Mitochondrial DNA phylogeography of the three-spined stickleback (Gasterosteus aculeatus) in Europe-Evidence for multiple glacial refugia

Molecular Phylogenetics and Evolution

Volumn 46, Issue 1, 2008, Pages 167-182

  Makinen H S ^a   Merila J ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Gasterosteus aculeatus; IM coalescent; mtDNA; Phylogeography; Population expansion

Indexed keywords

CYTOCHROME C; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; EUROPE; EVOLUTION; GENETICS; GEOGRAPHY; MOLECULAR EVOLUTION; PHYLOGENY; SMEGMAMORPHA;

ANIMALS; CYTOCHROMES C; DNA, MITOCHONDRIAL; EUROPE; EVOLUTION; EVOLUTION, MOLECULAR; GEOGRAPHY; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SMEGMAMORPHA;

GASTEROSTEUS ACULEATUS;

EID: 37249086149     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2007.06.011     Document Type: Article

References (55)

1. Aljanabi S.M., and Martinez I. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res. 25 (1997) 4692-4693
2. Arbogast B.S., Edwards S.V., Wakeley J., Beerli P., and Slowinski J.B. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annu. Rev. Ecol. Syst. 33 (2002) 707-740
3. Banarescu P. Zoogeography of Freshwaters vol. 1 (1990), AULA-Verlag, Wiesbaden
4. Bazin E., Glemin S., and Galtier N. Population size does not influence mitochondrial genetic diversity in animals. Science 312 (2006) 570-572
5. Bernatchez L., and Wilson C.C. Comparative phylogeography of Nearctic and Palearctic fishes. Mol. Ecol. 7 (1998) 431-452
6. Bell M.A., and Foster S.A. Introduction to the evolutionary biology of the threespine stickleback. In: Bell M.A., and Foster S.A. (Eds). The Evolutionary Biology of the Threespine Stickleback (1994), Oxford University Press, Oxford 1-26
7. Berry O.F., Wares J.P., Barber P.H., Ross-Ibarra J., Sotka E.E., Toonen R.J., Bazin E., Glemin S., et al. Mitochondrial DNA and population size. Science 314 (2006) 1388-1390
8. Clement M., Posada D., and Crandall K.A. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9 (2000) 1657-1659
9. Colosimo P.F., Hosemann K.E., Balabhadra S., Villarreal Jr. G., Dickson M., Grimwood J., Schmutz J., Myers R.M., Schluter D., and Kingsley D.M. Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science 307 (2005) 1928-1933
10. Crandall K.A., and Templeton A.R. Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics 134 (1993) 959-969
11. Dawson A.G. Ice Age Earth (1992), Routledege Press, London
12. Elphinstone M.S., Hinten G.N., Anderson M.J., and Nock C.J. An inexpensive and high-throughput procedure to extract and purify total genomic DNA for population studies. Mol. Ecol. Notes 3 (2003) 317-320
13. Fu Y.X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147 (1997) 915-925
14. Grant W., and Bowen B. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J. Hered. 89 (1998) 415-426
15. Haglund T.R., Buth D.G., and Lawson R. Allozyme variation and phylogenetic relationships of Asian, North American, and European populations of the threespine stickleback, Gasterosteus aculeatus. Copeia 1992 (1992) 432-443
16. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41 (1999) 95-98
17. Hasegawa M., Kishino H., and Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22 (1985) 160-174
18. Hewitt G. The genetic legacy of the Quaternary ice ages. Nature 405 (2000) 907-913
19. Hey J. On the number of new world founders: a population genetic portrait of the peopling of the Americas. PLoS Biol. 3 (2005) 965-975
20. Hey J., and Nielsen R. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167 (2004) 747-760
21. Hickerson M.J., and Cunningham C.W. Nearshore fish (Pholis gunnellus) persists across the North Atlantic through multiple glacial episodes. Mol. Ecol. 15 (2006) 4095-4107
22. Ho S.Y.W., and Larson G. Molecular clocks: when times are a-changin'. Trends Genet. 22 (2006) 79-83
23. Hänfling B., Hellemans B., Volckaert F.A., and Carvalho G.R. Late glacial history of the cold-adapted freshwater fish Cottus gobio, revealed by microsatellites. Mol. Ecol. 11 (2002) 1717-1729
24. Johnson L.S., and Taylor E.B. The distribution of divergent mitochondrial DNA lineages of threespine stickleback (Gasterosteus aculeatus) in the northeastern Pacific basin: post-glacial dispersal and lake accessibility. J. Biogeogr. 31 (2004) 1073-1083
25. Kuhner M.K., Yamato J., and Felsenstein J. Maximum likelihood estimation of population growth rates based on the coalescent. Genetics 149 (1998) 429-434
26. Lessa E.P., Cook J.A., and Patton J.L. Genetic footprints of demographic expansion in North America, but not Amazonia, during the Late Quaternary. Proc. Natl. Acad. Sci. USA 100 (2003) 10,331-10,334
