A comparison of variability and population structure for major histocompatibility complex and microsatellite loci in California coastal steelhead (Oncorhynchus mykiss Walbaum)

Molecular Ecology

Volumn 15, Issue 4, 2006, Pages 923-937

  Aguilar, Andres ^a   Garza, John Carlos ^a  

^a NONE

Author keywords

FST outlier; Major histocompatibility complex (MHC); Microsatellites; Selection; Steelhead

Indexed keywords

MICROSATELLITE DNA;

ALLELE; ANIMAL; ARTICLE; COMPARATIVE STUDY; GENETIC DRIFT; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; GENOTYPE; GEOGRAPHY; GROWTH, DEVELOPMENT AND AGING; HETEROZYGOTE; MAJOR HISTOCOMPATIBILITY COMPLEX; RAINBOW TROUT; UNITED STATES;

ALLELES; ANIMALS; CALIFORNIA; GENETIC DRIFT; GENOTYPE; GEOGRAPHY; HETEROZYGOTE; MAJOR HISTOCOMPATIBILITY COMPLEX; MICROSATELLITE REPEATS; ONCORHYNCHUS MYKISS; SELECTION (GENETICS); VARIATION (GENETICS);

ONCORHYNCHUS MYKISS; SALMONIDAE; VERTEBRATA;

EID: 33645034358     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2006.02843.x     Document Type: Article

References (69)

