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Rębała, Krzysztof et al. ; Homogeneous Proto-Slavic genetic substrate and/or extensive mixing after World War II were suggested to explain homogeneity of contemporary Polish paternal lineages. Alternatively, Polish local populations might have displayed pre-war genetic heterogeneity owing to genetic drift and/or gene flow with neighbouring populations. Although sharp genetic discontinuity along the political border between Poland and Germany indisputably results from war-mediated resettlements and homogenisation, it remained unknown whether Y-chromosomal diversity in ethnically/linguistically defined populations was clinal or discontinuous before the war. In order to answer these questions and elucidate early Slavic migrations, 1156 individuals from several Slavic and German populations were analysed, including Polish pre-war regional populations and an autochthonous Slavic population from Germany. Y chromosomes were assigned to 39 haplogroups and genotyped for 19 STRs. Genetic distances revealed similar degree of differentiation of Slavic-speaking pre-war populations from German populations irrespective of duration and intensity of contacts with German speakers. Admixture estimates showed minor Slavic paternal ancestry (∼20%) in modern eastern Germans and hardly detectable German paternal ancestry in Slavs neighbouring German populations for centuries. BATWING analysis of isolated Slavic populations revealed that their divergence was preceded by rapid demographic growth, undermining theory that Slavic expansion was primarily linguistic rather than population spread. Polish pre-war regional populations showed within-group heterogeneity and lower STR variation within R-M17 subclades compared with modern populations, which might have been homogenised by war resettlements. Our results suggest that genetic studies on early human history in the Vistula and Oder basins should rely on reconstructed pre-war rather than modern populations. © 2013 Macmillan Publishers Limited All rights reserved. ; KR was supported by the Foundation for Polish Science within the KOLUMB Programme and by the 'Crescendum Est – Polonia' Foundation. BM-C and DC were supported by MCINN grant CGL2010-14944/BOS. ; Peer Reviewed

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia. ; D.F. and M.N. were supported by Irish Research Council grants GOIPG/2013/36 and GOIPD/2013/1, respectively. Q.F. was funded by the Bureau of International Cooperation of the Chinese Academy of Sciences, the National Natural Science Foundation of China (L1524016) and the Chinese Academy of Sciences Discipline Development Strategy Project (2015-DX-C-03). The Scottish diversity data was funded by the Chief Scientist Office of the Scottish Government Health Directorates (CZD/16/6), the Scottish Funding Council (HR03006), and a project grant from the Scottish Executive Health Department, Chief Scientist Office (CZB/4/285). M.S., A.Tön., M.B. and P.K. were supported by the German Research Foundation (CRC 1052; B01, B03, C01). M.S.-P. was funded by a Wenner-Gren Foundation Dissertation Fieldwork grant (9005), and by the National Science Foundation DDRIG (BCS-1455744). P.K. was funded by the Federal Ministry of Education and Research, Germany (FKZ: 01EO1501). J.F.W. acknowledge the MRC 'QTL in Health and Disease' programme grant. The Romanian diversity data was supported by the EC Commission, Directorate General XII (Supplementary Agreement ERBCIPDCT 940038 to the Contract ERBCHRXCT 920032, coordinated by A. Piazza, Turin, Italy). O.S. and A.Tor. were supported by the University of Pavia (MIGRAT-IN-G) and the Italian Ministry of Education, University and Research: Progetti Ricerca Interesse Nazionale 2012. The Raqefet Cave Natufian project was supported by funds from the National Geographic Society (grant 8915-11), the Wenner-Gren Foundation (grant 7481) and the Irene Levi-Sala CARE Foundation, while radiocarbon dating on the samples was funded by the Israel Science Foundation (grant 475/10; E. Boaretto). R.P. was supported by ERC starting grant ADNABIOARC (263441). D.R. was supported by NIH grant GM100233 and by NSF HOMINID BCS-1032255

