SequenceMatrix: Concatenation software for the fast assembly of multi-gene datasets with character set and codon information

Cladistics

Volumn 27, Issue 2, 2011, Pages 171-180

  Vaidya, Gaurav ^a   Lohman, David J ^a,b   Meier, Rudolf ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b CITY COLLEGE OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATA SET; GENETIC ANALYSIS; SOFTWARE; TAXONOMY;

MALUS X DOMESTICA;

EID: 79952406380     PISSN: 07483007     EISSN: 10960031     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2010.00329.x     Document Type: Article

References (31)

1. Ang, Y., Puniamoorthy, N., Meier, R., 2008. Secondarily reduced foreleg armature in Perochaeta dikowi sp.n. (Diptera: Cyclorrhapha: Sepsidae) due to a novel mounting technique. Syst. Entomol. 33, 552-559.
2. Balke, M., Ribera, I., Hendrich, L., Miller, M.A., Sagata, K., Posman, A., Vogler, A.P., Meier, R., 2009. New Guinea highland origin of a widespread arthropod supertramp. Proc. R. Soc. Lond. B Biol. Sci. 276, 2359-2367.
3. Dunn, C.W., Hejnol, A., Matus, D.Q., Pang, K., Browne, W.E., Smith, S.A., Seaver, E., Rouse, G.W., Obst, M., Edgecombe, G.D., Sorensen, M.V., Haddock, S.H.D., Schmidt-Rhaesa, A., Okusu, A., Kristensen, R.M., Wheeler, W.C., Martindale, M.Q., Giribet, G., 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452, 745-749.
4. Goloboff, P.A., Farris, J.S., Nixon, K.S., 2008. TNT, a free program for phylogenetic analysis. Cladistics 24, 774-786.
5. Huang, D.W., Meier, R., Todd, P.A., Chou, L.M., 2009. More evidence for pervasive paraphyly in scleractinian corals: systematic study of Southeast Asian Faviidae (Cnidaria; Scleractinia) based on molecular and morphological data. Mol. Phylogenet. Evol. 50, 102-116.
6. Jones, M., Blaxter, M., 2006. TaxMan: a taxonomic database manager. BMC Bioinformatics 7, 536.
7. Kutty, S.N., Bernasconi, M.V., Sifner, F., Meier, R., 2007. Sensitivity analysis, molecular systematics and natural history evolution of Scathophagidae (Diptera: Cyclorrhapha: Calyptratae). Cladistics 23, 64-83.
8. Kutty, S.N., Pape, T., Pont, A., Wiegmann, B.M., Meier, R., 2008. The Muscoidea (Diptera: Calyptratae) are paraphyletic: evidence from four mitochondrial and four nuclear genes. Mol. Phylogenet. Evol. 49, 639-652.
9. Kutty, S.N., Pape, T., Wiegmann, B.M., Meier, R., 2010. Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine"s Fly. Syst. Entomol., in press, doi.
10. Laamanen, T.R., Meier, R., Miller, M.A., Hille, A., Wiegmann, B.M., 2005. Phylogenetic analysis of Themira (Sepsidae: Diptera): sensitivity analysis, alignment, and indel treatment in a multigene study. Cladistics 21, 258-271.
11. Lim, G.S., Hwang, W.S., Kutty, S.N., Meier, R., Grootaert, P., 2010. Mitochondrial and nuclear markers support the monophyly of Dolichopodidae and suggest a rapid origin of the subfamilies (Diptera: Empidoidea). Syst. Entomol. 35, 59-70.
12. Lohman, D.J., Peggie, D., Pierce, N.E., Meier, R., 2008. Phylogeography and genetic diversity of a widespread Old World butterfly, Lampides boeticus (Lepidoptera: Lycaenidae). BMC Evol. Biol. 8, 301.
13. Lohman, D.J., Ingram, K.K., Prawiradilaga, D.M., Winker, K., Sheldon, F.H., Moyle, R.G., Ng, P.K.L., Ong, P.S., Wang, L.K., Brailee, T.M., Astuti, D., Meier, R., 2010. Cryptic genetic diversity in "widespread" Southeast Asian bird species suggests that Philippine avian endemism is gravely underestimated. Biol. Conserv. 143, 1885-1890.
