Ancient DNA: A Window to the Past of Europe

Deguilloux, Marie‐France; Mendisco, Fanny

doi:10.1159/000356933

Cited by 11 publications

(11 citation statements)

References 36 publications

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“…Ancient mitochondrial samples from different areas in Europe have been studied independently, and most analyses have revealed an absence of regional population continuity over time, either from prehistoric times until today, or between two ancient periods (Deguilloux & Mendisco, ). However, the coalescent‐based methods used to date are able to provide only a dichotomous answer (i.e., reject or accept full population continuity) but are unable to differentiate among different amount of genetic contribution (or replacement) from one period to the other.…”

Section: Introductionmentioning

confidence: 99%

Bayesian estimation of partial population continuity using ancient DNA and spatially explicit simulations

Silva

Rio

Kreutzer

et al. 2018

Evolutionary Applications

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The retrieval of ancient DNA from osteological material provides direct evidence of human genetic diversity in the past. Ancient DNA samples are often used to investigate whether there was population continuity in the settlement history of an area. Methods based on the serial coalescent algorithm have been developed to test whether the population continuity hypothesis can be statistically rejected by analysing DNA samples from the same region but of different ages. Rejection of this hypothesis is indicative of a large genetic shift, possibly due to immigration occurring between two sampling times. However, this approach is only able to reject a model of full continuity model (a total absence of genetic input from outside), but admixture between local and immigrant populations may lead to partial continuity. We have recently developed a method to test for population continuity that explicitly considers the spatial and temporal dynamics of populations. Here, we extended this approach to estimate the proportion of genetic continuity between two populations, using ancient genetic samples. We applied our original approach to the question of the Neolithic transition in Central Europe. Our results confirmed the rejection of full continuity, but our approach represents an important step forward by estimating the relative contribution of immigrant farmers and of local hunter‐gatherers to the final Central European Neolithic genetic pool. Furthermore, we show that a substantial proportion of genes brought by the farmers in this region were assimilated from other hunter‐gatherer populations along the way from Anatolia, which was not detectable by previous continuity tests. Our approach is also able to jointly estimate demographic parameters, as we show here by finding both low density and low migration rate for pre‐Neolithic hunter‐gatherers. It provides a useful tool for the analysis of the numerous ancient DNA data sets that are currently being produced for many different species.

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Section: Introductionmentioning

confidence: 99%

Bayesian estimation of partial population continuity using ancient DNA and spatially explicit simulations

Silva

Rio

Kreutzer

et al. 2018

Evolutionary Applications

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“…As discussed in this volume [9] , current debates among geneticists still focus, for example, on the real contributions of modern humans' settlements at either the Neolithic or Paleolithic periods, and recent results of ancient DNA studies are also examined in this context [see, e.g. 10 ]. Another key issue to understand the patterns of genetic variation observed in Europe is the role of environmental factors.…”

Section: Introductionmentioning

confidence: 99%

A New HLA Map of Europe: Regional Genetic Variation and Its Implication for Peopling History, Disease-Association Studies and Tissue Transplantation

Sanchez‐Mazas

Bühler

Nunes³

2013

Hum Hered

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Objectives: HLA genes are highly polymorphic in human populations as a result of diversifying selection related to their immune function. However, HLA geographic variation worldwide suggests that demographic factors also shaped their evolution. We here analyzed in detail HLA genetic variation in Europe in order to identify signatures of migration history and/or natural selection. Methods: Relationships between HLA diversity and geography were analyzed at 7 loci through several approaches including linear regression on gene diversity and haplotype frequencies. Regional variation was also assessed on HLA multi-locus phenotypes through structure analysis. Deviation from neutrality was tested by resampling. Results: Geographic distance was a strong predictor of HLA variation at 5 loci (A, B, C, DRB1 and DPB1) in Europe, and latitude significantly shaped HLA gene diversity and haplotype frequencies. Whereas the main level of genetic diversity was found within populations, both HLA gene frequencies and phenotypic profiles revealed regional variation, Southeast Europe, Great Britain and Finland being the most distinctive. Effects of natural selection were suggested at the DQ loci. Conclusions: HLA regional variation was observed in Europe and can be related to population history, locus HLA-A providing by far the strongest signals. This new HLA map of Europe represents an invaluable reference for disease-association studies and tissue transplantation.

