Molecular signatures of Pleistocene sea-level changes that affected connectivity among freshwater shrimp in Indo-Australian waters

Molecular Ecology

Volumn 16, Issue 20, 2007, Pages 4295-4307

  De Bruyn, Mark ^a,b   Mather, Peter B ^b  

^a DURHAM UNIVERSITY   (United Kingdom)

^b QUEENSLAND UNIVERSITY OF TECHNOLOGY   (Australia)

Author keywords

Biogeography; Climate change; Dispersal; Evolution; Last Glacial Maximum; Phylogeography

Indexed keywords

FRESH WATER; MICROSATELLITE DNA; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; AUSTRALIA; BIOLOGICAL MODEL; CHEMISTRY; CLASSIFICATION; CLIMATE; DECAPODA (CRUSTACEA); DNA SEQUENCE; GENE FREQUENCY; GENETIC VARIABILITY; GENETICS; GENOTYPE; GEOGRAPHY; GROWTH, DEVELOPMENT AND AGING; HAPLOTYPE; INDONESIA; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION GENETICS; TIME;

ANIMALS; AUSTRALIA; CLIMATE; DECAPODA (CRUSTACEA); DNA, MITOCHONDRIAL; FRESH WATER; GENE FREQUENCY; GENETICS, POPULATION; GENOTYPE; GEOGRAPHY; HAPLOTYPES; INDONESIA; MICROSATELLITE REPEATS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; TIME FACTORS; VARIATION (GENETICS);

CRUSTACEA; DECAPODA (CRUSTACEA); MACROBRACHIUM ROSENBERGII;

EID: 34848880041     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2007.03481.x     Document Type: Article

References (69)

