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Sena Karachanak,
Viola Grugni,
Simona Fornarino,
Desislava Nesheva,
Nadia Al-Zahery,
Vincenza Battaglia,
Valeria Carossa,
Yordan Yordanov,
Antonio Torroni,
Angel S Galabov,
Draga Toncheva, Ornella Semino
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ABSTRACT: To better define the structure and origin of the Bulgarian paternal gene pool, we have examined the Y-chromosome variation in 808 Bulgarian males. The analysis was performed by high-resolution genotyping of biallelic markers and by analyzing the STR variation within the most informative haplogroups. We found that the Y-chromosome gene pool in modern Bulgarians is primarily represented by Western Eurasian haplogroups with ∼ 40% belonging to haplogroups E-V13 and I-M423, and 20% to R-M17. Haplogroups common in the Middle East (J and G) and in South Western Asia (R-L23*) occur at frequencies of 19% and 5%, respectively. Haplogroups C, N and Q, distinctive for Altaic and Central Asian Turkic-speaking populations, occur at the negligible frequency of only 1.5%. Principal Component analyses group Bulgarians with European populations, apart from Central Asian Turkic-speaking groups and South Western Asia populations. Within the country, the genetic variation is structured in Western, Central and Eastern Bulgaria indicating that the Balkan Mountains have been permeable to human movements. The lineage analysis provided the following interesting results: (i) R-L23* is present in Eastern Bulgaria since the post glacial period; (ii) haplogroup E-V13 has a Mesolithic age in Bulgaria from where it expanded after the arrival of farming; (iii) haplogroup J-M241 probably reflects the Neolithic westward expansion of farmers from the earliest sites along the Black Sea. On the whole, in light of the most recent historical studies, which indicate a substantial proto-Bulgarian input to the contemporary Bulgarian people, our data suggest that a common paternal ancestry between the proto-Bulgarians and the Altaic and Central Asian Turkic-speaking populations either did not exist or was negligible.
PLoS ONE 01/2013; 8(3):e56779. · 4.09 Impact Factor
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Siiri Rootsi,
Natalie M Myres,
Alice A Lin,
Mari Järve,
Roy J King,
Ildus Kutuev,
Vicente M Cabrera,
Elza K Khusnutdinova,
Kärt Varendi,
Hovhannes Sahakyan, [......],
Massoud Houshmand,
Mohammad H Sanati,
Draga Toncheva,
Antonella Lisa, Ornella Semino,
Jacques Chiaroni,
Julie Di Cristofaro,
Richard Villems,
Toomas Kivisild,
Peter A Underhill
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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.European Journal of Human Genetics advance online publication, 16 May 2012; doi:10.1038/ejhg.2012.86.
European journal of human genetics: EJHG 05/2012; · 3.56 Impact Factor
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Maria Pala,
Anna Olivieri,
Alessandro Achilli,
Matteo Accetturo,
Ene Metspalu,
Maere Reidla,
Erika Tamm,
Monika Karmin,
Tuuli Reisberg,
Baharak Hooshiar Kashani, [......],
Vincent Macaulay,
Luísa Pereira,
Scott R Woodward,
William Davies,
Clive Gamble,
Douglas Baird, Ornella Semino,
Richard Villems,
Antonio Torroni,
Martin B Richards
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ABSTRACT: Human populations, along with those of many other species, are thought to have contracted into a number of refuge areas at the height of the last Ice Age. European populations are believed to be, to a large extent, the descendants of the inhabitants of these refugia, and some extant mtDNA lineages can be traced to refugia in Franco-Cantabria (haplogroups H1, H3, V, and U5b1), the Italian Peninsula (U5b3), and the East European Plain (U4 and U5a). Parts of the Near East, such as the Levant, were also continuously inhabited throughout the Last Glacial Maximum, but unlike western and eastern Europe, no archaeological or genetic evidence for Late Glacial expansions into Europe from the Near East has hitherto been discovered. Here we report, on the basis of an enlarged whole-genome mitochondrial database, that a substantial, perhaps predominant, signal from mitochondrial haplogroups J and T, previously thought to have spread primarily from the Near East into Europe with the Neolithic population, may in fact reflect dispersals during the Late Glacial period, ∼19-12 thousand years (ka) ago.
