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Effects of coancestry on accuracy of individual assignments to population of origin: examples using Great Lakes lake trout (Salvelinus namaycush)

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Abstract

Methods for assigning individuals to population of origin are widely used in ecological genetics, resources management, and forensics. Characteristics of genetic data obtained from putative source populations that enhance accuracy of assignment are well established. How non-independence within and among unknown individuals to be classified [i.e., gene correlations within individual (inbreeding) and gene correlations among individuals within group (coancestry)] affect assignment accuracy is poorly understood. We used empirical data for six microsatellite loci and offspring from full-sib crosses of hatchery strains of lake trout (Salvelinus namaycush; Salmonidae) representing known levels of coancestry (mean θ = 0.006 and 0.06) within families to investigate how gene correlations can affect assignment. Additional simulations were conducted to further investigating the influence of allelic diversity (2, 6 or 10 alleles per locus) and inbreeding (F = 0.00, 0.05, and 0.15) on assignment accuracy for cases of low and high inter-population variance in allele frequency (mean F st = 0.01 and 0.1, respectively). Inbreeding had no effect on accuracy of assignments. In contrast, variance in assignment accuracy across replicated simulations, and for each empirical case study increased with increasing coancestry, reflecting non-independence of probabilities of correct assignment among members of kin groups. Empirical estimates of assignment error rates should be interpreted with caution if appreciable levels of coancestry are suspected. Additional emphasis should be placed on sampling designs (spatially and temporally) that define or minimize the potential for sampling related individuals.

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References

  • B. Angers L. Bernatchez (1996) ArticleTitleUsefulness of heterologous microsatellites obtained from brood charr, Salvelinus fontinalis Mitchill, in other Salvelinus species Mol. Ecol. 5 317–319 Occurrence Handle8673280 Occurrence Handle1:STN:280:DyaK283jvFKmsg%3D%3D Occurrence Handle10.1046/j.1365-294X.1996.00105.x

    Article  PubMed  CAS  Google Scholar 

  • K.E. Arnold (2000) ArticleTitleKin recognition in rainbow fish (Melanotaenia eachamensis): sex, sibs and shoalings Behav. Ecol. Sociobiol. 48 385–391 Occurrence Handle10.1007/s002650000253

    Article  Google Scholar 

  • D. Bekkevold M.M. Hansen V. Loeschke (2002) ArticleTitleMale reproductive competition in spawning aggregations of cod (Gadus morhua, L.) Mol. Ecol. 11 91–102 Occurrence Handle11903907 Occurrence Handle1:STN:280:DC%2BD387ntVWjtw%3D%3D Occurrence Handle10.1046/j.0962-1083.2001.01424.x

    Article  PubMed  CAS  Google Scholar 

  • Belkhir, K., P. Borsa, L. Chikhi, N. Raufaste & F. Bonhomme, 2001. Genetix 4.02, logiciel sous Windows™ pour la génétique des populations. UMR CNRS 5171 Génome, Populations et Interactions, Université des Sciences et Techniques du Languedoc, Montpellier, France

  • L. Bernatchez P. Duchesne (2000) ArticleTitleIndividual-based genotype analysis in studies of parentage and population assignment: how many loci, how many alleles? Can. J. Fish. Aquat. Sci. 57 1–12 Occurrence Handle10.1139/cjfas-57-1-1

    Article  Google Scholar 

  • O. Berry M.D. Tocher S.D. Sarre (2004) ArticleTitleCan assignment tests measure dispersal? Mol. Ecol. 13 551–561 Occurrence Handle14871360 Occurrence Handle10.1046/j.1365-294X.2004.2081.x

    Article  PubMed  Google Scholar 

  • V. Castric L. Bernatchez (2004) ArticleTitleIndividual assignment test reveals differential restriction to dispersal between two salmonids despite no increase of genetic differences with distance Mol. Ecol. 13 1299–1312 Occurrence Handle15078465 Occurrence Handle1:CAS:528:DC%2BD2cXktl2rtrg%3D Occurrence Handle10.1111/j.1365-294X.2004.02129.x

    Article  PubMed  CAS  Google Scholar 

  • V. Castric L. Bernatchez K. Belkhir F. Bonhomme (2002) ArticleTitleHeterozygote deficiences in small lacustrine populations of brook charr Salvelinus fontinalis Mitchill (Pisces, Salmonidae): a test of alternative hypotheses Heredity 89 26–35

