Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide single nucleotide polymorphism genotyping

Molecular Ecology

Volumn 22, Issue 7, 2013, Pages 1917-1932

  Deagle, Bruce E ^a,d   Jones, Felicity C ^b,e   Absher, Devin M ^c   Kingsley, David M ^b   Reimchen, Thomas E ^a  

^a UNIVERSITY OF VICTORIA   (Canada)

^b STANFORD UNIVERSITY   (United States)

^c HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

^d AUSTRALIAN ANTARCTIC DIVISION   (Australia)

^e FRIEDRICH MIESCHER LABORATORY OF THE MAX PLANCK SOCIETY   (Germany)

Author keywords

Gasterosteus; population structure; single nucleotide polymorphism

Indexed keywords

FRESH WATER; MITOCHONDRIAL DNA;

ADAPTATION; ALLELE; ANIMAL; ARTICLE; CANADA; CLASSIFICATION; DNA SEQUENCE; ECOSYSTEM; EVOLUTION; GENETICS; GENOMICS; HETEROZYGOTE; LAKE; PHENOTYPE; PHYLOGEOGRAPHY; PRINCIPAL COMPONENT ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SMEGMAMORPHA;

ADAPTATION, PHYSIOLOGICAL; ALLELES; ANIMALS; BIOLOGICAL EVOLUTION; CANADA; DNA, MITOCHONDRIAL; ECOSYSTEM; FRESH WATER; GENOMICS; HETEROZYGOTE; LAKES; PHENOTYPE; PHYLOGEOGRAPHY; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ANALYSIS, DNA; SMEGMAMORPHA;

GASTEROSTEUS;

EID: 84875364944     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12215     Document Type: Article

References (61)

