Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships

Molecular Phylogenetics and Evolution

Volumn 66, Issue 3, 2013, Pages 776-789

  Shen, Hong ^a   Braband, Anke ^a   Scholtz, Gerhard ^a  

^a HUMBOLDT UNIVERSITY   (Germany)

Author keywords

Aliscore; Mitochondrial genomes; Reptantia; Thalassinidans

Indexed keywords

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; BIOLOGY; CLASSIFICATION; DECAPODA (CRUSTACEA); DNA SEQUENCE; GENETICS; MITOCHONDRIAL GENOME; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPECIES DIFFERENCE; STATISTICAL MODEL;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; COMPUTATIONAL BIOLOGY; DECAPODA (CRUSTACEA); GENOME, MITOCHONDRIAL; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

ASTACIDEA; BRACHYURA; CALOCARIS MACANDREAE; CARIDEA; CORALLIANASSA; CRUSTACEA; CRYPTOLITHODES SITCHENSIS; DECAPODA (CRUSTACEA); DENDROBRANCHIATA; DROMIA PERSONATA; ENOPLOMETOPUS OCCIDENTALIS; EUPHAUSIACEA; HOMARUS GAMMARUS; NEAXIUS ACANTHUS; PANULIRUS; PANULIRUS VERSICOLOR; POLYCHELES TYPHLOPS; PROCAMBARUS; PROCAMBARUS FALLAX; REPTANTIA; SCYLLARIDES LATUS; STENOPODIDEA; STENOPUS HISPIDUS; STOMATOPODA; UPOGEBIA MAJOR;

EID: 84873183172     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.11.002     Document Type: Article

References (85)

