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Peter A Underhill - One of the best experts on this subject based on the ideXlab platform.
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the phYlogenetic and geographic structure of Y Chromosome Haplogroup r1a
European Journal of Human Genetics, 2015Co-Authors: Peter A Underhill, Siiri Rootsi, Natalie M Myres, Mari Jarve, Roy King, David G Poznik, Jianbin Wang, Ben Passarelli, Jad Kanbar, Julie Di CristofaroAbstract:R1a-M420 is one of the most widelY spread Y-Chromosome Haplogroups; however, its substructure within Europe and Asia has remained poorlY characterized. Using a panel of 16 244 male subjects from 126 populations sampled across Eurasia, we identified 2923 R1a-M420 Y-Chromosomes and analYzed them to a highlY granular phYlogeographic resolution. Whole Y-Chromosome sequence analYsis of eight R1a and five R1b individuals suggests a divergence time of ∼25 000 (95% CI: 21 300–29 000) Years ago and a coalescence time within R1a-M417 of ∼5800 (95% CI: 4800–6800) Years. The spatial frequencY distributions of R1a sub-Haplogroups conclusivelY indicate two major groups, one found primarilY in Europe and the other confined to Central and South Asia. BeYond the major European versus Asian dichotomY, we describe several Younger sub-Haplogroups. Based on spatial distributions and diversitY patterns within the R1a-M420 clade, particularlY rare basal branches detected primarilY within Iran and eastern TurkeY, we conclude that the initial episodes of Haplogroup R1a diversification likelY occurred in the vicinitY of present-daY Iran.
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population genomic analYsis of ancient and modern genomes Yields new insights into the genetic ancestrY of the tYrolean iceman and the genetic structure of europe
PLOS Genetics, 2014Co-Authors: Martin Sikora, Peter A Underhill, Brenna M Henn, Meredith L Carpenter, Andres Morenoestrada, Federico Sanchezquinto, Ilenia Zara, Maristella Pitzalis, C Sidore, Fabio BusoneroAbstract:Genome sequencing of the 5,300-Year-old mummY of the TYrolean Iceman, found in 1991 on a glacier near the border of ItalY and Austria, has Yielded new insights into his origin and relationship to modern European populations. A keY finding of that studY was an apparent recent common ancestrY with individuals from Sardinia, based largelY on the Y Chromosome Haplogroup and common autosomal SNP variation. Here, we compiled and analYzed genomic datasets from both modern and ancient Europeans, including genome sequence data from over 400 Sardinians and two ancient Thracians from Bulgaria, to investigate this result in greater detail and determine its implications for the genetic structure of Neolithic Europe. Using whole-genome sequencing data, we confirm that the Iceman is, indeed, most closelY related to Sardinians. Furthermore, we show that this relationship extends to other individuals from cultural contexts associated with the spread of agriculture during the Neolithic transition, in contrast to individuals from a hunter-gatherer context. We hYpothesize that this genetic affinitY of ancient samples from different parts of Europe with Sardinians represents a common genetic component that was geographicallY widespread across Europe during the Neolithic, likelY related to migrations and population expansions associated with the spread of agriculture.
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separating the post glacial coancestrY of european and asian Y Chromosomes within Haplogroup r1a
European Journal of Human Genetics, 2010Co-Authors: Peter A Underhill, Siiri Rootsi, Natalie M Myres, Alice A Lin, Lev A Zhivotovsky, Roy King, Mait Metspalu, Cherylemiliane T ChowAbstract:Human Y-Chromosome Haplogroup structure is largelY circumscribed bY continental boundaries. One notable exception to this general pattern is the Young Haplogroup R1a that exhibits post-Glacial coalescent times and relates the paternal ancestrY of more than 10% of men in a wide geographic area extending from South Asia to Central East Europe and South Siberia. Its origin and dispersal patterns are poorlY understood as no marker has Yet been described that would distinguish European R1a Chromosomes from Asian. Here we present frequencY and haplotYpe diversitY estimates for more than 2000 R1a Chromosomes assessed for several newlY discovered SNP markers that introduce the onset of informative R1a subdivisions bY geographY. Marker M434 has a low frequencY and a late origin in West Asia bearing witness to recent gene flow over the Arabian Sea. ConverselY, marker M458 has a significant frequencY in Europe, exceeding 30% in its core area in Eastern Europe and comprising up to 70% of all M17 Chromosomes present there. The diversitY and frequencY profiles of M458 suggest its origin during the earlY Holocene and a subsequent expansion likelY related to a number of prehistoric cultural developments in the region. Its primarY frequencY and diversitY distribution correlates well with some of the major Central and East European river basins where settled farming was established before its spread further eastward. ImportantlY, the virtual absence of M458 Chromosomes outside Europe speaks against substantial patrilineal gene flow from East Europe to Asia, including to India, at least since the mid-Holocene.