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“…Haplogroups T and K appeared in hunter-gatherers only after 6,500 yrBP, indicating a degree of admixture in some places between farmers and hunter-gatherers. Farmers before and after 6,500 yrBP in Europe had haplogroups W, HV*, H, T, K, and these are also found in individuals buried at Verteba Cave (Table 5) [32]. Therefore, our data point to a common ancestry with early European farmers.…”

Section: Discussionmentioning

confidence: 55%

Analysis of ancient human mitochondrial DNA from Verteba Cave, Ukraine: insights into the origins and expansions of the Late Neolithic-Chalcolithic Cututeni-Tripolye Culture

Wakabayashi

Schmidt

Gakuhari

et al. 2017

Preprint

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1 Background: The Eneolithic (~ 5,500 yrBP) site of Verteba Cave in Western Ukraine contains 2 the largest collection of human skeletal remains associated with the archaeological 3 Cucuteni-Tripolye Culture. Their subsistence economy is based largely on agro-pastoralism and 4 had some of the largest and most dense settlement sites during the Middle Neolithic in all of 5 Europe. To help understand the evolutionary history of the Tripolye people, we performed 6 mtDNA analyses on ancient human remains excavated from several chambers within the cave.7Results: Burials at Verteba Cave are largely commingled and secondary in nature. A total of 68 8 individual bone specimens were analyzed. Most of these specimens were found in association 9 with well-defined Tripolye artifacts. We determined 28 mtDNA D-Loop (368 bp) sequences 10 and defined 8 sequence types, belonging to haplogroups H, HV, W, K, and T. These results do 11 not suggest continuity with local pre-Eneolithic peoples, but rather complete population 12 replacement. We constructed maximum parsimonious networks from the data and generated 13 population genetic statistics. Nucleotide diversity (π) is low among all sequence types and our 14 network analysis indicates highly similar mtDNA sequence types for samples in chamber G3. 15Using different sample sizes due to the uncertainly in number of individuals (11, 28, or 15), we 16 found Tajima's D statistic to vary. When all sequence types are included (11 or 28), we do not 17 find a trend for demographic expansion (negative but not significantly different from zero); 18 however, when only samples from Site 7 (peak occupation) are included, we find a significantly 19 negative value, indicative of demographic expansion.20 Conclusions: Our results suggest individuals buried at Verteba Cave had overall low mtDNA 21 diversity, most likely due to increased conflict among sedentary farmers and nomadic 22 pastoralists to the East and North. Early Farmers tend to show demographic expansion. We find 23 different signatures of demographic expansion for the Tripolye people that may be caused by 24 existing population structure or the spatiotemporal nature of ancient data. Regardless, peoples of 25 the Tripolye Culture are more closely related to early European farmers and lack genetic 26 continuity with Mesolithic hunter-gatherers or pre-Eneolithic groups in Ukraine.28 29 30 31 32 33 3 Background 1 Profound cultural transitions accompanied the Neolithic and Bronze Age in Europe. 2 These transitions were catalyzed initially through large-scale migrations of agriculturists from 3 the West Asia (modern day Anatolia) during the Neolithic, and later through the migrations of 4 steppe herders from the Pontic-Caspian and Volga regions of modern Ukraine during the 5 Bronze Age [1-4]. A continuing question of debate among researchers is how these migrations 6 affected the genetic composition of modern-day Europe [5, 6]. A key question in this debate is 7 whether these migrations that brought about cultural changes were the results of mo...

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Ancient DNA: A Window to the Past of Europe

Cited by 11 publications

References 36 publications

Bayesian estimation of partial population continuity using ancient DNA and spatially explicit simulations

Bayesian estimation of partial population continuity using ancient DNA and spatially explicit simulations

A New HLA Map of Europe: Regional Genetic Variation and Its Implication for Peopling History, Disease-Association Studies and Tissue Transplantation

Analysis of ancient human mitochondrial DNA from Verteba Cave, Ukraine: insights into the origins and expansions of the Late Neolithic-Chalcolithic Cututeni-Tripolye Culture

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