1. Abascal F., Zardoya R., Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 2005, 21:2104-2105.
2. Abele L.G. Comparison of morphological and molecular phylogeny of the Decapoda. Mem. Queensl. Mus. 1991, 31:101-108.
3. Abele L.G., Felgenhauer B.E. Phylogenetic and phenetic relationships among the lower Decapoda. J. Crust. Biol. 1986, 6:385-400.
4. Ahyong S.T. Phylogeny of the clawed lobsters (Decapoda Homarida). Zootaxa 2006, 1109:1-14.
5. Ahyong S.T., O'Meally D. Phylogeny of the Decapoda Reptantia: resolution using three molecular loci and morphology. Raffles Bull. Zool. 2004, 52:673-693.
6. Ahyong S.T., Lai J.C.Y., Sharkey D., Colgan D.J., Ng P.K.L. Phylogenetics of the brachyuran crabs (Crustacea: Decapoda): the status of Podotremata based on small subunit nuclear ribosomal RNA. Mol. Phylogenet. Evol. 2007, 45:576-586.
7. Ahyong S.T., Schnabel K.E., Maas E.W. Anomuran phylogeny: new insights from molecular data. Decapod Crustacean Phylogenetics (Crustacean Issues 18) 2009, 399-414. CRC Press, Boca Raton. J.W. Martin, D.L. Felder, K.A. Crandall (Eds.).
8. Baurain D., Brinkmann H., Philippe H. Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors?. Mol. Biol. Evol. 2007, 24:6-9.
9. Bergsten J. A review of long-branch attraction. Cladistics 2005, 21:163-193.
10. Boas, J.E.V., 1880. Studier over Decapodernes Slaegtskabsforhold. Vidensk. Selsk. Skr. 6. Raekke, naturvid. math. Afd. I, 2, 25-210.
11. Boisselier-Dubayle M.-C., Bonillo C., Cruaud C., Couloux A., Richer de Forges B., Vidal N. The phylogenetic position of the 'living fossils' Neoglyphea and Laurentaeglyphea (Decapoda: Glypheidea). C.R. Biologies 2010, 333:755-759.
12. Boore J.L., Macey J.R., Medina M. Sequencing and comparing whole mitochondrial genomes of animals. Meth. Enzymol. 2005, 395:311-348.
13. Borradaile L.A. On the classification of the decapod crustaceans. Ann. Mag. Nat. Hist. 1907, 19:457-486.
14. Braband A., Kawai T., Scholtz G. The phylogenetic position of the East Asian freshwater crayfish Cambaroides within the Northern Hemisphere Astacoidea (Crustacea, Decapoda, Astacida) based on molecular data. J. Zool. Syst. Evol. Res. 2006, 44:17-24.
15. Braband A., Cameron S.L., Podsiadlowski L., Daniels S.R., Mayer G. The mitochondrial genome of the onychophoran Opisthopatus cinctipes (Peripatopsidae) reflects the ancestral mitochondrial gene arrangement of Panarthropoda and Ecdysozoa. Mol. Phylogenet. Evol. 2010, 57:285-292.
16. Bracken H.D., Toon A., Felder D.L., Martin J.W., Finley M., Rasmussen J., Palero F., Crandall K.A. The decapod tree of life: compiling the data and moving toward a consensus of decapod evolution. Arthr. Syst. Phylog. 2009, 67:99-116.
17. Brinkmann H., Philippe H. Animal phylogeny and large-scale sequencing: progress and pitfalls. J. Syst. Evol. 2008, 46:274-286.
18. Brösing A., Richter S., Scholtz G. Phylogenetic analysis of the Brachyura (Crustacea, Decapoda) based on characters of the foregut with establishment of a new taxon. J. Zool. Syst. Evol. Res. 2007, 45:20-32.
19. Burkenroad M.D. The evolution of the Eucarida (Crustacea, Eumalacostraca), in relation to the fossil record. Tulane Stud. Geol. 1963, 2:1-17.
20. Burkenroad M.D. The higher taxonomy and evolution of Decapoda (Crustacea). Trans. San Diego Soc. Nat. Hist. 1981, 19:251-268.
21. Bybee S.M., Bracken-Grissom H.D., Hermansen R.A., Clement M.J., Crandall K.A., Felder D.L. Directed next generation sequencing for phylogenetics: an example using Decapoda. Zool. Anz. 2011, 250:497-506.
22. Cameron S.L., Sullivan J., Song H., Miller K.B., Whiting M.F. A mitochondrial genome phylogeny of the Neuropterida (lace-wings, alderflies and snakeflies) and their relationship to the other holometabolous insect orders. Zool. Script. 2009, 38:575-590.
