117 results on '"Underhill PA"'
Search Results
2. The complex Y-chromosome landscape of East and south-east Europe
- Author
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Battaglia, V, Fornarino, S, Achilli, Alessandro, Marjanovic, AL ZAHERY, N, Underhill, Pa, SANTACHIARA BENERECETTI AS, and Semino, O.
- Published
- 2006
3. Origin and diffusion of the Y-chromosome haplogroups E, I and J in the European and the Mediterranean area populations
- Author
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Semino, O, Magri, C, Benuzzi, G, Battaglia, V, Fornarino, S, Montagna, S, AL ZAHERY, N, Achilli, Alessandro, Primorac, D, Torroni, A, Underhill, Pa, and SANTACHIARA BENERECETTI AS
- Published
- 2004
4. Peopling of three Mediterranean islands (Corsica, Sardinia, and Sicily) inferred by Y-chromosome biallelic variability
- Author
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Francalacci, P, Morelli, L, Underhill, Pa, Lillie, As, Passarino, G, Useli, A, Madeddu, R, Paoli, G, Tofanelli, S, Calò, Cm, Ghiani, Me, Varesi, L, Memmi, M, Vona, G, Lin, Aa, Oefner, P, and Cavalli-Sforza, Ll
- Subjects
Male ,Y-chromosome ,population genetics ,Mediterranean populations ,Chromosomes, Human, Y ,Mediterranean Islands ,Genetics, Population ,Haplotypes ,Italy ,Humans ,France ,Sicily ,Phylogeny - Abstract
An informative set of biallelic polymorphisms was used to study the structure of Y-chromosome variability in a sample from the Mediterranean islands of Corsica and Sicily, and compared with data on Sardinia to gain insights into the ethnogenesis of these island populations. The results were interpreted in a broader Mediterranean context by including in the analysis neighboring populations previously studied with the same methodology. All samples studied were enclosed in the comparable spectrum of European Y-chromosome variability. Pronounced differences were observed between the islands as well as in the percentages of haplotypes previously shown to have distinctive patterns of continental phylogeography. Approximately 60% of the Sicilian haplotypes are also prevalent in Southern Italy and Greece. Conversely, the Corsican sample had elevated levels of alternative haplotypes common in Northern Italy. Sardinia showed a haplotype ratio similar to that observed in Corsica, but with a remarkable difference in the presence of a lineage defined by marker M26, which approaches 35% in Sardinia but seems absent in Corsica. Although geographically adjacent, the data suggest different colonization histories and a minimal amount of recent gene flow between them. Our results identify possible ancestral continental sources of the various island populations and underscore the influence of founder effect and genetic drift. The Y-chromosome data are consistent with comparable mtDNA data at the RFLP haplogroup level of resolution, as well as linguistic and historic knowledge.
- Published
- 2003
5. Defining Microsatellite Alleles by Genotyping Global Indigenous Human Populations and Non-Human Primates
- Author
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Jin, L, Underhill, PA, Buoncristiani, M, and Robertson, JM
- Abstract
Polymorphisms at variable number of tandem repeat (VNTR) loci have been used in forensic science for almost decade. Microsatellite loci, especially tri-, tetra-, and pentanucleotide repeat loci, have shown great potential in personal identification and paternity testing. In this report, we describe results of genotyping three tetranucleotide repeat loci (D5S818, D7S820, D13S317) in 16 worldwide indigenous human populations and one chimpanzee population which were being developed for forensic applications. We demonstrate the utility of typing globally diverse populations in defining microsatellite alleles: Specifically (i) investigating the measurement errors of each allele using semi-automatic genotyping instrumentation and software, (ii) assessing the range of alleles, (iii) understanding the extent of allele frequency differences across worldwide populations, and (iv) identifying possible anomalous alleles with complex structures.
- Published
- 1997
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6. Modeling Nutrient Regeneration in the Ocean with an Aquarium System
- Author
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Sharp, JH, primary, Frake, AC, additional, Hillier, GB, additional, and Underhill, PA, additional
- Published
- 1982
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7. Differential Greek and northern African migrations to Sicily are supported by genetic evidence from the Y chromosome
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Mauro Gasparini, N. Cerutti, Peter A. Underhill, Carlo Torre, Francesco Calì, Giuseppe Matullo, S. Inturri, Alberto Piazza, Sarah Gino, Cornelia Di Gaetano, Simonetta Guarrera, F. Crobu, Valentino Romano, Alfredo Salerno, Roy J. King, Carlo Robino, Di Gaetano, C, Cerutti, N, Crobu, F, Robino, C, Inturri, S, Gino, S, Guarrera, S, Underhill, PA, King, RJ, Romano, V, Cali, F, Gasparini, M, Matullo, G, Salerno, A, Torre, C, and Piazza, A
- Subjects
Most recent common ancestor ,Gene Flow ,haplotype ,Population genetics ,Ancient Greek ,Haplogroup ,Article ,Modal haplotype ,Genetic Heterogeneity ,Africa, Northern ,Settore BIO/13 - Biologia Applicata ,Y chromosome, siciy greek and phoenician legacy ,Genetic variation ,Genetics ,Humans ,Sicily ,genetics of Sicily (Italy) ,Genetics (clinical) ,Phylogeny ,Settore MED/04 - Patologia Generale ,Analysis of Variance ,Principal Component Analysis ,Chromosomes, Human, Y ,Greece ,Y chromosome ,Genetic Variation ,population genetics ,short tandem repeats ,haplogroups ,Gene Pool ,Emigration and Immigration ,language.human_language ,humanities ,Geography ,Haplotypes ,Evolutionary biology ,language ,Gene pool ,Sicilian ,Microsatellite Repeats - Abstract
The presence or absence of genetic heterogeneity in Sicily has long been debated. Through the analysis of the variation of Y-chromosome lineages, using the combination of haplogroups and short tandem repeats from several areas of Sicily, we show that traces of genetic flows occurred in the island, due to ancient Greek colonization and to northern African contributions, are still visible on the basis of the distribution of some lineages. The genetic contribution of Greek chromosomes to the Sicilian gene pool is estimated to be about 37% whereas the contribution of North African populations is estimated to be around 6%. In particular, the presence of a modal haplotype coming from the southern Balkan Peninsula and of its one-step derivates associated to E3b1a2-V13, supports a common genetic heritage between Sicilians and Greeks. The estimate of Time to Most Recent Common Ancestor is about 2380 years before present, which broadly agrees with the archaeological traces of the Greek classic era. The Eastern and Western part of Sicily appear to be significantly different by the χ2-analysis, although the extent of such differentiation is not very high according to an analysis of molecular variance. The presence of a high number of different haplogroups in the island makes its gene diversity to reach about 0.9. The general heterogeneous composition of haplogroups in our Sicilian data is similar to the patterns observed in other major islands of the Mediterranean, reflecting the complex histories of settlements in Sicily.
