Inference of Historical Changes in Migration Rate From the Lengths of Migrant Tracts

Department of Statistics, University of California, Berkeley, California 94720, USA.
Genetics (Impact Factor: 5.96). 02/2009; 181(2):711-9. DOI: 10.1534/genetics.108.098095
Source: PubMed


After migrant chromosomes enter a population, they are progressively sliced into smaller pieces by recombination. Therefore, the length distribution of "migrant tracts" (chromosome segments with recent migrant ancestry) contains information about historical patterns of migration. Here we introduce a theoretical framework describing the migrant tract length distribution and propose a likelihood inference method to test demographic hypotheses and estimate parameters related to a historical change in migration rate. Applying this method to data from the hybridizing subspecies Mus musculus domesticus and M. m. musculus, we find evidence for an increase in the rate of hybridization. Our findings could indicate an evolutionary trajectory toward fusion rather than speciation in these taxa.

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    • "However, violations of the assumptions of the single-pulse model can result in substantial departure between expected and observed rates of decay of coancestry with respect to time. Models incorporating multiple admixture times, or sustained migration (Pool and Nielsen 2009; Gravel 2012; Hellenthal et al. 2014; Liang and Nielsen 2014b), have been built to address more complex admixture scenarios in single populations. However, these do not incorporate the fact that admixture often occurs in a geographic context—beginning at a given point in time, then spreading across space. "
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    ABSTRACT: Recent genomic studies have highlighted the important role of admixture in shaping genome-wide patterns of diversity. Past admixture leaves a population genomic signature of linkage disequilibrium (LD), reflecting the mixing of parental chromosomes by segregation and recombination. These patterns of LD can be used to infer the timing of admixture, but the results of inference can depend strongly on the assumed demographic model. Here, we introduce a theoretical framework for modeling patterns of LD in a geographic contact zone where two differentiated populations have come into contact and are mixing by diffusive local migration. Assuming that this secondary contact is recent enough that genetic drift can be ignored, we derive expressions for the expected LD and admixture tract lengths across geographic space as a function of the age of the contact zone and the dispersal distance of individuals. We develop an approach to infer age of contact zones using population genomic data from multiple spatially sampled populations by fitting our model to the decay of LD with recombination distance. To demonstrate an application of our model, we use our approach to explore the fit of a geographic contact zone model to three human genomic datasets from populations in Indonesia, Central Asia and India and compare our results to inference under different demographic models. We obtain substantially different results to the commonly used model of panmictic admixture, highlighting the sensitivity of admixture timing results to the choice of demographic model. Copyright © 2015, The Genetics Society of America.
    Genetics 07/2015; 201(1). DOI:10.1534/genetics.115.179838 · 5.96 Impact Factor
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    • "These methods vary in their effectiveness. Simple empirical criteria perform surprisingly well for admixture between species (as for the mouse admixture zone studied by Pool and Nielsen 2009). Similarly, most of these methods tend to be highly accurate for recent admixture between well-separated human groups (such as African Americans or American Latinos ). "
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    ABSTRACT: Admixture between long-separated populations is a defining feature of the genomes of many species. The mosaic block structure of admixed genomes can provide information about past contact events, including the time and extent of admixture. Here, we describe an improved wavelet-based technique that better characterizes ancestry block structure from observed genomic patterns. Principal Components Analysis is first applied to genomic data to identify the primary population structure, followed by wavelet decomposition to develop a new characterization of local ancestry information along the chromosomes. For testing purposes, this method is applied to human genome-wide genotype data from Indonesia, as well as virtual genetic data generated using genome-scale sequential coalescent simulations under a wide range of admixture scenarios. Time of admixture is inferred using an approximate Bayesian computation framework, providing robust estimates of both admixture times and their associated levels of uncertainty. Crucially, we demonstrate that this revised wavelet approach, which we have released as the R package adwave, provides improved statistical power over existing wavelet-based techniques and can be used to address a broad range of admixture questions. Copyright © 2015, The Genetics Society of America.
    Genetics 04/2015; 200(2). DOI:10.1534/genetics.115.176842 · 5.96 Impact Factor
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    • "For example, sampling of genomewide DNA sequence polymorphisms strengthens Correspondence: Ryan C. Garrick, Fax: +1 662-915-5144; E-mail: and Bryan C. Carstens, Fax: +1 614-292-2030; E-mail: our ability to distinguish between recent vs. historical migration and admixture (Pool & Nielsen 2009), and yields previously unattainable insights into both neutral and selective processes (Gompert et al. 2014). Even prior to the recent application of next-generation sequencing in phylogeography, a transformation in the basic approaches used to draw historical inferences from molecular data was underway (Brito & Edwards 2009; Hickerson et al. 2010). "
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    ABSTRACT: Empirical phylogeographic studies have progressively sampled greater numbers of loci over time, in part motivated by theoretical papers showing that estimates of key demographic parameters improve as the number of loci increases. Recently, next-generation sequencing has been applied to questions about organismal history, with the promise of revolutionizing the field. However, no systematic assessment of how phylogeographic datasets have changed over time with respect to overall size and information content has been performed. Here, we quantify the changing nature of these genetic datasets over the past 20 years, focusing on papers published in Molecular Ecology. We found that the number of independent loci, the total number of alleles sampled, and the total number of single nucleotide polymorphisms (SNPs) per dataset has improved over time, with particularly dramatic increases within the past five years. Interestingly, uniparentally-inherited organellar markers (e.g., animal mitochondrial and plant chloroplast DNA) continue to represent an important component of phylogeographic data. Single-species studies (cf. comparative studies) that focus on vertebrates (particularly fish and to some extent, birds) represent the gold standard of phylogeographic data collection. Based on the current trajectory seen in our survey data, forecast modelling indicated that the median number of SNPs per dataset for studies published by the end of the year 2016 may approach ~20,000. This survey provides baseline information for understanding the evolution of phylogeographic datasets, and underscores the fact that development of analytical methods for handling very large genetic datasets will be critical for facilitating growth of the field.This article is protected by copyright. All rights reserved.
    Molecular Ecology 02/2015; 24(6):n/a-n/a. DOI:10.1111/mec.13108 · 6.49 Impact Factor
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