Evolution Research - General Evolution News

Evolutionary history of vespid wasps rewritten by New study

2007-03-05T12:02:00.000+00:00

Scientists at the University of Illinois have conducted a genetic analysis of vespid wasps that revises the vespid family tree and challenges long-held views about how the wasps' social behaviors evolved. In the study [1], published in the February 21, 2007 Proceedings of the National Academy of Sciences journal, the researchers found genetic evidence that eusociality (the reproductive specialization seen in some insects and other animals) evolved independently in two groups of vespid wasps.

These findings contradict an earlier model of vespid wasp evolution, which placed the groups together in a single lineage with a common ancestor.

Eusocial behavior is quite rare, and generally involves the breeding of different reproductive classes within a colony. The sterile members of the group perform tasks that support their fertile counterparts. Eusociality occurs in only a few species of insects, rodents, crustaceans and other arthropods.

The evolution of eusociality in wasps has long been a source of debate, said U. of I. entomology graduate student Heather Hines and entomology professor Sydney Cameron, who is the principal investigator of the study. A prior model of vespid wasp evolution placed three subfamilies of wasps - the Polistinae, Vespinae and Stenogastrinae - together in a single evolutionary group with a common ancestor. This model did not rely on a genetic analysis of the wasps, but instead classified them according to several physical and behavioral traits.

Cameron's team included University of Missouri biology professor James H. Hunt, an expert on the evolution of social behavior in the vespid wasps. Hunt observed that many behavioral characteristics of the vespid wasps contradicted this model of the vespid family tree.

Hunt's observations, along with those of other behavioral experts in the field, prompted the new analysis.

Instead of affirming a linear, step-wise evolution of social behavior from solitary to highly social, Cameron said, her team's analysis shows that the Polistinae and Vespinae wasp subfamilies evolved their eusocial characteristics separately from the eusocial Stenogastrinae subfamily of vespid wasps.

Experts on vespid wasp behavior have long noted the significant behavioral differences between the Stenogastrinae subfamily and the group that includes Polistinae and Vespinae. And others have tried, unsuccessfully, to challenge the earlier non-genetic model of vespid wasp evolution. In 1998, German researchers J. Schmitz and R. Moritz also used a genetic analysis to propose that the subfamily Stenogastrinae was evolutionarily distinct from the Polistinae and Vespinae subfamilies.

Proponents of the non-genetic model criticized their work, however, because it relied on an analysis of less than 600 base pairs from two genes (one ribosomal RNA, the other mitochondrial DNA) and included very few representative species, some of which were unsuitable for the analysis.

The new study examined variations in fragments of four genes across 30 species of vespid wasps. Four independent statistical analyses tested the reliability of the pattern of relationships that emerged from the data.

This work confirms the ideas of Schmitz and Moritz, said Cameron, by adding to the weight of evidence that their hypothesis was accurate.

The fact that eusociality evolved independently in two groups of vespid wasps also sheds light on the complexity of evolutionary processes, Cameron said.

"Scientists attempt to make generalizations and simplify the world. But the world isn't always simple and evolution isn't simple. This finding points to the complexity of life."

Source (adapted): University of Illinois at Urbana-Champaign PR "New study rewrites evolutionary history of vespid wasps" March 1 2007

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[1] Based on the PNAS paper:

Multigene phylogeny reveals eusociality evolved twice in vespid wasps

Heather M. Hines, James H. Hunt, Timothy K. O'Connor, Joseph J. Gillespie, and Sydney A. Cameron

Published online before print February 21, 2007, 10.1073/pnas.0610140104
PNAS | February 27, 2007 | vol. 104 | no. 9 | 3295-3299

Eusocial wasps of the family Vespidae are thought to have derived their social behavior from a common ancestor that had a rudimentary caste-containing social system. In support of this behavioral scenario, the leading phylogenetic hypothesis of Vespidae places the eusocial wasps (subfamilies Stenogastrinae, Polistinae, and Vespinae) as a derived monophyletic clade, thus implying a single origin of eusocial behavior. This perspective has shaped the investigation and interpretation of vespid social evolution for more than two decades. Here we report a phylogeny of Vespidae based on data from four nuclear gene fragments (18S and 28S ribosomal DNA, abdominal-A and RNA polymerase II) and representatives from all six extant subfamilies. In contrast to the current phylogenetic perspective, our results indicate two independent origins of vespid eusociality, once in the clade Polistinae+Vespinae and once in the Stenogastrinae. The stenogastrines appear as an early diverging clade distantly related to the vespines and polistines and thus evolved their distinctive form of social behavior from a different ancestor than that of Polistinae+Vespinae. These results support earlier views based on life history and behavior and have important implications for interpreting transitional stages in vespid social evolution.

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Of related interest:

Eusociality: Origin and consequences

Edward O. Wilson, and Bert Holldobler

Published online before print September 12, 2005, 10.1073/pnas.0505858102
PNAS | September 20, 2005 | vol. 102 | no. 38 | 13367-13371

In this new assessment of the empirical evidence, an alternative to the standard model is proposed: group selection is the strong binding force in eusocial evolution; individual selection, the strong dissolutive force; and kin selection (narrowly defined), either a weak binding or weak dissolutive force, according to circumstance. Close kinship may be more a consequence of eusociality than a factor promoting its origin. A point of no return to the solitary state exists, as a rule when workers become anatomically differentiated. Eusociality has been rare in evolution, evidently due to the scarcity of environmental pressures adequate to tip the balance among countervailing forces in favor of group selection. Eusociality in ants and termites in the irreversible stage is the key to their ecological dominance and has (at least in ants) shaped some features of internal phylogeny. Their colonies are consistently superior to solitary and preeusocial competitors, due to the altruistic behavior among nestmates and their ability to organize coordinated action by pheromonal communication.

In eusociality, an evolutionarily advanced level of colonial existence, adult colonial members belong to two or more overlapping generations, care cooperatively for the young, and are divided into reproductive and nonreproductive (or at least less-reproductive) castes. The phenomenon is well marked and nearly confined to insects, especially ants, bees, wasps, and termites, where it has been subject to a large body of mostly specialized research scattered across disciplines from genetics to paleontology. It has long been the conviction of researchers on social insects that common principles exist at the organismic and superorganismic levels, thus between individual insects and the tightly integrated colonies they compose. Parallels have been persuasively drawn between the self-construction of organisms from molecules and tissues and that of superorganisms from interacting entire organisms. The principles can be further parsed into two segments of the time scale: the developmental decision rules that assemble organisms and colonies in each generation and the origin of these rules through evolutionary time.

Focusing here on the second principle, evolutionary process, we suggest how three seemingly disparate evolutionary phenomena can be causally linked: the selection forces that generate and shape eusociality, the rareness of the origin of eusociality, and the ecological hegemony of eusocial insects.

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Technorati: vespid, wasps, family tree, social, behavior, pnas, insects, eusociality, evolution, colony, sterile, entomology, common ancestor, traits, dna, complexity, history, phylogeny, rna, kin, selection, workers, evolutionary, process

Scientists say Climate Change caused Neanderthal extinction in Iberia

2007-03-03T14:30:00.000+00:00

Summary:

Recent studies carried out in Gorham's cave*, on Gibraltar, proved to be definitive for this work.

Results show that the Neanderthal extinction could have been greatly determined by environmental and climate changes and not by competitiveness with modern humans.

The research work has been published in Quaternary Science Reviews journal.

Main Text

Climate - and not modern humans - was the cause of the Neanderthal extinction in the Iberian Peninsula (Cave Art). Such is the conclusion of the University of Granada research group RNM 179 - Mineralogy and Geochemistry of sedimentary and metamorphic environments, headed by professor Miguel Ortega Huertas and whose members Francisco Jose Jimenez Espejo, Francisca Martínez Ruiz and David Gallego Torres work jointly at the department of Mineralogy and Petrology of the University of Granada (Universidad de Granada) and the Andalusian Regional Institute of Earth Sciences (CSIC-UGR).

Together with other scientists from the Gibraltar Museum, Stanford University and the Japan Marine Science and Technology Center (JAMSTEC), the Spanish scientists published in the scientific journal Quaternary Science Reviews an innovative work representing a considerable step forward in the knowledge of human ancestral history.

The results of this multidisciplinary research are an important contribution to the understanding of the Neanderthal extinction and the colonisation of the European continent by Homo Sapiens.

During the last Ice Age, the Iberian Peninsula was a refuge for Neanderthals, who had survived in local pockets during previous Ice Ages, bouncing back to Europe when weather conditions improved.

Climate reconstructions

The study is based upon climate reconstructions elaborated from marine records and using the experience of Spanish and international research groups on Western Mediterranean paleoceanography. The conclusions point out that Neanderthal populations did suffer fluctuations related to climate changes before the first Homo Sapiens arrived in the Iberian Peninsula. Cold, arid and highly variable climate was the least favourable weather for Neanderthals and 24,000 years ago they had to face the worst weather conditions in the last 250,000 years.

The most important about these data is that they differ from the current scientific paradigm which makes Homo Sapiens responsible for the Neanderthal extinction. This work is a contribution to a new scientific current - leaded by Dr. Clive Finlayson, from the Gibraltar Museum - according to which Neanderthal isolation and, possibly, extinction were due to environmental factors.

These studies on climate variability are part of the work of the group RNM 179, funded by the excellence project RNM 0432 of the Andalusian Regional Government's Department for Innovation, Science and Business and by the MARCAL project of the Spanish Ministry of Education and Science, both linked to the Andalusian Environment Centre (CEAMA - Centro Andaluz de Medio Ambiente).

Source (adapted): University of Granada PR "Spanish scientists point at climate changes as the cause of the Neanderthal extinction in the Iberian Peninsula" February 25 2007 [alt. Neandertal, Neandertals]

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[1] Based on the paper:

Climate forcing and Neanderthal extinction in Southern Iberia: insights from a multiproxy marine record

Francisco J. Jimenez-Espejo, Francisca Martínez-Ruiz, Clive Finlayson, Adina Paytan, Tatsuhiko Sakamoto, Miguel Ortega-Huertas, Geraldine Finlayson, Koichi Iijima, David Gallego-Torres and Darren Fa

Quaternary Science Reviews (Article in Press)
doi:10.1016/j.quascirev.2006.12.013

Paleoclimate records from the western Mediterranean have been used to further understand the role of climatic changes in the replacement of archaic human populations inhabiting South Iberia. Marine sediments from the Balearic basin (ODP Site 975) was analysed at high resolution to obtain both geochemical and mineralogical data. These data were compared with climate records from nearby areas. Baexcces was used to characterize marine productivity and then related to climatic variability. Since variations in productivity were the consequence of climatic oscillations, climate/productivity events have been established. Sedimentary regime, primary marine productivity and oxygen conditions at the time of population replacement were reconstructed by means of a multiproxy approach. Climatic/oceanographic variations correlate well with Homo spatial and occupational patterns in Southern Iberia. It was found that low ventilation (U/Th), high river supply (Mg/Al), low aridity (Zr/Al) and low values of Baexcess coefficient of variation, may be linked with Neanderthal hospitable conditions. We attempt to support recent findings which claim that Neanderthals populations continued to inhabit southern Iberia between 30 and approx 28 ky cal BP and that this persistence was due to the specific characteristics of South Iberian climatic refugia. Comparisons of our data with other marine and continental records appear to indicate that conditions in South Iberia were highly inhospitable approx 24 ky cal BP. Thus, it is proposed that the final disappearance of Neanderthals in this region could be linked with these extreme conditions.

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*History of Gorham's Cave

[Spain, Anthropology, Archaeology]

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Study: Why Do Birds Migrate?

2007-03-02T11:59:00.000+00:00

Why do some birds fly thousands of miles back and forth between breeding and non-breeding areas every year whereas others never travel at all?

One textbook explanation suggests either eating fruit or living in non-forested environments were the precursors needed to evolve migratory behavior.

Not so, report a pair of ecologists from The University of Arizona in Tucson. The pressure to migrate comes from seasonal food scarcity.

"It's not just whether you eat insects, fruit, nectar or candy bars or where you eat them -- it matters how reliable that food source is from day-to-day," said W. Alice Boyle. "For example, some really long-distance migrants like arctic terns are not fruit-eaters."

Boyle, an adjunct lecturer in UA's department of ecology and evolutionary biology and co-author Courtney J. Conway, a UA assistant professor of natural resources and a research scientist with the U.S. Geological Survey, reported their findings in the March 2007 issue of American Naturalist [1].

To figure out the underlying pressures that drive some birds to leave home for the season, the team wanted to examine a related set of species and compare their size, food type, habitat, migratory behavior and whether they fed in flocks.

Boyle and Conway focused on 379 species of New World flycatchers from the suborder Tyranni. One of the largest groups of New World birds, the Tyranni includes kingbirds, flycatchers, phoebes and such southern Arizona birdwatchers' delights as vermillion flycatchers and rose-throated becards. Tropical members include manakins and cotingas.

First the scientists had to construct the first "supertree" for New World flycatchers.

"No one has ever compiled all those birds together into one megafamily tree," Boyle said, adding that "supertree" is a technical term among evolutionary biologists.

Having the tree let the researchers compare a variety of traits across the many species of Tyranni by using a computer analysis called phylogenetic independent contrasts.

The technique allowed the scientists to sort out whether a bird was migratory because that's what species on their side of the family tree always did or whether the bird's travel habits had some ecological correlates.

Food scarcity was the number one issue that predicted a species' migratory behavior, the team found. Boyle said, "Food availability is the underlying process, not diet and habitat."

One strategy for dealing seasonal changes in food availability is migration. The team also found that species that forage in flocks are less likely to migrate.

"If you are faced with food scarcity, you have two options," Boyle said. "You can either forage with other birds or you can migrate."

When birds band together to search for food, the group is more likely to find a new patch of food than is one lone individual, she said. "Flocking can be an alternative way to deal with food shortages."

A universal assumption about bird migration has been that short-distance migration is an evolutionary stepping stone to long-distance migration. The team's work contradicts that idea by showing that short-distance migrants are inherently different from their globe-trotting cousins.

The National Science Foundation and the Natural Sciences and Engineering Research Council of Canada funded the work.

Source: University of Arizona PR March 1 2007 [Ornithology]

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[1] Based on the paper:

Why Migrate? A Test of the Evolutionary Precursor Hypothesis

W. Alice Boyle and Courtney J. Conway

Am. Nat. 2007. Vol. 169, pp. 344-359.
0003-0147/2007/16903-41953$15.00

The question of why birds migrate is still poorly understood despite decades of debate. Previous studies have suggested that use of edge habitats and a frugivorous diet are precursors to the evolution of migration in Neotropical birds. However, these studies did not explore other ecological correlates of migration and did not control for phylogeny at the species level. We tested the evolutionary precursor hypothesis by examining the extent to which habitat and diet are associated with migratory behavior, using a species-level comparative analysis of the Tyranni. We used both migratory distance and sedentary versus migratory behavior as response variables. We also examined the influences of foraging group size, membership in mixed-species flocks, elevational range, and body mass on migratory behavior. Raw species analyses corroborated some results from studies that put forth the evolutionary precursor hypothesis, but phylogenetically independent contrast analyses highlighted an important interaction between habitat and diet and their roles as precursors to migration. Foraging group size was consistently associated with migratory behavior in both raw species and independent contrast analyses. Our results lead to a resource variability hypothesis that refines the evolutionary precursor hypothesis and reconciles the results of several studies examining precursors to migration in birds.

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A 2006 related paper:

Phylogenetic tests of hypotheses for the evolution of avian migration: a case study using the Motacillidae

Diana C Outlaw and Gary Voelker

The Auk April 2006 123:455-466

The evolution of avian migration continues to be an intriguing research subject, even though relationships between migration and factors such as seasonality clearly exist. The question remains whether these relationships are evident within phylogenies containing both sedentary and migratory taxa. We explore the evolution of migration in the family Motacillidae by evaluating existing hypotheses for the evolution of migration in a comparative, phylogenetic framework at the interspecific level. Many hypotheses to explain the evolution of avian migration - such as the "evolutionary precursor" hypothesis (Levey and Stiles 1992, Chesser and Levey 1998) and the "stepping-stone" hypothesis (Cox 1968, 1985) - are based on New World migratory systems. The central components of these hypotheses should apply across biogeographic realms (i.e. the Old World), given that seasonality and habitat regimes are similar in the New and Old worlds. Using a molecular phylogeny containing most species in the Motacillidae, we investigated the potential interactions of seasonality and ecology with migratory and sedentary behavior. Our results suggest that habitat and migration are not correlated in the manner predicted by the evolutionary precursor hypothesis, but they also suggest the importance of increasing seasonality in explaining the patterns of the evolution of migration, an expected but previously unexamined evolutionary relationship. While understanding the limitations of applying generalizations to a complex evolutionary system such as migration, we have delineated here a broad methodology for testing hypotheses about the evolution of migration within a phylogenetic context.

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Genes and Genius: Confirmation of association between Gene and Intelligence

2007-03-01T08:40:00.000+00:00

A team of scientists, led by psychiatric geneticists at Washington University School of Medicine in St. Louis, has gathered the most extensive evidence to date that a gene that activates signaling pathways in the brain influences one kind of intelligence. They have confirmed a link between the gene, CHRM2, and performance IQ, which involves a person's ability to organize things logically.

"This is not a gene for intelligence," says Danielle M. Dick, Ph.D., assistant professor of psychiatry and lead author on the study. "It's a gene that's involved in some kinds of brain processing, and specific alterations in the gene appear to influence IQ. But this single gene isn't going to be the difference between whether a person is a genius or has below-average intelligence."

Dick's team comprehensively studied the DNA along the gene and found that several variations within the CHRM2 gene could be correlated with slight differences in performance IQ scores, which measure a person's visual-motor coordination, logical and sequential reasoning, spatial perception and abstract problem solving skills. When people had more than one positive variation in the gene, the improvements in performance IQ were cumulative. The study's findings are available online in Behavioral Genetics and will appear in an upcoming print issue of that journal [1].

IQ tests also measure verbal skills and typically include many subtests. For this study, subjects took five verbal subtests and four performance subtests, but the genetic variations influenced only performance IQ scores.

"One way to measure performance IQ may be to ask people to order pictures correctly to tell a story," Dick explains. "A simple example might be pictures of a child holding a vase, the vase broken to bits on the floor and the child crying. The person taking the test would have to put those pictures into an order that tells the story of how the child dropped the vase and broke it and then cried."

The researchers studied DNA gathered as part of the Collaborative Study on the Genetics of Alcoholism (COGA). In this multi-center study, people who have been treated for alcohol dependence and members of their families provide DNA samples to researchers, who isolated DNA regions related to alcohol abuse and dependence, as well as a variety of other outcomes.

Some of the participants in the study also took the Wechsler Adult Intelligence Scale-Revised, a traditional IQ test. In all, members of 200 families, including more than 2,150 individuals, took the Wechsler test, and those results were matched to differences in individuals' DNA.

By comparing individual differences embedded in DNA, the team zeroed in on CHRM2, the neuronal receptor gene on chromosome 7. The CHRM2 gene activates a multitude of signaling pathways in the brain involved in learning, memory and other higher brain functions. The research team doesn't yet understand how the gene exerts its effects on intelligence.

