Evolution Research - Wanted Papers

Re: 'Wanted: Epigenetic variation and inheritance in mammals'

2006-10-03T12:18:00.000+01:00

Current Opinion in Genetics and Development:

Epigenetic variation and inheritance in mammals (Review Article)

In Press, Corrected Proof, Available online 26 September 2006

Vardhman K Rakyan and Stephan Beck.

Abstract:

What determines phenotype is one of the most fundamental questions in biology. Historically, the search for answers had focused on genetic or environmental variants, but recent studies in epigenetics have revealed a third mechanism that can influence phenotypic outcomes, even in the absence of genetic or environmental heterogeneity. Even more surprisingly, some epigenetic variants, or epialleles, can be inherited by the offspring, indicating the existence of a mechanism for biological heredity that is not based on DNA sequence. Recent work from mouse models, human monozygotic twin studies, and large-scale epigenetic profiling suggests that epigenetically determined phenotypes and epigenetic inheritance are more common than previously appreciated.
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I've managed to get a copy from one of the authors! (via the Abstract link on the original post: "Wanted: Epigenetic variation and inheritance in mammals")

Technorati: current, opinion, genetics, development, epigenetic, variation, inheritance, mammals, review, article, abstract, phenotype, biology, genetic, environmental, variants, epigenetics, mechanism, phenotypic, epigenetic, offspring, biological, heredity, dna, sequence, mouse, models, human, twins, studies, large, scale, profiling, phenotypes

Wanted: Epigenetic variation and inheritance in mammals

2006-10-01T09:19:00.000+01:00

Current Opinion in Genetics and Development:

Epigenetic variation and inheritance in mammals (Review Article)

In Press, Corrected Proof, Available online 26 September 2006

Vardhman K Rakyan and Stephan Beck.

Abstract:

Re: 'Wanted: Inherited epigenetic variation - revisiting soft inheritance'

2006-08-21T20:56:00.000+01:00

Perspective: Nature Reviews Genetics 7, 395-401 (May 2006) | doi:10.1038/nrg1834

Opinion: Inherited epigenetic variation - revisiting soft inheritance

Eric J. Richards

Phenotypic variation is traditionally parsed into components that are directed by genetic and environmental variation. The line between these two components is blurred by inherited epigenetic variation, which is potentially sensitive to environmental inputs. Chromatin and DNA methylation-based mechanisms mediate a semi-independent epigenetic inheritance system at the interface between genetic control and the environment. Should the existence of inherited epigenetic variation alter our thinking about evolutionary change?

[Associated Washington University of St. Louis news release]
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The full text of "Inherited epigenetic variation - revisiting soft inheritance" is now available as a pdf file here.

[Original Post: 'Wanted: Inherited epigenetic variation - revisiting soft inheritance']

technorati tags: nature, reviews, genetics, inherited, epigenetic, variation, inheritance, soft, phenotypic, chromatin, dna, environment, evolutionary, washington, st.+louis

Wanted: Inherited epigenetic variation - revisiting soft inheritance

2006-08-04T06:15:00.000+01:00

Perspective: Nature Reviews Genetics 7, 395-401 (May 2006) | doi:10.1038/nrg1834

Opinion: Inherited epigenetic variation - revisiting soft inheritance

Eric J. Richards

[Associated Washington University of St. Louis news release]

technorati tags: nature, reviews, genetics, inherited, epigenetic, variation, inheritance, soft, phenotypic, chromatin, dna, environment, evolutionary, washington, st.+louis

Wanted: Evolution of the ear and hearing: issues and questions

2006-03-18T23:30:00.000+00:00

Popper, A.N. and Fay, R.R. (1997) Evolution of the ear and hearing: Issues and questions. Brain, Behav, Evol, 50:213-221.

