Published: Genomic islands of differentiation across 3 warbler species pairs


Today, published in Molecular Ecology: our paper comparing patterns of genomic differentiation across three hybridizing species pairs of warblers. This paper is the culmination of many years of work by a great group of 10 collaborators.

The citation:

Irwin, D.E., B. Milá, D.P.L. Toews, A. Brelsford, H.L. Kenyon, A.N. Porter, C. Grossen, K.E. Delmore, M. Alcaide, and J.H. Irwin. 2018. A comparison of genomic islands of differentiation across three young avian species pairs. Molecular Ecology, online Early View:

The Abstract:

Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions of high relative differentiation (i.e., “islands of differentiation” in FST), but there is much debate regarding the causes of this pattern. We briefly review the prominent models of genomic islands of differentiation and compare patterns of genomic differentiation in three closely related pairs of New World warblers with the goal of evaluating support for the four models. Each pair (MacGillivray’s/mourning warblers; Townsend’s/black‐throated green warblers; and Audubon’s/myrtle warblers) consists of forms that were likely separated in western and eastern North American refugia during cycles of Pleistocene glaciations and have now come into contact in western Canada, where each forms a narrow hybrid zone. We show strong differences between pairs in their patterns of genomic heterogeneity in FST, suggesting differing selective forces and/or differing genomic responses to similar selective forces among the three pairs. Across most of the genome, levels of within‐group nucleotide diversity (πWithin) are almost as large as levels of between‐group nucleotide distance (πBetween) within each pair, suggesting recent common ancestry and/or gene flow. In two pairs, a pattern of the FSTpeaks having low πBetween suggests that selective sweeps spread between geographically differentiated groups, followed by local differentiation. This “sweep‐before‐differentiation” model is consistent with signatures of gene flow within the yellow‐rumped warbler species complex. These findings add to our growing understanding of speciation as a complex process that can involve phases of adaptive introgression among partially differentiated populations.

New publication: ZW sex chromosomes and speciation


Darren has published a review of sex chromosomes evolution and speciation in birds and other ZW systems. This is an invited submission for a special issue of Molecular Ecology, on “Sex Chromosomes and Speciation.”

Here’s the citation and link:

Irwin, D.E. 2018. Sex chromosomes and speciation in birds and other ZW systems. Molecular Ecology, online Early View:

Brelsford, Toews & Irwin: Proceedings B paper on genomic basis of colour


Congrats to Alan Brelsford and David Toews, co-first authors on our new paper on the loci underlying colour pattern differences across the Audubon’s / myrtle warbler hybrid zone.

The paper:
Brelsford, A.*, D.P.L. Toews*, and D.E. Irwin. 2017. Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration. Proceedings B 284: 20171106. *Shared first authorship.  Link

The UBC Science press releaseLink

The key figure from the paper, showing the result of a genome-wide association study of colour differences between the two forms:

The Abstract:
Identifying the genetic bases for colour patterns has provided important insights into the control and expression of pigmentation and how these characteristics influence fitness. However, much more is known about the genetic bases for traits based on melanin pigments than for traits based on another major class of pigments, carotenoids. Here, we use natural admixture in a hybrid zone between Audubon’s and myrtle warblers (Setophaga coronata auduboni/S. c. coronata) to identify genomic regions associated with both types of pigmentation. Warblers are known for rapid speciation and dramatic differences in plumage. For each of five plumage coloration traits, we found highly significant associations with multiple single-nucleotide polymorphisms (SNPs) across the genome and these were clustered in discrete regions. Regions near significantly associated SNPs were enriched for genes associated with keratin filaments, fibrils that make up feathers. A carotenoid-based trait that differs between the taxa—throat colour—had more than a dozen genomic regions of association. One cluster of SNPs for this trait overlaps the Scavenger Receptor Class F Member 2 (SCARF2) gene. Other scavenger receptors are presumed to be expressed at target tissues and involved in the selective movement of carotenoids into the target cells, making SCARF2 a plausible new candidate for carotenoid processing. In addition, two melanin-based plumage traits—colours of the eye line and eye spot—show very strong associations with a single genomic region mapping to chromosome 20 in the zebra finch. These findings indicate that only a subset of the genomic regions differentiated between these two warblers are associated with the plumage differences between them and demonstrate the utility of reduced-representation genomic scans in hybrid zones.


