RT Journal
A1 Burri, Reto
A1 Nater, Alexander
A1 Kawakami, Takeshi
A1 Mugal, Carina F.
A1 Olason, Pall I.
A1 Smeds, Linnea
A1 Suh, Alexander
A1 Dutoit, Ludovic
A1 Bureš, Stanislav
A1 Garamszegi, Laszlo Z.
A1 Hogner, Silje
A1 Moreno, Juan
A1 Qvarnström, Anna
A1 Ružić, Milan
A1 Sæther, Stein-Are
A1 Sætre, Glenn-Peter
A1 Török, Janos
A1 Ellegren, Hans
T1 Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
JF Genome Research 
JO Genome Research 
YR 2015 
FD November 01 
VO 25 
IS 11 
SP 1656 
OP 1665 
DO 10.1101/gr.196485.115 
UL http://genome.cshlp.org/content/25/11/1656.abstract 
AB Speciation is a continuous process during which genetic changes gradually accumulate in the genomes of diverging species. Recent studies have documented highly heterogeneous differentiation landscapes, with distinct regions of elevated differentiation (“differentiation islands”) widespread across genomes. However, it remains unclear which processes drive the evolution of differentiation islands; how the differentiation landscape evolves as speciation advances; and ultimately, how differentiation islands are related to speciation. Here, we addressed these questions based on population genetic analyses of 200 resequenced genomes from 10 populations of four Ficedula flycatcher sister species. We show that a heterogeneous differentiation landscape starts emerging among populations within species, and differentiation islands evolve recurrently in the very same genomic regions among independent lineages. Contrary to expectations from models that interpret differentiation islands as genomic regions involved in reproductive isolation that are shielded from gene flow, patterns of sequence divergence (dxy and relative node depth) do not support a major role of gene flow in the evolution of the differentiation landscape in these species. Instead, as predicted by models of linked selection, genome-wide variation in diversity and differentiation can be explained by variation in recombination rate and the density of targets for selection. We thus conclude that the heterogeneous landscape of differentiation in Ficedula flycatchers evolves mainly as the result of background selection and selective sweeps in genomic regions of low recombination. Our results emphasize the necessity of incorporating linked selection as a null model to identify genome regions involved in adaptation and speciation.