A molecular phylogeny of the genus Gammarus (Crustacea: Amphipoda) based on mitochondrial and nuclear gene sequences

Molecular Phylogenetics and Evolution

Volumn 45, Issue 2, 2007, Pages 596-611

  Hou, Zhonge ^a,b   Fu, Jinzhong ^b   Li, Shuqiang ^a  

^a INSTITUTE OF ZOOLOGY   (China)

^b UNIVERSITY OF GUELPH   (Canada)

Author keywords

16S rRNA; 18S rRNA; 28S rRNA; COI; Gammarus; Molecular phylogeny; Phylogeography

Indexed keywords

CYTOCHROME C OXIDASE; PROTEIN SUBUNIT; RNA 16S; RNA 18S; RNA 28S;

AMPHIPODA; ANIMAL; ARTICLE; CELL NUCLEUS; CLASSIFICATION; DNA SEQUENCE; EUROPE; GENETICS; MITOCHONDRIAL GENE; MOLECULAR EVOLUTION; NORTH AMERICA; PHYLOGENY; SPECIES DIFFERENTIATION; TIME;

AMPHIPODA; ANIMALS; CELL NUCLEUS; ELECTRON TRANSPORT COMPLEX IV; EUROPE; EVOLUTION, MOLECULAR; GENES, MITOCHONDRIAL; GENETIC SPECIATION; NORTH AMERICA; PHYLOGENY; PROTEIN SUBUNITS; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 18S; RNA, RIBOSOMAL, 28S; SEQUENCE ANALYSIS, DNA; TIME FACTORS;

AMPHIPODA; CRUSTACEA; GAMMARUS;

EID: 34948834130     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2007.06.006     Document Type: Article

References (59)

