Differentiating salmon populations at broad and fine geographical scales with microsatellites and single nucleotide polymorphisms

Molecular Ecology

Volumn 17, Issue 15, 2008, Pages 3464-3477

  Narum, S R ^a   Banks, M ^b   Beacham, T D ^c   Bellinger, M R ^b   Campbell, M R ^d   Dekoning, J ^e   Elz, A ^f   Guthrie III, C M ^g   Kozfkay, C ^d   Miller, K M ^c   Moran, P ^f   Phillips, R ^e   Seeb, L W ^h,k   Smith, C T ^h,l   Warheit, K ⁱ   Young, S F ⁱ   Garza, J C ^j  

^a Hagerman Fish Culture Experiment Station ^*  (United States)

^b OREGON STATE UNIVERSITY   (United States)

^c PACIFIC BIOLOGICAL STATION   (Canada)

^d IDAHO DEPARTMENT OF FISH AND GAME   (United States)

^e WASHINGTON STATE UNIVERSITY   (United States)

^f ALASKA FISHERIES SCIENCE CENTER   (United States)

^g NATIONAL MARINE FISHERIES SERVICE   (United States)

^h ALASKA DEPARTMENT OF FISH AND GAME   (United States)

ⁱ WASHINGTON DEPARTMENT OF FISH AND WILDLIFE   (United States)

^j SOUTHWEST FISHERIES SCIENCE CENTER   (United States)

^k UNIVERSITY OF WASHINGTON   (United States)

^l ABERNATHY FISH TECHNOLOGY CENTER   (United States)

more..

Author keywords

Assignment tests; Chinook salmon; Differentiation; Genetic markers; Microsatellites; SNPs

Indexed keywords

MICROSATELLITE DNA;

ANIMAL; ARTICLE; CLASSIFICATION; GENETIC MARKER; GENETICS; GEOGRAPHY; NORTH AMERICA; PHYLOGENY; POPULATION GENETICS; SALMON; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; GENETIC MARKERS; GENETICS, POPULATION; GEOGRAPHY; MICROSATELLITE REPEATS; NORTH AMERICA; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SALMON;

ONCORHYNCHUS TSHAWYTSCHA;

EID: 47649120138     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2008.03851.x     Document Type: Article

References (55)