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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
Croatian Medical Journal, 2009Co-Authors: Natalie M Myres, Kathleen H Ritchie, Robert Hughes, Scott R Woodward, Peter A UnderhillAbstract: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.
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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
Croatian Medical Journal, 2009Co-Authors: Natalie M Myres, Kathleen H Ritchie, Robert Hughes, Scott R Woodward, Alice A Lin, Peter A UnderhillAbstract: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.
Natalie M Myres - One of the best experts on this subject based on the ideXlab platform.
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the phYlogenetic and geographic structure of Y Chromosome Haplogroup r1a
European Journal of Human Genetics, 2015Co-Authors: Peter A Underhill, Siiri Rootsi, Natalie M Myres, Mari Jarve, Roy King, David G Poznik, Jianbin Wang, Ben Passarelli, Jad Kanbar, Julie Di CristofaroAbstract:R1a-M420 is one of the most widelY spread Y-Chromosome Haplogroups; however, its substructure within Europe and Asia has remained poorlY characterized. Using a panel of 16 244 male subjects from 126 populations sampled across Eurasia, we identified 2923 R1a-M420 Y-Chromosomes and analYzed them to a highlY granular phYlogeographic resolution. Whole Y-Chromosome sequence analYsis of eight R1a and five R1b individuals suggests a divergence time of ∼25 000 (95% CI: 21 300–29 000) Years ago and a coalescence time within R1a-M417 of ∼5800 (95% CI: 4800–6800) Years. The spatial frequencY distributions of R1a sub-Haplogroups conclusivelY indicate two major groups, one found primarilY in Europe and the other confined to Central and South Asia. BeYond the major European versus Asian dichotomY, we describe several Younger sub-Haplogroups. Based on spatial distributions and diversitY patterns within the R1a-M420 clade, particularlY rare basal branches detected primarilY within Iran and eastern TurkeY, we conclude that the initial episodes of Haplogroup R1a diversification likelY occurred in the vicinitY of present-daY Iran.
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the first peopling of south america new evidence from Y Chromosome Haplogroup q
PLOS ONE, 2013Co-Authors: Vincenza Battaglia, Viola Grugni, Ugo A. Perego, Alessandro Achilli, Natalie M Myres, Scott R Woodward, Norman Angerhofer, Edgar J Gomezpalmieri, Antonio TorroniAbstract:Recent progress in the phYlogenetic resolution of the Y-Chromosome phYlogenY permits the male demographic dYnamics and migratorY events that occurred in Central and Southern America after the initial human spread into the Americas to be investigated at the regional level. To delve further into this issue, we examined more than 400 Native American Y Chromosomes (collected in the region ranging from Mexico to South America) belonging to Haplogroup Q – virtuallY the onlY branch of the Y phYlogenY observed in modern-daY Amerindians of Central and South America – together with 27 from Mongolia and Kamchatka. Two main founding lineages, Q1a3a1a-M3 and Q1a3a1-L54(xM3), were detected along with novel sub-clades of Younger age and more restricted geographic distributions. The first was also observed in Far East Asia while no Q1a3a1-L54(xM3) Y Chromosome was found in Asia except the southern Siberian-specific sub-clade Q1a3a1c-L330. Our data not onlY confirm a southern Siberian origin of ancestral populations that gave rise to Paleo-Indians and the differentiation of both Native American Q founding lineages in Beringia, but support their concomitant arrival in Mesoamerica, where Mexico acted as recipient for the first wave of migration, followed bY a rapid southward migration, along the Pacific coast, into the Andean region. Although Q1a3a1a-M3 and Q1a3a1-L54(xM3) displaY overlapping general distributions, theY show different patterns of evolution in the Mexican plateau and the Andean area, which can be explained bY local differentiations due to demographic events triggered bY the introduction of agriculture and associated with the flourishing of the Great Empires.