The American Journal of Human Genetics 05/2012; 90(5):915-24. · 10.60 Impact Factor
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Alessandro Achilli,
Anna Olivieri,
Pedro Soares,
Hovirag Lancioni,
Baharak Hooshiar Kashani,
Ugo A Perego,
Solomon G Nergadze,
Valeria Carossa,
Marco Santagostino,
Stefano Capomaccio, [......],
M Cecilia T Penedo,
Andrea Verini-Supplizi,
Massoud Houshmand,
Scott R Woodward, Ornella Semino,
Maurizio Silvestrelli,
Elena Giulotto,
Luísa Pereira,
Hans-Jürgen Bandelt,
Antonio Torroni
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ABSTRACT: Archaeological and genetic evidence concerning the time and mode of wild horse (Equus ferus) domestication is still debated. High levels of genetic diversity in horse mtDNA have been detected when analyzing the control region; recurrent mutations, however, tend to blur the structure of the phylogenetic tree. Here, we brought the horse mtDNA phylogeny to the highest level of molecular resolution by analyzing 83 mitochondrial genomes from modern horses across Asia, Europe, the Middle East, and the Americas. Our data reveal 18 major haplogroups (A-R) with radiation times that are mostly confined to the Neolithic and later periods and place the root of the phylogeny corresponding to the Ancestral Mare Mitogenome at ~130-160 thousand years ago. All haplogroups were detected in modern horses from Asia, but F was only found in E. przewalskii--the only remaining wild horse. Therefore, a wide range of matrilineal lineages from the extinct E. ferus underwent domestication in the Eurasian steppes during the Eneolithic period and were transmitted to modern E. caballus breeds. Importantly, now that the major horse haplogroups have been defined, each with diagnostic mutational motifs (in both the coding and control regions), these haplotypes could be easily used to (i) classify well-preserved ancient remains, (ii) (re)assess the haplogroup variation of modern breeds, including Thoroughbreds, and (iii) evaluate the possible role of mtDNA backgrounds in racehorse performance.
Proceedings of the National Academy of Sciences 02/2012; 109(7):2449-54. · 9.68 Impact Factor
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Baharak Hooshiar Kashani,
Ugo A Perego,
Anna Olivieri,
Norman Angerhofer,
Francesca Gandini,
Valeria Carossa,
Hovirag Lancioni, Ornella Semino,
Scott R Woodward,
Alessandro Achilli,
Antonio Torroni
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ABSTRACT: Recent analyses of mitochondrial genomes from Native Americans have brought the overall number of recognized maternal founding lineages from just four to a current count of 15. However, because of their relative low frequency, almost nothing is known for some of these lineages. This leaves a considerable void in understanding the events that led to the colonization of the Americas following the Last Glacial Maximum (LGM). In this study, we identified and completely sequenced 14 mitochondrial DNAs belonging to one extremely rare Native American lineage known as haplogroup C4c. Its age and geographical distribution raise the possibility that C4c marked the Paleo-Indian group(s) that entered North America from Beringia through the ice-free corridor between the Laurentide and Cordilleran ice sheets. The similarities in ages andgeographical distributions for C4c and the previously analyzed X2a lineage provide support to the scenario of a dual origin for Paleo-Indians. Taking into account that C4c is deeply rooted in the Asian portion of the mtDNA phylogeny and is indubitably of Asian origin, the finding that C4c and X2a are characterized by parallel genetic histories definitively dismisses the controversial hypothesis of an Atlantic glacial entry route into North America.
