Microsatellite and mtDNA analysis of lake trout, Salvelinus namaycush, from Great Bear Lake, Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems
Article first published online: 26 FEB 2013
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Ecology and Evolution
Volume 3, Issue 1, pages 145–161, January 2013
How to Cite
Ecology and Evolution 2013; 3(1): 145–161
- Issue published online: 26 FEB 2013
- Article first published online: 26 FEB 2013
- Manuscript Accepted: 29 OCT 2012
- Manuscript Revised: 22 OCT 2012
- Manuscript Received: 11 JUN 2012
- The Polar Continental Shelf Project
- 2004. Incipient speciation driven by phenotypic plasticity? Evidence from sympatric populations of Arctic charr. Biol. J. Linn. Soc. 81:611–618. , and .
- 2006. Microsatellite analysis of the phylogeography, Pleistocene history and secondary contact hypotheses for the killifish, Fundulus heteroclitus. Mol. Ecol. 15:1109–1123. , , and .
- 2007. Chinook salmon seasonal movements in Lake Huron determined from coded wire tag recoveries. North Am. J. Fish. Manag. 27:792–803. , , , , and .
- 2009. Phylogeography and sympatric differentiation of the Arctic charr Salvelinus alpinus (L.) complex in Siberia as revealed by mtDNA sequence analysis. J. Fish Biol. 75:368–392. , , , , , , et al.
- 2004. Evidence for two morphotypes of lake charr, Salvelinus namaycush, from Great Bear Lake, Northwest Territories, Canada. Environ. Biol. Fishes 71:21–32.
- 1998. Combined use of SMM and non-SMM methods to infer fine structure and evolutionary history of closely related brook charr (Salvelinus fontinalis, Salmonidae) populations from microsatellites. Mol. Biol. Evol. 15:143–159. , and .
- 2006. Comparison of Bayesian and maximum likelihood inference of population genetic parameters. Bioinformatics 22:341–345.
- 2008. Migrate-N, version 3.0.3. Available at http://popgen.scs.fsu.edu/Migraten.html/ (accessed March 12, 2012). .
- 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations using a coalescent approach. Proc. Natl Acad. Sci. USA 98:4563–4568. , and .
- 2004. Genetix 4.05, logiciel sous windows TM pour la ge′ne′tique des populations, version 4.05. Laboratoire Ge′nome, Populations, Interactions, CNRS UMR 5000, Universite′ de Montpellier II, Montpellier, France. , , , , and .
- 1991. Phylogeographic structure in mitochondrial-DNA of the lake whitefish (Coregonus-Clupeaformis) and its relation to Pleistocene glaciations. Evolution 45:1016–1035. , and .
- 1998. Comparative phylogeography of Nearctic and Palearctic fishes. Mol. Ecol. 7:431–452. , and .
- 1989. Population bottlenecks influence on mitochondrial-DNA diversity and its effect in Coregonine stock discrimination. J. Fish Biol. 35:233–244. , , and .
- 2003. Evidence for resource polymorphism in the lake charr (Salvelinus namaycush) population of Great Bear Lake, Northwest Territories, Canada. Ecoscience 10:509–514. , , and .
- 2001. Holartic phyogeography of Arctic charr (Salvelinus alpinus L.) inferred from mitochondrial DNA sequences. Evolution 55:573–586. , , , , and .
- 1993. Intralacustrine spe- ciation of Salvelinus namaycush in Lake Superior: an investigation of genetic and morphological varia- tion and evolution of lake trout in the Laurentian Great Lakes. Unpubl. Ph.D. diss., University of Michigan, Ann Arbor. .
- 2000. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9:1657–1660. , , and .
- 2005. Asymmetric gene flow and the evolutionary maintenance of genetic diversity in small, peripheral Atlantic salmon populations. Conserv. Genet. 6:823–842. , , , and .
- 2012. Genetic perspectives on Arctic biodiversity. Chapter 7. in H. Meltofte, ed 2013. Arctic biodiversity assessment. Status and trends in Arctic biodiversity. Conservation of Arctic Flora and Fauna, Akureyri. , , , , , , et al.