    Google Scholar 

  • R.K. Chesser (1991a) ArticleTitleGene diversity and female philopatry Genetics 127 437–447 Occurrence Handle1:STN:280:DyaK3M7mvFaqtg%3D%3D

    CAS  Google Scholar 

  • R.K. Chesser (1991b) ArticleTitleInfluence of gene flow and breeding tactics on gene diversity within populations Genetics 129 573–583 Occurrence Handle1:STN:280:DyaK38%2FnslCjsQ%3D%3D

    CAS  Google Scholar 

  • C.C. Cockerham (1969) ArticleTitleVariance of gene frequencies Evolution 23 72–84 Occurrence Handle10.2307/2406485

    Article  Google Scholar 

  • C.C. Cockerham (1973) ArticleTitleAnalysis of gene frequencies Genetics 74 679–700 Occurrence Handle1:STN:280:DC%2BC3crpt1CrtA%3D%3D Occurrence Handle17248636

    CAS  PubMed  Google Scholar 

  • J.-M. Cornuet S. Piry G. Luikart A. Estoup M. Solignac (1999) ArticleTitleNew methods employing multilocus genotypes to select or exclude populations as origins of individuals Genetics 153 1989–2000 Occurrence Handle10581301 Occurrence Handle1:STN:280:DC%2BD3c%2FltVKqsw%3D%3D

    PubMed  CAS  Google Scholar 

  • B. Efron (1983) ArticleTitleEstimating the error rate of a prediction rule: improvement of cross-validation J. Am. Stat. Assoc. 78 316–330 Occurrence Handle10.2307/2288636

    Article  Google Scholar 

  • D. Falush M. Stephens J.K. Pritchard (2003) ArticleTitleInference of population structure using multilocus genotype data: linked loci and correlated allele frequencies Genetics 164 1567–1587 Occurrence Handle12930761 Occurrence Handle1:CAS:528:DC%2BD3sXnvF2ntrk%3D

    PubMed  CAS  Google Scholar 

  • P.-M. Fontaine J.J. Dodson (1999) ArticleTitleAn analysis of the distribution of juvenile Atlantic salmon (Salmo salar) in nature as a function of relatedness using microsatellite Mol. Ecol. 8 189–198 Occurrence Handle10.1046/j.1365-294X.1999.00550.x

    Article  Google Scholar 

  • D.J. Fraser P. Duchesne L. Bernatchez (2005) ArticleTitleMigratory charr schools exhibit population and kin associations beyond juvenile stages Mol. Ecol. 14 3133–3146 Occurrence Handle16101779 Occurrence Handle1:CAS:528:DC%2BD2MXhtVGltLfM Occurrence Handle10.1111/j.1365-294X.2005.02657.x

    Article  PubMed  CAS  Google Scholar 

  • G. Gerlach U. Schardt R. Eckmann A. Meyer (2001) ArticleTitleKin-structured subpopulations in Eurasian perch (Perca fluviatilis L.) Heredity 86 213–221 Occurrence Handle11380667 Occurrence Handle1:CAS:528:DC%2BD3MXkvFelsb0%3D Occurrence Handle10.1046/j.1365-2540.2001.00825.x

    Article  PubMed  CAS  Google Scholar 

  • S.W. Guo E.A. Thompson (1992) ArticleTitlePerforming the exact test of Hardy–Weinberg proportion for multiple alleles Biometrics 48 361–372 Occurrence Handle1637966 Occurrence Handle1:STN:280:DyaK38zksFGgsA%3D%3D Occurrence Handle10.2307/2532296

    Article  PubMed  CAS  Google Scholar 

  • B. Guinand K.T. Scribner A. Topchy K.S. Page W. Punch M.K. Burnham-Curtis (2004) ArticleTitleSampling issues affecting accuracy of likelihood-based classification using genetical data Environ. Biol. Fish. 69 245–249 Occurrence Handle10.1023/B:EBFI.0000022869.72448.cd

    Article  Google Scholar 

  • M.M. Hansen L.F. Jensen (2005) ArticleTitleSibship within samples of brown trout (Salmo trutta) and implications for supportive breeding Conserv. Genet. 6 297–305 Occurrence Handle10.1007/s10592-004-7827-5

    Article  Google Scholar 

  • M.M. Hansen E.E. Nielsen K.L.D. Mensberg (1997) ArticleTitleThe problem of sampling families rather than populations: relatedness among individuals in samples of juvenile brown trout Salmo trutta L Mol. Ecol. 6 469–474 Occurrence Handle1:CAS:528:DyaK2sXjsFOiu7Y%3D Occurrence Handle10.1046/j.1365-294X.1997.t01-1-00202.x

