Molecular systematics of the Kakaducarididae (Crustacea: Decapoda: Caridea)

Molecular Phylogenetics and Evolution

Volumn 46, Issue 3, 2008, Pages 1003-1014

  Page, Timothy J ^a   Short, John W ^b   Humphrey, Christopher L ^c   Hillyer, Mia J ^a   Hughes, Jane M ^a  

^a GRIFFITH UNIVERSITY   (Australia)

^b BioAccess Australia   (Australia)

^c ENVIRONMENTAL RESEARCH INSTITUTE OF THE SUPERVISING SCIENTIST   (Australia)

Author keywords

16S; 18S; 28S; COI; Histone; Kakaducarididae; Kakaducaris; Leptopalaemon; Mitochondrial DNA; Nuclear DNA; Palaemonidae; Phylogenetics

Indexed keywords

HISTONE; MITOCHONDRIAL DNA; RNA 16S; RNA 18S; RNA 28S;

ANIMAL; ARTICLE; CELL NUCLEUS; CHEMISTRY; CLASSIFICATION; DECAPODA (CRUSTACEA); DNA SEQUENCE; GENE FLOW; GENETIC VARIABILITY; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ANIMALS; CELL NUCLEUS; DECAPODA (CRUSTACEA); DNA, MITOCHONDRIAL; GENE FLOW; HISTONES; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 18S; RNA, RIBOSOMAL, 28S; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

CARIDEA; CRUSTACEA; DECAPODA (CRUSTACEA); KAKADUCARIDIDAE; MACROBRACHIUM; PALAEMONIDAE;

EID: 40849114501     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2007.12.020     Document Type: Article

References (46)