American Journal of Physical Anthropology 01/2012; 147(1):35-9. · 2.82 Impact Factor
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Viola Grugni,
Vincenza Battaglia,
Baharak Hooshiar Kashani,
Silvia Parolo,
Nadia Al-Zahery,
Alessandro Achilli,
Anna Olivieri,
Francesca Gandini,
Massoud Houshmand,
Mohammad Hossein Sanati,
Antonio Torroni, Ornella Semino
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ABSTRACT: Knowledge of high resolution Y-chromosome haplogroup diversification within Iran provides important geographic context regarding the spread and compartmentalization of male lineages in the Middle East and southwestern Asia. At present, the Iranian population is characterized by an extraordinary mix of different ethnic groups speaking a variety of Indo-Iranian, Semitic and Turkic languages. Despite these features, only few studies have investigated the multiethnic components of the Iranian gene pool. In this survey 938 Iranian male DNAs belonging to 15 ethnic groups from 14 Iranian provinces were analyzed for 84 Y-chromosome biallelic markers and 10 STRs. The results show an autochthonous but non-homogeneous ancient background mainly composed by J2a sub-clades with different external contributions. The phylogeography of the main haplogroups allowed identifying post-glacial and Neolithic expansions toward western Eurasia but also recent movements towards the Iranian region from western Eurasia (R1b-L23), Central Asia (Q-M25), Asia Minor (J2a-M92) and southern Mesopotamia (J1-Page08). In spite of the presence of important geographic barriers (Zagros and Alborz mountain ranges, and the Dasht-e Kavir and Dash-e Lut deserts) which may have limited gene flow, AMOVA analysis revealed that language, in addition to geography, has played an important role in shaping the nowadays Iranian gene pool. Overall, this study provides a portrait of the Y-chromosomal variation in Iran, useful for depicting a more comprehensive history of the peoples of this area as well as for reconstructing ancient migration routes. In addition, our results evidence the important role of the Iranian plateau as source and recipient of gene flow between culturally and genetically distinct populations.
PLoS ONE 01/2012; 7(7):e41252. · 4.09 Impact Factor
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Michelle de Saint Pierre,
Francesca Gandini,
Ugo A Perego,
Martin Bodner,
Alberto Gómez-Carballa,
Daniel Corach,
Norman Angerhofer,
Scott R Woodward, Ornella Semino,
Antonio Salas,
Walther Parson,
Mauricio Moraga,
Alessandro Achilli,
Antonio Torroni,
Anna Olivieri
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ABSTRACT: WITH ANALYSES OF ENTIRE MITOGENOMES, STUDIES OF NATIVE AMERICAN MITOCHONDRIAL DNA (MTDNA) VARIATION HAVE ENTERED THE FINAL PHASE OF PHYLOGENETIC REFINEMENT: the dissection of the founding haplogroups into clades that arose in America during and after human arrival and spread. Ages and geographic distributions of these clades could provide novel clues on the colonization processes of the different regions of the double continent. As for the Southern Cone of South America, this approach has recently allowed the identification of two local clades (D1g and D1j) whose age estimates agree with the dating of the earliest archaeological sites in South America, indicating that Paleo-Indians might have reached that region from Beringia in less than 2000 years. In this study, we sequenced 46 mitogenomes belonging to two additional clades, termed B2i2 (former B2l) and C1b13, which were recently identified on the basis of mtDNA control-region data and whose geographical distributions appear to be restricted to Chile and Argentina. We confirm that their mutational motifs most likely arose in the Southern Cone region. However, the age estimate for B2i2 and C1b13 (11-13,000 years) appears to be younger than those of other local clades. The difference could reflect the different evolutionary origins of the distinct South American-specific sub-haplogroups, with some being already present, at different times and locations, at the very front of the expansion wave in South America, and others originating later in situ, when the tribalization process had already begun. A delayed origin of a few thousand years in one of the locally derived populations, possibly in the central part of Chile, would have limited the geographical and ethnic diffusion of B2i2 and explain the present-day occurrence that appears to be mainly confined to the Tehuelche and Araucanian-speaking groups.
