Divergence genetics analysis reveals historical population genetic processes leading to contrasting phylogeographic patterns in co-distributed species

Molecular Ecology

Volumn 19, Issue 22, 2010, Pages 5043-5060

  McGovern, Tamara M ^a,d   Keever, Carson C ^b   Saski, Christopher A ^c   Hart, Michael W ^b   Marko, Peter B ^a  

^a CLEMSON UNIVERSITY   (United States)

^b SIMON FRASER UNIVERSITY   (Canada)

^c CLEMSON UNIVERSITY   (United States)

^d Limestone College   (United States)

Author keywords

ancestral polymorphism; biogeography; coalescence; divergence time; gene flow; glaciation; larval development; pseudo congruence; vicariance

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; DNA SEQUENCE; GENE FLOW; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; MOLECULAR GENETICS; PHYLOGENY; POPULATION DENSITY; POPULATION GENETICS; SNAIL; STARFISH;

ANIMALS; DNA, MITOCHONDRIAL; GENE FLOW; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; MOLECULAR SEQUENCE DATA; PHYLOGENY; POPULATION DENSITY; SEQUENCE ANALYSIS, DNA; SNAILS; STARFISH;

ASTERINA MINIATA; CANIS FAMILIARIS; GASTROPODA; NUCELLA LAMELLOSA;

EID: 78449282381     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2010.04854.x     Document Type: Article

References (85)

