Out of Borneo: Neogene diversification of Sundaic freshwater crabs (Crustacea: Brachyura: Gecarcinucidae: Parathelphusa)

Journal of Biogeography

Volumn 40, Issue 1, 2013, Pages 63-74

  Klaus, Sebastian ^a,b   Selvandran, Sathyajothi ^a   Goh, Jun W ^a   Wowor, Daisy ^c   Brandis, Dirk ^d   Koller, Peter ^e   Schubart, Christoph D ^e   Streit, Bruno ^b   Meier, Rudolf ^a   Ng, Peter K L ^a   Yeo, Darren C J ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b GOETHE UNIVERSITY   (Germany)

^c INDONESIAN INSTITUTE OF SCIENCES   (Indonesia)

^d UNIVERSITY OF KIEL   (Germany)

^e UNIVERSITY OF REGENSBURG   (Germany)

Author keywords

Dispersal; Glacial period; Historical biogeography; Miocene; Pleistocene; Pliocene; Southeast Asia; Sundaland; Vicariance

Indexed keywords

BIOGEOGRAPHY; COLONIZATION; CRAB; DISPERSAL; FRESHWATER ENVIRONMENT; GLACIAL ENVIRONMENT; NEOGENE; PARAMETERIZATION; PHYLOGENETICS; PLEISTOCENE; SEA LEVEL CHANGE; SPECIES OCCURRENCE; SPECIES RICHNESS; VICARIANCE;

BORNEO; GREATER SUNDA ISLANDS; PHILIPPINES; SUNDA ISLES;

BRACHYURA; CRUSTACEA; DECAPODA (CRUSTACEA); GECARCINUCIDAE; PARATHELPHUSA;

EID: 84871310945     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/j.1365-2699.2012.02771.x     Document Type: Article

References (79)