PLoS ONE 01/2012; 7(12):e51311. · 4.09 Impact Factor
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Sena Karachanak,
Valeria Carossa,
Desislava Nesheva,
Anna Olivieri,
Maria Pala,
Baharak Hooshiar Kashani,
Viola Grugni,
Vincenza Battaglia,
Alessandro Achilli,
Yordan Yordanov,
Angel S Galabov, Ornella Semino,
Draga Toncheva,
Antonio Torroni
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ABSTRACT: To define the matrilineal relationships between Bulgarians and other European populations, we have evaluated the mitochondrial DNA (mtDNA) variation in a sample of 855 Bulgarian subjects from the mtDNA perspective. The molecular survey was performed by sequencing ∼750 bp of the control region, which resulted in 557 different haplotypes, and by a subsequent restriction fragment length polymorphism analysis to confirm haplogroup/subhaplogroup affiliation. The classification was carried out according to the most updated criteria as reported by van Oven and Kayser (Hum Mutat 30:386-394, 2009), allowing the identification of 45 mitochondrial clades. The observed pattern of mtDNA variation indicates that the Bulgarian mitochondrial pool is geographically homogeneous across the country, and that is characterized by an overall extremely high frequency of western Eurasian lineages. In the principal component analysis, Bulgarians locate in an intermediate position between Eastern European and Mediterranean populations, which is in agreement with historical events. Thus, while the Mediterranean legacy could be attributed to the Thracians, indigenous people that firstly inhabited the Balkans, the Eastern contribution is likely due to the Proto-Bulgarians originating from the Middle East and to the Slavs migrating from northeast Europe.
Deutsche Zeitschrift für die Gesamte Gerichtliche Medizin 06/2011; 126(4):497-503. · 2.59 Impact Factor
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Roy J King,
Julie Di Cristofaro,
Anastasia Kouvatsi,
Costas Triantaphyllidis,
Walter Scheidel,
Natalie M Myres,
Alice A Lin,
Alexandre Eissautier,
Michael Mitchell,
Didier Binder, Ornella Semino,
Andrea Novelletto,
Peter A Underhill,
Jacques Chiaroni
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ABSTRACT: 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).
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.
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.
BMC Evolutionary Biology 03/2011; 11:69. · 3.52 Impact Factor
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Alessandro Achilli,
Anna Olivieri,
Maria Pala,
Baharak Hooshiar Kashani,
Valeria Carossa,
Ugo A Perego,
Francesca Gandini,
Aurelia Santoro,
Vincenza Battaglia,
Viola Grugni, [......],
Massimo Boemi,
Ivano Testa, Ornella Semino,
Antonio Ceriello,
Liana Spazzafumo,
Maria Nicola Gadaleta,
Maurizio Marra,
Roberto Testa,
Claudio Franceschi,
Antonio Torroni
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ABSTRACT: Mitochondrial dysfunction has been implicated in rare and common forms of type 2 diabetes (T2DM). Additionally, rare mitochondrial DNA (mtDNA) mutations have been shown to be causal for T2DM pathogenesis. So far, many studies have investigated the possibility that mtDNA variation might affect the risk of T2DM, however, when found, haplogroup association has been rarely replicated, even in related populations, possibly due to an inadequate level of haplogroup resolution. Effects of mtDNA variation on diabetes complications have also been proposed. However, additional studies evaluating the mitochondrial role on both T2DM and related complications are badly needed. To test the hypothesis of a mitochondrial genome effect on diabetes and its complications, we genotyped the mtDNAs of 466 T2DM patients and 438 controls from a regional population of central Italy (Marche). Based on the most updated mtDNA phylogeny, all 904 samples were classified into 57 different mitochondrial sub-haplogroups, thus reaching an unprecedented level of resolution. We then evaluated whether the susceptibility of developing T2DM or its complications differed among the identified haplogroups, considering also the potential effects of phenotypical and clinical variables. MtDNA backgrounds, even when based on a refined haplogroup classification, do not appear to play a role in developing T2DM despite a possible protective effect for the common European haplogroup H1, which harbors the G3010A transition in the MTRNR2 gene. In contrast, our data indicate that different mitochondrial haplogroups are significantly associated with an increased risk of specific diabetes complications: H (the most frequent European haplogroup) with retinopathy, H3 with neuropathy, U3 with nephropathy, and V with renal failure.
