Publications

PEER-REVIEWED PUBLICATIONS

Hahlbeck N, Anlauf-Dunn K, Piotrowski S, Ortega J, Tinniswood W, Eliason E, O'Malley KG, Sloat M, Wyatt M, Hereford M, Ramirez B, Armstrong J. (In review). Habitat fragmentation drives divergent survival strategies of a cold-water fish in a warm landscape. Ecosphere.

Dayan DI, Mazur S, Green LJ, Bohn S, Johnson MA, Van Dyke DJ, Samarin PA, Battleson RD, O'Malley KG (In review) Genetic diversity within and among migratory groups of steelhead Oncorhynchus mykiss in the Rogue River, Oregon. Conservation Genetics

Rasmuson LK, Jackson TM, Edwards CA, O'Malley KG, Shanks A (2022) A decade of modeled dispersal of Dungeness crab (Cancer magister) larvae in the California Current. Marine Ecology Progress Series. DOI: 10.3354/meps13993

Waples RW, Ford MJ, Nichols K, Kardos M, Myers J, Thompson TQ, Anderson EC, Koche IJ, McKinney G, Miller MR, Naish K, Narum SR, O'Malley KG, Pearse D, Pess GR, Quinn TP, Seamons TR, Spidle A, Warheit K, Willis SC. (2022) Implications of large-effect loci for conservation: a review and case study with Pacific salmon. Journal of Heredity. Web PDF

Song W, Xie Y, Sun M, Li X, Fitzpatrick CK, Vaux F, O'Malley KG, Zhang Q, Qi J, He Y. (2021) A duplicated amh is the putative master sex-determining gene in Northwest Pacific Sebastes rockfishes. Open Biology. Web PDF

Vaux F, Bohn S, Hyde JR, O’Malley KG (2021) Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation. Evolutionary Applications, 14:1343–1364. DOI:10.1111/eva.13202. Web PDF

Jensen AJ, Schreck CB, Hess JE, Bohn S, O'Malley KG, Peterson JT (2020) Application of genetic stock identification and parentage-based tagging in a mixed-stock recreational Chinook salmon fishery. North American Journal of Fisheries Management, 41:130–141. DOI:10.1002/nafm.10542. Web

Lee EMJ and O'Malley KG (2020)  Fine-scale spatial and temporal genomic variation among Dungeness crab (Cancer magister) larval recruits in the California Current Ecosystem. Marine Ecology Progress Series, 649:67-81. DOI:10.3354/meps13453. Web

Vaux F, Aycock HM, Bohn S, Rasmuson LK, O'Malley KG (2020) Sex identification PCR-RFLP assay tested in eight species of Sebastes rockfish. Conservation Genetics Resources, 12:541–544. DOI: 10.1007/s12686-020-01150-y. Web

Lee EMJ and O'Malley KG (2020) Big fishery, big data, and little crabs: Using genomic methods to examine the seasonal recruitment patterns of early life stage Dungeness crab (Cancer magister) in the California Current Ecosystem.  Frontiers in Marine Science, 6:836. DOI: 10.3389/fmars.2019.00836. Web

Vaux F, Rasmuson LK, Kautzi LA, Rankin PS, Blume MTO, Lawrence K, Bohn S, O'Malley KG (2019) Sex matters: Otolith shape and genomic variation in Deacon Rockfish (Sebastes diaconus). Ecology and Evolution, 9, 13153–13173. DOI:10.1002/ece3.5763. Web

Madsen RPA, Jacobsen MW, O'Malley KG, Nygaard R, Praebel K, Jonsson B, Pujolar JM, Fraser DJ, Bernatchez L, Hansen MM (2019) Genetic population structure and variation at phenology-related genes in anadromous Arctic char (Salvelinus alpinus). Ecology of Freshwater Fish, 29, 170-183. DOI: 10.1111/eff.12504 Web

Evans ML, Hard JJ, Black AN, Sard NM, O’Malley KG (2019) A quantitative genetic analysis of life-history traits and lifetime reproductive success in reintroduced Chinook salmon.  Conservation Genetics, 20, 781-799. Web

O’Malley KG, Vaux F, Black AN (2019) Characterizing neutral and adaptive genomic differentiation in a changing climate: the most northerly freshwater fish as a model. Ecology and Evolution, 9, 2004-2017. DOI: 10.1002/ece3.4891 Web

Jackson TM, Roegner GC, O’Malley KG (2017) Evidence for inter-annual variation in genetic structure of Dungeness crab (Cancer magister) along the California Current System, 27, 352-368. Molecular Ecology, doi: 10.1111/mec.14443. Web

O’Malley KG, Corbett K, Beacham TD, Jacobson DP, Jackson TM, Roegner C (2017) Genetic connectivity of the Dungeness crab (Cancer magister) across oceanographic regimes. Journal of Shellfish Research, 36(2), 1-12. Web

