Admixture, Population Structure, and <i>F</i>-Statistics

Peter, Benjamin M.

doi:10.1534/genetics.115.183913

Cited by 254 publications

(303 citation statements)

References 48 publications

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“…Consequently, high values of F ST will not necessary mean that the breed has high inbreeding, but also that one of the ancestral populations is genetically far away from the group (Peter, 2016). It should be mentioned the possibility of admixture with other populations not investigated in this study.…”

Section: Discussionmentioning

confidence: 84%

Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

Mastrangelo

Portolano

Gerlando

et al. 2017

Animal

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Analysis of genomic data is becoming increasingly common in the livestock industry and the findings have been an invaluable resource for effective management of breeding programs in small and endangered populations. In this paper, with the goal of highlighting the potential of genomic analysis for small and endangered populations, genome-wide levels of linkage disequilibrium, measured as the squared correlation coefficient of allele frequencies at a pair of loci, effective population size, runs of homozygosity (ROH) and genetic diversity parameters, were estimated in Barbaresca sheep using Illumina OvineSNP50K array data. Moreover, the breed's genetic structure and its relationship with other breeds were investigated. Levels of pairwise linkage disequilibrium decreased with increasing distance between single nucleotide polymorphisms. An average correlation coefficient <0.25 was found for markers located up to 50 kb apart. Therefore, these results support the need to use denser single nucleotide polymorphism panels for high power association mapping and genomic selection efficiency in future breeding programs. The estimate of past effective population size ranged from 747 animals 250 generations ago to 28 animals five generations ago, whereas the contemporary effective population size was 25 animals. A total of 637 ROH were identified, most of which were short (67%) and ranged from 1 to 10 Mb. The genetic analyses revealed that the Barbaresca breed tended to display lower variability than other Sicilian breeds. Recent inbreeding was evident, according to the ROH analysis. All the investigated parameters showed a comparatively narrow genetic base and indicated an endangered status for Barbaresca. Multidimensional scaling, model-based clustering, measurement of population differentiation, neighbor networks and haplotype sharing distinguished Barbaresca from other breeds, showed a low level of admixture with the other breeds considered in this study, and indicated clear genetic differences compared with other breeds. Attention should be given to the conservation of Barbaresca due to its critical conservation status. In this context, genomic information may have a crucial role in management of small and endangered populations.

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Section: Discussionmentioning

confidence: 84%

Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

Mastrangelo

Portolano

Gerlando

et al. 2017

Animal

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“…Conceptually, our ontogenetic phylogeny approach could be extended to work with admixture graphs (Patterson et al, 2012;Pickrell and Pritchard, 2012) by adapting the pruning algorithm for calculating likelihoods to the dependence structure introduced by admixture. However, given the small size of current heteroplasmy frequency datasets compared to large whole-genome SNP datasets, detecting admixture with f -statistics (Patterson et al, 2012;Peter, 2016) or a more typical population phylogeny inference procedure (e.g., Treemix, Pickrell and Pritchard, 2012) would likely be more suitable.…”

Section: Discussionmentioning

confidence: 99%

A Population Phylogenetic View of Mitochondrial Heteroplasmy

et al. 2018

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The mitochondrion has recently emerged as an active player in a myriad of cellular processes. Additionally, it was recently shown that more than 200 diseases are known to be linked to variants in mitochondrial DNA or in nuclear genes interacting with mitochondria. This has reinvigorated interest in its biology and population genetics. Mitochondrial heteroplasmy, or genotypic variation of mitochondria within an individual, is now understood to be common in humans and important in human health. However, it is still not possible to make quantitative predictions about the inheritance of heteroplasmy and its proliferation within the body, partly due to the lack of an appropriate model. Here, we present a population-genetic framework for modeling mitochondrial heteroplasmy as a process that occurs on an ontogenetic phylogeny, with genetic drift and mutation changing heteroplasmy frequencies during the various developmental processes represented in the phylogeny. Using this framework, we develop a Bayesian inference method for inferring rates of mitochondrial genetic drift and mutation at different stages of human life. Applying the method to previously published heteroplasmy frequency data, we demonstrate a severe effective germline bottleneck comprised of the cumulative genetic drift occurring between the divergence of germline and somatic cells in the mother and the separation of germ layers in the offspring. Additionally, we find that the two somatic tissues we analyze here undergo tissue-specific bottlenecks during embryogenesis, less severe than the effective germline bottleneck, and that these somatic tissues experience little additional genetic drift during adulthood. We conclude with a discussion of possible extensions of the ontogenetic phylogeny framework and its possible applications to other ontogenetic processes in addition to mitochondrial heteroplasmy.

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“…The f 3 ‐statistic is based on the quantification of genetic drift (change of allele frequencies) between pairs of populations in a tree using variance in allele frequencies (Patterson et al, ; Peter, ; Reich, Thangaraj, Patterson, Price, & Singh, ). The f 3 ‐statistic can provide evidence of admixture, even if gene flow events occurred hundreds of generations ago (Patterson et al, ).…”

Section: Methodsmentioning

confidence: 99%

Killer whale genomes reveal a complex history of recurrent admixture and vicariance

et al. 2019

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Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree‐like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non‐Antarctic lineages is further driven by ancestry segments with up to four‐fold older coalescence time than the genome‐wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome‐wide data to sample the variation in ancestry within individuals.

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Admixture, Population Structure, and F-Statistics

Cited by 254 publications

References 48 publications

Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

A Population Phylogenetic View of Mitochondrial Heteroplasmy

Killer whale genomes reveal a complex history of recurrent admixture and vicariance

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