- Published
- 2009
8. Correction: Determination of the phylogenetic origins of the Árpád Dynasty based on Y chromosome sequencing of Béla the Third.
- Author
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Nagy PL, Olasz J, Neparáczki E, Rouse N, Kapuria K, Cano S, Chen H, Di Cristofaro J, Runfeldt G, Ekomasova N, Maróti Z, Jeney J, Litvinov S, Dzhaubermezov M, Gabidullina L, Szentirmay Z, Szabados G, Zgonjanin D, Chiaroni J, Behar DM, Khusnutdinova E, Underhill PA, and Kásler M
- Published
- 2021
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9. Determination of the phylogenetic origins of the Árpád Dynasty based on Y chromosome sequencing of Béla the Third.
- Author
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Nagy PL, Olasz J, Neparáczki E, Rouse N, Kapuria K, Cano S, Chen H, Di Cristofaro J, Runfeldt G, Ekomasova N, Maróti Z, Jeney J, Litvinov S, Dzhaubermezov M, Gabidullina L, Szentirmay Z, Szabados G, Zgonjanin D, Chiaroni J, Behar DM, Khusnutdinova E, Underhill PA, and Kásler M
- Subjects
- Female, Human Migration, Humans, Hungary, Male, Sequence Analysis, DNA methods, Chromosomes, Human, Y genetics, Famous Persons, Pedigree, Phylogeny, Polymorphism, Single Nucleotide
- Abstract
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.
- Published
- 2021
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10. The radial expansion of the Diego blood group system polymorphisms in Asia: mark of co-migration with the Mongol conquests.
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Petit F, Minnai F, Chiaroni J, Underhill PA, Bailly P, Mazières S, and Costedoat C
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- Asia, Chromosomes, Human, Y genetics, Female, Haplotypes, Humans, Male, Anion Exchange Protein 1, Erythrocyte genetics, Asian People genetics, Human Migration, Polymorphism, Genetic
- Abstract
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
a 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.- Published
- 2019
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11. Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe.
- Author
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Fregel R, Méndez FL, Bokbot Y, Martín-Socas D, Camalich-Massieu MD, Santana J, Morales J, Ávila-Arcos MC, Underhill PA, Shapiro B, Wojcik G, Rasmussen M, Soares AER, Kapp J, Sockell A, Rodríguez-Santos FJ, Mikdad A, Trujillo-Mederos A, and Bustamante CD
- Subjects
- Africa, Northern, Agriculture history, Chromosomes, Human, Y genetics, DNA, Mitochondrial genetics, Ethnicity history, Europe, Gene Flow, Gene Library, Genetics, Population, History, Ancient, Humans, Middle East, Morocco, Sequence Analysis, DNA, Spain ethnology, Ethnicity genetics, Genome, Human, Human Migration history
- Abstract
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., Competing Interests: The authors declare no conflict of interest.
- Published
- 2018
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12. Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families.
- Author
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Ilumäe AM, Reidla M, Chukhryaeva M, Järve M, Post H, Karmin M, Saag L, Agdzhoyan A, Kushniarevich A, Litvinov S, Ekomasova N, Tambets K, Metspalu E, Khusainova R, Yunusbayev B, Khusnutdinova EK, Osipova LP, Fedorova S, Utevska O, Koshel S, Balanovska E, Behar DM, Balanovsky O, Kivisild T, Underhill PA, Villems R, and Rootsi S
- Subjects
- Asia, Europe, Humans, Phylogeography, Time Factors, Chromosomes, Human, Y genetics, Haplotypes genetics, Language
- Abstract
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., (Copyright © 2016 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)
- Published
- 2016
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13. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.
- Author
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Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, Gymrek M, Malhotra A, Louzada S, Desalle R, Ritchie GR, Cerveira E, Fitzgerald TW, Garrison E, Marcketta A, Mittelman D, Romanovitch M, Zhang C, Zheng-Bradley X, Abecasis GR, McCarroll SA, Flicek P, Underhill PA, Coin L, Zerbino DR, Yang F, Lee C, Clarke L, Auton A, Erlich Y, Handsaker RE, Bustamante CD, and Tyler-Smith C
- Subjects
- Haplotypes, Humans, Male, Mutation, Phylogeny, Polymorphism, Single Nucleotide, Chromosomes, Human, Y, Demography
- Abstract
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.
- Published
- 2016
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14. Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements.
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Voskarides K, Mazières S, Hadjipanagi D, Di Cristofaro J, Ignatiou A, Stefanou C, King RJ, Underhill PA, Chiaroni J, and Deltas C
- Abstract
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.
- Published
- 2016
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15. A recent bottleneck of Y chromosome diversity coincides with a global change in culture.
- Author
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Karmin M, Saag L, Vicente M, Wilson Sayres MA, Järve M, Talas UG, Rootsi S, Ilumäe AM, Mägi R, Mitt M, Pagani L, Puurand T, Faltyskova Z, Clemente F, Cardona A, Metspalu E, Sahakyan H, Yunusbayev B, Hudjashov G, DeGiorgio M, Loogväli EL, Eichstaedt C, Eelmets M, Chaubey G, Tambets K, Litvinov S, Mormina M, Xue Y, Ayub Q, Zoraqi G, Korneliussen TS, Akhatova F, Lachance J, Tishkoff S, Momynaliev K, Ricaut FX, Kusuma P, Razafindrazaka H, Pierron D, Cox MP, Sultana GN, Willerslev R, Muller C, Westaway M, Lambert D, Skaro V, Kovačevic L, Turdikulova S, Dalimova D, Khusainova R, Trofimova N, Akhmetova V, Khidiyatova I, Lichman DV, Isakova J, Pocheshkhova E, Sabitov Z, Barashkov NA, Nymadawa P, Mihailov E, Seng JW, Evseeva I, Migliano AB, Abdullah S, Andriadze G, Primorac D, Atramentova L, Utevska O, Yepiskoposyan L, Marjanovic D, Kushniarevich A, Behar DM, Gilissen C, Vissers L, Veltman JA, Balanovska E, Derenko M, Malyarchuk B, Metspalu A, Fedorova S, Eriksson A, Manica A, Mendez FL, Karafet TM, Veeramah KR, Bradman N, Hammer MF, Osipova LP, Balanovsky O, Khusnutdinova EK, Johnsen K, Remm M, Thomas MG, Tyler-Smith C, Underhill PA, Willerslev E, Nielsen R, Metspalu M, Villems R, and Kivisild T
- Subjects
- Base Sequence, DNA, Mitochondrial genetics, Genetic Variation genetics, Genetics, Population, Haplotypes genetics, Humans, Male, Models, Genetic, Phylogeny, Sequence Analysis, DNA, Chromosomes, Human, Y genetics, Evolution, Molecular, Racial Groups genetics
- Abstract
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., (© 2015 Karmin et al.; Published by Cold Spring Harbor Laboratory Press.)
