Plumage Genes and Little Else Distinguish the Genomes of Hybridizing Warblers

Abstract

When related taxa hybridize extensively, their genomes may become increasingly homogenized over time. This mixing via hybridization creates conservation challenges when it reduces genetic or phenotypic diversity and when it endangers previously distinct species via genetic swamping [1]. However, hybridization also facilitates admixture mapping of traits that distinguish each species and the associated genes that maintain distinctiveness despite ongoing gene flow [2]. We address these dual aspects of hybridization in the golden-winged/blue-winged warbler complex, two phenotypically divergent warblers that are indistinguishable using traditional molecular markers and that draw substantial conservation attention [3-5]. Whole-genome comparisons show that differentiation is extremely low: only six small genomic regions exhibit strong differences. Four of these divergence peaks occur in proximity to genes known to be involved in feather development or pigmentation: agouti signaling protein (ASIP), follistatin (FST), ecodysplasin (EDA), wingless-related integration site (Wnt), and beta-carotene oxygenase 2 (BCO2). Throat coloration-the most striking plumage difference between these warblers-is perfectly associated with the promoter region of agouti, and genotypes at this locus obey simple Mendelian recessive inheritance of the black-throated phenotype characteristic of golden-winged warblers. The more general pattern of genomic similarity between these warblers likely results from a protracted period of hybridization, contradicting the broadly accepted hypothesis that admixture results from solely anthropogenic habitat change in the past two centuries [4]. Considered in concert, these results are relevant to both the genetic architecture of avian feather pigmentation and the evolutionary history and conservation challenges associated with these declining songbirds.

Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration

“…Given that the plumage traits differing between myrtle and Audubon's warblers are most strongly expressed in males in the breeding season, and that sex chromosomes have been identified in previous research as often being involved in avian plumage traits [18,[30][31][32], we expected the Z chromosome to account for more of the plumage differences between myrtle and Audubon's warblers. Recent anonymous genome scans of phenotypically distinct birds that have also investigated pigmentation have identified both a large proportion of differentiation peaks on the Z chromosome and many that include pigmentation genes [18,28,52]. For example, among Vermivora warblers and Sporophila seedeaters, two of six (33%) and 10 of 25 divergent regions (40%) were associated with the Z chromosome, respectively [18,28].…”

“…Our goal was to quantify the genomic substrate that leads to phenotypic divergence between these warblers, in this case by identifying regions of the genome significantly associated with plumage traits and possible candidate genes within these regions. Several recent anonymous genome scans have found differentiation peaks between closely related avian taxa disproportionately populated with pigmentation genes [18,28,29]. Yet, these studies have been focused on taxon comparisons with exceptionally low levels of genome-wide divergence.…”

“…First, we identified genes containing or located close to SNPs significantly associated with the five plumage characters. We relied on the annotation of the myrtle warbler genome [18], which used gene annotation data from the zebra finch genome [49]. We identified all of the features marked as genes in the annotation file that contained at least one SNP associated with a plumage trait, with a significance cut-off of 2log 10 ( p) .…”

“…We then used AdapterRemoval (v. 1.5.4; [38]) to merge overlapping paired reads. We used BOWTIE2 (v. 2.2.8; [39]) to map each of the individual reads to the myrtle warbler genome [18]. For this mapping, we used the 'very sensitive local' set of alignment pre-sets.…”

“…These advances have largely been facilitated by anonymous genome scans, which avoid the need to focus on previously identified candidate genes (e.g. [15,18]). …”