User menu

DNA analyses reveal abundant homoplasy in taxonomically important morphological characters of Eusiroidea (Crustacea,Amphipoda)

Bibliographic reference Verheye, Marie ; Martin, Patrick ; Backeljau, Thierry ; d’Udekem d’Acoz, Cédric. DNA analyses reveal abundant homoplasy in taxonomically important morphological characters of Eusiroidea (Crustacea,Amphipoda). In: Zoologica Scripta : an international journal of systematic zoology, Vol. 45, no. 3, p. 1-22 (2015)
Permanent URL
  1. Abouheif Ehab, Zardoya Rafael, Meyer Axel, Limitations of Metazoan 18S rRNA Sequence Data: Implications for Reconstructing a Phylogeny of the Animal Kingdom and Inferring the Reality of the Cambrian Explosion, 10.1007/pl00006397
  2. Anderson Frank E., Swofford David L., Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA, 10.1016/j.ympev.2004.06.015
  3. Barnard, The Annals and Magazine of Natural History, Vol. 7: Tenth Series, 425 (1931)
  4. Barnard, Amphipoda. Discovery Reports, Vol. 5 (1932)
  5. Laurens Barnard J., Revision of Some Families, Genera and Species of Gammaridean Amphipoda, 10.1163/156854064x00263
  6. Barnard J. L., Gammaridean Amphipoda of the rocky intertidal of California: Monterey Bay to La Jolla, 10.5479/si.03629236.258.1
  7. Barnard, Proceedings of the Biological Society of Washington, 102, 701 (1989)
  8. Barnard, Freshwater Amphipoda of the World. I. Evolutionary Patterns (1983)
  9. Barnard J.L., Karaman Gordan S., The Higher Classification in Amphipods, 10.1163/156854075x01206
  10. Barnard, Papers from the Conference on the Biology and Evolution of Crustacea. Australian Museum Memoir 18, 45 (1984)
  11. Barnard J. Laurens, Karaman Gordan S., The families and genera of marine gammaridean Amphipoda (except marine gammaroids). Part 1, 10.3853/j.0812-7387.13.1991.91
  12. Bellan-Santini, Traité de Zoologie: Anatomie, Systématique, Biologie, 93 (1999)
  13. Berge, Crustaceans and the Biodiversity Crisis. Proceedings of the Fourth International Crustacean Congress, 239 (1999)
  14. Bergsten Johannes, A review of long-branch attraction, 10.1111/j.1096-0031.2005.00059.x
  15. Bousfield, Crustaceana, Suppl. 4, 282 (1977)
  16. Bousfield, Transactions of the Royal Society of Canada Series, 4, 343 (1978)
  17. Bousfield, Crustacean Phylogeny, 257 (1983)
  18. Bousfield, Amphipacifica, 1, 17 (1994)
  19. Bousfield, Amphipacifica, 1, 3 (1995)
  20. Bousfield, Amphipacifica, 1, 76 (1994)
  21. Browne W. E., Haddock S. H. D., Martindale M. Q., Phylogenetic analysis of lineage relationships among hyperiid amphipods as revealed by examination of the mitochondrial gene, cytochrome oxidase I (COI), 10.1093/icb/icm093
  22. Coleman Ch. O., On the nutrition of two Antarctic acanthonotozomatidae (Crustacea: Amphipoda) : Gut contents and functional morphology of mouthparts, 10.1007/bf00287425
  23. Coleman, Bulletin de l'Institut Royal des Sciences Naturelles de Belgique, 77, 1 (2007)
  24. Coleman, Proceedings of the Biological Society of Washington, 104, 253 (1991)
  25. Coleman, Organisms Diversity & Evolution, 6, 1 (2006)
  26. Corrigan, Evolutionary Biology, 41, 154 (2014)
  27. Darriba Diego, Taboada Guillermo L, Doallo Ramón, Posada David, jModelTest 2: more models, new heuristics and parallel computing, 10.1038/nmeth.2109
  28. Dauby Patrick, Scailteur Yves, De Broyer Claude, 10.1023/a:1017596120422
  29. De Broyer, A Checklist of the Amphipoda (Crustacea) of the Southern Ocean (1993)
  30. De Broyer, Bulletin de l'Institut Royal des Sciences Naturelles de Belgique, 77, 1 (2007)
  31. Englisch , U. 2001 Analyse der Phylogenie der Amphipoda (Crustacea, Malacostraca) mit Hilfe von Sequenzen des Gens der RNA der kleinen ribosomalen Untereinheit. Ph.D. Dissertation. Fakultät für Biologie 1 158 Bochum, Germany Ruhr-Universität Bochum