    Article  CAS  Google Scholar 

  • M.M. Hansen E. Kenchington E.E. Nielsen (2001a) ArticleTitleAssigning individual fish to populations using microsatellite DNA markers Fish Fish. 2 93–112

    Google Scholar 

  • M.M. Hansen D.E. Ruzzante E.E. Nielsen K.L.D. Mensberg (2001b) ArticleTitleBrown trout (Salmo trutta) stocking impact assessment using microsatellite DNA markers Ecol. Appl. 11 148–160

    Google Scholar 

  • D. Hedgecock (1994) Does variance in reproductive success limit effective population sizes of marine organisms? A.R. Beaumont (Eds) Genetics and Evolution of Marine Organisms Chapman & Hall London 122–134

    Google Scholar 

  • T.L. King S.T. Kalinowski W.B. Schill A.P. Spidle B. Lubinski (2001) ArticleTitlePopulation structure of Atlantic salmon (Salmo salar L.): a range-wide perspective from microsatellite DNA variation Mol. Ecol. 10 807–821 Occurrence Handle11348491 Occurrence Handle1:CAS:528:DC%2BD3MXjvVensLY%3D Occurrence Handle10.1046/j.1365-294X.2001.01231.x

    Article  PubMed  CAS  Google Scholar 

  • N. Kolm E.A. Hoffman J. Olsson A. Berglund A.G. Jones (2005) ArticleTitleGroup stability and homing behavior but no kin group structures in a coral reef fish Behav. Ecol. 16 521–527 Occurrence Handle10.1093/beheco/ari022

    Article  Google Scholar 

  • M.T. Koskinen J. Piironen C.R. Primmer (2001) ArticleTitleInterpopulation genetic divergence in European grayling (Thymallus thymallus, Salmonidae) at a microgeographic scale: implications for conservation Conserv. Genet. 2 133–143 Occurrence Handle10.1023/A:1011814528664

    Article  Google Scholar 

  • J. Krause R.K. Butlin N. Peukhuri V.L. Pritchard (2001) ArticleTitleThe social organization of fish shoals: a test of the predictive power of laboratory experiments for the field Biol. Rev. Camb. Phil. Soc. 75 477–501 Occurrence Handle10.1111/j.1469-185X.2000.tb00052.x

    Article  Google Scholar 

  • G. Luikart P.R. England (1999) ArticleTitleStatistical analysis of microsatellite DNA data Trends Ecol. Evol. 14 253–256 Occurrence Handle10370259 Occurrence Handle10.1016/S0169-5347(99)01632-8

    Article  PubMed  Google Scholar 

  • S. Manel O.E. Gaggiotti R.S. Waples (2005) ArticleTitleAssignment methods: matching biological questions with appropriate techniques Trends Ecol. Evol. 20 136–142 Occurrence Handle16701357 Occurrence Handle10.1016/j.tree.2004.12.004

    Article  PubMed  Google Scholar 

  • J.L. Martinez J. Dumas E. Beall E. Garcia-Vazquez (2001) ArticleTitleAssessing introgression of foreign strains in wild Atlantic salmon populations: variation in microsatellites assessed in historic scale collections Freshwat. Biol. 46 835–844 Occurrence Handle10.1046/j.1365-2427.2001.00711.x

    Article  Google Scholar 

  • E.E. Nielsen M.M. Hansen C. Schmidt D. Meldrup P. Grønkjaer (2001) ArticleTitlePopulation of origin of Atlantic cod Nature 413 272 Occurrence Handle11565021 Occurrence Handle1:CAS:528:DC%2BD3MXnt1KjtbY%3D Occurrence Handle10.1038/35095112

    Article  PubMed  CAS  Google Scholar 

  • E.E. Nielsen M.M. Hansen D.E. Ruzzante D. Meldrup P. Grønkjaer (2003) ArticleTitleEvidence of a hybrid-zone in Atlantic cod (Gadus morhua) in the Baltic and the Danish Belt Sea revealed by individual admixture analysis Mol. Ecol. 12 1497–1508 Occurrence Handle12755878 Occurrence Handle10.1046/j.1365-294X.2003.01819.x

    Article  PubMed  Google Scholar 

  • J.B. Olsen P. Bentzen J.E. Seeb (1998) ArticleTitleCharacterization of seven microsatellite loci derived from pink salmon Mol. Ecol. 7 1087–1089 Occurrence Handle9711869 Occurrence Handle1:CAS:528:DyaK1cXlslGmtL0%3D

