Adaptation of redband trout in desert and montane environments

Molecular Ecology

Volumn 19, Issue 21, 2010, Pages 4622-4637

  Narum, Shawn R ^a   Campbell, Nathan R ^a   Kozfkay, Christine C ^b   Meyer, Kevin A ^b  

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

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

Author keywords

genome scan; local adaptation; Oncorhynchus mykiss; thermal tolerance

Indexed keywords

ADAPTATION; ANIMAL; ARTICLE; ECOSYSTEM; ENVIRONMENT; GENE FREQUENCY; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; GENOTYPE; MOLECULAR EVOLUTION; POPULATION GENETICS; RAINBOW TROUT; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED STATES;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; ECOSYSTEM; ENVIRONMENT; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENETIC VARIATION; GENETICS, POPULATION; GENOTYPE; IDAHO; ONCORHYNCHUS MYKISS; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION, GENETIC;

ONCORHYNCHUS MYKISS;

EID: 78149421770     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2010.04839.x     Document Type: Article

References (84)

1. Aguilar A, Garza JC, (2008) Isolation of 15 single nucleotide polymorphisms from coastal steelhead, Oncorhynchus mykiss (Salmonidae). Molecular Ecology Resources, 8, 659 - 662.
2. Airaksinen S, Rabergh CMI, Sistonen L, Nikinmaa M, (1998) Effects of heat shock and hypoxia on protein synthesis in rainbow trout (Oncorhynchus mykiss) cells. The Journal of Experimental Biology, 201, 2543 - 2551.
3. Akey JM, (2009) Constructing genomic maps of positive selection in humans: where do we go from here? Genome Research, 19, 711 - 722.
4. Akey JM, Zhang G, Zhang K, et al. (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Research, 12, 1805 - 1814.
5. Antao T, Lopes A, Lopes RJ, et al. (2008) LOSITAN: a workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinformatics, 9, 323.
6. Beacham TD, Murray CB, (1990) Temperature, egg size, and development of embryos and alevins of five species of Pacific salmon: a comparative analysis. Transactions of the American Fisheries Society, 119, 927 - 945.
7. Beaumont MA, Balding DJ, (2004) Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology, 13, 969 - 980.
8. Beaumont MA, Nichols RA, (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society of London Series B, 263, 1619 - 1626.
9. Beer WN, Anderson JJ, (2001) Effect of spawning day and temperature on salmon emergence: interpretations of a growth model for Methow River Chinook. Canadian Journal of Fisheries and Aquatic Sciences, 58, 943 - 949.
10. Benjamini Y, Yekutieli D, (2001) The control of false discovery rate under dependency. Annals of Statistics, 29, 1165 - 1188.
11. Berthold P, Helbig AJ, Mohr G, et al. (1992) Rapid microevolution of migratory behaviour in a wild bird species. Nature, 360, 668 - 670.
12. Bilodeau AL, Waldbieser GC, (2005) Activation of TLR3 and TLR5 in channel catfish exposed to virulent Edwardsiella ictaluri. Developmental and Comparative Immunology, 29, 713 - 721.
13. Bradshaw WE, Holzapfel CM, (2008) Genetic response to rapid climate change: its seasonal timing that matters. Molecular Ecology, 17, 157 - 166.
14. Bradshaw WE, Zani PA, Holzapfel CM, (2004) Adaptation to temperate climates. Evolution, 58, 1748 - 1762.
15. Brannon EL, (1987) Mechanisms stabilizing salmonid fry emergence timing. Canadian Special Publication of Fisheries and Aquatic Sciences, 96, 120 - 124.
16. Buckley BA, Somero GN, (2009) cDNA microarray analysis reveals the capacity of the cold-adapted Antarctic fish Trematomus bernacchii to alter gene expression in response to heat stress. Polar Biology, 32, 403 - 415.
17. Campbell NR, Narum SR, (2009a) Quantitative PCR assessment of microsatellite and SNP genotyping with variable quality DNA extracts. Conservation Genetics, 10, 779 - 784.