1. Archbold NW, Pigram CJ, Ratman N, Hakim S (1982) Indonesian Permian Brachipod fauna and Gondwana - South-East Asia relationships. Nature, 296, 556 558.
2. Audley-Charles MG (1983) Reconstruction of eastern Gondwanaland. Nature, 306, 48 50.
3. Avise JC (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, Massachusetts.
4. Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37 48.
5. Bennett KJ (1997) Evolution and Ecology: the Pace of Life. Cambridge University Press, Cambridge, UK.
6. Bermingham E, Avise JC (1986) Molecular zoogeography of freshwater fishes in the southeastern United States. Genetics, 113 (4 939 965.
7. Birky CW, Fuerst P, Maruyama T (1989) Organelle gene diversity under migration, mutation, and drift: equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells, and comparison to nuclear genes. Genetics, 121, 613 627.
8. Bohonak AJ (2002) ibd (isolation by distance): a program for analyses of isolation by distance. Journal of Heredity, 93, 153 154.
9. Brandon-Jones D (1998) Pre-glacial Bornean primate impoverishment and Wallace's Line. In : Biogeography and Geological Evolution of SE Asia (eds Holloway JD, Hall R pp. 393 404. Backhuys Publishers, Leiden, The Netherlands.
10. Briggs JC (2000) Centrifugal speciation and centres of origin. Journal of Biogeography, 27, 1183 1188.
11. Brown RM, Guttman SI (2002) Phylogenetic systematics of the Rana signata complex of Philippine and Bornean stream frogs: reconsideration of Huxley's modification of Wallace's Line at the Oriental-Australian faunal zone interface. Biological Journal of the Linnean Society, 76, 393 461.
12. de Bruyn M, Wilson JC, Mather PB (2004a) Huxley's line demarcates extensive genetic divergence between eastern and western forms of the giant freshwater prawn, Macrobrachium rosenbergii. Molecular Phylogenetics and Evolution, 30, 251 257.
13. de Bruyn M, Wilson JC, Mather PB (2004b) Reconciling geography and genealogy: phylogeography of giant freshwater prawns from the Lake Carpentaria region. Molecular Ecology, 13, 3515 3526.
14. de Bruyn M, Nugroho E, Hossain Md. M, Wilson JC, Mather PB (2005) Phylogeographic evidence for the existence of an ancient biogeographic barrier: the Isthmus of Kra Seaway. Heredity, 94, 370 378.
15. Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. American Journal of Human Genetics, 19, 233 257.
16. Chand V, de Bruyn M, Mather PB (2005) Microsatellite loci in the eastern form of the giant freshwater prawn (Macrobrachium rosenbergii). Molecular Ecology Notes, 5, 308 310.
17. Chappell J, Shackleton NJ (1986) Oxygen isotopes and sea level. Nature, 324, 137 140.
18. Clement M, Posada D, Crandall KA (2000) tcs: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657 1659.
19. Coope GR (1994) The response of insect faunas to glacial-interglacial climatic fluctuations. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 344, 19 26.
20. Cowie RH, Holland BS (2006) Dispersal is fundamental to biogeography and the evolution of biodiversity on oceanic islands. Journal of Biogeography, 33, 193 198.
21. Darwin C (1859) The Origin of Species. John Murray, London.
22. Davis MB, Shaw RG (2001) Range shifts and adaptive responses to Quaternary climate change. Science, 292, 673 679.
23. Epica Community Members (2004) Eight glacial cycles from an Antarctic ice core. Nature, 429, 623 628.
24. Felsenstein J (1993) phylip Version. 3.5 (Phylogeny Inference Package). University of Washington, Seattle.
25. Gathorne-Hardy FJ, Syaukani Davies RG, Eggleton P, Jones DT (2002) Quaternary rainforest refugia in south-east Asia: using termites (Isoptera) as indicators. Biological Journal of the Linnean Society, 75, 453-466.
26. Goudet J (1995) fstat, version 1.2: a computer program to calculate F-statistics. Journal of Heredity, 86, 485 486.
27. Guthrie RD (2003) Rapid body size decline in Alaskan Pleistocene horses before extinction. Nature, 426, 169 171.
28. Hall R (1998) The plate tectonics of Cenozoic SE Asia and the distribution of land and sea. In : Biogeography and Geological Evolution of SE Asia (eds Hall R, Holloway JD pp. 99 131. Backhuys Publishers, Leiden, The Netherlands.
29. Hall R (2001) Cenozoic reconstructions of SE Asia and the SW Pacific: changing patterns of land and sea. In : Faunal and Floral Migrations and Evolution in SE Asia-Australasia (eds Metcalfe I, Smith JMB, Morwood M, Davidson I pp. 35 56. A.A. Balkema Publishers, Lisse, The Netherlands.
30. Hall R (2002) Cenozoic geological and plate tectonic evolution of SE Asia and the SW Pacific: computer-based reconstructions, model and animations. Journal of Asian Earth Sciences, 20, 353 431.
31. Hallam A (1984) Pre-Quaternary sea-level changes. Annual Review of Earth and Planetary Sciences, 12, 205 243.
32. Heaney LR (1986) Biogeography of mammals in SE Asia: estimates of rates of colonization, extinction and speciation. Biological Journal of the Linnean Society, 28, 127 165.
33. Hewitt G (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907 913.
34. 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.
35. Ho SYW, Phillips MJ, Cooper A, Drummond AJ (2005) Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Molecular Biology and Evolution, 22 (7 1561 1568.
