Dienekes' Anthropology Blog

Genetic Variation and Recent Positive Selection with 1 million SNPs

2009-11-23T09:00:00.000+02:00

On the left Figure S4 shows PCA and frappe analysis for Eurasia. From the paper:

When just the Central/South Asia, Middle East, North Africa, and European groups are analyzed, PC1 (Fig. S4A) distinguishes the Mozabite (North Africa), Middle East, and Europe groups from the Central/South Asian groups, while PC2 separates the Mozabite and Middle East groups from the Europe groups, with no overlap among individuals from the different North Africa/Middle East/Europe groups. By contrast, there is overlap among individuals from the different Central/South Asia groups; in addition, the Makrani and Sindhi individuals identified in the worldwide analysis as having experienced recent sub-Saharan African admixture are clearly differentiated by PC2. The frappe analysis at K = 5 (Fig. S4B) indicates ancestry components corresponding to the Mozabite, Kalash, Hazara/Uygur, other Central/South Asia, and Europe groups. The three Middle East groups have varying amounts of the Europe, Mozabite, and Central/South Asia ancestry components. The three Italian groups are alone among European groups in having low amounts of the Mozabite ancestry component, possibly indicating gene flow across the Mediterranean. The Sardinians differ from continental European groups in lacking any Asian ancestry component, while the Russians and Adygei differ from other European groups in having appreciable amounts of the Hazara/Uygur and other Central/South Asia ancestry components, respectively, indicating more gene flow and/or ancestry with these groups (Fig. S4B).

Also from the paper, referring to Figure 3 and Figure S3:

Second, many of the subsequent statistically-significant PCs (Fig. 3 and Fig. S3) distinguish among various combinations of the sub-Saharan African groups (or among individuals within such groups), despite the fact that there are only six such groups in the analysis. This disproportionate impact of structure within sub-Saharan Africa on analyses of worldwide genetic diversity clearly emphasizes both the importance of such structure and the great need for further in-depth genetic characterization of sub-Saharan African populations [22]; we would hardly expect that these six groups encompass all of the genetic diversity in sub-Saharan Africa.

PLoS ONE doi:10.1371/journal.pone.0007888

Genetic Variation and Recent Positive Selection in Worldwide Human Populations: Evidence from Nearly 1 Million SNPs

David López Herráez et al.

Abstract

Background
Genome-wide scans of hundreds of thousands of single-nucleotide polymorphisms (SNPs) have resulted in the identification of new susceptibility variants to common diseases and are providing new insights into the genetic structure and relationships of human populations. Moreover, genome-wide data can be used to search for signals of recent positive selection, thereby providing new insights into the genetic adaptations that occurred as modern humans spread out of Africa and around the world.

Methodology
We genotyped approximately 500,000 SNPs in 255 individuals (5 individuals from each of 51 worldwide populations) from the Human Genome Diversity Panel (HGDP-CEPH). When merged with non-overlapping SNPs typed previously in 250 of these same individuals, the resulting data consist of over 950,000 SNPs. We then analyzed the genetic relationships and ancestry of individuals without assigning them to populations, and we also identified candidate regions of recent positive selection at both the population and regional (continental) level.

Conclusions
Our analyses both confirm and extend previous studies; in particular, we highlight the impact of various dispersals, and the role of substructure in Africa, on human genetic diversity. We also identified several novel candidate regions for recent positive selection, and a gene ontology (GO) analysis identified several GO groups that were significantly enriched for such candidate genes, including immunity and defense related genes, sensory perception genes, membrane proteins, signal receptors, lipid binding/metabolism genes, and genes involved in the nervous system. Among the novel candidate genes identified are two genes involved in the thyroid hormone pathway that show signals of selection in African Pygmies that may be related to their short stature.

Link

Ancestry-related assortative mating in latino populations (Risch et al. 2009)

2009-11-22T09:00:00.001+02:00

When different races admix, then in the first few generations there is a spectrum of ancestry proportions, ranging from pure individuals of the constituent races to admixed individuals with varying proportions of ancestry.

If there is random mating, then over several generations all individuals tend to have similar ancestry proportions, determined by the number of founders from the two constituent races. Mix 30,000 Europeans with 70,000 Africans, randomly mate them for 10-20 generations, and pretty soon almost everyone will have 30:70 European/African ancestral proportions with a little variation.

However, if there is assortative mating, then this process takes much longer to complete, as matings of individuals with very different ancestry proportions are rare, and the spectrum of varying individual ancestry is maintained. In the above-mentioned example, if there is perfect assortative mating, then after 10-20 generations you will still have 30% of the population having 100% European genes, and 70% of them having 100% African ones.

Previously, I had argued that the fact that Latin Americans, unlike Central Asian Turkic populations (such as the Uyghurs), have such a wide spectrum of ancestry proportions is due to the more recent admixture in the Americas than in Central Asia (less time for homogenization to take place), and the continued importation of Europeans.

Assortative mating is a third factor that may be behind this phenomenon. A stronger parallel may be found in South Asia, where the two constituents have been co-existing for a much longer time, but under a rigid, formalized regime of assortative mating (the caste system), homogenization has not taken place.

Genome Biology doi:10.1186/gb-2009-10-11-r132

Ancestry-related assortative mating in latino populations

Neil Risch et al.

Abstract

Background

While spouse correlations have been documented for numerous traits, no prior studies have assessed assortative mating for genetic ancestry in admixed populations.

Results

Using 104 ancestry informative markers, we examined spouse correlations in genetic ancestry for Mexican spouse pairs recruited from Mexico City and the San Francisco Bay Area, and Puerto Rican spouse pairs recruited from Puerto Rico and New York City. In the Mexican pairs, we found strong spouse correlations for European and Native American ancestry, but no correlation in African ancestry. In the Puerto Rican pairs, we found significant spouse correlations for African ancestry and European ancestry but not Native American ancestry. Correlations were not attributable to variation in socioeconomic status or geographic heterogeneity. Past evidence of spouse correlation was also seen in the strong evidence of linkage disequilibrium between unlinked markers, which was accounted for in regression analysis by ancestral allele frequency difference at the pair of markers (European versus Native American for Mexicans, European versus African for Puerto Ricans). We also observed an excess of homozygosity at individual markers within the spouses, but this provided weaker evidence, as expected, of spouse correlation. Ancestry variance is predicted to decline in each generation, but less so under assortative mating. We used the current observed variances of ancestry to infer even stronger patterns of spouse ancestry correlation in previous generations.

Conclusions

Assortative mating related to genetic ancestry persists in Latino populations to the current day, and has impacted on the genomic structure in these populations.

Link

Orientation of ancient Greek temples

2009-11-21T09:00:00.000+02:00

From the paper:

One reason for the difference in results might be the context of their construction. Temples in Greece were frequently built upon sites that had been sacred for generations, reaching back into the Bronze Age at places like Thermon, where the later classical temples were built over the remains of Mycenaean era megaron. [21] There was the matter of historical tradition which meant that temples built in the archaic and classical periods might be built not only according to the cosmology of the time of construction, but also within the restraints of prior religious thought. The temples in Sicily were built in cities that, at the time of building, saw themselves as immigrants in a distant land. [22] Therefore there was no historical precedent to shape the construction of the temples. They were much more likely to be purely the products of seventh-, sixth- and fifth-century cosmology. The lack of prior foundations gave the Sicilian Greeks more freedom to express current thought in religious practice through their temples.

The self-identification of Sicilian Greeks as Greeks living overseas may have also made adherence to a Greek ideal more of an imperative to reassure both themselves and visitors from the homeland that their location made them no less Greek. It is interesting to note that Greek sanctuaries in Greece could be out in the hinterland tying territory to the city, while Sicilian temples were all built in urban or suburban sites. An ‘astronomical fingerprint’ may, along with other elements such as the architectural form and religious practice, have been part of a drive to prove the Hellenic character of a settlement. Hence, perhaps, the stronger results in Sicily than Greece. This could be testable by comparison with temple alignments in other locations like the Black Sea colonies or Hellenistic Asia. A lack of a similar adherence to astronomical orientation for temples in these regions would be a surprising result given the emphatic nature of the results in Sicily and Greece.

Related: Soil and Greek temples

PLoS ONE doi:10.1371/journal.pone.0007903

The Astronomical Orientation of Ancient Greek Temples

Alun M. Salt

Abstract

Despite its appearing to be a simple question to answer, there has been no consensus as to whether or not the alignments of ancient Greek temples reflect astronomical intentions. Here I present the results of a survey of archaic and classical Greek temples in Sicily and compare them with temples in Greece. Using a binomial test I show strong evidence that there is a preference for solar orientations. I then speculate that differences in alignment patterns between Sicily and Greece reflect differing pressures in the expression of ethnic identity.

