Publications by authors named "Peter A Underhill"

75 Publications

Determination of the phylogenetic origins of the Árpád Dynasty based on Y chromosome sequencing of Béla the Third.

Eur J Hum Genet 2021 Jan 7;29(1):164-172. Epub 2020 Jul 7.

National Institute of Oncology, Budapest, Hungary.

We set out to identify the origins of the Árpád Dynasty based on genome sequencing of DNA derived from the skeletal remains of Hungarian King Béla III (1172-1196) and eight additional individuals (six males, two females) originally interred at the Royal Basilica of Székesfehérvár. Y-chromosome analysis established that two individuals, Béla III and HU52 assign to haplogroups R-Z2125 whose distribution centres near South Central Asia with subsidiary expansions in the regions of modern Iran, the Volga Ural region and the Caucasus. Out of a cohort of 4340 individuals from these geographic areas, we acquired whole-genome data from 208 individuals derived for the R-Z2123 haplogroup. From these data we have established that the closest living kin of the Árpád Dynasty are R-SUR51 derived modern day Bashkirs predominantly from the Burzyansky and Abzelilovsky districts of Bashkortostan in the Russian Federation. Our analysis also reveals the existence of SNPs defining a novel Árpád Dynasty specific haplogroup R-ARP. Framed within the context of a high resolution R-Z2123 phylogeny, the ancestry of the first Hungarian royal dynasty traces to the region centering near Northern Afghanistan about 4500 years ago and identifies the Bashkirs as their closest kin, with a separation date between the two populations at the beginning of the first millennium CE.
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http://dx.doi.org/10.1038/s41431-020-0683-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7809292PMC
January 2021

The radial expansion of the Diego blood group system polymorphisms in Asia: mark of co-migration with the Mongol conquests.

Eur J Hum Genet 2019 01 24;27(1):125-132. Epub 2018 Aug 24.

Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France.

Red cell polymorphisms can provide evidence of human migration and adaptation patterns. In Eurasia, the distribution of Diego blood group system polymorphisms remains unaddressed. To shed light on the dispersal of the Di antigen, we performed analyses of correlations between the frequencies of DI*01 allele, C2-M217 and C2-M401 Y-chromosome haplotypes ascribed as being of Mongolian-origin and language affiliations, in 75 Eurasian populations including DI*01 frequency data from the HGDP-CEPH panel. We revealed that DI*01 reaches its highest frequency in Mongolia, Turkmenistan and Kyrgyzstan, expanding southward and westward across Asia with Altaic-speaking nomadic carriers of C2-M217, and even more precisely C2-M401, from their homeland presumably in Mongolia, between the third century BCE and the thirteenth century CE. The present study has highlighted the gene-culture co-migration with the demographic movements that occurred during the past two millennia in Central and East Asia. Additionally, this work contributes to a better understanding of the distribution of immunogenic erythrocyte polymorphisms with a view to improve transfusion safety.
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http://dx.doi.org/10.1038/s41431-018-0245-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303257PMC
January 2019

Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe.

Proc Natl Acad Sci U S A 2018 06 12;115(26):6774-6779. Epub 2018 Jun 12.

Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305.

The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals' genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (∼5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb.
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http://dx.doi.org/10.1073/pnas.1800851115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6042094PMC
June 2018

Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families.

Am J Hum Genet 2016 07;99(1):163-73

Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia. Electronic address:

The paternal haplogroup (hg) N is distributed from southeast Asia to eastern Europe. The demographic processes that have shaped the vast extent of this major Y chromosome lineage across numerous linguistically and autosomally divergent populations have previously been unresolved. On the basis of 94 high-coverage re-sequenced Y chromosomes, we establish and date a detailed hg N phylogeny. We evaluate geographic structure by using 16 distinguishing binary markers in 1,631 hg N Y chromosomes from a collection of 6,521 samples from 56 populations. The more southerly distributed sub-clade N4 emerged before N2a1 and N3, found mostly in the north, but the latter two display more elaborate branching patterns, indicative of regional contrasts in recent expansions. In particular, a number of prominent and well-defined clades with common N3a3'6 ancestry occur in regionally dissimilar northern Eurasian populations, indicating almost simultaneous regional diversification and expansion within the last 5,000 years. This patrilineal genetic affinity is decoupled from the associated higher degree of language diversity.
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http://dx.doi.org/10.1016/j.ajhg.2016.05.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5005449PMC
July 2016

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.

Nat Genet 2016 06 25;48(6):593-9. Epub 2016 Apr 25.

Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26 worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants contribute the greatest predicted functional impact. We constructed a calibrated phylogenetic tree on the basis of binary single-nucleotide variants and projected the more complex variants onto it, estimating the number of mutations for each class. Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations.
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http://dx.doi.org/10.1038/ng.3559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4884158PMC
June 2016

Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements.

Investig Genet 2016 11;7. Epub 2016 Feb 11.

Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus.

Background: The archeological record indicates that the permanent settlement of Cyprus began with pioneering agriculturalists circa 11,000 years before present, (ca. 11,000 y BP). Subsequent colonization events followed, some recognized regionally. Here, we assess the Y-chromosome structure of Cyprus in context to regional populations and correlate it to phases of prehistoric colonization.

Results: Analysis of haplotypes from 574 samples showed that island-wide substructure was barely significant in a spatial analysis of molecular variance (SAMOVA). However, analyses of molecular variance (AMOVA) of haplogroups using 92 binary markers genotyped in 629 Cypriots revealed that the proportion of variance among the districts was irregularly distributed. Principal component analysis (PCA) revealed potential genetic associations of Greek-Cypriots with neighbor populations. Contrasting haplogroups in the PCA were used as surrogates of parental populations. Admixture analyses suggested that the majority of G2a-P15 and R1b-M269 components were contributed by Anatolia and Levant sources, respectively, while Greece Balkans supplied the majority of E-V13 and J2a-M67. Haplotype-based expansion times were at historical levels suggestive of recent demography.

Conclusions: Analyses of Cypriot haplogroup data are consistent with two stages of prehistoric settlement. E-V13 and E-M34 are widespread, and PCA suggests sourcing them to the Balkans and Levant/Anatolia, respectively. The persistent pre-Greek component is represented by elements of G2-U5(xL30) haplogroups: U5*, PF3147, and L293. J2b-M205 may contribute also to the pre-Greek strata. The majority of R1b-Z2105 lineages occur in both the westernmost and easternmost districts. Distinctively, sub-haplogroup R1b- M589 occurs only in the east. The absence of R1b- M589 lineages in Crete and the Balkans and the presence in Asia Minor are compatible with Late Bronze Age influences from Anatolia rather than from Mycenaean Greeks.
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http://dx.doi.org/10.1186/s13323-016-0032-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4750176PMC
February 2016

A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

Authors:
Monika Karmin Lauri Saag Mário Vicente Melissa A Wilson Sayres Mari Järve Ulvi Gerst Talas Siiri Rootsi Anne-Mai Ilumäe Reedik Mägi Mario Mitt Luca Pagani Tarmo Puurand Zuzana Faltyskova Florian Clemente Alexia Cardona Ene Metspalu Hovhannes Sahakyan Bayazit Yunusbayev Georgi Hudjashov Michael DeGiorgio Eva-Liis Loogväli Christina Eichstaedt Mikk Eelmets Gyaneshwer Chaubey Kristiina Tambets Sergei Litvinov Maru Mormina Yali Xue Qasim Ayub Grigor Zoraqi Thorfinn Sand Korneliussen Farida Akhatova Joseph Lachance Sarah Tishkoff Kuvat Momynaliev François-Xavier Ricaut Pradiptajati Kusuma Harilanto Razafindrazaka Denis Pierron Murray P Cox Gazi Nurun Nahar Sultana Rane Willerslev Craig Muller Michael Westaway David Lambert Vedrana Skaro Lejla Kovačevic Shahlo Turdikulova Dilbar Dalimova Rita Khusainova Natalya Trofimova Vita Akhmetova Irina Khidiyatova Daria V Lichman Jainagul Isakova Elvira Pocheshkhova Zhaxylyk Sabitov Nikolay A Barashkov Pagbajabyn Nymadawa Evelin Mihailov Joseph Wee Tien Seng Irina Evseeva Andrea Bamberg Migliano Syafiq Abdullah George Andriadze Dragan Primorac Lubov Atramentova Olga Utevska Levon Yepiskoposyan Damir Marjanovic Alena Kushniarevich Doron M Behar Christian Gilissen Lisenka Vissers Joris A Veltman Elena Balanovska Miroslava Derenko Boris Malyarchuk Andres Metspalu Sardana Fedorova Anders Eriksson Andrea Manica Fernando L Mendez Tatiana M Karafet Krishna R Veeramah Neil Bradman Michael F Hammer Ludmila P Osipova Oleg Balanovsky Elza K Khusnutdinova Knut Johnsen Maido Remm Mark G Thomas Chris Tyler-Smith Peter A Underhill Eske Willerslev Rasmus Nielsen Mait Metspalu Richard Villems Toomas Kivisild

Genome Res 2015 Apr 13;25(4):459-66. Epub 2015 Mar 13.

Estonian Biocentre, Tartu, 51010, Estonia; Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.
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http://dx.doi.org/10.1101/gr.186684.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381518PMC
April 2015

Genetics and the history of the Samaritans: Y-chromosomal microsatellites and genetic affinity between Samaritans and Cohanim.

Hum Biol 2013 Dec;85(6):825-58

Department of Biology, Stanford University, Stanford, CA.

