Probing marine Gammarus (Amphipoda) taxonomy with DNA barcodes

Systematics and Biodiversity

Volumn 7, Issue 4, 2009, Pages 365-379

  Costa, F O ^a,d   Henzler, C M ^b,e   Lunt, D H ^c   Whiteley, N M ^a   Rock, J ^a,c  

^a BANGOR UNIVERSITY   (United Kingdom)

^b DUKE UNIVERSITY   (United States)

^c UNIVERSITY OF HULL   (United Kingdom)

^d UNIVERSITY OF MINHO   (Portugal)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Amphipoda; Brackish; Cox1; Cryptic species; Cytochrome c oxidase I; DNA barcoding; Echinogammarus; Gammarus; Marine; Phylogenetics; Phylogeography

Indexed keywords

AMPHIPODA; CRUSTACEA; ECHINOGAMMARUS; ECHINOGAMMARUS MARINUS; GAMMARUS; GAMMARUS AEQUICAUDA; GAMMARUS DUEBENI; GAMMARUS INSENSIBILIS; GAMMARUS MARINUS; GAMMARUS OCEANICUS;

EID: 77949772352     PISSN: 14772000     EISSN: 14780933     Source Type: Journal    
DOI: 10.1017/S1477200009990120     Document Type: Article

References (69)