  32. Farris James S., Källersjö Mari, Kluge Arnold G., Bult Carol, Constructing a Significance Test for Incongruence, 10.1093/sysbio/44.4.570
  33. Havermans Charlotte, Nagy Zoltán T., Sonet Gontran, De Broyer Claude, Martin Patrick, Incongruence between molecular phylogeny and morphological classification in amphipod crustaceans: A case study of Antarctic lysianassoids, 10.1016/j.ympev.2009.10.025
  34. Hou Zhonge, Fu Jinzhong, Li Shuqiang, A molecular phylogeny of the genus Gammarus (Crustacea: Amphipoda) based on mitochondrial and nuclear gene sequences, 10.1016/j.ympev.2007.06.006
  35. Hou Z., Sket B., Fiser C., Li S., Eocene habitat shift from saline to freshwater promoted Tethyan amphipod diversification, 10.1073/pnas.1104636108
  36. Just J, Vicmusia duplocoxa, gen. et sp.nov., (Crustacea : Amphipoda : Gammaridea) of the new family Vicmusiidae from Australian upper bathyal waters, 10.1071/it9890925
  37. Katoh K., Standley D. M., MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, 10.1093/molbev/mst010
  38. Kim C. B., Kim W., Phylogenetic relationships among gammaridean families and amphipod suborders, 10.1080/00222939300770571
  39. Kolaczkowski Bryan, Thornton Joseph W., Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics, 10.1371/journal.pone.0007891
  40. Krapp Rupert H., Berge Jørgen, Flores Hauke, Gulliksen Bjørn, Werner Iris, Sympagic occurrence of Eusirid and Lysianassoid amphipods under Antarctic pack ice, 10.1016/j.dsr2.2007.12.018
  41. Kück Patrick, Mayer Christoph, Wägele Johann-Wolfgang, Misof Bernhard, Long Branch Effects Distort Maximum Likelihood Phylogenies in Simulations Despite Selection of the Correct Model, 10.1371/journal.pone.0036593
  42. Letsch Harald O., Kück Patrick, Stocsits Roman R., Misof Bernhard, The Impact of rRNA Secondary Structure Consideration in Alignment and Tree Reconstruction: Simulated Data and a Case Study on the Phylogeny of Hexapods, 10.1093/molbev/msq140
  43. Lincoln, British Marine Amphipoda: Gammaridea (1979)
  44. Lincoln, Bulletin of the British Museum of Natural History, 40, 103 (1981)
  45. Lowry, Xth International Colloquium on Amphipoda, 30 (2000)
  46. LOWRY J. K., MYERS A. A., A Phylogeny and Classification of the Senticaudata subord. nov. Crustacea: Amphipoda), 10.11646/zootaxa.3610.1.1
  47. Macdonald III Kenneth S., Yampolsky Lev, Duffy J. Emmett, Molecular and morphological evolution of the amphipod radiation of Lake Baikal, 10.1016/j.ympev.2005.01.013
  48. Martin, An Updated Classification of the Recent Crustacea (2001)
  49. Misof Bernhard, Misof Katharina, A Monte Carlo Approach Successfully Identifies Randomness in Multiple Sequence Alignments : A More Objective Means of Data Exclusion, 10.1093/sysbio/syp006
  50. Moore P. G., A functional interpretation of coxal morphology in Epimeria cornigera (Crustacea: Amphipoda: Paramphithoidae), 10.1017/s0025315400048189
  51. Myers A. A., Lowry J. K., A Phylogeny and a New Classification of the Corophiidea Leach, 1814 (Amphipoda), 10.1163/20021975-99990353
  52. Oshel PE, Steele DH, Amphipod Paramphithoe hystrix: a micro-predator on the sponge Haliclona ventilabrum , 10.3354/meps023307
  53. Parks Sarah L., Goldman Nick, Maximum Likelihood Inference of Small Trees in the Presence of Long Branches, 10.1093/sysbio/syu044
  54. Rambaut , A. Drummond , A. 2005 Tracer, a program for analyzing results from Bayesian MCMC programs such as Beast & MrBayes, version 1.3 Oxford http://evolve/zoo.Ox.Ac.Uk/software.Html?Id=tracer/
  55. Ronquist F., Huelsenbeck J. P., MrBayes 3: Bayesian phylogenetic inference under mixed models, 10.1093/bioinformatics/btg180
  56. Serejo Cristiana S., Cladistic revision of talitroidean amphipods (Crustacea, Gammaridea), with a proposal of a new classification, 10.1111/j.0300-3256.2004.00163.x