The Samaritans are a group of some 750 indigenous Middle Eastern people, about half of whom live in Holon, a suburb of Tel Aviv, and the other half near Nablus. The Samaritan population is believed to have numbered more than a million in late Roman times but less than 150 in 1917. The ancestry of the Samaritans has been subject to controversy from late Biblical times to the present. In this study, liquid chromatography/electrospray ionization/quadrupole ion trap mass spectrometry was used to allelotype 13 Y-chromosomal and 15 autosomal microsatellites in a sample of 12 Samaritans chosen to have as low a level of relationship as possible, and 461 Jews and non-Jews. Estimation of genetic distances between the Samaritans and seven Jewish and three non-Jewish populations from Israel, as well as populations from Africa, Pakistan, Turkey, and Europe, revealed that the Samaritans were closely related to Cohanim. This result supports the position of the Samaritans that they are descendants from the tribes of Israel dating to before the Assyrian exile in 722-720 BCE. In concordance with previously published single-nucleotide polymorphism haplotypes, each Samaritan family, with the exception of the Samaritan Cohen lineage, was observed to carry a distinctive Y-chromosome short tandem repeat haplotype that was not more than one mutation removed from the six-marker Cohen modal haplotype.
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http://dx.doi.org/10.3378/027.085.0601DOI Listing
December 2013

Population genomic analysis of ancient and modern genomes yields new insights into the genetic ancestry of the Tyrolean Iceman and the genetic structure of Europe.

PLoS Genet 2014 May 8;10(5):e1004353. Epub 2014 May 8.

Department of Genetics, Stanford University, Stanford, California, United States of America.

Genome sequencing of the 5,300-year-old mummy of the Tyrolean Iceman, found in 1991 on a glacier near the border of Italy and Austria, has yielded new insights into his origin and relationship to modern European populations. A key finding of that study was an apparent recent common ancestry with individuals from Sardinia, based largely on the Y chromosome haplogroup and common autosomal SNP variation. Here, we compiled and analyzed genomic datasets from both modern and ancient Europeans, including genome sequence data from over 400 Sardinians and two ancient Thracians from Bulgaria, to investigate this result in greater detail and determine its implications for the genetic structure of Neolithic Europe. Using whole-genome sequencing data, we confirm that the Iceman is, indeed, most closely related to Sardinians. Furthermore, we show that this relationship extends to other individuals from cultural contexts associated with the spread of agriculture during the Neolithic transition, in contrast to individuals from a hunter-gatherer context. We hypothesize that this genetic affinity of ancient samples from different parts of Europe with Sardinians represents a common genetic component that was geographically widespread across Europe during the Neolithic, likely related to migrations and population expansions associated with the spread of agriculture.
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http://dx.doi.org/10.1371/journal.pgen.1004353DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014435PMC
May 2014

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a.

Eur J Hum Genet 2015 Jan 26;23(1):124-31. Epub 2014 Mar 26.

1] Estonian Biocentre and the Department of Evolutionary Biology, University of Tartu, Tartu, Estonia [2] Estonian Academy of Sciences, Tallinn, Estonia.

R1a-M420 is one of the most widely spread Y-chromosome haplogroups; however, its substructure within Europe and Asia has remained poorly characterized. Using a panel of 16 244 male subjects from 126 populations sampled across Eurasia, we identified 2923 R1a-M420 Y-chromosomes and analyzed them to a highly granular phylogeographic resolution. Whole Y-chromosome sequence analysis of eight R1a and five R1b individuals suggests a divergence time of ∼25,000 (95% CI: 21,300-29,000) years ago and a coalescence time within R1a-M417 of ∼5800 (95% CI: 4800-6800) years. The spatial frequency distributions of R1a sub-haplogroups conclusively indicate two major groups, one found primarily in Europe and the other confined to Central and South Asia. Beyond the major European versus Asian dichotomy, we describe several younger sub-haplogroups. Based on spatial distributions and diversity patterns within the R1a-M420 clade, particularly rare basal branches detected primarily within Iran and eastern Turkey, we conclude that the initial episodes of haplogroup R1a diversification likely occurred in the vicinity of present-day Iran.
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http://dx.doi.org/10.1038/ejhg.2014.50DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266736PMC
January 2015

Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites.

Nat Commun 2013 ;4:2928

Department of Genetics, Stanford University, Stanford, California 94305, USA.

Previous Y-chromosome studies have demonstrated that Ashkenazi Levites, members of a paternally inherited Jewish priestly caste, display a distinctive founder event within R1a, the most prevalent Y-chromosome haplogroup in Eastern Europe. Here we report the analysis of 16 whole R1 sequences and show that a set of 19 unique nucleotide substitutions defines the Ashkenazi R1a lineage. While our survey of one of these, M582, in 2,834 R1a samples reveals its absence in 922 Eastern Europeans, we show it is present in all sampled R1a Ashkenazi Levites, as well as in 33.8% of other R1a Ashkenazi Jewish males and 5.9% of 303 R1a Near Eastern males, where it shows considerably higher diversity. Moreover, the M582 lineage also occurs at low frequencies in non-Ashkenazi Jewish populations. In contrast to the previously suggested Eastern European origin for Ashkenazi Levites, the current data are indicative of a geographic source of the Levite founder lineage in the Near East and its likely presence among pre-Diaspora Hebrews.
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http://dx.doi.org/10.1038/ncomms3928DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905698PMC
July 2014

Afghan Hindu Kush: where Eurasian sub-continent gene flows converge.

