Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Lin, Feng Jiau ^a   Liu, Yuan ^b   Sha, Zhongli ^b   Tsang, Ling M ^c   Chu, Ka H ^c   Chan, Tin Yam ^d   Liu, Ruiyu ^b   Cui, Zhaoxia ^b  

^a NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

^b INSTITUTE OF OCEANOLOGY   (China)

^c CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

^d NATIONAL TAIWAN OCEAN UNIVERSITY   (Taiwan)

Author keywords

Evolution; Gene order; Mitochondrial genome; Mud shrimps; Phylogenetics

Indexed keywords

RIBOSOME RNA; TRANSFER RNA;

AMINO ACID SEQUENCE; ARTICLE; AUSTINOGEBIA EDULIS; CONTROLLED STUDY; CRUSTACEA; DNA BASE COMPOSITION; EVOLUTION; GENE LOCATION; GENE ORDER; GENE REARRANGEMENT; MITOCHONDRIAL GENOME; MONOPHYLY; NEAXIUS GLYPTOCERCUS; NIHONOTRYPAEA THERMOPHILUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PCG GENE; PHYLOGENY; SPECIES DIFFERENTIATION; THALASSINA KELANANG; UPOGEBIA MAJOR;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BIOLOGICAL EVOLUTION; DECAPODA (CRUSTACEA); DNA, MITOCHONDRIAL; GENES, RRNA; GENOME, MITOCHONDRIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL; RNA, TRANSFER; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA;

CRUSTACEA; DECAPODA (CRUSTACEA); NEAXIUS GLYPTOCERCUS; NIHONOTRYPAEA; PANCRUSTACEA; THALASSINA; THALASSINIDEA; UPOGEBIA MAJOR; UPOGEBIIDAE;

EID: 84869051904     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-631     Document Type: Article

References (99)