We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages. ; J. Kr., A.M. and C.P. are grateful for support from DFG grant number KR 4015/1-1, the Carl-Zeiss Foundation and the Baden Württemberg Foundation. S. P., G. R., Q. F., C. F., K. P., S.C. and J.Ke. acknowledge support from the Presidential Innovation Fund of the Max Planck Society. G.R. was supported by an NSERC fellowship. J.G.S. acknowledges use of the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by NSF grant number OCI-1053575. E.B. and O.B. were supported by RFBR grants 13-06-00670, 13-04-01711, 13-04-90420. B.M. was supported by grants OTKA 73430 and 103983. A.Saj. was supported by a Finnish Professor Pool (Paulo Foundation) Grant. The Lithuanian sampling was supported by the LITGEN project (VP1-3.1-ŠMM-07-K-01-013), funded by the European Social Fund under the Global Grant Measure. A.S. was supported by Spanish grants SAF2011-26983 and EM 2012/045. O.U. was supported by Ukrainian SFFS grant F53.4/071. S.A.T. was supported by NIH Pioneer Award 8DP1ES022577-04 and NSF HOMINID award BCS-0827436. K.T. was supported by an Indian CSIR Network Project (GENESIS: BSC0121). L.S. was supported by an Indian CSIR Bhatnagar Fellowship. R.V., M.M., J.P. and E.M. were supported by the European Union Regional Development Fund through the Centre of Excellence in Genomics to the Estonian Biocentre and University of Tartu and by an Estonian Basic Research grant SF0270177As08. M.M. was additionally supported by Estonian Science Foundation grant number 8973. J.G.S. and M.S. were supported by NIH grant GM40282. P.H.S. and E.E.E. were supported by NIH grants HG004120 and HG002385. D.R. and N.P. were supported by NSF HOMINID award BCS-1032255 and NIH grant GM100233. This project has been funded in part with federal funds from the National Cancer Institute, National Institutes of Health, under contract HHSN26120080001E. This Research was supported in part by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research

Boattini, Alessio et al.-- The Genographic Consortium ; Located in the center of the Mediterranean landscape and with an extensive coastal line, the territory of what is today Italy has played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean Basin. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia (involving the overlapping of different cultural and demic strata) has shaped the pattern of the modern Italian genetic structure. With the aim of disentangling this pattern and understanding which processes more importantly shaped the distribution of diversity, we have analyzed the uniparentally-inherited markers in ∼900 individuals from an extensive sampling across the Italian peninsula, Sardinia and Sicily. Spatial PCAs and DAPCs revealed a sex-biased pattern indicating different demographic histories for males and females. Besides the genetic outlier position of Sardinians, a North West-South East Y-chromosome structure is found in continental Italy. Such structure is in agreement with recent archeological syntheses indicating two independent and parallel processes of Neolithisation. In addition, date estimates pinpoint the importance of the cultural and demographic events during the late Neolithic and Metal Ages. On the other hand, mitochondrial diversity is distributed more homogeneously in agreement with older population events that might be related to the presence of an Italian Refugium during the last glacial period in Europe. © 2013 Boattini et al. ; This study was supported by Strategic Project 2006-09 from the University of Bologna to DP and from MIUR PRIN 2007 and 2009 Grants to DP. The project was also supported by the Spanish Government grant CGL2010-14944/BOS. ; Peer Reviewed

