Papers by Peter Underhill
BMC Genetics, Sep 22, 2009
Background: Human origins and migration models proposing the Horn of Africa as a prehistoric exit... more Background: Human origins and migration models proposing the Horn of Africa as a prehistoric exit route to Asia have stimulated molecular genetic studies in the region using uniparental loci. However, from a Y-chromosome perspective, Saudi Arabia, the largest country of the region, has not yet been surveyed. To address this gap, a sample of 157 Saudi males was analyzed at high resolution using 67 Y-chromosome binary markers. In addition, haplotypic diversity for its most prominent J1-M267 lineage was estimated using a set of 17 Y-specific STR loci. Results: Saudi Arabia differentiates from other Arabian Peninsula countries by a higher presence of J2-M172 lineages. It is significantly different from Yemen mainly due to a comparative reduction of sub-Saharan Africa E1-M123 and Levantine J1-M267 male lineages. Around 14% of the Saudi Arabia Y-chromosome pool is typical of African biogeographic ancestry, 17% arrived to the area from the East across Iran, while the remainder 69% could be considered of direct or indirect Levantine ascription. Interestingly, basal E-M96* (n = 2) and J-M304* (n = 3) lineages have been detected, for the first time, in the Arabian Peninsula. Coalescence time for the most prominent J1-M267 haplogroup in Saudi Arabia (11.6 ± 1.9 ky) is similar to that obtained previously for Yemen (11.3 ± 2) but significantly older that those estimated for Qatar (7.3 ± 1.8) and UAE (6.8 ± 1.5). The Y-chromosome genetic structure of the Arabian Peninsula seems to be mainly modulated by geography. The data confirm that this area has mainly been a recipient of gene flow from its African and Asian surrounding areas, probably mainly since the last Glacial maximum onwards. Although rare deep rooting lineages for Y-chromosome haplogroups E and J have been detected, the presence of more basal clades supportive of the southern exit route of modern humans to Eurasian, were not found.
American Journal of Human Genetics, Sep 1, 2005
The prehistoric peopling of East Asia by modern humans remains controversial with respect to earl... more The prehistoric peopling of East Asia by modern humans remains controversial with respect to early population migrations. Here, we present a systematic sampling and genetic screening of an East Asian-specific Y-chromosome haplogroup (O3-M122) in 2,332 individuals from diverse East Asian populations. Our results indicate that the O3-M122 lineage is dominant in East Asian populations, with an average frequency of 44.3%. The microsatellite data show that the O3-M122 haplotypes in southern East Asia are more diverse than those in northern East Asia, suggesting a southern origin of the O3-M122 mutation. It was estimated that the early northward migration of the O3-M122 lineages in East Asia occurred ∼25,000-30,000 years ago, consistent with the fossil records of modern humans in East Asia.
Science, Aug 2, 2013
The Y chromosome and the mitochondrial genome (mtDNA) have been used to estimate when the common ... more The Y chromosome and the mitochondrial genome (mtDNA) 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 longstanding ambiguity deep within the tree. Applying equivalent methodologies to the Y and mtDNA, we estimate the time to the most recent common ancestor (T MRCA ) of the Y chromosome to be 120-156 thousand years and the mtDNA T MRCA to be 99-148 ky. Our findings suggest that, contrary to prior claims, male lineages do not coalesce significantly more recently than female lineages.
Résumé de la 1833e réunion scientifique de la société d'Anthroplogie de Paris "Autour de... more Résumé de la 1833e réunion scientifique de la société d'Anthroplogie de Paris "Autour de la Méditerranée, de la préhistoire à nos jours. - Hommes et peuplements/interactions bioculturelles - Marseille 23-25 Janvier 2008 dans Bulletins et Mémoires de la Société d'Anthropologie de Paris, n.s. , t.19 , 3-4, 265-29
Introduction: Comprehensive Croatian Y-chromosome short tandem repeat (STR) haplotype database on... more Introduction: Comprehensive Croatian Y-chromosome short tandem repeat (STR) haplotype database on national and regional levels is important to get an insight into Y-chromosome genetic variability. The aim of this study was the detailed analysis of haplotype and haplogroup diversification in Croatian population. Methods: We carried out a statistical analysis of the data from previously performed genetic a analyses collected during routine forensic work by the Forensic Science Centre ‘‘Ivan Vucetic’’. A total of 1100 men from eastern, western, central, southern and northern Croatia were typed using AmpFISTR Yfiler PCR amplification kit. We estimated Y-chromosomal haplogroups from Croatian Y-STR haplotype data using Whit Atheys’ Haplogroup Predictor. Median-Joining Network (MJN) included all 17 Y-STR loci, and was constructed with Network 4.60 software. Software Splitstree 4.10 was used for creating the Neighbor-Joining (NJ) tree based on RST pair-wise distances between the Croatian an...