1. De Grave S, Deam Pentcheff N, Ahyong ST, Chan TY, Crandall KA, Dworschak PC, Felder DL, Feldmann RM, Fransen CHJM, Goulding LYD, et al. A classification of living and fossil genera of decapod crustaceans. The Raffles Bulletin of Zoology 2009, 21:1-109.
2. Tudge CC. Phylogeny of the Anomura (Decapoda, Crustacea): Spermatozoa and spermatophore morphological evidence. Contrib Zool 1997, 67(2):125-141.
3. Morrison CL, Harvey AW, Lavery S, Tieu K, Huang Y, Cunningham CW. Mitochondrial gene rearrangements confirm the parallel evolution of the crab-like form. P Roy Soc Lond B Bio 2002, 269(1489):345-350.
4. Tsang LM, Ma KY, Ahyong ST, Chan TY, Chu KH. Phylogeny of Decapoda using two nuclear protein-coding genes: origin and evolution of the Reptantia. Mol Phylogenet Evol 2008, 48(1):359-368. 10.1016/j.ympev.2008.04.009, 18501643.
5. Chu KH, Tsang LM, Ma KY, Chan TY, Ng PKL. Decapod phylogeny: what can protein-coding genes tell us. Decapod Crustacean Phylogenetics 2009, 89-99. New York: CRC Press, Martin JW, Crandall KA, Felder DL.
6. Bracken HD, Toon A, Felder DL, Martin JW, Finley M, Rasmussen J, Palero F, Crandall KA. The decapod tree of life: compiling the data and moving toward a consensus of decapod evolution. Arthropod Systematics & Phylogeny 2009, 67(1):99-116.
7. Bracken HD, De Grave S, Toon A, Felder DL, Crandall KA. Phylogenetic position, systematic status, and divergence time of the Procarididea (Crustacea: Decapoda). Zoologica Scripta 2010, 39(2):198-212.
8. Robles R, Tudge CC, Dworschak PC, Poore GCB, Felder DL. Molecular phylogeny of the Thalassinidea based on nuclear and mitochondrial genes. Decapod Crustacean Phylogenetics 2009, 309-326. New York: CRC Press, Martin JW, Crandall KA, Felder DL.
9. Poore GCB. A phylogeny of the families of Thalassinidea (Crustacea: Decapoda) with keys to families and genera. Memoirs of the Museum of Victoria 1994, 54:79-120.
10. Scholtz G, Richter S. Phylogenetic systematics of the reptantian Decapoda (Crustacea, Malacostraca). Zool J Linn Soc-Lond 1995, 113(3):289-328.
11. Crandall KA, Harris DJ, Fetzner JW. The monophyletic origin of freshwater crayfish estimated from nuclear and mitochondrial DNA sequences. P Roy Soc Lond B Bio 2000, 267(1453):1679-1686.
12. Schram FR. Phylogeny of decapods: moving towards a consensus. Hydrobiologia 2001, 449(1-3):1-20.
13. Martin JW, Davis GE. An updated classification of the recent crustacea. Natural History Museum of Los Angeles County: Science Series 2001, 39:1-124.
14. Dixon CJ, Ahyong ST, Schram FR. A new hypothesis of decapod phylogeny. Crustaceana 2003, 76:935-975.
15. Ahyong ST, O'Meally D. Phylogeny of the Decapoda reptantia: Resolution using three molecular loci and morphology. Raffles B Zool 2004, 52(2):673-693.
16. Schram FR, Dixon CJ. Decapod phylogeny: addition of fossil evidence to a robust morphological cladistic data set. Bulletin of the Mizunami Fossil Museum 2004, 31:1-19.
17. Borradaile LA. On the classification of the Thalassinidea. The Annals and Magazine of Natural History, series 7 1903, 12:534-551.
18. Borradaile LA. On the classification of the decapod crustaceans. The Annals and Magazine of Natural History, series 7 1907, 19:457-486.
19. De Man JG. The Decapoda of the Siboga-expedition. Part 7. The Thalassinidae and Callianassidae collected by the Siboga-expedition with some remarks on the Laomediidae. Siboga Expéditie 1928, 39(A6):1-187.
20. Bouvier E-L. Décapodes marcheurs. Faune de France 1940, 37:1-407.
21. Zariquiey-Álvarez R. Crustáceos decápodos ibéricos. Investig Pesq 1968, 32:1-510.
22. Porter ML, Perez-Losada M, Crandall KA. Model-based multi-locus estimation of decapods phylogeny and divergence times. Mol Phylogenet Evol 2005, 37:355-369. 10.1016/j.ympev.2005.06.021, 16112880.
