The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

Abstract

The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception-a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence.

Genomics and the challenging translation into conservation practice

“…It is becoming increasingly clear that many genes with small effects underlie phenotypic variation of fitness relevance [41,42], which makes their detection difficult. A further challenge is that the loci underlying homogenous genomes with only a few regions of presumed fitness significance [26]. Thus while genome-wide data provides access to the adaptive genomic landscape, the signatures of adaptation vary on case-by-case basis and could simply go undetected.…”

“…nearly all outlier peaks were likely not the result of selection imposed by the environment, but instead reflected areas of low diversity generated by linked purifying selection [39,45]. Signals, perhaps prematurely associated with local adaptation, could instead be caused by a number of other processes, such as mate choice [26], selfish alleles or background selection acting on a heterogeneous recombination landscape [46][47][48][49]. 120…”

“…While targeting candidate genes (presumed adaptive) or serendipitously finding neutral markers linked to adaptive loci have not been uncommon in the conservation genetics era, given the low level of linkage disequilibrium often seen in natural populations [23] and polygenic nature of many traits [24], screening the entire genome holds considerably more power. Importantly, experimental systems have given us clues as to the signatures adaptive evolution leaves on the genome [25] and the 85 academic interest in using genomics to explore local adaptation in the wild has grown considerably (e.g., [26,27]). …”

Linkage mapping of a polymorphic plumage locus associated with intermorph incompatibility in the Gouldian finch (Erythrura gouldiae)

“…Colour polymorphisms are often associated with other physiological and behavioural traits (McKinnon and Pierotti, 2010), which may generate incompatibilities between morphs, thus facilitating speciation (Hugall and Stuart-Fox, 2012;Poelstra et al, 2014). One of the explanations for these associations is pleiotropy, in which the colour polymorphism is controlled by transcription factors or hormones that influence multiple physically unlinked genes (McKinnon and Pierotti, 2010).…”

Genome-wide introgression among distantly relatedHeliconiusbutterfly species

“…1 The geographical distribution of Heliconius butterfly species. The distributions of Heliconius melpomene-cydno-timareta and silvaniform clades are shown in different colors, along with wing pattern images of focal taxa lizards, Zimmerius flycatchers and crows [16,[40][41][42][43]. Here, we examine genome-wide patterns of divergence and introgression in Heliconius butterflies using full genome resequencing data, focusing on potential adaptive introgression between H. melpomene and H. besckei.…”