PLoS ONE 01/2011; 6(6):e21029. · 4.09 Impact Factor
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ABSTRACT: For millennia, the southern part of the Mesopotamia has been a wetland region generated by the Tigris and Euphrates rivers before flowing into the Gulf. This area has been occupied by human communities since ancient times and the present-day inhabitants, the Marsh Arabs, are considered the population with the strongest link to ancient Sumerians. Popular tradition, however, considers the Marsh Arabs as a foreign group, of unknown origin, which arrived in the marshlands when the rearing of water buffalo was introduced to the region.
To shed some light on the paternal and maternal origin of this population, Y chromosome and mitochondrial DNA (mtDNA) variation was surveyed in 143 Marsh Arabs and in a large sample of Iraqi controls. Analyses of the haplogroups and sub-haplogroups observed in the Marsh Arabs revealed a prevalent autochthonous Middle Eastern component for both male and female gene pools, with weak South-West Asian and African contributions, more evident in mtDNA. A higher male than female homogeneity is characteristic of the Marsh Arab gene pool, likely due to a strong male genetic drift determined by socio-cultural factors (patrilocality, polygamy, unequal male and female migration rates).
Evidence of genetic stratification ascribable to the Sumerian development was provided by the Y-chromosome data where the J1-Page08 branch reveals a local expansion, almost contemporary with the Sumerian City State period that characterized Southern Mesopotamia. On the other hand, a more ancient background shared with Northern Mesopotamia is revealed by the less represented Y-chromosome lineage J1-M267*. Overall our results indicate that the introduction of water buffalo breeding and rice farming, most likely from the Indian sub-continent, only marginally affected the gene pool of autochthonous people of the region. Furthermore, a prevalent Middle Eastern ancestry of the modern population of the marshes of southern Iraq implies that if the Marsh Arabs are descendants of the ancient Sumerians, also the Sumerians were most likely autochthonous and not of Indian or South Asian ancestry.
BMC Evolutionary Biology 01/2011; 11:288. · 3.52 Impact Factor
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Ugo A Perego,
Norman Angerhofer,
Maria Pala,
Anna Olivieri,
Hovirag Lancioni,
Baharak Hooshiar Kashani,
Valeria Carossa,
Jayne E Ekins,
Alberto Gómez-Carballa,
Gabriela Huber, [......],
Daniel Corach,
Nora Babudri,
Fausto Panara,
Natalie M Myres,
Walther Parson, Ornella Semino,
Antonio Salas,
Scott R Woodward,
Alessandro Achilli,
Antonio Torroni
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ABSTRACT: Pan-American mitochondrial DNA (mtDNA) haplogroup C1 has been recently subdivided into three branches, two of which (C1b and C1c) are characterized by ages and geographical distributions that are indicative of an early arrival from Beringia with Paleo-Indians. In contrast, the estimated ages of C1d--the third subset of C1--looked too young to fit the above scenario. To define the origin of this enigmatic C1 branch, we completely sequenced 63 C1d mitochondrial genomes from a wide range of geographically diverse, mixed, and indigenous American populations. The revised phylogeny not only brings the age of C1d within the range of that of its two sister clades, but reveals that there were two C1d founder genomes for Paleo-Indians. Thus, the recognized maternal founding lineages of Native Americans are at least 15, indicating that the overall number of Beringian or Asian founder mitochondrial genomes will probably increase extensively when all Native American haplogroups reach the same level of phylogenetic and genomic resolution as obtained here for C1d.