- Published
- 2015
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16. The phylogenetic and geographic structure of Y-chromosome haplogroup R1a.
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Underhill PA, Poznik GD, Rootsi S, Järve M, Lin AA, Wang J, Passarelli B, Kanbar J, Myres NM, King RJ, Di Cristofaro J, Sahakyan H, Behar DM, Kushniarevich A, Sarac J, Saric T, Rudan P, Pathak AK, Chaubey G, Grugni V, Semino O, Yepiskoposyan L, Bahmanimehr A, Farjadian S, Balanovsky O, Khusnutdinova EK, Herrera RJ, Chiaroni J, Bustamante CD, Quake SR, Kivisild T, and Villems R
- Subjects
- Asia, Ethnicity genetics, Europe, Evolution, Molecular, Gene Frequency, Genetic Linkage, Humans, Male, Microsatellite Repeats, Polymorphism, Single Nucleotide, Spatial Analysis, Alleles, Chromosomes, Human, Y, Haplotypes, Phylogeny, Phylogeography
- Abstract
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.
- Published
- 2015
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17. 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.
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Sikora M, Carpenter ML, Moreno-Estrada A, Henn BM, Underhill PA, Sánchez-Quinto F, Zara I, Pitzalis M, Sidore C, Busonero F, Maschio A, Angius A, Jones C, Mendoza-Revilla J, Nekhrizov G, Dimitrova D, Theodossiev N, Harkins TT, Keller A, Maixner F, Zink A, Abecasis G, Sanna S, Cucca F, and Bustamante CD
- Subjects
- Europe, Female, Humans, Polymorphism, Single Nucleotide, Fossils, Genetics, Population, Genome, Human
- Abstract
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.
- Published
- 2014
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18. Genetics and the history of the Samaritans: Y-chromosomal microsatellites and genetic affinity between Samaritans and Cohanim.
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Oefner PJ, Hölzi G, Shen P, Shpirer I, Gefel D, Lavi T, Woolf E, Cohen J, Cinnioglu C, Underhill PA, Rosenberg NA, Hochrein J, Granka JM, Hillel J, and Feldman MW
- Subjects
- Genetic Variation genetics, Genetics, Population, Genotype, History, Ancient, Humans, Israel ethnology, Jews history, Male, Polymerase Chain Reaction, Polymorphism, Single Nucleotide genetics, Sequence Analysis, DNA, Spectrometry, Mass, Electrospray Ionization, Chromosomes, Human, Y genetics, Jews genetics, Microsatellite Repeats genetics
- Abstract
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., (Copyright © 2014 Wayne State University Press, Detroit, Michigan 48201-1309.)
- Published
- 2013
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19. Afghan Hindu Kush: where Eurasian sub-continent gene flows converge.
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Di Cristofaro J, Pennarun E, Mazières S, Myres NM, Lin AA, Temori SA, Metspalu M, Metspalu E, Witzel M, King RJ, Underhill PA, Villems R, and Chiaroni J
- Subjects
- Afghanistan ethnology, Analysis of Variance, Asia ethnology, Asian People genetics, DNA, Mitochondrial chemistry, DNA, Mitochondrial classification, Europe ethnology, Genetic Variation, Genetics, Population methods, Geography, Haplotypes, Humans, Phylogeny, Phylogeography methods, Principal Component Analysis, Sequence Analysis, DNA, White People genetics, Chromosomes, Human, Y genetics, DNA, Mitochondrial genetics, Ethnicity genetics, Gene Flow
- Abstract
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.
- Published
- 2013
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20. Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females.
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Poznik GD, Henn BM, Yee MC, Sliwerska E, Euskirchen GM, Lin AA, Snyder M, Quintana-Murci L, Kidd JM, Underhill PA, and Bustamante CD
- Subjects
- Black People genetics, Evolution, Molecular, Female, Genome, Mitochondrial genetics, Haploidy, Humans, Male, Mutation, Phylogeny, Sequence Analysis, DNA, Time Factors, Chromosomes, Human, Y classification, Chromosomes, Human, Y genetics, Genetic Variation
- Abstract
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.
- Published
- 2013
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21. Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites.
- Author
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Rootsi S, Behar DM, Järve M, Lin AA, Myres NM, Passarelli B, Poznik GD, Tzur S, Sahakyan H, Pathak AK, Rosset S, Metspalu M, Grugni V, Semino O, Metspalu E, Bustamante CD, Skorecki K, Villems R, Kivisild T, and Underhill PA
- Subjects
- Europe, Eastern, Genetic Variation, Humans, Male, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Chromosomes, Human, Y, Gene Frequency, Haplotypes, Jews genetics, Phylogeny
- Abstract
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.
- Published
- 2013
- Full Text
- View/download PDF
22. Distinguishing the co-ancestries of haplogroup G Y-chromosomes in the populations of Europe and the Caucasus.
- Author
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Rootsi S, Myres NM, Lin AA, Järve M, King RJ, Kutuev I, Cabrera VM, Khusnutdinova EK, Varendi K, Sahakyan H, Behar DM, Khusainova R, Balanovsky O, Balanovska E, Rudan P, Yepiskoposyan L, Bahmanimehr A, Farjadian S, Kushniarevich A, Herrera RJ, Grugni V, Battaglia V, Nici C, Crobu F, Karachanak S, Hooshiar Kashani B, Houshmand M, Sanati MH, Toncheva D, Lisa A, Semino O, Chiaroni J, Di Cristofaro J, Villems R, Kivisild T, and Underhill PA
- Subjects
- Armenia, Chromosomes, Human, 21-22 and Y classification, Chromosomes, Human, Y classification, Europe, Evolution, Molecular, Gene Frequency, Humans, Middle East, Polymorphism, Single Nucleotide, Chromosomes, Human, 21-22 and Y genetics, Chromosomes, Human, Y genetics, Phylogeny, White People genetics
- Abstract
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.
