45 SNP universal genetic identification

Forensic geneticists currently use the highly polymorphic CODIS microsatellite markers for DNA sample identification. This paper shows that a unique DNA id for a human can be achieved by a panel of 45 SNPs.

Human Genetics doi:10.1007/s00439-009-0771-1

SNPs for a universal individual identification panel

Andrew J. Pakstis et al.

Abstract

An efficient method to uniquely identify every individual would have value in quality control and sample tracking of large collections of cell lines or DNA as is now often the case with whole genome association studies. Such a method would also be useful in forensics. SNPs represent the best markers for such purposes. We have developed a globally applicable resource of 92 SNPs for individual identification (IISNPs) with extremely low probabilities of any two unrelated individuals from anywhere in the world having identical genotypes. The SNPs were identified by screening over 500 likely/candidate SNPs on samples of 44 populations representing the major regions of the world. All 92 IISNPs have an average heterozygosity >0.4 and the F _st values are all less than 0.06 on our 44 populations making these a universally applicable panel irrespective of ethnicity or ancestry. No significant linkage disequilibrium (LD) occurs for all unique pairings of 86 of the 92 IISNPs (median LD = 0.011) in all of the 44 populations. The remaining 6 IISNPs show strong LD in most of the 44 populations for a small subset (7) of the unique pairings in which they occur due to close linkage. 45 of the 86 SNPs are spread across the 22 human autosomes and show very loose or no genetic linkage with each other. These 45 IISNPs constitute an excellent panel for individual identification including paternity testing with associated probabilities of individual genotypes less than 10⁻¹⁵, smaller than achieved with the current panels of forensic markers. This panel also improves on an interim panel of 40 IISNPs previously identified using 40 population samples. The unlinked status of the subset of 45 SNPs we have identified also makes them useful for situations involving close biological relationships. Comparisons with random sets of SNPs illustrate the greater discriminating power, efficiency, and more universal applicability of this IISNP panel to populations around the world. The full set of 86 IISNPs that do not show LD can be used to provide even smaller genotype match probabilities in the range of 10⁻³¹–10⁻³⁵ based on the 44 population samples studied.

Link

Γιατί ψηφίζουμε Ντόρα Μπακογιάννη στις 29 Νοεμβρίου

Στηρίζουμε Ντόρα Μπακογιάννη, γιατί δεν θέλουμε αύριο η Νέα Δημοκρατία να κυβερνάται από τη δυαρχία των πρώην αρχηγών αποτυχημένων κομμάτων και να έχει ηγετική ομάδα τους Μανώλη/Παπακώστα/Παναγιωτόπουλο/Πιπιλή/Μιχαλολιάκο/Μαρκόπουλο/Γεροντόπουλο/Γκιουλέκα. Στηρίζουμε Ντόρα Μπακογιάννη γιατί δεν θέλουμε να μείνουμε στην αντιπολίτευση ως το 2017 και βλέπουμε. Στηρίζουμε Ντόρα Μπακογιάννη γιατί ήταν μαζί μας στον αγώνα της 4ης Οκτωβρίου ενώ ο Μεσσήνιος Μεσσίας διατηρούσε το προσωπικό του ίματζ άφθαρτο και κρυβόταν στην εκλογική του περιφέρεια. Στηρίζουμε Ντόρα Μπακογιάννη γιατί ζήτησε διάλογο και πήρε άρνηση, δεσμεύτηκε για θητεία και προκριμματικές εκλογές και πήρε "ίσως", βγήκε σε όλα τα μέσα, φίλια και εχθρικά, και δεν κρύφτηκε σε μονολόγους μπροστά σε χειροκροτητές. Στηρίζουμε Ντόρα Μπακογιάννη γιατί δεν κοιτούσε 8 χρόνια τους τοίχους του σπιτιού της. Στηρίζουμε Ντόρα Μπακογιάννη γιατί δεν έκανε 7 ερωτήσεις 3 χρόνια ευρωβουλευτής. Στηρίζουμε Ντόρα Μπακογιάννη γιατί αυτός που πάτωσε το κόμμα του και οδήγησε σε αύξηση της Αριστεράς το 1996 δεν θα δώσει ιδεολογική λάμψη στην Κεντροδεξιά το 2013. Στηρίζουμε Ντόρα Μπακογιάννη γιατί δεν έχει πορεία εκκρεμούς, να είναι υπερβατική κεντρώα το 1993 και Σαρκοζική δεξιά το 2009. Στηρίζουμε Ντόρα Μπακογιάννη γιατί δεν θέλουμε να ξεχάσουμε την ιστορία μας και τους τρεις μας αρχηγούς εναντίον των οποίων κατέβηκε ο Σαμαράς στις εκλογές. Στηρίζουμε Ντόρα Μπακογιάννη γιατί ο Εθνάρχης πέταξε έξω τον Σαμαρά από το Προεδρικό Μέγαρο. Στηρίζουμε Ντόρα Μπακογιάννη γιατί μας έκανε για πρώτη φορά μετά από χρόνια να χαμογελάσουμε για το Σκοπιανό. Στηρίζουμε Ντόρα Μπακογιάννη γιατί το καπρίτσιο του Σαμαρά ανέτρεψε την βούληση τριών εκατομμυρίων Νεοδημοκρατών ψηφοφόρων. Στηρίζουμε Ντόρα Μπακογιάννη γιατί το μεγαλύτερο πολιτικό της επίτευγμα τα τελευταία 15 χρόνια δεν είναι που στερέωσε το πόδι της Ίριδας στο νέο Μουσείο. Για τον Παύλο, για την Ευρυτανία, για το Υπουργείο Πολιτισμού, για την Α' Αθηνών, για το Δήμο Αθηναίων, για το ΥΠΕΞ, για την εργατικότητα της, για την ευφυΐα της, για τη μαχητικότητα της, για την πίστη της, για την αδιάλειπτη παρουσία της σε καλές και κακές στιγμές, Ντόρα Μπακογιάννη στις 29 Νοεμβρίου.