Mendizabal, Isabel et al. ; The Romani, the largest European minority group with approximately 11 million people [1], constitute a mosaic of languages, religions, and lifestyles while sharing a distinct social heritage. Linguistic [2] and genetic [3-8] studies have located the Romani origins in the Indian subcontinent. However, a genome-wide perspective on Romani origins and population substructure, as well as a detailed reconstruction of their demographic history, has yet to be provided. Our analyses based on genome-wide data from 13 Romani groups collected across Europe suggest that the Romani diaspora constitutes a single initial founder population that originated in north/northwestern India ∿1.5 thousand years ago (kya). Our results further indicate that after a rapid migration with moderate gene flow from the Near or Middle East, the European spread of the Romani people was via the Balkans starting ∿0.9 kya. The strong population substructure and high levels of homozygosity we found in the European Romani are in line with genetic isolation as well as differential gene flow in time and space with non-Romani Europeans. Overall, our genome-wide study sheds new light on the origins and demographic history of European Romani. © 2012 Elsevier Ltd. ; I.M. was supported by a PhD grant by the Basque Government (Hezkuntza, Unibertsitate eta Ikerketa Saila, Eusko Jaurlaritza, BFI107.4). O.L., A.W., and M.K. were supported by the Erasmus MC University Medical Center Rotterdam. U.M.M. was supported by a PhD grant by Universitat Pompeu Fabra. M.G.N. was supported by a Vici grant of the Netherlands Organization of Scientific Research. L.G. was supported by an Invited Professor grant from CAPES/Brazil. A.M. was supported by the Estonian Government grant SF0180142s08. This study was supported in parts by Spanish Government MCINN grant CGL2010-14944/BOS to D.C., Czech Republic Ministry of Health grants CZ.2.16/3.1.00/24022 and 00064203 to M.M., Republic of Serbia Ministry of Education and Science grant ON173008 to D.R., Belgium University of Antwerp grant IWS BOFUA 2008/23064 to A.J., and Portuguese Foundation for Science and Technology (FCT) project grant PTDC/ANT/70413/2006 to L.G. IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Education and Science and is partially supported by the FCT. ; Peer Reviewed

This article is published with open access at Springerlink.com.-- This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited. ; African Pygmies are hunter-gatherer populations from the equatorial rainforest that present the lowest height averages among humans. The biological basis and the putative adaptive role of the short stature of Pygmy populations has been one of the most intriguing topics for human biologists in the last century, which still remains elusive. Worldwide convergent evolution of the Pygmy size suggests the presence of strong selective pressures on the phenotype. We developed a novel approach to survey the genetic architecture of phenotypes and applied it to study the genomic covariation between allele frequencies and height measurements among Pygmy and non-Pygmy populations. Among the regions that were most associated with the phenotype, we identified a significant excess of genes with pivotal roles in bone homeostasis, such as PPPT3B and the height associated SUPT3H-RUNX2. We hypothesize that skeletal remodeling could be a key biological process underlying the Pygmy phenotype. In addition, we showed that these regions have most likely evolved under positive selection. These results constitute the first genetic hint of adaptive evolution in the African Pygmy phenotype, which is consistent with the independent emergence of the Pygmy height in other continents with similar environments. © 2012 Springer-Verlag. ; IM was supported by a PhD fellowship by the Basque Government (Hezkuntza, Unibertsitate eta Ikerketa Saila, Eusko Jaurlaritza, BFI107.4); UMM was supported by a PhD fellowship from Universitat Pompeu Fabra. This work was partially supported by the Spanish Ministry of Science and Innovation (Grant CGL2010-14944/BOS), Direcció General de Recerca, Generalitat de Catalunya (2009SGR-1101) and by the Netherlands Forensic Institute (NFI), the Erasmus MC University Medical Center Rotterdam, and the Netherlands Genomics Initiative (NGI)/Netherlands Organization for Scientific Research (NWO) within the framework of the Forensic Genomics Consortium Netherlands (FGCN). ; Peer Reviewed

Genetic patterns of inter-population variation are a result of different demographic and adaptive histories, which gradually shape the frequency distribution of the variants. However, the study of clinically relevant mutations has a Eurocentric bias. The Romani, the largest transnational minority ethnic group in Europe, originated in South Asia and received extensive gene flow from West Eurasia. Most medical genetic studies have only explored founder mutations related to Mendelian disorders in this population. Here we analyze exome sequences and genome-wide array data of 89 healthy Spanish Roma individuals to study complex traits and disease. We apply a different framework and focus on variants with both increased and decreased allele frequencies, taking into account their local ancestry. We report several OMIM traits enriched for genes with deleterious variants showing increased frequencies in Roma or in non-Roma (e.g., obesity is enriched in Roma, with an associated variant linked to South Asian ancestry; while non-insulin dependent diabetes is enriched in non-Roma Europeans). In addition, previously reported pathogenic variants also show differences among populations, where some variants segregating at low frequency in non-Roma are virtually absent in the Roma. Lastly, we describe frequency changes in drug-response variation, where many of the variants increased in Roma are clinically associated with metabolic and cardiovascular-related drugs. These results suggest that clinically relevant variation in Roma cannot only be characterized in terms of founder mutations. Instead, we observe frequency differences compared to non-Roma: some variants are absent, while other have drifted to higher frequencies. As a result of the admixture events, these clinically damaging variants can be traced back to both European and South Asian-related ancestries. This can be attributed to a different prevalence of some genetic disorders or to the fact that genetic susceptibility variants are mostly studied in populations of European descent, and can differ in individuals with different ancestries. ; This study was supported by the Spanish Ministry of Science, Innovation and Universities (MCIU), Agencia Estatal de Investigación (AEI) grant number PID2019-106485GB-I00/AEI/10.13039/501100011033, and "Unidad de Excelencia María de Maeztu" (AEI, CEX2018-000792-M). NF-P was supported by a FPU17/03501 fellowship. ; With funding from the Spanish government through the "Severo Ochoa Centre of Excellence" accreditation (CEX2018-000792-M). ; Peer reviewed