American Journal of …, 1995
(1989) (Zysk KG [ed/ann]) The origin and develop-ment of classical Hinduism. Beacon, Boston Kosam... more (1989) (Zysk KG [ed/ann]) The origin and develop-ment of classical Hinduism. Beacon, Boston Kosambi DD (1950) On the origin of Brahmin gotras. J Asiatic Soc (Bombay) 26:21-80 (1956) An introduction to the study of Indian history. Popular Book Depot, Bombay ...
European Journal of Human Genetics, Aug 13, 2002
The genetic composition of the Norwegian population was investigated by analysing polymorphisms a... more The genetic composition of the Norwegian population was investigated by analysing polymorphisms associated with both the mitochondrial DNA (mtDNA) and Y chromosome loci in a sample of 74 Norwegian males. The combination of their uniparental mode of inheritance and the absence of recombination make these haplotypic stretches of DNA the tools of choice in evaluating the different components of a population's gene pool. The sequencing of the Dloop and two diagnostic RFLPs (AluI 7025 and HinfI at 12 308) allowed us to classify the mtDNA molecules in 10 previously described groups. As for the Y chromosome the combination of binary markers and microsatellites allowed us to compare our results to those obtained elsewhere in Europe. Both mtDNA and Y chromosome polymorphisms showed a noticeable genetic affinity between Norwegians and central Europeans, especially Germans. When the phylogeographic analysis of the Y chromosome haplotypes was attempted some interesting clues on the peopling of Norway emerged. Although Y chromosome binary and microsatellite data indicate that 80% of the haplotypes are closely related to Central and western Europeans, the remainder share a unique binary marker (M17) common in eastern Europeans with informative microsatellite haplotypes suggesting a different demographic history. Other minor genetic influences on the Norwegian population from Uralic speakers and Mediterranean populations were also highlighted.
Genome Research, Nov 1, 2002
Each independently evolving segment of the genomes of a sexually reproducing organism has a separ... more Each independently evolving segment of the genomes of a sexually reproducing organism has a separate history reflecting part of the evolutionary history of that organism. Uniparentally or clonally inherited DNA segments such as the mitochondrial and chloroplast genomes and the nonrecombining portion of the Y chromosome have provided, to date, most of the known data regarding compound haplotypic variation within and among populations. These comparatively small segments include numerous polymorphic sites and undergo little or no recombination. Recombining autosomes, however, comprise the major repository of genetic variation. Technical challenges and recombination have limited large-scale application of autosomal haplotypes. We have overcome this barrier through development of a general approach to the assessment of short autosomal DNA segments. Each such segment includes one or more single nucleotide polymorphisms (SNPs) and exactly one short tandem repeat (STR) locus. With dramatically different mutation rates, these two types of genetic markers provide complementary evolutionary information. We call the combination of a SNP and a STR polymorphism a SNPSTR, and have developed a simple, rapid method for empirically determining gametic phase for double and triple heterozygotes. Here, we illustrate the approach with two SNPSTR systems. Although even one system provides insight into population history, the power of the approach lies in combining results from multiple SNPSTR systems.
Genomic Diversity, 1999
ABSTRACT In an attempt to investigate the origin of the present-day Pakistani populations, we hav... more ABSTRACT In an attempt to investigate the origin of the present-day Pakistani populations, we have analysed a microsatellite locus (DYS19) and the Alu insertion polymorphism (YAP) in a sample of nine ethnic groups from the Northern (viz., Punjabi, Burusho, Pathan, Kalash, and Hazara) and the Southern (Brahui, Baloch, Makrani, and Sindhi) parts of the country. A north-south divide among the populations is evident. This separation is not only due to their geographic location but these two regional groups might have originated as a result of two ...
Nature, 2015
A global reference for human genetic variation The 1000 Genomes Project Consortium* The 1000 Geno... more A global reference for human genetic variation The 1000 Genomes Project Consortium* The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes .99% of SNP variants with a frequency of .1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.
American journal of human genetics, 1995
The demographic history of India was examined by comparing mtDNA sequences obtained from members ... more The demographic history of India was examined by comparing mtDNA sequences obtained from members of three culturally divergent Indian subpopulations (endogamous caste groups). While an inferred tree revealed some clustering according to caste affiliation, there was no clear separation into three genetically distinct groups along caste lines. Comparison of pairwise nucleotide difference distributions, however, did indicate a difference in growth patterns between two of the castes. The Brahmin population appears to have undergone either a rapid expansion or steady growth. The low-ranking Mukri caste, however, may have either maintained a roughly constant population size or undergone multiple bottlenecks during that period. Comparison of the Indian sequences to those obtained from other populations, using a tree, revealed that the Indian sequences, along with all other non-African samples, form a starlike cluster. This cluster may represent a major expansion, possibly originating in so...