1. Audzijonyte A., Damgaard J., Varvio S.L., Vainio J.K., and Väinölä R. Phylogeny of Mysis (Crustacea, Mysida): history of continental invasions inferred from molecular and morphological data. Cladistics 21 (2005) 575-596
2. Baker R.H., and DeSalle R. Multiple sources of character information and the phylogeny of Hawaiian Drosophilids. Syst. Biol. 46 (1997) 654-673
3. Baker R.H., Wilkinson G.S., and DeSalle R. Phylogenetic utility of different types of molecular data used to infer evolutionary relationships among stalk-eyed flies (Diopsidae). Syst. Biol. 50 (2001) 87-105
4. Barnard J.L., and Barnard C.M. Freshwater Amphipoda of the World I & II (1983), Hayfield Associates, Mt. Vernon, VA 471pp
5. Berschick P. One primer pair amplifies small subunit ribosomal DNA from mitochondria, plastids and bacteria. Biotechniques 23 (1997) 494-498
6. Bousfield E.L. A new look at the systematics of gammaroidean amphipods of the world. Crustaceana Suppl. 4 (1977) 282-316
7. Cerling T.E., Wang Y., and Quade J. Expansion of C4 ecosystems as an indicator of global ecological changes in the Late Miocene. Nature 361 (1993) 344-345
8. Chen Y., Xiao H., Fu J., and Huang D.W. A molecular phylogeny of eurytomid wasps inferred from DNA sequence data of 28S, 18S, 16S and COI genes. Mol. Phylogenet. Evol. 31 (2004) 300-307
9. Chung S.L., Lo C.H., Lee T.Y., Zhang Y., Xie Y., Li X., Wang K.L., and Wang P.L. Diachronous uplift of the Tibetan Plateau staring 40 Mys ago. Nature 394 (1998) 769-773
10. Crease T.J., and Colbourne J.K. The unusually long small-subunit ribosomal RNA of the crustacean, Daphnia pulex: sequence and predicted secondary structure. J. Mol. Evol. 46 (1998) 307-313
11. Cristescu M.E.A., and Hebert P.D.N. The "Crustacean Seas"-an evolutionary perspective on the Ponto-Caspian peracarids. Can. J. Fish. Aquat. Sci. 62 (2005) 505-517
12. Englisch U., and Koenemann S. Preliminary phylogenetic analysis of selected subterranean amphipod crustaceans, using small subunit rDNA gene sequences. Org. Divers. Evol. 1 (2001) 139-145
13. Englisch U., Coleman C.O., and Wägele J.W. First observations on the phylogeny of the families Gammaridae, Crangonyctidae, Melitidae, Niphargidae, Megaluropidae and Oedicerotidae (Amphipoda, Crustacea), using small subunit rDNA gene sequences. J. Nat. Hist. 37 (2003) 2461-2486
14. Farris J.S., Kallersjo M., Kluge A.G., and Bult C. Constructing a significance test for incongruence. Syst. Biol. 44 (1995) 570-572
15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
16. Fong D.W., Kane T.C., and Culver D.C. Vestigialization and loss of nonfunctional characters. Annu. Rev. Ecol. Syst. 26 (1995) 249-268
17. Folmer O., Black M., Hoeh W., and Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3 (1994) 294-299
18. Grant T., and Kluge G. Data exploration in phylogenetic inference: scientific, heuristic, or neither. Cladistics 19 (2003) 379-418
19. Harrison T.M., Copeland P., Kidd W.S.F., and Yin A. Raising Tibet. Science 255 (1992) 1663-1670
20. Hillis D.M., Mable B.K., Larson A., Davis S.K., and Zimmer E.A. Nucleic Acids IV: sequencing and cloning. In: Hillis D.M., Moritz C., and Mable B.K. (Eds). Molecular Systematics (1996), Sinauer Associates, Sunderland, MA 321-381
21. Hou, Z., 2002. Systematics of Chinese Freshwater Amphipoda. Ph.D. Dissertation. Graduate University of Chinese Academy of Sciences, Beijing.
22. Hou Z., and Li S. Two new species of troglobitic amphipod crustaceans (Gammaridae) from Hubei Province, China. Raffles B. Zool. 50 (2002) 27-36
23. Hou Z., and Li S. Gammarus species from Tibet Plateau, China (Crustacea: Amphipoda: Gammaridae). Raffles B. Zool. 52 (2004) 147-170
24. Hou Z., Li S., and Morino H. Three new species of the genus Gammarus (Crustacea, Amphipoda, Gammaridae) from Yunnan, China. Zool. Sci. 19 (2002) 939-960
25. Hou Z., Li S., and Platvoet D. Three new species of the genus Gammarus from Ili River, China. Rev. Suisse Zool. 111 (2004) 257-284
26. Karaman G.S. Remarks to the freshwater Gammarus species (Fam. Gammaridae) from Korea, China, Japan and some adjacent regions (Contribution to the knowledge of the Amphipoda 134). Montenegrin Acad. Sci. Arts. Glasnik. Sec. Nat. Sci. 4 (1984) 139-162
27. Karaman G.S., and Pinkster S. Freshwater Gammarus species from Europe, North Africa and adjacent regions of Asia (Crustacea-Amphipoda). Part I. Gammarus pulex-group and related species. Bijdr. Dierk. 47 (1977) 1-97
28. Karaman G.S., and Pinkster S. Freshwater Gammarus species from Europe, North Africa and adjacent regions of Asia (Crustacea-Amphipoda).Part II. Gammarus roeseli-group and related species. Bijdr. Dierk. 47 (1977) 165-196