The Iberian Peninsula is a well-delimited geographic region with a rich and complex human history. However, the causes of its genetic structure and past migratory dynamics are not yet fully understood. In order to shed light on them, here we evaluated the gene flow and genetic structure throughout the Iberian Peninsula with spatially explicit modelling applied to a georeferenced genetic dataset composed of genome-wide SNPs from 746 individuals belonging to 17 different regions of the Peninsula. We found contrasting patterns of genetic structure throughout Iberia. In particular, we identified strong patterns of genetic differentiation caused by relevant barriers to gene flow in northern regions and, on the other hand, a large genetic similarity in central and southern regions. In addition, our results showed a preferential north to south migratory dynamics and suggest a sex-biased dispersal in Mediterranean and southern regions. The estimated genetic patterns did not fit with the geographical relief of the Iberian landscape and they rather seem to follow political and linguistic territorial boundaries.

The Iberian Peninsula is a well-delimited geographic region with a rich and complex human history. However, the causes of its genetic structure and past migratory dynamics are not yet fully understood. In order to shed light on them, here we evaluated the gene flow and genetic structure throughout the Iberian Peninsula with spatially explicit modelling applied to a georeferenced genetic dataset composed of genome-wide SNPs from 746 individuals belonging to 17 different regions of the Peninsula. We found contrasting patterns of genetic structure throughout Iberia. In particular, we identified strong patterns of genetic differentiation caused by relevant barriers to gene flow in northern regions and, on the other hand, a large genetic similarity in central and southern regions. In addition, our results showed a preferential north to south migratory dynamics and suggest a sex-biased dispersal in Mediterranean and southern regions. The estimated genetic patterns did not fit with the geographical relief of the Iberian landscape and they rather seem to follow political and linguistic territorial boundaries. ; IPATIMUP integrates the i3S Research Unit, which is partially supported by FCT in the framework of the project "Institute for Research and Innovation in Health Sciences" (POCI-01-0145-FEDER-007274). J.P. and A.M.L. are funded by the Portuguese Government through the FCT fellowship SFRH/BD/97200/2013 and the research contract IF/01262/2014, respectively. M.A. was supported by the "Ramón y Cajal" grant RYC-2015-18241 from the Spanish Government. D.C. was supported by the Spanish grant CGL2016-75389-P (AEI, MINEICO/FEDER, UE), and "Unidad María de Maeztu" funded by the MINECO (MDM-2014-0370).

