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2. Genome-wide association analysis of the resistance to infectious hematopoietic necrosis virus in two rainbow trout aquaculture lines confirms oligogenic architecture with several moderate effect quantitative trait loci

Author

Palti, Yniv, primary, Vallejo, Roger L., additional, Purcell, Maureen K., additional, Gao, Guangtu, additional, Shewbridge, Kristy L., additional, Long, Roseanna L., additional, Setzke, Christopher, additional, Fragomeni, Breno O., additional, Cheng, Hao, additional, Martin, Kyle E., additional, and Naish, Kerry A., additional

Published
2024
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4. Sex-dependent dominance maintains migration supergene in rainbow trout

Author

Pearse, Devon E., Barson, Nicola J., Nome, Torfinn, Gao, Guangtu, Campbell, Matthew A., Abadía-Cardoso, Alicia, Anderson, Eric C., Rundio, David E., Williams, Thomas H., Naish, Kerry A., Moen, Thomas, Liu, Sixin, Kent, Matthew, Moser, Michel, Minkley, David R., Rondeau, Eric B., Brieuc, Marine S. O., Sandve, Simen Rød, Miller, Michael R., Cedillo, Lucydalila, Baruch, Kobi, Hernandez, Alvaro G., Ben-Zvi, Gil, Shem-Tov, Doron, Barad, Omer, Kuzishchin, Kirill, Garza, John Carlos, Lindley, Steven T., Koop, Ben F., Thorgaard, Gary H., Palti, Yniv, and Lien, Sigbjørn

Published
2019
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5. For the love of fish, nature and people: A tribute to Professor Louis Bernatchez (1960–2023)

Author

Wellenreuther, Maren, primary, Ferchaud, Anne‐Laure, additional, Beheregaray, Luciano B., additional, Bierne, Nicolas, additional, Correa, Alberto Soares, additional, Elmer, Kathryn, additional, Fraser, Dylan, additional, Gifford, Danna, additional, Gompert, Zachariah, additional, Johnson, Marc, additional, Kassen, Rees, additional, Martin, Ryan, additional, Meek, Mariah, additional, Mergeay, Joachim, additional, Mérot, Claire, additional, Naish, Kerry, additional, Narum, Shawn, additional, Sunnucks, Paul, additional, Thomas, Frédéric, additional, Thrall, Peter, additional, Yáñez, José Manuel, additional, Zhan, Jiasui, additional, and Zhan, Xiangjiang, additional

Published
2023
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8. Harnessing the Power of Genomics to Secure the Future of Seafood

Author

Bernatchez, Louis, Wellenreuther, Maren, Araneda, Cristián, Ashton, David T., Barth, Julia M.I., Beacham, Terry D., Maes, Gregory E., Martinsohn, Jann T., Miller, Kristina M., Naish, Kerry A., Ovenden, Jennifer R., Primmer, Craig R., Young Suk, Ho, Therkildsen, Nina O., and Withler, Ruth E.

Published
2017
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9. Population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome

Author

Rondeau, Eric B, primary, Christensen, Kris A, additional, Minkley, David R, additional, Leong, Jong S, additional, Chan, Michelle T T, additional, Despins, Cody A, additional, Mueller, Anita, additional, Sakhrani, Dionne, additional, Biagi, Carlo A, additional, Rougemont, Quentin, additional, Normandeau, Eric, additional, Jones, Steven J M, additional, Devlin, Robert H, additional, Withler, Ruth E, additional, Beacham, Terry D, additional, Naish, Kerry A, additional, Yáñez, José M, additional, Neira, Roberto, additional, Bernatchez, Louis, additional, Davidson, William S, additional, and Koop, Ben F, additional

Published
2023
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11. Publisher Correction: Sex-dependent dominance maintains migration supergene in rainbow trout

Author

Pearse, Devon E., Barson, Nicola J., Nome, Torfinn, Gao, Guangtu, Campbell, Matthew A., Abadía-Cardoso, Alicia, Anderson, Eric C., Rundio, David E., Williams, Thomas H., Naish, Kerry A., Moen, Thomas, Liu, Sixin, Kent, Matthew, Moser, Michel, Minkley, David R., Rondeau, Eric B., Brieuc, Marine S. O., Sandve, Simen Rød, Miller, Michael R., Cedillo, Lucydalila, Baruch, Kobi, Hernandez, Alvaro G., Ben-Zvi, Gil, Shem-Tov, Doron, Barad, Omer, Kuzishchin, Kirill, Garza, John Carlos, Lindley, Steven T., Koop, Ben F., Thorgaard, Gary H., Palti, Yniv, and Lien, Sigbjørn

