Multidisciplinary population monitoring when demographic data are sparse: a case study of remote trout populations
Article first published online: 8 NOV 2013
© 2013 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Ecology and Evolution
Volume 3, Issue 15, pages 4954–4969, December 2013
How to Cite
Ecology and Evolution 2013; 3(15): 4954–4969
- Issue published online: 10 DEC 2013
- Article first published online: 8 NOV 2013
- Manuscript Accepted: 30 SEP 2013
- Manuscript Received: 23 SEP 2013
- Niskamoon Corporation, Quebec
- 1973. Information theory as an extension of the maximum likelihood principle. Pp. 267–281 in B. N. Petrov and F. Csaki, eds. Second international symposium on information theory. Akademiai Kiado, Budapest, Hungary.
- 2011. Genome-wide mapping of Sox6 binding sites in skeletal muscles reveals both direct and indirect regulation of muscle terminal differentiation by Sox6. BMC Dev. Biol. 11:59. , , and .
- 1995. Specific microsatellite loci for brook charr reveal strong population subdivision on a microgeographic scale. Fish Biol. 47:47(Suppl. A)177–185. , , , and .
- 2010. Early detection of population declines: high power of genetic monitoring using effective population size estimators. Evol. Appl. 4:144–154. , , and .
- 2003. Demographic and genetic estimates of effective population size (Ne) reveals genetic compensation in steelhead trout. Mol. Ecol. 12:35–49. and .
- 2004. GENETIX 4.02, logiciel sous Windows™ pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UPR 9060, Université de Montpellier II, Montpellier, France. , , , , and .
- 2012. Concurrent habitat and life history influences on effective/census population size ratios in stream-dwelling trout. Ecol. Evol. 2:562–573. , , , , , and .
- 1999. Sacred ecology: traditional ecological knowledge and resource management. Taylor and Francis, Philadelphia, PA.
- 2002. Model selection and inference: a practical information-theoretic approach. Springer Verlag, New York, NY. and .
- 2000. Characterization of microsatellite and minisatellite loci in Atlantic salmon (Salmo salar L.) and cross-species amplification in other salmonids. Mol. Ecol. 9:2155–2234. , , and .
- 2011. Census and genetically effective population size in a lake resident population of brown trout Salmo trutta. J. Fish Biol. 79:2074–2082. , , , , and .
- 2013. Population genetics of the American eel (Anguilla rostrata): FST = 0 and NAO effects on demographic fluctuations of a panmictic species. Mol. Ecol. 22:1763–1776. , , , , , and .
- 2011. Temporal genetic stability and high effective population size despite fisheries-induced life-history trait evolution in the North Sea sole. Mol. Ecol. 20:3555–3568. , , , , and .
- 2010. The power of genetic monitoring for studying demography, ecology and genetics of a reintroduced bear population. Mol. Ecol. 19:3938–3951. , , , , , , et al.
- 2005. Characterization of 20 highly variable tetranucleotide microsatellite loci for bull trout (Salvelinus confluentus) and cross-amplification in other Salvelinus species. Mol. Ecol. Notes 5:582–585. and .
- 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol. Bioinform. Online 1:47–50. , , and .
- 1997. Collection and analysis of traditional ecological knowledge about a population of Arctic tundra caribou. Arctic 50:17–28. and .
- 2008. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 180:977–993. and .
- 2005. Adaptive migratory divergence among sympatric brook charr populations. Evolution 59:611–624. and .
- 2004. Consequences of unequal population size, asymmetric gene flow, and sex-biased dispersal for population structure in brook charr (Salvelinus fontinalis). Mol. Ecol. 13:67–80. , , and .
- 2005. Migratory charr schools exhibit population and kin associations beyond juvenile stages. Mol. Ecol. 14:3133–3146. , , and .
- 2006. Integrating traditional and evolutionary knowledge in biodiversity conservation: a population level case study. Ecol. Soc. 11:4. , , , , and .
- 2007a. Comparative estimation of effective population sizes and temporal gene flow in two contrasting population systems. Mol. Ecol. 16:3866–3889. , , , , , and .
- 2007b. Loss of historical immigration and the unsuccessful rehabilitation of extirpated salmon populations. Conserv. Genet. 8:527–546. , , , and .
- 2011. Extent and scale of local adaptation in salmonid fishes: review and meta-analysis. Heredity 106:404–420. , , , , and .
- 2012. Allele frequency stability in large, wild exploited populations over multiple generations: insights from Alaska sockeye salmon (Oncorhynchus nerka). Can. J. Fish. Aquat. Sci. 69:916–929. , , , and .
- 2006. Genetic restoration of a stocked brown trout Salmo trutta population using microsatellite DNA analysis of historical and contemporary samples. J. Appl. Ecol. 43:669–679. , , , , and .
- 2012. Monitoring adaptive genetic responses to climate change. Mol. Ecol. 21:1311–1329. , , , , and the GeM Working Group.
- 2001. Is catch-per-unit-effort proportional to abundance? Can. J. Fish. Aquat. Sci. 58:1760–1772. , , and .
