Signals of adaptive genetic variation in BC’s nearshore rockfish: implicat ions for population connectivity Matthew Siegle Introduction Degradation of the world’s oceans, including fishery overexploitation (Botsford et al. 1997), loss of marine biodiversity (Worm et al. 2006), increases in eutrophication (Rabalais et al. 2009), and the effects of climate change (Lotze et al. 2006) have forced scientists and resource managers to rethink current approaches to the maintenance of marine ecosystems (Lubchenco et al. 2003, Hughes et al. 2005). Changes from single species to ecosystem level management methods have provided insight into the usefulness ofmarine reserves for the preservation of marine ecosystem services (Agardy 1994, Halpern 2003, Lubchenco et al. 2003). Reserves are able to mitigate human pressures through a variety of measures, including the protection of vulnerable life stages, mating and nursery grounds, providing spatial refuge for harvested species and exporting individuals into depleted areas. However, Allison et al. (1998) warn against viewing marine reserves as a magic bullet, and highlight that communities residing in marine reserves are highly influenced by the continuous flow of water through reserve areas, and thus susceptible to threats originating outside reserve boundaries (e.g. pollution). Nevertheless, marine reserves remain a powerful tool in conservation and management. The empirical data showing the positive role reserves have in increasing biodiversity, abundances and densities within their boundaries is reasonably well established (Castilla and Bustamante 1989, Roberts 1995, Halpern and Warner 2002, Halpern 2003). What is less clear, however, is the role reserves play in exporting these benefits to outside areas (Agardy 1994, Palumbi 2003). Understanding how reserves function in the greater ecosystem beyond their
22
Embed
Signals of Adaptive Genetic Variation in BC’s Nearshore Rockfish: Implications
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
8/14/2019 Signals of Adaptive Genetic Variation in BC’s Nearshore Rockfish: Implications
environmental gradients, including salinity, depth, primary production,
varying ocean current patterns and a latitudinal cline. It is likely that
these environmental factors promote further population subdivision
than was provided by investigating neutral genetic structure.
Questions
Yelloweye
• Are there signatures of adaptive differentiation between“inside” and “outside” YE DUs?
• Do estimates of adaptive differentiation provide evidence forfurther substructure within each YE DU?
• Is adaptive differentiation correlated along any environmentalgradients?
Quillback
•
Do estimates of adaptive differentiation provide evidence forgenetic structure among coast-wide samples?o If so, is adaptive differentiation correlated along any
environmental gradients?Interspecific
• Does the degree of adaptive differentiation observed reflectthe varying levels of gene flow suggested in the Yamanaka etal. reports?
• If adaptive differentiation is found to occur along anyenvironmental gradients, do YE and QB rockfish share thesame pattern of differentiation?
Methods Sampling
Approximately 2500 YE individuals and 1500 QB individuals were
collected by DFO longline surveys from all over the BC coast (Figure
3a, b). Morphological and age data were collected in addition to
genetic tissue samples, and are included in the Yamanaka et al.
(2006a, b) reports.
Molecular Methods
I will utilize amplified fragment length polymorphisms (AFLPs)modified from Vos et al. (1995) to identify signatures of selection
across the genome of yelloweye and quillback rockfish. AFLPs utilize
restriction enzymes to cut the genome at known sequences. Primer
adapters (DNA sequences with 3’ overhangs complementary to the
single-strand 5’ overhangs left over from the restriction enzymes) are
8/14/2019 Signals of Adaptive Genetic Variation in BC’s Nearshore Rockfish: Implications
Figure 4: AFLP screening schematic. (1) Individual fish from the same
area will be pooled together. (2) Different groups will be screened foroutlier loci with many primer pairs. (3) Primer pairs that amplify outlierloci will be identified. (4) The groups will be screened at the individuallevel with the primer pairs known to amplify candidate loci.
8/14/2019 Signals of Adaptive Genetic Variation in BC’s Nearshore Rockfish: Implications
sufficient for marine conservation. Ecological Applicatinos (8)1 Supplement pp. S79-S92.
Antao, T., Lopes, A., Lopes, R.J., Beja-Pereira, A., Luikart, G. (2008) LOSITAN: Aworkbench to detect molecular adaptation based on a Fst-outlier method. BMCBioinformatics (9)323, doi:10.1186/1471-2105-9-323
Beaumont, M.A. and Nichols, R.A. (1996) Evaluating loci for use in the geneticanalysis of population structure. Proceedings of the Royal Society of London, Series B(263) pp. 1619-1626.
