Phylogenetic and biogeographic relationships of subterranean and surface genera of Australian Atyidae (Crustacea:Decapoda:Caridea) inferred with mitochondrial DNA

Invertebrate Systematics

Volumn 21, Issue 2, 2007, Pages 137-145

  Page, Timothy J ^a   Von Rintelen, Kristina ^b   Hughes, Jane M ^a  

^a GRIFFITH UNIVERSITY   (Australia)

^b HUMBOLDT UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOGEOGRAPHY; CLADISTICS; CRUSTACEAN; DNA FINGERPRINTING; ENDEMIC SPECIES; MITOCHONDRIAL DNA; MORPHOLOGY; PHYLOGENETICS; SUBTERRANEAN ENVIRONMENT;

ASIA; AUSTRALASIA; AUSTRALIA; EURASIA; INDIAN OCEAN; INDIAN OCEAN ISLANDS; MADAGASCAR; PHILIPPINES; SOUTHEAST ASIA;

ATYA; ATYIDAE (CRUSTACEANS); ATYOIDA; ATYOPSIS; AUSTRALATYA; CARIDEA; CARIDINA; CRUSTACEA; DECAPODA (CRUSTACEA); PARATYA; PARISIA;

EID: 34249032981     PISSN: 14455226     EISSN: None     Source Type: Journal    
DOI: 10.1071/IS06023     Document Type: Article

References (63)