The Iberian Peninsula is a well-delimited geographic region with a rich and complex human history. However, the causes of its genetic structure and past migratory dynamics are not yet fully understood. In order to shed light on them, here we evaluated the gene flow and genetic structure throughout the Iberian Peninsula with spatially explicit modelling applied to a georeferenced genetic dataset composed of genome-wide SNPs from 746 individuals belonging to 17 different regions of the Peninsula. We found contrasting patterns of genetic structure throughout Iberia. In particular, we identified strong patterns of genetic differentiation caused by relevant barriers to gene flow in northern regions and, on the other hand, a large genetic similarity in central and southern regions. In addition, our results showed a preferential north to south migratory dynamics and suggest a sex-biased dispersal in Mediterranean and southern regions. The estimated genetic patterns did not fit with the geographical relief of the Iberian landscape and they rather seem to follow political and linguistic territorial boundaries. ; IPATIMUP integrates the i3S Research Unit, which is partially supported by FCT in the framework of the project "Institute for Research and Innovation in Health Sciences" (POCI-01-0145-FEDER-007274). J.P. and A.M.L. are funded by the Portuguese Government through the FCT fellowship SFRH/BD/97200/2013 and the research contract IF/01262/2014, respectively. M.A. was supported by the "Ramón y Cajal" grant RYC-2015-18241 from the Spanish Government. D.C. was supported by the Spanish grant CGL2016-75389-P (AEI, MINEICO/FEDER, UE), and "Unidad María de Maeztu" funded by the MINECO (MDM-2014-0370).

The geostrategic location of North Africa as a crossroad between three continents and as a stepping-stone outside Africa has evoked anthropological and genetic interest in this region. Numerous studies have described the genetic landscape of the human population in North Africa employing paternal, maternal, and biparental molecular markers. However, information from these markers which have different inheritance patterns has been mostly assessed independently, resulting in an incomplete description of the region. In this study, we analyze uniparental and genome-wide markers examining similarities or contrasts in the results and consequently provide a comprehensive description of the evolutionary history of North Africa populations. Our results show that both males and females in North Africa underwent a similar admixture history with slight differences in the proportions of admixture components. Consequently, genome-wide diversity show similar patterns with admixture tests suggesting North Africans are a mixture of ancestral populations related to current Africans and Eurasians with more affinity towards the out-of-Africa populations than to sub-Saharan Africans. We estimate from the paternal lineages that most North Africans emerged ~15,000 years ago during the last glacial warming and that population splits started after the desiccation of the Sahara. Although most North Africans share a common admixture history, the Tunisian Berbers show long periods of genetic isolation and appear to have diverged from surrounding populations without subsequent mixture. On the other hand, continuous gene flow from the Middle East made Egyptians genetically closer to Eurasians than to other North Africans. We show that genetic diversity of today's North Africans mostly captures patterns from migrations post Last Glacial Maximum and therefore may be insufficient to inform on the initial population of the region during the Middle Paleolithic period. ; This study was supported in parts by Spanish Government MCINN grant CGL2010-14944/BOS and Programa de Cooperación Interuniversitaria e Investigación Científica, Spanish Ministry of Foreign Affairs and Cooperation grants A75180/06, A/8394/07, B/018514/08, A1/040218/11. ; Peer Reviewed

The Iberian Peninsula is a well-delimited geographic region with a rich and complex human history. However, the causes of its genetic structure and past migratory dynamics are not yet fully understood. In order to shed light on them, here we evaluated the gene flow and genetic structure throughout the Iberian Peninsula with spatially explicit modelling applied to a georeferenced genetic dataset composed of genome-wide SNPs from 746 individuals belonging to 17 different regions of the Peninsula. We found contrasting patterns of genetic structure throughout Iberia. In particular, we identified strong patterns of genetic differentiation caused by relevant barriers to gene flow in northern regions and, on the other hand, a large genetic similarity in central and southern regions. In addition, our results showed a preferential north to south migratory dynamics and suggest a sex-biased dispersal in Mediterranean and southern regions. The estimated genetic patterns did not fit with the geographical relief of the Iberian landscape and they rather seem to follow political and linguistic territorial boundaries. ; IPATIMUP integrates the i3S Research Unit, which is partially supported by FCT in the framework of the project "Institute for Research and Innovation in Health Sciences" (POCI-01-0145-FEDER-007274). J.P. and A.M.L. are funded by the Portuguese Government through the FCT fellowship SFRH/BD/97200/2013 and the research contract IF/01262/2014, respectively. M.A. was supported by the "Ramón y Cajal" grant RYC-2015-18241 from the Spanish Government. D.C. was supported by the Spanish grant CGL2016-75389-P (AEI, MINEICO/FEDER, UE), and "Unidad María de Maeztu" funded by the MINECO (MDM-2014-0370) ; SI