- Published
- 2012
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- View/download PDF
23. Afghanistan from a Y-chromosome perspective.
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Lacau H, Gayden T, Regueiro M, Chennakrishnaiah S, Bukhari A, Underhill PA, Garcia-Bertrand RL, and Herrera RJ
- Subjects
- Afghanistan ethnology, Ethnicity genetics, Gene Frequency, Haplotypes, Humans, Male, Microsatellite Repeats, Phylogeny, Polymorphism, Single Nucleotide, Chromosomes, Human, Y genetics
- Abstract
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.
- Published
- 2012
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24. Y-chromosome diversity in Native Mexicans reveals continental transition of genetic structure in the Americas.
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Sandoval K, Moreno-Estrada A, Mendizabal I, Underhill PA, Lopez-Valenzuela M, Peñaloza-Espinosa R, Lopez-Lopez M, Buentello-Malo L, Avelino H, Calafell F, and Comas D
- Subjects
- Americas, Genetic Variation, Haplotypes genetics, Humans, Indians, North American statistics & numerical data, Male, Mexico, Microsatellite Repeats, Phylogeny, Chromosomes, Human, Y, Indians, North American genetics
- Abstract
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., (Copyright © 2012 Wiley Periodicals, Inc.)
- Published
- 2012
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25. Neolithic patrilineal signals indicate that the Armenian plateau was repopulated by agriculturalists.
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Herrera KJ, Lowery RK, Hadden L, Calderon S, Chiou C, Yepiskoposyan L, Regueiro M, Underhill PA, and Herrera RJ
- Subjects
- Armenia ethnology, Gene Flow, Gene Frequency, Haplotypes, Humans, Microsatellite Repeats, Phylogeny, Phylogeography, Polymorphism, Single Nucleotide, Chromosomes, Human, Y, Genetic Variation, Genetics, Population
- Abstract
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.
- Published
- 2012
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26. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing.
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Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, Maixner F, Leidinger P, Backes C, Khairat R, Forster M, Stade B, Franke A, Mayer J, Spangler J, McLaughlin S, Shah M, Lee C, Harkins TT, Sartori A, Moreno-Estrada A, Henn B, Sikora M, Semino O, Chiaroni J, Rootsi S, Myres NM, Cabrera VM, Underhill PA, Bustamante CD, Vigl EE, Samadelli M, Cipollini G, Haas J, Katus H, O'Connor BD, Carlson MR, Meder B, Blin N, Meese E, Pusch CM, and Zink A
- Subjects
- Base Sequence, Borrelia burgdorferi genetics, Chromosome Mapping, DNA, Mitochondrial genetics, Genetic Predisposition to Disease, History, Ancient, Humans, Lyme Disease history, Mitochondria genetics, Paleontology, Phenotype, Sequence Analysis, DNA, Vascular Calcification, Genome, Human, Genome, Mitochondrial, Mummies microbiology
- Abstract
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.
- Published
- 2012
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- View/download PDF
27. Increased Y-chromosome resolution of haplogroup O suggests genetic ties between the Ami aborigines of Taiwan and the Polynesian Islands of Samoa and Tonga.
- Author
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Mirabal S, Herrera KJ, Gayden T, Regueiro M, Underhill PA, Garcia-Bertrand RL, and Herrera RJ
- Subjects
- Humans, Microsatellite Repeats, Phylogeny, Samoa, Taiwan, Tonga, Chromosomes, Human, Y, Haplotypes, Phylogeography
- Abstract
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., (Copyright © 2011 Elsevier B.V. All rights reserved.)
- Published
- 2012
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28. The phylogeography of Y-chromosome haplogroup h1a1a-m82 reveals the likely Indian origin of the European Romani populations.
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Rai N, Chaubey G, Tamang R, Pathak AK, Singh VK, Karmin M, Singh M, Rani DS, Anugula S, Yadav BK, Singh A, Srinivasagan R, Yadav A, Kashyap M, Narvariya S, Reddy AG, van Driem G, Underhill PA, Villems R, Kivisild T, Singh L, and Thangaraj K
- Subjects
- Asia, DNA, Mitochondrial, Europe, Humans, Phylogeny, Chromosomes, Human, Y, Ethnicity genetics, Haplotypes, Microsatellite Repeats, Phylogeography, White People genetics
- Abstract
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.
- Published
- 2012
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- View/download PDF
29. The Caucasus as an asymmetric semipermeable barrier to ancient human migrations.
- Author
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Yunusbayev B, Metspalu M, Järve M, Kutuev I, Rootsi S, Metspalu E, Behar DM, Varendi K, Sahakyan H, Khusainova R, Yepiskoposyan L, Khusnutdinova EK, Underhill PA, Kivisild T, and Villems R
- Subjects
- Algorithms, Anthropology, Physical, Asian People genetics, Chromosomes, Human, Y, Cluster Analysis, DNA, DNA, Mitochondrial genetics, Genetics, Population, History, Ancient, Humans, Linguistics, Transcaucasia, White People genetics, Emigration and Immigration history, Gene Flow
- Abstract
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.
- Published
- 2012
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- View/download PDF
30. Croatian genetic heritage: Y-chromosome story.
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Primorac D, Marjanović D, Rudan P, Villems R, and Underhill PA
- Subjects
- Agriculture, Croatia, DNA, Mitochondrial genetics, Ethnicity, Europe, Humans, Male, Molecular Biology, Mutation, Phylogeography, Chromosomes, Human, Y genetics, Genetics, Population statistics & numerical data, Haplotypes genetics
- Abstract
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.
- Published
- 2011
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31. Hunter-gatherer genomic diversity suggests a southern African origin for modern humans.
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Henn BM, Gignoux CR, Jobin M, Granka JM, Macpherson JM, Kidd JM, Rodríguez-Botigué L, Ramachandran S, Hon L, Brisbin A, Lin AA, Underhill PA, Comas D, Kidd KK, Norman PJ, Parham P, Bustamante CD, Mountain JL, and Feldman MW
- Subjects
- Africa, Culture, Ethnicity genetics, Genome, Human, Humans, Linkage Disequilibrium, Biological Evolution, Black People genetics, Genetic Variation, Genetics, Population, Polymorphism, Single Nucleotide
- Abstract
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.
- Published
- 2011
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- View/download PDF
32. The coming of the Greeks to Provence and Corsica: Y-chromosome models of archaic Greek colonization of the western Mediterranean.
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King RJ, Di Cristofaro J, Kouvatsi A, Triantaphyllidis C, Scheidel W, Myres NM, Lin AA, Eissautier A, Mitchell M, Binder D, Semino O, Novelletto A, Underhill PA, and Chiaroni J
- Subjects
- France, Greece, Haplotypes, Humans, Male, Mediterranean Region, Phylogeny, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Chromosomes, Human, Y genetics, Genetics, Population
- Abstract
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.