23. Boisselier-Dubayle MC, Bonillo C, Cruaud C, Couloux A, de Forges BR, Vidal N. The phylogenetic position of the 'living fossils' Neoglyphea and Laurentaeglyphea (Decapoda: Glypheidea). Comptes Rendus Biologies 2010, 333(10):755-759. 10.1016/j.crvi.2010.08.007, 20965445.
24. Holthuis LB. FAO species catalog. Vol. 13. Marine lobsters of the world. An annotated and illustrated catalogue of species of interest to fisheries known to date. FAO Fisheries Synopsis. vol. 125 1991, 292. Rome: Food and Agriculture Organization of the United Nations.
25. Gurney R. Larvae of decapod crustacea. Part 5. Nephropsidea and thalassinidea. Discovery Reports 1938, 17:291-344.
26. Gurney R. Larvae of decapod Crustacea 1942, London: Ray Society.
27. De Saint Laurent M. Versune nouvelle classification des Crustaces Decapodes Reptantia. Bulletin de I'Office National des Peches Republique Tunisienne, Ministere de UAgriculture 1979, 3:15-31.
28. De Saint Laurent M. Sur la classification et la phylogenie des Thalassinides: definitions de la superfamille des Axioidea, de la sous-famille des Thomassiniinae et de deux genres nouveaux (Crustacea Decapoda). C R Hebd Acad Sci 1979, 288:1395-1397.
29. Tudge C. Ultrastructure and phylogeny of the spermatozoa of the infraorders Thalassinidea and Anomura (Decapoda, Crustacea). Advances in Spermatozoal Phylogeny and Taxonomy 1995, 251-263. Paris: Mémoires du Muséum National d'Histoire Naturelle, Jamieson BGM, Ausio J, Justin JL, vol. 166.
30. Tsang LM, Lin FJ, Chu KH, Chan TY. Phylogeny of Thalassinidea (Crustacea, Decapoda) inferred from three rDNA sequences: implications for morphological evolution and superfamily classification. J Zool Syst Evol Res 2008, 46(3):216-223.
31. Harrison MK, Crespi BJ. Phylogenetics of Cancer crabs (Crustacea: Decapoda: Brachyura). Mol Phylogenet Evol 1999, 12(2):186-199. 10.1006/mpev.1998.0608, 10381321.
32. Ptacek MB, Sarver SK, Childress MJ, Herrnkind WF. Molecular phylogeny of the spiny lobster genusPanulirus(Decapoda: Palinuridae). Mar Freshwater Res 2001, 52(8):1037-1047.
33. Munasinghe DHN, Burridge CP, Austin CM. Molecular phylogeny of the spiny lobster genusPanulirus(Decapoda: Palinuridae). Biol J Linn Soc 2004, 81(4):553-563.
34. Shih HT, Ng PKL, Schubart CD, Chang HW. Phylogeny and phylogeography of the genus Geothelphusa (Crustacea: Decapoda, Brachyura, Potamidae) in southwestern Taiwan based on two mitochondrial genes. Zool Sci 2007, 24(1):57-66. 10.2108/zsj.24.57, 17409717.
35. Roe AD, Sperling FAH. Patterns of evolution of mitochondrial cytochrome c oxidase I and II DNA and implications for DNA barcoding. Mol Phylogenet Evol 2007, 44(1):325-345. 10.1016/j.ympev.2006.12.005, 17270468.
36. Boore JL. Animal mitochondrial genomes. Nucleic Acids Res 1999, 27(8):1767-1780. 10.1093/nar/27.8.1767, 148383, 10101183.
37. Kilpert F, Podsiadlowski L. The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features. BMC Genomics 2006, 7:241-258. 10.1186/1471-2164-7-241, 1590035, 16987408.
38. Gissi C, Iannelli F, Pesole G. Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity 2008, 101(4):301-320. 10.1038/hdy.2008.62, 18612321.
39. Wilson AC, Cann RL, Carr SM, George M, Gyllensten UB, Helmbychowski KM, Higuchi RG, Palumbi SR, Prager EM, Sage RD, et al. Mitochondrial DNA and two perspectives on evolutionary genetics. Biol J Linn Soc 1985, 26:375-400.
40. Boore JL, Collins TM, Stanton D, Daehler LL, Brown WM. Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature 1995, 376(6536):163-165. 10.1038/376163a0, 7603565.
41. Avise JC. Phylogeography: The history and formation of species 2000, Cambridge, MA: Harvard Univ Press.
