REFERENCES
Alexander, D.H., Novembre, J. & K. Lange. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19:1655–1664.
Ali, O.A., O’Rourke S.M., Amish, S.J., Meek, M.H., Gordon, L., Carson, J. and Miller, M. R. (2016). RAD Capture (Rapture): Flexible and efficient sequence-based genotyping. Genetics 202(2): 389-400.
Andrews, K., Good, J., Miller, M, Luikart, G, & Hohenlohe, P. (2016). Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics 17, 81-92.
Andrews, K.R., Adams J, Cassirer F, Plowright R, Gardner C, Dwire M, Hohenlohe PA, & Waits L. (2018). A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data. Molecular Ecology Resources 18: 1263-1281.
Barrio, A.M., Lamichhaney, S., Fan, G., Rafati, N., Pettersson, M., Zhang, H., Dainat, J., Ekman, D., Höppner, M., Jern, P. & Martin, M., (2016). The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. eLife 2016;5:e12081.
Beamish, R. J. (1979). New information on the longevity of Pacific ocean perch (Sebastes alutus ). Journal of the Fisheries Board of Canada, 36(11), 1395-1400.
Bell, G. (2010). Fluctuating selection: the perpetual renewal of adaptation in variable environments. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1537), 87-97.
Berkeley, S. A., Hixon, M. A., Larson, R. J., & Love, M. S. (2004). Fisheries sustainability via protection of age structure and spatial distribution of fish populations. Fisheries, 29(8), 23-32.
Brendonck L, De Meester L. 2003. Egg banks in freshwater zooplankton: evolutionary and ecological archives in the sediment. Hydrobiologia, 491: 65-84.
Carlson, H. R., & Haight, R. E. (1972). Evidence for a home site and homing of adult yellowtail rockfish, Sebastes flavidus . Journal of the Fisheries Board of Canada, 29(7), 1011-1014.
Carlson, H. R., & Haight, R. E. (1976). Juvenile life of Pacific ocean perch, Sebastes alutus , in coastal fiords of southeastern Alaska: Their environment, growth, food habits, and schooling behavior. Transactions of the American Fisheries Society, 105(2): 191-201.
Carlson, H. R., Haight, R. E., & Helle, J. H. (1995). Initial behavior of displaced yellowtail rockfish Sebastes flavidus in Lynn Canal, Southeast Alaska. Alaska Fisheries Research Bulletin, 2(1): 76-80.
Cattell, R. B. (1966). The scree test for the number of factors. Multivariate Behavioral Research, 1, 245-276.
Catchen, J.M., Hohenlohe, P.A., Bassham, S, Amores, A, Cresko, WA. (2013). Stacks: an Analysis tool set for population genomics. Molecular Ecology 22: 3124-3140.
Catchen, J., Hohenlohe, P.A., Bernatchez, L., Funk, W.C., Andrews, K.R., & Allendorf, F. (2017). Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations. Molecular Ecology Resources 17: 362-365
Cavole, L. M., Demko, A. M., Diner, R. E., Giddings, A., Koester, I., Pagniello, C. M., Paulsen, M-L., Ramirez-Valdez, A., Schwenck, S. M., Yen, N. K., Zill, M. E., & Franks, P. J. S. (2016). Biological impacts of the 2013–2015 warm-water anomaly in the Northeast Pacific: winners, losers, and the future. Oceanography, 29(2), 273-285.
Chabrol, E., Charonnet R (1937) Une novelle reaction pour l’etude des lipides. Presse Med 45:1713
Conrath, C. L., & Knoth, B. (2013). Reproductive biology of Pacific ocean perch in the Gulf of Alaska. Marine and Coastal Fisheries, 5(1), 21-27.
Cure, K., Thomas, L., Hobbs, J. P. A., Fairclough, D. V., & Kennington, W. J. (2017). Genomic signatures of local adaptation reveal source-sink dynamics in a high gene flow fish species. Scientific Reports, 7(1), 8618.
Davey, J. W., & Blaxter, M. L. (2010). RADSeq: next-generation population genetics. Briefings in Functional Genomics, 9(5-6), 416-423.
Dray S, Dufour A (2007). The ade4 package: Implementing the duality diagram for ecologists. Journal of Statistical Software, 22(4), 1–20. doi: 10.18637/jss.v022.i04.
Ellner S, Hairston NG. 1994. Role of overlapping generations in maintaining genetic variation in a fluctuating environment. The American Naturalist, 143: 403-417.
Folch, Jordi, M. Lees, & G. H. Sloane Stanley. (1957). A simple method for the isolation and purification of total lipides from animal tissues. Journal of Biological Chemistry, 226(1): 497-509.
Frichot, E., Mathieu, F., Trouillon, T., Bouchard, G., & François, O. (2014). Fast and efficient estimation of individual ancestry coefficients. Genetics, 196(4), 973-983.