1. Arbogast BS, Kenagy GJ, (2001) Comparative phylogeography as an integrative approach to historical biogeography. Journal of Biogeography, 28, 819-825.
2. Arbogast BS, Browne RA, Weigl PD, (2001) Evolutionary genetics and Pleistocene biogeography of North American tree squirrels (Tamiasciurus). Journal of Mammology, 82, 302-319.
3. Arbogast BS, Edwards SV, Wakeley J, Beerli P, Slowinski JB, (2002) Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annual Review of Ecology and Systematics, 33, 707-740.
4. Arndt A, Smith MJ, (1998) Genetic diversity and population structure in two species of sea cucumber: differing patterns according to mode of development. Molecular Ecology, 7, 1053-1064.
5. Avise JC, (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, MA.
6. Avise JC, (2004) Molecular Markers, Natural History and Evolution, 2nd edn. Sinauer Associates, Sunderland, MA.
7. Avise JC, Arnold J, Ball RM, etal. (1987) Intraspecific phylogeography: the mitochondrial-DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics, 18, 489-522.
8. Ayre DJ, Minchinton TE, Perrin C, (2009) Does life history predict past and current connectivity for rocky intertidal invertebrates across a marine biogeographic barrier- Molecular ecology, 18, 1887-1903.
9. Barber PH, Erdmann MV, Palumbi SR, (2006) Comparative phylogeography of three co-distributed stomatopods: origins and timing of regional lineage diversification in the coral triangle. Evolution, 60, 1825-1839.
10. Barrowclough GF, Zink RM, (2009) Funds enough, and time: mtDNA, nuDNA and the discovery of divergence. Molecular Ecology, 18, 2934-2936.
11. Basch LV, (1996) Effects of algal and larval densities on development and survival of asteroid larvae. Marine Biology, 126, 693-701.
12. Becquet C, Przeworski M, (2007) A new approach to estimate parameters of speciation models with application to apes. Genome research, 17, 1505-1519.
13. Benzie JAH, (1999) Genetic structure of coral reef organisms: Ghosts of dispersal past. American Zoologist, 39, 131-145.
14. Bermingham E, Moritz C, (1998) Comparative phylogeography: concepts and applications. Molecular Ecology, 7, 367-369.
15. Blakeslee AM, Byers JE, Lesser MP, (2008) Solving cryptogenic histories using host and parasite molecular genetics: the resolution of Littorina littorea's North American origin. Molecular ecology, 17, 16.
16. Briggs JC, (1974) Marine Zoogeography. McGraw-Hill, New York.
17. Brooks DR, (1981) Hennig's parasitological method: A proposed solution. Systematic Zoology, 30, 229-249.
18. Brooks DR, (1990) Parsimony analysis in historical biogeography and coevolution: methodological and theoretical update. Systematic Zoology, 39, 14-30.
19. Brundin L, (1966) Transantarctic relationships and their significance as evidenced by midges. Kungliga Svenska Vetenskapsakademiens Handlinger (Series 4) 11, 1-472.
20. Brundin LZ, (1988) Phylogenetic biogeography. In: Analytical Biogeography (ed., Myers AA,), pp. 343-369, Chapman and Hall, New York.
21. Burton RS, (1983) Protein polymorphisms and genetic dif-ferentiation of marine invertebrate populations. Marine Biology Letters, 4, 193-206.
22. Campbell CA, (1978) Genetic divergence between populations of Thais lamellosa (Gmelin). In: Marine Organisms: Genetics Ecology, and Evolution (eds, Battaglia B, Beardmore JA,), pp. 157-170. Plenum Press, New York. 4, 193-206.
23. Chenna R, Sugawara H, Koike T, etal. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Research, 31, 3497-3500.
24. Clague JJ, James TS, (2002) History and isostatic effects of the last ice sheet in southern British Columbia. Quaternary Science Reviews, 21, 71-87.
25. Clague JJ, Froese D, Hutchinson I, James TS, Simon KM, (2005) Early growth of the last Cordilleran ice sheet deduced from glacio-isostatic depression in southwest British Columbia, Canada. Quaternary Research, 63, 53-59.
26. Collins TM, Frazer K, Palmer AR, Vermeij GJ, Brown WM, (1996) Evolutionary history of northern hemisphere Nucella (Gastropoda, Muricidae): molecules, ecology, and fossils. Evolution, 50, 2287-2304.
27. Crandall ED, Frey MA, Grosberg RK, Barber PH, (2008) Contrasting demographic history and phylogeographical patterns in two Indo-Pacific gastropods. Molecular ecology, 17, 2.
28. Cummins PF, Freeland HJ, (2007) Variability of the North Pacific current and its bifurcation. Progress in Oceanography, 75, 253-265.
29. Cunningham CW, Collins TM, (1994) Developing model systems for molecular biogeography: vicariance and inter- change in marine invertebrates. In: Molecular Ecology and Evolution: Approaches and Application (eds, Schier water B, Streit B, Wagner GP, DeSalle R,), pp. 405-433. Birkhauser Verlad, Basel, Switzerland.
30. Donoghue MJ, Moore BR, (2003) Toward an integrative historical biogeography. Integrative and Comparative Biology, 43, 261-270.
31. Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutio-nary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
32. Edwards SV, Beerli P, (2000) Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution, 54, 1839-1854.
33. Edwards S, Bensch S, (2009) Looking forwards or looking backwardsin avian phylogeograph- A comment on Zink and Barrowclough 2008. Molecular Ecology, 18, 2930-2933.
34. Excoffier L, Laval G, Schneider S, (2005) Arlequin (Version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47-50.
35. Freeland HJ, Cummins PF, (2005) Argo: a new tool for environmental monitoring and assessment of the world's oceans, an example from the NE Pacific. Progress in Oceanography, 664, 31-44.
36. Funk VA, Wagner WL, (1995) Biogeographic patterns in the Hawaiian Islands. In: Hawaiian Biogeography: Evolution on a Hot Spot Archipelago (eds, Wagner WL, Funk VA,), pp. 379-419. Smithsonian Institution Press, Washington, D.C.
37. Galbreath KE, Hafner DJ, Zamudio KR, (2009) When cold is better: climate-driven elevation shifts yield complex patterns of diversification and demography in an alpine specialist (American pika, Ochotona princeps). Evolution, 63, 2848-2863.
38. Grosberg RK, Levitan DR, Cameron BB, (1996) Characterization of genetic structure and genealogies using RAPD-PCR markers: a random primer for the novice and nervous. In: Molecular Zoology: Advances, Strategies, and Protocols (eds, Ferraris JD, Palumbi SR,), pp. 67-100. Wiley-Liss, New York.
39. Hart MW, Byrne M, Smith MJ, (1997) Molecular phylogenetic analysis of life-history evolution in asterinid starfish. Evolution, 51, 1848-1861.
40. Hasegawa M, Kishino H, Yano TA, (1985) Dating of the human ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22, 160-174.