Toews, Heavyside & Irwin publish paper on migration of myrtle warblers


Congrats to co-authors David Toews and Julian Heavyside on our publication showing that the Myrtle Warblers (a form of Yellow-rumped Warbler) migrating down the Pacific Coast of North America are primarily breeding in Alaska, the Yukon, and northern BC, rather than further east.

The UBC Science press release: Isotope fingerprints in feathers reveal songbirds’ secret breeding grounds

The citation:

Toews, D.P.L., J. Heavyside, and D.E. Irwin. 2017. Linking the wintering and breeding grounds of warblers along the Pacific Flyway. Ecology and Evolution, online Early View.  DOI: 10.1002/ece3.3222   Link (open access!)

The Abstract:
Long-distance migration is a behavior that is exhibited by many animal groups. The evolution of novel migration routes can play an important role in range expansions, ecological interactions, and speciation. New migration routes may evolve in response to selection in favor of reducing distance between breeding and wintering areas, or avoiding navigational barriers. Many migratory changes are likely to evolve gradually and are therefore difficult to study. Here, we attempt to connect breeding and wintering populations of myrtle warblers (Setophaga coronata coronata) to better understand the possible evolution of distinct migration routes within this species. Myrtle warblers, unlike most other warblers with breeding ranges primarily in eastern North America, have two disjunct overwintering concentrations—one in the southeastern USA and one along the Pacific Coast—and presumably distinct routes to-and-from these locations. We studied both myrtle and Audubon’s warblers (S. c. auduboni) captured during their spring migration along the Pacific Coast, south of the narrow region where these two taxa hybridize. Using stable hydrogen isotopes and biometric data, we show that those myrtle warblers wintering along the southern Pacific Coast of North America are likely to breed at high latitudes in Alaska and the Yukon rather than in Alberta or further east. Our interpretation is that the evolution of this wintering range and migration route along the Pacific Coast may have facilitated the breeding expansion of myrtle warblers into northwestern North America. Moreover, these data suggest that there may be a migratory divide within genetically similar populations of myrtle warblers.

Myrtle warbler (copyright: Darren Irwin)


Ildiko Szabo et al.: First House Swift in Americas


Congrats to lead author Ildiko Szabo and coauthors Kimberly Walters and James Rourke on our publication documenting the first specimen of House Swift in the Americas:

Szabo, I., K. Walters, J. Rourke, and D.E. Irwin. 2017. First record of House Swift (Apus nipalensis) in the Americas. Wilson Journal of Ornithology 129: 411-416.  Link

The Abstract:
A carcass of a House Swift (Apus nipalensis) found in Ladner, British Columbia on 18 May 2012 appears to be the first documented record of this species in the Americas. Identification is based on DNA sequencing and morphometric characters. University of British Columbia Beaty Biodiversity Museum Cowan Tetrapod Collection catalogue number B017056 has been assigned to this specimen (round study skin, spread wing, partial skeleton, and tissue samples).

Feel free to email me for a PDF of the full publication.

Grossen et al.: Genomic variation in sapsuckers


Congrats to coauthors Christine Grossen, Sampath Seneviratne, and Daniel Croll on our publication about genomic variation in three species of sapsuckers and two hybrid zones.