Genome Research 09/2010; 20(9):1174-9. · 13.61 Impact Factor
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Doron M Behar,
Bayazit Yunusbayev,
Mait Metspalu,
Ene Metspalu,
Saharon Rosset,
Jüri Parik,
Siiri Rootsi,
Gyaneshwer Chaubey,
Ildus Kutuev,
Guennady Yudkovsky, [......],
Oleg Balanovsky, Ornella Semino,
Luisa Pereira,
David Comas,
David Gurwitz,
Batsheva Bonne-Tamir,
Tudor Parfitt,
Michael F Hammer,
Karl Skorecki,
Richard Villems
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ABSTRACT: Contemporary Jews comprise an aggregate of ethno-religious communities whose worldwide members identify with each other through various shared religious, historical and cultural traditions. Historical evidence suggests common origins in the Middle East, followed by migrations leading to the establishment of communities of Jews in Europe, Africa and Asia, in what is termed the Jewish Diaspora. This complex demographic history imposes special challenges in attempting to address the genetic structure of the Jewish people. Although many genetic studies have shed light on Jewish origins and on diseases prevalent among Jewish communities, including studies focusing on uniparentally and biparentally inherited markers, genome-wide patterns of variation across the vast geographic span of Jewish Diaspora communities and their respective neighbours have yet to be addressed. Here we use high-density bead arrays to genotype individuals from 14 Jewish Diaspora communities and compare these patterns of genome-wide diversity with those from 69 Old World non-Jewish populations, of which 25 have not previously been reported. These samples were carefully chosen to provide comprehensive comparisons between Jewish and non-Jewish populations in the Diaspora, as well as with non-Jewish populations from the Middle East and north Africa. Principal component and structure-like analyses identify previously unrecognized genetic substructure within the Middle East. Most Jewish samples form a remarkably tight subcluster that overlies Druze and Cypriot samples but not samples from other Levantine populations or paired Diaspora host populations. In contrast, Ethiopian Jews (Beta Israel) and Indian Jews (Bene Israel and Cochini) cluster with neighbouring autochthonous populations in Ethiopia and western India, respectively, despite a clear paternal link between the Bene Israel and the Levant. These results cast light on the variegated genetic architecture of the Middle East, and trace the origins of most Jewish Diaspora communities to the Levant.
Nature 07/2010; 466(7303):238-42. · 36.28 Impact Factor
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ABSTRACT: A new timescale has recently been established for human mitochondrial DNA (mtDNA) lineages, making mtDNA at present the most informative genetic marker system for studying European prehistory. Here, we review the new chronology and compare mtDNA with Y-chromosome patterns, in order to summarize what we have learnt from archaeogenetics concerning five episodes over the past 50,000 years which significantly contributed to the settlement history of Europe: the pioneer colonisation of the Upper Palaeolithic, the Late Glacial re-colonisation of the continent from southern refugia after the Last Glacial Maximum, the postglacial re-colonization of deserted areas after the Younger Dryas cold snap, the arrival of Near Easterners with an incipient Neolithic package, and the small-scale migrations along continent-wide economic exchange networks beginning with the Copper Age. The available data from uniparental genetic systems have already transformed our view of the prehistory of Europe, but our knowledge of these processes remains limited. Nevertheless, their legacy remains as sedimentary layers in the gene pool of modern Europeans, and our understanding of them will improve substantially when more mtDNAs are completely sequenced, the Y chromosome more thoroughly analysed, and haplotype blocks of the autosomal genome become amenable to phylogeographic studies.
Current biology: CB 02/2010; 20(4):R174-83. · 10.99 Impact Factor
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Peter A Underhill,
Natalie M Myres,
Siiri Rootsi,
Mait Metspalu,
Lev A Zhivotovsky,
Roy J King,
Alice A Lin,
Cheryl-Emiliane T Chow, Ornella Semino,
Vincenza Battaglia, [......],
Marian Baldovic,
Rene J Herrera,
Kumarasamy Thangaraj,
Vijay Singh,
Lalji Singh,
Partha Majumder,
Pavao Rudan,
Dragan Primorac,
Richard Villems,
Toomas Kivisild
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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.Keywords: Y chromosome; haplogroup R1a; human evolution; population genetics
European Journal of HumanGenetics 11/2009; 18(4):479-484. · 4.40 Impact Factor
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Jacques Chiaroni,
Roy J King,
Natalie M Myres,
Brenna M Henn,
Axel Ducourneau,
Michael J Mitchell,
Gilles Boetsch,
Issa Sheikha,
Alice A Lin,
Mahnoosh Nik-Ahd,
Jabeen Ahmad,
Francesca Lattanzi,
Rene J Herrera,
Muntaser E Ibrahim,
Aaron Brody, Ornella Semino,
Toomas Kivisild,
Peter A Underhill
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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.
