Jamie Clarke, an undergraduate researcher in our group, teamed up with a reporter from Trek Magazine, Rachel Glassman, to write an article about Jamie’s summer research on sapsuckers. Jamie worked closely with PhD student Libby Natola on a study of 3 species of hybridizing sapsuckers (Red-breasted, Red-naped, and Yellow-bellied Sapsuckers) in central British Columbia.

Here’s a link to the article: https://trekmagazine.alumni.ubc.ca/2019/summer-2019/features/how-to-catch-a-woodpecker/

Congratulations to PhD candidate Silu Wang for being awarded the Ruth Patrick Student Poster Award (awarded by the American Society of Naturalists) at the Evolution 2019 conference!

Here is Silu’s poster, which is beautiful both visually and in terms of scientific content:

Please note that the manuscript behind this poster is currently under review, thus the analysis/content might be subject to change.

On February 10th, we had a great time snowshoeing at Cypress Mountain. As a very experienced snowshoer, Silu led the way. Rashika in particular had fun, as it was her first time experiencing snow. And Maddie was enthusiastic, sort of a pre-celebration of her upcoming and now very successful MSc defence. Libby, Kenny, Ellen and I all had fun too.

Congrats to Madelyn (“Maddie”) Ore for her excellent M.Sc. defence! Maddie’s thesis is titled “Geographic variation in song and genetics in the Townsend’s Warbler (Setophaga townsendi).” Maddie defended her thesis on March 1, and will be entering the Ph.D. program at Cornell University in September 2019.

Dr. Geraldes did a great job with interviews on two CBC Radio stations, both on January 21st. You can listen here:

These are both about our recent paper (open access!) on genomic variation in Northern Goshawks:

Geraldes, A.*, K. Askelson*, E. Nikelski, F.I. Doyle, W.L. Harrower, K. Winker, and D.E. Irwin. 2018. Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii. Evolutionary Applications, online Early View: https://doi.org/10.1111/eva.12754. (*Shared first authorship)

For more about this paper, see: https://www.zoology.ubc.ca/~irwin/irwinlab/published-genomic-differentiation-of-goshawks/

This week, our paper on genomic differentiation of Northern Goshawks was published. Sylvia Heredia of UBC Biology produced this wonderful graphic that summarizes the paper:

The Abstract:

Accurate knowledge of geographic ranges and genetic relationships among populations is important when managing a species or population of conservation concern. Along the western coast of Canada, a subspecies of the northern goshawk (Accipiter gentilis laingi) is legally designated as Threatened. The range and distinctness of this form, in comparison with the broadly distributed North American subspecies (Accipiter gentilis atricapillus), is unclear. Given this morphological uncertainty, we analyzed genomic relationships in thousands of single nucleotide polymorphisms identified using genotyping‐by‐sequencing of high‐quality genetic samples. Results revealed a genetically distinct population of northern goshawks on the archipelago of Haida Gwaii and subtle structuring among other North American sampling regions. We then developed genotyping assays for ten loci that are highly differentiated between the two main genetic clusters, allowing inclusion of hundreds of low‐quality samples and confirming that the distinct genetic cluster is restricted to Haida Gwaii. As the laingi form was originally described as being based on Haida Gwaii (where the type specimen is from), further morphological analysis may result in this name being restricted to the Haida Gwaii genetic cluster. Regardless of taxonomic treatment, the distinct Haida Gwaii genetic cluster along with the small and declining population size of the Haida Gwaii population suggests a high risk of extinction of an ecologically and genetically distinct form of northern goshawk. Outside of Haida Gwaii, sampling regions along the coast of BC and southeast Alaska (often considered regions inhabited by laingi) show some subtle differentiation from other North American regions. These results will increase the effectiveness of conservation management of northern goshawks in northwestern North America. More broadly, other conservation‐related studies of genetic variation may benefit from the two‐step approach we employed that first surveys genomic variation using high‐quality samples and then genotypes low‐quality samples at particularly informative loci.

The citation and link:

Geraldes, A.*, K. Askelson*, E. Nikelski, F.I. Doyle, W.L. Harrower, K. Winker, and D.E. Irwin. 2018. Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii. Evolutionary Applications, online Early View: https://doi.org/10.1111/eva.12754. (*Shared first authorship)

The UBC press release: https://science.ubc.ca/news/haida-gwaiis-northern-goshawks-highly-distinct-and-risk

Media coverage:
CBC Radio interviews
CBC article by The Canadian Press

We thank the many sample contributors for their contributions to this study (see the Acknowledgements section of the paper).

This research was funded by grants from Genome British Columbia; British Columbia Ministry of Forests, Lands and Natural Resource Operations; Coast Forest Products Association; Western Forest Products; and the Natural Sciences and Engineering Research Council of Canada.

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 27:4839-4855. Link

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 F_ST), 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 F_ST, 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 (π_Within) are almost as large as levels of between-group nucleotide distance (π_Between) within each pair, suggesting recent common ancestry and/or gene flow. In two pairs, a pattern of the F_ST peaks having low π_Between 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.

Congrats to Kenneth Askelson for his excellent M.Sc. defence! Kenny’s thesis is titled “Genomic Differentiation of Northern Goshawks in Coastal British Columbia.” Kenny is continuing as a Ph.D. student in the Irwin lab.

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: https://doi.org/10.1111/mec.14537

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 release: Link

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.