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- Mattila, Tiina M., et al.
(författare)
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Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe
- 2023
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Ingår i: Communications Biology. - : Springer Nature. - 2399-3642. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show similar patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic, and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10,000 years ago. We found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4000 years, from the Mesolithic to the end of the Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River. Genome-wide sequencing of 56 ancient hunter-gatherer and early farmer individuals from Stone Age Central and Eastern Europe reveals striking population continuity in the east in contrast to central Europe that displays extensive admixture.
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- McKenna, James, 1987-, et al.
(författare)
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Detecting population continuity and ghost admixture among ancient genomes
- 2022
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Ingår i: biorxiv. - 2692-8205.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Ancient DNA (aDNA) can prove a valuable resource when investigating theevolutionary relationships between ancient and modern populations. Per-forming demographic inference using datasets that include aDNA sampleshowever, requires statistical methods that explicitly account for the differ-ences in drift expected among a temporally distributed sample. Such driftdue to temporal structure can be challenging to discriminate from admix-ture from an unsampled, or “ghost”, population, which can give rise to verysimilar summary statistics and confound methods commonly used in pop-ulation genetics. Sequence data from ancient individuals also have uniquecharacteristics, including short fragments, increased sequencing-error rates,and often limited genome-coverage that poses further challenges. Here wepresent a novel and conceptually simple approach for assessing questionsof population continuity among a temporally distributed sample. We notethat conditional on heterozygote sites in an individual genome at a particu-lar point in time, the mean proportion of derived variants at those sites inother individuals has different expectations forwards in time and backwardsin time. The difference in these processes enables us to construct a statis-tic that can detect population continuity in a temporal sample of genomes.We can show that the statistic is sensitive to historical admixture eventsfrom un-sampled populations. Simulations are used to evaluate the power ofthis approach. We investigate a set of ancient genomes from Early NeolithicScandinavia to assess levels of population continuity to an earlier Mesolithicindividual. Individuals from hunter-gathering Neolithic Pitted Ware cultureshow marked continuity with the Mesolithic individual, whereas the contem-porary Neolithic individuals from the and farming Funnel Beaker culturedisplay much less continuity.
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| 4. |
- McKenna, James, 1987-
(författare)
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Divergence, admixture and continuity in the human past : Demographic inference using ancient and modern genomes
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Demographic forces shaping the genetic variation we observe today can include population divergences, admixture events and continuity through time. The advancement of high-throughput sequencing technologies, together with developments in molecular and bio-informatics methods, mean the number of ancient genomes available for inference has risen steeply. To make effective use of aDNA however, inference tools need to be developed that account for temporal as well as geographic sampling of genomes. Here I have developed, evaluated and applied methods for estimating divergence times between ancient and modern populations. I used simulation to study the sensitivity of these approaches to violations of model assumptions, before applying them to study the history of population divergence between pairs of populations from a global panel. Non-tree-like demography is common in the human past, with evidence of ancestral structure in the form of archaic admixture in the genomes of all non-African modern humans. Using SNP-array data collected from 118 ethnic groups in the Philippines, I show that the highest levels of Denisovan ancestry are found among the Ayta Magbukon, further highlighting the complex history between modern human groups and the archaic hominins occupying Eurasia before our arrival. Among the most important contributions population genetics has made to the study of the human past is the demonstration that cultural transitions and spread of technologies were often associated with migrating groups of people. This can result in the admixture, displacement or replacement of populations, and aDNA provides us with the opportunity to assess these trends directly through time. I developed a statistical tool to detect population continuity through time, evaluating its performance using simulation. Applied to a dataset of ancient genomes from Early Neolithic Scandinavia, I demonstrate population continuity in the hunter-gathering Pitted Ware culture, despite these people overlapping both geographically and temporally with farmers of the Funnel Beaker culture. In another study of the hunter-gatherer ancestors of the San people of southern Africa, I show evidence that this group exhibited long-term population isolation, remaining unaffected by admixture from outside southern Africa until surprisingly recent times. Using these ancient genomes, I provide further evidence that all modern Khoe-San populations exhibit significant levels of admixture with people of non-Khoe-San ancestry, demonstrating the strong impact migrations in this region have had in the past ~2,000 years.
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