- 2002. Temporal change in genetic structure and effective population size in steelhead trout (Oncorhynchus mykiss). Mol. Ecol. 11:197–214. , , , and .
- 2011. Evolutionary principles and their practical application. Evol. Appl. 4:159–183. , , , , , , et al.
- 2000. Using traditional ecological knowledge in science: methods and applications. Ecol. Appl. 10:1270–1274.
- 2008. The nature of fisheries- and farming-induced evolution. Mol. Ecol. 17:294–313. and .
- 2011. Historical changes in genotypic frequencies at the Pantophysin locus in Atlantic cod (Gadus morhua) in Icelandic waters: evidence for fisheries-induced selection? Evol. Appl. 4:562–573. , , , , , , et al.
- 2007. Managing evolving fish stocks. Science 318:1247–1248. , , , , , , et al.
- 2012. Dynamics of introgressive hybridization assessed by coding genes SNP population genomics in stocked brook charr (Salvelinus fontinalis). Mol. Ecol. 21:2877–2895. , , , and .
- 2002. Estimating allelic richness: effects of sample size and bottlenecks. Mol. Ecol. 11:2445–2449.
- 2004. Ten polymorphic microsatellite markers from Arctic charr (Salvelinus alpinus): linkage analysis and amplification in other salmonids. Anim. Genet. 35:479–481. , , , , , and .
- 2009. Wolf survival and population trend using non-invasive mark-recapture techniques in the Western Alps. J. Appl. Ecol. 46:1003–1010. , , , , , and .
- 1990. Application of native knowledge in EIA: Inuit, elders, and Hudson Bay oil. Canadian Environmental Assessment Research Council, Ottawa, ON.
- 2011. Comparison of FST outlier tests for SNP loci under selection. Mol Ecol Resour 11:184–194. and .
- 2009. Population genomics of marine fishes: identifying adaptive variation in space and time. Mol. Ecol. 18:3128–3150. , , , and .
- 2012. Genetic monitoring and complex population dynamics: insights from a 12-year study of Rio Grande silvery minnow. Evol. Appl. 5:553–574. , , and .
- 2012. Effective/census population size ratio estimation: a compendium and appraisal. Ecol. Evol. 2:2357–2365. and .
- 2002. Dynamic pool models I: Interpreting the past using Virtual Population Analysis. Pp. 127–136 in P. J. B. Hart and J. D. Reynolds, eds. Handbook of fish biology and fisheries. Blackwell Science, Oxford, U.K.
- 1980. The brook charr, Salvelinus fontinalis. Pp. 141–203 in E. K. Balon, ed. Charrs: Salmonid fishes of the genus Salvelinus. Dr W. Junk Publishers, The Hague, the Netherlands.
- 1995. GENEPOP (version 3.1): population genetics software for exact tests and ecumenicism. J. Hered. 86:248–249. and .
- 2008. A roadmap for coasters: landscapes, life histories and conservation of brook trout. Trans. Am. Fish. Soc. 137:1179–1191.
- 2012a. Coding gene SNP mapping reveals QTL related to growth and stress response in brook charr (Salvelinus fontinalis). G3 (Bethesda) 2:707–720. , , , and .
- 2012b. Coding gene SNP mapping and QTL detection for physiological reproductive traits in brook charr, Salvelinus fontinalis. G3 (Bethesda) 2:379–392. , , , , and .
- 2010. Population diversity and the portfolio effect in an exploited species. Nature 465:609–613. , , , , , , et al.
- 2007. Genetic monitoring as a promising tool for conservation and management. Trends Ecol. Evol. 22:25–33. , , and .
- 2003. Census vs. effective population size in chinook salmon: large- and small-scale environmental perturbation effects. Mol. Ecol. 12:2571–2583. and .
- Statistics Canada. 2012. 2011 Census of population. Statistics Canada, Mistissini, QC.
- 2012. What can patterns of differentiation across plant genomes tell us about adaptation and speciation? Philos. Trans. R. Soc. Lond. B Biol. Sci. 367:364–373. , , , , , and .
- 2010. When are genetic methods useful for estimating contemporary abundance and detecting population trends? Mol Ecol Resour 10:684–692. , , , et al.
- 2012. Detecting population recovery using gametic disequilibrium-based effective population size estimates. Conserv. Genet. Resour. 4:987–989. , , , and .
- 1999. Species pairs of north temperate freshwater fishes: taxonomy, evolution, and conservation. Rev. Fish Biol. Fisheries 9:299–324.
- 2012. A simulation study on the performance of differentiation-based methods to detect selected loci using linked neutral markers. J. Evol. Biol. 25:1364–1376. , , and .
- 2001. A pseudo-likelihood method for estimating effective population size from temporally placed samples. Genet. Res. 78:243–257.
- 2003. Estimating effective population size and migration rates from genetic samples over space and time. Genetics 163:429–446. and .
- 1990. Conservation genetics of Pacific salmon III. Estimating effective population size. J. Hered. 81:277–289.
- 2010. Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evol. Appl. 3:244–262. and .
- 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370. and .