Abstract:

The ear appears to have arisen early in the evolution of the vertebrates. While there are significant interspecific differences in ear structure, it appears that receptor cell structure and the basic function of the ear and auditory system are similar among all vertebrate groups. In this paper we present the evolution of the sensory hair cells of the ear, the origins of the ear itself, and selected functions of the sense of hearing. We argue that there have been strong selective pressures in most vertebrate groups for the sorts of sound encoding and processing abilities that result in the efficient detection, localization, and identification of sound sources in noisy environments. Many of the encoding and processing strategies underlying these functions are shared as well.

technorati tags: ear, evolution, brain, vertebrates, sound

Wanted: Punctuated Equilibria - The Tempo and Mode of Evolution Reconsidered

2006-03-15T11:30:00.000+00:00

Punctuated Equilibria: The Tempo and Mode of Evolution Reconsidered
Stephen Jay Gould, Niles Eldredge
Paleobiology, Vol. 3, No. 2 (Spring, 1977) , pp. 115-151

Abstract:

We believe that punctuational change dominates the history of life: evolution is concentrated in very rapid events of speciation (geologically instantaneous, even if tolerably continuous in ecological time). Most species, during their geological history, either do not change in any appreciable way, or else they fluctuate mildly in morphology, with no apparent direction. Phyletic gradualism is very rare and too slow, in any case, to produce the major events of evolution. Evolutionary trends are not the product of slow, directional transformation within lineages; they represent the differential success of certain species within a clade - speciation may be random with respect to the direction of a trend (Wright's rule).

As an a priori bias, phyletic gradualism has precluded any fair assessment of evolutionary tempos and modes. It could not be refuted by empirical catalogues constructed in its light because it excluded contrary information as the artificial result of an imperfect fossil record. With the model of punctuated equilibria, an unbiased distribution of evolutionary tempos can be established by treating stasis as data and by recording the pattern of change for all species in an assemblage. This distribution of tempos can lead to strong inferences about modes. If, as we predict, the punctuational tempo is prevalent, then speciation - not phyletic evolution - must be the dominant mode of evolution.

We argue that virtually none of the examples brought forward to refute our model can stand as support for phyletic gradualism; many are so weak and ambiguous that they only reflect the persistent bias for gradualism still deeply embedded in paleontological thought. Of the few stronger cases, we concentrate on Gingerich's data for Hyopsodus and argue that it provides an excellent example of species selection under our model. We then review the data of several studies that have supported our model since we published it five years ago. The record of human evolution seems to provide a particularly good example: no gradualism has been detected within any hominid taxon, and many are long-ranging; the trend to larger brains arises from differential success of essentially static taxa. The data of molecular genetics support our assumption that large genetic changes often accompany the process of speciation.

Phyletic gradualism was an a priori assertion from the start - it was never "seen" in the rocks; it expressed the cultural and political biases of 19th century liberalism. Huxley advised Darwin to eschew it as an "unnecessary difficulty." We think that it has now become an empirical fallacy. A punctuational view of change may have wide validity at all levels of evolutionary processes. At the very least, it deserves consideration as an alternate way of interpreting the history of life.

technorati tags: punctuated+equilibria, gould, eldredge, calde, fossil, evolution, genetics, darwin, huxley

Wanted: Inverse Correlation between an Organ's Cancer Rate and Its Evolutionary Antiquity

2006-03-12T23:05:00.000+00:00

Journal: Organogenesis
Title:
Inverse Correlation between an Organ's Cancer Rate and Its Evolutionary Antiquity

Author(s):
Jamie A. Davies
View Article Vol: 1 | Issue: 2 | oct/nov/dec 2004 | pgs: 60-63 | Brief Communication

Abstract:

Human cancer rates vary dramatically across the range of internal organs in the body, but there is no single model to explain the variation and there is also no obvious overall pattern to it. Theories have been proposed to account for high rates in particularly cancer-prone organs, and they usually concentrate on the peculiar vulnerability of certain cells to mutation (eg lung cells' direct exposure to airborne carcinogens). These explanations are valuable for understanding mechanisms of disease and also for cancer prevention, but they neither address the overall distribution of cancers nor the possibility that some states of differentiation may be intrinsically less stable than others to the effects of random mutation, a possibility predicted on purely theoretical grounds many years ago. This brief report describes an overall pattern to human organ-specific cancer incidence data and shows that organ-specific cancer rates correlate negatively with an organ's evolutionary antiquity. Although the relationship may just be coincidental, it suggests the possibility that recently-evolved differentiation states may be intrinsically more vulnerable to neoplastic change. Extrapolation of the regression line to a cancer incidence of zero equates to a level of tissue organization typical of 660Myr ago; the inferred beginning of neoplasia therefore coincides with the rise of complex multicellular animals.