42. Boore JL, Macey JR, Medina M. Sequencing and comparing whole mitochondrial genomes of animals. Molecular Evolution: Producing the Biochemical Data, Part B 2005, 395:311-348.
43. Cui ZX, Liu YA, Li CP, Chu KH. Species delineation in Pampus (Perciformes) and the phylogenetic status of the Stromateoidei based on mitogenomics. Mol Biol Rep 2011, 38(2):1103-1114. 10.1007/s11033-010-0207-y, 20574712.
44. Yamauchi MM, Miya MU, Machida RJ, Nishida M. PCR-based approach for sequencing mitochondrial genomes of decapod crustaceans, with a practical example from kuruma prawn (Marsupenaeus japonicus). Mar Biotechnol 2004, 6(5):419-429. 10.1007/s10126-003-0036-2, 15791487.
45. Elson JL, Lightowlers RN. Mitochondrial DNA clonality in the dock: can surveillance swing the case?. Trends Genet 2006, 22(11):603-607. 10.1016/j.tig.2006.09.004, 16979783.
46. Qian G, Zhao Q, Wang AN, Zhu LIN, Zhou K, Sun H. Two new decapod (Crustacea, Malacostraca) complete mitochondrial genomes: bearings on the phylogenetic relationships within the Decapoda. Zool J Linn Soc-Lond 2011, 162(3):471-481.
47. Boore JL, Brown WM. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr Opin Genet Dev 1998, 8(6):668-674. 10.1016/S0959-437X(98)80035-X, 9914213.
48. Dowton M. Relationships among the cyclostome braconid (Hymenoptera: Braconidae) subfamilies inferred from a mitochondrial tRNA gene rearrangement. Mol Phylogenet Evol 1999, 11(2):283-287. 10.1006/mpev.1998.0580, 10191072.
49. Simon C, Buckley TR, Frati F, Stewart JB, Beckenbach AT. Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annu Rev Ecol Evol S 2006, 37:545-579.
50. Kim S, Kim J, Choi HG, Park JK, Min GS. Complete mitochondrial genome of the northern mauxia shrimp Acetes chinensis (Decapoda, Dendrobranchiata, Sergestoidae). Mitochondrial DNA 2012, 23(1):28-30. 10.3109/19401736.2011.643878, 22295863.
51. Kim S, Park MH, Jung JH, Ahn DH, Sultana T, Park JK, Choi HG, Min GS. The mitochondrial genomes of Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae): the phylogenetic implications for Reptantia. Zoologica Scripta 2012, 41(3):281-292.
52. Shi H, Liu R, Sha Z, Ma J. Complete mitochondrial DNA sequence of Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) and a novel tRNA gene cluster. Marine Genomics 2012, 6:7-15.
53. Kim S, Kim T, Choi HG, Park JK, Ahn DH, Min GS. The complete mitochondrial genome of the Japanese mud shrimp Upogebia major (Crustacea, Decapoda). Mitochondrial DNA 2011, 22(4):94-96. 10.3109/19401736.2011.624609, 22040075.
54. Wolstenholme DR. Animal mitochondrial DNA: Structure and Evolution. Int Rev Cytol 1992, 141:173-216.
55. Boore JL, Lavrov DV, Brown WM. Gene translocation links insects and crustaceans. Nature 1998, 392(6677):667-668. 10.1038/33577, 9565028.
56. Sun H, Zhou K, Song D. Mitochondrial genome of the Chinese mitten crab Eriocheir japonica sinenesis (Brachyura: Thoracotremata: Grapsoidea) reveals a novel gene order and two target regions of gene rearrangements. Gene 2005, 349:207-217.
57. Yang JS, Nagasawa H, Fujiwara Y, Tsuchida S, Yang WJ. The complete mitochondrial genome sequence of the hydrothermal vent galatheid crab Shinkaia crosnieri (Crustacea: Decapoda: Anomura): a novel arrangement and incomplete tRNA suite. BMC Genomics 2008, 9:257. 10.1186/1471-2164-9-257, 2442616, 18510775.
58. Ki JS, Dahms HU, Hwang JS, Lee JS. The complete mitogenome of the hydrothermal vent crab Xenograpsus testudinatus (Decapoda, Brachyura) and comparison with brachyuran crabs. Comp Biochem Physiol Part D Genomics Proteomics 2009, 4(4):290-299. 10.1016/j.cbd.2009.07.002, 20403751.