1. ANISIMOVA, M.&GASCUEL, O. 2006. Approximate likelihood ratio test for branches: A fast, accurate and powerful alternative. Systematic Biology 55, 539-552.
2. BELLAN-SANTINI, D.&COSTELLO, M.J. 2001. Amphipoda. In: COSTELLO, M.J. et al., Eds., European register of marine species: a check-list of the marine species in Europe and a bibliography of guides to their identification. Collection Patrimoines Naturels 50, 295-308.
3. BOUSFIELD, E.E. 1973. Shallow-water gammaridean Amphipoda of New England. Comstock Publishing, Cornell University Press, London.
4. CHRISTIE, H. &KRAUFVELIN, P. 2003. Mechanisms regulating amphipod population density within macroalgal communities with low predator impact. Scientia Marina 68, 189-198.
5. CLASON, B.&ZAUKE, G.-P. 2000. Bioaccumulation of trace metals in marine and estuarine amphipods: evaluation and verification of toxicokinetic models. Canadian Journal of Fisheries and Aquatic Sciences 57, 1410-1422.
6. COSTA, F.O.&COSTA, M.H. 2000. Review of the ecology of Gammarus locusta (L.). Polish Archives of Hydrobiology 48, 541-559.
7. COSTA, F.O., CUNHA, M.R., NEUPARTH, T., THEODORAKIS, C.W., COSTA, M.H.&SHUGART, L.R. 2004a. Application of RAPD DNA fingerprinting in taxonomic identification of amphipods: a case-study with Gammarus species (Crustacea: Amphipoda). Journal of the Marine Biological Association of the United Kingdom 84, 171-178.
8. COSTA, F.O., DEWAARD, J.R., BOUTILLIER, J., RATNASINGHAM, S., DOOH, R.T., HAJIBABAEI, M.&HEBERT, P.D.N. 2007. Biological identifications through DNA barcodes: the case of the Crustacea. Canadian Journal of Fisheries and Aquatic Sciences 64, 272-295.
9. COSTA, F.O., NEUPARTH, T., CORREIA, A.D.&COSTA, M.H. 2005. Multi-level assessment of chronic toxicity of estuarine sediments with the amphipod Gammarus locusta: II. Organism and population-level endpoints. Marine Environmental Research 60, 93-110.
10. COSTA, F.O., NEUPARTH, T., THEODORAKIS, C.W., COSTA, M.H.&SHUGART, L.R. 2004b. RAPD analysis of southern populations of Gammarus locusta: comparisonwith allozyme data and ecological inferences. Marine Ecology-Progress Series 277, 197-207.
11. CRISTESCU,M.E.A. &HEBERT, P.D.N. 2005. The 'Crustacean Seas' - an evolutionary perspective on the Ponto-Caspian peracarids. Canadian Journal of Fisheries and Aquatic Sciences 62, 505-517.
12. CRISTESCU, M.E.A., WITT, J.D.S., GRIGOROVICH, I.A., HEBERT, P.D.N.&MACISAAC, H.J. 2004. Dispersal of the Ponto-Caspian amphipod Echinogammarus ischnus: invasion waves from the Pleistocene to the present. Heredity 92, 197-203.
13. DICK, J.T.A., JOHNSON, M.P., MCCAMBRIDGE, S., JOHNSON, J., CARSON, V.E.E., KELLY, D.W.&MACNEIL, C. 2005. Predatory nature of the littoral amphipod Echinogammarus marinus: gut content analysis and effects of alternative food and substrate heterogeneity. Marine Ecology-Progress Series 291, 151-158.
14. ENGLISCH, U., COLEMAN, C.O.&WÄGELE, J.W. 2003. First observations on the phylogeny of the families Gammaridae, Crangonyctidae, Melitidae, Niphargidae, Megaluropidae and Oedicerotidae (Amphipoda, Crustacea), using small subunit rDNA gene sequences. Journal of Natural History 37, 2461-2486.
15. FIALKOWSKI, W.&RAINBOW, P.S. 2006. The discriminatory power of two biomonitors of trace metal bioavailabilities in freshwater streams. Water Research 40, 1805-1810.
16. FLOYD, R., ABEBE, E., PAPERT, A.&BLAXTER, M. 2002. Molecular barcodes for soil nematodes identification. Molecular Ecology 11, 839-850.
17. FOLMER, O., BLACK, M., HOEH, W., LUTZ, R.&VRIJENHOEK, R. 1994.DNAprimers for amplification ofmitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3, 294-297.
18. FREDSTED, T., WINCENTZ, T.&VILLESEN, P. 2006. Introgression of mountain hare (Lepus timidus) mitochondrial DNA into wild brown hares (Lepus europaeus) in Denmark. BioMed Central Ecology 6, 17.
19. GASTON, K.J.&SPICER, J.I. 2001. The relationship between range size and niche breadth: a test using five species of Gammarus (Amphipoda). Global Ecology and Biogeography 10, 179-188.
20. GRABOWSKI, M., JAZDZEWSKI, K.&KONOPACKA, A. 2007. Alien Crustacea in Polish waters - Amphipoda. Aquatic Invasions 2, 25-38.
21. GUINDON, S.&GASCUEL, O. 2003. PhyML - A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52, 696-704.
