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, Nick Patterson, Nick Patterson … (2015)

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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Massive migration from the steppe was a source for Indo-European languages in Europe

Wolfgang Haak, Iosif Lazaridis, Nick Patterson … (2015)

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ∼8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ∼24,000-year-old Siberian. By ∼6,000-5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ∼4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ∼75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ∼3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin of at least some of the Indo-European languages of Europe.

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Inferring human population size and separation history from multiple genome sequences

Stephan Schiffels, Richard Durbin (2014)

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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Author and article information

Journal

Journal ID (nlm-journal-id): 9216904

Journal ID (pubmed-jr-id): 2419

Journal ID (nlm-ta): Nat Genet

Journal ID (iso-abbrev): Nat. Genet.

Title: Nature genetics

ISSN (Print): 1061-4036

ISSN (Electronic): 1546-1718

Publication date Nihms-submitted: 1 August 2018

Publication date (Electronic): 17 September 2018

Publication date (Print): October 2018

Publication date PMC-release: 17 March 2019

Volume: 50

Issue: 10

Pages: 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

Manuscript ID: NIHMS1502262

DOI: 10.1038/s41588-018-0215-8

PMC ID: 6168346

PubMed ID: 30224645

SO-VID: fea11df7-60c4-41bb-a3ec-3ac940e0f055

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Genomic history of the Sardinian population

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Most cited references 70

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

Massive migration from the steppe was a source for Indo-European languages in Europe

Inferring human population size and separation history from multiple genome sequences

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