1. Alfaro, M.E., Karns, D.R., Voris, H.K., Brock, C.D. & Stuart, B.L. (2008) Phylogeny, evolutionary history, and biogeography of Oriental-Australian rear-fanged water snakes (Colubroidea, Homalopsidae) inferred from mitochondrial and nuclear DNA sequences. Molecular Phylogenetics and Evolution, 46, 576-593.
2. Ayres, J.M. & Clutton-Brock, T.H. (1992) River boundaries and species range size in Amazonian primates. The American Naturalist, 140, 531-537.
3. Bird, M.I., Taylor, D. & Hunt, C. (2005) Palaeoenvironments of insular Southeast Asia during the Last Glacial Period, a savanna corridor in Sundaland? Quaternary Science Reviews, 24, 2228-2242.
4. Blackburn, D.C., Bickford, D.P., Diesmos, A.C., Iskandar, D.T. & Brown, R.M. (2010) An ancient origin for the enigmatic flat-headed frogs (Bombinatoridae: Barbourula) from the islands of Southeast Asia. PLoS ONE, 5, e12090.
5. Bohlen, J., Šlechtová, V., Tan, H.H. & Britz, R. (2011) Phylogeny of the Southeast Asian freshwater fish genus Pangio (Cypriniformes; Cobitidae). Molecular Phylogenetics and Evolution, 61, 854-865.
6. Cannon, C.H., Morley, R.J. & Bush, A.B.G. (2009) The current refugial rainforests of Sundaland are unrepresentative of their biogeographic past and highly vulnerable to disturbance. Proceedings of the National Academy of Sciences USA, 106, 11188-11193.
7. Colgan, D.J., McLauchlan, C., Wilson, G.D.F., Livingston, S.P., Edgecombe, G.D., Macaranas, J., Cassis, G. & Gray, M.R. (1998) Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution. Australian Journal of Zoology, 46, 419-437.
8. Cumberlidge, N. & Ng, P.K.L. (2009) Systematics, evolution, and biogeography of freshwater crabs. Decapod crustacean phylogenetics (ed. by J.W. Martin, K.A. Crandall and D.L. Felder), pp. 491-508. Crustacean Issues, Francis and Taylor/CRC Press, Boca Raton, FL.
9. Daniels, S.R. (2003) Examining the genetic structure among populations of the common Cape river crab Potamonautes perlatus from river systems in South Africa reveals hydrographic boundaries. Journal of Crustacean Biology, 23, 936-950.
10. Daniels, S.R. (2011) Reconstructing the colonisation and diversification history of the endemic freshwater crab (Seychellum alluaudi) in the granitic and volcanic Seychelles Archipelago. Molecular Phylogenetics and Evolution, 61, 534-542.
11. Daniels, S.R., Gouws, G. & Crandall, K.A. (2006a) Phylogeographic patterning in a freshwater crab species (Decapoda, Potamonautidae, Potamonautes) reveals the signature of historical climatic oscillations. Journal of Biogeography, 33, 1538-1549.
12. Daniels, S.R., Cumberlidge, N., Pérez-Losada, M., Marijnissen, S.A.E. & Crandall, K.A. (2006b) Evolution of Afrotropical freshwater crab lineages obscured by morphological convergence. Molecular Phylogenetics and Evolution, 40, 227-235.
13. Dodson, J.J., Colombani, F. & Ng, P.K.L. (1995) Phylogeographic structure in mitochondrial DNA of South-east Asian freshwater fish, Hemibagrus nemurus (Siluroidae: Bagridae) and Pleistocene sea-level changes on the Sunda shelf. Molecular Evolution, 4, 331-346.
14. Drummond, A.J. & Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
15. Drummond, A.J., Ho, S.Y.W., Phillips, M.J. & Rambaut, A. (2006) Relaxed phylogenetics and dating with confidence. PLoS Biology, 4, e88.
16. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792-1797.
17. Esselstyn, J.A., Timm, R.M. & Brown, R.M. (2009) Do geological or climatic processes drive speciation in dynamic archipelagos? The tempo and mode of diversification in Southeast Asian shrews. Evolution, 63, 2595-2610.
18. Felsenstein, J. (2009) PHYLIP: phylogeny inference package, version 3.9. University of Washington, Seattle, WA.
19. Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294-299.
20. Gorog, A.J., Sinaga, M.H. & Engstrom, M.D. (2004) Vicariance or dispersal? Historical biogeography of three Sunda shelf murine rodents (Maxomys surifer, Leopoldamys sabanus and Maxomys whiteheadi). Biological Journal of the Linnean Society, 81, 91-109.