18. Campbell NR, Narum SR, (2009b) Identification and characterization of heat shock response related single nucleotide polymorphisms in O.mykiss and O.tschawytscha. Molecular Ecology Resources, 9, 1460 - 1559.
19. Campbell NR, Overturf K, Narum SR, (2009) Characterization of 22 novel single nucleotide polymorphism markers in steelhead and rainbow trout. Molecular Ecology Resources, 9, 318 - 322.
20. Cavalli-Sforza LL, Edwards WWF, (1967) Phylogenetic analysis; models and estimation procedures. Evolution, 32, 550 - 570.
21. Charlesworth B, Nordborg M, Charlesworth D, (1997) The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations. Genetical Research, 70, 155 - 174.
22. Chase K, Jones P, Martin A, et al. (2009) Genetic mapping of fixed phenotypes: disease frequency as a breed characteristic. Journal of Heredity, 100, S37 - S41.
23. Ciardiello MA, Camardella L, Carratore V, Di Prisco G, (2000) l-Glutamate dehydrogenase from the Antarctic fish Chaenocephalus aceratus: primary structure, function and thermodynamic characterization: relationship with cold adaptation. Biochimica et Biophysica Acta - Protein Structure and Molecular Enzymology, 1543, 11 - 23.
24. Crozier LG, Hendry AP, Lawson PW, et al. (2008) Potential responses to climate change in organisms with complex life histories: evolution and plasticity in Pacific salmon. Evolutionary Applications, 1, 252 - 270.
25. De Roos APW, Hayes BJ, Goddard ME, (2009) Reliability of genomic predictions across multiple populations. Genetics, 183, 1545 - 1553.
26. Dionne M, Miller KM, Dodson JJ, et al. (2007) Clinal variation in MHC diversity with temperature: evidence for the role of host-pathogen interaction on local adaptation in Atlantic salmon. Evolution, 61, 2154 - 2167.
27. Dionne M, Caron F, Dodson JJ, Bernatchez L, (2008) Landscape genetics and hierarchical genetic structure in Atlantic salmon: the interaction of gene flow and local adaptation. Molecular Ecology, 17, 2382 - 2396.
28. Ebersole JL, Liss WJ, Frissell CA, (2001) Relationship between stream temperature, thermal refugia and rainbow trout Oncorhynchus mykiss abundance in arid-land streams in the northwestern United States. Ecology of Freshwater Fish, 10, 1 - 10.
29. Evanno G, Regnaut S, Goudet J, (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14, 2611 - 2620.
30. Excoffier L, Hofer T, Foll M, (2009) Detecting loci under selection in a hierarchically structured population. Heredity, 103, 285 - 298.
31. Foll M, Gaggiotti OE, (2008) A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics, 180, 977 - 993.
32. Fowler SL, Hamilton D, Currie S, (2009) A comparison of the heat shock response in juvenile and adult rainbow trout (Oncorhynchus mykiss) - implications for increased thermal sensitivity with age. Canadian Journal of Fisheries and Aquatic Sciences, 66, 91 - 100.
33. Gamperl AK, Rodnick KJ, Faust HA, et al. (2002) Metabolism, swimming performance, and tissue biochemistry of high desert redband trout (Oncorhynchus mykiss ssp.): evidence for phenotypic differences in physiological function. Physiological and Biochemical Zoology, 75, 413 - 431.
34. Hari RE, Livingstone DM, Siber R, et al. (2006) Consequences of climatic change for water temperature and brown trout populations in Alpine rivers and streams. Global Change Biology, 12, 10 - 26.
35. Heath DD, Busch C, Kelly J, Atagi DY, (2002) Temporal change in genetic structure and effective population size in steelhead trout (Oncorhynchus mykiss). Molecular Ecology, 11, 197 - 214.
36. Hendry AP, Hensleigh JE, Reisenbichler RR, (1998) Incubation temperature, developmental biology, and the divergence of sockeye salmon (Oncorhynchus nerka) within Lake Washington. Canadian Journal of Fisheries and Aquatic Sciences, 55, 1387 - 1394.
