Inference of historical changes in migration rate from the lengths of migrant tracts - PubMed (original) (raw)

Inference of historical changes in migration rate from the lengths of migrant tracts

John E Pool et al. Genetics. 2009 Feb.

Abstract

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.

PubMed Disclaimer

Figures

F<sc>igure</sc> 1.—

Figure 1.—

The distribution of migrant tract lengths after the advent of admixture. Models where previously isolated populations begin exchanging migrants at rate N_e_m = 0.1 100, 200, or 300 generations ago are compared against the case in which populations exchange migrants at a constant rate N_e_m = 0.1 with no prior isolation (the single migration rate, “equilibrium” model). Depicted here is the relative abundance of migrant tracts for 0.01-cM histogram bins between 0.5 (the minimum/threshold tract length) and 5 cM. Also shown is the agreement between theoretical predictions (lines) and tracts from 1000 simulated replicates with _N_e = 10,000 (shapes).

F<sc>igure</sc> 2.—

Figure 2.—

Power to test demographic hypotheses. Shown here first are tests comparing the migration rate change model to the null model of a constant migration rate, for histories involving decreasing (A) or increasing (B) migration rates. For histories involving decreasing migration rates, power to reject a model with _m_1 constrained to be zero is shown (C). For histories involving increasing migration rates, power to reject a model with _m_2 constrained to be zero is shown (D). Significance was gauged by comparing the difference in log-likelihood scores between models to data simulated under the null model. Each data set consisted of 100 simulated haploid genomes, and a threshold tract length of 0.5 cM was used.

F<sc>igure</sc> 3.—

Figure 3.—

Distribution of demographic parameter estimates. Results from the analysis of simulated migrant tract data are shown, including median estimates (diamonds) and 95% confidence intervals (the 2.5 and 97.5 percentiles of the distribution of estimates) for (A) _m_1, (B) _m_2, and (C) T. The order of parameter sets is the same in each panel (i.e., the far left estimates are for true values of _m_1 = 0, _m_2 = 1_E_−5, and T = 100).

F<sc>igure</sc> 4.—

Figure 4.—

Migrant tract lengths found in M. m. domesticus and M. m. musculus, compared to constant migration rate expectations.

Similar articles

Cited by

References

    1. Baines, J. F., and B. Harr, 2007. Reduced X-linked diversity in derived populations of house mice. Genetics 175 1911–1921. - PMC - PubMed
    1. Becquet, C., and M. Przeworski, 2007. A new approach to estimate parameters of speciation models with application to apes. Genome Res. 17 1505–1519. - PMC - PubMed
    1. Beerli, P., and J. Felsenstein, 2001. Maximum likelihood estimation of migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Natl. Acad. Sci. USA 98 4563–4568. - PMC - PubMed
    1. Boursot, P., and K. Belkhir, 2006. Mouse SNPs for evolutionary biology: beware of ascertainment biases. Genome Res. 16 1191–1192. - PubMed
    1. Boursot, P., J.-C. Auffray, J. Britton-Davidian and F. Bonhomme, 1993. The evolution of house mice. Annu. Rev. Ecol. Syst. 24 119–152.

Publication types

MeSH terms

Grants and funding

LinkOut - more resources