1. Bǎnǎrescu, P. (1990). 'Zoogeography of Freshwaters Vol. 1: General Distribution and Dispersal of Freshwater Animals.' (Aula-Verlag: Wiesbaden, Germany.)
2. Bergsten, J. (2005). A review of long-branch attraction. Cladistics 21, 163-193. doi:10.1111/j.1096-0031.2005.00059.x
3. Bishop, J. A. (1967). The zoogeography of the Australian freshwater decapod Crustacea. In 'Australian Inland Waters and Their Fauna'. (Ed. A. H. Weatherly.) pp. 107-122. (Australian National University: Canberra, Australia.)
4. Bouvier, E. L. (1925). 'Recherches sur la Morphologie, les Variations, la Distribution Géographique des Crevettes de la Famille des Atyidés.' (Paul Lechevalier: Paris, France.)
5. Bruce, A. J. (1992). Pycnisia raptor, a new genus and species of predatory troglobic shrimp (Crustacea: Decapoda: Atyidae) from Northern Australia. Invertebrate Taxonomy 6, 553-566. doi:10.1071/IT9920553
6. Buckley, T. R., Simon, C., Flook, P. K., and Misof, B. (2000). Secondary structure and conserved motifs of the frequently sequenced domains IV and V of the insect mitochondrial large subunit rRNA gene. Insect Molecular Biology 9, 565-580. doi:10.1046/j.1365-2583.2000.00220.x
7. Cai, Y. X. (2005). On a small collection of atyid shrimps from cave Lakata Zafera, western Madagascar, with a description of a new species (Decapoda: Atyidae). Proceedings. Biological Society of Washington 118, 312-318.
8. Cai, Y. X., and Anker, A. (2004). On a collection of freshwater shrimps (Crustacea Decapoda Caridea) from the Philippines, with descriptions of five new species. Tropical Zoology 17, 233-266.
9. Cai, Y. X., and Bahir, M. M. (2005). Lancaris, a new genus of freshwater shrimp from Sri Lanka (Crustacea: Decapoda: Atyidae). Raffles Bulletin of Zoology Supp. 12, 39-46.
10. Cai, Y. X., and Shokita, S. (2006). Report on a collection of freshwater shrimps (Crustacea: Decapoda: Caridea) from the Philippines, with descriptions of four new species. Raffles Bulletin of Zoology 54, 245-279.
11. Calman, W. (1926). On freshwater prawns of the family Atyidae from Queensland. Annals and Magazine of Natural History 17, 241-246.
12. Cannone, J. J., Subramanian, S., Schnare, M. N., Collett, J. R., D'Souza, L. M., Du, Y., Feng, B., Lin, N., Madabusi, L. V., Müller, K. M., Pande, N., Shang, Z., Yu, N., and Gutell, R. R. (2002). The Comparative RNA web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3, 1-31. doi:10.1186/1471-2105-3-1
13. Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17, 540-552.
14. Chace, F. A. (1983). The Atya-like shrimps of the Indo-Pacific region (Decapoda, Atyidae). Smithsonian Contributions to Zoology 384, 1-54.
15. Chace, F. A. (1992). On the classification of the Caridea (Decapoda). Crustaceana 63, 70-80.
16. Choy, S. C. (1996). Caridina spelunca, a new species of freshwater shrimp (Crustacea: Decapoda: Atyidae) from a Western Australian cave. Records of the Western Australian Museum 18, 103-107.
17. Choy, S. C., and Horowitz, P. (1995). Preliminary key to the species of Australian shrimps (Atyidae) found in inland waters. In 'Preliminary Key to the Species of Decapoda (Crustacea, Malacostraca) found in Australian Inland Waters'. (Ed. P. Horwitz.) pp. 51-59. (Co-operative Research Centre for Freshwater Ecology: Albury, Australia.)
18. Christoffersen, M. L. (1986). Phylogenetic relationships between Oplophoridae, Atyidae, Pasiphaeidae, Alvinocarididae fam. n., Bresiliidae, Psalidopodidae and Disciadidae (Crustacea Caridea Atyoidea). Boletim de Zoologie 10, 273-281.
19. Cooper, S. J. B., Hinze, S., Leys, R., Watts, C. H. S., and Humphreys, W. F. (2002). Islands under the desert: molecular systematics and evolutionary origins of stygobitic water beetles (Coleoptera: Dytiscidae) from central Western Australia. Invertebrate Systematics 16, 589-598. doi:10.1071/IT01039
20. Davie, P. J. F. (2002). Atyidae. In 'Crustacea: Malacostraca: Phyllocarida, Hoplocarida, Eucarida (Part 1), Vol. 19.3A'. (Ed. P. J. F. Davie.) pp. 222-229. (CSIRO Publishing: Melbourne, Australia.)
21. Dayrat, B. (2005). Towards integrative taxonomy. Biological Journal of the Linnean Society 85, 407-415. doi:10.1111/j.1095-8312.2005.00503. x