European journal of human genetics: EJHG 10/2009; 18(3):348-53. · 3.56 Impact Factor
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ABSTRACT: Central Asia and the Indian subcontinent represent an area considered as a source and a reservoir for human genetic diversity, with many markers taking root here, most of which are the ancestral state of eastern and western haplogroups, while others are local. Between these two regions, Terai (Nepal) is a pivotal passageway allowing, in different times, multiple population interactions, although because of its highly malarial environment, it was scarcely inhabited until a few decades ago, when malaria was eradicated. One of the oldest and the largest indigenous people of Terai is represented by the malaria resistant Tharus, whose gene pool could still retain traces of ancient complex interactions. Until now, however, investigations on their genetic structure have been scarce mainly identifying East Asian signatures.
High-resolution analyses of mitochondrial-DNA (including 34 complete sequences) and Y-chromosome (67 SNPs and 12 STRs) variations carried out in 173 Tharus (two groups from Central and one from Eastern Terai), and 104 Indians (Hindus from Terai and New Delhi and tribals from Andhra Pradesh) allowed the identification of three principal components: East Asian, West Eurasian and Indian, the last including both local and inter-regional sub-components, at least for the Y chromosome.
Although remarkable quantitative and qualitative differences appear among the various population groups and also between sexes within the same group, many mitochondrial-DNA and Y-chromosome lineages are shared or derived from ancient Indian haplogroups, thus revealing a deep shared ancestry between Tharus and Indians. Interestingly, the local Y-chromosome Indian component observed in the Andhra-Pradesh tribals is present in all Tharu groups, whereas the inter-regional component strongly prevails in the two Hindu samples and other Nepalese populations.The complete sequencing of mtDNAs from unresolved haplogroups also provided informative markers that greatly improved the mtDNA phylogeny and allowed the identification of ancient relationships between Tharus and Malaysia, the Andaman Islands and Japan as well as between India and North and East Africa. Overall, this study gives a paradigmatic example of the importance of genetic isolates in revealing variants not easily detectable in the general population.
BMC Evolutionary Biology 08/2009; 9:154. · 3.52 Impact Factor
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Maria Pala,
Alessandro Achilli,
Anna Olivieri,
Baharak Hooshiar Kashani,
Ugo A Perego,
Daria Sanna,
Ene Metspalu,
Kristiina Tambets,
Erika Tamm,
Matteo Accetturo, [......],
Francesca Brisighelli,
Scott R Woodward,
Paolo Francalacci,
Walther Parson,
Antonio Salas,
Doron M Behar,
Richard Villems, Ornella Semino,
Hans-Jürgen Bandelt,
Antonio Torroni
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ABSTRACT: There are extensive data indicating that some glacial refuge zones of southern Europe (Franco-Cantabria, Balkans, and Ukraine) were major genetic sources for the human recolonization of the continent at the beginning of the Holocene. Intriguingly, there is no genetic evidence that the refuge area located in the Italian Peninsula contributed to this process. Here we show, through phylogeographic analyses of mitochondrial DNA (mtDNA) variation performed at the highest level of molecular resolution (52 entire mitochondrial genomes), that the most likely homeland for U5b3-a haplogroup present at a very low frequency across Europe-was the Italian Peninsula. In contrast to mtDNA haplogroups that expanded from other refugia, the Holocene expansion of haplogroup U5b3 toward the North was restricted by the Alps and occurred only along the Mediterranean coasts, mainly toward nearby Provence (southern France). From there, approximately 7,000-9,000 years ago, a subclade of this haplogroup moved to Sardinia, possibly as a result of the obsidian trade that linked the two regions, leaving a distinctive signature in the modern people of the island. This scenario strikingly matches the age, distribution, and postulated geographic source of a Sardinian Y chromosome haplogroup (I2a2-M26), a paradigmatic case in the European context of a founder event marking both female and male lineages.
