Scott A. Pavey


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Peer-Reviewed Publications


25) Gaillard, M. S.A. Pavey, C.L. Côté, R. Tremblaya, L.Bernatchez, and C. Audet. 2016. Regional variation of gene regulation associated with storage lipid metabolism in American glass eels (Anguilla rostrata). Comparative Biochemistry and Physiology Part A. Accepted

24) Laporte M, S.A. Pavey, C. Rougeux, F. Pierrion, H. Budzinski, P. Couture, M. Baudrimont, L.   Bernatchez. 2016. RAD-sequencing reveals within-generation polygenic selection in response to anthropogenic organic and heavy metal contamination in North Atlantic Eels25:219-237. Laporte et al. 2016. S.A. Pavey co-first author.



23) Shedd, K.R. F.A. von Hippel, J.J. Willacker, T.R. Hamon, O.L. Schlei, J.K. Wenburg, J.L. Miller, S.A. Pavey. 2015. Competitive release leads to novel ontogenetic resource polymorphism in kokanee (Oncorhynchus nerka). Canadian Journal of Fisheries and Aquatic Sciences. 72:1718-1730 Shedd et al. 2015

22) Bracamonte S.E., S. Smith, M. Hammer, S.A. Pavey, P. Sunnucks, L. Beheregaray. Characterization of MHC class IIB for four endangered Australian freshwater fishes obtained from ecologically divergent populations. Fish and Shellfish Immunololgy 46:468-476.

21) Pavey, S.A., J. Gaudin, E. Normandeau, M. Castonguay, M. Dionne, C. Audet, L. Bernatchez. 2015. RAD-sequencing highlights polygenic discrimination of habitat ecotypes in the panmictic American Eel. Current Biology 25:1666-1671. S0960-9822(15)00548-5

20) Pavey, S.A. 2015. Perspective: High-throughput SNPs for all: Genotyping-in-thousands. 2015. Molecular Ecology Resources. 15:685-687

19) Boivin, B., M. Castonguay, C. Audet, S.A. Pavey, M. Dionne and L. Bernatchez. 2015. How does salinity influence habitat selection and growth in juvenile American eels Anguilla rostrata? Journal of Fish Biology 86:765-784.

18) Côté, C., S.A. Pavey, A. Céline, T. Pratt. and L. Bernatchez. 2015. Growth trajectories and sex ratios differ by sex and rearing environment in American eel (Anguilla rostrata) from wild observations and common garden experiments: Implications for stocking programs. Transactions of the American Fisheries Society 144:235-245. S.A. Pavey co-first author


17) Sevellec, M., S.A. Pavey, S. Boutin, N. Derome L. Bernatchez. 2014. Microbiome investigation in the ecological species context of Lake Whitefish (Coregonus clupeaformis) using next-generation sequencing. Journal of Evolutionary Biology 27:1029-1046. PDF

16) Lamaze, F., S.A. Pavey, E. Normandeau, G. Roy, D. Garant and L. Bernatchez. 2014. Neutral and selective processes shape MHC gene diversity and expression in stocked brook charr populations (Salvelinus fontinalis). Molecular Ecology 23:1730-1748. PDF


15) Pavey, S.A., M. Sevellec, W. Adam , E. Normandeau, F.C. Lamaze, P.-A. Gagnaire, M. Filteau, F.-O. Gagnon-Hébert, H. Maaroufi, and L. Bernatchez. 2013. Nonparallelism in MHC IIβ diversity accompanies nonparallelism in pathogen infection of lake whitefish (Coregonus clupeaformis) species pairs as revealed by next-generation sequencing. Molecular Ecology 22:3833-3849. PDF

14) Filteau, M., S.A. Pavey, J. St-Cyr, and L. Bernatchez. 2013. Gene co-expression networks reveal key drivers of phenotypic divergence in lake whitefish. Molecular Biology and Evolution 30:1384-1396. PDF

13) Gagnaire, P.-A., S.A. Pavey, E.Normandeau, and L. Bernatchez. 2013. The genetic architecture of reproductive isolation during speciation-with-gene-flow in lake whitefish species pairs assessed by RAD-sequencing. Evolution  67:2483-2497. PDF

12) Gagnaire, P.-A., E. Normandeau, S.A. Pavey, and L. Bernatchez. 2013. Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis). Molecular Ecology 22:3036-3048. PDF


11) Pavey, S.A., N. Aubin-Horth, L. Bernatchez, and C.R. Landry. 2012. What is needed for next-generation ecological and evolutionary genomics? Trends in Ecology and Evolution 27:673-678. Unformatted PDF (official PDF available from TREE)

10) Boutin, S., M. Sevellec, S.A. Pavey, L. Bernatchez, N. Derome. 2012. A fast, highly sensitive double-nested PCR-based method to screen fish immunobiomes. Molecular Ecology Resources 12:1037-1039. PDF