22. Fryer, G. (1977). Studies on the functional morphology and ecology of the atyid prawns of Dominica. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 277, 57-129. doi:10.1098/rstb.1977.0007
23. Glaessner, M. F. (1969). Decapoda. In 'Treatise on Invertebrate Palaeontology. Arthropoda. 4. Part R (2)'. (Ed. R. C. Moore.) pp. 399-533. (Geological Society of America and University of Kansas Press: Lawrence, KS, USA.)
24. Guindon, S., and Gascuel, O. (2003). A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52, 696-704. doi:10.1080/10635150390235520
25. Gurney, A. R. (1984). Freshwater shrimp genera Caridina and Parisia (Decapoda: Caridea: Atyidae) of Madagascar, with descriptions of four new species. Journal of Natural History 18, 567-590. doi:10.1080/00222938400770481
26. Hillis, D. M., and Wiens, J. J. (2000). Molecules versus morphology in systematics: conflicts, artifacts, and misconceptions. In 'Phylogenetic Analysis of Morphological Data'. (Ed. J. J. Wiens.) pp. 1-19. (Smithsonian Institution Press: Washington, DC, USA.)
27. Hobbs, H. H. (1994). Biogeography of subterranean decapods in north and central-America and the Caribbean region (Caridea, Astacidea, Brachyura). Hydrobiologia 287, 95-104. doi:10.1007/BF00006899
28. Holthuis, L. B. (1986). A new genus and species of subterranean shrimp from Western Australia. Zoologische Mededelingen 60, 103-111.
29. Holthuis, L. B. (1993). 'The Recent Genera of the Caridean and Stenopodidean Shrimps (Crustacea, Decapoda) with an Appendix on the Order Amphionidacea.' (Nationaal Natuurhistorisch Museum: Leiden, The Netherlands.)
30. Huelsenbeck, J. P., and Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755. doi:10.1093/bioinformatics/17.8.754
31. Humphreys, W. F. (2006). Aquifers: the ultimate groundwater-dependent ecosystems. Australian Journal of Botany 54, 115-132. doi:10.1071/BT04151
32. Huxley, T. H. (1880). 'The Crayfish - An Introduction to the Study of Biology.' (MIT Press: Cambridge, MA, USA.)
33. Ivey, J. L., and Santos, S. R. (in press). The complete mitochondrial genome of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis (Crustacea: Decapoda: Atyidae). Gene, . doi:10.1016/j.gene/2007.01.009
34. Johnson, D. S. (1961). Notes on the freshwater Crustacea of Malaya. I. The Atyidae. Bulletin of the Raffles Museum 26, 120-153.
35. Lee, M. S. Y. (2004). The molecularisation of taxonomy. Invertebrate Systematics 18, 1-6. doi:10.1071/IS03021
36. Lefébure, T., Douady, C. J., and Gibert, J. (2006). Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation. Molecular Phylogenetics and Evolution 40, 435-447. doi:10.1016/j.ympev.2006.03. 014
37. Martin, J. W., and Wicksten, M. K. (2004). Review and redescription of the freshwater atyid shrimp genus Syncaris Holmes, 1900, in California. Journal of Crustacean Biology 24, 447-462. doi:10.1651/C-2451
38. Munasinghe, D. H. N., Burridge, C. P., and Austin, C. M. (2004). The systematics of freshwater crayfish of the genus Cherax Erichson (Decapoda: Parastacidae) in eastern Australia re-examined using nucleotide sequences from 12S rRNA and 16S rRNA genes. Invertebrate Systematics 18, 215-225. doi:10.1071/IS03012
39. Murphy, N. P., and Austin, C. M. (2002). A preliminary study of 16S rRNA sequence variation in Australian Macrobrachium shrimps (Palaemonidae: Decapoda) reveals inconsistencies in their current classification. Invertebrate Systematics 16, 697-701. doi:10.1071/IT01031
40. Murphy, N. P., and Austin, C. M. (2004). Multiple origins of the endemic Australian Macrobrachium (Decapoda: Palaemonidae) based on 16S rRNA mitochondrial sequences. Australian Journal of Zoology 52, 549-559. doi:10.1071/ZO03062
41. Page, T. J., Baker, A. M., Cook, B. D., and Hughes, J. M. (2005a). Historical transoceanic dispersal of a freshwater shrimp: the colonization of the South Pacific by the genus Paratya (Atyidae). Journal of Biogeography 32, 581-593. doi:10.1111/j.1365-2699.2004.01226.x
42. Page, T. J., Choy, S. C., and Hughes, J. M. (2005b). The taxonomic feedback loop: symbiosis of morphology & molecules. Biology Letters 1, 139-142. doi:10.1098/rsbl.2005.0298