1. Beiko R.G., Harlow T.J., and Ragan M.A. Highways of gene sharing in prokaryotes. Proc. Natl. Acad. Sci. USA 102 (2005) 14332-14337
2. Bickford D., Lohman D.J., Sodhi N.S., Ng P.K.L., Meier R., Winker K., Ingram K.K., and Das I. Cryptic species as a window on diversity and conservation. Trends Ecol. Evol. 22 (2007) 148-155
3. Bruce A.J. Kakaducaris glabra gen. nov., sp. nov., a new freshwater shrimp from the Kakadu National Park, Northern Territory, Australia, Crustacea, Decapoda, Palaemonidae with the designation of a new subfamily Kakaducaridinae. Hydrobiologia 268 (1993) 27-44
4. Bruce A.J., and Short J.W. Leptopalaemon gagadjui gen. nov., sp. nov., a new freshwater palaemonid shrimp from Arnhem Land, and a re-evaluation of Palaemonetes holthuisi Strenth, with the designation of a new genus, Calathaemon. Hydrobiologia 257 (1993) 73-94
5. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17 (2000) 540-552
6. Chace Jr. F.A. On the classification of the Caridea (Decapoda). Crustaceana 63 (1992) 70-80
7. Chu K.H., Li C.P., and Qi J. Ribosomal RNA as molecular barcodes, a simple correlation analysis without sequence alignment. Bioinformatics 22 (2006) 1690-1701
8. Colgan D.J., McLauchlan A., Wilson G.D.F., Livingston S.P., Edgecombe G.D., Macaranas J., Cassis G., and Gray M.R. Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution. Aust. J. Zool. 46 (1998) 419-437
9. Costa F.O., deWaard J.R., Boutillier J., Ratnasingham S., Dooh R.T., Hajibabaei M., and Hebert P.D.N. Biological identifications through DNA barcodes, the case of Crustacea. Can. J. Fish. Aquat. Sci. 64 (2007) 272-295
10. Crandall K.A., Harris D.J., and Fetzner J.W. The monophyletic origin of freshwater crayfish estimated from nuclear and mitochondrial DNA sequences. Proc. R. Soc. B 267 (2000) 1679-1686
11. Dasmahapatra K.K., and Mallet J. DNA barcodes, recent successes and future prospects. Heredity 97 (2006) 254-255
12. Davie P.J.F. Palaemonidae. In: Davie P.J.F. (Ed). Crustacea: Malacostraca: Phyllocarida, Hoplocarida, Eucarida (Part 1) Vol. 19.3A (2002), CSIRO, Melbourne 288-341
13. de Bruyn M., Wilson J.A., and Mather P.B. Huxley's line demarcates extensive genetic divergence between eastern and western forms of the giant freshwater prawn, Macrobrachium rosenbergii. Mol. Phylogenet. Evol. 30 (2004) 251-257
14. DeSalle R., Egan M.G., and Siddall M. The unholy trinity, taxonomy, species delimitation and DNA barcoding. Philo. Trans. R. Soc. B 360 (2005) 1905-1916
15. Doyle J.J., and Doyle J.L. A rapid DNA isolation procedure for small quantities of leaf tissue. Phytochem. Bull. 19 (1987) 11-15
16. Finlayson C.M., Lowry J., Bellio M.G., Nou S., Pidgeon R., Walden D., Humphrey C., and Fox G. Biodiversity of the wetlands of the Kakadu Region, northern Australia. Aquat. Sci. 68 (2006) 374-399
17. Gillespie J.J., Munro J.B., Heraty J.M., Yoder M.J., Owen A.K., and Carmichael A.E. A secondary structural model of the 28S rRNA expansion segments D2 and D3 for chalcidoid wasps (Hymenoptera, Chalcidoidea). Mol. Biol. Evol. 22 (2005) 1593-1608
18. Giribet G., and Wheeler W.C. Some unusual small-subunit ribosomal RNA sequences of metazoans. Am. Mus. Novit. 3337 (2001) 1-14
19. Guindon S., and Gascuel O. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
20. Hebert P.D., and Gregory T.R. The promise of DNA barcoding for taxonomy. Syst. Biol. 54 (2005) 852-859
21. Huelsenbeck J.P., and Ronquist F. MrBayes, Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
22. Knowlton N., and Weigt L.A. New dates and new rates for divergence across the Isthmus of Panama. Proc. R. Soc. B 265 (1998) 2257-2263
23. Lefébure T., Douady C.J., and Gibert J. Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation. Mol. Phylogenet. Evol. 40 (2006) 435-447
24. Liu M.Y., Cai Y., and Tzeng C.S. Molecular systematics of the freshwater prawn genus Macrobrachium Bate, 1868 (Crustacea, Decapoda, Palaemonidae) from mtDNA sequences, with emphasis on East Asian species. Zool. Stud. 46 (2007) 272-289
25. Meyer C.P., and Paulay G. DNA barcoding, error rates based on comprehensive sampling. PLoS Biol. 3 (2005) 2229-2238
26. Miller A.D., Murphy N.P., Burridge C.P., and Austin C.M. Complete mitochondrial DNA sequences of the decapod crustaceans Pseudocarcinus gigas (Menippidae) and Macrobrachium rosenbergii (Palaemonidae). Mar. Biotechnol. 7 (2005) 339-349
27. Moritz C., and Cicero C. DNA barcoding, promise and pitfalls. PLoS Biol. 2 (2004) 1529-1531
28. Murphy N.P., and Austin C.M. Molecular taxonomy and phylogenetics of some species of Australian palaemonid shrimps. J. Crust. Biol. 23 (2003) 169-177
29. Murphy N.P., and Austin C.M. Multiple origins of the endemic Australian Macrobrachium (Decapoda: Palaemonidae) based on 16S rRNA mitochondrial sequences. Aust. J. Zool. 52 (2004) 549-559
30. Murphy N.P., and Austin C.M. Phylogenetic relationships of the globally distributed freshwater prawn genus Macrobrachium (Crustacea, Decapoda, Palaemonidae), biogeography, taxonomy and the convergent evolution of abbreviated larval development. Zool. Scr. 34 (2005) 187-197
31. Nielsen R., and Matz M. Statistical approaches for DNA barcoding. Syst. Biol. 55 (2006) 162-169
32. Page T.J., Choy S.C., and Hughes J.M. The taxonomic feedback loop: symbiosis of morphology & molecules. Biol. Lett. 1 (2005) 139-142
33. Page T.J., von Rintelen K., and Hughes J.M. Phylogenetic and biogeographic relationships of subterranean and surface genera of Australian Atyidae (Crustacea, Decapoda, Caridea) inferred with mitochondrial DNA. Invertebr. Syst. 21 (2007) 137-145
34. Palumbi S.R., Martin A., Romano S., McMillan W.O., Stice L., and Grabowski G. A Simple Fool's Guide to PCR (1991), University of Hawaii Press, Honolulu
35. Porter M.L., Pérez-Losada M., and Crandall K.A. Model-based multi-locus estimation of decapod phylogeny and divergence times. Mol. Phylogenet. Evol. 37 (2005) 355-369
36. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
37. Schubart C.D., Diesel R., and Hedges S.B. Rapid evolution to terrestrial life in Jamaican crabs. Nature 393 (1998) 363-365
38. Short, J.W., 2000. Systematics and biogeography of Australian Macrobrachium (Crustacea: Decapoda: Palaemonidae) with descriptions of other new freshwater Decapoda. Ph.D. Thesis, Department of Zoology and Entomology, University of Queensland, Brisbane.
39. Short J.W. A revision of Australian river prawns, Macrobrachium (Crustacea: Decapoda: Palaemonidae). Hydrobiologia 525 (2004) 1-100
40. Sturmbauer C., Levinton J.S., and Christy J. Molecular phylogeny analysis of fiddler crabs, test of the hypothesis of increasing behavioral complexity in evolution. Proc. Natl. Acad. Sci. USA 93 (1996) 10855-10857
41. * and other methods) (2002), Sinauer Associates, Sunderland, MA
42. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24 (1997) 4876-4882
43. von Rintelen K., von Rintelen T., Meixner M., Lüter C., Cai Y., and Glaubrecht M. Freshwater shrimp-sponge association from an ancient lake. Biol. Lett. 3 (2007) 262-264
44. Walker T.M., and Poore G.C.B. Rediagnosis of Palaemon and differentiation of southern Australian species (Crustacea, Decapoda, Palaemonidae). Mem. Mus. Vic. 60 (2003) 243-256
45. Whiting M.F., Carpenter J.C., Wheeler Q.D., and Wheeler W.C. The strepsiptera problem, phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology. Syst. Biol. 46 (1997) 1-68
46. Wowor D., and Ng P.K.L. The giant freshwater prawns of the Macrobrachium rosenbergii species group (Crustacea: Decapoda: Caridea: Palaemonidae). Raffles Bull. Zool. 55 (2007) 321-336