Intelligence was one of the first traits that attracted the attention of people interested in the interplay of genes and environmental influences. Early studies of adopted children, for example, showed that when children grow up away from their biological parents, their IQs are more closely correlated to biological parents, with whom they share genes, than adoptive parents, with whom they share an environment.

But in spite of the association between genes and intelligence, it has been difficult to find specific variations that influence intelligence. The genes identified in the past were those that had profoundly negative effects on intelligence - genes that cause mental retardation, for example. Those that contribute to less dramatic differences have been much harder to isolate.

Dick's team is not the first to notice a link between intelligence and the CHRM2 gene. In 2003, a group in Minnesota looked at a single marker in the gene and noted that the variation was related to an increase in IQ. A more recent Dutch study looked at three regions of DNA along the gene and also noticed influences on intelligence. In this new study, however, researchers tested multiple genetic markers throughout the gene.

"If we look at a single marker, a DNA variation might influence IQ scores between two and four points, depending on which variant a person carries," Dick explains. "We did that all up and down the gene and found that the variations had cumulative effects, so that if one person had all of the 'good' variations and another all of the 'bad' variations, the difference in IQ might be 15 to 20 points. Unfortunately, the numbers of people at those extremes were so small that the finding isn't statistically significant, but the point is we saw fairly substantial differences in our sample when we combined information across multiple regions of the gene."

Dick says the next step is to look at the gene and its numerous variants to learn what is going on biologically that might affect cognitive performance. Presently, she says it's too early to predict how small changes in the gene might be influencing communication in the brain to affect intelligence, and she says it's nearly certain CHRM2 is not the only gene involved.

"Perhaps as many as 100 genes or more could influence intelligence," she says. "I think all of the genes involved probably have small, cumulative effects on increasing or decreasing I.Q., and I expect overall intelligence is a function of the accumulation of all of these genetic variants, not to mention environmental influences ranging from socio-economic status to the value that's placed on learning when children are growing up."

Source: Washington University in St Louis School of Medicine PR "Genes and genius: Researchers confirm association between gene and intelligence" February 27 2007

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[1] Association of CHRM2 with IQ: Converging Evidence for a Gene Influencing Intelligence

Danielle M. Dick et al.

Behavior Genetics
ISSN 0001-8244 (Print) 1573-3297 (Online)
DOI 10.1007/s10519-006-9131-2

The cholinergic neurotransmitter system is thought to be involved in many aspects of memory, attention, and higher cognition. In the Collaborative Study on the Genetics of Alcoholism (COGA) sample, we have previously reported linkage and association to the cholinergic muscarinic 2 receptor gene (CHRM2) on chromosome 7 with evoked EEG oscillations (Jones et al. 2004), providing evidence that this gene may be involved in human brain dynamics and cognition. In addition, a small number of genetic markers were genotyped in CHRM2 in the Minnesota Twin and Family Study (Comings et al. 2003) and a Dutch family study (Gosso et al. 2006, in press) and both research groups found evidence that this gene may be involved in intelligence. In the COGA sample, we have extensively genotyped SNPs (single nucleotide polymorphisms) within and flanking the CHRM2 gene. We find evidence of association with multiple SNPs across CHRM2 and Performance IQ, as measured by the Wechsler Adult Intelligence Scale-Revised (WAIS-R). These results remain significant after taking into account alcohol dependence and depression diagnoses in the sample.

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Study: Early Europeans unable to stomach milk

2007-02-28T11:19:00.000+00:00

The first direct evidence that early Europeans were unable to digest milk has been found by scientists at UCL (University College London) and Mainz University.

In a study, published in the journal PNAS [1] (Proceedings of the National Academy of Sciences), the team shows that the gene that controls our ability to digest milk was missing from Neolithic skeletons dating to between 5840 and 5000 BC. However, through exposure to milk, lactose tolerance evolved extremely rapidly, in evolutionary terms (see lactose intolerance). Today, it is present in over ninety per cent of the population of northern Europe and is also found in some African and Middle Eastern populations but is missing from the majority of the adult population globally.

Dr Mark Thomas, UCL Biology, said: "The ability to drink milk is the most advantageous trait that's evolved in Europeans in the recent past. Without the enzyme lactase, drinking milk in adulthood causes bloating and diarrhoea. Although the benefits of milk tolerance are not fully understood yet, they probably include: the continuous supply of milk compared to the boom and bust of seasonal crops; its nourishing qualities; and the fact that it's uncontaminated by parasites, unlike stream water, making it a safer drink. All in all, the ability to drink milk gave some early Europeans a big survival advantage."

The team carried out DNA tests on Neolithic skeletons from some of the earliest organised farming communities in Europe. Their aim was to find out whether these early Europeans from various sites in central, northeast and southeast Europe, carried a version of the lactase gene that controls our ability to produce the essential enzyme lactase into adulthood. The team found that it was absent from their ancient bone DNA. This led the researchers to conclude that the consumption and tolerance of milk would have been very rare or absent at the time.

Scientists have known for decades that at some point in the past all humans were lactose intolerant. What was not known was just how recently lactose tolerance evolved.

Dr Thomas said: "To go from lactose tolerance being rare or absent seven to eight thousand years ago to the commonality we see today in central and northern Europeans just cannot be explained by anything except strong natural selection. Our study confirms that the variant of the lactase gene appeared very recently in evolutionary terms and that it became common because it gave its carriers a massive survival advantage. Scientists have inferred this already through analysis of genes in today's population but we've confirmed it by going back and looking at ancient DNA."

This study challenges the theory that certain groups of Europeans were lactose tolerant and that this inborn ability led the community to pursue dairy farming. Instead, they actually evolved their tolerance of milk within the last 8000 years due to exposure to milk.

Dr Thomas said: "There were two theories out there: one that lactose tolerance led to dairy farming and another that exposure to milk led to the evolution of lactose tolerance. This is a simple chicken or egg question but one that is very important to archaeologists, anthropologists and evolutionary biologists. We found that the lactose tolerance variant of the lactase gene only became common after dairy farming, which started around 9 thousand years ago in Europe.

"This is just one part of the picture researchers are gathering about lactose tolerance and the origins of Europeans. Next on the list is why there is such disparity in lactose tolerance between populations. It's striking, for example, that today around eighty per cent of southern Europeans cannot tolerate lactose even though the first dairy farmers in Europe probably lived in those areas. Through computer simulations and DNA testing we are beginning to get glimpses of the bigger early European picture."

Source: University College London PR February 27 2007

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[1] Based on the PNAS paper:

Absence of the lactase-persistence-associated allele in early Neolithic Europeans

J. Burger, M. Kirchner, B. Bramanti, W. Haak, and M. G. Thomas

Published online before print February 28, 2007
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0607187104

Lactase persistence (LP), the dominant Mendelian trait conferring the ability to digest the milk sugar lactose in adults, has risen to high frequency in central and northern Europeans in the last 20,000 years. This trait is likely to have conferred a selective advantage in individuals who consume appreciable amounts of unfermented milk. Some have argued for the "culture-historical hypothesis," whereby LP alleles were rare until the advent of dairying early in the Neolithic but then rose rapidly in frequency under natural selection. Others favor the "reverse cause hypothesis," whereby dairying was adopted in populations with preadaptive high LP allele frequencies. Analysis based on the conservation of lactase gene haplotypes indicates a recent origin and high selection coefficients for LP, although it has not been possible to say whether early Neolithic European populations were lactase persistent at appreciable frequencies. We developed a stepwise strategy for obtaining reliable nuclear ancient DNA from ancient skeletons, based on (i) the selection of skeletons from archaeological sites that showed excellent biomolecular preservation, (ii) obtaining highly reproducible human mitochondrial DNA sequences, and (iii) reliable short tandem repeat (STR) genotypes from the same specimens. By applying this experimental strategy, we have obtained high-confidence LP-associated genotypes from eight Neolithic and one Mesolithic human remains, using a range of strict criteria for ancient DNA work. We did not observe the allele most commonly associated with LP in Europeans, thus providing evidence for the culture-historical hypothesis, and indicating that LP was rare in early European farmers.

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Study reduces Chimpanzee-Human split to 4 million years ago

2007-02-25T10:48:00.000+00:00

Anthropology and Primatology - Excerpts from the February 23, 2007 PLoS Genetics paper "Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model" (Adapted) by Asger Hobolth, Ole F. Christensen, Thomas Mailund, and Mikkel H. Schierup:

[Related news story from Scientific American - "Humans, chimps split 4 million years ago: study": A new study, certain to be controversial, maintains that chimpanzees and humans split from a common ancestor just 4 million years ago - a much shorter time than current estimates of 5 million to 7 million years ago.]

Author Summary

Primate evolution is a central topic in biology and much information can be obtained from DNA sequence data. A key parameter is the time "when we became human," i.e., the time in the past when descendents of the human-chimp ancestor split into human and chimpanzee. Other important parameters are the time in the past when descendents of the human-chimp-gorilla ancestor split into descendents of the human-chimp ancestor and the gorilla ancestor, and population sizes of the human-chimp and human-chimp-gorilla ancestors. To estimate speciation times and ancestral population sizes we have developed a new methodology that explicitly utilizes the spatial information in contiguous genome alignments. Furthermore, we have applied this methodology to four long autosomal human-chimp-gorilla-orangutan alignments and estimated a very recent speciation time of human and chimp (around 4 million years) and ancestral population sizes much larger than the present-day human effective population size. We also analyzed X-chromosome sequence data and found that the X chromosome has experienced a different history from that of autosomes, possibly because of selection.

Citation: Hobolth A, Christensen OF, Mailund T, Schierup MH (2007) Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model. PLoS Genet 3(2): e7 doi:10.1371/journal.pgen.0030007

Abstract

The genealogical relationship of human, chimpanzee, and gorilla varies along the genome. We develop a hidden Markov model (HMM) that incorporates this variation and relate the model parameters to population genetics quantities such as speciation times and ancestral population sizes. Our HMM is an analytically tractable approximation to the coalescent process with recombination, and in simulations we see no apparent bias in the HMM estimates. We apply the HMM to four autosomal contiguous human-chimp-gorilla-orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human-chimp (4.1 plus/minus 0.4 million years), and fairly large ancestral effective population sizes (65,000 plus/minus 30,000 for the human-chimp ancestor and 45,000 plus/minus 10,000 for the human-chimp-gorilla ancestor). Furthermore, around 50% of the human genome coalesces with chimpanzee after speciation with gorilla. We also consider 250,000 base pairs of X-chromosome alignments and find an effective population size much smaller than 75% of the autosomal effective population sizes. Finally, we find that the rate of transitions between different genealogies correlates well with the region-wide present-day human recombination rate, but does not correlate with the fine-scale recombination rates and recombination hot spots, suggesting that the latter are evolutionarily transient.

Introduction

The recent evolutionary history of the human species can be investigated by comparative approaches using the genomes of the great apes: chimpanzee, gorilla, and orangutan. Nucleotide differences, accumulated by fixation of mutations, carry a wealth of information on important issues such as speciation times, properties of ancestral species (e.g., population sizes), and how speciation occurred. Genes or genomic fragments with unusual patterns of nucleotide differences and divergence may have been under strong natural selection during recent evolution of the human species. Sequence analyses can also aid interpretations of the incomplete primate fossil records and aid assignment of dated fossils to evolutionary lineages. For instance, it is still debated whether the Millennium man, Orrorin tugenensis, which has been dated to 6 million years (Myr) ago, and Sahelanthropus tchadensis, which has been dated to 6-7 Myr ago, belong to the human lineage or the human-chimp (HC) lineage.

Comparative analyses of multiple alignments of small fragments of human, chimpanzee, gorilla, and orangutan sequence have revealed that the human genome is more similar to the gorilla genome than to the chimpanzee genome for a considerable fraction of single genes. Such a conflict between species and gene genealogy is expected if the time span between speciation events is small measured in the number of 2N generations, where N is the effective population of the ancestral species (see Figure 1). In that case, N can be estimated from the proportion of divergent genealogies if one assumes that speciation is an instantaneous event. Indeed, this has been done in several studies that find a HC ancestral effective population size NHC of 2-10 times the human present-day effective population size NH = 10,000. Recently, Patterson et al. studied a very large number of small human-chimp-gorilla-orangutan-macaque alignments. They found, in agreement with O'hUigin et al., that a large proportion of sites supporting alternative genealogies are caused by hypermutability and that the fraction of the genome with alternative genealogies therefore has been overestimated in previous studies. After using a statistical correction for substitution rate heterogeneity, Patterson et al. found that the variance in coalescence times is too large to be accounted for by instant speciation and a large ancestral effective population size, and that the speciation process therefore must have been complex. Particularly, the X chromosome shows a deviant pattern, which also led them to conclude that HC gene flow ceased and final speciation occurred as recently as 4 Myr ago. This date is generally believed to be the most recent time compatible with the fossil record, if the Millennium man and Sahelanthropus are not on the human lineage.

Whole genome sequences of gorilla and orangutan will soon supplement the already available whole genome sequences of human and chimpanzee. These four genomes are so closely related that alignments of large contiguous parts of the genomes can be constructed. Analysis of such large fragments is challenging because different parts of the alignment will have different evolutionary histories (and thus different genealogies, see Figure 1) because of recombination. Ideally, one would like to infer the genealogical changes directly from the data and then analyze each type of genealogy separately. A natural approach to this challenge is to move along the alignment, and simultaneously compute the probabilities of different relationships and speciation times. While recombination has been considered in previous likelihood models, the spatial information along the alignment has largely been ignored.

In this paper we describe a hidden Markov model (HMM) that allows the presence of different genealogies along large multiple alignments. The hidden states are different possible genealogies (labeled HC1, HC2, HG, and CG in Figures 1 and 2). Parameters of the HMM include population genetics parameters such as the HC and human-chimp-gorilla (HCG) ancestral effective population sizes, NHC and NHCG, and speciation times tau1 and tau2 (see Figure 1). We therefore name our approach a coalescent HMM (coal-HMM). The statistical framework of HMMs yields parameter estimates with associated standard errors, and posterior probabilities of hidden states. We show by simulation studies that the coal-HMM recovers parameters from the coalescence with recombination process, and we apply the coal-HMM to five long contiguous human-chimp-gorilla-orangutan (HCGO) alignments obtained from the NIH Intramural Sequencing Center comparative sequencing program (Targets 1, 106, 121, and 122 on four different autosomes and Target 46 on the X chromosome). We consistently find very recent estimates of HC speciation times and a large variance in the time to common ancestry along the genome. Similar to Patterson et al., we find that the X chromosome has a smaller effective population size than expected. The mapping of genealogical states further allows us to correlate transitions in genealogies with properties of the genome, and here we focus on fine-scale and region-wide recombination rate estimates.

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Technorati: plos, genetics, human, chimpanzee, gorilla, markov, scientific american, split, study, chimpanzees, humans, common ancestor, biology, anthropology, primatology, genome, dna, chimp, ancestors, primate, evolution, hot spots

Hunting Chimpanzees may alter view of Human Evolution (+ Related video)

2007-02-24T21:08:00.000+00:00

Reporting findings that help shape our understanding of how tool use has evolved among primates, researchers have discovered evidence that chimpanzees, at least under some conditions, are capable of habitually fashioning and using tools to hunt mammalian prey. The work [1], reported by Jill Pruetz of Iowa State University and Paco Bertolani of the University of Cambridge, will appear online in the journal Current Biology on February 22nd 2007.

Chimpanzees are well known for their ingenuity in using tools for some tasks, such as obtaining invertebrate insects from logs or pounding open hard nuts, but there had been only fleeting evidence of chimpanzees brandishing tools for bona fide hunting.

In the new work, researchers observed tool use in hunting by the Fongoli community of savanna-dwelling chimpanzees (Pan troglodytes verus) in southeastern Senegal. Chimpanzees were observed making spear-like tools in a step-wise fashion, and subsequently using them with jabbing motions in an apparent effort to obtain lesser bushbabies (Galago senegalensis) from cavities in hollow branches or tree trunks. Bushbabies are nocturnal prosimians that retire to such hidden cavities during the day.

Although there was only one successful attempt in 22 recorded instances of the chimpanzees using the spear-like tools to find and obtain prey, the researchers observed that tool-crafting and associated hunting behavior was systematic and consistent, suggesting that it was habitual. The hunting behavior included forceful jabbing motions into branch or trunk hollows, and chimpanzees were seen to subsequently open the hollows by breaking wood off from a distance, suggesting that the jabbing actions were intended to immobilize bushbabies, rather than rouse them from their cavities (bushbabies move quickly and might otherwise easily evade chimpanzees once roused).

Two notable aspects of the behavior observed in the Fongoli group were that on the one hand, it is rare for chimpanzees to consume prosimian prey - in other study sites, red colobus monkeys, hunted mainly by males, are the chimps' most common prey - and on the other hand, the tool use appeared to be primarily restricted to females and immature individuals. These two behavior characteristics could both be related to the fact that the Fongoli community inhabits a mosaic savannah that is relatively dry, and where red colobus monkeys are absent. This habitat may promote efforts - such as the observed tool use - to obtain meat through other means.

The authors point out that the females and immature chimpanzees using the spear-like tools appear to be exploiting a niche relatively ignored by males, an observation that supports a previous hypothesis that female hominids played a role in the evolution of the earliest tool technology and suggests that this technology may have included tools for hunting. [Primatology, Anthropology]

Source: Cell Press / PhysOrg

Info on the Fongoli Savanna Chimpanzee Project (from the National Primate Research Center)

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[1] Based on:

Savanna Chimpanzees, Pan troglodytes verus, Hunt with Tools

Jill D. Pruetz and Paco Bertolani

Current Biology: Online Ahead of Issue - Full citation NYA

Although tool use is known to occur in species ranging from naked mole rats [1] to owls [2], chimpanzees are the most accomplished tool users [3, 4, 5]. The modification and use of tools during hunting, however, is still considered to be a uniquely human trait among primates. Here, we report the first account of habitual tool use during vertebrate hunting by nonhumans. At the Fongoli site in Senegal, we observed ten different chimpanzees use tools to hunt prosimian prey in 22 bouts. This includes immature chimpanzees and females, members of age-sex classes not normally characterized by extensive hunting behavior. Chimpanzees made 26 different tools, and we were able to recover and analyze 12 of these. Tool construction entailed up to five steps, including trimming the tool tip to a point. Tools were used in the manner of a spear, rather than a probe or rousing tool. This new information on chimpanzee tool use has important implications for the evolution of tool use and construction for hunting in the earliest hominids, especially given our observations that females and immature chimpanzees exhibited this behavior more frequently than adult males.

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Excerpt from Craig Stanford's (Department of Anthropology, University of Southern California) May/June 1995 American Scientist paper "Chimpanzee hunting behavior and human evolution":

In the early 1960s, when the british primatologist Jane Goodall first observed wild chimpanzees hunting and eating meat in Gombe National Park, Tanzania, it was widely believed that these animals were strict vegetarians. Skeptics suggested that the diet of the Gombe chimpanzees was aberrant. Others suggested that the quantity of meat the chimpanzees ate was trivial. After more than 30 years of research, however, it is now clear that meat is a natural part of the chimpanzees' diet. Indeed, hunting has been observed at most of the other sites where chimpanzees are studied across central Africa. And, it turns out, a chimpanzee community may eat several hundred kilograms of meat in a single year.