PLoS One 2013 18;8(10):e76748. Epub 2013 Oct 18.

Aix Marseille Université, ADES UMR7268, CNRS, EFS-AM, Marseille, France.

Despite being located at the crossroads of Asia, genetics of the Afghanistan populations have been largely overlooked. It is currently inhabited by five major ethnic populations: Pashtun, Tajik, Hazara, Uzbek and Turkmen. Here we present autosomal from a subset of our samples, mitochondrial and Y- chromosome data from over 500 Afghan samples among these 5 ethnic groups. This Afghan data was supplemented with the same Y-chromosome analyses of samples from Iran, Kyrgyzstan, Mongolia and updated Pakistani samples (HGDP-CEPH). The data presented here was integrated into existing knowledge of pan-Eurasian genetic diversity. The pattern of genetic variation, revealed by structure-like and Principal Component analyses and Analysis of Molecular Variance indicates that the people of Afghanistan are made up of a mosaic of components representing various geographic regions of Eurasian ancestry. The absence of a major Central Asian-specific component indicates that the Hindu Kush, like the gene pool of Central Asian populations in general, is a confluence of gene flows rather than a source of distinctly autochthonous populations that have arisen in situ: a conclusion that is reinforced by the phylogeography of both haploid loci.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0076748PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799995PMC
August 2014

Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females.

Science 2013 Aug;341(6145):562-5

Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, CA, USA.

The Y chromosome and the mitochondrial genome have been used to estimate when the common patrilineal and matrilineal ancestors of humans lived. We sequenced the genomes of 69 males from nine populations, including two in which we find basal branches of the Y-chromosome tree. We identify ancient phylogenetic structure within African haplogroups and resolve a long-standing ambiguity deep within the tree. Applying equivalent methodologies to the Y chromosome and the mitochondrial genome, we estimate the time to the most recent common ancestor (T(MRCA)) of the Y chromosome to be 120 to 156 thousand years and the mitochondrial genome T(MRCA) to be 99 to 148 thousand years. Our findings suggest that, contrary to previous claims, male lineages do not coalesce significantly more recently than female lineages.
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http://dx.doi.org/10.1126/science.1237619DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032117PMC
August 2013

The phylogeography of Y-chromosome haplogroup h1a1a-m82 reveals the likely Indian origin of the European Romani populations.

PLoS One 2012 28;7(11):e48477. Epub 2012 Nov 28.

CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India.

Linguistic and genetic studies on Roma populations inhabited in Europe have unequivocally traced these populations to the Indian subcontinent. However, the exact parental population group and time of the out-of-India dispersal have remained disputed. In the absence of archaeological records and with only scanty historical documentation of the Roma, comparative linguistic studies were the first to identify their Indian origin. Recently, molecular studies on the basis of disease-causing mutations and haploid DNA markers (i.e. mtDNA and Y-chromosome) supported the linguistic view. The presence of Indian-specific Y-chromosome haplogroup H1a1a-M82 and mtDNA haplogroups M5a1, M18 and M35b among Roma has corroborated that their South Asian origins and later admixture with Near Eastern and European populations. However, previous studies have left unanswered questions about the exact parental population groups in South Asia. Here we present a detailed phylogeographical study of Y-chromosomal haplogroup H1a1a-M82 in a data set of more than 10,000 global samples to discern a more precise ancestral source of European Romani populations. The phylogeographical patterns and diversity estimates indicate an early origin of this haplogroup in the Indian subcontinent and its further expansion to other regions. Tellingly, the short tandem repeat (STR) based network of H1a1a-M82 lineages displayed the closest connection of Romani haplotypes with the traditional scheduled caste and scheduled tribe population groups of northwestern India.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048477PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509117PMC
June 2013

Distinguishing the co-ancestries of haplogroup G Y-chromosomes in the populations of Europe and the Caucasus.

Eur J Hum Genet 2012 Dec 16;20(12):1275-82. Epub 2012 May 16.

Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia.