23. Christoffersen M.L. Phylogenetic systematics of the Eucarida (Crustacea, Malacostraca). Revist. Brasil. Zool. 1988, 5:325-351.
24. Chu K.H., Tsang L.M., Ma K.Y., Chan T.Y., Ng P.K.L. Decapod phylogeny: what can protein-coding genes tell us?. Decapod Crustacean Phylogenetics (Crustacean Issues 18) 2009, 88-99. CRC Press, Boca Raton. J.W. Martin, D.L. Felder, K.A. Crandall (Eds.).
25. Cox C., Foster P., Hirt R., Harris S.R., Embley T.M. The archaebacterial origin of eukaryotes. Proc. Natl. Acad. Sci. USA 2008, 105:20356-20361.
26. Crandall K.A., Harris D.J., Fetzner J.W. The monophyletic origin of freshwater crayfish estimated from nuclear and mitochondrial DNA sequences. Proc. R. Soc. Lond. B 2000, 267:1679-1686.
27. De Grave S.D., Pentcheff N.D., Ahyong S.T., Chan T.Y., Crandall K.A., Dworschak P.C., Felder D.L., Feldmann R.M., Fransen C.H.J.M., Goulding L.Y.D., Lemaitre R., Low M.E.Y., Martin J.W., Ng P.K.L., Schweitzer C.E., Tan S.H., Tshudy D., Wetzer R. A classification of living and fossil genera of decapod crustaceans. Raffles Bull. Zool. Suppl. 2009, 21:1-109.
28. De Saint Laurent M. Sur la systématique et la phylogénie des Thalassinidea: definitions des familles des Callianassidae et des Upogebiidae et diagnose de cinq genres nouveaux (Crustacea Decapoda). Compt. Rend. Acad. Sci. (D) 1973, 277:513-516.
29. De Saint Laurent M. Sur la classification et la phylogénie des Crustacés Décapodes Brachyoures. Podotremata Guinot, 1977, et Eubrachyura sect. nov. Compt. Rend. Acad. Sci. (D) 1980, 290:1265-1268.
30. Dixon C.J., Ahyong S.T., Schram F.R. A new hypothesis of decapod phylogeny. Crustaceana 2003, 76:935-975.
31. Folmer O., Black M., Hoeh W., Lutz R., Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome C oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 1994, 3:294-299.
32. Foster P. Modeling compositional heterogeneity. Syst. Biol. 2004, 53:485-495.
33. Guinot, D., 1978. Principles d'une classification èvolutive des crustacès dècapodes brachyoures (Principles of a new classification of the Crustacea Decapoda Brachyura). Bull. Biol. Fr. Belg., N. S. 112, 211-293.
34. Gurney R. Larvae of decapod Crustacea. Part 5. Nephropsidae and Thalassinidae. Discov. Rep. 1938, 17:291-344.
35. Hall, T.A., 1999. BiolEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. .
36. Hassanin A. Phylogeny of Arthropoda inferred from mitochondrial sequences: strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution. Mol. Phylogenet. Evol. 2006, 38:100-116.
37. Hassanin A., Leger N., Deutsch J. Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa, and consequences for phylogenetic inferences. Syst. Biol. 2005, 54:277-298.
38. HuaFeng S., RuiYu L., ZhongLi S., JiPing M. Complete mitochondrial DNA sequence of Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) and a novel tRNA gene cluster. Mar. Gen. 2012, 6:7-15.
39. Jamieson B.G.M., Guinot D., Richer de Forges B. Phylogeny of the Brachyura (Crustacea, Decapoda): evidence from spermatozoal ultrastructure. Mém. Mus. Nat. Hist. Nat. 1995, 166:265-283.
40. Jarman S.N., Nicol S., Elliott N.G., McMinn A. 28S rDNA evolution in the Eumalacostraca and the phylogenetic position of krill. Mol. Phylogenet. Evol. 2000, 17:26-36.
41. Karasawa H., Schweitzer C.E., Feldmann R.M. Phylogenetic analysis and revised classification of podotrematous Brachyura (Decapoda) including extinct and extant families. J. Crust. Biol. 2011, 31:523-565.
42. Karasawa H., Schweitzer C.E., Feldmann R.M. Phylogeny and systematics of extant and extinct lobsters. J. Crust. Biol. 2013, 33:78-123.