To many anthropologists this is a surprising development. Of all the higher primates, only human beings and chimpanzees hunt and eat meat on a regular basis. The similarities pose an intriguing prospect: Might the close evolutionary relationship between chimpanzees and human beings provide some clues to the evolution of our own behavior? We do know that the earliest bipedal hominids, the australopithecines, evolved in Africa about 5 million years ago and that they shared a common ancestor with modern chimpanzees shortly before that time. Unfortunately, the evidence for the occurrence of meat-eating among the early australopithecines is spotty at best. Primitive stone tools that were made 2.5 million years ago suggest that early hominids had the means to carve the flesh from large carcasses, but we know very little about their diets before that time. Were they hunters or perhaps, as many anthropologists now argue, scavengers? The behavior of chimpanzees may provide a window through which we can see much that has been lost in the fossil record.

There are also some interesting subtleties to the chimpanzees' hunting behavior that need to be addressed. Although chimpanzees can and do hunt alone, they often form large hunting parties consisting of more than 10 adult males, plus females and juveniles. Chimpanzees also go on "hunting binges" in which they kill a large number of monkeys and other animals over a period of several days or weeks. Such binges have always been a little mysterious. What could incite a chimpanzee to suddenly forgo plant foraging and turn to hunting? Are there social or ecological factors associated with the impetus to hunt? What ecological effects does the chimpanzees' predatory behavior have on their prey?

In the past five years I have been mindful of such questions as I observed the chimpanzees and their primary prey at Gombe, the red colobus monkey. Although we are only beginning to understand some of the causes and consequences of the chimpanzees' actions, what we have discovered is more complicated and more interesting than anyone suspected. For chimpanzees, meat is not only another way to get nutrients like fat and protein, but a means to make political bonds and gain access to sexually receptive females.

Citation 1995 Stanford, C.B. Chimpanzee hunting behavior and human evolution. American Scientist 83 (3): 256-261.

Also see The Bwindi-Impenetrable Great Ape Project

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David Attenborough video clip* showing how hunting chimpanzees co-ordinate their behavior in order to trap and kill (then eat) a colobus monkey:

*From The Trials of Life: A Natural History of Behaviour, a BBC nature documentary first broadcast in 1990

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The video footage below hasn't any commentary but is accompanied by the following text by kambizkamrani: "Adolescent female Tumbo isolates a potential spear and modifies it. She begins to jab it into a tree to spear her prey. She then climbs the tree and begins jumping on the large limb, which eventually breaks off, allowing her to reach in and retrieve the prey, a bushbaby (Galago senegalensis)." - watching the National Geographic video "Video: Chimps Make and Use 'Spears' to Hunt" first may help.

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Technorati: evolution, primatology, anthropology, chimpanzees, chimps, jane goodall, david attenborough, video, hunting, tools, evidence, bushbabies, biology, spear, monkeys, technology, primate, primates, behavior, human, trials, life

What is wrong with intelligent design?

2007-02-24T08:05:00.000+00:00

In a thought-provoking paper from the March 2007 issue of The Quarterly Review of Biology , Elliott Sober (University of Wisconsin) clearly discusses the problems with two standard criticisms of intelligent design: that it is unfalsifiable and that the many imperfect adaptations found in nature refute the hypothesis of intelligent design.

Biologists from Charles Darwin to Stephen Jay Gould have advanced this second type of argument. Stephen Jay Gould's well-known example of a trait of this type is the panda's thumb. If a truly intelligent designer were responsible for the panda, Gould argues, it would have provided a more useful tool than the stubby proto-thumb that pandas use to laboriously strip bamboo in order to eat it.

ID proponents have a ready reply to this objection. We do not know whether an intelligent designer intended for pandas to be able to efficiently strip bamboo. The "no designer worth his salt" argument assumes the designer would want pandas to have better eating implements, but the objection has no justification for this assumption. In addition, Sober points out, this criticism of ID also concedes that creationism is testable.

A second common criticism of ID is that it is untestable. To develop this point, scientists often turn to the philosopher Karl Popper's idea of falsifiability. According to Popper, a scientific statement must allow the possibility of an observation that would disprove it. For example, the statement "all swans are white" is falsifiable, since observing even one swan that isn't white would disprove it. Sober points out that this criterion entails that many ID statements are falsifiable; for example, the statement that an intelligent designer created the vertebrate eye entails that vertebrates have eyes, which is an observation.

This leads Sober to jettison the concept of falsifiability and to provide a different account of testability. "If ID is to be tested," he says, "it must be tested against one or more competing hypotheses." If the ID claim about the vertebrate eye is to be tested against the hypothesis that the vertebrate eye evolved by Darwinian processes, the question is whether there is an observation that can discriminate between the two. The observation that vertebrates have eyes cannot do this.

Sober also points out that criticism of a competing theory, such as evolution, is not in-and-of-itself a test of ID. Proponents of ID must construct a theory that makes its own predictions in order for the theory to be testable. To contend that evolutionary processes cannot produce "irreducibly complex" adaptations merely changes the subject, Sober argues.

"When scientific theories compete with each other, the usual pattern is that independently attested auxiliary propositions allow the theories to make predictions that disagree with each other," Sober writes. "No such auxiliary propositions allow … ID to do this." In developing this idea, Sober makes use of ideas that the French philosopher Pierre Duhem developed in connection with physical theories - theories usually do not, all by themselves, make testable predictions. Rather, they do so only when supplemented with auxiliary information. For example, the laws of optics do not, by themselves, predict when eclipses will occur; they do so when independently justified claims about the positions of the earth, moon, and sun are taken into account.

Similarly, ID claims make predictions when they are supplemented by auxiliary claims. The problem is that these auxiliary assumptions about the putative designer's goals and abilities are not independently justified. Surprisingly, this is a point that several ID proponents concede.

Source: University of Chicago Press Journals /Eureka Alert

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Lizards 'Shout' Against a Noisy Background Discovery

2007-02-22T10:21:00.000+00:00

Lizards that signal to rivals with a visual display "shout" to get their point across, UC Davis researchers have found.

Male anole lizards signal ownership of their territory by sitting up on a tree trunk, bobbing their heads up and down and extending a colorful throat pouch (dewlap). They can spot a rival lizard up to 25 meters away, said Terry Ord, a postdoctoral researcher at UC Davis who is working with Judy Stamps, professor of evolution and ecology.

The lizards' signals need to be strong enough for a rival to see, but not vivid enough to say "eat me" to a passing predator. But their forest home can be a visually noisy environment, with branches and leaves waving in the breeze and casting patterns of light and shade.

"They have to have a strategy to get their message across," Ord said.

Image: Postdoctoral researcher Terry Ord says anole lizards, such as this one, create a strategy to get their message across to rivals. (Courtesy photo UCD)

Ord videotaped two species of anole lizards, Anolis cristatellus and Anolis gundlachi, in the Caribbean National Forest in Puerto Rico. He found that the more "visual noise" in the background, the faster and more exaggerated the movements of the lizards.

Anole lizards are interesting to evolutionary biologists because different species are found on different islands all over the Caribbean. The lizards are not particularly closely related - they are separated by 30 million years of evolution - but they live in similar environments with the same obstacles to communication. So Ord is using them as a model to investigate the evolution of such signals.

The other authors on the paper, which is published online in Proceedings of the Royal Society part B, are Richard A. Peters, Australian National University, Canberra; and Barbara Clucas, a graduate student in animal behavior at UC Davis. The work was supported by grants from the National Geographic Society, the National Science Foundation and the Australian Research Council.

Source: University of California Davis PR February 21, 2007

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Lizards speed up visual displays in noisy motion habitats

Terry J. Ord, Richard A. Peters, Barbara Clucas, Judy A. Stamps

Proceedings of the Royal Society B: Biological Sciences
ISSN: 0962-8452 (Paper) 1471-2954 (Online)
Issue: FirstCite Early Online Publishing
DOI: 10.1098/rspb.2006.0263

Extensive research over the last few decades has revealed that many acoustically communicating animals compensate for the masking effect of background noise by changing the structure of their signals. Familiar examples include birds using acoustic properties that enhance the transmission of vocalizations in noisy habitats. Here, we show that the effects of background noise on communication signals are not limited to the acoustic modality, and that visual noise from windblown vegetation has an equally important influence on the production of dynamic visual displays. We found that two species of Puerto Rican lizard, Anolis cristatellus and A. gundlachi, increase the speed of body movements used in territorial signalling to apparently improve communication in visually 'noisy' environments of rapidly moving vegetation. This is the first evidence that animals change how they produce dynamic visual signals when communicating in noisy motion habitats. Taken together with previous work on acoustic communication, our results show that animals with very different sensory ecologies can face similar environmental constraints and adopt remarkably similar strategies to overcome these constraints.

The above paper references:

Evolution of Anoline Lizard Display Behavior

Thomas A Jennsen

American Zoologist* 1977 17(1):203-215; doi:10.1093/icb/17.1.203

Based on my conceptual framework of anoline display behavior, I am suggesting the following evolutionary trends. Lateral presentation during display was probably promoted by monocular vision. Along with lateral presentation, postures evolved to increase lateral outline. These postures which magnified body size were probably of selective advantage within aggressive social contexts since larger animals tend to dominate smaller ones through bluff. Body movement evolved along with lateral orientation and size-enhancing postures. These movements would be most effective if they complemented lateral orientation. Effectors available for such movements were primarily pre-adapted for vertical motion. The patterns of movement generated were probably simple oscillatory bobbing movements by the head which were weakly stereotyped, interspecifically similar, appearing in many contexts, and having a weakly defined information content. Events having selective advantage for species recognition promoted stereotypy of bobbing behavior into species-unique displays; each species had its unique signature display which served in a manifold communicatory capacity. The signature display appeared in assertion, courtship, and challenge contexts. Its information content varied depending upon context and recipient of the display (e.g., male or female). Besides the stereotyped aspects of the display, certain features remained variable with potential information significance. Core variability (see text) promotes individual recognition and may be the origin of new unique display patterns as sibling species emerge. Display modifiers (see text) are variable display features shared by members of a population (many being shared interspecifically) that provide a graded appearance to display performance; modifiers can indicate level of arousal and facilitate interspecific communication. For some species display repertoire size seems to have evolved from a single display (signature display) to repertoires of multiple displays; these subsequent displays are generally restricted to aggressive interactions.

*American Zoologist is now Integrative and Comparative Biology

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Technorati: environment, lizard, lizards, evolution, ecology, communication, anole, anoles, territory, university, california, davis, terry, ord, puerto rico, caribbean

An ancient retrovirus is resurrected

2007-02-21T10:35:00.000+00:00

Retroviruses have been around longer than humanity itself. In fact, the best-known family member, HIV, is a relative youngster, with its first known human infections occurring sometime in the mid-20th century. But although many retroviruses went extinct hundreds of thousands or millions of years ago, researchers studying the pathogens don't use the traditional tools of paleontologists: They need look only as far as our own DNA. Retroviruses infect cells and replicate by inserting their DNA into their host cell's genome. If that cell happens to be a germ cell, such as a sperm, an egg or their precursors, then the retroviral DNA is inherited by offspring just like a normal gene. Humans have many defunct retroviruses deposited in our DNA, remnants of ancient retroviruses that replicated in our ancestors millions of years ago. Now, researchers have brought one of those retroviruses back to life.

"In our DNA, there's a fossil record of retroviruses that used to infect us," says Paul Bieniasz, associate professor and head of the Laboratory of Retrovirology at Rockefeller University and the Aaron Diamond AIDS Research Center [Aids]. In fact, about eight percent of human DNA is made up of retroviral sequences. Bieniasz and Youngnam Lee, a graduate student in the Bieniasz lab, have excavated some of that DNA and - in an attempt to better understand how humans and retroviruses co-evolved - they have resurrected an ancient retrovirus, one that can create new viral particles and infect human cells. They describe their work in a paper published by PLoS Pathogens last month [1].

The extinct retroviruses embedded in our DNA can't reproduce because of mutations in one or more of their genes. The younger of these human endogenous retroviruses (or HERVs) have fewer changes, and judging by the paucity of genetic alterations, at least one subfamily - HERV-K - was likely still active less than a few hundred thousand years ago. Different members of this subfamily have slightly different mutations. "But as of a few months ago," Bieniasz says, "there was no replication-competent form of this virus."

To eliminate those mutations that kept HERV-K from replicating, the two researchers deduced a genetic sequence that was a consensus of 10 different HERV-K proviruses (provirus) and synthesized the whole viral genome from scratch. Then, they took that sequence (which they dubbed HERV-KCON) and inserted it into cultured human cells to see if it would result in the creation of HERV-K structural proteins. Their consensus sequence resulted in not only functional proteins, but in a retrovirus that was capable of creating new viral particles and integrating itself into a host cell's genome. "This is the first time this has been done with a viral genome that was effectively dead, and now is alive - or at least has all the functions that suggest it should replicate," Bieniasz says.

The project began, Lee says, because certain human and non-human primate cells produce proteins that appear to block HIV from replicating. "And the question is where did the proteins come from?" she asks. "By studying these extremely old viruses, we can tap into what happened in our ancestors millions and millions of years ago."

Source: Rockefeller University PR February 20, 2007

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[1] Reconstitution of an Infectious Human Endogenous Retrovirus

Young Nam Lee and Paul D. Bieniasz

Citation: Lee YN, Bieniasz PD (2007) Reconstitution of an Infectious Human Endogenous Retrovirus. PLoS Pathogens 3(1): e10 doi:10.1371/journal.ppat.0030010

Excerpts:

Authors Summary

Retrovirus genomes integrate into the genomes of host cells. If the target cells of a particular retrovirus include germ-line cells, e.g., sperm or egg cells, then retroviral genomes can be inherited like cellular genes. So-called endogenous retroviruses have accumulated throughout evolution in the genomes of many organisms, including humans. While all known endogenous retroviruses of modern humans are unable to replicate as retroviruses, the human genome represents a fossil record of ancient retroviruses that once infected our ancestors. In this study, a collection of "dead" endogenous retroviral genomes in modern human DNA was used to deduce the approximate sequence of an ancestral retrovirus, human endogenous retrovirus (HERV)-K, that is now thought to be extinct. A pseudo-ancestral HERV-K DNA sequence was synthesized and used to produce viral proteins and RNA that could reconstitute the HERV-K replication cycle. Thus, the replication and biology of a once-extinct retrovirus can now be studied in the laboratory. Interestingly, reconstituted HERV-K replication experiments, and comparison of the reconstituted HERV-K DNA sequence with the dead HERV-Ks in modern human DNA, suggests that HERV-K may have been extinguished in humans in part by host defenses that induce mutation of retroviral DNA and that the reconstitution of the pseudo-ancestral HERV-K reversed these changes.

Abstract

The human genome represents a fossil record of ancient retroviruses that once replicated in the ancestors of contemporary humans. Indeed, approximately 8% of human DNA is composed of sequences that are recognizably retroviral. Despite occasional reports associating human endogenous retrovirus (HERV) expression with human disease, almost all HERV genomes contain obviously inactivating mutations, and none are thought to be capable of replication. Nonetheless, one family of HERVs, namely HERV-K(HML-2), may have replicated in human ancestors less than 1 million years ago. By deriving a consensus sequence, we reconstructed a proviral clone (HERV-KCON) that likely resembles the progenitor of HERV-K(HML-2) variants that entered the human genome within the last few million years. We show that HERV-KCON Gag and protease proteins mediate efficient assembly and processing into retrovirus-like particles. Moreover, reporter genes inserted into the HERV-KCON genome and packaged into HERV-K particles are capable of infectious transfer and stable integration in a manner that requires reverse transcription. Additionally, we show that HERV-KCON Env is capable of pseudotyping HIV-1 particles and mediating entry into human and nonhuman cell lines. Furthermore, we show that HERV-KCON is resistant to inhibition by the human retrovirus restriction factors tripartite motif 5alpha and apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC) 3G but is inhibited by APOBEC 3F. Overall, the resurrection of this extinct infectious agent in a functional form from molecular fossils should enable studies of the molecular virology and pathogenic potential of this ancient human retrovirus.

Introduction

A characteristic that is unique to retroviruses is their propensity to integrate their genomes into host-cell DNA as an essential part of their replication cycle. Thus, if the target cell population of a given retrovirus includes germ cells or their progenitors, retroviral genomes can be inherited in a Mendelian manner as so-called "endogenous" forms (see [1] for review). Indeed, endogenous retroviruses have accumulated over time in the genomes of many organisms and are extraordinarily common in mammals, comprising approximately 8% of human DNA [2]. Nonetheless, while some avian, murine, and primate species harbor replication-competent retroviruses within their genomes, intact retroviruses are relatively infrequent and almost all endogenous retroviruses are obviously defective due to the presence of stop codons and frameshifts in one or more genes.

Among the numerous families of defective human endogenous retroviruses (HERVs) found in modern human DNA, the human mouse mammary tumor virus-like 2 (HML-2) subfamily of HERV-K proviruses is of special interest. Even though replication-competent forms of HERV-K(HML-2) have not been found, some proviruses were deposited in the human genome after speciation and represent some of the youngest HERVs known [3-6]. Also, occasional reports link their expression with human disease [7]. The age of an endogenous provirus can be roughly estimated by comparing sequence of the two long terminal repeats (LTRs). At integration, the two proviral LTRs should be identical, but during host DNA replication, each LTR independently accumulates mutations as a function of age, and it is estimated that one difference between two LTRs should occur every approximately 200,000 to 450,000 y. Several HERV-K(HML-2) proviruses have been identified in human DNA that have less than five differences between the two LTRs, suggesting deposition perhaps less than 1 million y ago [3-6]. HERV-K(HML-2)-related proviruses are found only in Old World primates genomes, and many are unique to humans, with nonhuman primate genomes containing empty preintegration sites at orthologous loci. Compellingly, polymorphism exists in humans with respect to the presence or absence of proviruses at some HERV-K integration sites, indicating insertion relatively recently in human evolution [3-6]. Furthermore, many of the younger HERV-K(HML-2) proviruses contain a subset of open reading frames (ORFs) with a few or no mutations [3,6,8]. However, all known HERV-K proviruses are replication defective.

There are several ways in which a defective provirus can proliferate in a host's genome, including via exogenous infection events following complementation in trans, where functional proteins are supplied by other endogenous or exogenous viruses. Alternatively, for some retroelements, envelope-independent retrotransposition can occur in cis, where an element copies itself and inserts into a new genomic locus within the same cell, forgoing the normal extracellular phase of the retroviral life cycle. Defective proviruses can also be proliferated as a result of long interspersed element retrotransposition [9]. However, most HERV-K(HML-2) replication appears to have been a consequence of autonomous infection by extracellular virions [10,11]. This conclusion is based on the comparatively low number of stop codons and ratio of nonsynonymous to synonymous changes (dN/dS) in HERV-K ORFs, indicating a purifying selection on all proteins. Notably, this finding holds for HERV-K Env [10], which should be required for replication that includes an extracellular step but not for any other mode of provirus proliferation.