1. Allender CJ, Seehausen O, Knight ME, Turner GF, Maclean N, (2003) Divergent selection during speciation of Lake Malawi cichlid fishes inferred from parallel radiations in nuptial coloration. Proceedings of the National Academy of Sciences, 100, 14074-14079.
2. Avise JC, (2006) Evolutionary Pathways in Nature: A Phylogenetic Approach. Cambridge University Press, Cambridge, UK.
3. Barrie JV, Conway KW, (1999) Late Quaternary glaciation and postglacial stratigraphy of the northern Pacific margin of Canada. Quaternary Research, 51, 113-123.
4. Beaumont MA, Balding DJ, (2004) Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology, 13, 969-980.
5. Bell MA, (1976) Evolution of phenotypic diversity in Gasterosteus aculeatus superspecies on pacific coast of North America. Systematic Zoology, 25, 211-227.
6. Bell MA, (2001) Lateral plate evolution in the threespine stickleback: getting nowhere fast. Genetica, 112, 445-461.
7. Bell MA, Foster SA, (1994) The Evolutionary Biology of the Threespine Stickleback. Oxford University Press, New York.
8. Berner D, Grandchamp AC, Hendry AP, (2009) Variable progress toward ecological speciation in parapatry: stickleback across eight lake-stream transitions. Evolution, 63, 1740-1753.
9. Caldera EJ, Bolnick DI, (2008) Effects of colonization history and landscape structure on genetic variation within and among threespine stickleback (Gasterosteus aculeatus) populations in a single watershed. Evolutionary Ecology Research, 10, 575-598.
10. Chan YF, Marks ME, Jones FC, et al,. (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science, 327, 302-305.
11. Colosimo PF, Peichel CL, Nereng K, et al,. (2004) The genetic architecture of parallel armor plate reduction in threespine sticklebacks. Plos Biology, 2, 635-641.
12. Colosimo PF, Hosemann KE, Balabhadra S, et al,. (2005) Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science, 307, 1928-1933.
13. Dasmahapatra KK, Walters JR, Briscoe AD, et al,. (2012) Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature, 487, 94-98.
14. Deagle BE, Reimchen TE, Levin DB, (1996) Origins of endemic stickleback from the Queen Charlotte Islands: mitochondrial and morphological evidence. Canadian Journal of Zoology, 74, 1045-1056.
15. Deagle BE, Jones FC, Chan YF, Absher DB, Kingsley DM, Reimchen TE, (2012) Population genomics of parallel phenotypic evolution in stickleback across stream-lake ecological transitions. Proceedings of the Royal Society of London Series B-Biological Sciences, 279, 1277-1286.
16. Dowling DK, Friberg U, Lindell J, (2008) Evolutionary implications of non-neutral mitochondrial genetic variation. Trends in Ecology & Evolution, 23, 546-554.
17. Elmer KR, Meyer A, (2011) Adaptation in the age of ecological genomics: insights from parallelism and convergence. Trends in Ecology & Evolution, 26, 298-306.
18. Gambling SJ, Reimchen TE, (2012) Prolonged life span among endemic Gasterosteus populations. Canadian Journal of Zoology, 90, 284-290.
19. Gao XY, Starmer J, (2007) Human population structure detection via multilocus genotype clustering. BMC Genetics, 8.
20. Gromping U, (2006) Relative importance for linear regression in R: the package relaimpo. Journal of Statistical Software, 17.
21. Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA, (2010) Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. Plos Genetics, 6, e1000862.
22. Jones FC, Chan YF, Schmutz J, et al,. (2012a) A genome-wide SNP genotyping array reveals patterns of global and species pair divergence in sticklebacks. Current Biology, 22, 83-90.
23. Jones FC, Grabherr MG, Chan YF, et al,. (2012b) The genomic basis of adaptive evolution in threespine sticklebacks. Nature, 484, 55-61.
24. Josenhans HW, Fedje DW, Conway KW, Barrie JV, (1995) Post glacial sea levels on the western canadian continental shelf-evidence for rapid change, extensive subaerial exposure, and early human habitation. Marine Geology, 125, 73-94.
25. Josenhans H, Fedje D, Pienitz R, Southon J, (1997) Early humans and rapidly changing Holocene sea levels in the Queen Charlotte Islands Hecate Strait, British Columbia, Canada. Science, 277, 71-74.
26. Keller LF, Jeffery KJ, Arcese P, et al,. (2001) Immigration and the ephemerality of a natural population bottleneck: evidence from molecular markers. Proceedings of the Royal Society of London Series B-Biological Sciences, 268, 1387-1394.
27. Kitano J, Mori S, Peichel CL, (2007) Phenotypic divergence and reproductive isolation between sympatric forms of Japanese threespine sticklebacks. Biological Journal of the Linnean Society, 91, 671-685.
28. Kocher TD, (2004) Adaptive evolution and explosive speciation: the cichlid fish model. Nature Reviews Genetics, 5, 288-298.
29. Leaver SD, Reimchen TE, (2012) Abrupt changes in defence and trophic morphology of the giant threespine stickleback (Gasterosteus sp.) following colonization of a vacant habitat. Biological Journal of the Linnean Society, 107, 494-509.
30. Losos J, (2009) Lizards in an Evolutionary Tree: Ecology and Adaptive Radiation of Anoles. University of California Press, Berkeley, California.
31. Losos JB, Jackman TR, Larson A, de Queiroz K, Rodriguez-Schettino L, (1998) Contingency and determinism in replicated adaptive radiations of island lizards. Science, 279, 2115-2118.