Published
2020
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14. Isolation-by-distance and population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome

Author

Rondeau, Eric B., primary, Christensen, Kris A., additional, Minkley, David R., additional, Leong, Jong S., additional, Chan, Michelle T.T., additional, Despins, Cody A., additional, Mueller, Anita, additional, Sakhrani, Dionne, additional, Biagi, Carlo A., additional, Rougemont, Quentin, additional, Normandeau, Eric, additional, Jones, Steven J.M., additional, Devlin, Robert H., additional, Withler, Ruth E., additional, Beacham, Terry D., additional, Naish, Kerry A., additional, Yáñez, José M., additional, Neira, Roberto, additional, Bernatchez, Louis, additional, Davidson, William S., additional, and Koop, Ben F., additional

Published
2022
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15. Long‐distance migration is a major factor driving local adaptation at continental scale in Coho salmon.

Author

Rougemont, Quentin, Xuereb, Amanda, Dallaire, Xavier, Moore, Jean‐Sébastien, Normandeau, Eric, Perreault‐Payette, Alysse, Bougas, Bérénice, Rondeau, Eric B., Withler, Ruth E., Van Doornik, Donald M., Crane, Penelope A., Naish, Kerry A., Garza, John Carlos, Beacham, Terry D., Koop, Ben F., and Bernatchez, Louis

Subjects
COHO salmon, SINGLE nucleotide polymorphisms, LONG-distance running, SPATIAL variation, LOCUS (Genetics)
Abstract

Inferring the genomic basis of local adaptation is a long‐standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species' homing behaviour may promote the establishment of local adaptation. We genotyped 7829 individuals representing 217 sampling locations at more than 100,000 high‐quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. The results indicated that genetic differentiation scans and genetic–environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidate single nucleotide polymorphisms associated with long‐distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications. see also the Perspective by Rebekah L. Horn and Shawn R. Narum [ABSTRACT FROM AUTHOR]

Published
2023
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17. Implications of Large-Effect Loci for Conservation: A Review and Case Study with Pacific Salmon

Author

Waples, Robin S, primary, Ford, Michael J, additional, Nichols, Krista, additional, Kardos, Marty, additional, Myers, Jim, additional, Thompson, Tasha Q, additional, Anderson, Eric C, additional, Koch, Ilana J, additional, McKinney, Garrett, additional, Miller, Michael R, additional, Naish, Kerry, additional, Narum, Shawn R, additional, O’Malley, Kathleen G, additional, Pearse, Devon E, additional, Pess, George R, additional, Quinn, Thomas P, additional, Seamons, Todd R, additional, Spidle, Adrian, additional, Warheit, Kenneth I, additional, and Willis, Stuart C, additional

Published
2022
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19. Long‐distance migration is a major factor driving local adaptation at continental scale in Coho salmon

Author

Rougemont, Quentin, primary, Xuereb, Amanda, additional, Dallaire, Xavier, additional, Moore, Jean‐Sébastien, additional, Normandeau, Eric, additional, Perreault‐Payette, Alysse, additional, Bougas, Bérénice, additional, Rondeau, Eric B., additional, Withler, Ruth E., additional, Van Doornik, Donald M., additional, Crane, Penelope A., additional, Naish, Kerry A., additional, Garza, John Carlos, additional, Beacham, Terry D., additional, Koop, Ben F., additional, and Bernatchez, Louis, additional

Published
2022
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20. Long distance migration is a major factor driving local adaptation at continental scale in Coho Salmon

Author

Rougemont, Quentin, primary, Xuereb, Amanda, additional, Dallaire, Xavier, additional, Moore, Jean-Sebastien, additional, Normandeau, Eric, additional, Rondeau, Eric B, additional, Withler, Ruth, additional, Van Doornik, Donald, additional, Crane, Penelope, additional, Naish, Kerry, additional, Garza, John-Carlos, additional, Beacham, Terry, additional, Koop, Ben F., additional, and Bernatchez, Louis, additional

Published
2021
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26. Correction: Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

Author

Rougemont, Quentin, primary, Moore, Jean-Sébastien, additional, Leroy, Thibault, additional, Normandeau, Eric, additional, Rondeau, Eric B., additional, Withler, Ruth E., additional, Van Doornik, Donald M., additional, Crane, Penelope A., additional, Naish, Kerry A., additional, Garza, John Carlos, additional, Beacham, Terry D., additional, Koop, Ben F., additional, and Bernatchez, Louis, additional

Published
2021
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28. Evidence for the existence of a native population of sockeye salmon (Oncorhynchus nerka) and subsequent introgression with introduced populations in a Pacific Northwest watershed

Author

Spies, Ingrid B., Anderson, Eric C., Naish, Kerry, and Bentzen, Paul

Subjects
Sockeye salmon -- Natural history -- Identification and classification -- Genetic aspects -- Environmental aspects, Invasive species -- Environmental aspects -- Genetic aspects, Fish populations -- Evaluation -- Genetic aspects -- Environmental aspects
Abstract

Abstract: The Lake Washington watershed (Washington, USA) has been the recipient of numerous transplantations of nonnative Oncorhynchus nerka (both sockeye salmon and their landlocked form, kokanee) over the past century [...]