Frichot E, Francois O. (2015). LEA: an R package for landscape and ecological association studies. Methods in Ecology and Evolution 6: 925– 929.
Froese, R. (2006). Cube law, condition factor and weight–length relationships: History, meta‐analysis and recommendations. Journal of Applied Ichthyology 22(4): 241-253.
Garvin, M.R., Marcotte, R.W., Palof, K.J., Riley, R.J., Kamin, L.M. & Gharrett, A.J. (2011) Diagnostic single nucleotide polymorphisms (SNPs) identify Pacific ocean perch and delineate blackspotted and rougheye rockfish. Trans. Am. Fish. Soc. 140:984–988.
Gentemann, C. L., Fewings, M. R., & García‐Reyes, M. (2017). Satellite sea surface temperatures along the West Coast of the United States during the 2014–2016 northeast Pacific marine heat wave. Geophysical Research Letters, 44(1), 312-319.
Gosselin, T. (2018) radiator: RADseq data exploration, manipulation and visualization using R. R package version 0.0.11. Retrieved from https://github.com/thierrygosselin/radiator.
Goudet, J. (2005). Hierfstat, a package for R to compute and test hierarchical F‐statistics. Molecular Ecology Notes, 5(1), 184-186.
Groot, C., & Margolis, L. (Eds.). (1991). Pacific salmon life histories. UBC Press. 608 p.
Hanselman, D., Heifetz, J., Fujioka, J. T., & Ianelli, J. N. (2005). Gulf of Alaska Pacific ocean perch. Stock assessment and fishery evaluation report for the groundfish fisheries of the Gulf of Alaska, 525-578. In  Stock Assessment and Fishery Evaluation Report for the Groundfish Resources of the Gulf of Alaska. North Pacific Fishery Management Council, 605W. 4th Ave., Suite 306, Anchorage, AK 99501-2252.
Heppell, S. S., Heppell, S. A., Spencer, P. D., Smith, W. D., & Arnold, L. (2010). Assessment of female reproductive effort and maternal effects in Pacific ocean perch Sebastes alutus : Do big old females matter? North Pacific Research Board Final Report, NPRB Project 629. Oregon Sea Grant College Program.
Hixon, M. A., Johnson, D. W., & Sogard, S. M. (2013). BOFFFFs: on the importance of conserving old-growth age structure in fishery populations. ICES Journal of Marine Science, 71(8), 2171-2185.
Hoey, A. S., & McCormick, M. I. (2004). Selective predation for low body condition at the larval-juvenile transition of a coral reef fish. Oecologia 139(1):23-29.
Hoffmann, A. A., & Sgro, C. M. (2011). Climate change and evolutionary adaptation. Nature, 470(7335), 479.
Huisman, J. (2017). Pedigree reconstruction from SNP data: parentage assignment, sibship clustering and beyond. Molecular Ecology Resources, 17(5): 1009-1024. R package version 1.0.2, Retrieved from https://github.com/JiscaH/sequoia.
Hulson, P.J., Hanselman, D.H., Lunsford, C.R. and Fissel, B. (2017). Assessment of the Pacific Ocean perch stock in the Gulf of Alaska. P. 913-992. In  Stock Assessment and Fishery Evaluation Report for the Groundfish Resources of the Gulf of Alaska. North Pacific Fishery Management Council, 605W. 4th Ave., Suite 306, Anchorage, AK 99501-2252.
Jasonowicz, A.J., Goetz, F.W., Goetz, G.W. & Nichols, K.M. (2016). Love the one you’re with: Genomic evidence of panmixia in the sablefish (Anoplopoma fimbria ). Canadian Journal of Fisheries and Aquatic Sciences, 999:1-11.
Jombart T., Devillard S., & Balloux F. (2010) Discriminant analysis of principal components: a New method for the analysis of genetically structured populations. BMC Genetics 11:94
Jones, T., Parrish, J. K., Peterson, W. T., Bjorkstedt, E. P., Bond, N. A., Ballance, L. T., Bowes, V. J., Hipfner, M., Burgess, H. K., Dolliver, J. E., Lindquist, K., Lindsey, J., Nevins, H. M., Robertson, R. R. Roletto, J., Wilson, L., Joyce, T., & J. Harvey. (2018). Massive mortality of a planktivorous seabird in response to a marine heatwave. Geophysical Research Letters, 45(7), 3193-3202.
Kamin, L. M., Palof, K. J., Heifetz, J., & Gharrett, A. J. (2014). Interannual and spatial variation in the population genetic composition of young‐of‐the‐year Pacific ocean perch (Sebastes alutus ) in the Gulf of Alaska. Fisheries Oceanography, 23(1), 1-17.
Kamvar, Z. N., Tabima, J.F., Grünwald, N.J. (2014) Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2:e281. https://doi.org/10.7717/peerj.281.
