Article,

The genomic landscape of species divergence in Ficedula flycatchers

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Nature, 491 (7426): 756--760 (November 2012)
DOI: 10.1038/nature11584

Abstract

Unravelling the genomic landscape of divergence between lineages is key to understanding speciation1. The naturally hybridizing col- lared flycatcher and pied flycatcher are important avian speciation models2–7 that show pre- as well as postzygotic isolation8,9. We sequenced and assembled the 1.1-Gb flycatcher genome, physically mapped the assembly to chromosomes using a low-density linkage map10 and re-sequenced population samples of each species. Here we show that the genomic landscape of species differentiation is highly heterogeneous with approximately 50 ‘divergence islands’ showing up to 50-fold higher sequence divergence than the geno- mic background. These non-randomly distributed islands, with between one and three regions of elevated divergence per chro- mosome irrespective of chromosome size, are characterized by reduced levels of nucleotide diversity, skewed allele-frequency spectra, elevated levels of linkage disequilibrium and reduced pro- portions of shared polymorphisms in both species, indicative of parallel episodes of selection. Proximity of divergence peaks to genomic regions resistant to sequence assembly, potentially including centromeres and telomeres, indicate that complex repeat structures may drive species divergence. A much higher back- ground level of species divergence of the Z chromosome, and a lower proportion of shared polymorphisms, indicate that sex chromosomes and autosomes are at different stages of speciation. This study provides a roadmap to the emerging field of speciation genomics.

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