  57. Sherbakov D.Yu., Kamaltynov R.M., Ogarkov O.B., Verheyen E., Patterns of Evolutionary Change in Baikalian Gammarids Inferred from DNA Sequences (Crustacea, Amphipoda), 10.1006/mpev.1997.0482
  58. Sherbakov D. Yu., Ogarkov, Kamaltynov, Verheyen, Vainio, Vainola, ON THE PHYLOGENY OF LAKE BAIKAL AMPHIPODS IN THE LIGHT OF MITOCHONDRIAL AND NUCLEAR DNA SEQUENCE DATA, 10.1163/156854099503816
  59. Stebbing Thomas Roscoe Rede, Amphipoda I. Gammaridea, by the Rev. T. R. R. Stebbing ..., 10.5962/bhl.title.1224
  60. Steele V. J., Steele D. H., Presence of Two Types of Calceoli on Gammarellus Angulosus (Amphipoda: Gammaridea), 10.2307/1548794
  61. Susko Edward, Bayesian Long Branch Attraction Bias and Corrections, 10.1093/sysbio/syu099
  62. Swofford, Paup*. Phylogenetic analysis using Parsimony (*and other methods). Version 4 (2003)
  63. Takezaki, Molecular Biology and Evolution, 12, 823 (1995)
  64. Tamura Koichiro, Stecher Glen, Peterson Daniel, Filipski Alan, Kumar Sudhir, MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0, 10.1093/molbev/mst197
  65. Väinölä R., Witt J. D. S., Grabowski M., Bradbury J. H., Jazdzewski K., Sket B., Global diversity of amphipods (Amphipoda; Crustacea) in freshwater, 10.1007/s10750-007-9020-6
  66. Wägele Johann, Mayer Christoph, Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects, 10.1186/1471-2148-7-147
  67. WITT JONATHAN D. S., THRELOFF DOUG L., HEBERT PAUL D. N., DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation : DNA BARCODING OF AMPHIPODS, 10.1111/j.1365-294x.2006.02999.x
  68. Xia Xuhua, DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution, 10.1093/molbev/mst064
  69. Xia Xuhua, Xie Zheng, Salemi Marco, Chen Lu, Wang Yong, An index of substitution saturation and its application, 10.1016/s1055-7903(02)00326-3
  70. Zwickl , D. J. 2006 Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the Maximum Likelihood criterion. Ph.D. Dissertation Austin University of Texas
  71. Bellan-Santini, European Register of Marine Species: A Check-list of the Marine Species in Europe and a Bibliography of Guides to their Identification, 295 (2001)
  72. Friedrich M., Tautz D., An episodic change of rDNA nucleotide substitution rate has occurred during the emergence of the insect order Diptera, 10.1093/oxfordjournals.molbev.a025804
  73. Havermans Charlotte, Sonet Gontran, d’Udekem d’Acoz Cédric, Nagy Zoltán T., Martin Patrick, Brix Saskia, Riehl Torben, Agrawal Shobhit, Held Christoph, Genetic and Morphological Divergences in the Cosmopolitan Deep-Sea Amphipod Eurythenes gryllus Reveal a Diverse Abyss and a Bipolar Species, 10.1371/journal.pone.0074218
  74. Ito Atsushi, Aoki Masakazu N., Yahata Kensuke, Wada Hiroshi, Complicated evolution of the caprellid (Crustacea: Malacostraca: Peracarida: Amphipoda) body plan, reacquisition or multiple losses of the thoracic limbs and pleons, 10.1007/s00427-011-0365-5
  75. Ito Atsushi, Wada Hiroshi, Aoki Masakazu N., Phylogenetic Analysis of Caprellid and Corophioid Amphipods (Crustacea) Based on the 18S rRNA Gene, With Special Emphasis on the Phylogenetic Position of Phtisicidae, 10.2307/25066674
  76. Ki Jang-Seu, Dahms Hans-Uwe, Kim Il-Chan, Park Heum Gi, Hop Haakon, Lee Jae-Seong, Molecular relationships of gammaridean amphipods from Arctic sea ice, 10.1007/s00300-011-1016-z
  77. Omilian A. R., Taylor D. J., Rate Acceleration and Long-branch Attraction in a Conserved Gene of Cryptic Daphniid (Crustacea) Species, 10.1093/oxfordjournals.molbev.a003767
  78. Philippe* and H., Germot A., Phylogeny of Eukaryotes Based on Ribosomal RNA: Long-Branch Attraction and Models of Sequence Evolution, 10.1093/oxfordjournals.molbev.a026362
  79. Spears, Arthropod Relationships, 169 (1997)