Published
2007

29. Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

Author

Rougemont, Quentin, primary, Moore, Jean-Sébastien, additional, Leroy, Thibault, additional, Normandeau, Eric, additional, Rondeau, Eric B., additional, Withler, Ruth E., additional, Van Doornik, Donald M., additional, Crane, Penelope A., additional, Naish, Kerry A., additional, Garza, John Carlos, additional, Beacham, Terry D., additional, Koop, Ben F., additional, and Bernatchez, Louis, additional

Published
2020
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37. Publisher Correction: Sex-dependent dominance maintains migration supergene in rainbow trout

Author

Pearse, Devon E., primary, Barson, Nicola J., additional, Nome, Torfinn, additional, Gao, Guangtu, additional, Campbell, Matthew A., additional, Abadía-Cardoso, Alicia, additional, Anderson, Eric C., additional, Rundio, David E., additional, Williams, Thomas H., additional, Naish, Kerry A., additional, Moen, Thomas, additional, Liu, Sixin, additional, Kent, Matthew, additional, Moser, Michel, additional, Minkley, David R., additional, Rondeau, Eric B., additional, Brieuc, Marine S. O., additional, Sandve, Simen Rød, additional, Miller, Michael R., additional, Cedillo, Lucydalila, additional, Baruch, Kobi, additional, Hernandez, Alvaro G., additional, Ben-Zvi, Gil, additional, Shem-Tov, Doron, additional, Barad, Omer, additional, Kuzishchin, Kirill, additional, Garza, John Carlos, additional, Lindley, Steven T., additional, Koop, Ben F., additional, Thorgaard, Gary H., additional, Palti, Yniv, additional, and Lien, Sigbjørn, additional

Published
2019
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39. Demographic history, linked selection, and recombination shape the genomic landscape of a broadly distributed Pacific salmon

Author

Rougemont, Quentin, Moore, Jean-Sébastien, Leroy, Thibault, Normandeau, Eric, Rondeau, Eric B., Withler, Ruth E., Van Doornik, Donald M., Crane, Penelope A., Naish, Kerry A., Garza, John Carlos, Beacham, Terry D., Koop, Ben F., and Bernatchez, Louis

Abstract

Understanding the impacts of current human activities on within-species genetic variation requires a thorough description of the historical factors that have shaped the genomic and geographical distribution of nucleotide diversity. Past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential under the nearly neutral theory. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon ( Oncoryhnchus kisutch ) to address three issues. First, we demonstrate that a single glacial refugium is the source of the majority of present-day genetic diversity, with minor but detectable inputs from secondary micro-refugia. We propose a scenario whereby several ancestral populations located south of the ice sheets expanded in postglacial time, swamping out most of the diversity from other putative micro-refugia. Following this expansion, we identify particular populations having undergone continuous declines in population size ( Ne ). Second, we combine multiple evidence from demographic modelling, analysis of recombination landscape, and genome-wide landscape of diversity to demonstrate that selection at linked sites and Hill-Robertson interference played a major role in shaping genetic diversity across the Coho salmon genome. Third, we demonstrate that this demographic history generated subtle differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations. Taken together, we found considerable support for the joint contributions of demographic history and linked selection in the load of deleterious mutations. We suggest that these inferences should be better integrated in conservation genetics of managed fish species which currently focuses largely on within-population adaptation. Author Summary Reconstruction of a species’ past demographic history from genome-wide data allows understanding how historical factors interact with intrinsic genomic properties to shape the distribution of genetic diversity along its genome and its geographic range. Here, we combine genotyping-by-sequencing and whole genome sequence data with demographic modelling to address these issues in the Coho salmon, a Pacific salmon species with rapidly declining census size in some parts of its range, notably in the south. Our demographic reconstructions indicate a linear decrease in genetic diversity towards the north of the species range, supporting the hypothesis of a major southern refugia for the Coho salmon and a northern route of postglacial recolonization. Accordingly, the number of candidate deleterious homozygous derived mutations was higher in northern populations. Demographic modelling also suggested the existence of cryptic refugia that may have been missed with the use of simpler summary statistics. We further showed that the species’ genome was shaped by linked selection and biased gene conversion. In particular, local variation in recombination rates have modulated the efficacy of natural selection. These processes, together with a complex demographic history, can contribute to the load of deleterious mutations – an effect we argue should be taken into account more routinely in conservation genetics studies.