Link

Y chromosome diversity, human expansion, drift, and cultural evolution (Chiaroni et al. 2009)

2009-11-20T09:00:00.001+02:00

The supplementary material has some very interesting maps of the distribution of all major Y-chromosome haplogroups, and lists the geographical centroids with the standard deviations of all haplogroups. For example, the centroid of haplogroup J is in the Mediterranean sea between Greece, Cyprus, and Turkey, while that of its sister haplogroup I is in Central Europe. However, the standard deviation (in degrees) of the two haplogroups is 27.45 and 13.58 respectively, which shows the limited geographical extent of the latter haplogroup (see map on left).

As I have mentioned before, the origin (in space and time) of different haplogroups is related to their current geographical extent and demographic sizes, as well as their Y-STR diversity. This paper offers important data in assessing the first of these three factors.

Also of great interest is the updated Y-chromosome phylogeny, with two new branches (star: M522 that join IJ and KT, and diamond: M525 that unifies KMNOPS):

I am not so sure that drift has played a major role in human Y-chromosome diversity. As I argue in a previous post, I believe that the combination of recent TMRCAs and large haplogroup demographic sizes is best explained by selection (reproductive inequality) rather than drift.

PNAS doi:10.1073/pnas.0910803106

Y chromosome diversity, human expansion, drift, and cultural evolution

Jacques Chiaroni et al.

Abstract

The relative importance of the roles of adaptation and chance in determining genetic diversity and evolution has received attention in the last 50 years, but our understanding is still incomplete. All statements about the relative effects of evolutionary factors, especially drift, need confirmation by strong demographic observations, some of which are easier to obtain in a species like ours. Earlier quantitative studies on a variety of data have shown that the amount of genetic differentiation in living human populations indicates that the role of positive (or directional) selection is modest. We observe geographic peculiarities with some Y chromosome mutants, most probably due to a drift-related phenomenon called the surfing effect. We also compare the overall genetic diversity in Y chromosome DNA data with that of other chromosomes and their expectations under drift and natural selection, as well as the rate of fall of diversity within populations known as the serial founder effect during the recent “Out of Africa” expansion of modern humans to the whole world. All these observations are difficult to explain without accepting a major relative role for drift in the course of human expansions. The increasing role of human creativity and the fast diffusion of inventions seem to have favored cultural solutions for many of the problems encountered in the expansion. We suggest that cultural evolution has been subrogating biologic evolution in providing natural selection advantages and reducing our dependence on genetic mutations, especially in the last phase of transition from food collection to food production.

Link

Genetic methods applied to linguistic diversity of the Sahul

2009-11-18T20:14:00.021+02:00

It is great to see cross-pollination between the sciences; in this case, use of STRUCTURE has led to insights about languages of the Sahul.

From the paper:

Although we cannot specify how many different migrations have colonized Sahul since the first settlement approximately 50,000 years ago, our results indicate ancient splits into seven major plausible groups: TNG, South-Papuan, North-West Papuan, North-East Papuan, West-Papuan, PN, and non-PN. The wide-spread families (TNG and PN) on both sides of the Torres Strait divide (~9,000 BP) are the result of more recent expansions of two of those groups, in the case of TNG probably linked to the development of agriculture, ~9,000 to 6,000 years ago, see [35],[37].

The AN expansion is much more recent and has only had effects in eastern Indonesia, along the north coast of New Guinea and the islands east of the New Guinea mainland. We know on the basis of the comparative method correlated with archaeological data that approximately 3,200 years ago the Oceanic subgroup dispersed from its homeland on New Britain in three directions [9]: (1) back along the north coast, (2) around the eastern tip of New Guinea along the south coast, and (3) much further into the Pacific. The results of our analysis capture some of the impact of this great expansion on the languages that were already in the region. We find that in the eastern islands there are clearly distinct AN and non-AN groups, with good evidence of a deep structural phylogenetic signal, albeit with some admixture [16]. In the western islands however there is considerably more typological convergence between AN and non-AN languages (see also [38]). The linguistic population identified as Red appears to have members along the north coast (Mairasi, I'saka, and Kamasau) and on New Britain, where again both AN (Mangseng) and Papuan languages (Kol and Sulka) have contributions from the same cluster. This finding suggests an area of millennia of contact between AN and Papuan non-TNG speaking groups.

Gene Expression has more.

PLoS Biology doi:10.1371/journal.pbio.1000241

Explaining the Linguistic Diversity of Sahul Using Population Models

Ger Reesink et al.

Abstract

The region of the ancient Sahul continent (present day Australia and New Guinea, and surrounding islands) is home to extreme linguistic diversity. Even apart from the huge Austronesian language family, which spread into the area after the breakup of the Sahul continent in the Holocene, there are hundreds of languages from many apparently unrelated families. On each of the subcontinents, the generally accepted classification recognizes one large, widespread family and a number of unrelatable smaller families. If these language families are related to each other, it is at a depth which is inaccessible to standard linguistic methods. We have inferred the history of structural characteristics of these languages under an admixture model, using a Bayesian algorithm originally developed to discover populations on the basis of recombining genetic markers. This analysis identifies 10 ancestral language populations, some of which can be identified with clearly defined phylogenetic groups. The results also show traces of early dispersals, including hints at ancient connections between Australian languages and some Papuan groups (long hypothesized, never before demonstrated). Systematic language contact effects between members of big phylogenetic groups are also detected, which can in some cases be identified with a diffusional or substrate signal. Most interestingly, however, there remains striking evidence of a phylogenetic signal, with many languages showing negligible amounts of admixture.

Link

Y chromosomes of NE Portuguese Jews

2009-11-18T11:00:00.000+02:00

American Journal of Physical Anthropology doi:10.1002/ajpa.21154

Phylogeographic analysis of paternal lineages in NE Portuguese Jewish communities

Inês Nogueiro et al.

Abstract

The establishment of Jewish communities in the territory of contemporary Portugal is archaeologically documented since the 3rd century CE, but their settlement in Trás-os-Montes (NE Portugal) has not been proved before the 12th century. The Decree of Expulsion followed by the establishment of the Inquisition, both around the beginning of the 16th century, accounted for a significant exodus, as well as the establishment of crypto-Jewish communities. Previous Y chromosome studies have shown that different Jewish communities share a common origin in the Near East, although they can be quite heterogeneous as a consequence of genetic drift and different levels of admixture with their respective host populations. To characterize the genetic composition of the Portuguese Jewish communities from Trás-os-Montes, we have examined 57 unrelated Jewish males, with a high-resolution Y-chromosome typing strategy, comprising 16 STRs and 23 SNPs. A high lineage diversity was found, at both haplotype and haplogroup levels (98.74 and 82.83%, respectively), demonstrating the absence of either strong drift or founder effects. A deeper and more detailed investigation is required to clarify how these communities avoided the expected inbreeding caused by over four centuries of religious repression. Concerning haplogroup lineages, we detected some admixture with the Western European non-Jewish populations (R1b1b2-M269, 28%), along with a strong ancestral component reflecting their origin in the Middle East [J1(xJ1a-M267), 12%; J2-M172, 25%; T-M70, 16%] and in consequence Trás-os-Montes Jews were found to be more closely related with other Jewish groups, rather than with the Portuguese non-Jewish population.

Link

Time-independent evolutionary mtDNA mutation rates in Penguins

2009-11-16T09:00:00.000+02:00

The study is reminiscent of another recent paper on Penguins, and strikes another blow against the idea that over long time periods genetic diversity accumulates at a slow rate.

Trends in Genetics, Volume 25, Issue 11, doi:10.1016/j.tig.2009.09.005

High mitogenomic evolutionary rates and time dependency

Sankar Subramanian et al.

Using entire modern and ancient mitochondrial genomes of Adélie penguins (Pygoscelis adeliae) that are up to 44000 years old, we show that the rates of evolution of the mitochondrial genome are two to six times greater than those estimated from phylogenetic comparisons. Although the rate of evolution at constrained sites, including nonsynonymous positions and RNAs, varies more than twofold with time (between shallow and deep nodes), the rate of evolution at synonymous sites remains the same. The time-independent neutral evolutionary rates reported here would be useful for the study of recent evolutionary events.