The American Journal of Human Genetics 07/2009; 84(6):814-21. · 10.60 Impact Factor
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Etienne Patin,
Guillaume Laval,
Luis B Barreiro,
Antonio Salas, Ornella Semino,
Silvana Santachiara-Benerecetti,
Kenneth K Kidd,
Judith R Kidd,
Lolke Van der Veen,
Jean-Marie Hombert,
Antoine Gessain,
Alain Froment,
Serge Bahuchet,
Evelyne Heyer,
Lluís Quintana-Murci
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ABSTRACT: The transition from hunting and gathering to farming involved a major cultural innovation that has spread rapidly over most of the globe in the last ten millennia. In sub-Saharan Africa, hunter-gatherers have begun to shift toward an agriculture-based lifestyle over the last 5,000 years. Only a few populations still base their mode of subsistence on hunting and gathering. The Pygmies are considered to be the largest group of mobile hunter-gatherers of Africa. They dwell in equatorial rainforests and are characterized by their short mean stature. However, little is known about the chronology of the demographic events-size changes, population splits, and gene flow--ultimately giving rise to contemporary Pygmy (Western and Eastern) groups and neighboring agricultural populations. We studied the branching history of Pygmy hunter-gatherers and agricultural populations from Africa and estimated separation times and gene flow between these populations. We resequenced 24 independent noncoding regions across the genome, corresponding to a total of approximately 33 kb per individual, in 236 samples from seven Pygmy and five agricultural populations dispersed over the African continent. We used simulation-based inference to identify the historical model best fitting our data. The model identified included the early divergence of the ancestors of Pygmy hunter-gatherers and farming populations approximately 60,000 years ago, followed by a split of the Pygmies' ancestors into the Western and Eastern Pygmy groups approximately 20,000 years ago. Our findings increase knowledge of the history of the peopling of the African continent in a region lacking archaeological data. An appreciation of the demographic and adaptive history of African populations with different modes of subsistence should improve our understanding of the influence of human lifestyles on genome diversity.
PLoS Genetics 05/2009; 5(4):e1000448. · 8.69 Impact Factor
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Ugo A Perego,
Alessandro Achilli,
Norman Angerhofer,
Matteo Accetturo,
Maria Pala,
Anna Olivieri,
Baharak Hooshiar Kashani,
Kathleen H Ritchie,
Rosaria Scozzari,
Qing-Peng Kong,
Natalie M Myres,
Antonio Salas, Ornella Semino,
Hans-Jürgen Bandelt,
Scott R Woodward,
Antonio Torroni
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ABSTRACT: It is widely accepted that the ancestors of Native Americans arrived in the New World via Beringia approximately 10 to 30 thousand years ago (kya). However, the arrival time(s), number of expansion events, and migration routes into the Western Hemisphere remain controversial because linguistic, archaeological, and genetic evidence have not yet provided coherent answers. Notably, most of the genetic evidence has been acquired from the analysis of the common pan-American mitochondrial DNA (mtDNA) haplogroups. In this study, we have instead identified and analyzed mtDNAs belonging to two rare Native American haplogroups named D4h3 and X2a.
Phylogeographic analyses at the highest level of molecular resolution (69 entire mitochondrial genomes) reveal that two almost concomitant paths of migration from Beringia led to the Paleo-Indian dispersal approximately 15-17 kya. Haplogroup D4h3 spread into the Americas along the Pacific coast, whereas X2a entered through the ice-free corridor between the Laurentide and Cordilleran ice sheets. The examination of an additional 276 entire mtDNA sequences provides similar entry times for all common Native American haplogroups, thus indicating at least a dual origin for Paleo- Indians.
A dual origin for the first Americans is a striking novelty from the genetic point of view, and it makes plausible a scenario positing that within a rather short period of time, there may have been several entries into the Americas from a dynamically changing Beringian source. Moreover, this implies that most probably more than one language family was carried along with the Paleo-Indians.
Current biology: CB 02/2009; 19(1):1-8. · 10.99 Impact Factor
