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The geography of recent genetic ancestry across Europe. PLoS Biol 11: e1001555
, 2013
"... The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are de ..."
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The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2257 Europeans (in the POPRES dataset) to conduct one of the first surveys of recent genealogical ancestry over the past three thousand years at a continental scale. We detected 1.9 million shared long genomic segments, and used the lengths of these to infer the distri-bution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 2–12 genetic common ancestors from the last 1500 years, and upwards of 100 genetic ancestors from the previous 1000 years. These numbers drop off exponentially with geographic distance, but since these genetic ancestors are a tiny fraction of common genealogical ancestors, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1000 years. There is also substantial regional variation in the number of shared genetic ancestors. For example, there are especially high numbers of common ancestors shared between many eastern populations
R (2014) Inferring human population size and separation history frommultiple genome sequences. Nature Genetics 46: 919–925. doi: 10.1038/ng.3015 PMID: 24952747
"... 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 rece ..."
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Cited by 11 (0 self)
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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. Human genome sequences are related to each other through common ancestors. Estimates of when these ancestors lived provide insight into ancestral population sizes and ancestral
Proofs to be sent to:
"... Strategies for calculating blockwise likelihoods under the coalescent ..."
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and recent population history of Native Americans
"... Genomic evidence for the Pleistocene ..."
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R E,2 B
"... gtem. One of the genes showing the strongest evi-dence of selection, APOB, encodes the primary which can comprise up to 50 % of the body weight of an individ-ual, depending on its nutritional state (Atkinson and Ramsay, 1995; Atkinson et al., 1996). lipoprotein component of low-density lipoprotein ( ..."
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gtem. One of the genes showing the strongest evi-dence of selection, APOB, encodes the primary which can comprise up to 50 % of the body weight of an individ-ual, depending on its nutritional state (Atkinson and Ramsay, 1995; Atkinson et al., 1996). lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain
mutation rates from large-sample genomic
"... inference of population size histories and locus-specific ..."
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A renewal theory approach to IBD sharing
"... A long genomic segment inherited by a pair of individuals from a single, recent common ancestor is said to be identical-by-descent (IBD). Shared IBD segments have numerous applications in genetics, from demographic inference to phasing, imputation, pedigree reconstruction, and disease mapping. Here, ..."
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A long genomic segment inherited by a pair of individuals from a single, recent common ancestor is said to be identical-by-descent (IBD). Shared IBD segments have numerous applications in genetics, from demographic inference to phasing, imputation, pedigree reconstruction, and disease mapping. Here, we provide a theoretical analysis of IBD sharing under Markovian approximations of the coalescent with recombination. We describe a general framework for the IBD process along the chromosome under the Markovian models (SMC/SMC’), as well as introduce and justify a new model, which we term the renewal approxi-mation, under which lengths of successive segments are assumed to be indepen-dent. Then, considering the infinite-chromosome limit of the IBD process, we recover previous results (for SMC) and derive new results (for SMC’) for the mean fraction of the chromosome found in long shared segments and the mean number of such segments. We then use renewal theory to derive an expression (in Laplace space) for the distribution of the number of shared segments and demonstrate implications for demographic inference. We also compute (again, in Laplace space) the distribution of the fraction of the chromosome shared, from which we obtain explicit expressions for the first two moments. Finally, we generalize all results to populations with a variable effective size.
CAN ONE HEAR THE SHAPE OF A POPULATION HISTORY?
, 2014
"... Reconstructing past population size from present day genetic data is a major goal of pop-ulation genetics. Recent empirical studies infer population size history using coalescent-based models applied to a small number of individuals. While it is known that the allelic spectrum is not sufficient to i ..."
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Reconstructing past population size from present day genetic data is a major goal of pop-ulation genetics. Recent empirical studies infer population size history using coalescent-based models applied to a small number of individuals. While it is known that the allelic spectrum is not sufficient to infer the population size history, the distribution of coalescence times is. Here we provide tight bounds on the amount of information needed to recover the population size history at a certain level of accuracy assuming data given either by exact coalescence times, or given blocks of non-recombinant DNA sequences whose loci have approximately equal times to coalescence. Importantly, we prove lower bounds showing that it is impossible to accurately deduce population histories given limited data. 1
RESEARCH ARTICLE A New Method to Scan Genomes for Introgression in a Secondary Contact Model
"... Secondary contact between divergent populations or incipient species may result in the ex-change and introgression of genomic material. We develop a simple DNA sequence mea-sure, calledGmin, which is designed to identify genomic regions experiencing introgression in a secondary contact model.Gmin is ..."
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Secondary contact between divergent populations or incipient species may result in the ex-change and introgression of genomic material. We develop a simple DNA sequence mea-sure, calledGmin, which is designed to identify genomic regions experiencing introgression in a secondary contact model.Gmin is defined as the ratio of the minimum between-popula-tion number of nucleotide differences in a genomic window to the average number of be-tween-population differences. Although it is conceptually simple, one advantage ofGmin is that it is computationally inexpensive relative to model-based methods for detecting gene flow and it scales easily to the level of whole-genome analysis. We compare the sensitivity and specificity ofGmin to those of the widely used index of population differentiation, FST, and suggest a simple statistical test for identifying genomic outliers. Extensive computer simulations demonstrate thatGmin has both greater sensitivity and specificity for detecting recent introgression than does FST. Furthermore, we find that the sensitivity ofGmin is robust with respect to both the population mutation and recombination rates. Finally, a scan ofGmin across the X chromosome of Drosophila melanogaster identifies candidate regions of intro-gression between sub-Saharan African and cosmopolitan populations that were previously missed by other methods. These results show thatGmin is a biologically straightforward, yet powerful, alternative to FST, as well as to more computationally intensive model-based methods for detecting gene flow.