    PubMed  CAS  Google Scholar 

  • P.T. O’Reilly L.C. Hamilton S.K. McConnel J.W. Wright (1996) ArticleTitleRapid analysis of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of dinucleotide and tetranucleotide microsatellite Can. J. Fish. Aquat. Sci. 53 2292–2298 Occurrence Handle1:CAS:528:DyaK2sXhtFGhsbo%3D Occurrence Handle10.1139/cjfas-53-10-2292

    Article  CAS  Google Scholar 

  • D. Paetkau W. Calvert I. Stirling C. Strobeck (1995) ArticleTitleMicrosatellite analysis of population structure in Canadian polar bears Mol. Ecol. 4 347–354 Occurrence Handle7663752 Occurrence Handle1:CAS:528:DyaK2MXntValu78%3D

    PubMed  CAS  Google Scholar 

  • D. Paetkau R. Slade M. Burden A. Estoup (2004) ArticleTitleGenetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power Mol. Ecol. 13 55–65 Occurrence Handle14653788 Occurrence Handle1:CAS:528:DC%2BD2cXhs1WksLY%3D Occurrence Handle10.1046/j.1365-294X.2004.02008.x

    Article  PubMed  CAS  Google Scholar 

  • Page, K.S., 2001. Genetic diversity and interrelationships of wild and hatchery lake trout in the upper Great Lakes: inferences for broodstock management and development of restoration strategies. M.S. Thesis, 121 pp. Department of Fisheries and Wildlife, Michigan State University, East Lansing

  • K.S. Page K.T. Scribner K.R. Bennett L.M. Garzel (2003) ArticleTitleGenetic assessment of strain-specific sources of lake trout recruitment in the Great Lakes Trans. Am. Fish. Soc. 132 877–894 Occurrence Handle10.1577/T02-092

    Article  Google Scholar 

  • S. Planes P. Lenfant (2002) ArticleTitleTemporal change in the genetic structure between and within cohorts of a marine fish, Diplodus sargus, induced by a large variance in individual reproductive success Mol. Ecol. 11 1515–1524 Occurrence Handle12144670 Occurrence Handle1:STN:280:DC%2BD38zps1Ghuw%3D%3D Occurrence Handle10.1046/j.1365-294X.2002.01521.x

    Article  PubMed  CAS  Google Scholar 

  • S. Planes G. Lecaillon P. Lenfant M. Meekan (2002) ArticleTitleGenetic and demographic variation in new recruits of Naso unicornis J. Fish Biol. 61 1033–1049 Occurrence Handle10.1111/j.1095-8649.2002.tb01861.x

    Article  Google Scholar 

  • L. Pouyaud E. Desmarais A. Chenuil J.-F. Agnèse F. Bonhomme (1999) ArticleTitleKin cohesiveness and possible inbreeding in the mouthbrooding tilapia Sarotherodon melanotheron (Pisces Cichlidae) Mol. Ecol. 8 803–812 Occurrence Handle10.1046/j.1365-294X.1999.00632.x

    Article  Google Scholar 

  • C.R. Primmer M.T. Koskinen J. Piironen (2000) ArticleTitleThe one that did not get away: individual assignment using microsatellite data detects a case of fishing competition fraud Proc. R. Soc. Biol. Sci. B267 1699–1704 Occurrence Handle10.1098/rspb.2000.1197

    Article  Google Scholar 

  • J.K. Pritchard M. Stephens P. Donnelly (2000) ArticleTitleInference of population structure using multi-locus genotype data Genetics 155 945–959 Occurrence Handle10835412 Occurrence Handle1:STN:280:DC%2BD3cvislKrtA%3D%3D

    PubMed  CAS  Google Scholar 

  • D.C. Queller K.F. Goodnight (1989) ArticleTitleEstimating relatedness using genetic markers Evolution 43 258–275 Occurrence Handle10.2307/2409206

    Article  Google Scholar 

  • M. Raymond F. Rousset (1995) ArticleTitleGenepop (Version 1.2): population genetics software for exact tests and ecumenicism J. Hered. 86 248–249

    Google Scholar 

  • W.R. Rice (1989) ArticleTitleAnalysing tables of statistical tests Evolution 43 223–225 Occurrence Handle10.2307/2409177

    Article  Google Scholar 

  • S. Roques P. Duchesne L. Bernatchez (1999) ArticleTitlePotential of microsatellites for individual assignment: the North Atlantic redfish (genus Sebastes) species complex as a case study Mol. Ecol. 8 1703–1717 Occurrence Handle10583833 Occurrence Handle1:STN:280:DC%2BD3c%2FltFamsg%3D%3D Occurrence Handle10.1046/j.1365-294x.1999.00759.x