22. HAJIBABAEI, M., SINGER, G.A.C.&HICKEY, D.A. 2006. Benchmarking DNA barcodes: an assessment using available primate sequences. Genome 49, 851-854.
23. HEBERT, P.D.N., CYWINSKA, A.,BALL, S.L.&DEWAARD, J.R. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B-Biological Sciences 270, 313-321.
24. HENZLER, C.M. 2006. Rafting and refugia in North Atlantic amphipods: understanding the effects of Pleistocene climate change on low-dispersal marine species. Ph.D. thesis, Duke University, Durham, NC.
25. HICKERSON, M.J., MEYER, C.P.&MORITZ, C. 2006. J.M. DNA barcoding will often fail to discover new animal species over broad parameter space. Systematic Biology 55, 729-739.
26. HOU, Z., FU, J.&LI, S. 2007. A molecular phylogeny of the genus Gammarus (Crustacea: Amphipoda) based on mitochondrial and nuclear gene sequences. Molecular Phylogenetics and Evolution 45, 596-611.
27. IRONSIDE, J.E., SMITH, J.E., HATCHER, H.J., SHARPE, R.G., ROLLINSON, D.&DUNN, A.M. 2003. Two species of feminizing microsporidian parasite coexist in populations of Gammarus duebeni. Journal of Evolutionary Biology 16, 467-473.
28. JAZDZEWSKI, K. 1973. Ecology of gammarids in the Bay of Puck. Oikos Suppl. 15, 121-126.
29. JONES,D.T., TAYLOR,W.R.ÞTON, J.M. 1992. The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8, 275-282.
30. KEANE, T.M., CREEVEY, C.J., PENTONY, M.M., NAUGHTON, T.J.&MCINERNEY, J.O. 2006. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evolutionary Biology 6, 29.
31. KELLY, D.W., BAILEY, R.J., MACNEIL, C., DICK, J.T.A.&MCDONALD, R.A. 2006a. Invasion by the amphipod Gammarus pulex alters community composition of native freshwatermacroinvertebrates. Diversity and Distributions 12, 525-534.
32. KELLY, D.W.&DICK, J.T.A. 2005. Effects of environment and an introduced invertebrate species on the structure of benthic macroinvertebrate species at the catchment level. Archiv f̈ur Hydrobiologie 164, 69-88.
33. KELLY, D.W., DICK, J.T.A.&MONTGOMERY, I. 2002. The functional role of Gammarus (Crustacea, Amphipoda): shredders, predators or both? Hydrobiologia 485, 199-203.
34. KELLY, D.W.,MACISAAC, H.J.&HEATH, D.D. 2006b. Vicariance and dispersal effects on phylogeographic structure and speciation in a widespread estuarine invertebrate. Evolution 60, 257-267.
35. KINNE, O. 1954. Die Gammarus-Arten der Kieler Butch. Zoologische Jahrbuecher Abteilung fuer Systematik Oekologie und Geographie der Tiere 82, 405-424.
36. KLEKOWSKI, R.&WESLAWSKI, J. 1990. Atlas of the Marine Fauna of Southern Spitsbergen. 1. Vertebrates. Polish Academy of Science Press, Gdansk, Poland.
37. KOSTADINOVA, A.&MAVRODIEVA, R.S. 2005. Microphallids in Gammarus insensibilis Stock, 1966 from a Black Sea lagoon: host response to infection. Parasitology 131, 347-354.
38. LINCOLN,R.J. 1979. Britishmarine Amphipoda: Gammaridea.British Museum (Natural History), London.
39. LEF́EBURE, T.,DOUADY, C.J.&GIBERT, F.M. 2007. Testing dispersal and cryptic diversity in a widely distributed groundwater amphipod (Niphargus rhenorhodanensis). Molecular Phylogenetics and Evolution 42, 676-686.
40. MACDONALD, K.S., YAMPOLSKY, L.&DUFFY, J.E. 2005. Molecular and morphological evolution of the amphipod radiation of Lake Baikal. Molecular Phylogenetics and Evolution 35, 323-343.
41. MACNEIL, C.,DICK, J.T.A., JOHNSON,M.P., HATCHER, M.J.&DUNN, A.M. (2004) A species invasion mediated through habitat structure, intraguild predation, and parasitism. Limnology and Oceanography 49, 1848-1856.
42. MALLET, J.&WILLMOTT, K. 2003. Taxonomy: Renaissance or Tower of Babel? Trends in Ecology and Evolution 18, 57-59.
43. MEYRAN, J.C., MONNEROT, M.&TABERLET, P. 1997. Taxonomic status and phylogenetic relationships of some species of Gammarus (Crustacea, amphipoda) deduced from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 8, 1-10.
44. MILLER, S.A., DYKES, D.D.&POLESKY, H.F. 1988. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Research 16, 1215.
45. M̈ULLER, J., PARTSCH, E.&LINK, A. 2000. Differentiation in morphology and habitat partitioning of genetically characterized Gammarus fossarum forms (Amphipods) across a contact zone. Biological Journal of the Linnean Society 69, 41-53.