- 2003. The influence of history and contemporary stream hydrology on the evolution of genteic diversity within species: and examination of microsatellite DNA variaton in bull trout, Salvelinus confluentus, (Pisces: Salmonidae). Evolution 57:328–344. , , , , and .
- 2008. Genetic population structure among source populations for coaster brook trout in Nipigon Bay, Lake Superior. Trans. Am. Fish. Soc. 137:1213–1228. , and .
- 1996. Sources and sinks in population biology. Trends Ecol. Evol. 11:326–330.
- 2008. Landscape genetics and hierarchical genetic structure in Atlantic salmon: the interaction of gene flow and local adaptation. Mol. Ecol. 17:2382–2396. , , , and .
- 1996. Homing in Pacific salmon: mechanisms and ecological basis. J. Exp. Biol. 199:83–91. , and .
- 1999. Genetic and morphological variation between two forms of lacustrine brook charr. J. Fish Biol. 54:955–972. , , , and .
- 1953. The movement of tagged lake trout in Lake Superior, 1950–1952. Trans. Am. Fish. Soc. 82:68–77. , , and .
- 1998. Microsatellites and minisatellites for molecular ecology: theoretical and empirical considerations. Pp. 55–86 in G. Carvalho, ed. Advances in molecular ecology. IOS Press, Amsterdam, the Netherlands. , and .
- 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:2611–2620. , , and .
- 2005. Arlequin. Version 3.0. An integrated software package for population genetics data analysis. Evol. Bioinform. 1:47–50. , , and .
- 2004. Consequences of unequal population size, asymmetric gene flow and sex-biased dispersal on population structure in brook charr (Salvelinus fontinalis). Mol. Ecol. 13:67–80. , , and .
- 2009. Interaction of landscape and life history attributes on genetic diversity, neutral divergence and gene flow in a pristine community of salmonids. Mol. Ecol. 18:4854–4869. , , and .
- 2002. FSTAT: a program to estimate and test gene diversities and fixation indices. Version 184.108.40.206. Available at http://www.unil.ch/izea/softwares/fstat.html (accessed November 2, 2011). .
- 1996. Testing differentiation in diploid populations. Genetics 144:1933–1940. , , , and .
- 2003. Genetic variation over space and time: analyses of extinct and remnant lake trout populations in the Upper Great Lakes. Proc. R Soc. Lond. B Biol. Sci. 270:425–433. , , , and .
- 2006. Effects of coancestry on accuracy of individual assignments to population of origin: examples using Great Lakes lake trout (Salvelinus namaycush). Genetica 127:329–340. , , , , , and .
- 1992. Performing the exact test of Hardy–Weinberg proportion for multiple alleles. Biometrics 48:361–372. , and .
- 2008. Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster. PLoS Biol. 6:1706–1714. , , , , , and .
- 2006. Concordant genetic estimators of migration reveal anthropogenically enhanced source-sink population structure in the River Sculpin, Cottus gobio. Genetics 173:1487–1501. , and .
- 1999. Postglacial recolonization patterns and genetic relationships among whitefish (Coregonus sp.) populations in Denmark, inferred from mitochondrial DNA and microsatellite markers. Mol. Ecol. 8:239–252. , , and .
- 2002. SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol. Ecol. Notes 2:618–620. , and .
- 2003. Microsatellite allele sizes: a simple test to assess their significance on genetic differentiation. Genetics 163:1467–1482. , , , and .
- 2010a. Pleistocene glaciations and contemporary genetic diversity in a Beringian fish, the broad whitefish, Coregonus nasus (Pallas): inferences from microsatellite DNA variation. J. Evol. Biol. 23:72–86. , and .
- 2010b. Genetic population structure of broad whitefish, Coregonus nasus, from the Mackenzie River, Northwest Territories: implications for subsistence fishery management. Can. J. Fish. Aquat. Sci. 67:905–918. , and .