Αποτίμηση αποτελέσματος: 29/11/09: η νέα αρχή για τη Νέα Δημοκρατία

Y chromosomes of Andalusians from Huelva

Annals of Human Biology

The Andalusian population from Huelva reveals a high diversification of Y-DNA paternal lineages from haplogroup E: Identifying human male movements within the Mediterranean space.

B. Ambrosio et al.

Abstract

Gene flow among human populations is generally interpreted in terms of complex patterns, with the observed gene frequencies being the consequence of the entire genetic and demographic histories of the population. Aims: This study performs a high-resolution analysis of the Y-chromosome haplogroup E in Western Andalusians (Huelva province). The genetic information presented here provides new insights into migration processes that took place throughout the Mediterranean space and tries to evaluate its impact on the current genetic composition of the most southwestern population of Spain. Subjects and methods: 167 unrelated males were previously typed for the presence/absence of the Y-chromosome Alu polymorphism (YAP). The group of YAP (+) Andalusians was genotyped for 16 Y-SNPs and also characterized for 16 Y-STR loci. Results: The distribution of E-M81 haplogroup, a Berber marker, was found at a frequency of 3% in our sample. The distribution of M81 frequencies in Iberia seems to be not concordant with the regions where Islamic rule was most intense and long-lasting. The study also showed that most of M78 derived allele (6.6%) led to the V13* subhaplogroup. We also found the most basal and rare paragroup M78* and others with V12 and V65 mutations. The lineage defined by M34 mutation, which is quite frequent in Jews, was detected as well. Conclusions: The haplogroup E among Western Andalusians revealed a complex admixture of genetic markers from the Mediterranean space, with interesting signatures of populations from the Middle East and the Balkan Peninsula and a surprisingly low influence by Berber populations compared to other areas of the Iberian Peninsula.

Link

Τwo papers on Genetic structure of Han Chinese in AJHG

A couple of new papers on population structure in the Han Chinese have just appeared in the American Journal of Human Genetics. My comments will follow once I read the two papers.

UPDATE (on Chen et al.):

The PCA plot on the left from Chen et al. shows clearly the north-south cline of genetic variation in China. While there are no apparent barriers within the Han ethnic group, it is clear that subsets of Han Chinese can be perfectly distinguished from each other by just looking at the first two principal components.

From the paper:

The one-dimensional subpopulation structure of the Han Chinese population (along PC1) showed a close resemblance to their sampling location son a geographic map, and there is a very high correlation of 0.93 between the mean PC1 values of samples and the median latitudes of the provinces

The results of the STRUCTURE analysis are also very interesting as they show the expected clinality of variation within China rather than sharp distinctions, paralleling the situation in the landmass of Europe. However, at K=3 the major component of the Japanese (JPT) is shown to be a low-level component within the Chinese. It's hard to interpret this, but a first hypothesis could be that the Japanese are descended from an earlier Mongoloid genetic stratum that has since been admixed in the Asian mainland with other Mongoloid groups, but retained its "purity" in the Japanese islands.

The American Journal of Human Genetics, 25 November 2009
doi:10.1016/j.ajhg.2009.10.016

Genetic Structure of the Han Chinese Population Revealed by Genome-wide SNP Variation

Jieming Chen et al.