46. PAPADOPOULOS, L.N., PEIJNENBURG,K.T.C.A.&LUTTIKHUIZEN, P.C. 2005. Phylogeography of the calanoid copepods Calanus helgolandicus and Calanus euxinus suggests Pleistocene divergences between Atlantic, Mediterranean, and Black Sea populations. Marine Biology 147, 1353-1365.
47. PATARNELLO, T.,VOLCKAERT, F.A.M.J.&CASTILHO, R. 2007. Pillars of Hercules: Is the Atlantic-Mediterranean transition a phylogeographic break? Molecular Ecology 16, 4426-4444.
48. PEIJNENBURG, K.T.C.A., BREEUWER, J.A.J., PIERROT-BULTS, A.C.&MENKEN, S.B.J. 2004. Phylogeography of the planktonic chaetognath Sagitta setosa reveals isolation in European seas. Evolution 58, 1472-1487.
49. PISCART, C.,MANACH, A., COPP, G.H.&MARMONIER, P. 2007. Distribution and microhabitats of native and non-native gammarids (Amphipoda, Crustacea) in Brittany, with particular reference to the endangered endemic sub-species Gammarus duebeni celticus. Journal of Biogeography 34, 524-533.
50. PRATO, E., DI LEO, A., BIANDOLINO, F.&CARDELLICCHIO, N. 2006. Sediment toxicity tests using two species of marine amphipods: Gammarus aequicauda and Corophium insidiosum. Bulletin of Environmental Contamination and Toxicology 76, 629-636.
51. RATNASINGHAM, S.&HEBERT, P.D.N. 2007. BOLD: The Barcode of Life Data System (www.barcodinglife.org). Molecular Ecology Notes 7, 355-364.
52. ROCK, J., IRONSIDE, J., POTTER, T., WHITELEY, N.M.&LUNT, D.H. 2007. Phylogeography and environmental diversification of a highly adaptable marine amphipod, Gammarus duebeni. Heredity 99, 102-111.
53. ROLBIECKI, L.&NORMANT, M. 2005. The first record of parasites in Gammarus tigrinus Sexton, 1939 - a recent newcomer to the Gulf of Gdansk. Oceanologia 47, 283-287.
54. SEGERSTRALE, S.G. 1947. New observations on the distribution and morphology of the amphipod Gammarus zaddachi Sexton with notes on related species. Journal of the Marine Biological Association of the United Kingdom 27, 219-244.
55. SEGERSTRALE, S.G. 1971. A note on the occurrence of Gammarus locusta (L.) and Gammarus inaequicauda Stock (Amphipoda, Gammaridae) in the Baltic Sea. Annales Zoologici Fennici 8, 324-325.
56. SEZGIN, M.&KATAGAN, T. 2007. An account of our knowledge of the Amphipod fauna of the Black Sea. Crustaceana 80, 1-11.
57. SKADSHEIM, A.&SIEGISMUND, H.R. 1986. Genetic relationships among north-western European Gammaridea (Amphipoda). Crustaceana 51, 163-175.
58. SPOONER, G.M. 1947. The distribution of Gammarus species in estuaries. Part I. Journal of the Marine Biological Association of the United Kingdom 27, 1-52.
59. STAMATAKIS,A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690.
60. STAMATAKIS, A.,HOOVER, P.&ROUGEMONT, J. 2008. A Rapid Bootstrap Algorithm for the RAxMLWeb-Servers. Systematic Biology, 57, 758-771.
61. STEVENS, M.I., HOGG, I.D.&PILDITCH, C.A. 2006. Evidence for female-biased juvenile dispersal in corophiid amphipods from a New Zealand estuary. Journal of Experimental Marine Biology and Ecology 331, 9-20.
62. STOCK, J.H. 1967. A revision of the European species of the Gammarus locusta - group (Crustacea, Amphipoda). Zoologische Verhandelingen 90, 1-56.
63. TAMURA, K.,DUDLEY, J.,NEI, M.&KUMAR, S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24, 1596-1599.
64. V̈ AIN ̈OL̈A, R., VAINIO, J.K.&PALO, J.U. 2001. Phylogeography of 'glacial relict' Gammaracanthus (Crustacea, Amphipoda) from boreal lakes and the Caspian andWhite seas. Canadian Journal of Fisheries and Aquatic Sciences 58, 2247-2257.
65. V̈ AIN ̈OL̈A, R., WITT, J.D.S., GRABOWSKI, M., BRADBURY, J.H., JAZDZEWSKI, K.&SKET, B. 2008. Global diversity of amphipods (Amphipoda; Crustacea) in freshwater. Hydrobiologia 595, 241-255.
66. WARD, R.D. 2009. DNA barcode divergence among species and genera of birds and fishes. Molecular Ecology Resources 9, 1077-1085.
67. WARD, R.D., ZEMLAK, T.S., INNES, B.H., LAST, P.R.&HEBERT, P.D.N. 2005. Barcoding Australia's fish species. Philosophical Transactions of the Royal Society of London B 360, 1847-1857.
68. WARES, J.P.&CUNNINGHAM, C.W. (2001) Phylogeography and historical ecology of theNorth Atlantic intertidal. Evolution 55, 2455-2469.
69. WITT, J.D.S., THRELOFF, D.L.&HEBERT, P.D.N. 2006. DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation. Molecular Ecology 15, 3073-3082.