Haplogroup G, together with J2 clades, has been associated with the spread of agriculture, especially in the European context. However, interpretations based on simple haplogroup frequency clines do not recognize underlying patterns of genetic diversification. Although progress has been recently made in resolving the haplogroup G phylogeny, a comprehensive survey of the geographic distribution patterns of the significant sub-clades of this haplogroup has not been conducted yet. Here we present the haplogroup frequency distribution and STR variation of 16 informative G sub-clades by evaluating 1472 haplogroup G chromosomes belonging to 98 populations ranging from Europe to Pakistan. Although no basal G-M201* chromosomes were detected in our data set, the homeland of this haplogroup has been estimated to be somewhere nearby eastern Anatolia, Armenia or western Iran, the only areas characterized by the co-presence of deep basal branches as well as the occurrence of high sub-haplogroup diversity. The P303 SNP defines the most frequent and widespread G sub-haplogroup. However, its sub-clades have more localized distribution with the U1-defined branch largely restricted to Near/Middle Eastern and the Caucasus, whereas L497 lineages essentially occur in Europe where they likely originated. In contrast, the only U1 representative in Europe is the G-M527 lineage whose distribution pattern is consistent with regions of Greek colonization. No clinal patterns were detected suggesting that the distributions are rather indicative of isolation by distance and demographic complexities.
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http://dx.doi.org/10.1038/ejhg.2012.86DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3499744PMC
December 2012

Y-chromosome diversity in Native Mexicans reveals continental transition of genetic structure in the Americas.

Am J Phys Anthropol 2012 Jul 11;148(3):395-405. Epub 2012 May 11.

Institut de Biologia Evolutiva, CEXS-UPF-PRBB, Barcelona, Catalonia, Spain.

The genetic characterization of Native Mexicans is important to understand multiethnic based features influencing the medical genetics of present Mexican populations, as well as to the reconstruct the peopling of the Americas. We describe the Y-chromosome genetic diversity of 197 Native Mexicans from 11 populations and 1,044 individuals from 44 Native American populations after combining with publicly available data. We found extensive heterogeneity among Native Mexican populations and ample segregation of Q-M242* (46%) and Q-M3 (54%) haplogroups within Mexico. The northernmost sampled populations falling outside Mesoamerica (Pima and Tarahumara) showed a clear differentiation with respect to the other populations, which is in agreement with previous results from mtDNA lineages. However, our results point toward a complex genetic makeup of Native Mexicans whose maternal and paternal lineages reveal different narratives of their population history, with sex-biased continental contributions and different admixture proportions. At a continental scale, we found that Arctic populations and the northernmost groups from North America cluster together, but we did not find a clear differentiation within Mesoamerica and the rest of the continent, which coupled with the fact that the majority of individuals from Central and South American samples are restricted to the Q-M3 branch, supports the notion that most Native Americans from Mesoamerica southwards are descendants from a single wave of migration. This observation is compatible with the idea that present day Mexico might have constituted an area of transition in the diversification of paternal lineages during the colonization of the Americas.
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http://dx.doi.org/10.1002/ajpa.22062DOI Listing
July 2012

Afghanistan from a Y-chromosome perspective.

Eur J Hum Genet 2012 Oct 18;20(10):1063-70. Epub 2012 Apr 18.

Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL 33199, USA.

Central Asia has served as a corridor for human migrations providing trading routes since ancient times. It has functioned as a conduit connecting Europe and the Middle East with South Asia and far Eastern civilizations. Therefore, the study of populations in this region is essential for a comprehensive understanding of early human dispersal on the Eurasian continent. Although Y- chromosome distributions in Central Asia have been widely surveyed, present-day Afghanistan remains poorly characterized genetically. The present study addresses this lacuna by analyzing 190 Pathan males from Afghanistan using high-resolution Y-chromosome binary markers. In addition, haplotype diversity for its most common lineages (haplogroups R1a1a*-M198 and L3-M357) was estimated using a set of 15 Y-specific STR loci. The observed haplogroup distribution suggests some degree of genetic isolation of the northern population, likely due to the Hindu Kush mountain range separating it from the southern Afghans who have had greater contact with neighboring Pathans from Pakistan and migrations from the Indian subcontinent. Our study demonstrates genetic similarities between Pathans from Afghanistan and Pakistan, both of which are characterized by the predominance of haplogroup R1a1a*-M198 (>50%) and the sharing of the same modal haplotype. Furthermore, the high frequencies of R1a1a-M198 and the presence of G2c-M377 chromosomes in Pathans might represent phylogenetic signals from Khazars, a common link between Pathans and Ashkenazi groups, whereas the absence of E1b1b1a2-V13 lineage does not support their professed Greek ancestry.
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http://dx.doi.org/10.1038/ejhg.2012.59DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3449065PMC
October 2012

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing.

Nat Commun 2012 Feb 28;3:698. Epub 2012 Feb 28.

Department of Human Genetics, Saarland University, 66421 Homburg, Saar, Germany.