- 2004. Evolution illuminated: salmon and their relatives. Oxford University Press, Oxford, U.K. , and , eds.
- 1996. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol. J. Linn. Soc. 58:247–276.
- 2004. Genetic consequences of climatic oscillations in the Quaternary. Philos. Trans. R Soc. Lond. B Biol. Sci. 359:183–195.
- 2009. Inferring weak population structure with the assistance of sample group information. Mol. Ecol. Resour. 9:1322–1332. , , , and .
- 1999. Correlation of pairwise genetic and geographic distance measures: inferring the relative Influences of gene flow and drift on the distribution of genetic variability. Evolution 53:1898–1914. , and .
- 1996. Microsatellites, from molecules to populations and back. Trends Ecol. Evol. 11:424–429. , and .
- 1975a. Physical and chemical characteristics of Great Bear Lake, Northwest territories. J. Fish. Res. Board Can. 32:1971–1987.
- 1975b. Distribution of fish species in Great Bear Lake, Northwest Territories, with reference to zooplankton, benthic invertebrates, and environmental conditions. J. Fish. Res. Board Can. 32:1989–2004.
- 2003. Contrasting patterns of mitochondrial and microsatellite population structure in fragmented populations of greater prairie-chickens. Mol. Ecol. 12:3335–33347. , , and .
- 2005. HP-RARE 1.0: a computer program for performing rarefaction on measures of allelic richness. Mol. Ecol. Notes 5:187–189.
- 2007. The origins of ecotypic variation of rainbow trout: a test of environmental vs. genetically based differences in morphology. J. Evol. Biol. 20:725–736. , , and .
- 1963. Movement of tagged Great Slave Lake fish. J. Fish. Res. Board Can. 20:319–326.
- 2002. Microsatellite data resolve phylogeographic patterns in European grayling, Thymallus thymallus, Salmonidae. Heredity 88:391–401. , , , , , and .
- 1995. Review of genetics of lake trout in the great lakes: history, molecular genetics, physiology, strain comparisons, and restoration management. J. Great Lakes Res. 21:348–363. , and .
- 2005. Adaptive and neutral genetic variation and colonization history of Atlantic salmon, Salmo salar. Environ. Biol. Fishes 74:297–308.
- 2008. The landscape genetics of yellow perch (Perca flavescens) in a large fluvial ecosystem. Mol. Ecol. 17:1702–1717. , , , and .
- 1986. Zoogeography of fishes of the Yukon and Mackenzie basins. Pp. 639–674 in C. H. Hocutt and E. O. Wiley, eds. The zoogeography of North American freshwater fishes. Wiley, New York. , and .
- 2001. Contrasting patterns of mitochondrial DNA and microsatellite introgressive hybridization between lineages of lake whitefish (Coregonus clupeaformis); relevance for speciation. Mol. Ecol. 10:965–985. , , and .
- 1998. Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conserv. Biol. 12:228–237. , and .
- 1967. The detection of disease clustering and a generalized regression approach. Cancer Res. 27:209–220.
- 2001. Delineation of sympatric morphotypes of lake trout in Lake Superior. Trans. Am. Fish. Soc. 130:1233–1240. , and .
- 2008. Habitat use and movement patterns of brook trout in Nipigon Bay, Lake Superior. Trans. Am. Fish. Soc. 137:1203–1212. , and .
- 2006. Beyond Bonferroni: less conservative analysis for conservation genetics. Conserv. Genet. 7:783–787.
- 1977. Drift variances of Fst and Gst statistics obtained from a finite number of isolated populations. Theor. Popul. Biol. 11:307–325. , and .
- 2006. Fine-scale natal homing and localized movement as shaped by sex and spawning habitat in Chinook salmon: insights from spatial autocorrelation analysis of individual genotypes. Mol. Ecol. 15:4589–4602. , , , , and .
