A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy

Corbett-Detig, Russell; Nielsen, Rasmus

doi:10.1371/journal.pgen.1006529

Cited by 128 publications

(173 citation statements)

References 99 publications

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“…These estimations confirmed similar conclusions reached earlier using microsatellite data [76]. This very recent secondary contact between African and European lineages is likely responsible for the North- [78,79]. In samples with a predominant European genetic background, their results identify significant differences in the proportion of African ancestry between functional classes of genomic loci.…”

Section: Out Of Africasupporting

confidence: 89%

Population Genomics on the Fly: Recent Advances in Drosophila

Haudry

Laurent

Kapun

2020

Methods in Molecular Biology

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Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of genetic tools that allow to uncover mechanistic links between genotype and phenotype. Moreover, given its world-wide distribution in diverse habitats and its moderate genome-size, Drosophila has proven very powerful for population genetics inference and was one of the first eukaryotes whose genome was fully sequenced. In this bookchapter, we provide a brief historical overview of research in Drosophila and then focus on recent advances during the genomic era. After describing different types and sources of genomic data, we discuss mechanisms of neutral evolution including the demographic history of Drosophila and the effects of recombination and biased gene conversion. Then, we review recent advances in detecting genome-wide signals of selection, such as soft and hard selective sweeps. We further provide a brief introduction to background selection, selection of non-coding DNA and codon usage and focus on the role of structural variants, such as transposable elements and chromosomal inversions, during the adaptive process. Finally, we discuss how genomic data helps to dissect neutral and adaptive evolutionary mechanisms that shape genetic and phenotypic variation in natural populations along environmental gradients. In summary, this book chapter serves as a starting point to Drosophila population genomics and provides an introduction to the system and an overview to data sources, important population genetic concepts and recent advances in the field.

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Section: Out Of Africasupporting

confidence: 89%

Population Genomics on the Fly: Recent Advances in Drosophila

Haudry

Laurent

Kapun

2020

Methods in Molecular Biology

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“…Such an introgression event is common termed an "ancestry pulse" in related works (e.g. [7], [2]). We assume that allele A was fixed in the donor population, and that prior to admixture, allele a was fixed in the recipient population.…”

Section: 2mentioning

confidence: 99%

“…Let ω (i) be the logistic trajectory for selection coefficient s i . We condition on the observed allele frequencies at time t 0 , hence ω (1) (t 0 ) = ω (2) Figure 3. Dependence of the expected tract length on the strength of selection for different times of introgression.…”

Section: 3mentioning

confidence: 99%

“…These two features of genetic variation are the primary units of demographic model inference within admixed populations. For example, the decay of LD [25] and the ancestry tract length distribution [7], [2] are commonly used for timing the onset of admixture assuming a neutral model during admixture. For example, in [34], alleles private to Papuans relative to European and African populations were used to call the Denisovan-like and Neanderthallike ancestry tracts in admixed Papuan genomes.…”

Section: Introductionmentioning

confidence: 99%

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On the distribution of tract lengths during adaptive introgression

Shchur

Svedberg

Medina

et al. 2019

Preprint

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Admixture is increasingly being recognized as an important factor in evolutionary genetics. The distribution of genomic admixture tracts, and the resulting effects on admixture linkage disequilibrium, can be used to date the timing of admixture between species or populations. However, the theory used for such prediction assumes selective neutrality despite the fact that many famous examples of admixture involve natural selection acting for or against admixture. In this paper, we investigate the effects of positive selection on the distribution of tract lengths. We develop a theoretical framework that relies on approximating the trajectory of the selected allele using a logistic function. By numerically calculating the expected allele trajectory, we also show that the approach can be extended to cases where the logistic approximation is poor due to the effects of genetic drift. Using simulations, we show that the model is highly accurate under most scenarios. We use the model to show that positive selection on average will tend to increase the admixture tract length. However, perhaps counter-intuitively, conditional on the allele frequency at the time of sampling, positive selection will actually produce shorter expected tract lengths. We discuss the consequences of our results in interpreting the timing of the introgression of EPAS1 from Denisovans into the ancestors of Tibetans.

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“…It is also likely that selection acts to maintain parental gene combinations against recombination (Bierne et al, 2006;Simon et al, 2018). Both effects, gene flow and selection, tend to bias the date estimates towards more recent times (Corbett-Detig & Nielsen, 2017). A precise estimation of the admixture event will require a recombination map in mussels and the distribution of ancestry track lengths along the genome of admixed individuals.…”

Section: The Introduction Of Dock Mussels and The Timing Of Admixturementioning

confidence: 99%

Replicated anthropogenic hybridisations reveal parallel patterns of admixture in marine mussels

Simon

Arbiol

Nielsen

et al. 2019

Evolutionary Applications

106

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Human‐mediated transport creates secondary contacts between genetically differentiated lineages, bringing new opportunities for gene exchange. When similar introductions occur in different places, they provide informally replicated experiments for studying hybridisation. We here examined 4,279 Mytilus mussels, sampled in Europe and genotyped with 77 ancestry‐informative markers. We identified a type of introduced mussels, called “dock mussels,” associated with port habitats and displaying a particular genetic signal of admixture between M. edulis and the Mediterranean lineage of M. galloprovincialis. These mussels exhibit similarities in their ancestry compositions, regardless of the local native genetic backgrounds and the distance separating colonised ports. We observed fine‐scale genetic shifts at the port entrance, at scales below natural dispersal distance. Such sharp clines do not fit with migration‐selection tension zone models, and instead suggest habitat choice and early‐stage adaptation to the port environment, possibly coupled with connectivity barriers. Variations in the spread and admixture patterns of dock mussels seem to be influenced by the local native genetic backgrounds encountered. We next examined departures from the average admixture rate at different loci, and compared human‐mediated admixture events, to naturally admixed populations and experimental crosses. When the same M. galloprovincialis background was involved, positive correlations in the departures of loci across locations were found; but when different backgrounds were involved, no or negative correlations were observed. While some observed positive correlations might be best explained by a shared history and saltatory colonisation, others are likely produced by parallel selective events. Altogether, genome‐wide effect of admixture seems repeatable and more dependent on genetic background than environmental context. Our results pave the way towards further genomic analyses of admixture, and monitoring of the spread of dock mussels both at large and at fine spacial scales.

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A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy

Cited by 128 publications

References 99 publications

Population Genomics on the Fly: Recent Advances in Drosophila

Population Genomics on the Fly: Recent Advances in Drosophila

On the distribution of tract lengths during adaptive introgression

Replicated anthropogenic hybridisations reveal parallel patterns of admixture in marine mussels

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