The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Ötztal Alps. Here we report the complete genome sequence of the Iceman and show 100% concordance between the previously reported mitochondrial genome sequence and the consensus sequence generated from our genomic data. We present indications for recent common ancestry between the Iceman and present-day inhabitants of the Tyrrhenian Sea, that the Iceman probably had brown eyes, belonged to blood group O and was lactose intolerant. His genetic predisposition shows an increased risk for coronary heart disease and may have contributed to the development of previously reported vascular calcifications. Sequences corresponding to ~60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis.
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http://dx.doi.org/10.1038/ncomms1701DOI Listing
February 2012

Neolithic patrilineal signals indicate that the Armenian plateau was repopulated by agriculturalists.

Eur J Hum Genet 2012 Mar 16;20(3):313-20. Epub 2011 Nov 16.

Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL 33199, USA.

Armenia, situated between the Black and Caspian Seas, lies at the junction of Turkey, Iran, Georgia, Azerbaijan and former Mesopotamia. This geographic position made it a potential contact zone between Eastern and Western civilizations. In this investigation, we assess Y-chromosomal diversity in four geographically distinct populations that represent the extent of historical Armenia. We find a striking prominence of haplogroups previously implicated with the Agricultural Revolution in the Near East, including the J2a-M410-, R1b1b1(*)-L23-, G2a-P15- and J1-M267-derived lineages. Given that the Last Glacial Maximum event in the Armenian plateau occured a few millennia before the Neolithic era, we envision a scenario in which its repopulation was achieved mainly by the arrival of farmers from the Fertile Crescent temporally coincident with the initial inception of farming in Greece. However, we detect very restricted genetic affinities with Europe that suggest any later cultural diffusions from Armenia to Europe were not associated with substantial amounts of paternal gene flow, despite the presence of closely related Indo-European languages in both Armenia and Southeast Europe.
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http://dx.doi.org/10.1038/ejhg.2011.192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3286660PMC
March 2012

Increased Y-chromosome resolution of haplogroup O suggests genetic ties between the Ami aborigines of Taiwan and the Polynesian Islands of Samoa and Tonga.

Gene 2012 Jan 3;492(2):339-48. Epub 2011 Nov 3.

College of Medicine, Florida International University, Miami, FL 33199, USA.

The Austronesian expansion has left its fingerprint throughout two thirds of the circumference of the globe reaching the island of Madagascar in East Africa to the west and Easter Island, off the coast of Chile, to the east. To date, several theories exist to explain the current genetic distribution of Austronesian populations, with the "slow boat" model being the most widely accepted, though other conjectures (i.e., the "express train" and "entangled bank" hypotheses) have also been widely discussed. In the current study, 158 Y chromosomes from the Polynesian archipelagos of Samoa and Tonga were typed using high resolution binary markers and compared to populations across Mainland East Asia, Taiwan, Island Southeast Asia, Melanesia and Polynesia in order to establish their patrilineal genetic relationships. Y-STR haplotypes on the C2 (M38), C2a (M208), O1a (M119), O3 (M122) and O3a2 (P201) backgrounds were utilized in an attempt to identify the differing sources of the current Y-chromosomal haplogroups present throughout Polynesia (of Melanesian and/or Asian descent). We find that, while haplogroups C2a, S and K3-P79 suggest a Melanesian component in 23%-42% of the Samoan and Tongan Y chromosomes, the majority of the paternal Polynesian gene pool exhibits ties to East Asia. In particular, the prominence of sub-haplogroup O3a2c* (P164), which has previously been observed at only minimal levels in Mainland East Asians (2.0-4.5%), in both Polynesians (ranging from 19% in Manua to 54% in Tonga) and Ami aborigines from Taiwan (37%) provides, for the first time, evidence for a genetic connection between the Polynesian populations and the Ami.
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http://dx.doi.org/10.1016/j.gene.2011.10.042DOI Listing
January 2012

The Caucasus as an asymmetric semipermeable barrier to ancient human migrations.

Mol Biol Evol 2012 Jan 13;29(1):359-65. Epub 2011 Sep 13.

Estonian Biocentre, Tartu, Estonia.

The Caucasus, inhabited by modern humans since the Early Upper Paleolithic and known for its linguistic diversity, is considered to be important for understanding human dispersals and genetic diversity in Eurasia. We report a synthesis of autosomal, Y chromosome, and mitochondrial DNA (mtDNA) variation in populations from all major subregions and linguistic phyla of the area. Autosomal genome variation in the Caucasus reveals significant genetic uniformity among its ethnically and linguistically diverse populations and is consistent with predominantly Near/Middle Eastern origin of the Caucasians, with minor external impacts. In contrast to autosomal and mtDNA variation, signals of regional Y chromosome founder effects distinguish the eastern from western North Caucasians. Genetic discontinuity between the North Caucasus and the East European Plain contrasts with continuity through Anatolia and the Balkans, suggesting major routes of ancient gene flows and admixture.
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http://dx.doi.org/10.1093/molbev/msr221DOI Listing
January 2012

Croatian genetic heritage: Y-chromosome story.