59. Liu Y, Cui Z. The complete mitochondrial genome of the mantid shrimp Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda): Novel non-coding regions features and phylogenetic implications of the Stomatopoda. Comp Biochem Physiol Part D Genomics Proteomics 2010, 5(3):190-198. 10.1016/j.cbd.2010.04.001, 20510661.
60. Cook CE, Yue QY, Akam M. Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic. Proceedings of the Royal Society B-Biological Sciences 2005, 272(1569):1295-1304.
61. Yamauchi MM, Miya MU, Nishida M. Complete mitochondrial DNA sequence of the Japanese spiny lobster,Panulirus japonicus(Crustacea: Decapoda). Gene 2002, 295(1):89-96. 10.1016/S0378-1119(02)00824-7, 12242015.
62. 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(1):403-410. 10.1007/s11033-010-0122-2, 20352347.
63. Boore JL. The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals. Comparative genomics, computational biology series Volume 1 2000, 133-147. Kluwer, Dordrecht: Academic Publishers, Sankoff D, Nadeau J.
64. Lavrov DV, Boore JL, Brown WM. Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: Duplication and nonrandom loss. Mol Biol Evol 2002, 19(2):163-169. 10.1093/oxfordjournals.molbev.a004068, 11801744.
65. Lunt DH, Hyman BC. Animal mitochondrial DNA recombination. Nature 1997, 387(6630):247. 10.1038/387247a0, 9153388.
66. Shao RF, Barker SC. The highly rearranged mitochondrial genome of the plague thrips,Thrips imaginis(Insecta: thysanoptera): Convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes. Mol Biol Evol 2003, 20(3):362-370. 10.1093/molbev/msg045, 12644556.
67. Wang MX, Sun S, Li CL, Shen X. Distinctive mitochondrial genome of Calanoid copepodCalanus sinicuswith multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies. BMC Genomics 2011, 12:73. 10.1186/1471-2164-12-73, 3041745, 21269523.
68. Higgs PG, Jameson D, Jow H, Rattray M. The evolution of tRNA-Leu genes in animal mitochondrial genomes. J Mol Evol 2003, 57(4):435-445. 10.1007/s00239-003-2494-6, 14708576.
69. Krebes L, Bastrop R. The mitogenome of Gammarus duebeni (Crustacea Amphipoda): A new gene order and non-neutral sequence evolution of tandem repeats in the control region. Comp Biochem Phys D 2012, 7(2):201-211.
70. Ito A, Aoki MN, Yokobori S, Wada H. The complete mitochondrial genome of Caprella scaura (Crustacea, Amphipoda, Caprellidea), with emphasis on the unique gene order pattern and duplicated control region. Mitochondrial DNA 2010, 21(5):183-190. 10.3109/19401736.2010.517834, 20958227.
71. Segawa RD, Aotsuka T. The mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Crustacea: Brachyura): Evidence for its evolution via gene duplication. Gene 2005, 355:28-39.
72. Tavares C, Serejo C, Martin JW. A preliminary phylogenetic anaylsis of the Dendrobranchiata based on morphological characters. Decapod Crustacean Phylogenetics 2009, 261-279. London, New York: CRC Press, Taylor & Francis Group, Martin JW, Crandall KA, Felder DL, Boca R.
73. Tsang LM, Chan TY, Ahyong ST, Chu KH. Hermit to king, or hermit to all: multiple transitions to crab-like forms from hermit crab ancestors. Syst Biol 2011, 60(5):616-629. 10.1093/sysbio/syr063, 21835822.
74. 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(5):294-299.
75. Lavrov DV, Brown WM, Boore JL. Phylogenetic position of the Pentastomida and (pan)crustacean relationships. P Roy Soc Lond B Bio 2004, 271(1538):537-544.
76. Schubart CD, Neigel JE, Felder DL. Use of the mitochondrial 16S rRNA gene for phylogenetic and population studies of Crustacea. Crustacean Iss 2000, 12:817-830.
77. Boore JL, Brown WM. Mitochondrial genomes of Galathealinum, Helobdella, and Platynereis: Sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa. Mol Biol Evol 2000, 17(1):87-106. 10.1093/oxfordjournals.molbev.a026241, 10666709.