Link

Cambyses' army found in Egypt

2009-11-14T09:00:00.002+02:00

VANISHED PERSIAN ARMY SAID FOUND IN DESERT

Bones, jewelry and weapons found in Egyptian desert may be the remains of Cambyses' army that vanished 2,500 years ago.

The remains of a mighty Persian army said to have drowned in the sands of the western Egyptian desert 2,500 years ago might have been finally located, solving one of archaeology's biggest outstanding mysteries, according to Italian researchers.

Bronze weapons, a silver bracelet, an earring and hundreds of human bones found in the vast desolate wilderness of the Sahara desert have raised hopes of finally finding the lost army of Persian King Cambyses II. The 50,000 warriors were said to be buried by a cataclysmic sandstorm in 525 B.C.

"We have found the first archaeological evidence of a story reported by the Greek historian Herodotus," Dario Del Bufalo, a member of the expedition from the University of Lecce, told Discovery News.

According to Herodotus (484-425 B.C.), Cambyses, the son of Cyrus the Great, sent 50,000 soldiers from Thebes to attack the Oasis of Siwa and destroy the oracle at the Temple of Amun after the priests there refused to legitimize his claim to Egypt.

After walking for seven days in the desert, the army got to an "oasis," which historians believe was El-Kharga. After they left, they were never seen again.

"A wind arose from the south, strong and deadly, bringing with it vast columns of whirling sand, which entirely covered up the troops and caused them wholly to disappear," wrote Herodotus.

A century after Herodotus wrote his account, Alexander the Great made his own pilgrimage to the oracle of Amun, and in 332 B.C. he won the oracle's confirmation that he was the divine son of Zeus, the Greek god equated with Amun.

Video on the Lost Army of Cambyses. Another video.

UPDATE: Rogue Classicism is skeptical.

mtDNA haplogroup H and maximal oxygen uptake

2009-11-12T15:00:00.000+02:00

Mitochondrion. 2009 Nov 6. [Epub ahead of print]

Human mitochondrial haplogroup H: the highest VO(2max) consumer. Is it a paradox?

Martínez-Redondo D et al.

Mitochondrial background has been demonstrated to influence maximal oxygen uptake (VO(2max), in mL.kg(-1).min(-1)), but this genetic influence can be compensated for by regular exercise. A positive correlation among electron transport chain (ETC) coupling, ATP and reactive oxygen species (ROS) production has been established, and mitochondrial variants have been reported to show differences in their ETC performance. In this study, we examined in detail the VO(2max) differences found among mitochondrial haplogroups. We recruited 81 healthy male Spanish Caucasian individuals and determined their mitochondrial haplogroup. Their VO(2max) was determined using incremental cycling exercise (ICE). VO(2max) was lower in J than in non-J haplogroup individuals (P=0.04). The H haplogroup was responsible for this difference (VO(2max); J vs. H; P=0.008) and this group also had significantly higher mitochondrial oxidative damage (mtOD) than the J haplogroup (P=0.04). In agreement with these results, VO(2max) and mtOD were positively correlated (P=0.01). Given that ROS production is the major contributor to mtOD and consumes four times more oxygen per electron than the ETC, our results strongly suggest that ROS production is responsible for the higher VO(2max) found in the H variant. These findings not only contribute to a better understanding of the mechanisms underneath VO(2max), but also help to explain some reported associations between mitochondrial haplogroups and mtOD with longevity, sperm motility, premature aging and susceptibility to different pathologies.

Link

Spouse selection in Sardinia

2009-11-11T15:00:00.000+02:00

American Journal of Physical Anthropology doi:10.1002/ajpa.21150

Spouse selection by health status and physical traits. Sardinia, 1856-1925

M. Manfredini et al.

Abstract

Military medical information and data from civil registers of death and marriage have been used to study the role of physical characteristics and health conditions in explaining access to marriage for the male population of Alghero, a small city located in Sardinia Island (Italy), at the turn of 19th century. Literature data about contemporary populations have already demonstrated the influence of somatic traits in the mate choice. The results presented here show that men with low height and poor health status at the age of 20 were negatively selected for marriage. This holds true also in a society where families often arranged marriages for their children. This pattern of male selection on marriage was found to be particularly marked among the richest and wealthiest SES groups. Our hypothesis is that this social group carefully selected for marriage those individuals who were apparently healthier and therefore more likely to guarantee good health status and better life conditions to offspring. In evolutionary terms, the mate choice component of sexual selection suggests that the height of prospective partners could be claimed as one of the determinants, along with other environmental causes, of the observed higher stature of men belonging to the wealthiest social strata of the Alghero population.

Link

Ottoman terror in 15th c. Croatia

2009-11-10T15:00:00.002+02:00

Peaceful co-existence, Islamic tolerance, Ottoman benevolence in action...

American Journal of Physical Anthropology doi:10.1002/ajpa.21152

The harsh life on the 15th century Croatia-Ottoman Empire military border: Analyzing and identifying the reasons for the massacre in epin

Mario laus et al.

Abstract

Excavation of the historic period cemetery in epin, Croatia revealed the presence of a large number of perimortem injuries distributed among males, females, and subadults. Archaeological and historical data suggest these individuals were victims of a raid carried out by Turkish akinji light cavalry in 1441. Comparisons with the frequencies of perimortem trauma in 12 other, temporally congruent skeletal series from the Balkans (n = 2,123 skeletons) support this assumption. The role of the akinji in the Ottoman army was twofold: to supply war captives, and to terrorize and disperse local populations before the advance of regular troops. This article tests the hypothesis that the purpose of the 1441 raid was the latter. To accomplish this, perimortem trauma in the series were analyzed by sex, age, location, and depth of the injury. A total of 82 perimortem injuries were recorded in 12 males, 7 females, and 3 subadults. The demographic profile of the victims suggests that young adults were specifically targeted in the attack. Significant sex differences are noted in the number, distribution, and pattern of perimortem trauma. Females exhibit significantly more perimortem injuries per individual, and per bone affected, than males. The morphology and pattern of perimortem trauma in females is suggestive of gratuitous violence. Cumulatively, analysis of the osteological data suggest that the objective of the 1441 akinji raid was to spread terror and panic in the epin area, either as revenge for recent military setbacks, or as part of a long-term strategy intended to depopulate the area around Osijek.

Link

Common variant for straight hair in Europeans

2009-11-10T15:00:00.001+02:00

American Journal of Human Genetics doi:10.1016/j.ajhg.2009.10.009

Common Variants in the Trichohyalin Gene Are Associated with Straight Hair in Europeans

Sarah E. Medland et al.

Abstract

Hair morphology is highly differentiated between populations and among people of European ancestry. Whereas hair morphology in East Asian populations has been studied extensively, relatively little is known about the genetics of this trait in Europeans. We performed a genome-wide association scan for hair morphology (straight, wavy, curly) in three Australian samples of European descent. All three samples showed evidence of association implicating the Trichohyalin gene (TCHH), which is expressed in the developing inner root sheath of the hair follicle, and explaining ∼6% of variance (p = 1.5 × 10⁻³¹). These variants are at their highest frequency in Northern Europeans, paralleling the distribution of the straight-hair EDAR variant in Asian populations.

Link

Population affinities of Parsis

2009-11-09T15:00:00.000+02:00

International Journal of Osteoarchaeology doi:10.1002/oa.1123

Population affinities of Parsis in the Indian subcontinent

Manjari Jonnalagadda et al.

Abstract

The present study was an attempt to document changes in frequencies of dental morphology traits and understand phenetic affinities of Parsis, who migrated to the Indian subcontinent around the 8th century. Despite successfully integrating themselves into the Indian society, they have retained their ethnicity and distinct cultural practices. This study was conceived as a result of an excavation at the site of Sanjan, Gujarat which, as per historical records, is believed to be the first town in the Indian subcontinent with a large Parsi settlement thereby facilitating a diachronic comparison between the ancestral and extant Parsi groups. We compared and analysed dental traits between the two groups expecting a very close relationship between them owing to their ancestor-descendent relationship. Eleven discrete dental traits were selected and scored using the Arizona State University Dental Anthropology System (ASUDAS). Frequency changes were assessed by comparing trait frequencies; whereas phenetic affinity between Parsis was assessed by statistically comparing them with 13 populations using Smith's mean measure of divergence (MMD) statistic. Comparison of dental trait frequencies between Sanjan and extant Parsi samples show significant differences in incisor morphology, Carabelli cusp and Hypocone development. Trait frequencies, MMD values and 2D multidimensional scaling (MDS) plot indicate that extant Parsis and Sanjan samples are distantly separated from each other. Extant Parsis show closer affinity to low caste Mahars and tribal Madia Gonds than South and Central Asian groups. Sanjan is distant from all other groups including extant Parsis. It is likely that genetic drift accentuated by their small numbers and strict endogamy has resulted in divergence of Parsi groups. Similarly, their convergence with Maharashtran groups indicates admixture of Parsis with local groups, which supports earlier conducted mtDNA studies.