Ancient retroviruses are of interest, in part because they likely imposed selective pressure on host defenses in human ancestors. Indeed, the tripartite motif (TRIM) 5alpha and apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC) 3 proteins that provide part of the host defense against modern retroviruses have been under positive selection for much of primate evolution [12-16]. As a retrovirus that appears to have replicated in the ancestors of modern Old World monkeys, apes, and humans, HERV-K may be partly responsible for this pressure. Moreover, it is conceivable that HERV-K exists today in an undetected replication-competent form in rare humans [4]. However, no studies of the virology or pathogenic potential of this ancient human virus have been possible because a contemporary, replication-competent HERV-K strain has not been identified and may not exist at all.

Despite some functional degradation due to mutation during deposition or during human DNA replication, HERV-K(HML-2) proviruses that have been deposited in human DNA in the past few million years should be reasonably well preserved and have relatively few inactivating mutations. Indeed, various studies have shown that individual proteins from certain HERV-K proviruses can function in vitro [17-25]. We reasoned that it might be possible to resurrect HERV-K(HML-2) in replication-competent form using proviruses that are thought to have most recently entered the human genome as a template. Therefore, we constructed a HERV-K strain whose genome sequence is a consensus of a subset of HERV-K(HML-2) proviruses. Importantly, we demonstrate that all viral proteins necessary for viral replication encoded by this provirus are functional and that proteins and genomes based on the reconstructed HERV-K(HML-2) viral genome can be used to generate infectious exogenous retrovirus particles.

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Studies of population genetics, evolution are an exercise in bad taste

2007-02-20T11:18:00.000+00:00

Scientific studies of why foods such as Brussels sprouts and stout beer are horribly bitter-tasting to some people but palatable to others are shedding light on a number of questions, from the mechanisms of natural selection to understanding how our genes affect our dietary habits (see "Origins and Evolution of Human Diet").

Dr. Stephen Wooding, a population geneticist at UT Southwestern Medical Center in Dallas, studies how slight variations in genes give rise to variations in traits among a given human population.

Part of Dr. Wooding's research focuses on variations in the genes responsible for bitter-taste receptors, tiny receptacles on the tongue that intercept harsh-tasting chemicals from food. Each of these genes comes in several forms, and the forms you carry help determine how you perceive bitter-tasting compounds.

The ability to taste or not taste bitter foods might have played a role in human evolution and may today account for such health-related behaviors as smoking and vegetable consumption, Dr. Wooding said. He presented an overview of his research on the bitter-taste receptor in San Francisco at the 2007 annual meeting of the American Association for the Advancement of Science (AAAS). The title of his talk is "Evolution: A Study in Bad Taste?" [1]

In the 1930s, scientists discovered differences in the ability of humans to taste a bitter synthetic compound called phenylthiocarbamide, or PTC, and they determined that the trait was controlled by genetics (the actual gene for PTC sensitivity was discovered in 2003). For PTC "tasters," even tiny concentrations of the compound are extremely bitter, while "nontasters" experience little or no taste to the same concentration of PTC.

"In some ways, bitter-taste sensitivity seems to be a trivial trait, but early geneticists recognized that this trait was special, for a variety of reasons," said Dr. Wooding, an assistant professor with UT Southwestern's Eugene McDermott Center for Human Growth and Development.

"Bitter-taste sensitivity is crucially important in protecting the human body from toxins in the environment. By enabling us to perceive noxious chemicals in potential foods - especially toxins used by plants to defend themselves against herbivores - bitter taste probably helped our early ancestors avoid poisoning," he said.

If that is the case, then why are both tasters and nontasters still present in the human population? Based on the rules of natural selection, shouldn't all of the nontasters have died off early in our evolution?

The answer is complex, Dr. Wooding said, noting that some things that taste bitter are used as medicine, such as compounds in certain tree barks that help protect against malaria.

He and his colleagues - Drs. Dennis Drayna and Un-kyung Kim at the National Institutes of Health, along with Drs. Lynn Jorde and Michael Barnshad at the University of Utah - analyzed the gene for PTC sensitivity for certain "signatures" of natural selection that would tell them how the gene has changed over time. They found very strong evidence that within humans, a process called "balancing natural selection" has taken place.

"This is a kind of natural selection that keeps two different forms of the same gene active in a population," Dr. Wooding said. "In this case they are the taster and the nontaster forms. In the absence of this type of natural selection, you would expect one form to dominate. That hasn't happened here because for some reason, there is not a strong advantage of one over the other. It's an unusual situation."

One hypothesis is that PTC nontasters can taste something that tasters can't.

"When we look at the nontaster form of the PTC receptor, it looks functional, so we think it probably responds to something," Dr. Wooding said. "One explanation could be that, long ago, it conferred some sort of protection from a different compound in these people."

Follow-up studies of variation in other bitter-taste receptor genes have revealed that different genes show different patterns of diversity. These might match up with other person-to-person differences in taste, Dr. Wooding said.

Regardless of the form of the PTC gene an individual carries, Dr. Wooding - who genetically is a taster - emphasized that taste preferences, upbringing and cultural issues clearly play very important roles in a person's diet.

"I personally like a little bit of bitter taste," he said.

Source (Adapted): University of Texas Southwestern Medical Center February 16, 2007

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[1] See the 2005 Current Biology paper:

Evolution: A Study in Bad Taste?

Stephen Wooding

Current Biology Volume 15, Issue 19, 11 October 2005, Pages R805-R807
doi:10.1016/j.cub.2005.09.021

Abstract

Bitter tastes are among the most salient of life's experiences - who can forget one's first encounter with dandelion milk or a stout beer? Studies of the genes underlying these tastes are providing new perspectives on human origins and health.

Excerpt

Bitter-taste sensitivity, of course, begins on the tongue. Concentrated at the back of the tongue, on disc-like structures called circumvallate papillae, specialized bitter-taste receptor cells await contact with potentially bitter compounds. Upon exposure to an appropriate ligand, these receptor cells depolarize, generating a signal that is conveyed via the facial and glossopharyngeal nerves to the brain (Figure 1A). In principle, any mechanism that stimulates this neural pathway will lead to the sensation of bitter taste; however, recent studies have highlighted the importance of a small group of G-protein-coupled receptors encoded by the TAS2R (also called T2R) gene family.

In humans, this family includes roughly 25 functional genes and eight pseudogenes, each roughly a kilobase in length, found in three clusters on chromosomes 5, 7 and 12. The protein products of these genes are concentrated at the apex of bitter-taste receptor cells, near the taste pore, where they are positioned to bind bitter ligands as they wash past, dissolved in saliva (Figure 1A). Upon ligand binding, these receptors catalyze a series of reactions leading to the efflux of intracellular calcium, and the cascade of events leading to taste perception begins (Figure 1B).

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Michigan Researcher Hopes to Unlock Evolutionary Secrets

2007-02-19T10:18:00.000+00:00

Roughly 2 1/2 billion years ago, some algae began to photosynthesize, an astonishing development that led to the creation of plants and a myriad of complex life forms, including, incidentally, mankind.

Today, Eric Linton, a Central Michigan University assistant professor of biology, is studying the gene makeup of single-celled euglenoids - single-celled organisms that acquired the ability to photosynthesize from algae - to learn whether that evolutionary step was a single hallmark moment or a series of events over time.

Eventually, Linton hopes to learn whether dormant genes that once controlled photosynthesis in certain euglenoids can reactivate, shedding light on whether scientists can jumpstart long-dormant genes in other organisms, such as in humans to fight a host of diseases.

With a 354,000 dollar grant from the National Science Foundation, Linton has begun a three-year project to perform complete genome sequencing of six forms of euglenoids, some of which long ago lost the ability to photosynthesize.

A focus of Linton's research is chloroplasts - components of euglenoid cells that serve as an engine for photosynthesis, or the synthesis of sugar from light, carbon dioxide and water. Some of the euglenoids under study have functioning chloroplasts, enabling photosynthesis; in others, the chloroplasts apparently are dormant.

By examining the genes for chloroplasts from six different euglenoids, Linton hopes to learn whether all acquired the ability to photosynthesize from the same ancestor, or multiple ancestors. Also, Linton wants to deduce how the genes are transferred, lost or evolved when two genomes are combined.

The discovery of supposedly dormant genes in the euglenoids raises questions about whether such genes - both in euglenoids and humans - can receive a man-made jump-start one day.

"If they are keeping these genes around," Linton said, "they must be achieving something."

Most genome sequencing will occur off-campus, but Linton plans on using a 50,000 dollar differential interference contrast microscope - which provides near 3D imaging - for much of the study. A graduate student and two undergraduates will assist him.

Linton, who joined CMU in July 2006, earned his doctorate in 2000 from Rutgers University in New Jersey.

Source: Central Michigan University PR January 31, 2007

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An earlier paper co-authored by Eric Linton:

Pattern of diversity in the genomic region near the maize domestication gene tb1

Richard M. Clark, Eric Linton, Joachim Messing, and John F. Doebley

PNAS | January 20, 2004 | vol. 101 | no. 3 | 700-707

Domesticated maize and its wild ancestor (teosinte) differ strikingly in morphology and afford an opportunity to examine the connection between strong selection and diversity in a major crop species. The tb1 gene largely controls the increase in apical dominance in maize relative to teosinte, and a region of the tb1 locus 5' to the transcript sequence was a target of selection during maize domestication. To better characterize the impact of selection at a major "domestication" locus, we have sequenced the upstream tb1 genomic region and systematically sampled nucleotide diversity for sites located as far as 163 kb upstream to tb1. Our analyses define a selective sweep of {approx}60-90 kb 5' to the tb1 transcribed sequence. The selected region harbors a mixture of unique sequences and large repetitive elements, but it contains no predicted genes. Diversity at the nearest 5' gene to tb1 is typical of that for neutral maize loci, indicating that selection at tb1 has had a minimal impact on the surrounding chromosomal region. Our data also show low intergenic linkage disequilibrium in the region and suggest that selection has had a minor role in shaping the pattern of linkage disequilibrium that is observed. Finally, our data raise the possibility that maize-like tb1 haplotypes are present in extant teosinte populations, and our findings also suggest a model of tb1 gene regulation that differs from traditional views of how plant gene expression is controlled.

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Out of Africa - Bacteria, as well (Helicobacter pylori)

2007-02-18T15:10:00.000+00:00

When man made his way out of Africa some 60,000 years ago to populate the world, he was not alone: He was accompanied by the bacterium Helicobacter pylori, which causes gastritis in many people today. Together, man and the bacterium spread throughout the entire world. This is the conclusion reached by an international team of scientists led by Mark Achtman from the Max Planck Institute for Infection Biology in Berlin, Germany. The researchers also discovered that differences developed in the genetic makeup of the bacteria populations, just as it did in that of the various peoples of the world. This has also given scientists new insight into the paths taken by man as he journeyed across the Earth.

The migration paths taken by modern man as he colonized the world. 60,000 years ago, Homo sapiens left his original home in East Africa - taking the bacterium Helicobacter pylori with him. The abbreviation kyears stands for thousand years. Image: Max Planck Institute for Infection Biology

More than half of all human beings are infected with Helicobacter pylori, a bacterium that can cause stomach ulcers. Like humans, the bacteria are also split up into numerous regional populations. A team of scientists led by Mark Achtman at the Max Planck Institute for Infection Biology, François Balloux at the University of Cambridge and Sebastian Suerbaum at Hanover Medical University have found signs of the parallel evolution of man and H. pylori. Using mathematical simulations, the researchers demonstrated that H. pylori must have left East Africa at the same time as man - around 60,000 years ago. This astonishing conformity was uncovered by scientists when they compared the nucleotide sequencing patterns in the DNA of human and H. pylori populations.

In order to characterise the individual populations, the scientists employed the principle of isolation by distance. According to this principle, the genetic distance between two populations has a linear correlation with the length of the migration paths taken since they were separated. "It's actually quite logical," explains Dr. Mark Achtman, "because in the time that elapses after a population leaves its point of origin, the number of mutations in its genetic makeup continually increases."

However, while man was spreading throughout the world, human populations had to repeatedly pass through what scientists call genetic bottlenecks: when a population shrinks, the gene pool also becomes smaller. These losses in genetic diversity linger, even when the population starts once again to increase in number. Since the Homo sapiens populations usually had to pass through several genetic bottlenecks on their way across the globe, their genetic diversity declined the further they journeyed from their origin in East Africa.

Scientists have now uncovered similar signs of historical population migration in the genetic makeup of H. pylori. However, the genetic diversity of the bacteria is larger than that of man. This paves the way for researchers to use H. pylori data to work out the migratory movements of modern man. "The parallels between the spread of man and of H. pylori are truly astonishing," says Achtman. "This bacterium could help us attain further information on aspects of human history that are still hotly disputed today if we analyzed H. pylori in conjunction with human data." For example, after leaving East Africa, the H. pylori population spread through limited localities in southern Africa, West Africa, Northeast Africa, India and East Asia. The genes of bacteria isolated in Europe, for instance, reveal influences from Central Asia - an indication that human immigrants came to Europe from Asia.

Source: Max Planck Society PR "Out of Africa - Bacteria, as well" News B / 2007 (14) February 14th, 2007

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Based on:

An African origin for the intimate association between humans and Helicobacter pylori

Bodo Linz, François Balloux, Yoshan Moodley, Andrea Manica, Hua Liu, Philippe Roumagnac, Daniel Falush, Christiana Stamer, Franck Prugnolle, Schalk W. van der Merwe, Yoshio Yamaoka, David Y. Graham, Emilio Perez-Trallero, Torkel Wadstrom, Sebastian Suerbaum and Mark Achtman

Nature advance online publication 7 February 2007 | doi:10.1038/nature05562; Received 4 October 2006; Accepted 22 December 2006; Published online 7 February 2007

Infection of the stomach by Helicobacter pylori is ubiquitous among humans. However, although H. pylori strains from different geographic areas are associated with clear phylogeographic differentiation, the age of an association between these bacteria with humans remains highly controversial. Here we show, using sequences from a large data set of bacterial strains that, as in humans, genetic diversity in H. pylori decreases with geographic distance from east Africa, the cradle of modern humans. We also observe similar clines of genetic isolation by distance (IBD) for both H. pylori and its human host at a worldwide scale. Like humans, simulations indicate that H. pylori seems to have spread from east Africa around 58,000 yr ago. Even at more restricted geographic scales, where IBD tends to become blurred, principal component clines in H. pylori from Europe strongly resemble the classical clines for Europeans described by Cavalli-Sforza and colleagues. Taken together, our results establish that anatomically modern humans were already infected by H. pylori before their migrations from Africa and demonstrate that H. pylori has remained intimately associated with their human host populations ever since.

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Birth rate, competition are major players in hominid extinctions

2007-02-17T21:32:00.000+00:00

Modern human mothers are probably happy that they typically have one, maybe two babies at a time, but for early hominids, low birth numbers combined with competition often spelled extinction.

"The lineages of primates have some traits that make it hard for them to respond to rapid perturbations in the environment," says Dr. Nina G. Jablonski [1], professor of anthropology and department head at Penn State. "Through time we see a lot of lineages become extinct when environments where the species are found become highly seasonal or unpredictable."

Primates evolved in the Paleocene and Eocene when worldwide climate was less seasonal. The beneficial environment allowed primates to evolve as relatively brainy animals that reproduce slowly. However, when climate changed so that tropical forests shrunk and the environment became patchy, many species including primate species became extinct.

"While past primate populations moved with the forest, early hominid cultures 2.5 million years ago show signs of the ability to live in marginal areas and live on more dynamic, seasonal landscapes," Jablonski told attendees on February 16 2007 at the annual meeting of the American Association for the Advancement of Science/AAAS in San Francisco.

Through time, the human lineage evolved to fill a wide variety of ecological niches, but those species that filled narrow environments, were less able to withstand the effects of climate change. Paranthropus boisei, a Pleistocene hominid, thrived around 2.5 million years ago, but disappears from the fossil record a million years ago. Paranthropus boisei became extinct when it was unable to compete with other mammals.

A specialized feeder, Paranthropus boisei dined on hard objects like seeds, tubers and bones. While it had a variety of food sources, they all required the crunching, grinding force of its teeth. Unfortunately, bush pigs and hyenas had great grinding and crushing teeth, too, and went after the same food. Paranthropus could not compete because it produced one offspring a year at most, while the others had large litters and could increase their populations at a much faster rate. Paranthropus simply could not compete reproductively and could not alter its choice of food.

"We find that the early members of the genus Homo who succeeded were super ecological opportunists," says Jablonski. "They would eat vegetation and scavenge, kill small animals and forage."

Cultural adaptations helped these opportunists to take advantage of whatever food was available. But culture did not seem to help the Neandertal (alt. Neanderthal). Tremendously successful from about 200 to 50 thousand years ago, they suffered a gradual decrease and extinction from about 30 to 26 thousand years ago.

"Neandertal was extremely adept culturally," says Jablonski. "They had big brains, a wide variety of tools and were extremely successful as active, aggressive hunters of large game. We see evidence of hunting, kill sites, butchery and even herding off cliffs. We find thrusting spears and butchering knives."

The Neandertal encountered increasing environmental seasonality with longer cold seasons and shorter periods of warm weather. Leading up to and during the last glacial maximum about 18,000 years ago, the grassy plains disappeared, taking with them the animals that relied on large expanses of grass for grazing. These animals were the prime food source for Neandertal.

At the same time, modern Homo sapiens experienced the same reduction in large animal game, but switched to also fishing, snaring small mammals like rabbits and capturing turtles and birds.

"Rather than being a specialized large mammal predator, modern humans would eat anything they could get their hands on. They eked out a living even if it meant eating grasshoppers or whatever," says Jablonski. "Even with this, modern humans barely hung on from 12 to 16,000 years ago.

"Why did Neandertal not adapt culturally?" she asks. "Why did they not start eating bunnies? They did begin fishing."

Jablonski believes that competition from modern humans was already too strong. The environment was marginal and modern humans were already foraging and small-animal collecting.

"I think they were out-competed at the very end," says Jablonski. "Modern humans simply did it better, more nimbly."

She adds that modern humans may have had storage capabilities that Neandertal did not. There is evidence that modern humans did have the capacity to store food and water in the late Pleistocene. No evidence exists that Neandertal could store either.

Both Neandertal and modern humans suffered from the primate curses of single births widely spaced. For Neandertal, cultural adaptation was not sufficient to overcome and compete with modern humans, just as Paranthropus boisei could not compete with the likes of bush pigs and hyenas.

" Can we, today, control our cultural behavior to ensure our environmental success,” says Jablonski. "Can we control growth and population density, or come up with new technology to overcome the problems we will face from the global climate change we have created?"

"We clearly have the cultural ability to do either," says the Penn State researcher. "But both require forethought and planning to face the demographic and climate change. A degree of honesty, our species is not known for." [Primatology]

Source: Penn State University PR Friday, February 16, 2007

[Neandertals, Neanderthals]

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[1] A Conversation With Nina G. Jablonski
Always Revealing, Human Skin Is an Anthropologist's Map
Published January 9, 2007 in the International Herald Tribune and The New York Times

...QUESTION: You made news in 2004 when you discovered the world's oldest chimpanzee fossil [2]. These were chimp teeth about a half-million years old. Where did you find them?