37. Hendry AP, Farrugia TJ, Kinnison MT, (2008) Human influences on rates of phenotypic change in wild animal populations. Molecular Ecology, 17, 20 - 29.
38. Hermisson J, (2009) Who believes in whole-genome scans for selection? Heredity, 103, 283 - 284.
39. Hoekstra HE, Hirschmann RJ, Bundey RA, et al. (2006) A single amino acid mutation contributes to adaptive beach mouse color pattern. Science, 313, 101 - 104.
40. Hoffmann AA, Hallas RJ, Dean JA, Schiffer M, (2003) Low potential for climatic stress adaptation in a rainforest Drosophila species. Science, 301, 100 - 102.
41. Holt RA, Amandi A, Rohovec JS, Fryer JL, (1989) Relation of water temperature to bacterial cold-water disease in coho salmon, Chinook salmon, and rainbow trout. Journal of Aquatic Animal Health, 1, 94 - 101.
42. Huber M, Guderley H, (1993) The effect of thermal acclimation and exercise upon the binding of glycolytic enzymes in muscle of the goldfish Carassius auratus. Journal of Experimental Biology, 175, 195 - 209.
43. Hubisz MJ, Falush D, Stephens M, Pritchard JK, (2009) Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources, 9, 1322 - 1332.
44. Jakobsson M, Rosenberg NA, (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23, 1801 - 1806.
45. Jensen LF, Hansen MM, Pertoldi C, et al. (2008) Local adaptation in brown trout early life-history traits: implications for climate change adaptability. Proceeding of the Royal Society of London Series B, 275, 2859 - 2868.
46. Joost S, Kalbermatten M, Bonin A, (2008) Spatial Analysis Method (SAM): a software tool combining molecular and environmental data to identify candidate loci for selection. Molecular Ecology Resources, 8, 957 - 960.
47. Kassahn KS, Crozier RH, Ward AC, et al. (2007) From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis. BMC Genomics, doi:.
48. Lande R, Thompson R, (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics, 124, 743 - 756.
49. Lander ES, Schork NJ, (1994) Genetic dissection of complex traits. Science, 265, 2037 - 2048.
50. Langella O, (2001) Populations 1.2.24: population genetic structure (individuals or populations distances, phylogenetic trees). Available:.
51. Lee SH, Van Der Werf JHJ, Hayes BJ, et al. (2008) Predicting unobserved phenotypes for complex traits from whole-genome SNP Data. PLoS Genetics, 4: e1000231, doi:.
52. Luikart G, England PR, Tallmon D, et al. (2003) The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics, 4, 981 - 994.
53. Lyman RF, Mackay TFC, (1998) Candidate quantitative trait loci and naturally occurring phenotypic variation for bristle number in Drosophila melanogaster: the delta-hairless gene region. Genetics, 149, 983 - 998.
54. Marcogliese DJ, (2001) Implications of climate change for parasitism of animals in the aquatic environment. Canadian Journal of Zoology, 79, 1331 - 1352.
55. Meyer KA, Lamansky J, Schill DJ, (2010) Biotic and abiotic factors related to redband trout occurrence and abundance in desert and montane streams. Western North American Naturalist, 70, 67 - 76.
56. Morin PA, Luikart G, Wayne RK, SNP Workshop Group (2004) SNPs in ecology, evolution and conservation. Trends in Ecology & Evolution, 19, 208 - 216.
57. Morrill JC, Bales RC, Conklin MH, (2005) Estimating stream temperature from air temperature: implications for future water quality. Journal of Environmental Engineering, 131, 139 - 146.
58. Morrison AC, Bare LA, Chambless LE, et al. (2007) Prediction of coronary heart disease risk using a genetic risk score: the atherosclerosis risk in communities study. American Journal of Epidemiology, 166, 28 - 35.
59. Narum SR, (2006) Beyond Bonferroni: less conservative analyses for conservation genetics. Conservation Genetics, 7, 783 - 787.
60. Narum SR, Zendt J, Graves D, Sharp B, (2008) Influence of landscape on resident and anadromous life history types of Oncorhynchus mykiss. Canadian Journal of Fisheries and Aquatic Sciences, 65, 1013 - 1023.