    Article  PubMed  CAS  Google Scholar 

  • K.G. Ross (2001) ArticleTitleMolecular ecology of social behaviour: analyses of breeding systems and genetic structure Mol. Ecol. 10 265–284 Occurrence Handle11298944 Occurrence Handle1:STN:280:DC%2BD3M3gvVanuw%3D%3D Occurrence Handle10.1046/j.1365-294x.2001.01191.x

    Article  PubMed  CAS  Google Scholar 

  • S.T. Russell J.L. Kelley J.A. Graves A.E. Magurran (2004) ArticleTitleKin structure and shoal composition dynamics in the guppy (Poecilia reticulata) Oïkos 106 520–526

    Google Scholar 

  • D.E. Ruzzante M.M. Hansen D. Meldrup (2001) ArticleTitleDistribution of individual inbreeding coefficients, relatedness and influence of stocking on native anadromous brown trout (Salmo trutta) population structure Mol. Ecol. 10 2107–2128 Occurrence Handle11555255 Occurrence Handle1:STN:280:DC%2BD3MrgslWjug%3D%3D Occurrence Handle10.1046/j.1365-294X.2001.01352.x

    Article  PubMed  CAS  Google Scholar 

  • N. Ryman F.W. Allendorf G. Ståhl (1979) ArticleTitleReproductive isolation with little genetic divergence in sympatric populations of brown trout (Salmo trutta) Genetics 92 247–262 Occurrence Handle499765 Occurrence Handle1:STN:280:DyaL3c%2FkslOktA%3D%3D

    PubMed  CAS  Google Scholar 

  • J.F. Storz (1999) ArticleTitleGenetic consequences of mammalian social structure J. Mammal. 80 553–569

    Google Scholar 

  • D.W. Sugg R.K. Chesser F.S. Dobson J.L. Hoogland (1996) ArticleTitlePopulation genetics meets behavioral ecology Trends Ecol. Evol. 11 338–342 Occurrence Handle10.1016/0169-5347(96)20050-3

    Article  Google Scholar 

  • E.B. Taylor A. Kuiper P.M. Troffe D.J. Hoysak S. Pollard (2000) ArticleTitleVariation in developmental biology and microsatellite DNA in reproductive ecotypes of kokanee, Oncorhynchus nerka: implications for declining populations in a large British Columbia lake Conserv. Genet. 1 213–249 Occurrence Handle10.1023/A:1011553705015

    Article  Google Scholar 

  • E.B. Taylor Z. Redenbach A.B. Costello S.J. Pollard C.J. Pacas (2001) ArticleTitleNested analysis of genetic variation in northwestern North American char, Dolly Varden (Salvelinus malma) and bull trout (S. confluentus) Can. J. Fish. Aquat. Sci. 58 406–420 Occurrence Handle1:CAS:528:DC%2BD3MXislagsbk%3D Occurrence Handle10.1139/cjfas-58-2-406

    Article  CAS  Google Scholar 

  • P.M. Waser C. Strobeck (1998) ArticleTitleGenetic signatures of interpopulation dispersal Trends Ecol. Evol. 13 43–44 Occurrence Handle10.1016/S0169-5347(97)01255-X

    Article  Google Scholar 

  • B.S. Weir (1979) ArticleTitleInferences about linkage disequilibrium Biometrics 25 235–254 Occurrence Handle10.2307/2529947

    Article  Google Scholar 

  • B.S. Weir C.C. Cockerham (1984) ArticleTitleEstimating F-statistics for the analysis of population structure Evolution 38 1358–1370 Occurrence Handle10.2307/2408641

    Article  Google Scholar 

  • S. Wright (1965) ArticleTitleThe interpretation of population structure by F-statistics with special regards to system of mating Evolution 19 395–420 Occurrence Handle10.2307/2406450

    Article  Google Scholar 

  • S. Wright (1969) Evolution and the Genetics of Populations. Vol. 2: the Theory of Gene Frequencies Chicago University Press Chicago

    Google Scholar 

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Guinand, B., Scribner, K.T., Page, K.S. et al. Effects of coancestry on accuracy of individual assignments to population of origin: examples using Great Lakes lake trout (Salvelinus namaycush). Genetica 127, 329–340 (2006). https://doi.org/10.1007/s10709-005-5365-9

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