1. Aguilar A, Garza JC (2006) A comparison of variability and population structure for major histocompatibility complex and microsatellite loci in California coastal steelhead (Oncorhynchus mykiss Walbaum). Molecular Ecology, 15, 923 937.
2. Banks MA, Blouin MS, Baldwin BA et al 1999) Isolation and inheritance of novel microsatellites in Chinook salmon. Journal of Heredity, 90, 281 288.
3. Beacham TD, Jonsen KL, Supernault J, Wetklo M, Deng L, Varnavskaya N (2006) Pacific Rim population structure of Chinook salmon as determined from microsatellite analysis. Transactions of the American Fisheries Society, 135, 1604 1621.
4. Beaumont MA, Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology, 13, 969 980.
5. Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society London. Series B, Biological Sciences, 263, 1619 1626.
6. Benjamini Y, Yekutieli D (2001) The control of false discovery rate under dependency. Annals of Statistics, 29, 1165 1188.
7. Bensch S, Åkesson S, Irwin DE (2002) The use of AFLP to find an informative SNP: genetic differences across a migratory divide in willow warblers. Molecular Ecology, 11, 2359 2366.
8. Bouck A, Vision T (2007) The molecular ecologist's guide to expressed sequence tags. Molecular Ecology, 16, 907 924.
9. Cairney M, Taggart JB, Hoyheim B (2000) Atlantic salmon (Salmo salar L.) and cross-species amplification in other salmonids. Molecular Ecology, 9, 2175 2178.
10. Cavalli-Sforza LL, Edwards WWF (1967) Phylogenetic analysis; models and estimation procedures. Evolution, 32, 550 570.
11. Clark AG, Hubisz MJ, Bustamante CD, Williamson SH, Nielsen R (2005) Ascertainment bias in studies of human genome-wide polymorphism. Genome Research, 15, 1496 1502.
12. Di Rienzo A, Peterson AC, Garza JC, Valdes AM, Slatkin M (1994) Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences, USA, 91, 3166 3170.
13. Dieringer D, Schlötterer C (2003) microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3, 167 169.
14. Estoup A, Tailliez C, Cornuet JM, Solignac M (1995) Size homoplasy and mutational processes of interrupted microsatellites in two bee species, Apis mellifera and Bombus terrestris (Apidae). Molecular Biology and Evolution, 12, 1074 1084.
15. Ford MJ (1998) Testing models of migration and isolation among populations of Chinook salmon (Oncorhynchus tshawytscha). Evolution, 52, 539 557.
16. Fouquet A, Vences M, Salducci MD et al 2007) Revealing cryptic diversity using molecular phylogenetics and phylogeography in frogs of the Scinax ruber and Rhinella margaritifera species groups. Molecular Phylogenetics and Evolution, 43, 567 582.
17. Gaines CA, Hare MP, Beck SE, Rosenbaum HC (2005) Nuclear markers confirm taxonomic status and relationships among highly endangered and closely related right whale species. Proceedings of the Royal Society B: Biological Sciences, 272, 533 542.
18. Garza JC, Freimer NB (1996) Homoplasy for size at microsatellite loci in humans and chimpanzees. Genome Research, 6, 211 217.
19. Greig C, Jacobson DP, Banks MA (2003) New tetranucleotide microsatellites for fine-scale discrimination among endangered Chinook salmon (Oncorhynchus tshawytscha). Molecular Ecology Notes, 3, 376 379.
20. Heath DD, Shrimpton JM, Hepburn RI, Jamieson SK, Brode SK, Docker MF (2006) Population structure and divergence using microsatellite and gene locus markers in Chinook salmon (Oncorhynchus tshawytscha) populations. Canadian Journal of Fisheries and Aquatic Sciences, 63, 1370 1383.
21. Hedrick PW (1999) Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution, 53, 313 318.
22. Hedrick PW (2005) A standardized genetic differentiation measure. Evolution, 59, 1633 1638.
23. Hoffman JI, Amos W (2005) Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion. Molecular Ecology, 14, 599 612.
24. Kalinowski ST (2002) How many alleles per locus should be used to estimate genetic distances? Heredity, 88, 62 65.
25. Kalinowski ST (2004) Genetic polymorphism and mixed stock fisheries analysis. Canadian Journal of Fisheries and Aquatic Sciences, 61, 1075 1082.
26. Kalinowski ST (2005) hp-rare 1.0: a computer program for performing rarefaction on measures of allelic richness. Molecular Ecology Notes, 5, 187 189.
27. Kuhner MK, Beerli P, Yamato J, Felsenstein J (2000) Usefulness of single nucleotide polymorphism data for estimating population parameters. Genetics, 156, 439 447.
28. Langella O (2001) Populations 1.2.24: population genetic structure (individuals or populations distances, phylogenetic trees). Available: http://bioinformatics.org/∼tryphon/populations/.