Beaumont, M.A. and Balding, D.J. (2004) Identifying adaptive genetic divergenceamong populations from genome scans. Molecular Ecology (13) pp. 969-980.
Bonin, A., Taberlet, P., Miaud, C., Pompanon, F. (2006) Explorative genome scan todetect candidate loci for adaptation along a gradient of altitude in the common frog(Rana temporaria). Molecular Biology and Evolution (23)4 pp. 773-783.
Botsford, L.W., Castilla, J.C., Peterson, C.H. (1997) The management of fisheries andmarine ecosystems. Science (277) pp. 509-515. Carvalho, G.R., Hauser, L. (1994) Molecular genetics and the stock concept infisheries. Reviews in Fish Biology and Fisheries (4)3 pp. 326-350.
Castilla, J.C. and Bustamante, R.H. (1989) Human exclusion from rocky intertidal of Las Cruces, central Chile: effects on Durvillaea Antarctica (Phaeophyta, Durvilleales).Marine Ecology Progress Series (50) pp. 203-214.
Conover, D.O., Clarke, L.M., Munch, S.B., Wagner, G.N. (2006) Spatial and temporalscales of adaptive divergence in marine fishes and the implications for conservation.
Journal of Fish Biology (69) Supplement C, pp. 21-47.
COSEWIC 2002. COSEWIC assessment and status report on the Bocaccio Sebastes paucispinis in Canada. Committee on the Status of Endangered Wildlife in Canada.Ottawa.
COSEWIC. 2007. COSEWIC assessment and status report on the canary rockfishSebastes pinniger in Canada. Committee on the Status of Endangered Wildlife inCanada. Ottawa. (www.sararegistry.gc.ca/status/status_e.cfm).
COSEWIC. 2008. COSEWIC assessment and status report on the YE Rockfish Sebastesruberrimus, Pacific Ocean inside waters population and Pacific Ocean outside waterspopulation, in Canada. Committee on the Status of Endangered Wildlife in Canada.Ottawa. (www.sararegistry.gc.ca/status/status_e.cfm).
DeMartini, E.E. (1993) Modeling the potential of fishery reserves for managing Pacific
coral reef fishes. Fishery Bulletin (91) pp. 414-427.
Federal Register (2008) Listing Endangered and Threatened Species and DesignatingCritical Habitat: Notice on Finding on a Petition to List Five Rockfish Species in PugetSound (WA) as Endangered or Threatened Species Under the Endangered SpeciesAct.”73(52).
Halpern, B.S. and Warner, R.R. (2002) Marine reserves have rapid and lasting effects.
8/14/2019 Signals of Adaptive Genetic Variation in BC’s Nearshore Rockfish: Implications
Halpern, B.S. (2003) The impact of marine reserves: do reserves work and doesreserve size matter? Ecological Applications (13)1 Supplement, pp. S117-S137.Hamilton, S.L., Regetz, J., Warner, R.R. (2008) Postsettlement survival linked to larvallife in a marine fish. Proceedings of the National Academy of Sciences. (105)5 pp.
1561-1566.
Hauser, L. and Carvalho, G.R. (2008) Paradigm shifts in marine fisheries genetics:ugly hypotheses slain by beautiful facts. Fish and Fisheries (9) pp. 333-362.
Hemmer-Hansen, J., Nielsen, E.E., Frydenberg, J., Loeschcke, V. (2007) Adaptivedivergence in a high gene flow environment: Hsc70 variation in the Europeanflounder (Platichthys flesus L.) Heredity (99) pp. 592-600.
Hughes, T.P., Bellwood, D.R., Foke, C., Steneck, R.S., Wilson, J. (2005) New paradigmsfor supporting the resilience of marine ecosystems. Trends in Ecology and Evolution(20)7 pp. 380-386.
Hyde J.R. and Vetter, R.D. (2007) The origin, evolution, and diversification of rockfishes of the genus Sevastes (Cuvier). Molecular Phylogenetics and Evolution (44)pp. 790-811.
Gagnaire, P.A., Albert, V., Jonsson, B., Bernatchez, L. (2009) Natural selectioninfluences AFLP intraspecific variability and introgression patterns in Atlantic eels.Molecular Ecology (18) pp. 1678-1691.
Lea, R.N., McAllister, R.D. VenTresca, D. (1999) Biological aspects of nearshorerockfishes of the genus Sebastes from Central California. State of CaliforniaDepartment of Fish and Game Fish Bulletin (177).
Levin, L.A. (2006) Recent progress in understanding larval dispersal: new directionsand digressions. Integrative and Comparative Biology 46(3) pp. 282-297.
