Eight thousand years of natural selection in Europe

Mathieson, Iain; Lazaridis, Iosif; Rohland, Nadin; Mallick, Swapan; Patterson, Nick; S, Alpaslan Roodenberg; Harney, Éadaoin; Stewardson, Kristin; Fernandes, Daniel; Novak, Mario; Sirak, Kendra; Gamba, Cristina; Er, Jones; Llamas, Bastien; Dryomov, Stanislav; Pickrell, Joseph K.; Jl, Arsuaga; Jmb, de Castro; Carbonell, Eudald; Gerritsen, Fokke; Khokhlov, Aleksandr; Kuznetsov, Pavel; Lozano, Marina; Meller, Harald; Mochalov, Oleg Dmitrievich; Moiseyev,; Guerra, Rojo; Roodenberg, Jacob; Jm, Verges; Krause, Johannes; Cooper, Alan; Kw, Alt; Brown, Dorcas; Anthony, David W.; Lalueza‐Fox, Carles; Haak, Wolfgang; Pinhasi, Ron; Reich, David

doi:10.1101/016477

Cited by 65 publications

(86 citation statements)

References 91 publications

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“…There is also evidence that these genes underwent selection more recently in the history of Europeans (Mathieson et al 2015), which could suggest an extended period of selection-perhaps influenced by migrations between Asia and Europe-or repeated selective events at the same locus.…”

Section: Selection In Eurasiansmentioning

confidence: 99%

Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation

Racimo

2015

Genetics

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A powerful way to detect selection in a population is by modeling local allele frequency changes in a particular region of the genome under scenarios of selection and neutrality and finding which model is most compatible with the data. A previous method based on a cross-population composite likelihood ratio (XP-CLR) uses an outgroup population to detect departures from neutrality that could be compatible with hard or soft sweeps, at linked sites near a beneficial allele. However, this method is most sensitive to recent selection and may miss selective events that happened a long time ago. To overcome this, we developed an extension of XP-CLR that jointly models the behavior of a selected allele in a three-population tree. Our method -called "3-population composite likelihood ratio" (3P-CLR) -outperforms XP-CLR when testing for selection that occurred before two populations split from each other and can distinguish between those events and events that occurred specifically in each of the populations after the split. We applied our new test to population genomic data from the 1000 Genomes Project, to search for selective sweeps that occurred before the split of Yoruba and Eurasians, but after their split from Neanderthals, and that could have led to the spread of modern-human-specific phenotypes. We also searched for sweep events that occurred in East Asians, Europeans, and the ancestors of both populations, after their split from Yoruba. In both cases, we are able to confirm a number of regions identified by previous methods and find several new candidates for selection in recent and ancient times. For some of these, we also find suggestive functional mutations that may have driven the selective events.

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Section: Selection In Eurasiansmentioning

confidence: 99%

Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation

Racimo

2015

Genetics

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“…BC or later. Genetic (3) and isotope data (4) have revealed that demographic movements brought these Neolithic novelties from the Near East into Europe through the process by which scarce Mesolithic foragers were either quickly replaced or assimilated into Neolithic lifeways. Isotope analyses have also suggested that Mesolithic diets were largely based on terrestrial, marine, or riverine protein-rich resources (5-7) with scanty evidence for the consumption of plants (8).…”

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confidence: 99%

Dental calculus reveals Mesolithic foragers in the Balkans consumed domesticated plant foods

Cristiani

Radini

Edinborough

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Researchers agree that domesticated plants were introduced into southeast Europe from southwest Asia as a part of a Neolithic "package," which included domesticated animals and artifacts typical of farming communities. It is commonly believed that this package reached inland areas of the Balkans by ∼6200 calibrated (cal.) BC or later. Our analysis of the starch record entrapped in dental calculus of Mesolithic human teeth at the site of Vlasac in the Danube Gorges of the central Balkans provides direct evidence that already by ∼6600 cal. BC, if not earlier, Late Mesolithic foragers of this region consumed domestic cereals, such as Triticum monococcum, Triticum dicoccum, and Hordeum distichon, which were also the main crops found among Early Neolithic communities of southeast Europe. We infer that "exotic" Neolithic domesticated plants were introduced to southern Europe independently almost half a millennium earlier than previously thought, through networks that enabled exchanges between inland Mesolithic foragers and early farming groups found along the Aegean coast of Turkey.Mesolithic foragers | starch analysis | domesticated cereals | forager/farmer interaction | human dental calculus

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“…The Khvalynsk culture contains mitochondrial haplotype U5a (together with U4 and H) (9). If the migrants moved via the mentioned territories, the found subclades of mt-DNA C in Mesolithic-Neolithic remains could be the evidence (as they preserved in Yuzhniy Oleni Ostrov and Dnieper-Donetsk area), but there are no such findings.…”

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confidence: 96%

On Localization of Ancient Bearers of Y-DNA R1a Haplotype in Eastern Europe Neolithic Cultures

2015

Russian Journal of Biological Research

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The work considers the problems of genetics, archeology, and anthropology connected with problem of localization of R1a* Y-DNA haplotype bearers in Meso-and Neolithic Pre-Corded Ware archaeologic sites. Based on the analysis of findings of 2014-2015 years (described in other works) this paper proposes a hypothesis that the areas of Comb Ware cultures of Eastern Europe could be the possible area of archaic Y-DNA R1a1 subclades spread. The ancient R1a1 Y-haplotype (M198-, M459+) bearers could be possibly accompanied with those with J2b Y-DNA haplotype. As for pre-Mesolitic time, the situation remains unclear as more Eastern and more Southern localizations of R1a* and R1a1* bearers are possible according to modern data.

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Eight thousand years of natural selection in Europe

Cited by 65 publications

References 91 publications

Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation

Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation

Dental calculus reveals Mesolithic foragers in the Balkans consumed domesticated plant foods

On Localization of Ancient Bearers of Y-DNA R1a Haplotype in Eastern Europe Neolithic Cultures

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