JABLONSKI: In a drawer at the National Museum of Kenya in Nairobi.

I was rummaging through this bag labeled "fossil monkeys" and I saw it. "This doesn't look like monkey," I thought. It turned out they were from an early chimp. That find proved important because there had been no chimpanzee this old in the fossil record. By analyzing it, we've learned that chimpanzees in their current form have probably existed for longer than previously thought. (Laughs) Since my find, people have been rummaging through dusty museum drawers everywhere!

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[2] First fossil chimpanzee
Sally McBrearty and Nina G. Jablonski

Nature 437, 105-108 (1 September 2005) | doi:10.1038/nature04008; Received 31 January 2005; ; Accepted 4 July 2005

There are thousands of fossils of hominins, but no fossil chimpanzee has yet been reported. The chimpanzee (Pan) is the closest living relative to humans. Chimpanzee populations today are confined to wooded West and central Africa, whereas most hominin fossil sites occur in the semi-arid East African Rift Valley. This situation has fuelled speculation regarding causes for the divergence of the human and chimpanzee lineages five to eight million years ago. Some investigators have invoked a shift from wooded to savannah vegetation in East Africa, driven by climate change, to explain the apparent separation between chimpanzee and human ancestral populations and the origin of the unique hominin locomotor adaptation, bipedalism. The Rift Valley itself functions as an obstacle to chimpanzee occupation in some scenarios. Here we report the first fossil chimpanzee. These fossils, from the Kapthurin Formation, Kenya, show that representatives of Pan were present in the East African Rift Valley during the Middle Pleistocene, where they were contemporary with an extinct species of Homo. Habitats suitable for both hominins and chimpanzees were clearly present there during this period, and the Rift Valley did not present an impenetrable barrier to chimpanzee occupation.

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Evidence of a Nonconscious Sibling Detection Mechanism (+ Podcast)

2007-02-17T06:56:00.000+00:00

Fundamental theories in evolutionary biology have long proposed that biological kinship is the foundation of the family unit. It not only creates the sense of altruism that exists among genetically related family members, but also establishes boundaries regarding sexual relations within the nuclear family. Questions have persisted, however, regarding the means by which humans recognize family members - particularly siblings - as close genetic relatives.

A team of researchers at the University of California, Santa Barbara, has found evidence of a nonconscious mechanism in the human brain that identifies genetic siblings on the basis of cues that guided our hunter-gatherer ancestors. Their findings will be published in the February 15 2007 issue of the science journal Nature [1].

In a study involving more than 600 test subjects, the researchers found that people felt more altruistic toward individuals this mechanism recognized as siblings, and, at the same time, felt a greater aversion to engaging in incestuous sexual relations with them.

"The old thinking was that Darwinism applied to humans physically, but not socially. Now we see the evolution of a mechanism that finely regulates important aspects of human social behavior," said John Tooby, professor of anthropology and co-director of the Center for Evolutionary Psychology at UCSB. He completed the study with Leda Cosmides, professor of psychology and also co-director of the Center for Evolutionary Psychology, and Debra Lieberman, a former student at the center and now a professor of psychology at the University of Hawaii. Mechanisms such as the one identified in the current study have been found in many species, he added, but their existence in humans had been a matter of controversy.

According to the researchers, the development of altruism between siblings is a result of natural selection, as are their aversions to sexual relations with one another and their aversion to sexual relations among siblings in general. The study's findings indicate these sensibilities are not primarily a result of socialization by parents or peers, but of motivational systems that evolved to respond to cues of genetic relatedness.

The question the researchers sought to answer was how siblings recognize their close genetic matches. Drawing on the socioecology of ancestral human foragers they found the answer in a set of cues that enable humans to identify their brothers and sisters as siblings. For older siblings, what the researchers refer to as "maternal perinatal association" - seeing their mothers care for infant siblings - activates the mechanism in the brain, which, in turn, increases feelings of both altruism and sexual aversion toward younger brothers and sisters.

This cue, however, is unavailable to younger siblings whose birth order precludes the opportunity of watching their mothers care for older brothers and sisters. For these siblings, the mechanism is triggered by the amount of time they live together as a family during the period from the younger siblings' infancy through adolescence. The researchers found that this "co-residence" regulates sibling altruism and sexual aversion toward adopted and step-siblings as well - individuals whom the subjects consciously believe to be genetically unrelated. "This shows that the mechanism operates independently of our beliefs about kinship," Cosmides said. "The cues regulate sibling altruism and sexual aversion, no matter what we believe."

The discovery of a mechanism designed to make family relationships non-erotic casts doubt on Sigmund Freud's view that family members are the first and most powerful objects of sexual desire, say the authors. It also helps to settle a long-running debate in anthropology about whether family relationships are socially created purely by culture, or whether evolved mechanisms in the brain play a role.

The results of the study could also have implications for health care professionals such as psychiatrists and psychologists who treat victims of incest and those who commit it.

"The theory gives a means of identifying who might be at risk," said Tooby. "Siblings who have lived separately for long periods of time have not been exposed to the cues the brain uses to determine who is a sibling. This may offer an explanation as to why someone might have an inclination toward incest." It also suggests, he says, ways of building families that would be more strongly and reliably linked together by bonds of affection.

Source: University of California PR "UCSB Study on Sibling Detection Mechanism Highlighted in 'Nature'" February 15, 2007

--------

[1] Based on:

The architecture of human kin detection
Debra Lieberman, John Tooby, and Leda Cosmides
Nature 445, 727-731 (15 February 2007) | doi:10.1038/nature05510; Received 22 July 2006; Accepted 5 December 2006

Evolved mechanisms for assessing genetic relatedness have been found in many species, but their existence in humans has been a matter of controversy. Here we report three converging lines of evidence, drawn from siblings, that support the hypothesis that kin detection mechanisms exist in humans. These operate by computing, for each familiar individual, a unitary regulatory variable (the kinship index) that corresponds to a pairwise estimate of genetic relatedness between self and other. The cues that the system uses were identified by quantitatively matching individual exposure to potential cues of relatedness to variation in three outputs relevant to the system's evolved functions: sibling altruism, aversion to personally engaging in sibling incest, and moral opposition to third party sibling incest. As predicted, the kin detection system uses two distinct, ancestrally valid cues to compute relatedness: the familiar other's perinatal association with the individual's biological mother, and duration of sibling coresidence.

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John Tooby and Leda Cosmides are authors of "Evolutionary Psychology: A Primer"

Listen to related Nature podcast on "HIV's Achilles heel, probing protein regulation, avoiding incest (with Debra Lieberman), the soppy side of science, new diabetes genes, and the darkest galaxies in the universe."

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Technorati: evolutionary, biology, biological, kinship, family, unit, foundation, altruism, sexual, relations, nuclear, siblings, genetic, relatives, nonconscious, mechanism, human, brain, science, nature, darwinism, evolution, hunter gatherer, ancestors, social, behavior, controversy, maternal, aversion, anthropology, culture, incest, kin, detection, selection, tooby, cosmides, psychology

The Nature of 'Regressive Evolution' in Cavefish Untangled

2007-02-16T18:20:00.000+00:00

"Regressive evolution," or the reduction of traits over time, is the result of either natural selection or genetic drift, according to a study on cavefish by researchers at New York University's Department of Biology, the University of California at Berkeley's Department of Integrative Biology, and the Harvard Medical School.

Previously, scientists could not determine which forces contributed to regressive evolution in cave-adapted species, and many doubt the role of natural selection in this process. Darwin himself, who famously questioned the role of natural selection in eye loss in cave fishes, said, "As it is difficult to imagine that eyes, although useless, could be in any way injurious to animals living in darkness, I attribute their loss wholly to disuse."

The research appears in the most recent issue of the journal Current Biology [A].

[Image: New York University]

Cave adaptations have evolved in many species independently, and each cave species can be considered a replicate of the same evolutionary experiment that asks how species change in perpetual darkness. This makes cavefish a rich source for the examination of the evolutionary process.

In this study, the researchers examined the genetic basis of regressive evolution in the eyes and pigmentation of Mexican cavefish. To do so, they mapped the quantitative trait loci (QTL) determining differences in eye and lens sizes as well as the melanophore - or pigment cell - number between cave and surface fish. These QTL represent genes where new mutations arose in cave populations. To better understand the genetic basis for regressive evolution, they focused on two alternative explanations for regression: natural selection, in which beneficial DNA mutations become more common over time, and genetic drift, in which the frequencies of these mutations can rise or fall over time due solely to statistical variation.

Their results suggested that eyes and pigmentation regressed through different mechanisms. Mutations in cave populations that affected eye or lens size invariably caused size reductions. This observation is consistent with evolution by natural selection and inconsistent with evolution by genetic drift. By contrast, mutations in cave populations that affected pigmentation sometimes caused increases instead of decreases in pigment cell density, consistent with evolution by random processes and genetic drift.

Allaying Darwin's doubts about the role of natural selection in eye loss, the researchers suggest that the high metabolic cost of maintaining the retina is the source of selection against eyes in the cave. By contrast, no such great cost is associated with pigmentation - thus, the two traits regress for different reasons.

Source: New York University Thursday, Feb 15, 2007 (N-280, 2006-07)

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[A] Based on the Current Biology paper:

Regressive Evolution in the Mexican Cave Tetra, Astyanax mexicanus

Meredith Protas, Melissa Conrad, Joshua B. Gross, Clifford Tabin, and Richard Borowsky
Current Biology
10.1016/j.cub.2007.01.051

The evolutionary forces driving the reduction of eyes and pigmentation in cave-adapted animals are unknown; Darwin famously questioned the role of natural selection in eye loss in cave fishes: "As it is difficult to imagine that eyes, although useless, could be in any way injurious to animals living in darkness, I attribute their loss wholly to disuse" [1]. We studied the genetics of eye and pigmentation regression in the Mexican cave tetra, Astyanax mexicanus, by mapping and quantitative trait loci (QTL) analysis. We also mapped QTL for the putatively constructive traits of jaw size, tooth number, and numbers of taste buds. The data suggest that eyes and pigmentation regressed through different mechanisms. Cave alleles at every eye or lens QTL we detected caused size reductions, consistent with evolution by natural selection but not with drift. QTL polarities for melanophore number were mixed, however, consistent with genetic drift. Arguments against a role for selection in the regression of cave-fish eyes cited the insignificant cost of their development [2, 3], but we argue that the energetic cost of their maintenance is sufficiently high for eyes to be detrimental in the cave environment. Regression can be caused either by selection or drift.

[1] Darwin, Charles. (1859). On the Origin of Species by Means of Natural Selection, or The Preservation of Favoured Races in the Struggle for Life (London: John Murray).

[2] Culver, D.C. (1982). Cave Life: Evolution and Ecology (Cambridge, MA: Harvard University Press).

[3] Eigenmann, C.H. (1909). Cave Vertebrates of America: A Study in Degenerative Evolution (Washington, D.C.: Carnegie Institution of Washington).

See Richard Borowsky's webpage The Evolutionary Biology of Cave Fishes

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Also see:

Embryonic Lens Prompts Eye Development
Elizabeth Pennisi
Science 28 July 2000: 522
DOI: 10.1126/science.289.5479.522b

A blind cave fish is providing new insight into how eyes come to be. In work reported on page 631 [B], two developmental biologists show that the lens plays a leading role in eye development in this fish. If it doesn't form properly, the researchers found, the embryo will not go on to make the cornea and other eye structures.

A copy of the above is available from www.bio.net/bionet/mm/cellbiol/2000-August/012893.html:

..The Maryland team has been studying the fish, which is called Astyanax mexicanus, for the past 6 years. Several dozen isolated populations of the species exist in northeastern Mexico, with some living in surface ponds and streams and others in caves and underground waterways. Over the past million years or so, the eyes of the underground fish have degenerated to varying degrees, while the surface fish have retained their large eyes.

To begin to understand this difference, Jeffery and Yamamoto first monitored eye development in the blind fish. They observed a precursor lens and the rudiments of the optic cup forming during the embryo's first 24 hours. But soon afterward, they found, the cells in the embryonic lens underwent programmed cell death. Other eye structures, such as the cornea and the iris, never appeared, and the retina never developed distinct, organized layers, as it does in normal eyes. The eyeball gradually sank back into the socket and was covered by a flap of skin.

Because eye development seemed to progress normally until the lens degenerated, Jeffery and Yamamoto wondered whether this disintegration was triggered by a signal from the embryo or from the lens itself. To find out, Yamamoto removed the embryonic lens from one eye of a blind cave fish embryo and replaced it with a lens from a surface fish embryo. He also did the opposite experiment, replacing the lens of an embryonic surface fish with one from a cave fish embryo. In all cases, he labeled the transplanted tissue with dye so he could track what happened to it. "It's not a complicated experiment, but it really [was] very elucidative," says Mathers.

In both types of transplants, the lens behaved as if it were still in its original embryo. The one from the cave fish degenerated, even though it was in an environment conducive to further development, whereas the lens from the surface fish thrived in the cave fish embryo and the eye differentiated, forming a cornea, anterior chamber, and iris. These results show that "the lens plays a central role" in determining whether the eye develops, comments David Beebe, a developmental biologist at Washington University School of Medicine in St. Louis. Jeffery doesn't know, however, whether the fish can actually see, as a vision test is quite difficult to devise..

[B] Related paper:

Central Role for the Lens in Cave Fish Eye Degeneration
Yoshiyuki Yamamoto, William R. Jeffery

Science 28 July 2000:
Vol. 289. no. 5479, pp. 631 - 633
DOI: 10.1126/science.289.5479.631

Astyanax mexicanus is a teleost with eyed surface-dwelling and eyeless cave-dwelling forms. Eye formation is initiated in cave fish embryos, but the eye subsequently arrests and degenerates. The surface fish lens stimulates growth and development after transplantation into the cave fish optic cup, restoring optic tissues lost during cave fish evolution. Conversely, eye growth and development are retarded following transplantation of a surface fish lens into a cave fish optic cup or lens extirpation. These results show that evolutionary changes in an inductive signal from the lens are involved in cave fish eye degeneration.

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Technorati: regressive, reverse, evolution, reduction, traits, trait, biology, darwin, cave, species, natural selection, eye, loss, cave, fishes, eyes, research, adaptations, evolutionary, process, mexican, cavefish, quantitative, loci, qtl, genetic, regression, dna, mutations, pigmentation, lens, drift, selection, origin, ecology, blind, mexico, development

DNA method gives new perspective on the Mysteries of Nature

2007-02-15T17:01:00.000+00:00

What caused the extinction of the mammoth [2] while other ice age mammals like the musk ox survived to present day? A new scientific methodological approach to detect genetic material will help researchers to solve the many mysteries of the past.

"I’m confident that the new methodological approach will be of great importance to molecular biology", says Professor Eske Willerslev at the Centre for Ancient Genetics, University of Copenhagen. One of his PhD students recently came up with a brilliant idea enabling researchers to get a full view of total ecosystems or populations dating thousands of years back in time. What usually has taken the DNA-researchers several years of laboratory work can now be done in just a few hours.

The automation of a long research process

Professor Eske Willerslev and his team find DNA traces of ancient life in areas where the ground is permanently frozen like in Siberia or Alaska. Here, inside the frozen ground, the team is able to find ancient DNA material from animals and plants that used to live in the area thousands of years ago. In order to detect the types of DNA material in a sample, the researchers normally use a DNA primer - a kind of 'fishing hook' attached to a specific piece of DNA. That particular piece of DNA is then being multiplied, cloned and sequenced (see "DNA Sequencing") which makes it possible for the researchers to identify it. However, this procedure is slow, and it takes years just to identify a fraction of the most common animals and plants available from the many DNA samples.

The technology

A new sequencing machine capable of interpreting millions of pieces of DNA in just a few hours was recently introduced. The machine alone brought in a revolution to the field, but has certain disadvantages and shortcomings. Firstly, an analysis made by the machine is quite expensive. Each analysis costs approximately DKK 45,000 and although the machine reads extensive amounts of DNA material, the cost is still considerable to a research project. Secondly, a vital problem arises when researchers try to benefit from the machine's enormous capacity by analysing samples from multiple locations or specimens in a single run in order to reduce costs. The machine simply cannot separate more than 16 samples from each other.

Eske Willerslev went to check out the machine for himself at the Danish Cattle Research Centre in Foulum - the only place in Denmark, which operates the new sequencing machine. He realised to his great disappointment that the researchers at the University of Copenhagen could not make use of the machine for their respective projects due to the disadvantages mentioned above.

A simple but brilliant idea!

Then Jonas Binladen, a PhD student from his team, came up with a simple but brilliant idea: By attaching a 'finger-print' to the tagged primers ('fishing hooks' used to amplify DNA from each sample), one should - in theory - be able to localise each of the million sequences produced in each run, to its original sample or specimen. By making it possible to process amplification products from multiple samples or specimens in the same run, the team could make use of the machine's great capacity.

The research team now wanted to test the idea. And it really did work! The results are now being published in the scientific web magazine PLoS ONE Publication [1].

According to Eske Willerslev, the new approach have great scientific potentials:

"Today, when using conventional methods to detect ancient DNA, we are only able to test a limited number of samples providing us with a somewhat random image of life in the past. Due to this new method, our knowledge will be put into a whole new perspective. For instance, finding out if species became endangered due to a dramatic change in the climate or if the decline in numbers started many years earlier than we originally thought or estimated".

Source: University of Copenhagen PR 15 February 2007

--------

[1] Based on:

Binladen J, Gilbert MTP, Bollback JP, Panitz F,
Bendixen C, et al. (2007) The Use of Coded PCR Primers Enables
High-Throughput Sequencing of Multiple Homolog Amplification Products
by 454 Parallel Sequencing. PLoS ONE 2(2): e197.
doi:10.1371/journal.pone.0000197

Abstract

Background

The invention of the Genome Sequence 20TM DNA Sequencing System (454 parallel sequencing platform) has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR) reactions and subsequent sequencing runs have been unable to combine template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources.

Methodology

We use conventional PCR with 5'-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through the high-throughput Genome Sequence 20TM DNA Sequencing System (GS20, Roche/454 Life Sciences). Each DNA sequence is subsequently traced back to its individual source through 5' tag-analysis.

Conclusions

We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate less than 0.4%). Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution of the sequences as sorted by the second nucleotide of the dinucleotide tags. As the results are based on a single GS20 run, the general applicability of the approach requires confirmation. However, our experiments demonstrate that 5' primer tagging is a useful method in which the sequencing power of the GS20 can be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of comparative genomics, complete mitochondrial analyses, population genetics, and phylogenetics.

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[2] Excerpt from "Supernova Explosion May Have Caused Mammoth Extinction"

A distant supernova that exploded 41,000 years ago may have led to the extinction of the mammoth, according to research conducted by nuclear scientist Richard Firestone of the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab).

Firestone, who collaborated with Arizona geologist Allen West on this study, unveiled this theory September 24, 2005 at the 2nd International Conference "The World of Elephants" in Hot Springs, South Dakota (see "Evidence of a Catastrophic Impact Event at the End of the Clovis Era"). Their theory joins the list of possible culprits responsible for the demise of mammoths, which last roamed North America roughly 13,000 years ago. Scientists have long eyed climate change, disease, or intensive hunting by humans as likely suspects.