Link

Γιατί υποστηρίζω την Ντόρα Μπακογιάννη για την προεδρία της Νέας Δημοκρατίας

2009-11-08T15:00:00.008+02:00

Δεν ασχολούμαι συνήθως με τα ζητήματα της τρέχουσας πολιτικής αλλά νιώθω την υποχρέωση να πάρω μια ξεκάθαρη θέση για το ζήτημα της διαδοχής στη Νέα Δημοκρατία.

Υποστηρίζω την κ. Ντόρα Μπακογιάννη για τέσσερις λόγους, έναν αρνητικό και τρεις θετικούς:

1. Αδυναμίες του αντιπάλου της

Αυτός που θέλει τάχα να πολεμήσει τους μηχανισμούς έγινε κατευθείαν βουλευτής λόγω οικογενειακού ονόματος στα 26, παριστάνει τον υπερπατριώτη αλλά έκανε μειωμένη «θητεία» παράλληλα με άλλες δουλείες, στο Ναυτικό, πρόδωσε τη Νέα Δημοκρατία ρίχνοντας την εκλεγμένη κυβέρνησή της, διέσπασε την παράταξη ιδρύοντας νέο κόμμα με το οποίο κατέβηκε ενάντια στη Νέα Δημοκρατία σε τέσσερις εκλογικές αναμετρήσεις και απέναντι σε τρεις διαφορετικούς αρχηγούς, οδήγησε το κόμμα του οποίου ηγήθηκε στην καταστροφή του 2.3% και τα παράτησε, απέτρεψε τις εκλογές το 1995 συνεργαζόμενος με το ΠΑΣΟΚ για να κρατήσει τη βουλευτική του καρέκλα αλλά συνάμα και τον ανήμπορο Ανδρέα Παπανδρέου στην πρωθυπουργία, διακήρυξε πως ο Κωνσταντίνος Καραμανλής ήταν «κατάκοπη ηγεσία» που έπρεπε να φύγει, τίμησε, τάχα, το «δάκρυ του Εθνάρχη» ενώ ο Εθνάρχης του είχε κλείσει την πόρτα του Προεδρικού Μεγάρου, αυτοπροσδιορίσθηκε, τη δεκαετία του '90 ως κεντρώος ενώ τώρα εμφανίζεται τώρα ως σκληρός κεντροδεξιός και οπαδός του Σαρκοζί αλλά και δεύτερος Έλληνας Ομπάμα (!), πίστευε (τότε) πως έπρεπε να γίνει η «Υπέρβαση» της Νέας Δημοκρατίας ενώ μας μιλάει (τώρα) για τη διαχρονικότητα της ιδρυτικής της διακήρυξης, θεωρεί εαυτόν δικαιωμένο παρά το γεγονός πως η πολιτική που απέρριψε πομπωδώς το 1993 για σύνθετη ονομασία της ΠΓΔΜ έχει γίνει επίσημη πολιτική της Νέας Δημοκρατίας, έμεινε οκτώ χρόνια άνευ βιοπορισμού και οιασδήποτε δραστηριότητας κοιτάζοντας τους τοίχους του σπιτιού τους, έλειπε στα δύσκολα χρόνια της αντιπολίτευσης και ήρθε στα εύκολα χρόνια της Κυβέρνησης όχι με ψήφο του λαού αλλά με διορισμό στην Ευρωβουλή, έκανε αρνητικό ρεκόρ με οκτώ ερωτήσεις τα τρία χρόνια που ήταν ευρωβουλευτής, δεν βγήκε μια φορά σε ένα κεντρικό δελτίο για να υποστηρίξει τη Νέα Δημοκρατία, αυτός που έλεγε ότι δεν θα δεχόταν ποτέ να επιστρέψει στη Νέα Δημοκρατία, ακόμα και αν του ζητούσαν να γίνει αρχηγός, αυτός λοιπόν απλά δεν έχει ηθικό δικαίωμα να γίνει πρόεδρός της, και θα έπρεπε να ντρέπεται που προσβάλει τη νοημοσύνη μας θέτοντας εαυτόν υποψήφιο.

2. Βιογραφικό

Γιατί η Ντόρα Μπακογιάννη υπήρξε πάντοτε παρούσα στους αγώνες της Νέας Δημοκρατίας, και στην Αντιπολίτευση, και στην Κυβέρνηση. Γιατί ήταν διαρκώς στα μέσα ενημέρωσης δίνοντας τη μάχη της ενημέρωσης. Γιατί κέρδισε για τη Νέα Δημοκρατία και την Ευρυτανία, και το Δήμο Αθηναίων, και πρώτευσε στην Α' Αθηνών. Γιατί πρότεινε την εκλογή προέδρου από τη βάση πριν από δέκα χρόνια και δεν ανακάλυψε την δημοκρατικότητα πριν από ένα μήνα όταν συνειδητοποίησε πως δεν της έβγαιναν τα συνεδριακά «κουκιά». Γιατί ανακάλυψε το Διαδίκτυο και τα Νέα Μέσα όταν οι άλλοι δεν έβγαιναν καν σε μια εφημερίδα ή τηλεόραση. Γιατί πέτυχε στα δύο χρόνια στο Δήμο να γίνουν άψογοι Ολυμπιακοί Αγώνες κατά το μερίδιο της ευθύνης της. Γιατί δεν δίστασε να τσακωθεί με την Υπουργό Εξωτερικών της Υπερδύναμης για την είσοδο της ΠΓΔΜ στο ΝΑΤΟ, και κατόρθωσε να επιβάλει μαζί με τον Κώστα Καραμανλή την Ελληνική θέση στο Μακεδονικό κάνοντας την συμμαχική θέση με την υπογραφή τόσο των Ηνωμένων Πολιτειών όσο και της Τουρκίας. Γιατί δεν υποχώρησε ποτέ στο ελάχιστο στα εθνικά θἐματα. Γιατί βίωσε τον ξεριζωμό από την Ελλάδα στα εφηβικά της χρόνια και την βία των τρομοκρατών στα νεανικά της αλλά σηκώθηκε, ξανάφτιαξε τη ζωή της και την αφιέρωσε στην υπηρεσία της Ελλάδας.

3. Προτάσεις για τη Νέα Δημοκρατία

Γιατί δεν ζητάει λευκή επιταγή και αποδέχεται να έχει θητεία σε αντίθεση με τον κύριο αντίπαλό της. Γιατί λέει το αυτονόητο, πως η ΝΔ είναι πολυσυλλεκτικό κόμμα που στηρίζεται σε ανθρώπους με διαφορετικά χαρακτηριστικά (συντηρητικούς, φιλελεύθερους, κεντρώους, δεξιούς) και δεν πρέπει να αυτοπεριχαρακωθεί. Γιατί αναλαμβάνει συγκεκριμένες δεσμεύσεις για την οργάνωση του κόμματος: αναλογικό σύστημα στην εκλογή των οργάνων του κόμματος έτσι ώστε να εκπροσωπούνται όλες οι τάσεις και να διασφαλίζεται η πολυσυλλεκτικότητα του, δημοσιοποίηση και ονομαστικοποίηση των εσόδων του κόμματος, αιρετό συμβούλιο δεοντολογίας, εκλογές για όλα τα αξιώματα και δημοψηφίσματα στα μέλη για ζητήματα πολιτικής, συχνή και τακτική λειτουργία των οργάνων για παραγωγή πολιτικής και όχι αυτοκρατορικό κόμμα όπου όλοι κρέμονται από τα χείλη του αρχηγού. Μόνο έτσι μπορεί η ΝΔ να αποτελεί όχημα σύνθεσης πολιτικών προτάσεων με προοπτική εξουσίας.