Abstract

Population stratification is a potential problem for genome-wide association studies (GWAS), confounding results and causing spurious associations. Hence, understanding how allele frequencies vary across geographic regions or among subpopulations is an important prelude to analyzing GWAS data. Using over 350,000 genome-wide autosomal SNPs in over 6000 Han Chinese samples from ten provinces of China, our study revealed a one-dimensional “north-south” population structure and a close correlation between geography and the genetic structure of the Han Chinese. The north-south population structure is consistent with the historical migration pattern of the Han Chinese population. Metropolitan cities in China were, however, more diffused “outliers,” probably because of the impact of modern migration of peoples. At a very local scale within the Guangdong province, we observed evidence of population structure among dialect groups, probably on account of endogamy within these dialects. Via simulation, we show that empirical levels of population structure observed across modern China can cause spurious associations in GWAS if not properly handled. In the Han Chinese, geographic matching is a good proxy for genetic matching, particularly in validation and candidate-gene studies in which population stratification cannot be directly accessed and accounted for because of the lack of genome-wide data, with the exception of the metropolitan cities, where geographical location is no longer a good indicator of ancestral origin. Our findings are important for designing GWAS in the Chinese population, an activity that is expected to intensify greatly in the near future.

Link

The American Journal of Human Genetics, 25 November 2009
doi:10.1016/j.ajhg.2009.10.015

Genomic Dissection of Population Substructure of Han Chinese and Its Implication in Association Studies

Shuhua Xu et al.

Abstract

To date, most genome-wide association studies (GWAS) and studies of fine-scale population structure have been conducted primarily on Europeans. Han Chinese, the largest ethnic group in the world, composing 20% of the entire global human population, is largely underrepresented in such studies. A well-recognized challenge is the fact that population structure can cause spurious associations in GWAS. In this study, we examined population substructures in a diverse set of over 1700 Han Chinese samples collected from 26 regions across China, each genotyped at ∼160K single-nucleotide polymorphisms (SNPs). Our results showed that the Han Chinese population is intricately substructured, with the main observed clusters corresponding roughly to northern Han, central Han, and southern Han. However, simulated case-control studies showed that genetic differentiation among these clusters, although very small (FST = 0.0002 ∼0.0009), is sufficient to lead to an inflated rate of false-positive results even when the sample size is moderate. The top two SNPs with the greatest frequency differences between the northern Han and southern Han clusters (FST > 0.06) were found in the FADS2 gene, which associates with the fatty acid composition in phospholipids, and in the HLA complex P5 gene (HCP5), which associates with HIV infection, psoriasis, and psoriatic arthritis. Ingenuity Pathway Analysis (IPA) showed that most differentiated genes among clusters are involved in cardiac arteriopathy (p less than 10−101). These signals indicating significant differences among Han Chinese subpopulations should be carefully explained in case they are also detected in association studies, especially when sample sources are diverse.

Link

Sex-biased admixture in the Americas (Stefflova et al. 2009)

PLoS ONE doi:10.1371/journal.pone.0007842

Evaluation of Group Genetic Ancestry of Populations from Philadelphia and Dakar in the Context of Sex-Biased Admixture in the Americas

Klara Stefflova et al.

Abstract

Background
Population history can be reflected in group genetic ancestry, where genomic variation captured by the mitochondrial DNA (mtDNA) and non-recombining portion of the Y chromosome (NRY) can separate female- and male-specific admixture processes. Genetic ancestry may influence genetic association studies due to differences in individual admixture within recently admixed populations like African Americans.

Principal Findings
We evaluated the genetic ancestry of Senegalese as well as European Americans and African Americans from Philadelphia. Senegalese mtDNA consisted of ~12% U haplotypes (U6 and U5b1b haplotypes, common in North Africa) while the NRY haplotypes belonged solely to haplogroup E. In Philadelphia, we observed varying degrees of admixture. While African Americans have 9–10% mtDNAs and ~31% NRYs of European origin, these results are not mirrored in the mtDNA/NRY pools of European Americans: they have less than 7% mtDNAs and less than 2% NRYs from non-European sources. Additionally, there is Additionally, there is less than 2% Native American contribution to Philadelphian African American ancestry and the admixture from combined mtDNA/NRY estimates is consistent with the admixture derived from autosomal genetic data. To further dissect these estimates, we have analyzed our samples in the context of different demographic groups in the Americas.

Conclusions
We found that sex-biased admixture in African-derived populations is present throughout the Americas, with continual influence of European males, while Native American females contribute mainly to populations of the Caribbean and South America. The high non-European female contribution to the pool of European-derived populations is consistently characteristic of Iberian colonization. These data suggest that genomic data correlate well with historical records of colonization in the Americas.

Link

Genetic Variation and Recent Positive Selection with 1 million SNPs

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)

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

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)

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

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

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

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

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

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.

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Spouse selection in Sardinia

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.

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Ottoman terror in 15th c. Croatia

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.

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