Now, a supernova may join the lineup. Firestone and West believe that debris from a supernova explosion coalesced into low-density, comet-like objects that wreaked havoc on the solar system long ago. One such comet may have hit North America 13,000 years ago, unleashing a cataclysmic event that killed off the vast majority of mammoths and many other large North American mammals. They found evidence of this impact layer at several archaeological sites throughout North America where Clovis hunting artifacts and human-butchered mammoths have been unearthed. It has long been established that human activity ceased at these sites about 13,000 years ago, which is roughly the same time that mammoths disappeared.

They also found evidence of the supernova explosion's initial shockwave: 34,000-year-old mammoth tusks that are peppered with tiny impact craters apparently produced by iron-rich grains traveling at an estimated 10,000 kilometers per second. These grains may have been emitted from a supernova that exploded roughly 7,000 years earlier and about 250 light years from Earth.

"Our research indicates that a 10-kilometer-wide comet, which may have been composed from the remnants of a supernova explosion, could have hit North America 13,000 years ago," says Firestone. "This event was preceded by an intense blast of iron-rich grains that impacted the planet roughly 34,000 years ago."

Source: Berkeley Lab PR September 23, 2005

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Technorati: extinction, mammoth, ice age, mammals, musk ox, new, scientific, method, molecular, biology, ancient, genetics, dna, researchers, life, siberia, alaska, sequencing, animals, plants, revolution, technology, analysis, theory, clovis, sample, specimen, plos one, species, endangered, climate, change, genome, nucleotide, phylogenetics, era

Ancient Chimpanzee Tools fuel Evolutionary Debate (Video)

2007-02-15T12:40:00.000+00:00

Researchers have found evidence that chimpanzees from West Africa were cracking nuts with stone tools before the advent of agriculture, thousands of years ago. The result suggests chimpanzees developed this behaviour on their own, or even that stone tool use was a trait inherited from our common ancestor.

Julio Mercader, Christophe Boesch and colleagues found the stones at the Noulo site in Cote d'Ivoire, the only known prehistoric chimpanzee settlement. The stones they excavated show the hallmarks of use as tools for smashing nuts when compared to ancient human or modern chimpanzee stone tools. Also, they found several types of starch grains on the stones; part of the residue derived from cracking local nuts.

The tools are 4300 years old, which, in human terms, corresponds to the Later Stone Age.

Image caption: Examples of some of the stones that were excavated. Analysis shows they were used by chimpanzees some 4,300 years ago to crack nuts. (Credit: University of Calgary)

Before this study [1], chimpanzees were first observed using stone tools in the 19th century. Now, thanks to this new archaeological find, tool use by chimpanzees has been pushed back thousands of years. The authors suggest this type of tool use could have originated with our common ancestor, instead of arising independently among hominins and chimpanzees or through imitation of humans by chimpanzees.

This study confirmed that chimpanzees and human ancestors share for thousands of years several cultural attributes once thought exclusive of humanity, including transport of raw materials across the landscape; selection and curation of raw materials for a specific type of work and projected usage; habitual reoccupation of sites where garbage and debris accumulate; and the use of locally available resources. Nut cracking behaviour in chimpanzees is transmitted socially, and the new discoveries presented in this study shows that such behaviour has been transmitted over the course of many chimpanzee generations. Chimpanzee prehistory has deep roots!

The study of our living closest relative, the chimpanzee, constantly highlights new aspects of human evolution, and a better protection of this endangered species will guarantee that we can continue uncovering new facets of our past. Relevant finds come from all parts of the African continent, including the rainforest, and not just the classical east African homeland.

Source: Max Planck Institute for Evolutionary Anthropology - "The Chimpanzee Stone Age" February 13th, 2007

[Primatology, Archaeology]

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Video of chimpanzees using stone tools to crack nuts:

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[1] Julio Mercader, Huw Barton, Jason Gillespie, Jack Harris, Steven Kuhn, Robert Tyler, and Christophe Boesch

4300-year-old chimpanzee sites and the origins of percussive stone technology.

Published online before print February 20, 2007
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0607909104

Archaeological research in the African rainforest reveals unexpected results in the search for the origins of hominoid technology. The ancient Panin sites from Cote d'Ivoire constitute the only evidence of prehistoric ape behavior known to date anywhere in the world. Recent archaeological work has yielded behaviorally modified stones, dated by chronometric means to 4,300 years of age, lodging starch residue suggestive of prehistoric dietary practices by ancient chimpanzees. The "Chimpanzee Stone Age" pre-dates the advent of settled farming villages in this part of the African rainforest and suggests that percussive material culture could have been inherited from an common human-chimpanzee clade, rather than invented by hominins, or have arisen by imitation, or resulted from independent technological convergence.

Also see:

Excavation of a Chimpanzee Stone Tool Site in the African Rainforest
Julio Mercader, Melissa Panger, Christophe Boesch

Science 24 May 2002:
Vol. 296. no. 5572, pp. 1452 - 1455
DOI: 10.1126/science.1070268

Chimpanzees from the Tai forest of Cote d'Ivoire produce unintentional flaked stone assemblages at nut-cracking sites, leaving behind a record of tool use and plant consumption that is recoverable with archaeological methods. About 40 kilograms of nutshell and 4 kilograms of stone were excavated at the Panda 100 site. The data unearthed show that chimpanzees transported stones from outcrops and soils to focal points, where they used them as hammers to process foodstuff. The repeated use of activity areas led to refuse accumulation and site formation. The implications of these data for the interpretation of the earliest hominin archaeological record are explored.

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Technorati: evidence, chimpanzees, west, africa, nuts, agriculture, stone, tool, trait, common ancestor, prehistoric, cote d'ivoire, settlement, tools, human, later, age, hominin, study, nut, prehistory, chimpanzee, evolution, video, evolutionary, anthropology, archaeology, primatology, technology, science, panda, site, primate, chimps

Antibiotic Resistance - Evolution by Any Other Name

2007-02-14T17:20:00.000+00:00

An open access article from PLoS Biology:

Evolution by Any Other Name: Antibiotic Resistance and Avoidance of the E-Word

Citation: Antonovics J, Abbate JL, Baker CH, Daley D, Hood ME, et al. (2007) Evolution by Any Other Name: Antibiotic Resistance and Avoidance of the E-Word. PLoS Biol 5(2): e30 doi:10.1371/journal.pbio.0050030

Published February 13, 2007

The increase in resistance of human pathogens to antimicrobial agents is one of the best-documented examples of evolution in action at the present time, and because it has direct life-and-death consequences, it provides the strongest rationale for teaching evolutionary biology as a rigorous science in high school biology curricula, universities, and medical schools. In spite of the importance of antimicrobial resistance, we show that the actual word "evolution" is rarely used in the papers describing this research. Instead, antimicrobial resistance is said to "emerge," "arise," or "spread" rather than "evolve." Moreover, we show that the failure to use the word "evolution" by the scientific community may have a direct impact on the public perception of the importance of evolutionary biology in our everyday lives.

To establish whether the word "evolution" is used with different frequency by evolutionary biologists versus researchers in the medical fields, we searched scientific journals published since 2000 for research papers and reviews dealing with antimicrobial resistance. To find these papers, we used standard search engines and databases to identify papers with "antimicrobial resistance" or "antibiotic resistance" (or with names of specific antibiotics) in the titles or abstract. We deliberately did not include the word "evolution" in the searches, so as not to bias our findings in favor of articles with this word. However, we chose for further analysis only those articles that were obviously describing the evolution of antimicrobial resistance, and excluded those that described, for example, the biochemical basis of resistance or the pharmacology of antimicrobial agents. The articles were chosen in an unbiased manner by several readers who each independently read the first papers they found that met these criteria. We compared 15 articles that were primarily published in evolutionary journals (such as Evolution, Genetics, and Proceedings of the Royal Society of London Series B) with 15 articles that were published in primarily medical journals (such as The Lancet, The New England Journal of Medicine, and The Journal of Antimicrobial Chemotherapy). (A list of the papers and articles that are the basis of the results reported here is available in Text S1.)

Each reader then read the articles in their entirety. In each paper we explicitly noted and counted the words or phrases (see below) that were used to describe the evolutionary process, in order to obtain the proportion of times that the actual word "evolution" (or its lexemes such as "evolutionary" or "evolving") was used when reference was being made to the evolutionary process. Although we deliberately read equal numbers of articles in the two types of journals, we actually found that by far the majority of publications on the evolution of antibiotic resistance are in the medical field, and not in academic evolutionary biology or genetics journals. The evolution of antibiotic resistance, while critically important from a medical viewpoint, is no longer in and of itself a novel finding in evolutionary biology.

The results of our survey showed a huge disparity in word use between the evolutionary biology and biomedical research literature (Figure 1). In research reports in journals with primarily evolutionary or genetic content, the word "evolution" was used 65.8% of the time to describe evolutionary processes (range 10%-94%, mode 50%-60%, from a total of 632 phrases referring to evolution). However, in research reports in the biomedical literature, the word "evolution" was used only 2.7% of the time (range 0%-75%, mode 0%-10%, from a total of 292 phrases referring to evolution), a highly significant difference (chi-square, p less than 0.001). Indeed, whereas all the articles in the evolutionary genetics journals used the word "evolution," ten out of 15 of the articles in the biomedical literature failed to do so completely. Instead, 60.0% of the time antimicrobial resistance was described as "emerging," "spreading," or "increasing" (range 0%-86%, mode 30%-40%); in contrast, these words were used only 7.5% of the time in the evolutionary literature (range 0%-25%, mode 0%-10%). Other nontechnical words describing the evolutionary process included "develop," "acquire," "appear," "trend," "become common," "improve," and "arise." Inclusion of technical words relating to evolution (e.g., "selection," "differential fitness," "genetic change," or "adaptation") did not substantially alter the picture: in evolutionary journals, evolution-related words were used 79.1% of the time that there was an opportunity to use them (range 26%-98%, mode 50%-60%), whereas in biomedical journals they were used only 17.8% of the time (range 0%-92%, mode 0%-10%).

Figure 1. Frequency of Use of Words to Describe the Evolutionary Process in Evolutionary Journals versus Biomedical Journals

The left-hand pair of bars show percentage use of the word "evolution," and the right-hand pair of bars show percentage use of the words "emerge," "arise," or "increase." Data shown are unweighted means and standard errors, based on 15 papers in evolution or genetics journals and 15 papers in biomedical journals.

In spite of the disparity in word use, we found that the papers in the medical literature generally included professional and competent descriptions of evolutionary processes. At times words such as "develop" or "acquire" did creep in, but egregiously misleading phrases were relatively rare. For example, once we found the wording "bacteria had learned to resist antibiotics" and at another time "the activity of antimicrobial agents had decreased" (which, if read literally, implies that the antimicrobials themselves were changing rather than that the pathogens were evolving). But these were exceptions.

In reading these papers, we found no evidence that deliberate efforts were being made by medical researchers to deny that evolutionary processes were involved in the increase of antibiotic resistance. The frequent use of the term "emergence" rather than "evolution" seemed more to be the result of a simplified phraseology that has "emerged and spread" out of habit and repeated usage. It may also be that many nonprofessional evolutionary biologists consider "evolution" to be a rather nonspecific word meaning "gradual change," and that "emergence" more explicitly incorporates the component aspects of the evolutionary process, namely, mutation, recombination, and/or horizontal transfer of resistance. The word "spread" may, similarly, appear to incorporate the component processes of transmission, horizontal transfer, and increase in allele frequency. While these processes are recognized by professional evolutionary biologists as important aspects of evolutionary change, biomedical researchers may have the sense that the word "evolution" is itself too imprecise. Indeed, evolutionary biologists are sometimes accused of focusing too much attention on "change in gene frequency" rather than on the origin of variants by mutation and recombination, or on the consequences of changes in allele frequency for numerical abundance and distribution.

There is also the possibility that the failure to use the word "evolution" may reflect the mistaken sense that evolution implies processes that are long past, slow, and imperceptible. This is more worrying, as it fails to acknowledge the importance of evolution as a powerful force in present-day populations of all organisms, and not only microbes.

A critical question is whether avoidance of the word "evolution" has had an impact on the public perception of science. To investigate this, we examined whether the use of the term "evolution" in the scientific literature affects the use of this word in the popular press, i.e., whether there is evidence for "cultural inheritance" of word use. We searched articles on antimicrobial resistance in national media outlets, such as The New York Times, The Washington Post, Fox News, and the BBC (Text S1). Our results showed that the proportion of times the word "evolution" was used in a popular article was highly correlated with how often it was used in the original scientific paper to which the popular article referred (Figure 2). This clearly shows that the public is more likely to be exposed to the idea of evolution and its real-world consequences if the word "evolution" is also being used in the technical literature.

Figure 2. Use of "Evolution" in Popular Articles Based on Research Papers

This graph shows the relationship between the frequency of use of the word "evolution" in popular press articles addressing antimicrobial resistance and the frequency of its use in the corresponding research article. Most of the articles included were in the biomedical literature (Text S1). The point at the origin represents nine pairs for which "evolution" was mentioned neither in the scientific nor in the popular version. The regression is highly significant (d.f. = 21, p less than 0.0001, beta = 0.76; weighted arcsine square root transformed; points and fitted line in figure represent untransformed data).

We wondered whether these patterns were changing, so we carried out a survey of the use of the word "evolution" from 1991 to 2005 in the titles and abstracts of papers published in 14 scientific journals, as well as in the titles of proposals funded by both the US National Science Foundation (Division of Environmental Biology) and the US National Institutes of Health (National Institute of General Medical Sciences). The results showed that the use of the word "evolution" was actually increasing in all fields of biology, with the greatest relative increases in the areas of general science and medicine (Figure 3). This reflects the growing importance of evolutionary concepts in the biomedical field, and highlights even more the strange rarity with which the word "evolution" is used in the biomedical literature dealing with antimicrobial resistance. It has been repeatedly rumored (and reiterated by one of the reviewers of this article) that both the National Institutes of Health and the National Science Foundation have in the past actively discouraged the use of the word "evolution" in titles or abstracts of proposals so as to avoid controversy. Indeed, we were told by one researcher that in the title of one proposal, the authors were urged to change the phrase "the evolution of sex" to the more arcanely eloquent wording "the advantage of bi-parental genomic recombination."

Figure 3. Change over Time in the Frequency of Use of the Word "Evolution" in Journals and Grant Proposals

This figure shows change in the frequency of use of the word "evolution" in (A) paper titles and abstracts for journals classified by type and (B) titles of funded research proposals classified by US federal granting agency. Note that the data for general science journals and medical journals are shown at 10 and 100 times their values, respectively. Analysis of covariance (log of arcsine square root transformed data) showed that the rate of increase of use of the word "evolution" was significantly greater in the journal categories of general science and medical than in the evolutionary category (p less than 0.002). Journal classification was as follows: evolutionary journals: Evolution, Genetics, Heredity, Journal of Evolutionary Biology, Journal of Molecular Evolution, Molecular Biology and Evolution; general science journals: Nature, Nature Genetics, and Science; medical journals: BMJ, Clinical Infectious Diseases, JAMA, The Lancet, and The New England Journal of Medicine. Funding data are from the online data retrieval systems of the National Science Foundation (Division of Environmental Biology) (NSF [DEB]) and National Institutes of Health (National Institute of General Medical Sciences) (NIH [GMS]).

Nowadays, medical researchers are increasingly realizing that evolutionary processes are involved in immediate threats associated with not only antibiotic resistance but also emerging diseases [1,2]. The evolution of antimicrobial resistance has resulted in 2- to 3-fold increases in mortality of hospitalized patients, has increased the length of hospital stays, and has dramatically increased the costs of treatment [3,4]. It is doubtful that the theory of gravity (a force that can neither be seen nor touched, and for which physicists have no agreed upon explanation) would be so readily accepted by the public were it not for the fact that ignoring it can have lethal results. This brief survey shows that by explicitly using evolutionary terminology, biomedical researchers could greatly help convey to the layperson that evolution is not a topic to be innocuously relegated to the armchair confines of political or religious debate. Like gravity, evolution is an everyday process that directly impacts our health and well-being, and promoting rather than obscuring this fact should be an essential activity of all researchers.

Supporting Information

Text S1. Accessory Materials

Acknowledgments

We wish to thank Dr. Mark Courtney of the National Science Foundation for help with accessing and collating the word-use data for National Science Foundation grants.

References

1. Culotta E, Pennisi E (2005) Breakthrough of the year: Evolution in action. Science 310: 1878-1879.
2. Nesse RM, Stearns SC, Omenn GS (2006) Medicine needs evolution. Science 311: 1071.
3. Schwaber MJ, Navon-Venezia S, Kaye KS, Ben-Ami R, Schwartz D, et al. (2006) Clinical and economic impact of bacteremia with extended-spectrum-beta-lactamase-producing Enterobacteriaceae. Antimicrob Agents Chemother 50: 1257-1262.
4. Carmeli Y, Mozaffari E (2006) Health and economic outcomes of vancomycin-resistant enterococci. Arch Int Med 162: 2223-2228.

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Recent posts include:

"Horizontal gene transfer adds to speed and complexity of evolution"

"How 'DNA parasites' can increase spread of antibiotic resistance"

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Current related paper:

Nature Reviews Microbiology 5, 175-186 (March 2007) | doi:10.1038/nrmicro1614

The antibiotic resistome: the nexus of chemical and genetic diversity

Gerard D. Wright

Abstract

Over the millennia, microorganisms have evolved evasion strategies to overcome a myriad of chemical and environmental challenges, including antimicrobial drugs. Even before the first clinical use of antibiotics more than 60 years ago, resistant organisms had been isolated. Moreover, the potential problem of the widespread distribution of antibiotic resistant bacteria was recognized by scientists and healthcare specialists from the initial use of these drugs. Why is resistance inevitable and where does it come from? Understanding the molecular diversity that underlies resistance will inform our use of these drugs and guide efforts to develop new efficacious antibiotics.

See "The Microbial "Resistome""

Technorati: open access, plos, biology, evolution, antibiotic, resistance, human, pathogens, evolutionary, antimicrobial, research, genetics, the lancet, journal, chemotherapy, genetic, change, adaptation, process, public, science, health, medical, nature, infectious, diseases, medicine

Intelligent Design - Fighting to keep Darwin in the classroom

2007-02-13T09:09:00.000+00:00

New journal Outreach and Education in Evolution will arm educators for battle with creationists:

Nearly a century ago, John Scopes [1] was found guilty of violating a Tennessee statute when he taught evolution in his classroom. Though an appeals court later reversed his conviction on a technicality, the law lingered on the books, joined by later laws promoting "scientific creationism," and, most recently, "intelligent design." The battle to keep religiously based explanations of the history of life - especially human life - out of the science curriculum continues unabated. And though a number of educational institutions and organizations have had notable success in combating intelligent design in the classroom, what is needed now is a fresh source of evolution materials and anti-creationism ammunition for our school teachers on the front lines of this ongoing battle. Today, on Charles Darwin's 198th birthday, Springer announces plans for a new journal which will do just that.