4. Πολιτική ταυτότητα και πρόταση

Γιατί δεν λαϊκίζει, είναι σοβαρή, αλλά όχι σοβαροφανής, έξυπνη, ετοιμόλογη, δημοφιλής εκτός της ΝΔ, με ξεκάθαρη φιλελεύθερη ιδεολογία και συγκεκριμένες θέσεις για την πολιτική: πιστεύει πως «εύτακτον το ελεύθερον», πως «ένα υπεύθυνο και αξιόπιστο κόμμα δεν κάνει πολιτική με δανεικά», πως το πανεπιστημιακό άσυλο πρέπει «να απαλλαγεί από όλα τα στοιχεία που το ευτελίζουν και το απονομιμοποιούν στη συνείδηση όλων μας», πως πρέπει να υπάρχει «αξιολόγηση των εκπαιδευτικών μονάδων και των διδασκόντων, σε κάθε βαθμίδα της εκπαίδευσης». Γιατί δίνει βήμα στους πολίτες, απαντάει στις ερωτήσεις τους, και διαμορφώνει νέες πολιτικές μαζί τους. Γιατί έχει όλα τα προσόντα να γίνει η πρώτη Ελληνίδα Πρωθυπουργός.

Δεδομένων αυτών των γεγονότων η επιλογή κάθε Νεοδημοκράτη για τις εκλογές της 29ης Οκτωβρίου είναι δεδομένη. Ψηφίζουμε Ντόρα και δίνουμε στη Νέα Δημοκρατία προοπτική νίκης το 2013.

Υστερόγραφο:

Γιατί ενδιαφέρομαι για την εκλογή προέδρου στη Νέα Δημοκρατία; Για τρεις λόγους:

1. Πιστεύω πως στις Δημοκρατίες οι πολίτες έχουν υποχρέωση να συμμετέχουν στα κοινά και πως όσοι δεν το κάνουν είναι άχρηστοι.

2. Πιστεύω στον συκοφαντημένο δικομματισμό, το σύστημα των μακροβιότερων κοινοβουλευτικών δημοκρατιών όπου:

τα κόμματα συνθέτουν απόψεις και παρουσιάζουν πρόγραμμα
το κόμμα που πρωτεύει εφαρμόζει το πρόγραμμα του για μια τετραετία και κρίνεται για αυτό, θετικά ή αρνητικά.
Απορρίπτω τις «κυβερνήσεις συνεργασίας» όπου μικρά κομματίδια με ελάχιστη κοινωνική απήχηση επιβάλλουν όρους διακυβέρνησης και οι πολιτικές αποφασίζονται με συμφωνίες κορυφής ανάμεσα σε αρχηγούς πίσω από κλειστές πόρτες.

3. Δεν είμαι σοσιαλιστής. Πιστεύω στο έθνος-κράτος, στην ελεύθερη οικονομία, στις παραδοσιακές Ελληνικές αξίες. Επομένως δεν μπορώ να υποστηρίξω το ΠΑΣΟΚ του κρατισμού, της φοροεπιδρομής και ψηφοθηρικής «αναδιανομής», της μαζικής απόδοσης ιθαγένειας σε πρώην λαθρομετανάστες και τα παιδιά τους, της αποβολής του επιθέτου «εθνική» από τα υπουργεία, του διαχωρισμού Εκκλησίας-Κράτους

Υποσημείωση: Είμαι απλός ψηφοφόρος της Νέας Δημοκρατίας (όχι ακόμα μέλος) και δεν έχω καμιά προσωπική σχέση ούτε με την κ. Μπακογιάννη, ούτε με κανέναν άλλο πολιτευτή της Νέας Δημοκρατίας, ούτε έχω λαμβάνειν ό,τιδήποτε σε ενδεχόμενη επικράτησή της.

Δείτε επίσης:

Αναγγελία της υποψηφιότητας για την ηγεσία της ΝΔ (video)

Ομιλία στην Κεντρική Επιτροπή της ΝΔ (video)

Ομιλία Ντόρας Μπακογιάννη στο Έκτακτο Συνέδριο της 7ης Νοεμβρίου (video)

Δευτερολογία Ντόρας Μπακογιάννη στο Έκτακτο Συνέδριο στις 8 Νοεμβρίου

Σχετικοί ιστότοποι:

H προσωπική σελίδα της Ντόρας Μπακογιάννη. Η Ντόρα στο ΥouΤube, στο Τwitter, και στο Facebook.

Ενημερώσεις άρθρου:

Genetic ancestry of Coloured South Africans

2009-11-08T09:00:00.000+02:00

Hum Mol Genet. 2009

Genetic structure of a unique admixed population: implications for medical research.

Patterson N, Petersen DC, van der Ross RE, Sudoyo H, Glashoff RH, Marzuki S, Reich D, Hayes VM.

Understanding human genetic structure has fundamental implications for understanding the evolution and impact of human diseases. In this study we describe the complex genetic substructure of a unique and recently admixed population arising approximately 350 years ago as a direct result of European settlement in South Africa. Analysis was performed using over 900,000 genome-wide single nucleotide polymorphisms in 20 unrelated ancestry-informative marker selected Coloured individuals and made comparisons with historically predicted founder populations. We show that there is substantial genetic contribution from at least four distinct population groups: Europeans, South Asians, Indonesians, and a population genetically close to the isiXhosa sub-Saharan Bantu. This is in good accord with the historical record. We briefly examine the implications of determining the genetic diversity of this population, not only for furthering understanding of human evolution out of Africa, but also for genome-wide association studies using admixture mapping. In conclusion, we define the genetic structure of a uniquely admixed population that holds great potential to advance genetic-based medical research.

Link

German and French newborns cry differently

2009-11-07T09:00:00.000+02:00

Current Biology, doi:10.1016/j.cub.2009.09.064

Newborns' Cry Melody Is Shaped by Their Native Language

Birgit Mampe et al.

Summary

Human fetuses are able to memorize auditory stimuli from the external world by the last trimester of pregnancy, with a particular sensitivity to melody contour in both music and language [1,2,3]. Newborns prefer their mother's voice over other voices [4,5,6,7,8] and perceive the emotional content of messages conveyed via intonation contours in maternal speech (“motherese”) [9]. Their perceptual preference for the surrounding language [10,11,12] and their ability to distinguish between prosodically different languages [13,14,15] and pitch changes [16] are based on prosodic information, primarily melody. Adult-like processing of pitch intervals allows newborns to appreciate musical melodies and emotional and linguistic prosody [17]. Although prenatal exposure to native-language prosody influences newborns' perception, the surrounding language affects sound production apparently much later [18]. Here, we analyzed the crying patterns of 30 French and 30 German newborns with respect to their melody and intensity contours. The French group preferentially produced cries with a rising melody contour, whereas the German group preferentially produced falling contours. The data show an influence of the surrounding speech prosody on newborns' cry melody, possibly via vocal learning based on biological predispositions.

Link

Finally, structure in haplogroup R1a (Underhill et al. 2009)

2009-11-05T15:00:00.003+02:00

I have lobbied for more structure in R1a to be discovered since the early days of this blog, and finally the R1a monolith seems to be cracking.

(Watch this space for my comments once I read the paper).

UPDATE (Nov 05):

This paper makes a very important contribution by studying the diversity and distribution of Y-chromosome marker M458 defining the new haplogroup R1a1a7.

R-M458 reaches high frequency and diversity in central and eastern Europe. It is virtually absent in northwestern Europe, the Near East, and Asia east of the Urals. The maximum frequency is reached in south (36.4%) and central (33.3%) Poland.

The earliest expansion time for R-M458 is found in Poland (10.7ky), but since the paper uses the effective mutation rate that I criticized elsewhere, this date should be divided by a factor of 3 giving an age of 3.6ky. This matches quite well the age for the Balto-Slavic split according to Gray and Atkinson. As with the recent paper on J-P58, adopting the germline rate makes excellent sense.

If R-M458 had started expanding 10.7ky ago, then by the time of the early dispersals of Kurgan groups east, it would have been present among them, and we would expect to find it east of the Urals and in the Near East/Central/South Asia. To reconcile this age with the archaeological picture of west-east movements across the steppe seems impossible. However, the situation resolves itself neatly when we realize that J-P58 is only 3-4 thousand years old, and was not in existence at the time of the Kurgan expansion.

However, the paper also is inconsistent with an origin of R-M17 either in a glacial refugium or with the expansion of the Kurgan culture, as the diversity of R1a1a*(xR1a1a7) is not particularly high in either Russia or the Ukraine and is much higher in India and Pakistan:

Analysis of associated STR diversity profiles revealed that among the R1a1a*(xM458) chromosomes the highest diversity is observed among populations of the Indus Valley yielding coalescent times above 14 KYA (thousands of years ago), whereas the R1a1a* diversity declines toward Europe where its maximum diversity and coalescent times of 11.2 KYA are observed in Poland, Slovakia and Crete.

Hopefully we will not have to wait another decade for the R1a1a* chromosomes to be further resolved, and thus yield signal(s) specific to the archaeologically attested trans-Ural spread of the Kurgan culture and/or the Indo-Iranians.

