Publications by authors named "Carolyn Tarpey"

4 Publications

  • Page 1 of 1

Evidence for selection and spatially distinct patterns found in a putative zona pellucida gene in Pacific cod, and implications for management.

Ecol Evol 2021 Dec 30;11(23):16661-16679. Epub 2021 Nov 30.

School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA.

Genetic differentiation has been observed in marine species even when no obvious barriers to gene flow exist, and understanding such differentiation is essential for effective fisheries management. Highly differentiated outlier loci can provide information on how genetic variation might not only contribute to local adaptation but may also be affected by historical demographic events. A locus which aligned to a predicted zona pellucida sperm-binding protein 3 gene (ZP3) in Atlantic cod () was previously identified as the highest outlier based on in a RADseq study of Pacific cod () across the West Coast of North America. However, because of the limited length of the RAD sequence and restricted geographic area of sampling, no conclusion on the functional significance of the observed variation was possible. In other marine species, ZP3 is involved in reproductive isolation, local adaptation, and has neofunctionalized as an antifreeze gene, and so it may provide important insights in functional population structure of Pacific cod. Here, we sequenced a 544-bp region of ZP3 in 230 Pacific cod collected from throughout their geographic range. We observed striking patterns of spatial structuring of ZP3 haplotypes, with a sharp break near Kodiak, Alaska, USA where populations within ~200 km of each other are nearly fixed for different haplotypes, contrasting a pattern of isolation by distance at other genetic markers in this region ( = 0.003). Phylogenetic analysis of ZP3 haplotypes revealed that the more southern haplotypes appear to be ancestral, with the northern haplotype evolving more recently, potentially in response to a novel selective pressure as Pacific cod recolonized northern latitudes after glaciation. The sharp break in haplotype frequencies suggests strong selective pressures are operating on small spatial scales and illustrates that selection can create high divergence even in marine species with ample opportunities for gene flow.
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http://dx.doi.org/10.1002/ece3.8284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8668774PMC
December 2021

The pink salmon genome: Uncovering the genomic consequences of a two-year life cycle.

PLoS One 2021 17;16(12):e0255752. Epub 2021 Dec 17.

Department of Biology, University of Victoria, Victoria, British Columbia, Canada.

Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A two-year life history of pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of a centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0255752PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8682878PMC
January 2022

Functional genetic diversity in an exploited marine species and its relevance to fisheries management.

Proc Biol Sci 2021 02 24;288(1945):20202398. Epub 2021 Feb 24.

School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle WA 98105, USA.

The timing of reproduction influences key evolutionary and ecological processes in wild populations. Variation in reproductive timing may be an especially important evolutionary driver in the marine environment, where the high mobility of many species and few physical barriers to migration provide limited opportunities for spatial divergence to arise. Using genomic data collected from spawning aggregations of Pacific herring () across 1600 km of coastline, we show that reproductive timing drives population structure in these pelagic fish. Within a specific spawning season, we observed isolation by distance, indicating that gene flow is also geographically limited over our study area. These results emphasize the importance of considering both seasonal and spatial variation in spawning when delineating management units for herring. On several chromosomes, we detected linkage disequilibrium extending over multiple Mb, suggesting the presence of chromosomal rearrangements. Spawning phenology was highly correlated with polymorphisms in several genes, in particular , which influences the development of retinal photoreceptors in vertebrates. is probably within a chromosomal rearrangement in Pacific herring and is also associated with spawn timing in Atlantic herring (). The observed genetic diversity probably underlies resource waves provided by spawning herring. Given the ecological, economic and cultural significance of herring, our results support that conserving intraspecific genetic diversity is important for maintaining current and future ecosystem processes.
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http://dx.doi.org/10.1098/rspb.2020.2398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7934995PMC
February 2021

Genetic evidence of a northward range expansion in the eastern Bering Sea stock of Pacific cod.

Evol Appl 2020 Feb 18;13(2):362-375. Epub 2019 Oct 18.

School of Aquatic and Fishery Sciences University of Washington Seattle ‎Washington.

Poleward species range shifts have been predicted to result from climate change, and many observations have confirmed such movement. Poleward shifts may represent a homogeneous shift in distribution, seasonal northward movement of specific populations, or colonization processes at the poleward edge of the distribution. The ecosystem of the Bering Sea has been changing along with the climate, moving from an arctic to a subarctic system. Several fish species have been observed farther north than previously reported and in increasing abundances. We examined one of these fish species, Pacific cod, in the northern Bering Sea (NBS) to assess whether they migrated from another stock in the eastern Bering Sea (EBS), Gulf of Alaska, or Aleutian Islands, or whether they represent a separate population. Genetic analyses using 3,599 single nucleotide polymorphism markers indicated that nonspawning cod collected in August 2017 in the NBS were similar to spawning stocks of cod in the EBS. This result suggests escalating northward movement of the large EBS stock during summer months. Whether the cod observed in the NBS migrate south during winter to spawn or remain in the NBS as a sink population is unknown.
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http://dx.doi.org/10.1111/eva.12874DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976961PMC
February 2020
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