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a major Y Chromosome Haplogroup r1b holocene era founder effect in central and western europe
European Journal of Human Genetics, 2011Co-Authors: Natalie M Myres, Siiri Rootsi, I A Kutuev, Alice A Lin, Mari Jarve, Roy King, Vicente M Cabrera, E K Khusnutdinova, Andrey PshenichnovAbstract:The phYlogenetic relationships of numerous branches within the core Y-Chromosome Haplogroup R-M207 support a West Asian origin of Haplogroup R1b, its initial differentiation there followed bY a rapid spread of one of its sub-clades carrYing the M269 mutation to Europe. Here, we present phYlogeographicallY resolved data for 2043 M269-derived Y-Chromosomes from 118 West Asian and European populations assessed for the M412 SNP that largelY separates the majoritY of Central and West European R1b lineages from those observed in Eastern Europe, the Circum-Uralic region, the Near East, the Caucasus and Pakistan. Within the M412 dichotomY, the major S116 sub-clade shows a frequencY peak in the upper Danube basin and Paris area with declining frequencY toward ItalY, Iberia, Southern France and British Isles. Although this frequencY pattern closelY approximates the spread of the Linearbandkeramik (LBK), Neolithic culture, an advent leading to a number of pre-historic cultural developments during the past ≤10 thousand Years, more complex pre-Neolithic scenarios remain possible for the L23(xM412) components in Southeast Europe and elsewhere.
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separating the post glacial coancestrY of european and asian Y Chromosomes within Haplogroup r1a
European Journal of Human Genetics, 2010Co-Authors: Peter A Underhill, Siiri Rootsi, Natalie M Myres, Alice A Lin, Lev A Zhivotovsky, Roy King, Mait Metspalu, Cherylemiliane T ChowAbstract:Human Y-Chromosome Haplogroup structure is largelY circumscribed bY continental boundaries. One notable exception to this general pattern is the Young Haplogroup R1a that exhibits post-Glacial coalescent times and relates the paternal ancestrY of more than 10% of men in a wide geographic area extending from South Asia to Central East Europe and South Siberia. Its origin and dispersal patterns are poorlY understood as no marker has Yet been described that would distinguish European R1a Chromosomes from Asian. Here we present frequencY and haplotYpe diversitY estimates for more than 2000 R1a Chromosomes assessed for several newlY discovered SNP markers that introduce the onset of informative R1a subdivisions bY geographY. Marker M434 has a low frequencY and a late origin in West Asia bearing witness to recent gene flow over the Arabian Sea. ConverselY, marker M458 has a significant frequencY in Europe, exceeding 30% in its core area in Eastern Europe and comprising up to 70% of all M17 Chromosomes present there. The diversitY and frequencY profiles of M458 suggest its origin during the earlY Holocene and a subsequent expansion likelY related to a number of prehistoric cultural developments in the region. Its primarY frequencY and diversitY distribution correlates well with some of the major Central and East European river basins where settled farming was established before its spread further eastward. ImportantlY, the virtual absence of M458 Chromosomes outside Europe speaks against substantial patrilineal gene flow from East Europe to Asia, including to India, at least since the mid-Holocene.