27. Mäkinen H.S., Cano J.M., and Merilä J. Genetic relationships among marine and freshwater populations of the European three-spined stickleback (Gasterosteus aculeatus) revealed by microsatellites. Mol. Ecol. 15 (2006) 1519-1534
28. Malhi R.S., Rhett G., and Bell A.M. Mitochondrial DNA evidence of an early Holocene population expansion of threespine sticklebacks from Scotland. Mol. Phylogenet. Evol. 40 (2006) 148-154
29. Mangerud J., Jakobsson M., Alexanderson H., Astakhov V., Clarke G.K.C., Henriksen M., Hjort C., Krinner G., Lunkka J., Möller P., et al. Ice-dammed lakes and rerouting of the drainage of northern Eurasia during the last glaciation. Quaternary Sci. Rev. 23 (2004) 1313-1332
30. Martens K. Speciation in ancient lakes. Trends Ecol. Evol. 12 (1997) 177-182
31. McKinnon J.S., and Rundle H.D. Speciation in nature: the threespine stickleback model systems. Trends Ecol. Evol. 17 (2002) 480-488
32. Miya M., Kawaguchi A., and Nishida M. Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Mol. Biol. Evol. 18 (2001) 1993-2009
33. Moritz C. Defining "Evolutionarily Significant Units" for conservation. Trends Ecol. Evol. 9 (1994) 373-375
34. Münzing J. The evolution of variation and distributional patterns in European populations of the three-spined stickleback, Gasterosteus aculeatus. Evolution 17 (1963) 320-332
35. Omland K.E., Baker J.M., and Peters J.L. Genetic signatures of intermediate divergence: population history of old and new world Holarctic ravens (Corvus corax). Mol. Ecol. 15 (2006) 795-808
36. Orti G., Bell M.A., Reimchen T.E., and Meyer A. Global survey of mitochondrial DNA sequences in the threespine stickleback: evidence for recent migrations. Evolution 48 (1994) 608-622
37. Paepke H.J. Gasterosteus aculeatus Linnaeus, 1758. In: Banarescu P., and Paepke H.J. (Eds). The Freshwater Fishes of Europe Cyprinidae vol. 5 (2001), Aula-Verlag 209-256
38. Peters J.L., Gretes W., and Omland K.E. Late Pleistocene divergence between eastern and western populations of wood ducks (Aix sponsa) inferred by the 'isolation with migration' coalescent method. Mol. Ecol. 14 (2005) 3407-3418
39. Posada D., and Crandall K.A. Intraspecific gene genealogies: trees grafting into networks. Trends Ecol. Evol. 16 (2001) 37-45
40. Rambaut, A., Drummond, A.J., 2003. Tracer v1.3, Available from: http://evolve.zoo.ox.ac.uk.
41. Reusch T.B., Wegner K.M., and Kalbe M. Rapid genetic divergence in postglacial populations of threespine stickleback (Gasterosteus aculeatus): the role of habitat type, drainage and geographical proximity. Mol. Ecol. 10 (2001) 2435-2445
42. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
43. Rozas J., Sanchez-DelBarrio J.C., Messeguer X., and Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 (2003) 2496-2497
44. Ryan W.B.F., Major C.O., Lericolais G., and Goldstein S.L. Catastrophic flooding of the Black Sea. Annu. Rev. Earth Planet. Sci. 31 (2003) 525-554
45. Ryan W.B.F., Pitman W.C., Major C.O., Shimkus K., Moskalenko V., Jones G.A., Dimitrov P., Gorür N., Sakinç M., and Yüce H. An abrupt drowning of the Black Sea shelf. Mar. Geol. 138 (1997) 119-126
46. Stärner H., Påhlsson C., and Lindén M. Tandem repeat polymorphism and heteroplasmy in the mitochondrial DNA control region of threespine stickleback (Gasterosteus aculeatus). Behaviour 141 (2004) 1357-1369
47. Svendsen J.I., Alexanderson H., Astakhov V.I., Demidov I., Dowdeswell J.A., Funder S., Gataullin V., Henriksen M., Hjort C., Houmark-Nielsen M., et al. Late Quaternary ice sheet history of northern Eurasia. Quaternary Sci. Rev. 23 (2004) 1229-1271
48. Swofford, D.L., 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, MA.
49. Taberlet P., Fumagalli L., Wust-Saucy A.G., and Cosson J.F. Comparative phylogeography and postglacial colonization routes in Europe. Mol. Ecol. 7 (1998) 453-464
50. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (1989) 585-595
51. Takahashi H., and Goto A. Evolution of East Asian ninespine sticklebacks as shown by mitochondrial DNA control region sequences. Mol. Phylogenet. Evol. 21 (2001) 135-155
52. Volckaert F.A.M., Hänfling B., Hellemans B., and Carvalho G.R. Timing of the population dynamics of bullhead Cottus gobio (Teleostei: Cottidae) during the Pleistocene. J. Evol. Biol. 15 (2002) 930-944
53. Wares J.P., Barber P.H., Ross-Ibarra J., Sotka E.E., and Toonen R.J. Mitochondrial DNA and population size. Science 314 (2006) 1388-1390 (author reply 1388-1390)
54. Watanabe K., Mori S., and Nishida M. Genetic relationships and origin of two geographic groups of the freshwater threespine stickleback, 'hariyo'. Zool. Sci. 20 (2003) 265-274
55. Zhang D.X., and Hewitt G.M. Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol. Ecol. 12 (2003) 563-584