Published
2019
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41. A Bridge to Marine Geosciences: A Learning Community for College Transfer Students.

Author

Dolliver, Jane, Guzmán, Jose M., Nuwer, Mikelle, Thompson, LuAnne A., and Naish, Kerry A.

Subjects
COMMUNITY college students, UNIVERSITY towns, EARTH sciences, LEARNING communities
Abstract

The article discusses a program called GEODUC that was developed to increase interest and retention in geosciences among community college transfer students. The program consists of three phases: recruitment, a bridge program, and a mentoring seminar series. The program was successful in recruiting historically excluded group participants, and the bridge program and seminar series were effective in increasing research skills, confidence, and creating a supportive community. The program also had early successes, with participants receiving fellowships and presenting at professional meetings. The authors provide lessons learned and plans for future iterations of the program. [Extracted from the article]

Published
2023
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44. Temporal variation in selection on body length and date of return in a wild population of coho salmon, Oncorhynchus kisutch

Author

Kodama Miyako, Hard Jeffrey J, and Naish Kerry A

Subjects
Selection, Temporal variation, Evolution, Environmental variation, Lifetime reproductive success, Oncorhynchus kisutch, QH359-425
Abstract

Abstract Background A number of studies have measured selection in nature to understand how populations adapt to their environment; however, the temporal dynamics of selection are rarely investigated. The aim of this study was to assess the temporal variation in selection by comparing the mode, direction and strength of selection on fitness-related traits between two cohorts of coho salmon (Oncorhynchus kisutch). Specifically, we quantified individual reproductive success and examined selection on date of return and body length in a wild population at Big Beef Creek, Washington (USA). Results Reproductive success and the mode, direction and strength of selection on date of return and body length differed between two cohorts sampled in 2006 and 2007. Adults of the first brood year had greater success over those of the second. In 2006, disruptive selection favored early and late returning individuals in 2-year-old males, and earlier returning 3-year-old males had higher fitness. No evidence of selection on date of return was detected in females. In 2007, selection on date of return was not observed in males of either age class, but stabilizing selection on date of return was observed in females. No selection on body length was detected in males of both age classes in 2006, and large size was associated with higher fitness in females. In 2007, selection favored larger size in 3-year-old males and intermediate size in females. Correlational selection between date of return and body length was observed only in 2-year-old males in 2006. Conclusions We found evidence of selection on body length and date of return to the spawning ground, both of which are important fitness-related traits in salmonid species, but this selection varied over time. Fluctuation in the mode, direction and strength of selection between two cohorts was likely to be due to factors such as changes in precipitation, occurrence of catastrophic events (flooding), the proportion of younger- versus older-maturing males, sex ratio and densities of spawners.

Published
2012
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45. Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

Author

Rougemont, Quentin, primary, Moore, Jean-Sébastien, additional, Leroy, Thibault, additional, Normandeau, Eric, additional, Rondeau, Eric B., additional, Withler, Ruth E., additional, Van Doornik, Donald M., additional, Crane, Penelope A., additional, Naish, Kerry A., additional, Garza, John Carlos, additional, Beacham, Terry D., additional, Koop, Ben F., additional, and Bernatchez, Louis, additional

Published
2019
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46. Sex-dependent dominance maintains migration supergene in rainbow trout

Author

Pearse, Devon E., primary, Barson, Nicola J., additional, Nome, Torfinn, additional, Gao, Guangtu, additional, Campbell, Matthew A., additional, Abadía-Cardoso, Alicia, additional, Anderson, Eric C., additional, Rundio, David E., additional, Williams, Thomas H., additional, Naish, Kerry A., additional, Moen, Thomas, additional, Liu, Sixin, additional, Kent, Matthew, additional, Minkley, David R., additional, Rondeau, Eric B., additional, Brieuc, Marine S. O., additional, Rød Sandve, Simen, additional, Miller, Michael R., additional, Cedillo, Lucydalila, additional, Baruch, Kobi, additional, Hernandez, Alvaro G., additional, Ben-Zvi, Gil, additional, Shem-Tov, Doron, additional, Barad, Omer, additional, Kuzishchin, Kirill, additional, Garza, John Carlos, additional, Lindley, Steven T., additional, Koop, Ben F., additional, Thorgaard, Gary H., additional, Palti, Yniv, additional, and Lien, Sigbjørn, additional

Published
2018
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