29. Liu N, Chen L, Wang S, Oh C, Zhao H (2005) Comparison of single-nucleotide polymorphisms and microsatellites in inference of population structure. BMC Genetics, 6 (S1 1471 2156.
30. Luikart G, England PR, Tallmon D, Jordan S, Taberlet P (2003) The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics, 4, 981 994.
31. Miller CR, Joyce P, Waits LP (2002) Assessing allelic dropout and genotype reliability using maximum likelihood. Genetics, 160, 357 366.
32. Miller KM, Withler RE, Beacham TD (1997) Molecular evolution at MHC genes in two populations of Chinook salmon Oncorhynchus tshawytscha. Molecular Ecology, 6, 937 954.
33. Morin PA, Luikart G, Wayne RK, SNP Workshop Group (2004) SNPs in ecology, evolution and conservation. Trends in Ecology & Evolution, 19, 208 216.
34. Narum SR (2006) Beyond Bonferroni: Less conservative analyses for onservation genetics. Conservation Genetics, 7, 783 787.
35. Narum SR, Powell MS, Talbot AJ (2004) A distinctive microsatellite locus that differentiates ocean-type from stream-type Chinook salmon in the interior Columbia River Basin. Transactions of the American Fisheries Society, 133, 1051 1055.
36. Olsen JB, Bentzen P, Seeb JE (1998) Characterization of seven microsatellite loci derived from pink salmon. Molecular Ecology, 7, 1083 1090.
37. Page RDM (1996) TreeView: an application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences, 12, 357 358.
38. Piry S, Alapetite A, Cornuet JM, Paetkau D, Baudouin L, Estoup A (2004) GENECLASS2: a software for genetic assignment and first-generation migrant detection. Journal of Heredity, 95, 536 539.
39. Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences, USA, 94, 9197 9221.
40. Raymond M, Rousset F (1995) genepop (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity, 86, 248 249.
41. Rexroad CE III, Coleman RL, Martin AM, Hershberger WK, Killefer J (2001) Thirty-five polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss). Animal Genetics, 32, 317 319.
42. Rice WR (1989) Analyzing tables of statistical tests. Evolution, 43, 223 225.
43. Rosenberg NA, Li LM, Ward R, Pritchard JK (2003) Informativeness of genetic markers for inference of ancestry. American Journal of Human Genetics, 73, 1402 1422.
44. Ryman N, Palm S (2006) powsim: a computer program for assessing statistical power when testing for genetic differentiation. Molecular Ecology Notes, 6, 600 602.
45. Ryynänen HJ, Tonteri A, Vasemägi A, Primmer CR (2007) A comparison of the efficiency of single nucleotide polymorphisms (SNPs) and microsatellites for the estimates of population and conservation genetic parameters in Atlantic salmon (Salmo salar). Journal of Heredity, 98, 692 704.
46. Sabeti PC, Schaffner SF, Fry B et al 2006) Positive natural selection in the human lineage. Science, 312, 1614 1620.
47. Seddon JM, Parker HG, Ostrander EA, Ellegren H (2005) SNPs in ecological and conservation studies: a test in the Scandinavian wolf population. Molecular Ecology, 14, 503 511.
48. Seeb LW, Antonovich A, Banks MA et al 2007) Development of a standardized DNA database for Chinook salmon. Fisheries, 32, 540 552.
49. Smith CT, Elfstrom CM, Seeb JE, Seeb LW (2005a) Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon. Molecular Ecology, 14, 4193 4203.
50. Smith CT, Seeb JE, Schwenke P, Seeb LW (2005b) Use of the 5′-nuclease reaction for single nucleotide polymorphism genotyping in Chinook salmon. Transactions of the American Fisheries Society, 134, 207 217.
51. Smith CT, Antonovich A, Elfstrom CM, Narum SR, Seeb LW (2007) Impacts of marker class bias relative to locus-specific variability on population inferences in Chinook salmon; a comparison of SNPs to STRs and allozymes. Transactions of the American Fisheries Society, 136, 1674 1687.
52. Waples RS, Teel DJ, Myers JM, Marshall AR (2004) Life-history divergence in Chinook salmon: historical contingency and parallel evolution. Evolution, 58, 386 403.
53. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358 1370.
54. Wilding CS, Butlin RK, Grahame J (2001) Differential gene exchange between parapatric morphs of Littorina saxatilis detected using AFLP markers. Journal of Evolutionary Biology, 14, 611 619.
55. Williamson KS, Cordes JF, May B (2002) Characterization of microsatellite loci in Chinook salmon (Oncorhynchus tshawytscha) and cross-species amplification in other salmonids. Molecular Ecology Notes, 2, 17 19.