43. Page, T. J., von Rintelen, K., and Hughes, J. M. (in press). 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. doi:10.1016/j.ympev.2006.08.007
44. Palumbi, S. R., Martin, A., Romano, S., McMillan, W. O., Stice, L., and Grabowski, G. (1991). 'A Simple Fool's Guide to PCR.' (University of Hawaii Press: Honolulu, HI, USA.)
45. Porter, M. L., Perez-Losada, M., and Crandall, K. A. (2005). Model-based multi-locus estimation of decapod phylogeny and divergence times. Molecular Phylogenetics and Evolution 37, 355-369. doi:10.1016/j.ympev.2005.06. 021
46. Posada, D., and Crandall, K. A. (1998). Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817-818. doi:10.1093/ bioinformatics/14.9.817
47. Posada, D., and Buckley, T. R. (2004). Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Systematic Biology 53, 793-808. doi:10.1080/10635150490522304
48. Proudlove, G., and Wood, P. J. (2003). The blind leading the blind: cryptic subterranean species and DNA taxonomy. Trends in Ecology & Evolution 18, 272-273. doi:10.1016/S0169-5347(03)00095-8
49. Quan, J., Zhuang, Z., Deng, J., Dai, J., and Zhang, Y. P. (2004). Phylogenetic relationships of 12 Penaeoidea shrimp species deduced from mitochondrial DNA sequences. Biochemical Genetics 42, 331-345. doi:10.1023/B:BIGI.0000039808.12069.ed
50. Riek, E. F. (1953). The Australian freshwater prawns of the family Atyidae. Records of the Australian Museum 23, 111-121.
51. Sanz, S., and Platvoet, D. (1995). New perspectives on the evolution of the genus Typhlatya (Crustacea, Decapoda): first record of a cavernicolous atyid in the Iberian Peninsula, Typhlatya miravetensis n. sp. Contributions to Zoology (Amsterdam, Netherlands : 1995) 65, 79-99.
52. Short, J. W., and Doumenq, E. (2003). Atyidae and Palaemonidae, freshwater shrimps. In 'The Natural History of Madagascar'. (Eds S. M. Goodman and J. P. Benstead.) pp. 603-608. (University of Chicago Press: Chicago, IL, USA.)
53. Smith, M. J., and Williams, W. D. (1981). The occurrence of Antecaridina lauensis (Edmondson) (Crustacea, Decapoda, Atyidae) in the Solomon Islands. An intriguing biogeographical problem. Hydrobiologia 85, 49-58. doi:10.1007/BF00011344
54. Smith, M. J., and Williams, W. D. (1982). Taxonomic revision of the Australian genus Caridinides Calman (Crustacea: Decapoda: Atyidae). Australian Journal of Marine and Freshwater Research 33, 575-587. doi:10.1071/MF9820575
55. Sorenson, M. D. (1999). 'TreeRot version 2.' (Boston University Press: Boston, MA, USA.)
56. Suzuki, H., and Davie, P. J. F. (2003). A new cavernicolous shrimp in Pycnisia Bruce, 1992 (Crustacea: Decapoda: Caridea: Atyidae) from northwestern Queensland. Memoirs of the Queensland Museum 49, 447-451.
57. Swofford, D. L. (2002). 'PAUP * version 4.0b5 - Phylogenetic Analysis Using Parsimony (* And Other Methods).' (Sinauer Associates: Sunderland, MA, USA.)
58. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G. (1997). The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25, 4876-4882. doi:10.1093/nar/25.24.4876
59. von Rintelen, K., von Rintelen, T., Meixner, M., Lüter, C., Cai, Y., and Glaubrecht, M. (in press). Freshwater shrimp-sponge association from an ancient lake. Biology Letters. doi:10.1093/nar/25.24.4876
60. Webb, M. S. (2003). Intraspecific relationships among the stygobitic shrimp Typhlatya mitchelli, by analyzing sequence data from mitochondrial DNA. Masters Thesis, Texas A&M University, College Station, TX, USA.
61. Williams, W. D. (1964). Subterranean freshwater prawns (Crustacea: Decapoda: Atyidae) in Australia. Australian Journal of Marine and Freshwater Research 15, 93-106. doi:10.1071/MF9640093
62. Williams, W. D., and Allen, G. R. (1987). Origins and adaptations of the fauna of inland waters. In 'Fauna of Australia: Vol 1A: General Articles'. (Eds G. R. Dyne and D. W. Walton.) pp. 184-201. (CSIRO: Canberra, Australia.)
63. Zakšek, V., Sket, B., and Trontelj, P. (2007). Phylogeny of the cave shrimp Troglocaris: evidence of a young connection between Balkans and Caucasus. Molecular Phylogenetics and Evolution 42, 223-235. doi:10.1016/j.ympev.2006.07.009