9) Pavey, S.A., B. Sutherland, J. Leong, A. Robb, K. von Schalburg, T. Hamon, B. Koop, and J. Nielsen. 2011. Ecological transcriptomics of lake-type and riverine sockeye salmon (Oncorhynchus nerka). BMC Ecology 11:31. PDF

8) Pavey, S.A., F.C. Lamaze, D. Garant, and L. Bernatchez. 2011. Full length MHC II beta exon 2 primers for salmonids: a new resource for next generation sequencing. Conservation Genetics Resources 3:665-667. PDF


7) Pavey, S.A., H. Collin, P. Nosil, S. Rogers. 2010. The role of gene expression in ecological speciation. Annals of the New York Academy of Sciences 1206:110-129. PDF

6) Pavey, S.A., J.L. Nielsen, R.H. Mackas, T.R. Hamon, F. Breden. 2010. Contrasting ecology shapes juvenile lake-type and riverine sockeye salmon. Transactions of the American Fisheries Society 139: 1584-1594. PDF

5) Nielsen, J.L. and S.A. Pavey. 2010. Gene expression in fisheries management. Current Zoology 56: 157-174. PDF

4) Pavey, S.A., J.L. Nielsen, and T.R Hamon. 2010. Recent ecological divergence despite migration in sockeye salmon (Oncorhynchus nerka). Evolution 64:1773-1783 PDF


3) Rajasingh, H., D.I. Vage, S.A. Pavey, S. Omholt. 2007. Why are salmonids pink? Canadian Journal of Fisheries and Aquatic Sciences 64:1614-1627. PDF

2) Pavey, S.A., T.R. Hamon, and J.L. Nielsen. 2007. Revisiting evolutionary dead ends in sockeye salmon (Oncorhynchus nerka) life history. Canadian Journal of Fisheries and Aquatic Sciences 64:1199-1208. PDF

1) Nielsen, J.L., S.A. Pavey, T. Wiacek, and I. Williams. 2005. Genetics of Central Valley O. mykiss populations: drainage and watershed scale analyses. San Francisco Estuary and Watershed Science 3:31 pp. PDF

Manuscripts in Preparation

Pavey, S.A., J. Gaudin, E. Normandeau, L. Létourneau, S. Boisvert, J. Corbeil, C. Audet and L. Bernatchez. Draft genome of the American Eel (Anguilla rostrata).

Bowles, E., J. Laroche, T.R. Hamon, S.A. Pavey and S.M. Rogers. Population genomics of the threespine stickleback (Gasterosteus aculeatus) in a unique system of aged lakes with and without gene flow with the contemporary marine ancestor in Southwest Alaska.


Pavey, S.A., M. Filteau, J. Leong, B. Koop, K. von Schalburg, T.R. Hamon and L. Bernatchez. Spawning ecological transcriptomics of muscle, liver and brain tissues in river and beach spawning habitats of recently colonized Sockeye Salmon (Oncorhynchus nerka).

Science Communcation and Public Outreach

Pavey, S.A., H. Collin, P. Nosil, S. Rogers. 2013. Something in the water. International Innovations: Life Fantastic volume:64-66. PDF

Pavey S.A. 2013. Genome 10K Workshop and Conference: The Great Challenge of Fish Genomes. American Fisheries Society Genetics Section Newsletter 26:4.

Hamon, T.R. and S.A. Pavey. 2012. Salmon in a volcanic landscape: How salmon survive and thrive on the Alaska Peninsula. Alaska Park Science 11:15-19. PDF

Pavey, S.A. and J. Dodson. 2012. At the interface of behaviour, ecology and evolution: Insights from the world of fishes. Current Zoology vol 58.

Pavey, S.A. 2010. Functional ecology and evolution of sockeye salmon (Oncorhynchus nerka) life history in the dynamic environments of Aniakchak and Katmai. PhD Dissertation. Simon Fraser University, Burnaby, BC Canada. 184 pp. PDF

Pavey, S.A. 2005. Book Review: Stock Enhancement and Sea Ranching: Development, Pitfalls and
Opportunities (eds. K.M. Leber, S. Kitada, H. L. Blankenship and T. Svasand). Reviews in Fish Biology
and Fisheries 15:163.

Hamon, T.R., S.A. Pavey, J. L. Miller, and J. L. Nielsen. 2005. Aniakchak sockeye salmon investigations. Alaska Park Science 3:35-39. PDF

Pavey, S.A. 2004. Genetic relationships of sockeye salmon (Oncorhynchus nerka) at Aniakchak National Monument and Preserve. Master's Thesis. University of Alaska Anchorage, Anchorage, AK 39 pp.

Nielsen, J.L., S A. Pavey, T. Waicek, G.K. Sage, and I. Williams. 2003. Genetic analyses of Central Valley trout populations. Field Technical Report, California Dept of Fish and Game and US Fish and Wildlife Service, Red Bluff Fish and Wildlife Office.


Contents are copyright ©2008-2015 Scott A. Pavey unless otherwise noted. All rights reserved.