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

Aside

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

Aside

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

Aside

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

Aside

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

Aside

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: Audubon.org; 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: http://dx.doi.org/10.1016/j.cub.2016.06.015. Link

Highlights:
• 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

Aside

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.

 

Kira Delmore publishes Proc B paper on migration and speciation

Aside

Congrats to Kira, Haley, and Ryan on a nice paper!

Delmore, K.E., L. Kenyon, R.R. Germain, and D.E. Irwin. 2015. Phenotypic divergence during speciation is inversely associated with differences in seasonal migration. Proceedings of the Royal Society of London B 282: 20151921. Link

Abstract:  Differences in seasonal migration might promote reproductive isolation and differentiation by causing populations in migratory divides to arrive on the breeding grounds at different times and/or produce hybrids that take inferior migratory routes. We examined this question by quantifying divergence in song, colour, and morphology between sister pairs of North American migratory birds. We predicted that apparent rates of phenotypic differentiation would differ between pairs that do and do not form migratory divides. Consistent with this prediction, results from mixed effects models and Ornstein–Uhlenbeck models of evolution showed different rates of divergence between these groups; surprisingly, differentiation was greater among non-divide pairs. We interpret this finding as a result of variable rates of population blending and fusion between partially diverged forms. Ancient pairs of populations that subsequently fused are now observed as a single form, whereas those that did not fuse are observable as pairs and included in our study. We propose that fusion of two populations is more likely to occur when they have similar migratory routes and little other phenotypic differentiation that would cause reproductive isolation. By contrast, pairs with migratory divides are more likely to remain reproductively isolated, even when differing little in other phenotypic traits. These findings suggest that migratory differences may be one among several isolating barriers that prevent divergent populations from fusing and thereby increase the likelihood that they will continue differentiating as distinct species.