14. Maddison, D.R., Maddison, W.P., 2001. MacClade 4: Analysis of Phylogeny and Character Evolution. Sinauer Associates, Sunderland, MA.
15. Maddison, W.P., Maddison, D.R. 2009. Mesquite: a modular system for evolutionary analysis. Version 2.72.
16. Maddison, D.R., Swofford, D.L., Maddison, W.P., 1997. NEXUS: an extensible file format for systematic information. Syst. Biol. 46, 590-621.
17. Meier, R., Baker, R., 2002. A cladistic analysis of Diopsidae (Diptera) based on morphological and DNA sequence data. Insect Syst. Evol. 33, 325-336.
18. Meier, R., Wiegmann, B.M., 2002. A phylogenetic analysis of Coelopidae (Diptera) based on morphological and DNA sequence data. Mol. Phylogenet. Evol. 25, 393-407.
19. Meier, R., Kwong, S., Vaidya, G., Ng, P.K.L., 2006. DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst. Biol. 55, 715-728.
20. Meier, R., Zhang, G.Y., Ali, F., 2008. The use of mean instead of smallest interspecific distances exaggerates the size of the "barcoding gap" and leads to misidentification. Syst. Biol. 57, 809-813.
21. Nixon, K.C., Wheeler, Q.D., 1992. Extinction and the origin of species. In: Novacek, M.J., Wheeler, Q.D. (Eds.), Extinction and Phylogeny. Columbia University Press, New York, pp. 117-143.
22. Petersen, F.T., Meier, R., Kutty, S.N., Wiegmann, B.M., 2007. The phylogeny and evolution of host choice in the Hippoboscoidea (Diptera) as reconstructed using four molecular markers. Mol. Phylogenet. Evol. 45, 111-122.
23. Puniamoorthy, N., Su, K.F.Y., Meier, R., 2008. Bending for love: losses and gains of sexual dimorphisms are strictly correlated with changes in the mounting position of sepsid flies (Sepsidae: Diptera). BMC Evol. Biol. 8, 155.
24. Puniamoorthy, N., Ismail, M.R.B., Tan, D.S.H., Meier, R., 2009. From kissing to belly stridulation: comparative analysis reveals surprising diversity, rapid evolution, and much homoplasy in the mating behaviour of 27 species of sepsid flies (Diptera: Sepsidae). J. Evol. Biol. 22, 2146-2156.
25. Roure, B., Rodriguez-Ezpeleta, N., Philippe, H., 2007. SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics. BMC Evol. Biol. 7, Suppl. 1, S2.
26. Smith, S.A., Dunn, C.W., 2008. Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 24, 715-716.
27. Su, K.F., Meier, R., Jackson, R.R., Harland, D.P., Li, D., 2007. Convergent evolution of eye ultrastructure and divergent evolution of vision-mediated predatory behaviour in jumping spiders. J. Evol. Biol. 20, 1478-1489.
28. Su, F.-Y.K., Kutty, S.N., Meier, R., 2008. Morphology versus molecules: the phylogenetic relationships of Sepsidae (Diptera: Cyclorrhapha) based on morphology and DNA sequence data from ten genes. Cladistics 24, 902-916.
29. Swofford, D.L., 2004. PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods). Sinauer Associates, Inc., Sunderland, MA.
30. Wowor, D., Muthu, V., Meier, R., Balke, M., Cai, Y.X., Ng, P.K.L., 2009. Evolution of life history traits in Asian freshwater prawns of the genus Macrobrachium (Crustacea: Decapoda: Palaemonidae) based on multilocus molecular phylogenetic analysis. Mol. Phylogenet. Evol. 52, 340-350.
31. Yeo, D.C.J., Shih, H.T., Meier, R., Ng, P.K.L., 2007. Phylogeny and biogeography of the freshwater crab genus Johora (Crustacea: Brachyura: Potamidae) from the Malay Peninsula, and the origins of its insular fauna. Zool. Scr. 36, 255-269.