32. Makinen HS, Cano JM, Merila J, (2006) Genetic relationships among marine and freshwater populations of the European three-spined stickleback (Gasterosteus aculeatus) revealed by microsatellites. Molecular Ecology, 15, 1519-1534.
33. McKinnon JS, Mori S, Blackman BK, et al,. (2004) Evidence for ecology's role in speciation. Nature, 429, 294-298.
34. Michel AP, Sim S, Powell T, Nosil P, Feder JL, (2010) Widespread genomic divergence during sympatric speciation. Proceedings of the National Academy of Sciences of the United States of America, 107, 9724-9729.
35. Miller CT, Beleza S, Pollen AA, et al,. (2007) cis-regulatory changes in kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans. Cell, 131, 1179-1189.
36. Miller MR, Brunelli JP, Wheeler PA, et al,. (2012) A conserved haplotype controls parallel adaptation in geographically distant salmonid populations. Molecular Ecology, 21, 237-249.
37. Moodie GEE, (1972) Morphology, life-history, and ecology of an unusual stickleback (Gasterosteus aculeatus) in Queen Charlotte Islands, Canada. Canadian Journal of Zoology, 50, 721-732.
38. Moodie GEE, Reimchen TE, (1976a) Glacial refugia, endemism, and stickleback populations of Queen Charlotte Islands, British Columbia. Canadian Field-Naturalist, 90, 471-474.
39. Moodie GEE, Reimchen TE, (1976b) Phenetic variation and habitat differences in Gasterosteus populations of Queen Charlotte Islands. Systematic Zoology, 25, 49-61.
40. O'Reilly P, Reimchen TE, Beech R, Strobeck C, (1993) Mitochondrial DNA in Gasterosteus and pleistocene glacial refugium on the Queen Charlotte Islands, British-Columbia. Evolution, 47, 678-684.
41. Orti G, Bell MA, Reimchen TE, Meyer A, (1994) Global survey of mitochondrial DNA sequences in the threespine stickleback evidence for recent migrations. Evolution, 48, 608-622.
42. Patterson N, Price AL, Reich D, (2006) Population structure and eigenanalysis. Plos Genetics, 2, 2074-2093.
43. R (2009) Development Core Team R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
44. Reimchen TE, (1980) Spine-deficiency and polymorphism in a population of Gasterosteus aculeatus: an adaptation to predators? Canadian Journal of Zoology, 58, 1232-1244.
45. Reimchen TE, (1983) Structural relationships between spines and lateral plates in threespine stickleback (Gasterosteus aculeatus). Evolution, 37, 931-946.
46. Reimchen TE, (1994) Predators and morphological evolution in threespine stickleback. In: The Evolutionary Biology of the Threespine Stickleback (eds, Bell MA, Foster SA,), pp. 240-276. Oxford University Press, New York.
47. Reimchen TE, (2000) Predator handling failures of lateral plate morphs in Gasterosteus aculeatus: implications for stasis and distribution of the ancestral plate condition. Behaviour, 137, 1081-1096.
48. Reimchen TE, Nosil P, (2002) Temporal variation in divergent selection on spine number in threespine stickleback. Evolution, 56, 2472-2483.
49. Reimchen TE, Stinson EM, Nelson JS, (1985) Multivariate differentiation of parapatric and allopatric populations of threespine stickleback in the Sangan River watershed, Queen Charlotte Islands. Canadian Journal of Zoology, 63, 2944-2951.
50. Reimchen TE, Byun A, (2005) The evolution of endemic species on Haida Gwaii. In: Haida Gwaii: Human History and Environment from the Time of Loon to the Time of the Iron People (eds, Fedje D, Mathewes R,), pp. 77-95. UBC press, Vancouver, British Columbia.
51. Reimchen TE, Bergstrom C, Nosil P, (2013) Adaptive radiation of Haida Gwaii stickleback. Evolutionary Ecology Research, in press.
52. Roesti M, Hendry AP, Salzburger W, Berner D, (2012) Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs. Molecular Ecology, 21, 2852-2862.
53. Schluter D, Conte GL, (2009) Genetics and ecological speciation. Proceedings of the National Academy of Sciences of the United States of America, 106, 9955-9962.
54. Spoljaric MA, Reimchen TE, (2007) 10 000 years later: evolution of body shape in Haida Gwaii three-spined stickleback. Journal of Fish Biology, 70, 1484-1503.
55. Sutherland-Brown A, Yorath CJ, (1989) Geology and non-renewable resources of Haida Gwaii. In: The Outer Shores (eds, Scudder GGE, Gessler N,), pp. 3-26. Queen Charlotte Island Museum, Queen Charlotte City, British Columbia.
56. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731-2739.
57. Taylor EB, McPhail JD, (1999) Evolutionary history of an adaptive radiation in species pairs of threespine sticklebacks (Gasterosteus): insights from mitochondrial DNA. Biological Journal of the Linnean Society, 66, 271-291.
58. Willing EM, Bentzen P, van Oosterhout C, et al,. (2010) Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies. Molecular Ecology, 19, 968-984.
59. Withler RE, McPhail JD, (1985) Genetic variability in freshwater and anadromous sticklebacks (Gasterosteus aculeatus) of southern British Columbia. Canadian Journal of Zoology, 63, 528-533.
60. Wootton R, (1976) The Biology of the Stickleback. Academic Press, London.
61. Yamada M, Higuchi M, Goto A, (2001) Extensive introgression of mitochondrial DNA found between two genetically divergent forms of threespine stickleback, Gasterosteus aculeatus, around Japan. Environmental Biology of Fishes, 61, 269-284.