- 2010. Population structure of lake trout (Salvelinus namaycush) in a large glacial-fed lake inferred from microsatellite DNA and morphological analysis. Can. J. Fish. Aquat. Sci. 67:1171–1186. , , and .
- 2004. Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes 4:535–538. , , , and .
- 2004. Direct, real-time estimation of migration rate using assignment methods: a simulation-based exploration of accuracy and power. Mol. Ecol. 13:55–65. , , , and .
- 2005. Genetic evaluation of a Great Lakes lake trout hatchery program. Trans. Am. Fish. Soc. 134:872–891.
- 2003. Genetic assessment of strain-specific sources of lake trout recruitment in the Great Lakes. Trans. Am. Fish. Soc. 132:877–894. , , , , and .
- 2004. Genetic diversity of wild and hatchery lake trout populations: relevance for management and restoration in the Great Lakes. Trans. Am. Fish. Soc. 133:674–691. , , and .
- 2007. Population structure and gene flow reversals in Atlantic salmon (Salmo salar) over contemporary and long-term temporal scales: effects of population size and life history. Mol. Ecol. 16:4504–4522. , , and .
- 2009. Gene flow and species delimitation. Trends Ecol. Evol. 24:386–393. , and .
- 1991. After the Ice Age. The return of life to glaciated North America. University of Chicago press, Chicago, IL.
- 2012. Microsatellite variation and genetic structure of brook trout (Salvelinus fontinalis) populations in Labrador and neighboring Atlantic Canada: evidence for ongoing gene flow and dual routes of post-Wisconsinan colonization. Ecol. Evol. 2:885–898. , , , , and .
- 2005. Conservation genetics of inland lake trout in the upper Mississippi River basin: stocked or native ancestry? Trans. Am. Fish. Soc. 134:789–802. , , , and .
- 1999. BOTTLENECK: a computer program for detecting recent reductions in effective population size using allele frequency data. J. Hered. 90:502–503. , , and .
- 2004. GeneClass2: a software for genetic assignment and first-generation migrant detection. J. Hered. 95:536–539. , , , , , and .
- 2009. Ecological and genetic differentiation among the Arctic charr of Lake Aigneau, Northern Québec. Ecol. Freshwat. Fish. 18:445–460. , , , and .
- 2000. Inference of population structure using multilocus genotype data. Genetics 155:945–959. , , and .
- 2005. The behavior and ecology of Pacific salmon and trout. University of Washington Press, Seattle, WA, USA.
- 2007. TRACER, Version 1.5: MCMC Trace Analysis Package. Available from http://tree.bio.ed.ac.uk/software/tracer/ (accessed March 15, 2012). , and .
- 1997. Detecting immigration by using multilocus genotypes. Proc. Natl Acad. Sci. USA 94:9197–9201. , and .
- 1998. Postglacial fish dispersal of fish from the Mississippi refuge to the Mackenzie River basin. Can. J. Fish. Aquat. Sci. 55:893–899. , and .
- 1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145:1219–1228.
- 2008. Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resour. 8:103–106.
- 1990. Growth, survival, and straying of the three lake trout strains stocked in the refuge of northern Lake Michigan. Michigan Department of Natural Resources Fisheries Research Report 1977, Ann Arbor, Michigan. .
- 2002. Lake trout movements in Northwestern Lake Michigan. North Am. J. Fish. Manag. 22:737–749. , , , , and .
- 1998. Freshwater fishes of Canada. Bull. Fish. Res. Board Can. 184:996pp. , and .
- 2011. Historic divergence with contemporary connectivity in a catadromous fish, the estuary perch (Macquaria colonorum). Can. J. Fish. Aquat. Sci. 68:304–318. , , , , , and .
- 1985. Gene Flow in Natural-Populations. Annu. Rev. Ecol. Syst. 16:393–430.
- 1987. Gene flow and the geographic structure of natural populations. Science 236:787–792.
- 1994. Glacial Lake Mcconnell - Paleogeography, Age, Duration, and Associated River Deltas, Mackenzie River Basin, Western Canada. Quatern. Sci. Rev. 13:829–843.