Croat Med J 2011 Jun;52(3):225-34

Dragan Primorac, University of Split School of Medicine, Soltanska 2, 21 000 Split, Croatia.

The aim of this article is to offer a concise interpretation of the scientific data about the topic of Croatian genetic heritage that was obtained over the past 10 years. We made a short overview of previously published articles by our and other groups, based mostly on Y-chromosome results. The data demonstrate that Croatian human population, as almost any other European population, represents remarkable genetic mixture. More than 3/4 of the contemporary Croatian men are most probably the offspring of Old Europeans who came here before and after the Last Glacial Maximum. The rest of the population is the offspring of the people who were arriving in this part of Europe through the southeastern route in the last 10,000 years, mostly during the neolithization process. We believe that the latest discoveries made with the techniques for whole-genome typing using the array technology, will help us understand the structure of Croatian population in more detail, as well as the aspects of its demographic history.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3118711PMC
http://dx.doi.org/10.3325/cmj.2011.52.225DOI Listing
June 2011

The coming of the Greeks to Provence and Corsica: Y-chromosome models of archaic Greek colonization of the western Mediterranean.

BMC Evol Biol 2011 Mar 14;11:69. Epub 2011 Mar 14.

Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, CA 94305, USA.

Background: The process of Greek colonization of the central and western Mediterranean during the Archaic and Classical Eras has been understudied from the perspective of population genetics. To investigate the Y chromosomal demography of Greek colonization in the western Mediterranean, Y-chromosome data consisting of 29 YSNPs and 37 YSTRs were compared from 51 subjects from Provence, 58 subjects from Smyrna and 31 subjects whose paternal ancestry derives from Asia Minor Phokaia, the ancestral embarkation port to the 6th century BCE Greek colonies of Massalia (Marseilles) and Alalie (Aleria, Corsica).

Results: 19% of the Phokaian and 12% of the Smyrnian representatives were derived for haplogroup E-V13, characteristic of the Greek and Balkan mainland, while 4% of the Provencal, 4.6% of East Corsican and 1.6% of West Corsican samples were derived for E-V13. An admixture analysis estimated that 17% of the Y-chromosomes of Provence may be attributed to Greek colonization. Using the following putative Neolithic Anatolian lineages: J2a-DYS445 = 6, G2a-M406 and J2a1b1-M92, the data predict a 0% Neolithic contribution to Provence from Anatolia. Estimates of colonial Greek vs. indigenous Celto-Ligurian demography predict a maximum of a 10% Greek contribution, suggesting a Greek male elite-dominant input into the Iron Age Provence population.

Conclusions: Given the origin of viniculture in Provence is ascribed to Massalia, these results suggest that E-V13 may trace the demographic and socio-cultural impact of Greek colonization in Mediterranean Europe, a contribution that appears to be considerably larger than that of a Neolithic pioneer colonization.
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http://dx.doi.org/10.1186/1471-2148-11-69DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068964PMC
March 2011

Hunter-gatherer genomic diversity suggests a southern African origin for modern humans.

Proc Natl Acad Sci U S A 2011 Mar 7;108(13):5154-62. Epub 2011 Mar 7.

Department of Genetics, Stanford University, Stanford, CA 94305, USA.

Africa is inferred to be the continent of origin for all modern human populations, but the details of human prehistory and evolution in Africa remain largely obscure owing to the complex histories of hundreds of distinct populations. We present data for more than 580,000 SNPs for several hunter-gatherer populations: the Hadza and Sandawe of Tanzania, and the ≠Khomani Bushmen of South Africa, including speakers of the nearly extinct N|u language. We find that African hunter-gatherer populations today remain highly differentiated, encompassing major components of variation that are not found in other African populations. Hunter-gatherer populations also tend to have the lowest levels of genome-wide linkage disequilibrium among 27 African populations. We analyzed geographic patterns of linkage disequilibrium and population differentiation, as measured by F(ST), in Africa. The observed patterns are consistent with an origin of modern humans in southern Africa rather than eastern Africa, as is generally assumed. Additionally, genetic variation in African hunter-gatherer populations has been significantly affected by interaction with farmers and herders over the past 5,000 y, through both severe population bottlenecks and sex-biased migration. However, African hunter-gatherer populations continue to maintain the highest levels of genetic diversity in the world.
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http://dx.doi.org/10.1073/pnas.1017511108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3069156PMC
March 2011

A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe.

Eur J Hum Genet 2011 Jan 25;19(1):95-101. Epub 2010 Aug 25.

Sorenson Molecular Genealogy Foundation, Salt Lake City, UT, USA.