There are also other useful conclusions that we may draw from this study:

1. The presence of R1a in Scandinavia does not reflect any sort of Balto-Slavic admixture, as R-M458 is lacking in them. This, coupled with the discovery of R1a chromosomes in ancient remains from Eulau and Lichtenstein in German territory suggests that R1a was present among ancient Germanic speakers. However, there is also structure in R-M458 frequency in Germany itself, with lowest percentages reached in the north and west; this suggests an admixture with Baltic and/or Slavic elements in present-day Germany itself.

2. In several Balkan samples the frequency of R-M458 ranges between 0-12% which is at most a third of its maximum frequency, suggesting that the extent of Slavic admixture in the Balkans is upper-bounded by about 1/3. The complete absence of R-M458 in Italy and its sub-1% representation in Anatolia further support the idea that R-M458 in the Balkans is of medieval and later origins.

3. The samples from Greece (N=263), Macedonian Greeks (N=57), and Crete (N=361) have R-M458 frequency of 4.2, 8.8, and 2.2%. Assuming a frequency of R-M458 at 36.4% in ancestral Slavs, as in south Poland, the admixture estimates are 11.5, 24, 6%. These should probably be interpreted as upper limits (plus statistical margins) because the highest present-day frequency of R-M458 is probably lower than that in early Slavs.

4. Interestingly, the Slavs of FYROM have an R-M458 frequency of 3.8%, barely different from that of Greeks at large, suggesting that (i) the claims of some Greek nationalists that they Slavs of FYROM are newcomers to the Balkans are wrong, just as (ii) the claim of some FYROMian nationalists that they are markedly different from Greeks are wrong. The actual truth is that the Slavs of FYROM are largely of old Balkan (pre-Slavic) stock who adopted a non-Balkan Slavic language, just as the modern Turks are largely of old Anatolian (pre-Turkish) stock who adopted a non-Anatolian Turkic language.

European Journal of Human Genetics doi:10.1038/ejhg.2009.194

Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a

Peter A Underhill et al.

Abstract

Human Y-chromosome haplogroup structure is largely circumscribed by continental boundaries. One notable exception to this general pattern is the young haplogroup R1a that exhibits post-Glacial coalescent times and relates the paternal ancestry of more than 10% of men in a wide geographic area extending from South Asia to Central East Europe and South Siberia. Its origin and dispersal patterns are poorly understood as no marker has yet been described that would distinguish European R1a chromosomes from Asian. Here we present frequency and haplotype diversity estimates for more than 2000 R1a chromosomes assessed for several newly discovered SNP markers that introduce the onset of informative R1a subdivisions by geography. Marker M434 has a low frequency and a late origin in West Asia bearing witness to recent gene flow over the Arabian Sea. Conversely, marker M458 has a significant frequency in Europe, exceeding 30% in its core area in Eastern Europe and comprising up to 70% of all M17 chromosomes present there. The diversity and frequency profiles of M458 suggest its origin during the early Holocene and a subsequent expansion likely related to a number of prehistoric cultural developments in the region. Its primary frequency and diversity distribution correlates well with some of the major Central and East European river basins where settled farming was established before its spread further eastward. Importantly, the virtual absence of M458 chromosomes outside Europe speaks against substantial patrilineal gene flow from East Europe to Asia, including to India, at least since the mid-Holocene.

Link

Maternal vs. Paternal grandmother and grandchild survival

2009-11-02T15:00:00.001+02:00

From the paper:

Grandsons and granddaughters differ in the proportion of their X-chromosomes shared with MGMs and PGMs (figure 1). According to our proposed X-linked grandmother hypothesis, if grandmothers invest in grandchildren because of their genetic relatedness with them, then their adaptive incentive to invest may vary in a way that mirrors this variation in genetic relatedness. As a consequence, grandmothers’ differential investment in grandchildren could cause differential survivorship of those grandchildren.

...

Therefore, MGMs and grandchildren are likely to share 25 per cent of their genomes, while PGM and granddaughter may share a total of approximately 31 per cent of their genes, with a likelihood of 27 per cent inheritance, while a PGM and grandson may share only approximately 23 per cent.

...

Genetic relatedness between kin is often used to explain behavioural phenomena associated with altruism and caretaking, as well as biological traits and developmental trends. The grandmother hypothesis is the prevailing theory to explain why human female longevity extends beyond menopause. It suggests that elderly women are able to contribute to their grandchildren's survivorship through nutritional provisioning, which would increase a woman's inclusive fitness because she shares one-quarter of her genes with a grandchild. In seven previously studied populations, separating grandchild survivorship rates by sex reveals that X-chromosome relatedness correlates with grandchild survival in the presences of MGMs and PGMs. In all seven populations, boys survive better in the presence of their MGM than PGM. In all bar one population, the PGM has a more beneficial effect on girls than on boys. Our X-linked grandmother hypothesis demonstrates how the effects of grandmothers could be sex-specific because of the unusual inheritance pattern of the X-chromosome. This provides a more universally applicable model to explain differential survival of grandchildren in the presence of their grandmothers.

Proceedings of the Royal Society B doi: 10.1098/rspb.2009.1660

Grandma plays favourites: X-chromosome relatedness and sex-specific childhood mortality

Molly Fox et al.

Abstract

Biologists use genetic relatedness between family members to explain the evolution of many behavioural and developmental traits in humans, including altruism, kin investment and longevity. Women's post-menopausal longevity in particular is linked to genetic relatedness between family members. According to the ‘grandmother hypothesis’, post-menopausal women can increase their genetic contribution to future generations by increasing the survivorship of their grandchildren. While some demographic studies have found evidence for this, others have found little support for it. Here, we re-model the predictions of the grandmother hypothesis by examining the genetic relatedness between grandmothers and grandchildren. We use this new model to re-evaluate the grandmother effect in seven previously studied human populations. Boys and girls differ in the per cent of genes they share with maternal versus paternal grandmothers because of differences in X-chromosome inheritance. Here, we demonstrate a relationship between X-chromosome inheritance and grandchild mortality in the presence of a grandmother. With this sex-specific and X-chromosome approach to interpreting mortality rates, we provide a new perspective on the prevailing theory for the evolution of human female longevity. This approach yields more consistent support for the grandmother hypothesis, and has implications for the study of human evolution.

Link

Coevolution of individualism–collectivism and the serotonin transporter gene

2009-10-29T21:00:00.001+02:00

From the paper:

Here, we demonstrate for the first time a robust association between cultural values of individualism–collectivism and allelic frequency of the serotonin transporter gene, controlling for associated economic and disease factors. Geographical regions characterized by cultural collectivism exhibit a greater prevalence of S allele carriers of the serotonin transporter gene, even when cultural regions rather than nations served as the unit of analysis. Additionally, we show that global variability in historical pathogen prevalence predicts global variability in individualism–collectivism owing to genetic selection of the S allele of the serotonin transporter gene in regions characterized by high collectivism. Importantly, we also reveal a novel and surprising negative association between individualism–collectivism, frequency of S allele carriers of the serotonin transporter gene and global prevalence of anxiety and mood disorder. Across nations, both collectivism and allelic frequency of the S allele negatively predict global prevalence of anxiety and mood disorders. Critically, our results further indicate that greater population frequency of S allele carriers is associated with decreased prevalence of anxiety and mood disorders due to increased cultural collectivism.

The current findings suggest a novel demonstration of culture–gene coevolution of human behaviour. Emphasizing social norms that increase social harmony and encourage giving social support to others, collectivism serves an ‘anti-psychopathology’ function by creating an ecological niche that lowers the prevalence of chronic life stress, protecting genetically susceptible individuals from environmental pathogens known to trigger negative emotion and psychopathology. These findings complement notions that cultural values of individualism and collectivism are adaptive and by-products of evolution, more broadly. For instance, recent evidence suggests that cultural values of collectivism also serve an ‘anti-pathogen defence’ whereby behavioural manifestations of collectivism, such as conformity and parochialism, function as buffers against the transmission and increased prevalence of disease-causing pathogens (e.g. malaria, typhus and tuberculosis) (Fincher et al. 2008). Our results provide novel evidence that geographical regions characterized by collectivistic cultural norms have a higher historical and contemporary prevalence of infectious diseases due, at least partially, to genetic selection of S allele carriers (Fincher et al. 2008). Taken together, these findings dovetail nicely as two examples of how cultural values serve adaptive functions by tuning societal behaviour so that social and environmental risk factors are reduced and physical and mental health of group members is maintained. Importantly, in the current study, we found that population frequency of the serotonin transporter gene was a singular predictor of cultural values of individualism–collectivism across nations, even when controlling for historical and contemporary pathogen prevalence. Hence, our findings illustrate that gene frequency plays a unique role in explaining global variation in the adoption of cultural norms and is fundamental to any comprehensive understanding of culture.