78. Hunter RL, Webb MS, Iliffe TM, Bremer JRA. Phylogeny and historical biogeography of the cave-adapted shrimp genus Typhlatya (Atyidae) in the Caribbean Sea and western Atlantic. J Biogeogr 2008, 35(1):65-75.
79. Podsiadlowski L, Bartolomaeus T. Organization of the mitochondrial genome of mantis shrimp Pseudosquilla ciliata (Crustacea: Stomatopoda). Mar Biotechnol 2005, 7(6):618-624. 10.1007/s10126-005-0017-8, 16088353.
80. Peregrino-Uriarte AB, Varela-Romero A, Muhlia-Almazan A, Anduro-Corona I, Vega-Heredia S, Gutierrez-Millan LE, De la Rosa-Velez J, Yepiz-Plascencia G. The complete mitochondrial genomes of the yellowleg shrimp Farfantepenaeus californiensis and the blue shrimp Litopenaeus stylirostris (Crustacea: Decapoda). Comp Biochem Physiol Part D Genomics Proteomics 2009, 4(1):45-53. 10.1016/j.cbd.2008.10.003, 20403743.
81. Miya M, Pietsch TW, Orr JW, Arnold RJ, Satoh TP, Shedlock AM, Ho HC, Shimazaki M, Yabe M, Nishida M. Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspective. BMC Evol Biol 2010, 10:58. 10.1186/1471-2148-10-58, 2836326, 20178642.
82. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8(3):186-194.
83. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998, 8(3):175-185.
84. Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res 1998, 8:195-202.
85. Wyman SK, Jansen RK, Boore JL. Automatic annotation of organellar genomes with DOGMA. Bioinformatics 2004, 20(17):3252-3255. 10.1093/bioinformatics/bth352, 15180927.
86. Lowe TM, Eddy SR. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25(5):955-964. 146525, 9023104.
87. Lupi R, de Meo PD, Picardi E, D'Antonio M, Paoletti D, Castrignano T, Pesole G, Gissi C. MitoZoa: A curated mitochondrial genome database of metazoans for comparative genomics studies. Mitochondrion 2010, 10(2):192-199. 10.1016/j.mito.2010.01.004, 20080208.
88. Bernt M, Merkle D, Ramsch K, Fritzsch G, Perseke M, Bernhard D, Schlegel M, Stadler PF, Middendorf M. CREx: inferring genomic rearrangements based on common intervals. Bioinformatics 2007, 23(21):2957-2958. 10.1093/bioinformatics/btm468, 17895271.
89. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The ClustalX windows interface flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25:4876-4882. 10.1093/nar/25.24.4876, 147148, 9396791.
90. Xia XH, Xie Z, Salemi M, Chen L, Wang Y. An index of substitution saturation and its application. Mol Phylogenet Evol 2003, 26(1):1-7. 10.1016/S1055-7903(02)00326-3, 12470932.
91. Xia X, Xie Z. DAMBE software package for data analysis in molecular biology and evolution. J Hered 2001, 92:371-373. 10.1093/jhered/92.4.371, 11535656.
92. Lartillot N, Lepage T, Blanquart S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 2009, 25(17):2286-2288. 10.1093/bioinformatics/btp368, 19535536.
93. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22(21):2688-2690. 10.1093/bioinformatics/btl446, 16928733.
94. Posada D. jModelTest: phylogenetic model averaging. Mol Biol Evol 2008, 25(7):1253-1256. 10.1093/molbev/msn083, 18397919.
95. Abascal F, Zardoya R, Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 2005, 21(9):2104-2105. 10.1093/bioinformatics/bti263, 15647292.
96. Lartillot N, Philippe H. A bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 2004, 21(6):1095-1109. 10.1093/molbev/msh112, 15014145.
97. Lartillot N, Brinkmann H, Philippe H. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol 2007, 7(1):S4. 10.1186/1471-2148-7-S1-S4, 1963479, 17767732.
98. Shimodaira H, Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 2001, 17(12):1246-1247. 10.1093/bioinformatics/17.12.1246, 11751242.
99. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst Biol 2002, 51(3):492-508. 10.1080/10635150290069913, 12079646.