- Published
- 2011
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33. A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe.
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Myres NM, Rootsi S, Lin AA, Järve M, King RJ, Kutuev I, Cabrera VM, Khusnutdinova EK, Pshenichnov A, Yunusbayev B, Balanovsky O, Balanovska E, Rudan P, Baldovic M, Herrera RJ, Chiaroni J, Di Cristofaro J, Villems R, Kivisild T, and Underhill PA
- Subjects
- Emigration and Immigration, Europe, Gene Flow, Haplotypes, Humans, Phylogeny, Asian People genetics, Biological Evolution, Chromosomes, Human, Y genetics, Founder Effect, Genetics, Population, White People genetics
- Abstract
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.
- Published
- 2011
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- View/download PDF
34. Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a.
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Underhill PA, Myres NM, Rootsi S, Metspalu M, Zhivotovsky LA, King RJ, Lin AA, Chow CE, Semino O, Battaglia V, Kutuev I, Järve M, Chaubey G, Ayub Q, Mohyuddin A, Mehdi SQ, Sengupta S, Rogaev EI, Khusnutdinova EK, Pshenichnov A, Balanovsky O, Balanovska E, Jeran N, Augustin DH, Baldovic M, Herrera RJ, Thangaraj K, Singh V, Singh L, Majumder P, Rudan P, Primorac D, Villems R, and Kivisild T
- Subjects
- Ethnicity, Gene Flow, Humans, Male, Polymorphism, Genetic, Asian People genetics, Biological Evolution, Chromosomes, Human, Y genetics, Genetics, Population, Haplotypes genetics, White People genetics
- Abstract
Human Y-chromosome haplogroup structure is largely circumscribed by continental boundaries. One notable exception to this general pattern is the young haplogroup R1a that exhibits post-Glacial coalescent times and relates the paternal ancestry of more than 10% of men in a wide geographic area extending from South Asia to Central East Europe and South Siberia. Its origin and dispersal patterns are poorly understood as no marker has yet been described that would distinguish European R1a chromosomes from Asian. Here we present frequency and haplotype diversity estimates for more than 2000 R1a chromosomes assessed for several newly discovered SNP markers that introduce the onset of informative R1a subdivisions by geography. Marker M434 has a low frequency and a late origin in West Asia bearing witness to recent gene flow over the Arabian Sea. Conversely, marker M458 has a significant frequency in Europe, exceeding 30% in its core area in Eastern Europe and comprising up to 70% of all M17 chromosomes present there. The diversity and frequency profiles of M458 suggest its origin during the early Holocene and a subsequent expansion likely related to a number of prehistoric cultural developments in the region. Its primary frequency and diversity distribution correlates well with some of the major Central and East European river basins where settled farming was established before its spread further eastward. Importantly, the virtual absence of M458 chromosomes outside Europe speaks against substantial patrilineal gene flow from East Europe to Asia, including to India, at least since the mid-Holocene.
- Published
- 2010
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- View/download PDF
35. The emergence of Y-chromosome haplogroup J1e among Arabic-speaking populations.
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Chiaroni J, King RJ, Myres NM, Henn BM, Ducourneau A, Mitchell MJ, Boetsch G, Sheikha I, Lin AA, Nik-Ahd M, Ahmad J, Lattanzi F, Herrera RJ, Ibrahim ME, Brody A, Semino O, Kivisild T, and Underhill PA
- Subjects
- Genetic Loci genetics, Geography, Humans, Microsatellite Repeats genetics, Arabs genetics, Chromosomes, Human, Y genetics, Ethnicity genetics, Genetics, Population, Haplotypes genetics, Language
- Abstract
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.
- Published
- 2010
- Full Text
- View/download PDF
36. Footprints of X-to-Y gene conversion in recent human evolution.
- Author
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Trombetta B, Cruciani F, Underhill PA, Sellitto D, and Scozzari R
- Subjects
- Cadherins genetics, Chromosomes, Human, X chemistry, Chromosomes, Human, Y chemistry, Humans, Nuclear Proteins genetics, Polymorphism, Single Nucleotide, Protocadherins, Sequence Homology, Nucleic Acid, Transducin genetics, Chromosomes, Human, X genetics, Chromosomes, Human, Y genetics, DNA Mutational Analysis methods, Evolution, Molecular, Gene Conversion
- Abstract
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.
- Published
- 2010
- Full Text
- View/download PDF
37. Y chromosome diversity, human expansion, drift, and cultural evolution.
- Author
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Chiaroni J, Underhill PA, and Cavalli-Sforza LL
- Subjects
- Founder Effect, Haplotypes genetics, Humans, Phylogeny, Selection, Genetic, Chromosomes, Human, Y genetics, Cultural Evolution, Genetic Drift, Genetic Variation, Genetics, Population, Population Dynamics
- 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.
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- 2009
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38. Y-chromosome distribution within the geo-linguistic landscape of northwestern Russia.
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Mirabal S, Regueiro M, Cadenas AM, Cavalli-Sforza LL, Underhill PA, Verbenko DA, Limborska SA, and Herrera RJ
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- Ethnicity, Genetics, Population, Genotype, Geography, Haplotypes, Humans, Linguistics, Mutation, Phylogeny, Polymorphism, Single Nucleotide, Russia, Siberia, Time Factors, Chromosomes, Human, Y classification, Chromosomes, Human, Y genetics, Polymorphism, Genetic
- Abstract
Populations of northeastern Europe and the Uralic mountain range are found in close geographic proximity, but they have been subject to different demographic histories. The current study attempts to better understand the genetic paternal relationships of ethnic groups residing in these regions. We have performed high-resolution haplotyping of 236 Y-chromosomes from populations in northwestern Russia and the Uralic mountains, and compared them to relevant previously published data. Haplotype variation and age estimation analyses using 15 Y-STR loci were conducted for samples within the N1b, N1c1 and R1a1 single-nucleotide polymorphism backgrounds. Our results suggest that although most genetic relationships throughout Eurasia are dependent on geographic proximity, members of the Uralic and Slavic linguistic families and subfamilies, yield significant correlations at both levels of comparison making it difficult to denote either linguistics or geographic proximity as the basis for their genetic substrata. Expansion times for haplogroup R1a1 date approximately to 18,000 YBP, and age estimates along with Network topology of populations found at opposite poles of its range (Eastern Europe and South Asia) indicate that two separate haplotypic foci exist within this haplogroup. Data based on haplogroup N1b challenge earlier findings and suggest that the mutation may have occurred in the Uralic range rather than in Siberia and much earlier than has been proposed (12.9+/-4.1 instead of 5.2+/-2.7 kya). In addition, age and variance estimates for haplogroup N1c1 suggest that populations from the western Urals may have been genetically influenced by a dispersal from northeastern Europe (eg, eastern Slavs) rather than the converse.