Proceedings of the Royal Society B doi:10.1098/rspb.2009.1650

Culture–gene coevolution of individualism–collectivism and the serotonin transporter gene

Joan Y. Chiao, and Katherine D. Blizinsky

Culture–gene coevolutionary theory posits that cultural values have evolved, are adaptive and influence the social and physical environments under which genetic selection operates. Here, we examined the association between cultural values of individualism–collectivism and allelic frequency of the serotonin transporter functional polymorphism (5-HTTLPR) as well as the role this culture–gene association may play in explaining global variability in prevalence of pathogens and affective disorders. We found evidence that collectivistic cultures were significantly more likely to comprise individuals carrying the short (S) allele of the 5-HTTLPR across 29 nations. Results further show that historical pathogen prevalence predicts cultural variability in individualism–collectivism owing to genetic selection of the S allele. Additionally, cultural values and frequency of S allele carriers negatively predict global prevalence of anxiety and mood disorder. Finally, mediation analyses further indicate that increased frequency of S allele carriers predicted decreased anxiety and mood disorder prevalence owing to increased collectivistic cultural values. Taken together, our findings suggest culture–gene coevolution between allelic frequency of 5-HTTLPR and cultural values of individualism–collectivism and support the notion that cultural values buffer genetically susceptible populations from increased prevalence of affective disorders. Implications of the current findings for understanding culture–gene coevolution of human brain and behaviour as well as how this coevolutionary process may contribute to global variation in pathogen prevalence and epidemiology of affective disorders, such as anxiety and depression, are discussed.

Link

Long live the 28th October 1940

2009-10-28T09:00:00.001+02:00

mtDNA in southern Italy

2009-10-27T15:00:00.000+02:00

Ann Hum Biol. 2009 Oct 25. [Epub ahead of print]

Human mitochondrial DNA variation in Southern Italy

Ottoni C, Martinez-Labarga C, Vitelli L, Scano G, Fabrini E, Contini I, Biondi G, Rickards O.

Background: Since prehistoric times Southern Italy has been a cultural crossroads of the Mediterranean basin. Genetic data on the peoples of Basilicata and Calabria are scarce and, particularly, no records on mtDNA variability have been published. Aim: In this study mtDNA haplotypes of populations from Basilicata, Calabria and Sicily are compared with those of other Italian and Mediterranean populations, so as to investigate their genetic relationships. Subjects and methods: A total of 341 individuals was analysed for mtDNA in order to provide their classification into haplogroups. Multivariate analysis was used to compare the studied populations with other Mediterranean samples; median-joining network analysis was applied to observe the relationship between the major lineages of the Southern Italians. Results: The haplogroup distribution in the Southern Italian samples falls within the typical pattern of mtDNA variability of Western Eurasia. The comparison with other Mediterranean countries showed a substantial homogeneity of the area, which is probably related to the historic contact through the Mediterranean Sea. Conclusion: The mtDNA analysis demonstrated that Southern Italy displays a typical pattern of Mediterranean basin variability, even though it appears plausible that Southern Italy was less affected by the effects of the Late Glacial Maximum, which reduced genetic diversity in Europe.

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Ancient Greeks introduced wine to France

2009-10-26T15:00:00.000+02:00

Related: Wikipedia article on the Vix Grave. Covered elsewhere: Greeks uncorked French passion for wine.

Ancient Greeks introduced wine to France, Cambridge study reveals

The original makers of Côtes-du-Rhône are said to have descended from Greek explorers who settled in southern France about 2500 years ago, it claimed.

The study, by Prof Paul Cartledge, suggested the world's biggest wine industry might never have developed had it not been for a “band of pioneering Greek explorers” who settled in southern France around 600 BC.

His study appears to dispel the theory that it was the Romans who were responsible for bringing viticulture to France.

The study found that the Greeks founded Massalia, now known as Marseilles, which they then turned into a bustling trading site, where local tribes of Ligurian Celts undertook friendly bartering.

Prof Cartledge said within a matter of generations the nearby Rhône became a major thoroughfare for vessels carrying terracotta amphorae that contained what was seen as a new, exotic Greek drink made from fermented grape juice.

He argued the new drink rapidly became a hit among the tribes of Western Europe, which then contributed to the French’s modern love of wine.

"I hope this will lay to rest an enduring debate about the historic origins of supermarket plonk,” he said.

"Although some academics agree the Greeks were central to founding Europe's wine trade, others argue the Etruscans or even the later Romans were the ones responsible for bringing viticulture to France.”

Archaeologists have discovered a five-foot high, 31.5 stone bronze vessel, the Vix Krater, which was found in the grave of a Celtic princess in northern Burgundy, France.

Prof Cartledge said there were two main points that proved it was the Greeks who introduced wine to the region.

"First, the Greeks had to marry and mix with the local Ligurians to ensure that Massalia survived, suggesting that they also swapped goods and ideas.

"Second, they left behind copious amounts of archaeological evidence of their wine trade (unlike the Etruscans and long before the Romans), much of which has been found on Celtic sites."

The research forms part of Professor Cartledge's study into where the boundaries of Ancient Greece began and ended.

Rather than covering the geographical area occupied by the modern Greek state, he argued Ancient Greece stretched from Georgia in the east to Spain in the west.

European population substructure and systemic lupus erythematosus

2009-10-25T15:00:00.000+02:00

Genes Immun. 2009 Oct 22. [Epub ahead of print]

European population substructure correlates with systemic lupus erythematosus endophenotypes in North Americans of European descent.

Richman IB, Chung SA, Taylor KE, Kosoy R, Tian C, Ortmann WA, Nititham J, Lee AT, Rutman S, Petri M, Manzi S, Behrens TW, Gregersen PK, Seldin MF, Criswell LA.

Previous work has demonstrated that Northern and Southern European ancestries are associated with specific systemic lupus erythematosus (SLE) manifestations. In this study, 1855 SLE cases of European descent were genotyped for 4965 single-nucleotide polymorphisms and principal components analysis of genotype information was used to define population substructure. The first principal component (PC1) distinguished Northern from Southern European ancestry, PC2 differentiated Eastern from Western European ancestry and PC3 delineated Ashkenazi Jewish ancestry. Compared with Northern European ancestry, Southern European ancestry was associated with autoantibody production (odds ratio (OR)=1.40, 95% confidence interval (CI) 1.07-1.83) and renal involvement (OR 1.41, 95% CI 1.06-1.87), and was protective for discoid rash (OR=0.51, 95% CI 0.32-0.82) and photosensitivity (OR=0.74, 95% CI 0.56-0.97). Both serositis (OR=1.46, 95% CI 1.12-1.89) and autoantibody production (OR=1.38, 95% CI 1.06-1.80) were associated with Western compared to Eastern European ancestry. Ashkenazi Jewish ancestry was protective against neurologic manifestations of SLE (OR=0.62, 95% CI 0.40-0.94). Homogeneous clusters of cases defined by multiple PCs demonstrated stronger phenotypic associations. Genetic ancestry may contribute to the development of SLE endophenotypes and should be accounted for in genetic studies of disease characteristics.

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Stephen Oppenheimer's bad science

2009-10-24T09:00:00.003+03:00

Stephen Oppenheimer is quoted in the Times Online in regard to some comments that BNP leader Nick Griffin recently made about indigenous Britons. From the article titled Nick Griffin's Bad Science.

Watching Nick Griffin's performance on Question Time last night, I was struck by more than his objectionable views and evasive answers. He also seems to have a distinctly sketchy grasp of science, which he misrepresents to support his idea that Britain belongs to its "indigenous people".

He described white English, Welsh, Scottish and Irish people as "Britain's aborigines", suggesting these groups are descended from an ancestral population that arrived 17,000 years ago. Scientists, he said, would happily confirm this.

His comments seem, so far as I can tell, to be based on the hypothesis advanced by Stephen Oppenheimer, of Oxford University, in his book The Origins of the British. This uses genetic data to suggest that about 75 per cent of British ancestry can be traced back to very ancient times, before the Anglo-Saxons, Romans and Celts -- the argument is summarised nicely in this Prospect piece.