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The emergence of Y-Chromosome Haplogroup J1e among Arabic-speaking populations
European Journal of Human Genetics, 2010Co-Authors: Jacques Chiaroni, Natalie M Myres, Roy J King, Brenna M Henn, Axel Ducourneau, Michael J Mitchell, Gilles Boetsch, Issa Sheikha, Jabeen Ahmad, Francesca LattanziAbstract: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.
Alena Kushniarevich - One of the best experts on this subject based on the ideXlab platform.
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origin and diffusion of human Y Chromosome Haplogroup j1 m267
Scientific Reports, 2021Co-Authors: Hovhannes Sahakyan, Ashot Margaryan, Lauri Saag, Monika Karmin, Rodrigo Flores, Marc Haber, Alena KushniarevichAbstract:Human Y Chromosome Haplogroup J1-M267 is a common male lineage in West Asia. One high-frequencY region-encompassing the Arabian Peninsula, southern Mesopotamia, and the southern Levant-resides ~ 2000 km awaY from the other one found in the Caucasus. The region between them, although has a lower frequencY, nevertheless demonstrates high genetic diversitY. Studies associate this Haplogroup with the spread of farming from the Fertile Crescent to Europe, the spread of mobile pastoralism in the desert regions of the Arabian Peninsula, the historY of the Jews, and the spread of Islam. Here, we studY past human male demographY in West Asia with 172 high-coverage whole Y Chromosome sequences and 889 genotYped samples of Haplogroup J1-M267. We show that this Haplogroup evolved ~ 20,000 Years ago somewhere in northwestern Iran, the Caucasus, the Armenian Highland, and northern Mesopotamia. The major branch-J1a1a1-P58-evolved during the earlY Holocene ~ 9500 Years ago somewhere in the Arabian Peninsula, the Levant, and southern Mesopotamia. Haplogroup J1-M267 expanded during the Chalcolithic, the Bronze Age, and the Iron Age. Most probablY, the spread of Afro-Asiatic languages, the spread of mobile pastoralism in the arid zones, or both of these events together explain the distribution of Haplogroup J1-M267 we see todaY in the southern regions of West Asia.
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Additional file 6: of Genes reveal traces of common recent demographic historY for most of the Uralic-speaking populations
2018Co-Authors: Kristiina Tambets, Siiri Rootsi, Bayazit Yunusbayev, Georgi Hudjashov, Anne-mai Ilumäe, Terhi Honkola, Outi Vesakoski, Quentin Atkinson, Pontus Skoglund, Alena KushniarevichAbstract:Table S5. Y Chromosome Haplogroup frequencies in Eurasia. (XLSX 22 kb
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human Y Chromosome Haplogroup n a non trivial time resolved phYlogeographY that cuts across language families
American Journal of Human Genetics, 2016Co-Authors: Annemai Ilumae, Lauri Saag, Monika Karmin, Alena Kushniarevich, Mari Jarve, Maere Reidla, Marina Chukhryaeva, Helen Post, A T AgdzhoyanAbstract: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.
Alessandro Achilli - One of the best experts on this subject based on the ideXlab platform.
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AnalYsis of the human Y-Chromosome Haplogroup Q characterizes ancient population movements in Eurasia and the Americas
BMC Biology, 2019Co-Authors: Viola Grugni, Linda Ongaro, Vincenza Battaglia, Giulia Colombo, Marco Rosario Capodiferro, B. Trombetta, Alessandro Raveane, Anna Olivieri, Alessandro Achilli, Ugo A. PeregoAbstract:BackgroundRecent genome studies of modern and ancient samples have proposed that Native Americans derive from a subset of the Eurasian gene pool carried to America bY an ancestral Beringian population, from which two well-differentiated components originated and subsequentlY mixed in different proportion during their spread in the Americas. To assess the timing, places of origin and extent of admixture between these components, we performed an analYsis of the Y-Chromosome Haplogroup Q, which is the onlY Pan-American Haplogroup and accounts for virtuallY all Native American Y Chromosomes in Mesoamerica and South America.ResultsOur analYses of 1.5 Mb of 152 Y Chromosomes, 34 re-sequenced in this work, support a “coastal and inland routes scenario” for the first entrance of modern humans in North America. We show a major phase of male population growth in the Americas after 15 thousand Years ago (kYa), followed bY a period of constant population size from 8 to 3 kYa, after which a secondarY sign of growth was registered. The estimated dates of the first expansion in Mesoamerica and the Isthmo-Colombian Area, mainlY revealed bY Haplogroup Q-Z780, suggest an entrance in South America prior to 15 kYa. During the global constant population size phase, local South American hints of growth were registered bY different Q-M848 sub-clades. These expansion events, which started during the Holocene with the improvement of climatic conditions, can be ascribed to multiple cultural changes rather than a steadY population growth and a single cohesive culture diffusion as it occurred in Europe.ConclusionsWe established and dated a detailed Haplogroup Q phYlogenY that provides new insights into the geographic distribution of its Eurasian and American branches in modern and ancient samples.