1. Aguilar A Roemer G Debenham S et al. 2004 High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal Proceedings of the National Academy of Sciences, USA 101 3490 3494
2. Allendorf FW Phelps SR 1981 Use of allelic frequencies to describe population structure Canadian Journal of Fisheries and Aquatic Sciences 38 1507 1514
3. Banks MA Rashbrook VK Calavetta MJ Dean CA Hedgecock D 2000 Analysis of microsatellite DNA resolves genetic structure and diversity of chinook salmon (Oncorhynchus tshawytscha) in California's Central Valley Canadian Journal of Fisheries and Aquatic Sciences 57 915 927
4. ST tell us? Trends in Ecology & Evolution 20 435 440
5. Beaumont MA Nichols RA 1996 Evaluating loci for use in the genetic analysis of population structure Proceedings of the Royal Society of LondonSeries B, Biological Sciences 263 1619 1626
6. Behnke RJ 1992 Native trout of western North America American Fisheries Society Monograph 6 275
7. TMpour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, Université de Montpellier II Montpellier, France
8. Bernatchez L Landry C 2003 MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years? Journal of Evolutionary Biology 16 363 377
9. Binz T Largiader C Muller R Wedekind C 2001 Sequence diversity of Mhc genes in lake whitefish Journal of Fish Biology 58 359 373
10. Bjorkstedt EP Spence BC Garza JC et al. 2005 ) An Analysis of Historical Population Structure for Evolutionarily Significant Units of Chinook Salmon, Coho Salmon, and Steelhead in the North-Central California Coast Recovery Domain. NOAA Technical Memorandum NMFS-SWFSC-382
11. Bonnet E Van de Peer Y 2002 zt : a software tool for simple and partial Mantel tests Journal of Statistical Software 7 1 10
12. Brown JH Jardetzky TS Gorga JC et al. 1993 3-Dimensional structure of the human class-II histocompatibility antigen HLA-DR1 Nature 364 33 39
13. Busby PJ Wainwright TC Bryant GJ et al. 1996 ) Status review of west coast steelhead from Washington, Idaho, Oregon, and California. NOAA Technical Memorandum NMFS-NWFSC-27
14. Cavalli-Sforza LL Edwards AWF 1967 Phylogenetic analysis: models and estimation procedures Evolution 32 550 570
15. Danzmann RG Jackson TR Ferguson MM 1999 Epistasis in allelic expression at upper temperature tolerance QTL in rainbow trout Aquaculture 173 45 58
16. Dorschner MO Duris T Bronte CR Burnham-Curtis MK Phillips RB 2000 High levels of MHC class II allelic diversity in lake trout from Lake Superior Journal of Heredity 91 359 363
17. Garrigan D Hedrick PW 2003 Perspective: detecting adaptive molecular polymorphism: lessons from the MHC Evolution 57 1707 1722
18. Garza JC 1998 Population genetics of the northern elephant seal PhD dissertation University of California Berkeley.
19. Garza JC Williamson EG 2001 Detection of reduction in population size using data from microsatellite loci Molecular Ecology 10 305 318
20. Garza JC Gilbert-Hovarth L Anderson J et al 2004 Population structure and history of steelhead trout in California, NPAFC Technical Report No. 5 129 131
21. Hedrick PW 1994 Evolutionary genetics of the major histocompatibility complex American Naturalist 143 945 964
22. Hedrick PW 1999 Perspective: highly variable loci and their interpretation in evolution and conservation Evolution 53 313 318
23. Hedrick PW 2005 A standardized genetic differentiation measure Evolution 59 1633 1638
24. Hedrick PW Parker KM Lee RN 2001 Using microsatellite and MHC variation to identify species, ESUs, and MUs in the endangered Sonoran topminnow Molecular Ecology 10 1399 1412
25. Hess CM Gasper J Hoekstra HE Hill CE Edwards SV 2000 MHC class II pseudogene and genomic signature of a 32-kb cosmid in the house finch (Carpodacus mexicanus) Genome Research 10 613 623
26. Hughes AL Nei M 1989 Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection Proceedings of the National Academy of Sciences, USA 86 958 962
27. Jarvi SI Tarr CL McIntosh CE Atkinson CT Fleischer RC 2004 Natural selection of the major histocompatibility complex (Mhc) in Hawaiian honeycreepers (Drepanidinae) Molecular Ecology 13 2157 2168
28. Kalinowski ST 2005 hp - rare 1.0: a computer program for performing rarefaction on measures of allelic richness Molecular Ecology Notes 5 187 189
29. Kim TJ Parker KM Hedrick PW 1999 Major histocompatibility complex differentiation in Sacramento River chinook salmon Genetics 151 1115 1122
30. Klein J 1986 Natural History of the Major Histocompatibility Complex John Wiley New York
31. Klein J O'hUigin C 1994 MHC polymorphism and parasites Philosophical Transactions of the Royal Society of LondonSeries B, Biological Sciences 346 351 358
32. Klein J Sato A Nagl S O'hUigin C 1998 Molecular trans-species polymorphism Annual Review of Ecology and Systematics 29 1 21
33. Kumar S Tamura K Nei M 2004 mega 3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment Briefings in Bioinformatics 5 150 163
34. Lancaster A Nelson MP Single RM Meyer D Thomson G 2003 pypop : a software framework for population genomics: analyzing large-scale multi-locus genotype data In Pacific Symposium on Biocomputing 8 (ed Altman RB et al. ), pp 514 525 World Scientific Singapore
35. Landry C Bernatchez L 2001 Comparative analysis of population structure across environments and geographical scales at major histocompatibility complex and microsatellite loci in Atlantic salmon (Salmo salar) Molecular Ecology 10 2525 2539