Part of Openheimer's response:

"About three quarters of the ancestors had arrived before the neolithic. Most of the rest arrived during the neolithic. There’s about 5 per cent from Anglo-Saxons, about 6 per cent from Vikings."

The idea of Paleolithic genetic continuity has been demolished recently, as I detail in Migrationism Strikes Back. Most of the mtDNA haplogroups, thought by scientists to have been in Europe since the Paleolithic, were absent when actual Paleolithic DNA was tested. Genetic continuity must be proven directly, and inferences from modern populations are suspect.

Oppenheimer bases his inferences on age calculations based on Y-chromosome STRs on modern populations, using an extreme evolutionary mutation rate that overestimates time depth by almost an order of magnitude, and leads to even more extreme time overestimates than the evoluationary rate that I criticized recently.

I had been positively inclined towards Oppenheimer's work, and I still consider it superior to other popularizing efforts, because of its data richness and clear effort to synthesize different strands of knowledge. In retrospect, however, it is flawed, as it is based on faulty mutation rates and faulty interpretation:

Oppenheimer's argument is a special case of what Francois Balloux described recently, and Guido Barbujani a long time ago. To make a long story short, it doesn't matter if a certain haplogroup found in Britons is 1,000 or 10,000 years old. Knowing this fact tells us nothing about when the patrilineage arrived in Britain: a 1,000-year old haplogroup may have developed from a British line of ancestors that were reduced to a single man 1,000 years ago, and a 10,000-year old haplogroup may have arrived in Britain only 10 years ago by a group of distantly related immigrants.

Nick Griffin is of course also wrong in inferring that Britons are descended from Paleolithic ancestors. But, he is wrong only in misquoting a date and in building a political case around a belief in Oppenheimer's inferences on Paleolithic origins of Britons.

Oppenheimer's political case is also flawed, however:

"He’s missed the point of the genetics in terms of his perspective that he can determine who is indigenous British. All British people are immigrants. As Bonnie Greer pointed out, the original Britons were Neanderthals. They were exterminated, then the Ice Age left a clean sheet. The modern population is essentially of north Iberian origin. So what’s British?"

Clearly the word "indigenous" cannot be taken literally and everyone living in Britain is descended from people who arrived there at some point or another. But, this is a gross oversimplification of the situation. Why do people speak of "native" Americans or Australian "aborigines"? They do not, certainly, mean that these people emerged from American or Australian soil. What they do mean, however, is that these people are the oldest recorded inhabitants of their homelands, the first people that can be named.

In the case of Britain, there are indeed indigenous people that can and are named by ancient writers, e.g. the Britons or Picts. No traditions for the immigration of these people exists, although their immigration can be inferred on linguistic grounds (Britons were IE speakers). There were certainly other people before them, whose names are lost to memory, but whose genetic trace may persist in the current inhabitants. There are also non-indigenous people that arrived there a long time ago, e.g., the Gaels, the Anglo-Saxons, the Norse, or the Normans, and their arrival was noted by historians. Finally, there are people that arrived in Great Britain more recently, e.g., Poles or Pakistanis.

Is there any way to distinguish between all these groups?

Clearly, one possible distinction is chronological: groups that arrived earlier are more indigenous than groups that arrived later. However, this is a relative difference, which does not allow us to make a sharp distinction between indigenous and foreign. 50 generations certainly earns you more "native" points than 2, but no obvious demarcation of indigeneity exists.

However, the main distinction is between groups that developed in situ and groups that arrived from elsewhere. The English are descended from a bunch of different sets of people, but as a people they developed in the country that came to be known as England.

In that sense the English are indigenous to England, not because their genes didn't arrive from elsewhere (they did), but in the sense that they became a people in the land itself. Different people were grafted onto the English over time, but they became English in an ethnic sense by being grafted onto them, and not by simply co-existing with them while retaining their own identity.

140,000-year divergence time between Eurasians and West Africans

2009-10-23T15:00:00.001+03:00

From the paper:

Perhaps our most interesting demographic results are the inferred divergence times. Other studies [11],[12] have estimated divergence times between Europeans and East Asians similar to the ≈23 kya we infer. Interestingly, archeological evidence places humans in Europe much earlier (≈40 kya) [1]. Our inferred divergence time of ≈22 kya between East Asians and Mexican-Americans is somewhat older than the oldest well-accepted New World archeological evidence [2]. The divergence we infer may reflect the settlement of Beringia, rather than the expansion into the New World proper [14]. Finally, the divergence time of ≈140 kya we infer between African and Eurasian populations is consistent with archeological evidence for modern humans in the Middle East ≈100 kya [1], but it is much older than other inferences of ≈50 kya divergence from mitochondrial DNA [1]. This discrepancy may be explained by our inclusion of migration in the model. Migration preserves correlation between population allele frequencies, so an observed correlation across the genome can be explained by either recent divergence without migration or ancient divergence with migration. In fact, the African-Eurasian migration rate we infer of ≈25×10−5 per generation is comparable to the ≈100×10−5 inferred from census records between modern continental Europe and Britain [55].

One difficulty in interpreting our divergence times is that the sampled populations may not best represent those in which historically important divergences occurred. For example, the Yoruba are a West African population, so the divergence time we infer between Yoruba and Eurasian ancestral populations may correspond to divergence within Africa itself. Future studies of more populations [56]–[58] will help alleviate this difficulty.

Some comments:

The 140ky divergence time between Eurasians and West Africans is consistent with my idea of Africans being divided into Palaeoafricans and Afrasians. The 140ky gap includes both divergence since Eurasians left Africa, as well as divergence between ancestral Eurasians ("Afrasians") and earlier African populations ("Palaeoafricans'). It remains to be seen whether the bulk of the 140ky occurred in Africa itself (in which case conventional Out of Africa c. 40kya is affirmed), or outside Africa (in which case Out of Africa c. 100kya, evidenced by early modern skulls acquires a new significance).
East Asian - Native American divergence of 22ky predates the known settlement of the Americas. But, this is not a problem, since we must split the 22ky into 15ky (since the settlement), and 8ky, which is reasonable time for divergence between the ancestors of the Chinese and the populations that headed north, and perhaps stayed in Beringia before crossing into the Americas.
East Asian - European divergence of 23ky suggests, in agreement with recent mtDNA evidence, that Europeans are not primarily descended from the earliest (or even the latest) Upper Paleolithic population of the continent. This seems to also be in agreement with Y-chromosome evidence that suggests interesting East-West connections in Eurasia that are not easily explained by a simple early divergence model with no subsequent link between east and west (e.g., western E vs. eastern D, western R vs. eastern Q, northern N vs. eastern O, etc.). It is also in agreement with the mtDNA picture (West Eurasian N dominance, East Eurasian mixed N/M).

Naturally, both the increased age of divergence of 140ky (compared to other studies), as well as the wide confidence intervals suggest that we must always treat genetic age estimates with the utmost caution.

PLoS Genet 5(10): e1000695. doi:10.1371/journal.pgen.1000695

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

Ryan N. Gutenkunst, Ryan D. Hernandez, Scott H. Williamson, Carlos D. Bustamante

Abstract

Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic variants within and between populations. For candidate models we numerically compute the expected spectrum using a diffusion approximation to the one-locus, two-allele Wright-Fisher process, involving up to three simultaneous populations. Our approach is a composite likelihood scheme, since linkage between neutral loci alters the variance but not the expectation of the frequency spectrum. We thus use bootstraps incorporating linkage to estimate uncertainties for parameters and significance values for hypothesis tests. Our method can also incorporate selection on single sites, predicting the joint distribution of selected alleles among populations experiencing a bevy of evolutionary forces, including expansions, contractions, migrations, and admixture. We model human expansion out of Africa and the settlement of the New World, using 5 Mb of noncoding DNA resequenced in 68 individuals from 4 populations (YRI, CHB, CEU, and MXL) by the Environmental Genome Project. We infer divergence between West African and Eurasian populations 140 thousand years ago (95% confidence interval: 40–270 kya). This is earlier than other genetic studies, in part because we incorporate migration. We estimate the European (CEU) and East Asian (CHB) divergence time to be 23 kya (95% c.i.: 17–43 kya), long after archeological evidence places modern humans in Europe. Finally, we estimate divergence between East Asians (CHB) and Mexican-Americans (MXL) of 22 kya (95% c.i.: 16.3–26.9 kya), and our analysis yields no evidence for subsequent migration. Furthermore, combining our demographic model with a previously estimated distribution of selective effects among newly arising amino acid mutations accurately predicts the frequency spectrum of nonsynonymous variants across three continental populations (YRI, CHB, CEU).

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