Inferring the demographic history of European Ficedula flycatcher populations

Abstract

Background: 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. 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.

Results: We 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.

Conclusions: Our 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.

Figure 1

European breeding distribution ranges for the pied flycatcher (Ficedula hypoleuca, light blue), the collared flycatcher (Ficedula albicollis, green), and regions where both species occur together (red). Unreservedly redrawn and adapted from range maps in Cramp & Perrins [27]. Circles indicate sampling sites and the number of birds collected on each site is given within the circle. Numbers for pied flycatchers are in blue font and numbers for collared flycatchers are in green font.

Figure 2

Posterior probability distributions of the six parameters estimated using the isolation-migration model. Left panel is current (pied flycatcher = blue, collared flycatcher = red) and ancestral (green) effective population size estimates in millions, middle panel is time of divergence in million years and right panel is post-divergence migration rates (per gene per generation) from pied flycatcher to collared flycatcher (red) and from collared flycatcher to pied flycatcher (blue). A) allopatric Spanish pied flycatcher and Italian collared flycatcher, B) allopatric Spanish pied flycatcher and Hungarian collared flycatcher, C) sympatric pied flycatcher and collared flycatcher from the Baltic Sea islands and D) between species comparison including data from all populations within each species.

Figure 3

The bars show assignments of individuals to populations as suggested by the STRUCTURE analysis for A) pied flycatcher populations and B) collared flycatcher populations. The three panels for each species represent results from independent runs with K = 2 (top), K = 3 (middle) and K = 4 (bottom). One vertical bar represents one individual and the proportional assignment of each individual to a specific population is coded by color. The population origin of the samples is specified below bars.

Figure 4

Plot of the principal component analysis with SMARTPCA including the three most informative principal components for each dataset: A)data from pied flycatchers only,B)data from collared flycatchers only andC)data from both species combined.