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analYsis of the human Y Chromosome Haplogroup q characterizes ancient population movements in eurasia and the americas
BMC Biology, 2019Co-Authors: Viola Grugni, Linda Ongaro, Vincenza Battaglia, Giulia Colombo, Marco Rosario Capodiferro, B. Trombetta, Alessandro Raveane, Anna Olivieri, Alessandro AchilliAbstract:Recent genome studies of modern and ancient samples have proposed that Native Americans derive from a subset of the Eurasian gene pool carried to America bY an ancestral Beringian population, from which two well-differentiated components originated and subsequentlY mixed in different proportion during their spread in the Americas. To assess the timing, places of origin and extent of admixture between these components, we performed an analYsis of the Y-Chromosome Haplogroup Q, which is the onlY Pan-American Haplogroup and accounts for virtuallY all Native American Y Chromosomes in Mesoamerica and South America. Our analYses of 1.5 Mb of 152 Y Chromosomes, 34 re-sequenced in this work, support a “coastal and inland routes scenario” for the first entrance of modern humans in North America. We show a major phase of male population growth in the Americas after 15 thousand Years ago (kYa), followed bY a period of constant population size from 8 to 3 kYa, after which a secondarY sign of growth was registered. The estimated dates of the first expansion in Mesoamerica and the Isthmo-Colombian Area, mainlY revealed bY Haplogroup Q-Z780, suggest an entrance in South America prior to 15 kYa. During the global constant population size phase, local South American hints of growth were registered bY different Q-M848 sub-clades. These expansion events, which started during the Holocene with the improvement of climatic conditions, can be ascribed to multiple cultural changes rather than a steadY population growth and a single cohesive culture diffusion as it occurred in Europe. We established and dated a detailed Haplogroup Q phYlogenY that provides new insights into the geographic distribution of its Eurasian and American branches in modern and ancient samples.
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Additional file 1: of AnalYsis of the human Y-Chromosome Haplogroup Q characterizes ancient population movements in Eurasia and the Americas
2019Co-Authors: Viola Grugni, Linda Ongaro, Vincenza Battaglia, Giulia Colombo, Marco Rosario Capodiferro, B. Trombetta, Alessandro Raveane, Anna Olivieri, Alessandro Achilli, Ugo PeregoAbstract:Table S1. List of the high coverage samples analYsed in this studY along with their geographic origin and Y-Chromosome Haplogroup affiliation. (XLSX 20 kb
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Additional file 10: of AnalYsis of the human Y-Chromosome Haplogroup Q characterizes ancient population movements in Eurasia and the Americas
2019Co-Authors: Viola Grugni, Linda Ongaro, Vincenza Battaglia, Giulia Colombo, Marco Rosario Capodiferro, B. Trombetta, Alessandro Raveane, Anna Olivieri, Alessandro Achilli, Ugo PeregoAbstract:Figure S4. PhYlogeographY of the branches Q-Y2659, Q-L53 and Q-L804 (panels a, b and c, respectivelY). Each panel illustrates the phYlogenetic relationships of the markers (in different colours) investigated per each branch and their pattern of frequencY distribution (complete list of samples in Additional file 8: Table S6). Circles without anY number refer to one subject. Larger circles refer to the number of specified subjects. Stars highlighted bY a greY shading refer to ancient samples: (1) [75]; (2) [38]; (3) [42]; their relative dating is also reported in italics. Dates reported below branches refer to BaYesian estimates of node ages. (PDF 1183 kb