43. Kim W., Bae G.J. Nucleotide analysis of 18S rRNA and molecular phylogeny of the Korean decapods. Korean J. Zool. 1992, 35:30-86.
44. Kück P., Garcia F.H., Misof B., Meusemann K. Improved phylogenetic analyses corroborate a plausible position of Martialis heureka in the ant tree of life. PLoS ONE 2010, 6(6):e21031.
45. Lartillot N., Philippe H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 2004, 21:1095-1109.
46. Liu Y., Cui Z. Complete mitochondrial genome of the Chinese spiny lobster Panulirus stimpsoni (Crustacea: Decapoda): genome characterization and phylogenetic considerations. Mol. Biol. Rep. 2011, 38:403-410.
47. Lowe T.M., Eddy S.R. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucl. Acids Res. 1997, 25:955-964.
48. Madsen O., Scally M., Douady C.J., Kao D.J., Debry R.W., Adkins R., Amrine H.M., Stanhope M.J., Jong W.W., Springer M.S. Parallel adaptive radiations in two major clades of placental mammals. Nature 2001, 409:610-614.
49. Martin J.W., Abele L.G. Phylogenetic relationships of the genus Aegla (Decapoda: Anomura: Aeglidae), with comments on anomuran phylogeny. J. Crust. Biol. 1986, 6:576-616.
50. Masta S.E., Longhorn S.J., Boore J.L. Arachnid relationships based on mitochondrial genomes: Asymmetric nucleotide and amino acid bias affects phylogenetic analyses. Mol. Phylogenet. Evol. 2009, 50:117-128.
51. Miller A.D., Austin C.M. The complete mitochondrial genome of the mantis shrimp Harpiosquilla harpax, and a phylogenetic investigation of the Decapoda using mitochondrial sequences. Mol. Phylogenet. Evol. 2006, 38:565-574.
52. Misof B., Misof K. A Monte Carlo approach successfully identifies randomness in multiple sequence alignments: a more objective means of data exclusion. Syst. Biol. 2009, 58:21-34.
53. Morrison C.L., Harvey A.W., Lavery S., Tieu K., Huang Y., Cunningham C.W. Mitochondrial gene rearrangements confirm the parallel evolution of the crab-like body form. Proc. Roy. Soc. Lond. B 2002, 269:345-350.
54. Philippe H., Snell E.A., Bapteste E., Lopez P., Holland P.W., Casane D. Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol. Biol. Evol. 2004, 21:1740-1752.
55. Poore G.C.B. A phylogeny of the families of Thalassinidea (Crustacea: Decapoda) with keys to families and genera. Mem. Qld. Mus. 1994, 54:79-120.
56. Porter M.L., Pérez-Losada M., Crandall K.A. Model-based multi-locus estimation of decapod phylogeny and divergence times. Mol. Phylogenet. Evol. 2005, 37:355-369.
57. Regier J.C., Shultz J.W., Zwick A., Hussey A., Ball B., Wetzer R., Martin J.W., Cunningham C.W. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 2010, 463:1079-1083.
58. Reimann A., Richter S., Scholtz G. Phylogeny of the anomala (Crustacea, Decapoda, Reptantia) based on the ossicles of the foregut. Zool. Anz. 2011, 250:316-342.
59. Richter S., Scholtz G. Phylogenetic analysis of the Malacostraca (Crustacea) J. Zool. Syst. Evol. Res. 2001, 39:113-136.
60. Robles R., Tudge C.C., Dworschak P.C., Poore G.C.B., Felder D.L. Molecular phylogeny of the Thalassinidea based on nuclear and mitochondrial genes. Decapod Crustacean Phylogenetics (Crustacean Issues 18) 2009, 309-326. CRC Press, Boca Raton. J.W. Martin, D.L. Felder, K.A. Crandall (Eds.).
61. Rokas A., Williams B.L., King N., Carroll S.B. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003, 425:798-804.
62. Rota-Stabelli O., Kayal E., Gleeson D., Daub J., Boore J.L., Telford M.J., Pisani D., Blaxter M., Lavrov D.V. Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda. Genome Biol. Evol. 2010, 2:425-440.
63. Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M.A., Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 2000, 16:944-945.