36. Hofreiter M, Serre D, Rohland N et al 2003) Lack of phylogeography in European mammals before the last glaciation. Proceedings of the National Academy of Sciences, USA, 101, 12963 12968.
37. 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.
38. Johnson DS (1973) Notes on some species of the genus Macrobrachium (Crustacea: Decapoda: Caridea: Palaemonidae). Journal of the Singapore National Academy of Sciences, USA, 3 (3 273 291.
39. Knowlton N, Weigt LA (1998) New dates and new rates for divergence across the Isthmus of Panama. Proceedings of the Royal Society of London. Series B, Biological Sciences, 265, 2257 2263.
40. Kumar S, Tamura K, Nei M (2004) mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics, 5, 150 163.
41. Lindenfelser ME (1984) Morphometric and allozymic congruence: evolution in the prawn Macrobrachium rosenbergii (Decapoda: Palaemonidae). Systematic Zoology, 33, 195 204.
42. 18O records. Paleoceanography, 20, PA1003, doi:.
43. McDonald JH, Kreitman ME (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature, 351, 652 654.
44. Meyers G, Bailey RJ, Worby AP (1995) Geostrophic transport of Indonesian Throughflow. Deep Sea Research, 42 (7 1163 1174.
45. Mittermeier RA, Myers N, Robles-Gil P, Mittermeier CG (1999) Hotspots: Earth's Biologically Richest and Most Endangered Terrestrial Ecoregions. Cemex, Conservation International, Agrupacion, Sierra Madre.
46. Morrison CL, Rió R, Duffy JE (2004) Phylogenetic evidence for an ancient rapid radiation of Caribbean sponge-dwelling snapping shrimps (Synalpheus). Molecular Phylogenetics and Evolution, 30, 563 581.
47. Moss SJ, Wilson MEJ (1998) Biogeographic implications of the Tertiary palaeogeographic evolution of Sulawesi and Borneo. In : Biogeography and Geological Evolution of SE Asia (eds Hall R, Holloway JD pp. 133 163. Backhuys Publishers, Leiden, The Netherlands.
48. Murphy NP, Austin CM (2005) Phylogenetic relationships of the globally distributed freshwater prawn genus Macrobrachium (Crustacea: Decapoda: Palaemonidae): biogeography, taxonomy and the convergent evolution of abbreviated larval development. Zoologica Scripta, 34, 187 197.
49. Myers N, Mittermeier RA, Mittermeier CG, de Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853 858.
50. Nielsen R, Wakeley J (2001) Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics, 158, 885 896.
51. Page TJ, Von Rintelen K, Hughes JM (2007) An island in the stream: Australia's place in the cosmopolitan world of Indo-West Pacific freshwater shrimp (Decapoda: Atyidae: Caridina). Molecular Phylogenetics and Evolution, 43, 645 659.
52. Palsbøll PJ, Bėrubė M, Aguilar A, Notarbartolo-Di-Sciara G, Nielsen R (2004) Discerning between recurrent gene flow and recent divergence under a finite-site mutation model applied to North Atlantic and Mediterranean Sea fin whale (Balaenoptera physalus) populations. Evolution, 58, 670 675.
53. Penny D (2005) Relativity for molecular clocks. Nature, 436, 183 184.
54. Posada D, Crandall KA (1998) modeltest: testing the model of DNA substitution. Bioinformatics, 14, 817 818.
55. Raymond M, Rousset F (1995) genepop (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity, 86, 248 249.
56. Ronquist F, Huelsenbeck JP (2003) mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572 1574.
57. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics, 145, 1219 1228.
58. Sandifer PA, Hopkins JS, Smith TIJ (1975) Observations on salinity tolerance and osmoregulation in laboratory-reared Macrobrachium rosenbergii postlarvae (Crustacea: Caridea). Aquaculture, 6, 103 114.
59. Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) tree-puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics, 18, 502 504.
60. Schmitt LH, Kitchener DJ, How RA (1995) A genetic perspective of mammalian variation and evolution in the Indonesian Archipelago: biogeographic correlates in the fruit bat genus Cynopterus. Evolution, 49, 399 412.
61. Schneider SD, Roessli D, Excoffier L (2000) arlequin, Version 2.0: A Software for Population Genetic Data Analysis. Genetics and Biometry Laboratory, University of Geneva, Geneva.
62. Shapiro B, Drummond AJ, Rambaut A et al 2004) Rise and fall of the Beringian steppe bison. Science, 306, 1561 1565.
63. Short JW (2004) A revision of Australian river prawns, Macrobrachium (Crustacea: Decapoda: Palaemonidae). Hydrobiologia, 525, 1 100.
64. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10, 512 526.
65. Unmack PJ (2001) Biogeography of Australian freshwater fishes. Journal of Biogeography, 28, 1053 1089.
66. Voris HK (2000) Maps of Pleistocene sea levels in South East Asia: shorelines, river systems, time durations. Journal of Biogeography, 27, 1153 1167.
67. Wallace AR (1862) Narrative of search after birds of paradise. Proceedings of the Zoological Society of London, 1862, 153 161.
68. Wallace AR (1869) The Malay Archipelago. Macmillan, London.
69. Wowor D (2004) A systematic revision of the freshwater prawns of the genus Macrobrachium (Crustacea: Decapoda: Caridea: Palaemonidae). PhD Thesis, National University of Singapore, Singapore.