Kamvar Z. N., Brooks JC & Grünwald NJ (2015) Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Front. Genet. 6:208.
Kawecki, T. J. (2000). The evolution of genetic canalization under fluctuating selection. Evolution, 54(1), 1-12.
Kendall, A.W., Kondzela, C., Li, Z., Clausen, D. & Gharrett, A.J. (2007) Genetic and morphological identification of pelagic juvenile rockfish collected from the Gulf of Alaska. U.S. Department of Commerce, NOAA Professional Paper NMFS 9, 26 p.
Kumar, G., & Kocour, M. (2017). Applications of next-generation sequencing in fisheries research: a Review. Fisheries Research, 186, 11-22.
Lande, R. (2007). Expected relative fitness and the adaptive topography of fluctuating selection. Evolution, 61(8), 1835-1846.
Langmead B, & Salzberg S. (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods. 9:357-359.
Levin, P.S, & C. Möllmann C. (2015) Marine ecosystem regime shifts: challenges and opportunities for ecosystem-based management. Philosophical Transactions of the Royal Society B: Biological Sciences. 370(1659):20130275.
Link, J.S. (2002) What does ecosystem-based fisheries management mean. Fisheries, 27(4):18-21.
Longhurst, A. (2002). Murphy’s Law revisited: Longevity as a factor in recruitment to fish populations. Fisheries Research, 56(2), 125-131.
Love, M. S., Yoklavich, M., & Thorsteinson, L. K. (2002). The Rockfishes of the Northeast Pacific. University of California Press. 416 p.
Major, R. L., and H. H. Shippen. (1970). Synopsis of biological data on Pacific ocean perch, Sebastodes alutus. FAO Fisheries Synopsis No. 79, NOAA Circular 347, 38 p.
Manel, S., Gaggiotti, O. E., & Waples, R. S. (2005). Assignment methods: Matching biological questions with appropriate techniques. Trends in Ecology & Evolution, 20(3), 136-142.
Marshall, T. C., Slate, J. B. K. E., Kruuk, L. E. B., & Pemberton, J. M. (1998). Statistical confidence for likelihood‐based paternity inference in natural populations. Molecular Ecology, 7(5), 639-655.
Matthews, K. R. (1990). A telemetric study of the home ranges and homing routes of copper and quillback rockfishes on shallow rocky reefs. Canadian Journal of Zoology, 68(11), 2243-2250.
McKinney, G. J., Larson, W. A., Seeb, L. W. & Seeb, J. E. (2017), RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al. (2016). Mol Ecol Resour, 17: 356–361. doi:10.1111/1755-0998.12649.
Megrey, B. A. (1988). Review and comparison of age-structured stock assessment models. NWAFC Processed Rep., 88-21, 116 p. Northwest and Alaska Fish. Cent., Natl. Mar. Fish. Serv., NOAA, 7600 Sand Point Way NE, Seattle, WA 98115-0070.
Narum, S. R., Buerkle, C. A., Davey, J. W., Miller, M. R., & Hohenlohe, P. A. (2013). Genotyping‐by‐sequencing in ecological and conservation genomics. Molecular Ecology, 22(11), 2841-2847.
Nei, M. (1987). Molecular Evolutionary Genetics. Columbia University Press. 512 p.
NOAA (2019). Commercial Fishery Statistics – Annual Commercial Landings by Group: https://www.fisheries.noaa.gov/national/sustainable-fisheries/commercial-fisheries-landings
Newman, D. L., Abney, M., McPeek, M. S., Ober, C., & Cox, N. J. (2001). The importance of genealogy in determining genetic associations with complex traits. The American Journal of Human Genetics, 69(5), 1146-1148.
Pacifici, M., Foden, W. B., Visconti, P., Watson, J. E., Butchart, S. H., Kovacs, K. M., Scheffers, B. R., Hole, D. G., Martin, T. G., Akçakaya, H. R., Corlett, R. T., Huntley, B., Bickford, D., Carr, J. A., Hoffmann, A. A., Midgley, G. F., Pearce-Kelly, P., Pearson, R. G., Williams, S. E., Willis, S. G. Young, B., & Rondinini, C. (2015). Assessing species vulnerability to climate change. Nature Climate Change, 5(3), 215.
Palof, K.J., Heifetz, J., & Gharrett, A.J. (2011). Geographic structure in Alaskan Pacific ocean perch (Sebastes alutus ) indicates limited life-time dispersal. Mar. Biol. 158:779-792.
Parker, S.J., Berkeley, S.A., Golden, J.T. et al (2000). Management of Pacific rockfish. Fisheries 25:22–29
Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945-959.