The phylogenetic relationships of numerous branches within the core Y-chromosome haplogroup R-M207 support a West Asian origin of haplogroup R1b, its initial differentiation there followed by a rapid spread of one of its sub-clades carrying the M269 mutation to Europe. Here, we present phylogeographically resolved data for 2043 M269-derived Y-chromosomes from 118 West Asian and European populations assessed for the M412 SNP that largely separates the majority of Central and West European R1b lineages from those observed in Eastern Europe, the Circum-Uralic region, the Near East, the Caucasus and Pakistan. Within the M412 dichotomy, the major S116 sub-clade shows a frequency peak in the upper Danube basin and Paris area with declining frequency toward Italy, Iberia, Southern France and British Isles. Although this frequency pattern closely approximates the spread of the Linearbandkeramik (LBK), Neolithic culture, an advent leading to a number of pre-historic cultural developments during the past ≤10 thousand years, more complex pre-Neolithic scenarios remain possible for the L23(xM412) components in Southeast Europe and elsewhere.
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http://dx.doi.org/10.1038/ejhg.2010.146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039512PMC
January 2011

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

Proc Natl Acad Sci U S A 2009 Dec 17;106(48):20174-9. Epub 2009 Nov 17.

Unité Mixte de Recherche 6578, Centre National de Recherche Scientifique, and Etablissement Français du Sang, Biocultural Anthropology, Medical Faculty,Université de Méditerranée, 13916 Marseille, France.

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.
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http://dx.doi.org/10.1073/pnas.0910803106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2787129PMC
December 2009

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

Eur J Hum Genet 2010 Apr 4;18(4):479-84. Epub 2009 Nov 4.

Division of Child and Adolescent Psychiatry and Child Development, Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA 94304-5485, USA.

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.
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http://dx.doi.org/10.1038/ejhg.2009.194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2987245PMC
April 2010

The emergence of Y-chromosome haplogroup J1e among Arabic-speaking populations.

Eur J Hum Genet 2010 Mar 14;18(3):348-53. Epub 2009 Oct 14.

UMR6578 (Université de la Méditerranée, CNRS, EFS) Anthropologie bio-culturelle, Faculté de médecine de Marseille, Marseille, France.

Haplogroup J1 is a prevalent Y-chromosome lineage within the Near East. We report the frequency and YSTR diversity data for its major sub-clade (J1e). The overall expansion time estimated from 453 chromosomes is 10,000 years. Moreover, the previously described J1 (DYS388=13) chromosomes, frequently found in the Caucasus and eastern Anatolian populations, were ancestral to J1e and displayed an expansion time of 9000 years. For J1e, the Zagros/Taurus mountain region displays the highest haplotype diversity, although the J1e frequency increases toward the peripheral Arabian Peninsula. The southerly pattern of decreasing expansion time estimates is consistent with the serial drift and founder effect processes. The first such migration is predicted to have occurred at the onset of the Neolithic, and accordingly J1e parallels the establishment of rain-fed agriculture and semi-nomadic herders throughout the Fertile Crescent. Subsequently, J1e lineages might have been involved in episodes of the expansion of pastoralists into arid habitats coinciding with the spread of Arabic and other Semitic-speaking populations.
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http://dx.doi.org/10.1038/ejhg.2009.166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2987219PMC
March 2010

Footprints of X-to-Y gene conversion in recent human evolution.

Mol Biol Evol 2010 Mar 6;27(3):714-25. Epub 2009 Oct 6.

Dipartimento di Genetica e Biologia Molecolare, Sapienza Università di Roma, Rome, Italy.

Different X-homologous regions of the male-specific portion of the human Y chromosome (MSY) are characterized by a different content of putative single nucleotide polymorphisms (SNPs), as reported in public databases. The possible role of X-to-Y nonallelic gene conversion in contributing to these differences remains poorly understood. We explored this issue by analyzing sequence variation in three regions of the MSY characterized by a different degree of X-Y similarity and a different density of putative SNPs: the PCDH11Y gene in the X-transposed (X-Y identity 99%, high putative SNP content); the TBL1Y gene in the X-degenerate (X-Y identity 86-88%, low putative SNP content); and VCY genes-containing region in the P8 palindrome (X-Y identity 95%, low putative SNP content). Present findings do not provide any evidence for gene conversion in the PCDH11Y and TBL1Y genes; they also strongly suggest that most putative SNPs of the PCDH11Y gene (and possibly the entire X-transposed region) are most likely X-Y paralogous sequence variants, which have been entered in the databases as SNPs. On the other hand, clear evidence for the VCY genes in the P8 palindrome having acted as an acceptor of X-to-Y gene conversion was obtained. A rate of 1.8 x 10(-7) X-to-Y conversions/bp/year was estimated for these genes. These findings indicate that in the VCY region of the MSY, X-to-Y gene conversion can be highly effective to increase the level of diversity among human Y chromosomes and suggest an additional explanation for the ability of the Y chromosome to retard degradation during evolution. Present data are expected to pave the way for future investigations on the role of nonallelic gene conversion in double-strand break repair and the maintenance of Y chromosome integrity.
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http://dx.doi.org/10.1093/molbev/msp231DOI Listing
March 2010