Lotze, H.K., Lenihan, H.S., Bourque, B.J., Bradbury, R.H., Cooke, R.G., Kay, M.C.,Kidwell, S.M., Kirby, M.X., Peterson, C.H., Jackson, J.B.C. (2006) Depletion,degradation and the recovery potential of estuaries and coastal seas. Science(312)5781 pp. 1806-1809.
Love, M.S., Yoklavich, M., Thorsteinson, L. (2002) The Rockfishes of the NortheastPacific. University of California Press, Los Angeles.
Lubchenco, J., Palumbi, S.R., Gaines, S.D., Andelman, S. (2003) Plugging a hole in theocean: the emerging science of marine reserves. Ecological Applications (13)1Supplement, pp. S3-S7.
McKay, J.K. and Latta, R.G. (2002) Adaptive population divergence: markers, QTL andtraits. Trends in Ecology and Evolution (17), pp. 285-291.
Palumbi, S.R. (1994) Genetic divergence, reproductive isolation, and marinespeciation. Annual Review of Ecology and Systematics (25) pp. 547-572.
Palumbi, S.R. (2003) Population genetics, demographic connectivity, and the designof marine reserves. Ecological Applications (13)1 Supplement, pp. S146-S158.
8/14/2019 Signals of Adaptive Genetic Variation in BC’s Nearshore Rockfish: Implications
Rabalais, N.N., Turner, R.E., Diaz, R.J., Justic, D. (2009) Global change and
eutrophication of coastal waters. ICES Journal of Marine Science (66) pp. 1528-1537.
Selkoe, K.A., Henzler, C.M., Gaines, S.D. (2008) Seascape genetics and the spatialecology of marine populations. Fish and Fisheries (9) pp. 363-377.
Slatkin, M. (1973) Gene flow and selection in a two-locus system. Genetics (81) pp.787-802.
Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., Frijters, A.,Pot, J., Peleman, J., Kuiper, M. et al. (1995) AFLP: a new technique for DNAfingerprinting. Nucleic Acids Research (23)21 pp. 4407-4414.
Waples, R.S. (1998) Separating the wheat from the chaff: patterns of geneticdifferentiation in high gene flow species. Genetics (89), pp. 438-450.
Ward, R.D., Woodwark, M., Skibinski, D.O.F. (1994) A comparison of genetic diversitylevels in marine, freshwater and anadromous fishes. Journal of Fish Biology (44)2 pp.213-232.
Warner, R.R. and Cowen, R.K. (2002) Local retention of production in marinepopulations: evidence, mechanisms, and consequences. Bulletin of Marine Science70(1) Supplement, pp. 245-259.
Whitlock, M.C. and McCauley, D.E. (1999) Indirect Measures of gene flow andmigration: Fst ≠ 1/(4Nm+1) Heredity (82) pp. 117-125.
Worm, B., Barbier, E.B., Beaumont, N., Duffy, J.E., Folke, C., Halpern, B.S., Jackson, J.B.C., Lotze, H.K., Micheli, F., Palumbi, S.R., Sala, E., Selkoe, K.A., Stachowicz, J.J.,Watson, R. (2006) Impacts of biodiversity loss on ocean ecosystem services. Science(314) pp. 787-790.
Wright, S. (1931) Evolution in Mendelian populations. Genetics (16) pp. 97-159.
Yamanaka, K.L. and Lacko, L.C. 2001. Inshore Rockfish (Sebastes ruberrimus, S.maliger, S. caurinus, S. melanops, S. nigrocinctus, and S. nebulosus) StockAssessment for the West Coast of Canada and Recommendations for Management.Canadian Science Advisory Secretariat Research Document 2001/139.
Yamanaka, K.L., Lacko, L.C., Withler, R., Grandin, C., Lockhead, J.K., Martin, J.C.,Olsen, N., Wallace, S.S. (2006a) A review of YE rockfish Sebastes ruberrimus along
the Pacific coast of Canada: biology, distribution and abundance trends. CanadianScience Advisory Secretariat . Research Document 2006/076.
Yamanaka, K.L., Lacko, L.C., Miller-Saunders, K., Grandin, C., Lochead, J.K., Martin, J.C., Olsen, N., Wallace, S.S. (2006b) A review of QB rockfish, Sebastes maliger , alongthe Pacific coast of Canada: biology, distribution and abundance trends. CanadianScience Advisory Secretariat . Research Document 2006/nnn.
Zhivotovsky, L. (1999) Estimating population structure in diploids with multilocus
8/14/2019 Signals of Adaptive Genetic Variation in BC’s Nearshore Rockfish: Implications