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Abstract

Isolation of organisms causes unequal patterns of genetic distances among populations called population structure, which is regarded as the potentially initial stage of speciation. However, it is not well documented how different parts of genomes contribute to population structure, which I term the genomic landscape of population structure. Comparisons among island and the continental populations are informative to understand population structure and speciation, because organisms are geographically and ecologically isolated after island colonisation events, often coupled with adaptation. Here, I demonstrate a mosaicism of the genomic landscape of population structure in the blackcap, a migratory songbird with population-specific adaptation to year-round resident on islands. By analysing the whole-genome resequencing data of the continental and island populations, I found that two genomic blocks contribute uniquely to the population structure. A subset group of the island populations are highly differentiated from the continental population at these regions. Multiple characteristics of these regions fit the properties of supergenes, a group of linked genes inherited as a single Mendelian locus, often associated with chromosomal rearrangements. Although demography analysis could not reveal detailed evolutionary history of the recent island colonisation events and loss of migration or the role of these supergene-like elements in them, further genomic and experimental studies might shed a light on the evolutionary role of supergenes in the initial stage of speciation.