Jackson TM and O’Malley KG (2017) Comparing genetic connectivity among Dungeness crab (Cancer magister) inhabiting Puget Sound and coastal Washington. Marine Biology, 164, 123. Web

Sard NM, Johnson MA, Jacobson DP, Hogansen MJ, O’Malley KG, Banks MA (2016) Genetic monitoring guides adaptive management of a migratory fish reintroduction program. Animal Conservation, 19, 570-577. Web

Evans ML, Johnson MA, Jacobson DP, Wang J, Hogansen M, O’Malley KG (2016) Evaluating a multi-generational reintroduction program for threatened spring Chinook salmon using genetic parentage analysis. Canadian Journal of Fisheries and Aquatic Sciences, 73, 844-852. Web

Evans ML, Shry S, Jacobson DP, Sard, N, O’Malley KG (2015) Functional gene diversity and migration timing in reintroduced Chinook salmon. Conservation Genetics, 16, 1455-1464. Web

Sard NM, O’Malley KG, Jacobson DP, Hogansen M, Schroeder K, Johnson MA, Banks MA (2015) Factors influencing spawner success in a spring Chinook salmon (Oncorhynchus tshawytscha) reintroduction program. Canadian Journal of Fisheries and Aquatic Sciences, 72, 1390-1397. Web

O’Malley KG, Perales B, Whitcomb AC (2015) Influence of immune-relevant genotype on the reproductive success of a salmonid alternative mating strategy. Journal of Fish Biology, 86, 871-881. Web

Whitcomb AC, Banks MA, O’Malley KG (2014) Influence of immune-relevant genes on mate choice and reproductive success in wild spawning hatchery-reared and wild coho salmon (Oncorhynchus kisutch). Canadian Journal of Fisheries and Aquatic Sciences, 71, 1000-1009. Web

Banks MA, Jacobson DP, Meusnier I, Greig C, Rashbrook V, Ardren W, Bernier-Latmani J, Van Sickle J, O’Malley KG (2014) Testing advances in molecular discrimination among Chinook salmon life histories: Evidence from a blind test. Animal Genetics, 45, 412-420. Web

O’Malley KG, Jacobson DP, Kurth R, Dill AJ, Banks MA (2013) Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow. Evolutionary Applications, 6, 1184-1194. Web

O’Malley KG, Cross TF, Bailie D, Carlsson J, Coughlan JP, Dillane E, Prodhol PA, McGinnity P (2013) Circadian clock gene (OtsClock1b) variation and time of ocean return in Atlantic salmon (Salmo salar). Fisheries Management and Ecology, 21, 82-87. Web

O’Malley KG, Markle D, Ardren W (2013) Timing of population fragmentation in a vulnerable minnow, the Umpqua chub, and the role of nonnative predators. Transactions of the American Fisheries Society, 142, 447-457. Web

O’Malley KG, Ford MJ, Hard JJ (2010) Clock polymorphism in Pacific salmon: Variable selection along a latitudinal gradient. Proceedings of the Royal Society B., 277, 3703-3714. Web

O’Malley KG, McClelland EK, Naish KA (2010) Clock genes localize to quantitative trait loci for stage-specific growth in juvenile coho salmon, Oncorhynchus kisutch. Journal of Heredity, 101, 628-632. Web

O’Malley KG, Banks MA (2008) A latitudinal cline in the Chinook salmon (Oncorhynchus tshawytscha) Clock gene: Evidence for selection on PolyQ length variants. Proceedings of the Royal Society B (Featured article), 275, 2813-2821. Web

O’Malley KG, Banks MA (2008) Duplicated Clock genes with unique polyglutamine domains provide evidence for nonhomologous recombination in Chinook salmon (Oncorhynchus tshawytscha). Genetica, 132, 87-94. Web

O’Malley KG, Camara MD, Banks MA (2007) Candidate loci reveal genetic differentiation between temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha). Molecular Ecology, 16, 4930-4941. Web

Ross K, Wang X, O’Malley KG, Gatlin III DM, Gold JR (2004) Microsatellite DNA markers for parental assignment in hybrid stripe bass (Morone saxatilis x Morone chrysops). Molecular Ecology Notes, 4, 156-159. Web

Saillant E, Cizdziel K, O’Malley KG, Turner TF, Pruett CL, Gold JR (2004) Microsatellite markers for red drum, Sciaenops ocellatus. Gulf of Mexico Science, 1, 101-107. PDF 

O’Malley KG, Abbey CA, Ross K, Gold JR (2003) Microsatellite DNA markers for kinship analysis and genetic mapping in red drum, Sciaenops ocellatus (Sciaenidae, Teleostei). Molecular Ecology Notes, 3, 155-158. Web

O’Malley KG, Sakamoto T, Danzmann RG, Ferguson MM (2003) Quantitative Trait Loci for spawning date and body weight in rainbow trout: Testing for conserved effects across ancestrally duplicated chromosomes. Journal of Heredity, 94, 273-284. Web