The paper:  Grossen, C., S.S. Seneviratne, D. Croll, and D.E. Irwin. 2016. Strong reproductive isolation and narrow genomic tracts of differentiation among three woodpecker species in secondary contact. Molecular Ecology, online Early View: doi:10.1111/mec.13751 Link

The Abstract:  Hybrid zones allow the measurement of gene flow across the genome, producing insight into the genomic architecture of speciation. Such analysis is particularly powerful when applied to multiple pairs of hybridizing species, as patterns of genomic differentiation can then be related to age of the hybridizing species, providing a view into the build-up of differentiation over time. We examined 33 809 single nucleotide polymorphisms (SNPs) in three hybridizing woodpecker species: Red-breasted, Red-naped and Yellow-bellied sapsuckers (Sphyrapicus ruber, Sphyrapicus nuchalis and Sphyrapicus varius), two of which (ruber and nuchalis) are much more closely related than each is to the third (varius). To identify positions of SNPs on chromosomes, we developed a localization method based on comparative genomics. We found narrow clines, bimodal distributions of hybrid indices and genomic regions with decreased rates of introgression. These results suggest moderately strong reproductive isolation among species and selection against specific hybrid genotypes. We found 19 small regions of strong differentiation between species, partly shared among species pairs, but no large regions of differentiation. An association analysis revealed a single strong-effect candidate locus associated with plumage, possibly explaining mismatch among the three species in genomic relatedness and plumage similarity. Our comparative analysis of species pairs of different age and their hybrid zones showed that moderately strong reproductive isolation can occur with little genomic differentiation, but that reproductive isolation is incomplete even with much greater genomic differentiation, implying there are long periods of time when hybridization is possible if diverging populations are in geographic contact.

Kira Delmore finds genetic basis for orientation


Congrats to Kira Delmore on the publication of her discovery of a genetic region underlying migratory orientation in Swainson’s Thrush. A massive accomplishment, involving migratory tracking, orientation experiments, and in-depth analysis of genomic variation.

The press release: Link

Articles:; IFLScience; Cosmos

CBC Radio’s interview of Kira Delmore
Global News’ television interview of Darren Irwin and Kira Delmore

The paper:

Delmore, K.E., D.P.L. Toews, R.R. Germain, G.L. Owens, and D.E. Irwin. 2016. The genetics of seasonal migration and plumage color. Current Biology, corrected proof available online: Link

• Variation in migratory route and plumage color is explained by genomic variation
• A region on chromosome 4 is strongly and additively associated with orientation
• This region includes circadian, nervous system, and cell signaling genes
• Recurrent selective sweeps have shaped variation in this region

Sampath Seneviratne publishes on Sapsucker hybridization


Congrats to Dr. Seneviratne on a nice publication about two sapsucker hybrid zones:

Seneviratne, S.S., P. Davidson, K. Martin, and D.E. Irwin. 2016. Low levels of hybridization across two contact zones among three species of woodpeckers (Sphyrapicus sapsuckers). Journal of Avian Biology, online Early View: doi: 10.1111/jav.00946.  Link

Abstract: Three species of closely related woodpeckers (sapsuckers; Sphyrapicus) hybridize where they come into contact, presenting a rare ‘λ-shape’ meeting of hybrid zones. Two of the three arms of this hybrid zone are located on either side of the Interior Plateau of British Columbia, Canada bordering the foothills of the Coast Mountains and the Rocky Mountains. The third arm is located in the eastern foothills of the Rocky Mountains. The zones of hybridization present high variability of phenotypes and alleles in relatively small areas and provide an opportunity to examine levels of reproductive isolation between the taxa involved. We examined phenotypes (morphometric traits and plumage) and genotypes of 175 live birds across the two hybrid zones. We used the Genotyping By Sequencing (GBS) method to identify 180 partially diagnostic single nucleotide polymorphisms (SNPs) to generate a genetic hybrid index (GHI) for each bird. Phenotypically diverged S. ruberand S. nuchalis are genetically closely related, while S. nuchalis and S. varius have similar plumage but are well separated at the genetic markers studied. The width of both hybrid zones is narrower than expected under neutrality, and analyses of both genotypes and phenotypes indicate that hybrids are rare in the hybrid zone. Rarity of hybrids indicates assortative mating and/or some form of fitness reduction in hybrids, which might maintain the species complex despite close genetic distance and introgression. These findings further support the treatment of the three taxa as distinct species.