International Congress Series, 2003
DNA typing of male-specific polymorphisms is a well-established procedure of molecular analysis. ... more DNA typing of male-specific polymorphisms is a well-established procedure of molecular analysis. A haplotype of eight different human male Y-specific short tandem repeats (STRs) has been intensively used for forensic casework. This haplotype has also been effectively used to address specific problems of population genetics. A collection of 50 male genomes from our laboratory previously genotyped for 8-Y-STR has been reinvestigated with a battery of eight single nucleotide polymorphisms (SNPs) mapping to the Y-chromosome. The addition of these biallelic markers provided additional identification power. Population investigation revealed genetic structure in Italy, with notably implications in Forensic Genetics.
genetic structure of the Iberian peninsula revealed by Y-chromosome analysis: implications for po... more genetic structure of the Iberian peninsula revealed by Y-chromosome analysis: implications for population demography
. PCR primers and conditions for amplifying CDY1a381 (sY1313) and CDY1284 (sY1314) have been depo... more . PCR primers and conditions for amplifying CDY1a381 (sY1313) and CDY1284 (sY1314) have been deposited in GenBank (accession numbers G73596 and G73597, respectively). When typing CDY1a381 by sequencing, ‘primer A’ in GenBank G73596 served as the sequencing primer. CDY1284 was typed by sequencing using ‘primer B’ in GenBank G73597. For the samples that showed evidence of gene conversion (Fig. 2 and Supplementary Figs 1‐3), we excluded the possibility of deletion of one copy of the variant site as discussed in Supplementary Note 1. Steady-state balance between mutations and gene-conversion To show that the combined action of mutation and gene conversion results in a steadystate level of arm-to-arm divergence, we use the following recursion: dna1aO1 2 cgUdna 2mg where d n is the sequence divergence between repeat copies at generation n, m g is the mutation rate per nucleotide per generation, and c g is the gene conversion rate per duplicated nucleotide per generation. We presume that d 0a 0, corresponding to no differences between sequence copies immediately after the initial duplication event. However, as 1 2 c g , 1, limn!1 d na 2m g/c g, for any value of d 0 small enough to support c g. Because m g and d are very small, mutations almost never occur at sites that already differ between the two palindrome arms, and this possibility can be ignored. As shown in Supplementary Note 2, our analysis is a special case of Ohta’s analysis 25
European Journal of Human Genetics, 2020
We set out to identify the origins of the Árpád Dynasty based on genome sequencing of DNA derived... more 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 s...
Molecular Biology and Evolution, 2006
The human settlement of the Pacific Islands represents one of the most recent major migration eve... more The human settlement of the Pacific Islands represents one of the most recent major migration events of mankind. Polynesians originated in Asia according to linguistic evidence or in Melanesia according to archaeological evidence. To shed light on the genetic origins of Polynesians, we investigated over 400 Polynesians from 8 island groups, in comparison with over 900 individuals from potential parental populations of Melanesia, Southeast and East Asia, and Australia, by means of Y chromosome (NRY) and mitochondrial DNA (mtDNA) markers. Overall, we classified 94.1% of Polynesian Y chromosomes and 99.8% of Polynesian mtDNAs as of either Melanesian (NRY-DNA: 65.8%, mtDNA: 6%) or Asian (NRY-DNA: 28.3%, mtDNA: 93.8%) origin, suggesting a dual genetic origin of Polynesians in agreement with the ''Slow Boat'' hypothesis. Our data suggest a pronounced admixture bias in Polynesians toward more Melanesian men than women, perhaps as a result of matrilocal residence in the ancestral Polynesian society. Although dating methods are consistent with somewhat similar entries of NRY/mtDNA haplogroups into Polynesia, haplotype sharing suggests an earlier appearance of Melanesian haplogroups than those from Asia. Surprisingly, we identified gradients in the frequency distribution of some NRY/mtDNA haplogroups across Polynesia and a gradual west-to-east decrease of overall NRY/mtDNA diversity, not only providing evidence for a west-to-east direction of Polynesian settlements but also suggesting that Pacific voyaging was regular rather than haphazard. We also demonstrate that Fiji played a pivotal role in the history of Polynesia: humans probably first migrated to Fiji, and subsequent settlement of Polynesia probably came from Fiji.
Background: The process of Greek colonization of the central and western Mediterranean during the... more 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 6 th 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.
Analysis of 89 biallelic polymorphisms in 523 Turkish Y chromosomes revealed 52 distinct haplotyp... more Analysis of 89 biallelic polymorphisms in 523 Turkish Y chromosomes revealed 52 distinct haplotypes with considerable haplogroup substructure, as exemplified by their respective levels of accumulated diversity at ten short tandem repeat (STR) loci. The major components
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Papers by Peter Underhill