21. Haffer, J. (1997) Alternative models of vertebrate speciation in Amazonia: an overview. Biodiversity and Conservation, 6, 451-477.
22. Hall, R. (2009) Southeast Asia's changing palaeogeography. Blumea, 54, 148-161.
23. Hutchison, C.S. (2005) Geology of north-west Borneo: Sarawak, Brunei and Sabah. Elsevier, Amsterdam.
24. Inger, R.F. & Voris, H.K. (2001) The biogeographical relations of the frogs and snakes of Sundaland. Journal of Biogeography, 28, 863-891.
25. Inger, R.F., Stuart, B.L. & Iskandar, D.T. (2009) Systematics of a widespread Southeast Asian frog, Rana chalconata (Amphibia: Anura: Ranidae). Zoological Journal of the Linnean Society, 155, 123-147.
26. Jesse, R., Schubart, C.D. & Klaus, S. (2010) Identification of a cryptic lineage within Potamon fluviatile (Herbst, 1785) (Crustacea: Brachyura: Potamidae). Invertebrate Systematics, 24, 348-356.
27. Jesse, R., Grudinski, M., Klaus, S., Streit, B. & Pfenninger, M. (2011) Evolution of freshwater crab diversity in the Aegean region (Crustacea: Brachyura: Potamidae). Molecular Phylogenetics and Evolution, 59, 23-33.
28. Karns, D.R., O'Bannon, A., Voris, H.K. & Weigt, L.A. (2000) Biogeographical implications of mitochondrial DNA variation in the Bockadam snake (Cerberus rynchops, Serpentes, Homalopsinae) in Southeast Asia. Journal of Biogeography, 27, 391-402.
29. Klaus, S., Schubart, C.D. & Brandis, D. (2006) Phylogeny, biogeography and a new taxonomy for the Gecarcinucoidea Rathbun, 1904 (Decapoda: Brachyura). Organisms, Diversity and Evolution, 6, 199-217.
30. Klaus, S., Brandis, D., Ng, P.K.L., Yeo, D.C.J. & Schubart, C.D. (2009) Phylogeny and biogeography of Asian freshwater crabs of the family Gecarcinucidae (Crustacea: Brachyura: Potamoidea). Decapod crustacean phylogenetics (ed. by J.W. Martin, K.A. Crandall and D.L. Felder), pp. 509-531. Crustacean Issues, Francis and Taylor/CRC Press, Boca Raton, FL.
31. Klaus, S., Schubart, C.D., Streit, B. & Pfenninger, M. (2010) When Indian crabs were not yet Asian - evidence for Eocene proximity of India and Southeast Asia from freshwater crab biogeography. BMC Evolutionary Biology, 10, 287.
32. Klaus, S., Böhme, M., Schneider, S., Prieto, J. & Phetsomphou, B. (2011) Evidence of the earliest freshwater decapod fossil from Southeast Asia (Crustacea: Decapoda: Brachyura). Raffles Bulletin of Zoology, 59, 47-51.
33. Lim, H.C., Rahman, M.A., Lim, S.L.H., Moyle, R.G. & Sheldon, F.H. (2010) Revisiting Wallace's haunt: coalescent simulations and comparative niche modeling reveal historical mechanisms that promoted avian population divergence in the Malay archipelago. Evolution, 65, 321-334.
34. Lohman, D.J., Ingram, K.K., Prawiradilaga, D.M., Winker, K., Sheldon, F.H., Moyle, R.G., Ng, P.K.L., Ong, P.S., Wang, L.K., Braile, T.M., Astuti, D. & Meier, R. (2010) Cryptic genetic diversity in "widespread" Southeast Asian bird species suggests that Philippine avian endemism is gravely underestimated. Biological Conservation, 143, 1885-1890.
35. Lohman, D.J., de Bruyn, M., Page, T., von Rintelen, K., Hall, R., Ng, P.K.L., Shih, H.-T., Carvalho, G.C. & von Rintelen, T. (2011) Beyond Wallace's Line: genetics and geology inform biogeographical insights in the Indo-Australian Archipelago. Annual Review of Ecology, Evolution, and Systematics, 42, 205-226.
36. Marijnissen, S.A.E., Michel, E., Kamermans, M., Olaya-Bosch, K., Kars, M., Cleary, D.F.R., van Loon, E.E., Rachello Dolmen, P.G. & Menken, S.B.J. (2008) Ecological correlates of species differences in the Lake Tanganyika crab radiation. Hydorobiologia, 615, 81-94.
37. Marks, B.D. (2010) Are lowland rainforests really evolutionary museums? Phylogeography of the green hylia (Hylia prasina) in the Afrotropics. Molecular Phylogenetics and Evolution, 55, 178-184.
38. Matsui, M., Hamidy, A., Murphy, R.W., Khonsue, W., Yambun, P., Shimada, T., Ahmad, N., Belabut, D.M. & Jiang, J.-P. (2010a) Phylogenetic relationships of megophryid frogs of the genus Leptobrachium (Amphibia, Anura) as revealed by mtDNA gene sequences. Molecular Phylogenetics and Evolution, 56, 259-272.