A father-and-son team - a world-renowned evolutionary biologist and a highly skilled and sophisticated science high school teacher - have decided it's time to help science educators fight back against the strong pressure creationists are exerting on public education. In the new journal Outreach and Education in Evolution, to be published by Springer starting in March 2008, editors-in-chief Niles and Greg Eldredge intend to fill the gap between scientific literature and curriculum materials normally available to educators and students.

Niles Eldredge has been a paleontologist on the curatorial staff of the American Museum of Natural History (AMNH) since 1969. His theory of "punctuated equilibria" (co-authored with Stephen jay Gould - an SJG Official Archive is under development) is a milestone in contemporary evolutionary biology. He has combated the creationist movement through lectures, articles and books and is the curator responsible for the content of the major exhibition Darwin which opened at the AMNH in New York in November 2005, drawing in over 500,000 visitors. Greg Eldredge has a Masters Degree in Education and has been a New York City school teacher for the past three years. He is a co-author of the children's book The Fossil Factory. The two are supported by an international editorial board, made up of some of the most renowned scientists in the field.

Niles and Greg Eldredge are in agreement: "Evolution remains the central unifying idea in biology and yet is still a source of contention and confusion in the classroom. In Outreach and Education in Evolution, we'll cover the gamut, from molecules to ecosystems and from ‘intelligent design' to natural selection. We aim to make a big difference in evolutionary education."

Amelia McNamara, Vice President, Publishing, Life Sciences and Biomedicine at Springer, said, "Springer stands behind evolutionary theory as a fundamental component of modern science education, especially now since the 'intelligent design' advocates have made worrying attempts to promote their views in public schools. We are committed to helping educators teach Darwin's theory to students at all levels. Outreach and Education in Evolution will provide them with the tools they need."

Outreach and Education in Evolution, a traditional peer-reviewed journal with non-traditional features, will address these concerns. Each quarterly issue will feature peer-reviewed articles on evolution, "letters from the trenches," interviews with prominent scientists and educators, lesson plans, critical essays, cartoons, puzzles, reviews on evolution in the media (books, movies, museum openings and exhibitions) and more. The full-color online edition will offer added value, for example chat rooms, teaching resources and blogging opportunities. In addition, Springer has committed up to 10,000 US dollars annually in grants and prizes for the best paper, the best lesson plan, etc. The journal, aimed at members of the educational, museum, and scientific community involved in the teaching of evolutionary theory, will be available at a very affordable price.

Kathleen K. Smith, Director, National Evolutionary Synthesis Center, said, "As an official partner of Outreach and Education in Evolution, NESCENT is pleased to support this important endeavor. Focusing on the issues and challenges surrounding evolution education, it will provide a much needed resource for teachers presenting this important but often poorly understood subject. I believe that it will fill a valuable niche."

Douglas J. Futuyma, Distinguished Professor at Stony Brook University and President of the American Institute of Biological Sciences, added, "Increasing public understanding of science is of utmost importance. This is most urgently required with respect to evolution, which commands acceptance by less than half the American public. Springer's new journal is very timely and indeed well overdue. It is sure to play a major role in science education in the United States and beyond."

Telmo Pievani, Professor of Philosophy of Science at the University of Milan, Italy, said, "Outreach and Education in Evolution is absolutely opportune in its mission. It is much needed today for European audiences as well, where some conservative and religious leaders have grasped the political power of the tricky ideas of 'intelligent design.' For such a project, education is the main pathway."

Springer is the second-largest publisher worldwide in the science, technology, and medicine (STM) sector. Springer is part of Springer Science+Business Media, one of the world's leading suppliers of scientific and specialist literature. The group publishes over 1,700 journals and more than 5,500 new books a year, as well as the largest STM eBook Collection worldwide. Springer has operations in over 20 countries in Europe, the USA, and Asia, and some 5,000 employees.

The editors-in-chief, Niles Eldredge and Greg Eldredge, are available for interviews.

Source: Springer Press Release (Adapted) - "Fighting to keep Darwin in the classroom" Heidelberg/New York, 12 February 2007

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[1] See Tennessee vs. John Scopes: The "Monkey Trial" 1925, The Butler Act, Film footage from the actual Trial, and the 2006 video Scopes Monkey Trial: Context for Controversy from Penn State.

From Clarence Seward Darrow's "The Story of my Life" (1932), Chapter 29, The Evolution Case:

In less than a year after the ending of the Loeb-Leopold case, a most uncommon series of events brought me into even wider notice than any that had happened before. I cannot say that in this case I had nothing to do with the immediate cause of all this publicity. For the first, the last, the only time in my life, I volunteered my services in a case; it was in the Scopes case in Tennessee that I did this, because I really wanted to take part in it.

...The little town of Dayton, Tennessee, had never been heard of very far away from home. A boy, twenty-one years old, had come from Kentucky and applied for a position as teacher in the high school. His name was John T. Scopes. And he was destined to be famous. He was a modest, studious, conscientious lad. His father was a locomotive engineer and formerly a member of the American Railway Union. For his membership in this organization he had been placed on the blacklist, and after the strike he went to Kentucky to look for a job. He was a man of courage and independence, and brought up his family to have their own opinions and to stand by them.

John was a good teacher. He had the respect of the whole town of Dayton and the affection of his pupils. Among other subjects, he taught biology; the work furnished as a textbook was "Hunter's Biology." It seems strange that the Dayton school board did not adopt the first and second chapters of Genesis as a modern textbook on biology. Anyhow, Scopes told the little boys and girls that the origin of life was in the slime and ooze of the sea; that life developed from a germ, and gradually grew and changed until it reached the various forms of the life of to-day.

For this he was indicted for the crime of teaching the truth. John T. Scopes was not the first man indicted for this most heinous offense. So far as I know, he was the last, up to the present time...

[Source: Project Gutenberg of Australia]

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'Inherit the Wind' (Spencer Tracy) Creationism v Evolution film/video excerpt (9 mins) - "That rock is not more than 6,000 years old":

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Recent posts include:

"Ken Ham's 'The Lie: Evolution' - Online Book (+ Video)"

"Britain boosts intelligent-design debate"

"The Root of All Evil: The God Delusion (Online Video)"

"Intelligent Design Video: 'Unlocking the Mystery of Life'"

"Intelligent Design: 'A War on Science' (BBC Horizon Video - 49 mins)"

"Bats in flight reveal unexpected aerodynamics"

"Genetic evidence for punctuated equilibrium"

"Evolution: A Scientific American Reader (Book)"

Technorati: new, journal, springer, outreach, education, evolution, john, scopes, tennessee, scientific, creationism, intelligent design, history, life, classroom, charles, darwin, niles, eldredge, stephen, jay, gould, evolutionary, biology, natural selection, theory, education, science, monkey, trial, clarence, darrow, inherit, wind, spencer tracy, film, video, excerpt

Study shows largest North America climate change in 65 million years

2007-02-12T07:47:00.000+00:00

The largest climate change in central North America since the age of the dinosaurs 65 million years ago, a temperature drop of nearly 15 degrees Fahrenheit, is documented within the fossilized teeth of horses and other plant-eating mammals, a new study reveals.

[Image: Mesohippus]

The overwhelming majority of previous climate-change studies on the 400,000-year transition from the Eocene to the Oligocene epochs, about 33.5 million years ago, focus on marine environments, but University of Florida vertebrate paleontologist Bruce MacFadden and his colleagues turned their attention to fossils from the Great Plains.

The study were published online on February 7 in the journal Nature and appeared in the February 8 print edition.

"If a temperature change of this magnitude occurred today, Florida would have weather similar to Washington, D.C., or even farther north," said MacFadden, a curator at the Florida Museum of Natural History.

The Eocene-to-Oligocene transition (or Eocene/Oligocene Boundary) is known in the fossil record as the Grande Coupure, the "Big Cut" in French, because it marks a massive extinction of life in both marine and land environments. Scientists believe the drop in temperature was likely due to changes in oceanic currents, MacFadden said.

"Fossil mammals are archives of ancient information," MacFadden said. "Their teeth are like little time capsules that allow us to analyze chemicals captured millions of years ago within the animals' skeletons."

MacFadden said 49 of the 68 fossil teeth analyzed came from the Florida Museum's vertebrate paleontology collection. Researchers analyzed oxygen and carbon isotopes in the preserved teeth and bones of primitive fossil horses and a primitive cloven-hoofed mammal called an oreodont. Isotopes are atoms of naturally occurring elements, characterized by varying numbers of neutrons but constant numbers of protons. Oxygen isotopes act as thermometers, telling scientists at what temperature they were formed; and carbon isotopes act as barometers, revealing relative humidity.

"A combined analysis of the isotope composition of bones and teeth is a new approach to studying this boundary in time," said Alessandro Zanazzi, a doctoral student in geology at the University of South Carolina and lead author of the paper. "Tooth enamel has very low porosity and low organic matter, so it maintains the isotopic composition of when it was formed."

Donald R. Prothero, a professor of geology at Occidental College and an expert on the Eocene-to-Oligocene transition, said, "We have long known that there were some dramatic climatic changes in the earliest Oligocene based on the record of marine plankton and isotopes. But we didn't know how much change there was in degrees, although the plant changes suggested it was indeed about 15 degrees."

Prothero also said gaps in the fossil record from Nebraska may have prevented researchers from obtaining detailed temperature data, and he hopes further studies will be completed at other sites such as Wyoming.

Source: University of Florida February 7, 2007 (Adapted).

[Evolution]

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Based on the journal Nature paper:

Large temperature drop across the Eocene-Oligocene transition in central North America
Alessandro Zanazzi, Matthew J. Kohn, Bruce J. MacFadden and Dennis O. Terry
doi:10.1038/nature05551

The Eocene-Oligocene transition towards a cool climate (approx33.5 million years ago) was one of the most pronounced climate events during the Cenozoic era. The marine record of this transition has been extensively studied. However, significantly less research has focused on continental climate change at the time, yielding partly inconsistent results on the magnitude and timing of the changes. Here we use a combination of in vivo stable isotope compositions of fossil tooth enamel with diagenetic stable isotope compositions of fossil bone to derive a high-resolution (about 40,000 years) continental temperature record for the Eocene-Oligocene transition. We find a large drop in mean annual temperature of 8.2 plus or minus 3.1 degrees C over about 400,000 years, the possibility of a small increase in temperature seasonality, and no resolvable change in aridity across the transition. The large change in mean annual temperature, exceeding changes in sea surface temperatures at comparable latitudes and possibly delayed in time with respect to marine changes by up to 400,000 years, explains the faunal turnover for gastropods, amphibians and reptiles, whereas most mammals in the region were unaffected. Our results are in agreement with modelling studies that attribute the climate cooling at the Eocene-Oligocene transition to a significant drop in atmospheric carbon dioxide concentrations.

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Recent posts include:

"Titanis walleri: 'Terror bird' arrived in North America before land bridge"

"The Eocene Epoch: Ancient insects used advanced camouflage"

"New theory for mass extinctions (Geological Society of America)"

"New Study Finds that Single Impact Killed Dinosaurs"

Technorati: climate change, central, north america, age, dinosaurs, temperature, teeth, horses, new, study, mammals, mesohippus, transition, eocene, oligocene, fossils, great plains, nature, boundary, fossil, vertebrate, primitive, oreodont, bones, time, nebraska, wyoming, south carolina, epochs, cenozoic, era, evolution, mass extinction, research, amphibians, reptiles

Which Genome Variants Matter?

2007-02-10T20:48:00.000+00:00

Global Survey of the Consequences of small and large DNA variants in our Genome:

Findings published February 9 2007 in Science (see below) will accelerate the search for genes involved in human disease. The report provides a first genome-wide view of how the unique composition of genetic variation within each of us leads to unique patterns of gene activity.

By defining those genetic variants with a biological effect, the results will help to prioritise regions of the genome that are investigated for association with disease. This is an important step to understanding links between genes and disease for individuals, and across populations.

The Human Genome Project gave us the instruction manual for building a human. The HapMap and Copy Number Variation (CNV) Projects developed indices of where to find differences in the manuals of different people. One of the challenges for research into variation and disease is that most variants have no consequence for our wellbeing.

The new study gives a global view of the consequences of those differences for gene activity. The work shows that activity of more than 1000 genes is affected by sequence variation and is the first map of human populations that identifies the most important fraction of DNA variation, that which directly affects gene activity.

The research was led by scientists from the Wellcome Trust Sanger Institute, together with colleagues from the University of Cambridge, Hospital for Sick Children/University of Toronto and Harvard Medical School/Brigham and Women's Hospital.

Using the HapMap series of cell samples from four populations, they measured the activity of more than 14,000 genes in cells grown in culture. The cell samples provide a snapshot of genetic activity in one cell type. The activity of each gene was then correlated with genetic variation nearby, as defined by the HapMap, an index of single-base changes (single nucleotide polymorphisms, or SNPs) and the new index of copy number variants (CNVs).

"We've been able to look back into our history and find changes that are older and likely to be shared among populations," explained Dr Manolis Dermitzakis, senior author and Project Leader at the Wellcome Trust Sanger Institute. "But we also find many that are newer and less widespread."

"These are part of our recent evolution and a step along the way to understanding the origin and personal consequences of genetic change, not least for our wellbeing. This is a first generation map of biologically important DNA sequence variation."

The understanding of the genetic basis of gene activity will help medical research to provide individuals with information about their personal predisposition to disease.

The study was a massive undertaking: it included HapMap genotype data on 700,000 SNPs located close to genes, as well as 25,000 sites interrogated for potential structural variation to examine copy-number differences, looking at the activity of 14,000 genes in 210 unrelated individuals.

SNP and CNV variation correlated with altered activity in almost 900 and 240 genes, respectively. The HapMap has been invaluable in detecting variants involved in many diseases and these results suggest that the CNV index will prove similarly useful.

"The remarkable finding was that there is such little overlap in the genes found by using the two indices," commented Dr Matthew Hurles, also a leader of the project at the Wellcome Trust Sanger Institute. "Only about 10% of the activity variants associated with a CNV were also associated with a SNP."

"This suggests that we must include CNV studies in our searches for genetic variation associated with disease or we will be missing a lot of the important genetic effects."

The results show that at least 10-20% of heritable variation in gene activity is due to CNVs. The team found associations that included previously known examples, such as UGT2B17, which has been associated with prostate cancer, proving that the new approach works well.

They also showed for the first time that activity of other genes, located close to UGT2B17, was affected. Finding other effects in this way will enhance the search for critical genes within a region of genetic possibilities.

Some associations were not found in all four populations, two-thirds (CNVs or SNPs) being found in only one population. A gene implicated in Spinal Muscular Atrophy showed an association in three populations, but not in Yoruba from Ibadan, Nigeria. Understanding population differences can help us understand our history.

Variation in copy number can affect gene activity by altering the 'dose' of a gene, by disrupting the active parts of a gene that contain the code for protein, or by disrupting the regulatory regions of the genome that control gene activity - the on/off and dimmer switches in our genome.

"Although the simplest model for a CNV affecting gene activity is where the variant is a deletion of a gene or part of a gene, we found examples where activity is affected from a distance," commented Barbara Stranger, first author and post-doctoral fellow at the Wellcome Trust Sanger Institute. "This may occur when the CNV reduces the effectiveness of a region that works to switch the genes on or off."

The survey gives the first global view of the effects of SNPs and CNVs on gene activity. The methods and resources developed will help researchers better understand the link between differences - large and small - in our genome and our health.

Source: Wellcome Trust Sanger Institute Press Releases 8th February 2007

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Based on:

Stranger BE et al. (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes.
Science 9 February 2007: Vol. 315. no. 5813, pp. 848 - 853 DOI: 10.1126/science.1136678
Matthew Hurles and Manolis Dermitzakis are corresponding authors.

Extensive studies are currently being performed to associate disease susceptibility with one form of genetic variation, namely, single-nucleotide polymorphisms (SNPs). In recent years, another type of common genetic variation has been characterized, namely, structural variation, including copy number variants (CNVs). To determine the overall contribution of CNVs to complex phenotypes, we have performed association analyses of expression levels of 14,925 transcripts with SNPs and CNVs in individuals who are part of the International HapMap project. SNPs and CNVs captured 83.6% and 17.7% of the total detected genetic variation in gene expression, respectively, but the signals from the two types of variation had little overlap. Interrogation of the genome for both types of variants may be an effective way to elucidate the causes of complex phenotypes and disease in humans.

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Recent posts include:

"Learning the language of gene expression"

"How 'DNA parasites' can increase spread of antibiotic resistance"

"Study Detects Recent Instance of Human Evolution"

"'Silent mutations' may not always be silent..."

"And the Evolutionary Beat Goes On..."

Technorati: dna, variants, genome, science, genes, human, disease, report, gene, activity, genetic, variation, human genome project, hapmap, copy, number, research, new, study, dna, populations, cells, history, origin, change, sequence, basis, snp, effects, evolution, cancer, regulatory, regions, expression, evolutionary, complex

Professor Contends Biological Underpinnings Of Darwinian Evolution Not Valid

2007-02-09T19:36:00.000+00:00

(Jeffrey H. Schwartz and Bruno Maresca's approach is consistent with a proposed testable 'Model of an Internal Evolutionary Mechanism' based on an extension to homeostasis - see [2])

Summary: Jeffrey H. Schwartz's most recent article, "Critique of Molecular Systematics," is the next step towards a counter evolutionary theory that takes a critical look at the theory of cellular and molecular change.

Pittsburgh - Jeffrey H. Schwartz, University of Pittsburgh professor of anthropology in the School of Arts and Sciences, is working to debunk a major tenet of Darwinian evolution. Schwartz believes that evolutionary changes occur suddenly as opposed to the Darwinian model of evolution, which is characterized by gradual and constant change. Among other scientific observations, gaps in the fossil record could bolster Schwartz's theory because, for Schwartz, there is no "missing link."

In an examination that further challenges the Darwinian model, Schwartz and cowriter Bruno Maresca, a professor of biochemistry at the University of Salerno, Italy, examine the history and development of what the writers dub the "Molecular Assumption" (MA) in the article "Do Molecular Clocks Run at All? A Critique of Molecular Systematics," [1] to be published in the Febuary 9 issue of Biological Theory. [Molecular Clock]

The MA became a veritable scientific theory when, in 1962, biochemists Emil Zuckerkandl and Linus Pauling demonstrated species similarity through utilizing immunological activity between the blood's serum and a constructed antiserum. Upon observing the intensity of the serum and antiserum reactivity between human, gorilla, horse, chicken, and fish blood, Zuckerkandl and Pauling deduced "special relatedness"-the more intense the reaction, the more closely related the species were supposed to be.

Fish blood was most dissimilar, so it was assumed that the fish line diverged long before the other species. Human and gorilla blood were the most similar, meaning both species had the least amount of time to diverge. Ultimately, the Darwinian model of constant evolutionary change was imposed upon the static observation made by Zuckerkandl and Pauling.

To date, the scientific community has accepted the MA as a scientific truth. It is this assumption, which Schwartz is contemplating: "That always struck me as being a very odd thing-that this model of constant change was never challenged." Schwartz has his own theories regarding evolution, which are backed by recent developments in molecular biology.