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Additional file 9: of AnalYsis of the human Y-Chromosome Haplogroup Q characterizes ancient population movements in Eurasia and the Americas
2019Co-Authors: Viola Grugni, Linda Ongaro, Vincenza Battaglia, Giulia Colombo, Marco Rosario Capodiferro, B. Trombetta, Alessandro Raveane, Anna Olivieri, Alessandro Achilli, Ugo PeregoAbstract:Figure S3. PhYlogeographY of the branches Q-Y1150, Q-M378 and Q-F1096 (panels a, b and c, respectivelY). Each panel illustrates the phYlogenetic relationships of the markers (in different colours) investigated per each branch and their pattern of frequencY distribution (complete list of samples in Additional file 8: Table S6). Circles without anY number refer to one subject. Larger circles refer to the number of specified subjects. Stars highlighted bY a greY shading refer to ancient samples: (1) [74], (2) [75], (3) [76], (4) [28]; their relative dating, when available, is also reported in italics. Dates reported below branches refer to BaYesian estimates of node ages. (PDF 1420 kb
Viola Grugni - One of the best experts on this subject based on the ideXlab platform.
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AnalYsis of the human Y-Chromosome Haplogroup Q characterizes ancient population movements in Eurasia and the Americas
BMC Biology, 2019Co-Authors: Viola Grugni, Linda Ongaro, Vincenza Battaglia, Giulia Colombo, Marco Rosario Capodiferro, B. Trombetta, Alessandro Raveane, Anna Olivieri, Alessandro Achilli, Ugo A. PeregoAbstract:BackgroundRecent genome studies of modern and ancient samples have proposed that Native Americans derive from a subset of the Eurasian gene pool carried to America bY an ancestral Beringian population, from which two well-differentiated components originated and subsequentlY mixed in different proportion during their spread in the Americas. To assess the timing, places of origin and extent of admixture between these components, we performed an analYsis of the Y-Chromosome Haplogroup Q, which is the onlY Pan-American Haplogroup and accounts for virtuallY all Native American Y Chromosomes in Mesoamerica and South America.ResultsOur analYses of 1.5 Mb of 152 Y Chromosomes, 34 re-sequenced in this work, support a “coastal and inland routes scenario” for the first entrance of modern humans in North America. We show a major phase of male population growth in the Americas after 15 thousand Years ago (kYa), followed bY a period of constant population size from 8 to 3 kYa, after which a secondarY sign of growth was registered. The estimated dates of the first expansion in Mesoamerica and the Isthmo-Colombian Area, mainlY revealed bY Haplogroup Q-Z780, suggest an entrance in South America prior to 15 kYa. During the global constant population size phase, local South American hints of growth were registered bY different Q-M848 sub-clades. These expansion events, which started during the Holocene with the improvement of climatic conditions, can be ascribed to multiple cultural changes rather than a steadY population growth and a single cohesive culture diffusion as it occurred in Europe.ConclusionsWe established and dated a detailed Haplogroup Q phYlogenY that provides new insights into the geographic distribution of its Eurasian and American branches in modern and ancient samples.
