Abstract
BackgroundInference of population and species histories and population stratification using genetic data is important for discriminating between different speciation scenarios and for correct interpretation of genome scans for signs of adaptive evolution and trait association. Here we use data from 24 intronic loci re-sequenced in population samples of two closely related species, the pied flycatcher and the collared flycatcher.ResultsWe applied Isolation-Migration models, assignment analyses and estimated the genetic differentiation and diversity between species and between populations within species. The data indicate a divergence time between the species of <1 million years, significantly shorter than previous estimates using mtDNA, point to a scenario with unidirectional gene-flow from the pied flycatcher into the collared flycatcher and imply that barriers to hybridisation are still permeable in a recently established hybrid zone. Furthermore, we detect significant population stratification, predominantly between the Spanish population and other pied flycatcher populations.ConclusionsOur results provide further evidence for a divergence process where different genomic regions may be at different stages of speciation. We also conclude that forthcoming analyses of genotype-phenotype relations in these ecological model species should be designed to take population stratification into account.
Highlights
Inference of population and species histories and population stratification using genetic data is important for discriminating between different speciation scenarios and for correct interpretation of genome scans for signs of adaptive evolution and trait association
Using genetic data to infer the demographic history of a species or a population is of importance for several reasons
We collected up to 13,164 bp of sequence data from 24 autosomal loci (Table 1) for a total of 64 pied flycatchers and 110 collared flycatchers sampled from four different locations throughout their respective breeding ranges (Figure 1, Table 1)
Summary
Inference of population and species histories and population stratification using genetic data is important for discriminating between different speciation scenarios and for correct interpretation of genome scans for signs of adaptive evolution and trait association. Using genetic data to infer the demographic history of a species or a population is of importance for several reasons. Of particular interest is the identification of genomic regions that evolve under pressure of natural selection and characterization of functional elements underlying fitness traits [1]. Since demographic events in the history of populations govern the distribution of alleles on a genome-wide scale, the design, analytical efficiency and interpretation of downstream population genetic analyses or genome scans to discover such regions can be enhanced if the population history is known in some detail [2,3,4]. A recently developed and powerful way of disentangling between alternative demographic hypotheses is the application of isolation migration model theory via a maximum likelihood analysis framework [eg. 11] of coalescence based models of population
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