41. Hedrick PW, (1999) Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution, 53, 313-318.
42. Hedrick PW, (2005) A standardized genetic differentiation measure. Evolution, 59, 1633-1638.
43. Hey J, (2007) Introduction to the IM and IM a computer programs:.
44. Hey J, Nielsen R, (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D.persimilis. Genetics, 167, 747-760.
45. Hey J, Nielsen R, (2007) Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences, 104, 2785-2790.
46. Hickerson MJ, Cunningham CW, (2005) Contrasting Quaternary histories in an ecologically divergent sister pair of low-dispersing intertidal fish (Xiphister) revealed by multilocus DNA analysis. Evolution, 59, 344-360.
47. Hickerson MJ, Meyer CP, (2008) Testing comparative phylo-geographic models of marine vicariance and dispersal using a hierarchical Bayesian approach. BMC evolutionary biology, 8, 322.
48. Hickerson MJ, Stahl EA, Lessios HA, (2006) Test for simultaneous divergence using approximate Bayesian computation. Evolution, 60, 2435-2453.
49. Hudson RR, Kaplan NL, (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics, 111, 147-164.
50. Jacobs DK, Haney TA, Louie KD, (2004) Genes, diversity, and geologic processes on the Pacific coast. Annual Review of Earth and Planetary Sciences, 3, 601-652.
51. Jennings WB, Edwards SV, (2005) Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution, 59, 2033-2047.
52. Keever CC, Sunday J, Puritz JB, etal. (2009) Discordant Distribution of Populations and Genetic Variation in a Sea Star with High Dispersal Potential. Evolution, 63, 3214-3227.
53. Kimura M, (1969) The number of heterozygous nucleotide sites maintained in a finite population due to a steady flux of mutations. Genetics, 61, 893-903.
54. Lessios HA, Kessing BD, Pearse JS, (2001) Population structure and speciation in tropical seas: global phylogeography of the sea urchin Diadema. Evolution, 55, 955-975.
55. Lomolino MV, Riddle BR, Brown JH, (2006) Biogeography, 3rd edn. Sinauer Associates, Inc., Sunderland, MA.
56. Lourie SA, Green DM, Vincent AC, (2005) Dispersal, habitat differences, and comparative phylogeography of Southeast Asian seahorses (Syngnathidae: Hippocampus). Molecular ecology, 14, 1073-1094.
57. Marko PB, (2004) 'What's larvae got to do with it-' Disparate patterns of post-glacial population structure in two benthic marine gastropods with identical dispersal potential. Molecular Ecology, 13, 597-611.
58. Marko PB, Barr KB, (2007) Basin-scale patterns of mtDNA differentiation and gene flow in the Bay Scallop, Argopecten irradians concentricus Say. Marine Ecology Progress Series, 349, 139-150.
59. Marko PB, Moran AL, (2009) Out of sight, out of mind: high cryptic diversity obscures the identities and histories of geminate species in the marine bivalve subgenus Acar. Journal of Biogeography, 36, 1861-1880.
60. Marko PB, Hoffman JM, Emme SA, McGovern TM, Keever C, Cox LN, (2010) The expansion-contraction model of Pleistocene demography: rocky shores suffer a sea change- Molecular Ecology, 19, 146-169.
61. Morris RH, Abbott DL, Haderlie EC, (1980) Intertidal inverte-brates of California. Stanford University Press, Stanford, CA.
62. Navascues M, Emerson BC, (2009) Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods. Molecular Ecology, 18, 4390-4397.
63. ST obs Conservation Genetics, 3, 167-173.
64. Nielsen R, Wakeley J, (2001) Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics, 158, 885-896.
65. Palumbi SR, (1997) Molecular biogeography of the Pacific. Coral Reefs, 16, S47-S52.
66. Platnick NI, Nelson G, (1978) A method of analysis for historical biogeography. Systematic Zoology, 27, 1-16.
67. Posada D, Crandall KA, (1998) Modeltest: testing the model of DNA substitution. Bioinformatics, 14, 817-818.
68. Rambaut A, (2002) Se-Al Sequence Alignment Editor v2.0 (Software). Department of Zoology, University of Oxford, Oxford, UK.
69. Riddle BR, (2005) Is biogeography emerging from its identity crisis- Journal of Biogeography, 32, 185-186.
70. Rocha LA, Bass Al, Robertson DR, Bowen BW, (2002) Adult habitat preferences, larval dispersal, and the comparative phylogeography of three Atlantic surgeonfishes (Teleostei: Acanthuridae). Molecular Ecology, 11, 243-252.
71. Rosen DE, (1978) Vicariant patterns and historical explanation in biogeography. Systematic Zoology, 27, 159-188.
72. Rumrill SS, (1989) Population size-structure, juvenile growth, and breeding periodicity of the sea star Asterina miniata in Barkley Sound, British Columbia. Marine Ecology Progress Series, 56, 37-47.
73. Sambrook J, Fritsch EF, Maniatis T, (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, London, pp. 1.25-1.28
74. Stephens M, Smith N, Donnelly P, (2001) A new statistical method for haplotype reconstruction from population data. American. Journal of Human Genetics, 68, 978-989.
75. Strasburg JL, Rieseberg LH, (2009) How robust are "Isolation with Migration" analyses to violations of the IM model- A simulation study. Molecular Biology and Evolution, 27, 297-310.
76. Strathmann MF, (1987) Reproduction and Development of Marine Invertebrates of the Northern Pacific Coast: Data and Methods for the Study of Eggs, Embryos, and Larvae. University of Washington Press, Seattle, WA.
77. Swofford DL, (2002) Phylogenetic Analysis Using Parsimony (and Other Methods) Paup 4.0b4. Sinauer Associates, Sunderland, Massachusetts.
78. Victoriano PF, Ortiz JC, Benavides E, Adams BJ, Sites JW, (2008) Phylogeography of codistributed species of Chilean Liolaemus (Squamata: Tropiduridae) from the central-southern Andean range. Molecular Ecology, 17, 2397-2416.
79. Waples RS, (1998) Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. Journal of Heredity, 89, 438-450.
80. Whitlock MC, McCauley DE, (1999) Short review: indirect measures of gene flow-Fst does not equal 1/(4Nm+1). Heredity, 82, 117-125.
81. Wiley EO, (1981) Phylogenetics: The Theory and Practice of Phylogenetic Systematics. John Wiley and Sons, New York.
82. Wiley EO, (1988) Vicariance biogeography. Annual Review of Ecology and Systematics, 19, 513-542.
83. Woerner AE, Cox MP, Hammer MF, (2007) Recombination-filtered genomic datasets by information maximization. Bioinformatics, 23, 1851-1853.
84. Wright S, (1978) Evolution and the Genetics of Populations. Volume 4: Variability Within and Among Natural Populations. University of Chicago Press, Chicago.
85. Zink RM, Barrowclough GF, (2008) Mitochondrial DNA under siege in avian phylogeography. Molecular Ecology, 17, 2107-2121.