64. Sakai K. The diphyletic nature of the infraorder Thalassinidea (Decapoda, Pleocyemata) as derived from the morphology of the gastric mill. Crustaceana 2004, 77:1117-1130.
65. Sandeman D., Scholtz G., Sandeman R. Brain evolution in decapod Crustacea. J. Exp. Zool. 1993, 295:112-133.
66. Scholtz G. Teloblasts in decapod embryos: an embryonic character reveals the monophyletic origin of freshwater crayfishes (Crustacea, Decapoda). Zool. Anz. 1993, 230:45-54.
67. Scholtz, G., 1995. Ursprung und Evolution der Flußkrebse (Crustacea, Astacida). Sitzber. naturforsch. Freunde Berlin (N.F.) 34, 93-115.
68. Scholtz G., McLay C.L. Is the Brachyura Podotremata a monophyletic group?. Decapod Crustacean Phylogenetics (Crustacean Issues 18) 2009, 417-435. CRC Press, Boca Raton. J.W. Martin, D.L. Felder, K.A. Crandall (Eds.).
69. Scholtz G., Richter S. Phylogenetic systematics of the reptantian Decapoda (Crustacea, Malacostraca). Zool. J. Lin. Soc. 1995, 113:289-328.
70. Schram F.R. Phylogeny of decapods: moving towards a consensus. Hydrobiologia 2001, 449:1-20.
71. Schram F.R., Dixon C.J. Decapod phylogeny: addition of fossil evidence to a robust morphological cladistic data set. Bull. Mizu. Fos. Mus. 2004, 31:1-19.
72. Spears T., Abele L.G., Kim W. The monophyly of brachyuran crabs: a phylogenetic study based on 18S rRNA. Syst. Biol. 1992, 41:446-461.
73. Stamatakis A., Hoover P., Rougemont J. A rapid bootstrap algorithm for the RAxML web-servers. Syst. Biol. 2008, 57:758-771.
74. Thompson J.D., Higgins D.G., Gibson T.J. Clustal-W improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weigh matrix choice. Nucl. Acids Res. 1994, 22:4673-4680.
75. Toon A., Finley M., Staples J., Crandall K.A. Decapod phylogenetics and molecular evolution. Decapod Crustacean Phylogenetics (Crustacean Issues 18) 2009, 15-30. CRC Press, Boca Raton. J.W. Martin, D.L. Felder, K.A. Crandall (Eds.).
76. Tsang L.M., Lin F.J., Chu K.H., Chan T.Y. Phylogeny of Thalassinidea (Crustacea, Decapoda) inferred from three rDNA sequences: implications for morphological evolution and superfamily classification. J. Zool. Syst. Evol. Res. 2008, 46:216-223.
77. Tsang L.M., Ma K.Y., Ahyong S.T., Chan T.Y., Chu K.H. Phylogeny of Decapoda using two nuclear protein-coding genes: origin and evolution of the Reptantia. Mol. Phylogenet. Evol. 2008, 48:359-368.
78. Tsang L.M., Chan T.-Y., Ahyong S.T., Chu K.H. Hermit to king, or hermit to all: multiple transitions to crab-like forms from hermit crab ancestors. Syst. Biol. 2011, 60:616-629.
79. Tshudy D., Babcock L.E. Morphology-based phylogenetic analysis of the clawed lobsters (family Nephopidae and the new family Chilenophoberidae). J. Crust. Biol. 1997, 17:253-263.
80. Tudge, C.C., 1995. Ultrastructure and Phylogeny of the spermatozoa of the infraorders Thalassinidea and Anomura (Decapoda, Crustacea). In: Jamieson, B.G.M., Ausio, J., Justine, J.-L. (Eds.), Advances in Spermatozoal Phylogeny and Taxonomy. Mém. Mus. Nat. Hist. nat. (Paris), 166, 251-263.
81. Tudge C.C., Cunningham C.W. Molecular phylogeny of the mud lobsters and mud shrimps (Crustacea: Decapoda: Thalassinidea) using nuclear 18s rDNA and mitochondrial 16s rDNA. Invert. Syst. 2002, 16:839-847.
82. von Sternberg R., Cumberlidge N. On the heterotreme-thoracotreme distinction in the Eubrachyura De Saint Laurent, 1980 (Decapoda: Brachyura). Crustaceana 2001, 74:321-338.
83. Wägele, J.W., Mayer, C., 2007. Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects. BMC Evol. Biol. 7, 1-24.
84. Wei S.-J., Shi M., Chen X.-X., Sharkey M.J., van Achterberg C., Ye G.-Y., He J.-H. New views on strand asymmetry in insect mitochondrial genomes. PloS One 2010, 5:9.
85. Xia X., Xie Z. DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 2001, 92:371-373.