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      Genomic history of the Sardinian population

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          Abstract

          The population of the Mediterranean island of Sardinia has made important contributions to genome-wide association studies of complex disease traits and, based on ancient DNA (aDNA) studies of mainland Europe, Sardinia is hypothesized to be a unique refuge for early Neolithic ancestry. To provide new insights on the genetic history of this flagship population, we analyzed 3,514 whole-genome sequenced individuals from Sardinia. We find Sardinian samples show elevated levels of shared ancestry with Basque individuals, especially samples from the more historically isolated regions of Sardinia. Our analysis also uniquely illuminates how levels of genetic similarity with mainland aDNA samples varies subtly across the island. Together, our results indicate within-island sub-structure and sex-biased processes have substantially impacted the genetic history of Sardinia. These results give new insight to the demography of ancestral Sardinians and help further the understanding of sharing of disease risk alleles between Sardinia and mainland populations.

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          Most cited references 70

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          Ancient human genomes suggest three ancestral populations for present-day Europeans

           Iosif Lazaridis,  Krause Johannes (corresponding) ,  Nick Patterson (2014)
          We sequenced genomes from a $\sim$7,000 year old early farmer from Stuttgart in Germany, an $\sim$8,000 year old hunter-gatherer from Luxembourg, and seven $\sim$8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had $\sim$44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.
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            Inferring human population size and separation history from multiple genome sequences

            The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) analyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe.
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              Massive migration from the steppe was a source for Indo-European languages in Europe

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                Author and article information

                Journal
                9216904
                2419
                Nat Genet
                Nat. Genet.
                Nature genetics
                1061-4036
                1546-1718
                1 August 2018
                17 September 2018
                October 2018
                17 March 2019
                : 50
                : 10
                : 1426-1434
                Affiliations
                [1 ]Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
                [2 ]Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Behavior, University of California, Los Angeles, Los Angeles, California, USA.
                [3 ]Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA.
                [4 ]Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.
                [5 ]Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy.
                [6 ]Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
                [7 ]Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA.
                [8 ]Laboratory of Genetics, National Institute on Aging, US National Institutes of Health, Baltimore, Maryland, USA.
                [9 ]Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy.
                Author notes

                AUTHOR CONTRIBUTIONS

                F.C. G.R.A., D.S., and J.N. conceived of the study; C.W.K.C., C.S., D.S., F.C. G.R.A., J.N. designed the study; C.W.K.C., J.H.M., C.S., H.A., A.B. performed the analyses; C.W.K.C., J.H.M., C.S., A.B., K.E.L., G.R.A., D.S., F.C., J.N. interpreted the data; C.S., M.Z., M.P., F.B., A.M., G.P., M.S., A.A., G.R.A., D.S., F.C. contributed in the data collection and initial preparation for population genetic analysis. C.W.K.C. and J.N. wrote the paper with input from all coauthors.

                Correspondence should be addressed to C.W.K.C. ( charleston.chiang@ 123456med.usc.edu ) and J.N. ( jnovembre@ 123456uchicago.edu )
                Article
                NIHMS1502262
                10.1038/s41588-018-0215-8
                6168346
                30224645

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                Genetics

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