technorati tags: random+mutations, organogenesis, cancer, evolution, antiquity

Wanted: Evolutionary morphology and Evo-devo: Hierarchy and novelty

2006-03-09T22:42:00.000+00:00

Theory in Biosciences
Volume 124, Issues 3-4 , 1 March 2006, Pages 317-333
Alan C. Love

Abstract

Although the role of morphology in evolutionary theory remains a subject of debate, assessing the contributions of morphological investigation to evolutionary developmental biology (Evo-devo) is a more circumscribed issue of direct relevance to ongoing research. Historical studies of morphologically oriented researchers and the formation of the Modern Synthesis in the Anglo-American context identify a recurring theme: the synthetic theory of evolution did not capture multiple levels of biological organization. When this feature is incorporated into a philosophical framework for explaining the origin of evolutionary innovations and novelties (a core domain of inquiry in Evo-devo) two specific roles for morphology can be described: (1) the conceptualization and operational identification of the targets of explanation; and (2) the elucidation of causal interactions at higher levels of organization during ontogeny and through evolutionary time. These roles are critical components of any adequate explanation of innovation and novelty though not exhaustive of the parts played by morphology in evolutionary investigation. They also invite reflection on what counts as an evolutionary cause in contemporary evolutionary biology.

technorati tags: morphology, modern+synthesis, innovation, development, evo-devo, biology

Wanted: Modularity and sense organs in the blind cavefish, Astyanax mexicanus.

2006-03-01T15:08:00.000+00:00

Franz-Odendaal TA, Hall BK
Modularity and sense organs in the blind cavefish, Astyanax mexicanus.
Evol Dev. 2006 Jan-Feb;8(1):94-100.

Mexican tetra (Astyanax mexicanus) exist as two morphs: a sighted (surface) form and a blind (cavefish) form. In the cavefish, some modules are lost, such as the eye and pigment modules, whereas others are expanded, such as the taste bud and cranial neuromast modules. We suggest that modularity can be viewed as being nested in a manner similar to Bauplane so that modules express unique sets of genes, cells, and processes. In terms of evolution, we conclude that natural selection can act on any of these hierarchical levels within modules or on all the sensory modules as a whole. We discuss interactions within and between modules with reference to the blind cavefish from both genetic and developmental perspectives. The cavefish represents an illuminating example of module interaction, uncoupling of modules, and module expansion.

I'm also interested in two other papers by Brian Hall. I only have the citations though:

Hall, B.K. (1984). Developmental mechanisms underlying the formation
of atavisms. Biol. Rev. Camb. Philos. Soc. 59, 89-124.

12. Hall, B.K. (1995). Atavisms and atavistic mutations. Nat. Genet.
10, 126-127.

John Latter

(guess who's learned to use blockquotes!)

UPDATE: Reprints of Modularity and sense organs in the blind cavefish can be requested from Tamara Franz-Odentaal at the email address here

technorati tags: modularity, cavefish, bauplane, genes, cells, modules, atavisms, atavistic, evolution

Wanted: The case of the one-eyed brine shrimp: are ancient atavisms possible?

2006-02-27T23:55:00.000+00:00

Journal of Natural History, Volume 33, Number 6, 1 June 1999, pp. 791-798(8)

Abstract:

In the cyclopean mutant of the anostracan branchiopod Artemia franciscana, paired stalked eyes are replaced by a single, median, sessile, eye resembling that found in certain monocular branchiopod orders. This eye, its nerve supply, and skeletal support, comprise a perfect unit which appears to be a spontaneous atavism. However, according to recent calculations this cannot be so. These suggest that while re-activation of long-silent genes, on which atavisms depend, can occur after a lapse of up to 6 million years (My), this is impossible after 10 My unless the gene is maintained by active selection, which cannot apply here. However, the Anostraca is an old group, and the atavism (if such it be) is clearly very ancient. Efficient DNA repair, not considered in the calculations, offers a possible explanation of how silent genes may survive for longer than the suggested period of viability. Particularly intriguing is that a binocular condition is primitive and the cyclopean derived, which has remarkable evolutionary implications. It suggests two reversals during the history of the Anostraca from paired sessile eyes to a long-extinct monocular condition such as prevails in certain other branchiopods, later to paired stalked eyes. Other ancient atavisms also challenge the claim that silent genes have short life spans. This problem, which has fundamental biological implications, is still sub-judice. [Evolution, shrimp]

technorati tags: mutant, eye, atavism, dna, silent, genes, evolution, shrimp, natural+history