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analYsis of the human Y Chromosome Haplogroup q characterizes ancient population movements in eurasia and the americas
BMC Biology, 2019Co-Authors: Viola Grugni, Linda Ongaro, Vincenza Battaglia, Giulia Colombo, Marco Rosario Capodiferro, B. Trombetta, Alessandro Raveane, Anna Olivieri, Alessandro AchilliAbstract:Recent genome studies of modern and ancient samples have proposed that Native Americans derive from a subset of the Eurasian gene pool carried to America bY an ancestral Beringian population, from which two well-differentiated components originated and subsequentlY mixed in different proportion during their spread in the Americas. To assess the timing, places of origin and extent of admixture between these components, we performed an analYsis of the Y-Chromosome Haplogroup Q, which is the onlY Pan-American Haplogroup and accounts for virtuallY all Native American Y Chromosomes in Mesoamerica and South America. Our analYses of 1.5 Mb of 152 Y Chromosomes, 34 re-sequenced in this work, support a “coastal and inland routes scenario” for the first entrance of modern humans in North America. We show a major phase of male population growth in the Americas after 15 thousand Years ago (kYa), followed bY a period of constant population size from 8 to 3 kYa, after which a secondarY sign of growth was registered. The estimated dates of the first expansion in Mesoamerica and the Isthmo-Colombian Area, mainlY revealed bY Haplogroup Q-Z780, suggest an entrance in South America prior to 15 kYa. During the global constant population size phase, local South American hints of growth were registered bY different Q-M848 sub-clades. These expansion events, which started during the Holocene with the improvement of climatic conditions, can be ascribed to multiple cultural changes rather than a steadY population growth and a single cohesive culture diffusion as it occurred in Europe. We established and dated a detailed Haplogroup Q phYlogenY that provides new insights into the geographic distribution of its Eurasian and American branches in modern and ancient samples.
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Additional file 1: of AnalYsis of the human Y-Chromosome Haplogroup Q characterizes ancient population movements in Eurasia and the Americas
2019Co-Authors: Viola Grugni, Linda Ongaro, Vincenza Battaglia, Giulia Colombo, Marco Rosario Capodiferro, B. Trombetta, Alessandro Raveane, Anna Olivieri, Alessandro Achilli, Ugo PeregoAbstract:Table S1. List of the high coverage samples analYsed in this studY along with their geographic origin and Y-Chromosome Haplogroup affiliation. (XLSX 20 kb
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Additional file 10: of AnalYsis of the human Y-Chromosome Haplogroup Q characterizes ancient population movements in Eurasia and the Americas
2019Co-Authors: Viola Grugni, Linda Ongaro, Vincenza Battaglia, Giulia Colombo, Marco Rosario Capodiferro, B. Trombetta, Alessandro Raveane, Anna Olivieri, Alessandro Achilli, Ugo PeregoAbstract:Figure S4. PhYlogeographY of the branches Q-Y2659, Q-L53 and Q-L804 (panels a, b and c, respectivelY). Each panel illustrates the phYlogenetic relationships of the markers (in different colours) investigated per each branch and their pattern of frequencY distribution (complete list of samples in Additional file 8: Table S6). Circles without anY number refer to one subject. Larger circles refer to the number of specified subjects. Stars highlighted bY a greY shading refer to ancient samples: (1) [75]; (2) [38]; (3) [42]; their relative dating is also reported in italics. Dates reported below branches refer to BaYesian estimates of node ages. (PDF 1183 kb
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Additional file 9: of AnalYsis of the human Y-Chromosome Haplogroup Q characterizes ancient population movements in Eurasia and the Americas
2019Co-Authors: Viola Grugni, Linda Ongaro, Vincenza Battaglia, Giulia Colombo, Marco Rosario Capodiferro, B. Trombetta, Alessandro Raveane, Anna Olivieri, Alessandro Achilli, Ugo PeregoAbstract:Figure S3. PhYlogeographY of the branches Q-Y1150, Q-M378 and Q-F1096 (panels a, b and c, respectivelY). Each panel illustrates the phYlogenetic relationships of the markers (in different colours) investigated per each branch and their pattern of frequencY distribution (complete list of samples in Additional file 8: Table S6). Circles without anY number refer to one subject. Larger circles refer to the number of specified subjects. Stars highlighted bY a greY shading refer to ancient samples: (1) [74], (2) [75], (3) [76], (4) [28]; their relative dating, when available, is also reported in italics. Dates reported below branches refer to BaYesian estimates of node ages. (PDF 1420 kb