- 2010. The Biology of Speciation. Evolution 64:295–315. , , , and .
- 2004. Phylogeographic lineages of Arctic grayling (Thymallus arcticus) in North America: divergence, origins and affinities with Eurasian Thymallus. Mol. Ecol. 13:1533–1549. , and .
- 2005. Population subdivison and genetic signatures of demographic changes in (Arctic grayling) from an impounded watershed. Can. J. Fish. Aquat. Sci. 62:2548–2559. , and .
- 2003. Evidence for fine-scale natal homing among island beach spawning sockeye salmon, Oncorhynchus nerka. Environ. Biol. Fishes 67:77–85. , , and .
- 2010. Genetic structure and diversity among brook trout from Isle Royale, Lake Nipigon, and three Minnesota tributaries of Lake Superior. North Am. J. Fish. Manag. 30:400–411. , , , and .
- 1989. Statistical methods to test for nucleotide mutation hypothesis by DNA polymorphism. Genetics 123:585–595.
- 2010. The influence of Wisconsinan glaciation and contemporary stream hydrology on microsatellite DNA variation in rainbow trout (Oncorhynchus mykiss). Can. J. Fish. Aquat. Sci. 67:919–935. , , and .
- 1992. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+ C-content biases. Mol. Biol. Evol. 9:678–687.
- 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731–2739. , , , , , and .
- 2008. Genetic analysis of sympatric char populations in western Alaska: Arctic char (Salvelinus alpinus) and Dolly Varden (Salvelinus malma) are not two sides of the same coin. J. Evol. Biol. 21:1609–1625. , , , , and .
- 2011. Connectivity among populations of pygmy whitefish (Prosopium coulterii) in northwestern North America inferred from microsatellite DNA analyses. Can. J. Zool. 89:255–266. , , , and .
- 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132:619–633. , , and .
- 2001a. Clinal variation at microsatellite loci reveals historical secondary intergredation between glacial races of Coregonus artedi (Teleostei: Coregoninae). Evolution 55:2274–2286. , and .
- 2001b. Mitochondrial DNA phylogeography of lake cisco (Coregonus artedi): evidence supporting extensive secondary contacts between two glacial races. Mol. Ecol. 10:987–1001. , and .
- 2007. Life-history and habitat features influence the within-river genetic structure of Atlantic salmon. Mol. Ecol. 16:2638–2654. , , , and .
- 2010. Recognizing the temporal distinctions between landscape genetics and phylogeography. Mol. Ecol. 19:2605–2608.
- 2010. Genetic clustering methods reveal bull trout (Salvelinus confluentus) fine-scale population structure as a spatially nested hierarchy. Conserv. Genet. 11:1421–1433. , , and .
- 2000. Phylogeography and arctic biodiversity: a review. Ann. Zool. Fenn. 37:217–231. , and .
- 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370. , and .
- 2010. Genetic variation and effective population size in isolated populations of coastal cutthroat trout. Conserv. Genet. 11:1929–1943. , , , , , and .
- 1996. Phylogeographic origins of lake trout (Salvelinus namaycush) in eastern North America. Can. J. Fish. Aquat. Sci. 53:2764–2775. , and .
- 1998. Phylogeography and postglacial dispersal of lake trout, Salvelinus namaycush, in North America. Can. J. Fish. Aquat. Sci. 55:1010–1024. , and .
- 2003. Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163:1177–1191. , and .
- 2010. The impact of Pleistocene glaciation across the range of a widespread European coastal species. Mol. Ecol. 19:4535–4553. , and .
- 1996. Phylogeography and postglacial dispersal of Arctic charr Salvelinus alpinus in North America. Mol. Ecol. 5:187–197. , , , and .
- 2011. Phylogeography and the origins of range disjunctions in a north temperate fish, the pygmy whitefish (Prosopium coulterii), inferred from mitochondrial and nuclear DNA sequence analysis. J. Biogeogr. 38:1557–1569. , , and .