61. Neuhauss SCF, Biehlmaier O, Seeliger MW, et al. (1999) Genetic disorders of vision revealed by a behavioral screen of 400 essential loci in zebrafish. Journal of Neuroscience, 19, 8603 - 8615.
62. Nosil P, Egan SP, Funk DJ, (2008) Heterogeneous genomic differentiation between walking-stick ecotypes: "isolation by adaptation" and multiple roles for divergent selection. Evolution, 62, 316 - 336.
63. Olsen JB, Bentzen P, Seeb JE, (1998) Characterization of seven microsatellite loci derived from pink salmon. Molecular Ecology, 7, 1083 - 1090.
64. Page RDM, (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences, 12, 357 - 358.
65. Piertney SB, Oliver MK, (2006) The evolutionary ecology of the major histocompatibility complex. Heredity, 96, 7 - 21.
66. Price AL, Patterson NJ, Plenge RM, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics, 38, 904 - 909.
67. Pritchard JK, Rosenberg NA, (1999) Use of unlinked genetic markers to detect population stratification in association studies. American Journal of Human Genetics, 65, 220 - 228.
68. Pritchard J, Stephens M, Donnelly P, (2000a) Inference of population structure using multilocus genotype data. Genetics, 155, 945 - 959.
69. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P, (2000b) Association mapping in structured populations. American Journal of Human Genetics, 67, 170 - 181.
70. Raymond M, Rousset F, (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity, 86, 248 - 249.
71. Rodnick KJ, Gamperl AK, Lizars KR, et al. (2004) Thermal tolerance and metabolic physiology among redband trout populations in south-eastern Oregon. Journal of Fish Biology, 64, 310 - 335.
72. Sprowles AE, Stephens MR, Clipperton NW, May BP, (2006) Fishing for SNPs: a targeted locus approach for single nucleotide polymorphism discovery in rainbow trout. Transactions of the American Fisheries Society, 135, 1698 - 1721.
73. Tate KW, Lancaster DL, Lile DF, (2007) Assessment of thermal stratification within stream pools as a mechanism to provide refugia for native trout in hot, arid rangelands. Environmental Monitoring and Assessment, 124, 289 - 300.
74. Taylor EB, (1995) Genetic variation at minisatellite DNA loci among North Pacific populations of steelhead trout and rainbow trout (Oncorhynchus mykiss). Journal of Heredity, 86, 354 - 363.
75. Torgerson DG, Boyko AR, Hermandez RD, et al. (2009) Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLoS Genetics, doi
76. Umina PA, Weeks AR, Kearney MR, et al. (2005) A rapid shift in a classic clinal pattern in Drosophila reflecting climate change. Science, 308, 691 - 693.
77. Vasemagi A, Primmer CR, (2005) Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies. Molecular Ecology, 14, 3623 - 3642.
78. Waples RS, (2006) A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conservation Genetics, 7, 167 - 184.
79. Waples RS, Do C, (2008) LDNE: a program for estimating effective population size from data on linkage disequilibrium. Molecular Ecology Resources, 8, 753 - 756.
80. Weir BS, Cockerham CC, (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, L1358 - L1370.
81. Wray NR, Goddard ME, Visscher PM, (2007) Prediction of individual genetic risk from genome-wide association studies. Genome Research, 17, 1520 - 1528.
82. Zhang F, Wang Y, Deng H, (2008) Comparison of population-based association study methods correcting for population stratification. PLoS ONE, doi:.
83. Zinn JL, Johnson KA, Sanders JE, Fryer JL, (1977) Susceptibility of salmonid species and hatchery strains of Chinook salmon (Oncorhynchus tshawytscha) to infections by Ceratomyxa shasta. Journal of the Fisheries Research Board of Canada, 34, 933 - 936.
84. Zoellick BW, (1999) Stream temperatures and the elevational distribution of redband trout in southwestern Idaho. Great Basin Naturalist, 59, 136 - 143.