Multicellular animals have large sections of genomes, the genetic material of an organism, which control their development. Schwartz argues that the structure of the genome does not keep changing, based on the presence of stress proteins, also known as heat shock proteins. These proteins are located in each cell, and their main function is to eliminate the potential for cellular error and change via maintaining normal cellular form through protein folding.

This regular cellular maintenance is what Schwartz points to regarding his refutation of constant cellular change. "The biology of the cell seems to run contrary to the model people have in their heads," says Schwartz, and he contends that if our molecules were constantly changing, it would threaten proper survival, and strange animals would be rapidly emerging all over the world. Consequentially, Schwartz argues that molecular change is brought about only by significant environmental stressors, such as rapid temperature change, severe dietary change, or even physical crowding.

If an organism's stress proteins are unable to cope with a significant change, the genomic structure can be modified. However, Schwartz notes, a mutation also can be recessive in an organism for many generations before it is displayed in its offspring. Whether or not the offspring survives is another matter. If it does in fact live, the presence of this genetically modified organism is not the product of gradual molecular change but a sudden display of the genetic mutation, which may have occurred myriad years prior.

However, it is not only the current molecular theory that intrigues Schwartz, but the failure of the scientific community to question an idea that is more than 40 years old: "The history of organ life is undemonstrable; we cannot prove a whole lot in evolutionary biology, and our findings will always be hypothesis. There is one true evolutionary history of life, and whether we will actually ever know it is not likely. Most importantly, we have to think about questioning underlying assumptions, whether we are dealing with molecules or anything else," says Schwartz.

Schwartz, who forensically reconstructed three life-size images of George Washington that are on display at Mt. Vernon, is a Fellow of the prestigious American Association for the Advancement of Science and the World Academy of Art and Science. He is the author of several books, including "The Red Ape: Orang-utans & Human Origins" (Westview Press, 2005) and "Sudden Origins: Fossils, Genes, and the Emergence of Species" (Wiley, 2000). He has spent more than 20 years contemplating the methods, theories, and philosophy of taking data and trying to interpret it for purposes of reconstructing evolutionary relationships.

Source: University of Pittsburgh News February 9, 2007

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[1] "Do Molecular Clocks Run at All? A Critique of Molecular Systematics,"
Jeffrey H. Schwartz and Bruno Maresca

Currently available as a PDF file from Orangutans and human origins at the Buffalo Museum of Science.

Abstract

Although molecular systematists may use the terminology of cladism, claiming that the reconstruction of phylogenetic relationships is based on shared derived states (synapomorphies), the latter is not the case. Rather, molecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change. Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the "molecular assumption."

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[2] Maresca, Bruno and Schwartz, Jeffrey H.
(2006) "Sudden Origins: a general mechanism of evolution based on stress protein concentration and rapid environmental change." The Anatomical Record, Part B: The New Anatomist, Vol. 289B: 38-46.

Abstract

A major theme in Darwinian evolutionary theory is that novelty arises through a process in which organisms and their features are gradually transformed. Morgan provided Darwinism and the evolutionary synthesis with the idea that minor mutations produce the minuscule morphological variations on which natural selection then acts, and that, although mutation is random, once a process of gradual genetic modification begins, it becomes directional and leads to morphological, and consequently organismal, transformation. In contrast, studies on the role of cell membrane physical states in regulating the expression of stress proteins in response to environmental shifts indicate the existence of a downstream mechanism that prevents or corrects genetic change (i.e., maintains "DNA homeostasis") (homeostasis). However, episodic spikes in various kinds of environmental stress that exceed an organism's cells' thresholds for expression of proper amounts of stress proteins responsible for protein folding (including stochastically occurring DNA repair) may increase mutation rate and genetic change, which in turn will alter the pattern of gene expression during development. If severe stress disrupts DNA homeostasis during meiosis (gametogenesis), this could allow for the appearance of significant mutational events that would otherwise be corrected or suppressed. In evolutionary terms, extreme spikes in environmental stress make possible the emergence of new genetic and consequent developmental and epigenetic networks, and thus also the emergence of potentially new morphological traits, without invoking geographic or other isolating mechanisms.

See "The Internal Evolutionary Mechanism: Basic Concept" (blog post - includes fibonacci analogy) and "Model of an Internal Evolutionary Mechanism" (original webpages).

And:

"An Error In Associating Lamarck With 'Adaptive Mutations'?"

"Why research an 'Internal Evolutionary Mechanism'? (1)"

"An Internal Evolutionary Mechanism and 'Direction in Evolution': Preliminary Notes"

"Common objections to 'Internal Evolutionary Mechanisms' (1)"

"Researcher gives hard thoughts on soft inheritance"

"Mother's Diet during Pregnancy can affect Grandchildren (Epigenetics)"

"'New Science' to be created at Florida State University Workshop"

"Evolution's 'Driving Force' Shifts Based on Behavior, Study Says"

Technorati: model, internal evolutionary mechanism, homeostasis, molecular, systematics, theory, change, darwinian, evolution, school, arts, anthropology, scientific, gaps, fossil, record, missing link, clock, biological, blood, human, gorilla, genome, offspring, history, origins, ape, fossils, genes, science, lamarck, evolutionary, mechanism, research, epigentics, dna

Human proteins evolving slowly thanks to multi-tasking genes

2007-02-07T09:27:00.000+00:00

Many human proteins are not as good as they might be because the gene sequences that code for them have a double role which slows down the rate at which they evolve, according to new research published in PLoS Biology.

By tweaking these dual role regions, scientists could develop gene therapy techniques that produce proteins that are even better than those found in nature, and could one day be used to help people recover from genetic disorders.

The stretch of DNA which codes for a specific protein is often interrupted by sections of apparently useless DNA - known as introns - which need to be edited out in order to produce a new protein.

Recently it has been discovered that some of the instructions on where to splice and re-splice the DNA in this editing process are contained in the coding section, or exon, of the DNA itself.

So, as well as spelling out which amino acids are needed to produce a specific protein, the part of the exon immediately next to the intron contains information that is essential for the gene editing process.

This means that these parts of genes evolve particularly slowly, making the proteins they encode for not as good as they could be had evolutionary processes been more able to improve them over time.

"Our research suggests that a gene with many exons would evolve at under half the rate of the same one that had no introns, simply owing to the need to specify where to remove introns," said Professor Laurence Hurst from the University of Bath (UK), who worked with colleagues from the University of Lausanne (Switzerland) on the project.

"This is one of the strongest predictors of rates of protein evolution known, indicating that this dual coding role is vastly more influential than previously believed."

The finding could have major implications for medicine and the development of gene therapy techniques in which people with a defective gene are given the correct version.

"Our results suggest that we could make the replacement gene even better than the normal version," said Professor Hurst, from the Department of Biology and Biochemistry at the University of Bath.

"We would just need to remove the introns and tweak the protein at the sites that were dual coding.

"We also found that genes that have lost their introns many millions of years ago evolve especially fast near where the introns once resided.

"This indicates that this tweaking of the dual role sections of genes is also what evolution does when introns are removed."

The research was funded by the Biotechnology and Biological Sciences Research Council, the Swiss National Science Foundation and the Center for Integrative Genomics at the University of Lausanne.

Source: University of Bath 6 February 2007

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Based on the paper "Splicing and the Evolution of Proteins in Mammals"

Citation:

Parmley JL, Urrutia AO, Potrzebowski L, Kaessmann H, Hurst LD (2007) Splicing and the Evolution of Proteins in Mammals. PLoS Biol 5(2): e14 doi:10.1371/journal.pbio.0050014

Excerpts:

Authors Summary

Most of the DNA in our genes is actually not involved in the specification of proteins. Rather, the bits with the protein-coding information (exons) are separated from each other by noncoding bits, introns. Before a gene can be translated into protein these introns are removed and the exons are spliced back together to be translated into protein. While information about which DNA to remove is largely in the introns themselves, parts of the exons near the intron - exon boundary can, for example, function as splice enhancer elements. In principle, then, these parts of exons have two functions: to specify the amino acids of the resulting protein and to enable the correct removal of introns. What impact might this have on a gene's evolution? We show that near intron - exon boundaries, amino acid usage is biased towards nucleotides involved in splice control. Moreover, these parts of genes evolve especially slowly. Indeed, we estimate that a gene with many exons would evolve at under half the rate of the same gene with no introns, simply owing to the need to specify where to remove introns. Likewise, genes that have lost their introns evolve especially fast near the former intron's location. Thus, human proteins may not be as optimised as they could be, as their sequence is serving two conflicting roles.

Abstract

It is often supposed that a protein's rate of evolution and its amino acid content are determined by the function and anatomy of the protein. Here we examine an alternative possibility, namely that the requirement to specify in the unprocessed RNA, in the vicinity of intron - exon boundaries, information necessary for removal of introns (e.g., exonic splice enhancers) affects both amino acid usage and rates of protein evolution. We find that the majority of amino acids show skewed usage near intron - exon boundaries, and that differences in the trends for the 2-fold and 4-fold blocks of both arginine and leucine show this to be owing to effects mediated at the nucleotide level. More specifically, there is a robust relationship between the extent to which an amino acid is preferred/avoided near boundaries and its enrichment/paucity in splice enhancers. As might then be expected, the rate of evolution is lowest near intron - exon boundaries, at least in part owing to splice enhancers, such that domains flanking intron - exon junctions evolve on average at under half the rate of exon centres from the same gene. In contrast, the rate of evolution of intronless retrogenes is highest near the domains where intron - exon junctions previously resided. The proportion of sequence near intron - exon boundaries is one of the stronger predictors of a protein's rate of evolution in mammals yet described. We conclude that after intron insertion selection favours modification of amino acid content near intron - exon junctions, so as to enable efficient intron removal, these changes then being subject to strong purifying selection even if nonoptimal for protein function. Thus there exists a strong force operating on protein evolution in mammals that is not explained directly in terms of the biology of the protein.

Introduction

Why do some parts of proteins evolve more slowly than others? Why, in turn, do some proteins evolve more slowly than others? Intragenic conserved regions are typically considered to reflect domains of functional importance to the protein [1]. Similarly, proteins with a high density of important functional sites should evolve slowly. There are, however, potentially multiple other correlates to rates of protein evolution [1]. The expression parameters of a gene (rate of expression, protein abundance, and number of tissues in which a gene is expressed) are consistently reported to be important predictors [2 - 5]. This may in part reflect selection to resist mistranslation [6]. Other possible covariates include essentiality and the number of protein interactions, but the issues here are more contentious, not least because of covariance with expression parameters [7 - 17]. Here we test the hypothesis that selection acting to ensure that introns are correctly removed skews amino acid content in predictable ways and imposes constraints on rates of protein evolution.

In mammalian genes, which are rich in introns [18], correct removal of introns often requires the presence, in the flanking exons, of splice-enhancer domains, these being short (six nucleotide) blocks required for binding of serine/arginine-rich proteins [19]. The need for splice enhancers can impact the use of synonymous codons in the domains flanking intron - exon junctions, such that when a synonymous codon is used commonly in splice enhancers it is preferred over its less commonly used synonym [20,21]. Moreover, selection to preserve splice enhancers affects both the synonymous single nucleotide polymorphism profile [22,23] and the rate of evolution at synonymous sites of splice-enhancer-associated domains [24].

Might the same forces also act to cause skews in amino acid usage in the vicinity of intron - exon junctions? In a preliminary analysis, we showed that there is a tendency for enrichment near boundaries of an amino acid whose codons are common in splice enhancers: lysine is coded by AAA and AAG, both of which are common in splice enhancers, and at both 5' and 3' ends of exons, lysine's proportional usage increases [24]. Is it more generally the case that an amino acid's usage increases near intron - exon junctions if it commonly features in splice enhancers? Conversely, are some amino acids avoided near such boundaries if they are rare in splice-enhancer domains? To address these issues, we derive patterns of amino acid preference in the vicinity of intron - exon boundaries and compare these patterns with a metric of enrichment of amino acids in splice enhancers relative to rates of usage in the genome. In turn, we ask whether selective constraints are stronger near intron - exon boundaries, and whether such constraints explain much of the variation between proteins in their rate of evolution.

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Recent posts include:

"Developmental Biology: Special Issue on the Sea Urchin Genome"

"Genetics of eye colour unlocked"

"'Silent mutations' may not always be silent..."

"Balancing Robustness and Evolvability"

"Evolution: RNA Silencing Sheds Light on the RNA World"

Technorati: human, proteins, gene, code, evolve, rate, new, research, plos, biology, therapy, nature, genetic, disorders, dna, protein, introns, exon, amino acids, intron, genes, evolution, defective, biochemistry, exons, introns, science, mammals, nucleotides, rna, sequence, genetics

Ken Ham's 'The Lie: Evolution' - Online Book (+ Video)

2007-02-06T09:45:00.000+00:00

The Education Resources page of Answers in Genesis currently lists (and links to) Ken Ham's "The Lie: Evolution" as a 'Featured Online Book'. No doubt it will eventually also be linked to from their Online resources page

Table of Contents

Foreword

By Luther D. Sunderland, author of Darwin's Enigma - Ebbing the Tide of Naturalism [1]:

..Mr. Ham shows that Genesis, in particular, is a dependable account of actual events that are supported by solid scientific evidence. Furthermore, he shows how the questioning of this foundational book of the Bible, even by many Christians, has led to the degeneration of society so that the only moral codes it accepts are based upon "survival of the fittest," "do your own thing," and "if it feels good, do it." There are no moral absolutes.

Introduction

..My parents knew that evolution was wrong because it was obvious from Genesis that God had given us the details of the creation of the world. These details were important foundational truths for the rest of Christianity. At that time, the current wealth of materials on the creation/evolution issue produced, for instance, by the Institute for Creation Research, were not available. I recall going to my local minister and asking him what to do about the problem. He told me to accept evolution but then add it to the Bible so that God used evolution to bring all forms of life into being. This was an unsatisfactory solution to the problem. If God did not mean what He said in Genesis, then how could one trust Him in the rest of the Scriptures?

Chapter 1: Christianity Is Under Attack

Chapter 2: Evolution Is Religion

..The term "evolutionist" is used extensively throughout the following chapters. In other parts of this book, we will discuss the ideas of Christians who try to marry the concepts of evolution and the Bible. However, because the majority of evolutionists are not Christians, I wish the reader to understand that the term "evolutionist" is used to mean those who believe that evolution - in the sense of time, chance, and struggle for survival - rather than the God of the Bible, is responsible for life.

Chapter 3: Creation Is Religion

..However, we no longer live in the world God originally created. Because our first parents placed human opinion above God's Word (as we continue to do), struggle and death entered the world, and God cursed the creation. Charles Darwin called this struggle to the death "natural selection" and offered his theory as a substitute for the Creator. Evolutionists later added accidental changes in heredity (mutations) to their theory. But death and accident do not create: instead they bring disease, defects, and decay into the world God created.

Chapter 4: The Root of the Problem

..Why do evolutionists not want to admit that evolution is really a religion?

It is related to the fact that whatever you believe about your origins does affect your whole world view, the meaning of life, etc. If there is no God and we are the result of chance random processes, it means there is no absolute authority. And if there is no one who sets the rules, then everyone can do whatever he likes or hopes he can get away with. Evolution is a religion which enables people to justify writing their own rules.

Chapter 5: Crumbling Foundations

..Students in most of our schools are given a totally anti-biblical foundation: the foundation of evolution. This foundation, of course, will not allow the Christian structure to stand. A structure of a different type - humanism - is the one built on this foreign foundation.

Chapter 6: Genesis Does Matter

..Atheistic evolutionary philosophy says: "There is no God. All is the result of chance and randomness. Death and struggle are the order of the day, not only now, but indefinitely into the past and future." If this is true, there is no basis for right and wrong. The more people believe in evolution, the more they are going to say, "There is no God. Why should I obey authority? Why should there be rules against aberrant sexual behavior? Why should there be rules concerning abortion? After all, evolution tells us we are all animals. So, killing babies by abortion is no worse than chopping the head off a fish or a chicken." It does matter whether you believe in evolution or creation! It affects every area of your life.

Chapter 7: Death: A Curse and a Blessing

..Each Lord's Day we rejoice in Christ's resurrection, and thus the conquering of sin and death.

But evolution destroys the very basis of this message of love. The evolutionary process is supposed to be one of death and struggle, cruelty, brutality, and ruthlessness. It is a ghastly fight for survival, elimination of the weak and deformed. This is what underlies evolution - death, bloodshed, and struggle bringing man into existence.

Chapter 8: The Evils of Evolution

..Particularly in the Western nations, where Christian ethics were once very prevalent, Darwinian evolution provided a justification for people not to believe in God and, therefore, to do those things which Christians would deem as wrong. As one non-Christian scientist said in a TV interview, "Darwinian evolution helped make atheism respectable."

Chapter 9: Evangelism in a Pagan World

..There is a war going on in society - a very real battle. The war is Christianity versus humanism, but we must wake up to the fact that, at the foundational level, it's really creation versus evolution.

Having agreed on all this, however, we must remember that our enemies are not the humanists and evolutionists themselves, but the powers of darkness that have deceived them.

Chapter 10: Wake Up, Shepherds!

..At one seminar, a lady told me that evolutionism had destroyed her faith in the Scriptures. She had such an emptiness in her life that she cried to the Lord and prayed for a solution to this problem. She was finding it impossible to trust the Scriptures. She was led to a library and happened to find a book on the Gap Theory. (The Gap Theory basically allows for billions of years between Genesis 1:1 and Genesis 1:2.) She was thrilled at this explanation and set about rebuilding her Christian life. At the end of the seminar, she came to me and exclaimed what a thrill it was to know she did not have to believe the Gap Theory.

Chapter 11: Creation, Flood, and Coming Fire

..There is a prophecy in 2 Peter 3 concerning the last days of this earth's history, and it very much relates to the whole creation/evolution issue:

Knowing this first, that there shall come in the last days scoffers, walking after their own lusts, and saying, Where is the promise of his coming? for since the fathers fell asleep, all things continue as they were from the beginning of the creation. For this they willingly are ignorant of, that by the word of God the heavens were of old, and the earth standing out of the water and in the water: Whereby the world that then was, being overflowed with water, perished: But the heavens and the earth, which are now, by the same word are kept in store, reserved unto fire against the day of judgment and perdition of ungodly men (2 Pet. 3:3–7).

Appendix 1: Twenty Reasons Why Genesis and Evolution Don't Mix

..For those who try to harmonize evolution with Genesis, the order of evolution must compare with the order of events in Genesis. There are a number of problems here. The basic tenets of evolution totally conflict with the order in Genesis. For instance, Genesis teaches that God created fruit trees before fish - plants on day three, fish on day five. Evolution teaches that fish came before fruit trees. Evolution teaches that first life began in the sea, and after millions of years life was established on the land. The Bible teaches that the earth was first created covered with water: evolutionary teaching is that the earth first began as a hot molten blob. There is no way that the order of events according to evolution and Genesis can be reconciled.

Appendix 2: Why Did God Take Six Days?

..Probably one of the major reasons people tend not to take the days of Genesis as ordinary days is because they believe that scientists have proved the earth to be billions of years old. But this is not true. There is no absolute age-dating method to determine how old the earth is. Besides this, there is much evidence consistent with a belief in a young age for the earth, perhaps only thousands of years.

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The Ken Ham video "Do Animals Evolve?":