- Published
- 2009
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39. Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions.
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Abu-Amero KK, Hellani A, González AM, Larruga JM, Cabrera VM, and Underhill PA
- Subjects
- Emigration and Immigration, Evolution, Molecular, Gene Flow, Geography, Haplotypes, Humans, Male, Polymorphism, Single Nucleotide, Saudi Arabia, Sequence Analysis, DNA, Black People genetics, Chromosomes, Human, Y genetics, Genetics, Population
- Abstract
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)., Conclusion: 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.
- Published
- 2009
- Full Text
- View/download PDF
40. Y-chromosome short tandem repeat intermediate variant alleles DYS392.2, DYS449.2, and DYS385.2 delineate new phylogenetic substructure in human Y-chromosome haplogroup tree.
- Author
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Myres NM, Ritchie KH, Lin AA, Hughes RH, Woodward SR, and Underhill PA
- Subjects
- Haplotypes, Humans, Sequence Analysis, DNA, Chromosomes, Human, Y genetics, Microsatellite Repeats genetics, Phylogeny
- Abstract
Aim: To determine the human Y-chromosome haplogroup backgrounds of intermediate-sized variant alleles displayed by short tandem repeat (STR) loci DYS392, DYS449, and DYS385, and to evaluate the potential of each intermediate variant to elucidate new phylogenetic substructure within the human Y-chromosome haplogroup tree., Methods: Molecular characterization of lineages was achieved using a combination of Y-chromosome haplogroup defining binary polymorphisms and up to 37 short tandem repeat loci. DNA sequencing and median-joining network analyses were used to evaluate Y-chromosome lineages displaying intermediate variant alleles., Results: We show that DYS392.2 occurs on a single haplogroup background, specifically I1*-M253, and likely represents a new phylogenetic subdivision in this European haplogroup. Intermediate variants DYS449.2 and DYS385.2 both occur on multiple haplogroup backgrounds, and when evaluated within specific haplogroup contexts, delineate new phylogenetic substructure, with DYS449.2 being informative within haplogroup A-P97 and DYS385.2 in haplogroups D-M145, E1b1a-M2, and R1b*-M343. Sequence analysis of variant alleles observed within the various haplogroup backgrounds showed that the nature of the intermediate variant differed, confirming the mutations arose independently., Conclusions: Y-chromosome short tandem repeat intermediate variant alleles, while relatively rare, typically occur on multiple haplogroup backgrounds. This distribution indicates that such mutations arise at a rate generally intermediate to those of binary markers and STR loci. As a result, intermediate-sized Y-STR variants can reveal phylogenetic substructure within the Y-chromosome phylogeny not currently detected by either binary or Y-STR markers alone, but only when such variants are evaluated within a haplogroup context.
- Published
- 2009
- Full Text
- View/download PDF
41. Y-chromosomal evidence of the cultural diffusion of agriculture in Southeast Europe.
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Battaglia V, Fornarino S, Al-Zahery N, Olivieri A, Pala M, Myres NM, King RJ, Rootsi S, Marjanovic D, Primorac D, Hadziselimovic R, Vidovic S, Drobnic K, Durmishi N, Torroni A, Santachiara-Benerecetti AS, Underhill PA, and Semino O
- Subjects
- Africa, Northern, Cultural Evolution, Europe, Genetic Markers, Genetic Variation, Geography, Humans, Male, Microsatellite Repeats genetics, Phylogeny, Agriculture, Chromosomes, Human, Y genetics, Genetics, Population
- Abstract
The debate concerning the mechanisms underlying the prehistoric spread of farming to Southeast Europe is framed around the opposing roles of population movement and cultural diffusion. To investigate the possible involvement of local people during the transition of agriculture in the Balkans, we analysed patterns of Y-chromosome diversity in 1206 subjects from 17 population samples, mainly from Southeast Europe. Evidence from three Y-chromosome lineages, I-M423, E-V13 and J-M241, make it possible to distinguish between Holocene Mesolithic forager and subsequent Neolithic range expansions from the eastern Sahara and the Near East, respectively. In particular, whereas the Balkan microsatellite variation associated to J-M241 correlates with the Neolithic period, those related to E-V13 and I-M423 Balkan Y chromosomes are consistent with a late Mesolithic time frame. In addition, the low frequency and variance associated to I-M423 and E-V13 in Anatolia and the Middle East, support an European Mesolithic origin of these two clades. Thus, these Balkan Mesolithic foragers with their own autochthonous genetic signatures, were destined to become the earliest to adopt farming, when it was subsequently introduced by a cadre of migrating farmers from the Near East. These initial local converted farmers became the principal agents spreading this economy using maritime leapfrog colonization strategies in the Adriatic and transmitting the Neolithic cultural package to other adjacent Mesolithic populations. The ensuing range expansions of E-V13 and I-M423 parallel in space and time the diffusion of Neolithic Impressed Ware, thereby supporting a case of cultural diffusion using genetic evidence.
- Published
- 2009
- Full Text
- View/download PDF
42. Differential Greek and northern African migrations to Sicily are supported by genetic evidence from the Y chromosome.
- Author
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Di Gaetano C, Cerutti N, Crobu F, Robino C, Inturri S, Gino S, Guarrera S, Underhill PA, King RJ, Romano V, Cali F, Gasparini M, Matullo G, Salerno A, Torre C, and Piazza A
- Subjects
- Africa, Northern, Analysis of Variance, Chromosomes, Human, Y genetics, Emigration and Immigration, Gene Pool, Genetic Heterogeneity, Greece, Haplotypes, Humans, Microsatellite Repeats, Phylogeny, Principal Component Analysis, Sicily, Gene Flow, Genetic Variation
- Abstract
The presence or absence of genetic heterogeneity in Sicily has long been debated. Through the analysis of the variation of Y-chromosome lineages, using the combination of haplogroups and short tandem repeats from several areas of Sicily, we show that traces of genetic flows occurred in the island, due to ancient Greek colonization and to northern African contributions, are still visible on the basis of the distribution of some lineages. The genetic contribution of Greek chromosomes to the Sicilian gene pool is estimated to be about 37% whereas the contribution of North African populations is estimated to be around 6%.In particular, the presence of a modal haplotype coming from the southern Balkan Peninsula and of its one-step derivates associated to E3b1a2-V13, supports a common genetic heritage between Sicilians and Greeks. The estimate of Time to Most Recent Common Ancestor is about 2380 years before present, which broadly agrees with the archaeological traces of the Greek classic era. The Eastern and Western part of Sicily appear to be significantly different by the chi(2)-analysis, although the extent of such differentiation is not very high according to an analysis of molecular variance. The presence of a high number of different haplogroups in the island makes its gene diversity to reach about 0.9. The general heterogeneous composition of haplogroups in our Sicilian data is similar to the patterns observed in other major islands of the Mediterranean, reflecting the complex histories of settlements in Sicily.
