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.

35 Reads
  • Source
    • "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). "
    [Show abstract] [Hide abstract]
    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
  • Source
    • "Alternatively, composite likelihood methods that exploit the SFS (Gutenkunst et al. 2009; Excoffier et al. 2013) assume the data comprise independent (i.e., unlinked) single nucleotide polymorphisms (SNPs), an unrealistic assumption for most genomic datasets that prevents such methods from exploiting information derived from linkage (e.g. Pool & Nielsen 2009). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Rapidly developing sequencing technologies and declining costs have made it possible to collect genome-scale data from population-level samples in non-model systems. Inferential tools for historical demography given these datasets are, at present, underdeveloped. In particular, approximate Bayesian computation (ABC) has yet to be widely embraced by researchers generating these data. Here, we demonstrate the promise of ABC for analysis of the large datasets that are now attainable from non-model taxa through current genomic sequencing technologies. We develop and test an ABC framework for model selection and parameter estimation given histories of three-population divergence with admixture. We then explore different sampling regimes to illustrate how sampling more loci, longer loci, or more individuals affects the quality of model selection and parameter estimation in this ABC framework. Our results show that inferences improved substantially with increases in the number and/or length of sequenced loci, while less benefit was gained by sampling large numbers of individuals. Optimal sampling strategies given our inferential models included at least 2000 loci, each approximately 2kb in length, sampled from five diploid individuals per population, although specific strategies are model- and question-dependent. We tested our ABC approach through simulation-based cross-validations and illustrate its application using previously analyzed data from the oak gall wasp, Biorhiza pallida.This article is protected by copyright. All rights reserved.
    Molecular Ecology 08/2014; 23(18). DOI:10.1111/mec.12881 · 6.49 Impact Factor
  • Source
    • "We find that the longest blocks were a maximum of 1.1 Mbp length. If admixture between species had taken place within the last hundreds of generations, we would expect longer tracts of shared DNA (Gravel, 2012; Pool and Nielsen, 2009). Hence the limited length of admixture blocks supports the hypothesis that admixture was an old event, and that enough time has passed for recombination to break up the long stretches of introgressed DNA. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyperlipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show that the species diverged only 479-343 thousand years BP. We find that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization of the cardiovascular system. One of the genes showing the strongest evidence of selection, APOB, encodes the primary lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain how polar bears are able to cope with life-long elevated LDL levels that are associated with high risk of heart disease in humans. PAPERCLIP:
    Cell 05/2014; 157(4):785-94. DOI:10.1016/j.cell.2014.03.054 · 32.24 Impact Factor
Show more


35 Reads
Available from