Wanted: Adaptive Evolution of Eye Degeneration in the Mexican Blind Cavefish

2006-02-24T22:44:00.000+00:00

Adaptive Evolution of Eye Degeneration in the Mexican Blind Cavefish -- Jeffery 96 (3): 185 -- Journal of Heredity:

"The evolutionary mechanisms responsible for eye degeneration in cave-adapted animals have not been resolved. Opposing hypotheses invoking neural mutation or natural selection, each with certain genetic and developmental expectations, have been advanced to explain eye regression, although little or no experimental evidence has been presented to support or reject either theory. Here we review recent developmental and molecular studies in the teleost Astyanax mexicanus, a single species consisting of a sighted surface-dwelling form (surface fish) and many blind cave-dwelling forms (cavefish), which shed new light on this problem. The manner of eye development and degeneration, the ability to experimentally restore eyes, gene expression patterns, and comparisons between different cavefish populations all provide important clues for understanding the evolutionary forces responsible for eye degeneration. A key discovery is that Hedgehog midline signaling is expanded and inhibits eye formation by inducing lens apoptosis in cavefish embryos. Accordingly, eyes could have been lost by default as a consequence of natural selection for constructive traits, such as feeding structures, which are positively regulated by Hh signaling. We conclude from these studies that eye degeneration in cavefish may be caused by adaptive evolution and pleiotropy."

technorati tags: evolution, eye, degeneration, mexican, blind, cavefish, neutral+mutation, natural+selection, genetic, regression, species, development, hedgehog, midline, signalling, embryos, adaptive, pleiotropy

Wanted: Mutation for Survival

2006-02-23T14:54:00.000+00:00

Rosenberg, S. M. (1997). "Mutation for survival." Current Opinion in Genetics & Development 7(6): 829-834.

Abstract:

Adaptive mutations appear in response to selection. In the best-studied system, the two most controversial issues were resolved this year. The mutations are neither Lamarckian nor a peculiarity of bacterial sex, as had been suggested. They occur genome-wide in a hypermutable subpopulation of stressed cells. Genomic 'hot' and 'cold' regions may explain previous failures to detect similar mutations in other systems and at other sites. Stationary phase specific limitation of mismatch repair has also been discovered.

technorati tags: mutation, survival, adaptive+mutations, lamarckian, sex, genome, hypermutable, cells, stressed

Wanted: The Development of Archosaurian First-Generation Teeth in a Chicken Mutant

2006-02-21T23:26:00.000+00:00

Current Biology, Vol 16, 371-377, 21 February 2006

Summary:

Modern birds do not have teeth. Rather, they develop a specialized keratinized structure, called the rhamphotheca, that covers the mandible, maxillae, and premaxillae. Although recombination studies have shown that the avian epidermis can respond to tooth-inductive cues from mouse or lizard oral mesenchyme and participate in tooth formation 1; 2, attempts to initiate tooth development de novo in birds have failed. Here, we describe the formation of teeth in the talpid2 chicken mutant, including the developmental processes and early molecular changes associated with the formation of teeth. Additionally, we show recapitulation of the early events seen in talpid2 after in vivo activation of β-catenin in wild-type embryos. We compare the formation of teeth in the talpid2 mutant with that in the alligator and show the formation of decidedly archosaurian (crocodilian) first-generation teeth in an avian embryo. The formation of teeth in the mutant is coupled with alterations in the specification of the oral/aboral boundary of the jaw. We propose an epigenetic model of the developmental modification of dentition in avian evolution; in this model, changes in the relative position of a lateral signaling center over competent odontogenic mesenchyme led to loss of teeth in avians while maintaining tooth developmental potential.