36. Langella O 2002 ) populations (version 1.2.28).
37. Lewontin RC Krakauer J 1973 Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms Genetics 74 175 195
38. 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
39. Maruyama T Fuerst PA 1985 Population bottlenecks and nonequilibrium models in population genetics. 3. Genic homozygosity in populations which experience periodic bottlenecks Genetics 111 691 703
40. McConnell SK O'Reilly P Hamilton L et al. 1995 Polymorphic microsatellite loci from Atlantic salmon (Salmo salar): genetic differentiation of North American and European populations Canadian Journal of Fisheries and Aquatic Sciences 52 1863 1872
41. Meyer D Thomson G 2001 How selection shapes variation of the human major histocompatibility complex: a review Annals of Human Genetics 65 1 26
42. Miller KM Withler RE 1996 Sequence analysis of a polymorphic Mhc class II gene in Pacific salmon Immunogenetics 43 337 351
43. 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
44. Miller KM Kaukinen KH Beacham TD Withler RE 2001 Geographic heterogeneity in natural selection on an MHC locus in sockeye salmon Genetica 111 237 257
45. Morris DB Richard KR Wright JM 1996 Microsatellites from rainbow trout (Oncorhynchus mykiss) and their use for genetic study of salmonids Canadian Journal of Fisheries and Aquatic Sciences 53 120 126
46. Nei M 1987 Molecular Evolutionary Genetics Columbia University Press
47. Nei M Kumar S 2000 Molecular Evolution and Phylogenetics Oxford University Press, Oxford
48. O'Reilly PT Hamilton LC McConnell SK Wright JM 1996 Rapid analysis of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of dinucleotide and tetranucleotide microsatellites Canadian Journal of Fisheries and Aquatic Sciences 53 2292 2298
49. Olsen KH Grahn M Lohm J 2002 Influence of MHC on sibling discrimination in Arctic char, Salvelinus alpinus (L.) Journal of Chemical Ecology 28 783 795
50. Ono H O'hUigin C Vincek V Klein J 1993 Exon-intron organization of fish major histocompatibility complex class II beta genes Immunogenetics 38 223 234
51. Penn DJ Potts WK 1999 The evolution of mating preferences and major histocompatibility complex genes American Naturalist 153 145 164
52. Rajakaruna RS Brown JA Kaukinen K Miller KM 2001 MHC genes influence the kin recognition in juvenile Atlantic salmon American Zoologist 41 1562 1562
53. Raymond M Rousset F 1995 genepop (version-1.2): population genetics software for exact tests and ecumenicism Journal of Heredity 86 248 249
54. Sakamoto T Danzmann RG Okamoto N Ferguson MM Ihssen PE 1999 Linkage analysis of quantitative trait loci associated with spawning time in rainbow trout (Oncorhynchus mykiss) Aquaculture 173 33 43
55. Salamon H Klitz W Easteal S et al. 1999 Evolution of HLA class II molecules: allelic and amino acid site variability across populations Genetics 152 393 400
56. Sato A Figueroa F O'hUigin C Steck N Klein J 1998 Cloning of major histocompatibility complex (MHC) genes from threespine stickleback, Gasterosteus aculeatus Molecular Marine Biology and Biotechnology 7 221 231
57. Schierup MH Charlesworth D Vekemans X 2000 The effect of hitch-hiking on genes linked to a balanced polymorphism in a subdivided population Genetical Research 76 63 73
58. Scribner KT Gust JR Fields RL 1996 Isolation and characterization of novel salmon microsatellite loci: cross-species amplification and population genetic applications Canadian Journal of Fisheries and Aquatic Sciences 53 833 841
59. Shapovalov L Taft A 1954 The life histories of the steelhead rainbow trout (Salmo gairdneri gairdneri) and silver salmon (Oncorhynchus kisutch) with special reference to Waddell Creek, California, and recommendations regarding their management California Department of Fish and Game, Fish Bulletin 98 375
60. Shum BP Guethlein L Flodin LR et al. 2001 Modes of salmonid MHC class I and II evolution differ from the primate paradigm Journal of Immunology 166 3297 3308
61. Slatkin M 1994 An exact test for neutrality based on the Ewens sampling distribution Genetical Research 64 71 74
62. Slatkin M 1996 A correction to the exact test based on the Ewens sampling distribution Genetical Research 68 259 260
63. Somorjai IML Danzmann RG Ferguson MM 2003 Distribution of temperature tolerance quantitative trait loci in Arctic charr (Salvelinus alpinus) and inferred homologies in rainbow trout (Oncorhynchus mykiss) Genetics 165 1443 1456
64. Storz JF 2005 Using genome scans of DNA polymorphism to infer adaptive population divergence Molecular Ecology 14 671 688
65. Sunnucks P Wilson ACC Beheregaray LB et al 2000 SSCP is not so difficult: the application and utility of single-stranded conformation polymorphism in evolutionary biology and molecular ecology Molecular Ecology 9 1699 1710
66. Watterson GA 1978 Homozygosity test of neutrality Genetics 88 405 417
67. Weir BS Cockerham CC 1984 Estimating F-statistics for the analysis of population structure Evolution 38 1358 1370
68. 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
69. Withler RE 1966 Variability in life history characteristics of steelhead trout (Salmo gairdneri) along the Pacific coast of North America Journal of the Fisheries Research Board of Canada 23 365 393