R Core Team (2016). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
Moss, J. H., Shotwell, S. K., Heintz, R. A., Atkinson, S., Debenham, C., Fournier, W., Golden, N., Heifetz, J., Mueter, F. J., Pirtle, J. L., Reid, J. A., Slater, L., Sreenivasan, A., Will, A., Zaleski, M., & Zimmermann, M. (2016). Surviving the Gauntlet: A comparative study of the pelagic, demersal, and spatial linkages that determine groundfish recruitment and diversity in the Gulf of Alaska ecosystem (NPRB GOA Project G81 Upper Trophic Level Final Report). North Pacific Research Board, Anchorage, AK.
Rooper, C. N., Boldt, J. L., Batten, S., & Gburski, C. (2012). Growth and production of Pacific ocean perch (Sebastes alutus ) in nursery habitats of the Gulf of Alaska. Fisheries Oceanography, 21(6), 415-429.
Saenz‐Agudelo, P., Jones, G. P., Thorrold, S. R., & Planes, S. (2009). Estimating connectivity in marine populations: an Empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios. Molecular Ecology, 18(8), 1765-1776.
Schindler, D. E., Hilborn, R., Chasco, B., Boatright, C. P., Quinn, T. P., Rogers, L. A., & Webster, M. S. (2010). Population diversity and the portfolio effect in an exploited species. Nature, 465(7298), 609.
Sigler, M. F., M. P. Eagleton, T. E. Helser, J. V. Olson, J. L. Pirtle, C. N. Rooper, S. C. Simpson, & R. P. Stone. (2017). Alaska Essential Fish Habitat Research Plan: A Research Plan for the National Marine Fisheries Service’s Alaska Fisheries Science Center and Alaska Regional Office. AFSC Processed Rep. 2015-05, 22 p. Alaska Fish. Sci. Cent., NOAA, Natl. Mar. Fish. Serv., 7600 Sand Point Way NE, Seattle WA 98115.
Simons, A. M. (2009). Fluctuating natural selection accounts for the evolution of diversification bet hedging. Proceedings of the Royal Society B: Biological Sciences, 276(1664), 1987-1992.
Stanley, R. D. (1986). A comparison of age estimates derived from the surface and cross-section methods of otolith reading for Pacific ocean perch (Sebastes alutus ), p. 187-196. In  Proceedings of the International Rockfish Symposium. Alaska Sea Grant College Program, AK-SG-87-02.
Stockhausen, W. T., & Hermann, A. J. (2007). Modeling larval dispersion of rockfish: a Tool for marine reserve design. Biology, assessment, and management of North Pacific rockfishes, 251-273.Alaska Sea Grant College Program, AK-SG-07-01.
Stockhausen, B. (2009). DisMELS: A Dispersal Model for Early Life History Stages. http://www.afsc.noaa.gov/Quarterly/jfm2009/divrptsREFM5.htm. Last accessed July 25, 2016.
Stockhausen, W. T., Coyle, K. O., Hermann, A. J., Doyle, M., Gibson, G. A., Hinckley, S., Ladd, C., & Parada, C. (2018). Running the gauntlet: Connectivity between natal and nursery areas for Pacific ocean perch (Sebastes alutus ) in the Gulf of Alaska, as inferred from a biophysical individual-based model. Deep-sea Research Part II: Topical Studies in Oceanography, 165:74-88.
Sunday, J. M., Crim, R. N., Harley, C. D., & Hart, M. W. (2011). Quantifying rates of evolutionary adaptation in response to ocean acidification. PLOS ONE, 6(8), e22881.
Valenzuela-Quiñonez, F., (2016). How fisheries management can benefit from genomics? Briefings in Functional Genomics, 15(5): 352-357. p.elw006.
Voight, B. F., & Pritchard, J. K. (2005). Confounding from cryptic relatedness in case-control association studies. PLOS Genetics. https://doi.org/10.1371/journal.pgen.0010032.
Wang, H.-Y., & Höök, T. O. (2009). Eco-genetic model to explore fishing-induced ecological and evolutionary effects on growth and maturation schedules. Evolutionary Applications, 2(3), 438–455.
Wenne, R., Boudry, P., Hemmer-Hansen, J., Lubieniecki, K.P., Was, A., & Kause, A. (2007). What role for genomics in fisheries management and aquaculture? Aquat. Living Resour., 20 3 241-255.
Westrheim, S. J. (1958). On the biology of the Pacific ocean perch,Sebastodes alutu s (Gilbert) (Doctoral dissertation, University of Washington).
Westrheim, S. J. (1975). Reproduction, maturation, and identification of larvae of some Sebastes (Scorpaenidae) species in the northeast Pacific Ocean. Journal of the Fisheries Board of Canada, 32(12), 2399-2411.
Withler, R., Beacham, T., Schulze, A., Richards, L., & Miller, K. (2001). Co-existing populations of Pacific ocean perch, Sebastes alutus , in Queen Charlotte Sound, British Columbia. Marine Biology, 139(1), 1-12.