29. Karaman G.S., and Pinkster S. Freshwater Gammarus species from Europe, North Africa and adjacent regions of Asia (Crustacea-Amphipoda). Part III. Gammarus balcanicus-group and related species. Bijdr. Dierk. 57 (1987) 207-260
30. Karaman G.S., and Ruffo S. Sinogammarus troglodytes n. gen. n. sp. A new troglobiont gammarid from China (Crustacea: Amphipoda). Int. J. Speleol. 23 (1995) 157-171
31. Kelly D.W., MacIsaac H.J., and Heath D.D. Vicariance and dispersal effects on phylogeographic structure and speciation in a widespread estuarine invertebrate. Evolution (2006) 257-267
32. Knowlton N., and Weigt L.A. New date and new rates for divergence across the Isthmus of Panama. Proc. R. Soc. Lond. B Biol. Sci. 265 (1998) 2257-2263
33. Knowlton N., Weigt L.A., Solorzan L.A., Mills D.K., and Bermingham E. Divergence in proteins, mitochondrial DNA, and reproductive compatibility across the Isthmus of Panama. Science 260 (1993) 1629-1632
34. Li J.J., and Fang X.M. Uplift of the Tibetan Plateau and environmental changes. Chin. Sci. Bull. 44 (1999) 2117-2124
35. Macdonald III K.S., Yampolsky L., and Duffy J.E. Molecular and morphological evolution of the amphipod radiation of Lake Baikal. Mol. Phylogenet. Evol. 35 (2005) 323-343
36. Maddison D.R., and Maddison W.P. MacClade 4: Analysis of Phylogeny and Character Evolution (2000), Sinauer Associates, Sunderland, MA
37. Meland K., and Willassen E. Molecular phylogeny and biogeography of the genus Pseudomma (Peracarida: Mysida). J. Crustacean Biol. 24 (2004) 541-557
38. Meyran J.C., Monnerot M., and Taberlet P. Taxonomic status and phylogenetic relationships of some species of the genus Gammarus (Crustacea, Amphipoda) deduced from mitochondrial DNA sequences. Mol. Phylogenet. Evol. 8 (1997) 1-10
39. Meyran J.C., and Taberlet P. Mitochondrial DNA polymorphism among alpine populations of Gammarus lacustris (Crustacea, Amphipoda). Freshwater Biol. 39 (1998) 259-265
40. Müller J. Mitochondrial DNA variation and the evolutionary history of cryptic Gammarus fossarum types. Mol. Phylogenet. Evol. 15 (2000) 260-268
41. Müller J.C., Schramm S., and Seitz A. Genetic and morphological differentiation of Dikerogammarus invaders and their invasion history in Central Europe. Freshwater Biol. 47 (2002) 2039-2048
42. Nylander J.A.A. MrModeltest v2. Program Distributed by the Author (2004), Evolutionary Biology Centre, Uppsala University
43. Palumbi S.R. Nucleic acids II: the polymerase chain reaction. In: Hillis D.M., Moritz C., and Mable B.K. (Eds). Molecular Systematics (1996), Sinauer Associates, Sunderland, MA 205-247
44. Peng Z., Ho S.Y.W., Zhang Y., and He S. Uplift of the Tibetan Plateau: evidence from divergence times of glyptosternoid catfishes. Mol. Phylogenet. Evol. 39 (2006) 568-572
45. Pinkster S. The value of morphological characters in taxonomy of Gammarus. Beaufortia 33 (1983) 15-28
46. Ronquist F., and Huelsenbeck J.P. MRBAYES 3: bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
47. Sorenson M.D. TreeRot, Version 2 (1999), Boston University, Boston, MA
48. Stock J.H. A revision of the European species of the Gammarus locusta-group (Crustacea, Amphipoda). Zoologische Verhandelingen 90 (1967) 1-56
49. Stock J.H., Mirzajani A.R., Vonk R., Naderi S., and Kiabi B.H. Limnic and brackish water Amphipoda (Crustacea) from Iran. Beaufortia 48 (1998) 173-234
50. Swofford D.L. PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods) (2002), Sinauer Associates, Sunderland, MA
51. Templeton A.R. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37 (1983) 221-244
52. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
53. Turner S., Hawkesworth C., Liu J., Rogers N., Kelley S., and van Calsteren P. Timing of Tibetan uplift constrained by analysis of volcanic rocks. Nature 364 (1993) 50-54
54. Vader, W., 2007. New amphipod species described in the period 1974-2006, ordered by family. Amphipod Newsletter 31. (http://uit.no/tmu/133/43).
55. Vainio J.K., and Väinölä R. Refugial races and postglacial colonization history of the freshwater amphipod Gammarus lacustris in Northern Europe. Biol. J. Linn. Soc. 79 (2003) 523-542
56. Väinölä, R., Witt, J.D.S., Grabowski, M., Bradbury, J.H., Jazdzewski, K., Sket, B., 2007. Global diversity of amphipods (Amphipoda; Crustacea) in freshwater. Hydrobiologia, in press.
57. Witt J.S., Threloff D.L., and Hebert P.D.N. DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation. Mol. Ecol. 15 (2006) 3037-3082
58. Wu Y.Q., Cui Z.J., Liu G.N., Ge D.K., Yin J.R., Xu Q.H., and Pang Q.Q. Quanternary geomorphological evolution of the Kunlun Pass areas and uplift of the Qinghai-Xizang (Tibet) Plateau. Geomorphology 36 (2001) 203-216
59. Zhang P., Chen Y.Q., Zhou H., Liu Y.F., Wang X.L., Papenfuss T.J., Wake D.B., and Qu L.H. Phylogeny, evolution and biogeography of Asiatic salamanders (Hynobiidae). PNAS 103 (2006) 7360-7365