39. Matsui, M., Tominaga, A., Liu, W., Khonsue, W., Grismer, L.L., Diesmos, A.C., Das, I., Sudin, A., Yambun, P., Yong, H., Sukumara, J. & Brown, R.M. (2010b) Phylogenetic relationships of Ansonia from Southeast Asia inferred from mitochondrial DNA sequences: systematic and biogeographic implications (Anura: Bufonidae). Molecular Phylogenetics and Evolution, 54, 561-570.
40. Meijaard, E. (2009) Solving mammalian riddles along the Indochinese-Sundaic zoogeographic transition: new insights from mammalian biogeography. Journal of Biogeography, 36, 801-802.
41. Miller, K.G., Kominz, M.A., Browning, J.V., Wright, J.D., Mountain, G.S., Katz, M.E., Sugarman, P.J., Cramer, B.S., Christie-Blick, N. & Pekar, S.F. (2005) The Phanerozoic record of global sea-level change. Science, 310, 1293-1298.
42. Morris, S. & van Aardt, W.J. (1998) Salt and water relations, and nitrogen excretion, in the amphibious African freshwater crab Potamonautes warreni in water and air. The Journal of Experimental Biology, 201, 883-893.
43. Moss, S.J. & Wilson, M.E.J. (1998) Biogeographic implications from the Tertiary palaeogeographic evolution of Sulawesi and Borneo. Biogeography and geological evolution of SE Asia (ed. by R. Hall and D. Holloway), pp. 133-155. Backhuys, Leiden.
44. Nee, S., Homes, E.C., May, R.M. & Harvey, P.H. (1994) Extinction rates can be estimated from molecular phylogenies. Philosophical Transactions of the Royal Society B: Biological Sciences, 344, 77-82.
45. Ng, P.K.L. (1988) The freshwater crabs of peninsular Malaysia and Singapore. Shinglee, Singapore.
46. Ng, P.K.L. (1990) The freshwater crabs and prawns of Singapore. Essays in zoology (ed. by L.M. Chou and P.K.L. Ng), pp. 189-204. Department of Zoology, National University of Singapore, Singapore.
47. Ng, P.K.L. & Chia, O.K.S. (2006) The freshwater crabs of Sulawesi with the description of two new genera and four new species (Crustacea, Decapoda, Brachyura, Parathelphusidae). Raffles Bulletin of Zoology, 54, 381-428.
48. Ng, P.K.L., Guinot, D. & Davie, P.J.F. (2008) Systema Brachyurorum, Part I. An annotated checklist of extant brachyuran crabs of the world. Raffles Bulletin of Zoology, 17, 1-286.
49. Ogg, J.G. & Gradstein, F.M. (2008) The concise geologic time scale. Cambridge University Press, Cambridge, UK.
50. Outlaw, D.C. & Voelker, G. (2008) Pliocene climatic change in insular Southeast Asia as an engine of diversification in Ficedula flycatchers. Journal of Biogeography, 35, 739-752.
51. Pagel, M., Meade, A. & Barker, D. (2004) Bayesian estimation of ancestral character states on phylogenies. Systematic Biology, 53, 673-684.
52. Paradis, E., Claude, J. & Strimmer, K. (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-290.
53. Posada, D. (2008) jModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253-1256.
54. Quek, S.-P., Davies, S.J., Ashton, P.S., Itino, T. & Pierce, N.E. (2007) The geography of diversification in mutualistic ants: a gene's-eye view into the Neogene history of Sundaland rain forests. Molecular Ecology, 16, 2045-2062.
55. R Development Core Team (2008) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna.
56. Rabosky, D.L. (2006) LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates. Evolutionary Bioinformatics Online, 2, 257-260.
57. Rabosky, D.L., Donnellan, S.C., Talaba, A.L. & Lovette, I.J. (2007) Exceptional among-lineage variation in diversification rates during the radiation of Australia's largest vertebrate clade. Proceedings of the Royal Society B: Biological Sciences, 274, 2915-2923.
58. Rambaut, A. & Drummond, A.J. (2007) Tracer v1.5. Available at: http://tree.bio.ed.ac.uk/software/tracer/.
59. Ree, H.R. & Smith, S.A. (2008) Maximum likelihood inference of geographic range evolution by dispersal, local extinction and cladogenesis. Systematic Biology, 57, 4-14.