- Published
- 2009
- Full Text
- View/download PDF
43. Y-chromosome variation among Sudanese: restricted gene flow, concordance with language, geography, and history.
- Author
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Hassan HY, Underhill PA, Cavalli-Sforza LL, and Ibrahim ME
- Subjects
- Genetic Markers, Haplotypes, Humans, Male, Phylogeny, Population Density, Population Dynamics, Social Isolation, Sudan, Black People genetics, Chromosomes, Human, Y chemistry, Gene Flow, Genetic Variation, Geography, Language
- Abstract
We study the major levels of Y-chromosome haplogroup variation in 15 Sudanese populations by typing major Y-haplogroups in 445 unrelated males representing the three linguistic families in Sudan. Our analysis shows Sudanese populations fall into haplogroups A, B, E, F, I, J, K, and R in frequencies of 16.9, 7.9, 34.4, 3.1, 1.3, 22.5, 0.9, and 13% respectively. Haplogroups A, B, and E occur mainly in Nilo-Saharan speaking groups including Nilotics, Fur, Borgu, and Masalit; whereas haplogroups F, I, J, K, and R are more frequent among Afro-Asiatic speaking groups including Arabs, Beja, Copts, and Hausa, and Niger-Congo speakers from the Fulani ethnic group. Mantel tests reveal a strong correlation between genetic and linguistic structures (r = 0.31, P = 0.007), and a similar correlation between genetic and geographic distances (r = 0.29, P = 0.025) that appears after removing nomadic pastoralists of no known geographic locality from the analysis. The bulk of genetic diversity appears to be a consequence of recent migrations and demographic events mainly from Asia and Europe, evident in a higher migration rate for speakers of Afro-Asiatic as compared with the Nilo-Saharan family of languages, and a generally higher effective population size for the former. The data provide insights not only into the history of the Nile Valley, but also in part to the history of Africa and the area of the Sahel.
- Published
- 2008
- Full Text
- View/download PDF
44. Y-chromosomal evidence of a pastoralist migration through Tanzania to southern Africa.
- Author
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Henn BM, Gignoux C, Lin AA, Oefner PJ, Shen P, Scozzari R, Cruciani F, Tishkoff SA, Mountain JL, and Underhill PA
- Subjects
- Chromatography, High Pressure Liquid, Genotype, Haplotypes genetics, History, Ancient, Humans, Male, Microsatellite Repeats genetics, Models, Genetic, Polymorphism, Single Nucleotide genetics, Tanzania, Agriculture history, Chromosomes, Human, Y genetics, Demography, Emigration and Immigration history, Genetics, Population
- Abstract
Although geneticists have extensively debated the mode by which agriculture diffused from the Near East to Europe, they have not directly examined similar agropastoral diffusions in Africa. It is unclear, for example, whether early instances of sheep, cows, pottery, and other traits of the pastoralist package were transmitted to southern Africa by demic or cultural diffusion. Here, we report a newly discovered Y-chromosome-specific polymorphism that defines haplogroup E3b1f-M293. This polymorphism reveals the monophyletic relationship of the majority of haplotypes of a previously paraphyletic clade, E3b1-M35*, that is widespread in Africa and southern Europe. To elucidate the history of the E3b1f haplogroup, we analyzed this haplogroup in 13 populations from southern and eastern Africa. The geographic distribution of the E3b1f haplogroup, in association with the microsatellite diversity estimates for populations, is consistent with an expansion through Tanzania to southern-central Africa. The data suggest this dispersal was independent of the migration of Bantu-speaking peoples along a similar route. Instead, the phylogeography and microsatellite diversity of the E3b1f lineage correlate with the arrival of the pastoralist economy in southern Africa. Our Y-chromosomal evidence supports a demic diffusion model of pastoralism from eastern to southern Africa approximately 2,000 years ago.
- Published
- 2008
- Full Text
- View/download PDF
45. New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree.
- Author
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Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, and Hammer MF
- Subjects
- Genetic Markers, Humans, Mutation, Chromosomes, Human, Y genetics, Haplotypes genetics, Phylogeny, Polymorphism, Genetic genetics
- Abstract
Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.
- Published
- 2008
- Full Text
- View/download PDF
46. Y-chromosome diversity characterizes the Gulf of Oman.
- Author
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Cadenas AM, Zhivotovsky LA, Cavalli-Sforza LL, Underhill PA, and Herrera RJ
- Subjects
- Haplotypes, Humans, Male, Microsatellite Repeats, Phylogeny, Qatar, United Arab Emirates, Yemen, Chromosomes, Human, Y
- Abstract
Arabia has served as a strategic crossroads for human disseminations, providing a natural connection between the distant populations of China and India in the east to the western civilizations along the Mediterranean. To explore this region's critical role in the migratory episodes leaving Africa to Eurasia and back, high-resolution Y-chromosome analysis of males from the United Arab Emirates (164), Qatar (72) and Yemen (62) was performed. The role of the Levant in the Neolithic dispersal of the E3b1-M35 sublineages is supported by the data, and the distribution and STR-based analyses of J1-M267 representatives points to their spread from the north, most likely during the Neolithic. With the exception of Yemen, southern Arabia, South Iran and South Pakistan display high diversity in their Y-haplogroup substructure possibly a result of gene flow along the coastal crescent-shaped corridor of the Gulf of Oman facilitating human dispersals. Elevated rates of consanguinity may have had an impact in Yemen and Qatar, which experience significant heterozygote deficiencies at various hypervariable autosomal STR loci.