Related terms: Evolution

John Latter

Model of an Internal Evolutionary Mechanism
http://members.aol.com/jorolat/index.html

UPDATE: Reprints can be requested from the email addresses here

technorati tags: birds, mandible, epidermis, mouse, lizard, tooth+formation, teeth, chicken, evolution, developmental, molecular, embryo, alligator, formation, epigenetic, jaw, recapitulation

Wanted: The origin of mutants

2006-02-19T18:56:00.000+00:00

[The origin of mutants: Cairns, Overbaugh & Miller, Nature, Sep '88]

Abstract:

Nucleic acids are replicated with conspicuous fidelity. Infrequently, however, they undergo changes in sequence, and this process of change (mutation) generates the variability that allows evolution. As the result of studies of bacterial variation, it is now widely believed that mutations arise continuously and without any consideration for their utility. In this paper, we briefly review the source of this idea and then describe some experiments suggesting that cells may have mechanisms for choosing which mutations will occur.

Related terms: Evolution, e. coli and bacteria, directed mutation.

John Latter

Model of an Internal Evolutionary Mechanism
http://members.aol.com/jorolat/index.html

UPDATE: I've now got a copy!

technorati tags: cairns, origin+of+mutants, nature, overbaugh, miller, nucleic+acids, evolution, mutations, bacteria, directed+mutation, e.+coli

Info wanted on two intriguing 'Lamarckian' experiments

2006-02-16T12:42:00.000+00:00

Details of the experiments have been posted on the 'Main Blog' at the above link. If you have any info about these (or similar) experiments/phenomena then please let me know: jorolat@gmail.com

Related terms: Lamarck and Lamarckian

John Latter (Jorolat)

technorati tags: lamarck, lamarckian, experiments, john+latter, jorolat

Wanted: Evolution of a Polyphenism by Genetic Accommodation (Science)

2006-02-03T08:10:00.000+00:00

[Suzuki & Nijhout, Science, Feb '06]

Abstract:

Polyphenisms are adaptations in which a genome is associatedwith discrete alternative phenotypes in different environments.Little is known about the mechanism by which polyphenisms originate.We show that a mutation in the juvenile hormone-regulatory pathwayin Manduca sexta enables heat stress to reveal a hidden reactionnorm of larval coloration. Selection for increased color changein response to heat stress resulted in the evolution of a larvalcolor polyphenism and a corresponding change in hormonal titersthrough genetic accommodation. Evidently, mechanisms that regulatedevelopmental hormones can mask genetic variation and act asevolutionary capacitors, facilitating the origin of novel adaptivephenotypes.

http://www.sciencemag.org/cgi/content/abstract/311/5761/650

John

Model of an Internal Evolutionary Mechanism
http://members.aol.com/jorolat/index.html

UPDATE: Reprints can be requested from Yuichiro Suzuki's email address here

Wanted: 'Obscure' 1889 Paper on Trilobite Eyes & The Fibonacci Series

2006-02-02T20:02:00.000+00:00

Can anyone help me find the 'obscure' paper by JM Clarke that Niles Eldredge refers to on page 64 of "Time Frames"? A scan of the page is available here:

http://members.aol.com/jorolat/trilobite.html

In fact I would be grateful for any information regarding the appearance of the fibonacci series in the lens arrangement of trilobite eyes!

If you know the citation (or better still, have a copy) then please email me or post here.

NB This isn't the paper I'm looking for:

CLARKE, J. M. 1889. The structure and development of the visual area in the trilobite Phacops rana Green. Journal of Morphology, 2:253270.)

Finally, I emailed Niles Eldredge and he said "I've lost touch with it [the paper]--journal such as American Naturalist..". I don't have a subsciption to Jstor. Someone did a search of American Naturalist on my behalf but couldn't find anything ('sigh').

John Latter

Model of an Internal Evolutionary Mechanism
http://members.aol.com/jorolat/index.html

technorati tags: trilobite, trilobite+eyes, time+frames, niles+eldredge, fibonacci, fibonacci+series, american+naturalist, jm+clarke, john+latter