60. Revell, L.J., Harmon, L.J. & Glor, R.E. (2005) Underparameterized model of sequence evolution leads to bias in the estimation of diversification rates from molecular phylogenies. Systematic Biology, 54, 973-983.
61. Rüber, L., Kottelat, M., Tan, H.H., Ng, P.K.L. & Britz, R. (2007) Evolution of miniaturization and the phylogenetic position of Paedocypris, comprising the world's smallest vertebrate. BMC Evolutionary Biology, 7, 38.
62. Schubart, C.D. & Huber, M.G.J. (2006) Genetic comparisons of German populations of the stone crayfish, Austropotamobius torrentium (Crustacea: Astacidae). Bulletin Français de la Pêche et de la Pisciculture, 380-381, 1019-1028.
63. Schubart, C.D., Diesel, R. & Hedges, S.B. (1998) Rapid evolution to terrestrial life in Jamaican crabs. Nature, 393, 363-365.
64. Schubart, C.D., Santl, T. & Koller, P. (2008) Mitochondrial patterns of intra- and interspecific differentiation among endemic freshwater crabs of ancient lakes in Sulawesi. Contributions to Zoology, 77, 83-90.
65. Sémah, F., Saleki, H. & Falguères, C. (2000) Did early man reach Java during the Late Pliocene? Journal of Archaeological Science, 27, 763-769.
66. Sheldon, F.H., Lohman, D.J., Lim, H.C., Zou, F., Goodman, S.M., Prawiradilaga, D.M., Winker, K., Braile, T.M. & Moyle, R.G. (2010) Phylogeography of the magpie-robin species complex (Aves: Turdidae: Copsychus) reveals a Philippine species, an interesting isolating barrier and unusual dispersal patterns in the Indian Ocean and Southeast Asia. Journal of Biogeography, 143, 1885-1890.
67. Shih, H.S., Naruse, T. & Yeo, D.C.J. (2008) A new species of Geothelphusa Stimpson, 1857, from Taiwan (Crustacea: Brachyura: Potamidae) based on morphological and molecular evidence, with notes on species from western Taiwan. Zootaxa, 1877, 37-48.
68. Shih, H.-T. & Shy, J.-Y. (2009) Geothelphusa makatao sp. nov. (Crustacea: Brachyura: Potamidae), a new freshwater crab from an uplifted Pleistocene reef in Taiwan. Zootaxa, 2106, 51-60.
69. Shih, H.T., Hung, H.C., Schubart, C.D., Chen, C.L.A. & Chang, H.W. (2006) Intraspecific genetic diversity of the endemic freshwater crab Candidiopotamon rathbunae (Decapoda, Brachyura, Potamidae) reflects five million years of the geological history of Taiwan. Journal of Biogeography, 33, 980-989.
70. Shih, H.T., Fang, S.H. & Ng, P.K.L. (2007) Phylogeny of the freshwater crab genus Somanniathelphusa Bott (Decapoda, Parathelphusidae) from Taiwan and the coastal regions of China, with notes on their biogeography. Invertebrate Systematics, 21, 29-37.
71. Shih, H.T., Ng, P.K.L., Naruse, T., Shokita, S. & Liu, M.Y. (2011) Pleistocene speciation of freshwater crabs (Crustacea: Potamidae: Geothelphusa) from northern Taiwan and southern Ryukyus, as revealed by phylogenetic relationships. Zoologischer Anzeiger, 250, 457-471.
72. Sodhi, N.S., Koh, L.P., Brook, B.W. & Ng, P.K.L. (2004) Southeast Asian biodiversity: an impending disaster. Trends in Ecology and Evolution, 19, 654-660.
73. Stamatakis, A. (2006a) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688-2690.
74. Stamatakis, A. (2006b) Phylogenetic models of rate heterogeneity: a high performance computing perspective. 20th IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS2006). Available at: http://www.hicomb.org/HiCOMB2008/papers/HICOMB2006-05.pdf (accessed July 2012).
75. Steiper, M.E. (2006) Population history, biogeography, and taxonomy of orangutans (Genus, Pongo) based on a population genetic meta-analysis of multiple loci. Journal of Human Evolution, 50, 509-522.
76. Sukumaran, J. & Holder, M.T. (2010) DendroPy: a Python library for phylogenetic computing. Bioinformatics, 26, 1569-1571.
77. 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.
78. den Tex, R.-J., Thorington, R., Maldonado, J.E. & Leonard, J.A. (2010) Speciation dynamics in the SE Asian tropics: putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus. Molecular Phylogenetics and Evolution, 55, 711-720.
79. Voris, H.K. (2000) Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. Journal of Biogeography, 27, 1153-1167.