- Published
- 2008
- Full Text
- View/download PDF
47. Differential Y-chromosome Anatolian influences on the Greek and Cretan Neolithic.
- Author
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King RJ, Ozcan SS, Carter T, Kalfoğlu E, Atasoy S, Triantaphyllidis C, Kouvatsi A, Lin AA, Chow CE, Zhivotovsky LA, Michalodimitrakis M, and Underhill PA
- Subjects
- Analysis of Variance, Cluster Analysis, DNA Primers genetics, Greece, Ancient, Haplotypes genetics, History, Ancient, Humans, Male, Principal Component Analysis, Turkey, Chromosomes, Human, Y genetics, Emigration and Immigration, Ethnicity genetics, Phylogeny, Polymorphism, Genetic, Population Dynamics
- Abstract
The earliest Neolithic sites of Europe are located in Crete and mainland Greece. A debate persists concerning whether these farmers originated in neighboring Anatolia and the role of maritime colonization. To address these issues 171 samples were collected from areas near three known early Neolithic settlements in Greece together with 193 samples from Crete. An analysis of Y-chromosome haplogroups determined that the samples from the Greek Neolithic sites showed strong affinity to Balkan data, while Crete shows affinity with central/Mediterranean Anatolia. Haplogroup J2b-M12 was frequent in Thessaly and Greek Macedonia while haplogroup J2a-M410 was scarce. Alternatively, Crete, like Anatolia showed a high frequency of J2a-M410 and a low frequency of J2b-M12. This dichotomy parallels archaeobotanical evidence, specifically that while bread wheat (Triticum aestivum) is known from Neolithic Anatolia, Crete and southern Italy; it is absent from earliest Neolithic Greece. The expansion time of YSTR variation for haplogroup E3b1a2-V13, in the Peloponnese was consistent with an indigenous Mesolithic presence. In turn, two distinctive haplogroups, J2a1h-M319 and J2a1b1-M92, have demographic properties consistent with Bronze Age expansions in Crete, arguably from NW/W Anatolia and Syro-Palestine, while a later mainland (Mycenaean) contribution to Crete is indicated by relative frequencies of V13.
- Published
- 2008
- Full Text
- View/download PDF
48. Co-introgression of Y-chromosome haplogroups and the sickle cell gene across Africa's Sahel.
- Author
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Bereir RE, Hassan HY, Salih NA, Underhill PA, Cavalli-Sforza LL, Hussain AA, Kwiatkowski D, and Ibrahim ME
- Subjects
- Africa, Northern, Anemia, Sickle Cell blood, Case-Control Studies, Gene Frequency, Humans, Male, Anemia, Sickle Cell genetics, Chromosomes, Human, Y genetics, Emigration and Immigration, Haplotypes genetics, Hemoglobin, Sickle genetics
- Abstract
The Sahel that extends from the Atlantic Ocean to the Ethiopian highland is a historical reservoir of Africa's cultures and grandest populations and a known arena of ancient and recent migrations. We are interested in the issue whether such migrations were also carriers of genetic traits and whether this introgression could be associated with population genetic markers. Based on analysis of Y-chromosome haplogroups, we present evidence that the sickle gene, one of the major protective polymorphisms known in malaria, has in fact found its way only recently to the gene pool of the populations in eastern Sahel. We discuss the possible dynamics of the process and give estimates of the age of the introduction of the S allele into eastern Sahel.
- Published
- 2007
- Full Text
- View/download PDF
49. Y-chromosome short tandem repeat DYS458.2 non-consensus alleles occur independently in both binary haplogroups J1-M267 and R1b3-M405.
- Author
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Myres NM, Ekins JE, Lin AA, Cavalli-Sforza LL, Woodward SR, and Underhill PA
- Subjects
- Alleles, Europe, Genetics, Population, Humans, Pakistan, Point Mutation, Polymorphism, Genetic, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Turkey, Chromosomes, Human, Y genetics, Gene Frequency, Haplotypes, Microsatellite Repeats
- Abstract
Aim: To determine the human Y-chromosome haplogroup backgrounds of non-consensus DYS458.2 short tandem repeat alleles and evaluate their phylogenetic substructure and frequency in representative samples from the Middle East, Europe, and Pakistan., Methods: Molecular characterization of lineages was achieved using a combination of Y-chromosome haplogroup defining binary polymorphisms and up to 37 short tandem repeat loci, including DYS388 to construct haplotypes. DNA sequencing of the DYS458 locus and median-joining network analyses were used to evaluate Y-chromosome lineages displaying the DYS458.2 motif., Results: We showed that the DYS458.2 allelic innovation arose independently on at least two distinctive binary haplogroup backgrounds and possibly a third as well. The partial allele length pattern was fixed in all haplogroup J1 chromosomes examined, including its known rare sub-haplogroups. Within the alternative R1b3 associated M405 defined sub-haplogroup, both DYS458.0 and DYS458.2 allele classes occurred. A single chromosome also allocated to the R1b3-M269*(xM405) classification. The physical position of the partial insertion/deletion occurrence within the normal tetramer tract differed distinctly in each haplogroup context., Conclusions: While unusual DYS458.2 alleles are informative, additional information for other linked polymorphic loci is required when using such non-conforming alleles to infer haplogroup background and common ancestry.
- Published
- 2007
50. Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis.
- Author
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Hudjashov G, Kivisild T, Underhill PA, Endicott P, Sanchez JJ, Lin AA, Shen P, Oefner P, Renfrew C, Villems R, and Forster P
- Subjects
- Africa, Australia, History, Ancient, Humans, Male, Molecular Sequence Data, New Guinea, Chromosomes, Human, Y genetics, DNA, Mitochondrial analysis, DNA, Mitochondrial genetics, Emigration and Immigration history, Phylogeny
- Abstract
Published and new samples of Aboriginal Australians and Melanesians were analyzed for mtDNA (n=172) and Y variation (n=522), and the resulting profiles were compared with the branches known so far within the global mtDNA and the Y chromosome tree. (i) All Australian lineages are confirmed to fall within the mitochondrial founder branches M and N and the Y chromosomal founders C and F, which are associated with the exodus of modern humans from Africa approximately 50-70,000 years ago. The analysis reveals no evidence for any archaic maternal or paternal lineages in Australians, despite some suggestively robust features in the Australian fossil record, thus weakening the argument for continuity with any earlier Homo erectus populations in Southeast Asia. (ii) The tree of complete mtDNA sequences shows that Aboriginal Australians are most closely related to the autochthonous populations of New Guinea/Melanesia, indicating that prehistoric Australia and New Guinea were occupied initially by one and the same Palaeolithic colonization event approximately 50,000 years ago, in agreement with current archaeological evidence. (iii) The deep mtDNA and Y chromosomal branching patterns between Australia and most other populations around the Indian Ocean point to a considerable isolation after the initial arrival. (iv) We detect only minor secondary gene flow into Australia, and this could have taken place before the land bridge between Australia and New Guinea was submerged approximately 8,000 years ago, thus calling into question that certain significant developments in later Australian prehistory (the emergence of a backed-blade lithic industry, and the linguistic dichotomy) were externally motivated.
- Published
- 2007
- Full Text
- View/download PDF
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