Phylogeny and biogeography of Triportheidae (Teleostei: Characiformes) based on molecular data

Molecular Phylogenetics and Evolution - Tập 96 - Trang 130-139 - 2016
T.C. Mariguela1, F.F. Roxo2, F. Foresti2, C. Oliveira2
1Departamento de Zoologia, Instituto de Biociências, Univ. Estadual Paulista – UNESP, Rio Claro, São Paulo, Brazil
2Departamento de Morfologia, Instituto de Biociências, Univ. Estadual Paulista – UNESP, Botucatu, São Paulo, Brazil

Tài liệu tham khảo

Abe, 2014, Systematic and historical biogeography of the Bryconidae (Ostariophysi: Characiformes) suggesting a new rearrangement of its genera and an old origin of Mesoamerican ichthyofauna, BMC Evol. Biol., 14, 152, 10.1186/1471-2148-14-152 Abe, 2013, Multilocus molecular phylogeny of Gasteropelecidae (Ostariophysi: Characiformes) reveals the existence of an unsuspected diversity, Mol. Phyl. Evol., 69, 1209, 10.1016/j.ympev.2013.07.005 Akaike, 1973, Information theory and an extension of the maximum likelihood principle, vol. 6, 267 Albert, 2011, Major biogeographic and phylogenetic patterns, 21 Arroyave, 2011, Phylogenetic relationships and the temporal context for the diversification of African characins of the family Alestidae (Ostariophysi: Characiformes): evidence from DNA sequence data, Mol. Phyl. Evol., 60, 385, 10.1016/j.ympev.2011.04.016 Assine, 2004, A bacia sedimentar do Pantanal Mato-Grossense, 61 Castro, 1990, Moojenichthys Miranda-Ribeiro (Pisces: Ostariophysi: Characidae), a phylogenetic reapraisal and redescription, Proc. Biol. Soc. Wash., 103, 525 Drummond, 2012, Bayesian phylogenetics with BEAUti and the BEAST 1.7, Mol. Biol. Evol., 29, 1969, 10.1093/molbev/mss075 Edgar, 2004, MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, 5, 113, 10.1186/1471-2105-5-113 Eschmeyer, W.N., Fong, J.D., 2015. Species by Family/Subfamily. <http://research.calacademy.org/research/ichthyology/catalog/SpeciesByFamily.asp> (electronic version accessed 10.07.15). Gregory, 1938, The phylogeny of the characin fishes, Zoologica, 23, 319 Hall, 1999, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucl. Acids Symp. Ser., 41, 95 Hoorn, 1995, Andean Tectonics as a Cause for changing drainage patterns in Miocene northern South-America, Geology, 23, 237, 10.1130/0091-7613(1995)023<0237:ATAACF>2.3.CO;2 Hoorn, 2010, Amazonia through time: andean uplift, climate change, landscape evolution, and biodiversity, Science, 33, 927, 10.1126/science.1194585 Landis, 2013, Bayesian analysis of biogeography when the number of areas is large, Syst. Biol., 10.1093/sysbio/syt040 Langeani, 2007, Diversidade da ictiofauna do Alto Rio Paraná: composição atual e perspectivas futura, Biota Neotrop, 7, 181, 10.1590/S1676-06032007000300020 Li, 2008, Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci, Syst. Biol., 57, 519, 10.1080/10635150802206883 Lima, 2011, Peixes da Estação Ecológica Serra Geral do Tocantins, bacias dos Rios Tocantins e São Francisco, com observações sobre as implicações biogeográficas das “águas emendadas” dos Rios Sapão e Galheiros, Biota Neotrop., 11, 231, 10.1590/S1676-06032011000100024 Lima, 1985, Etude palynilogique de la formation Tremembé, Tertiaire du Bassin de Taubaté, (Etat de São Paulo, Bresil), d’apres les echantillons du sondage n-42 du CNP. Coletânea de Trabalhos Paleontológicos, MME-DNPM, Sér. Zool., 27, 379 Lima, 2011, Continental-scale tectonic controls of biogeography and ecology, 145 Lopez-Fernández, 2011, Paleogene radiations, 105 Lundberg, 1998, The stage for Neotropical fish diversification: a history of tropical South American rivers, 13 Malabarba, 1998, Phylogeny of fossil Characiformes and paleobiogeography of the Tremembé Formation, São Paulo, Brazil, 69 Malabarba, 2004, Revision of the Neotropical genus Triportheus Cope, 1872 (Characiformes, Characidae), Neotrop. Ichthyol., 2, 167, 10.1590/S1679-62252004000400001 Mariguela, 2013, Historical biogeography and cryptic diversity in the Callichthyinae (Siluriformes, Callichthyidae), J. Zool. Syst. Evol. Res., 51, 308, 10.1111/jzs.12029 Matzke, 2013, Probabilistic historical biogeography: new models for founderevent speciation, imperfect detection, and fossils allow improved accuracy and model-testing, Front. Biogeogr., 5, 242, 10.21425/F55419694 Matzke, N.J., 2013b. BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts. Release R package version 0.2.2-2. <http://CRAN.R-project.org/package=BioGeoBEARS>. Miller, M.A., Pfeiffer, W., Schwartz, T., 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proc. Gat. Comp. Environ. Workshop (GCE), New Orleans, LA, pp. 1–8. Mirande, 2010, Phylogeny of the family Characidae (Teleostei: Characiformes): from characters to taxonomy, Neotrop. Ichthyol., 8, 385, 10.1590/S1679-62252010000300001 Oliveira, 2011, Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling, BMC Evol. Biol., 11, 275, 10.1186/1471-2148-11-275 Parham, 2012, Best practices for justifying fossil calibrations, Syst. Biol., 61, 346, 10.1093/sysbio/syr107 Pavanelli, 2007, Fishes from the Corumbá Reservoir, Paranaíba River drainage, upper Paraná River basin, State of Goiás, Brazil, Check List, 3, 58, 10.15560/3.1.58 Posada, 2004, Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests, Syst. Biol., 53, 793, 10.1080/10635150490522304 Rambaut, A., Drummond, A.J., 2007a. Tracer v1.5, Available from <http://beast.bio.ed.ac.uk/Tracer>. Rambaut, A., Drummond, A.J., 2007b. TreeAnnotator v1.8.0. Available from <http://beast.bio.ed.ac.uk/TreeAnnotator>. Ramos, 2014, Ichthyofauna of the Parnaíba River Basin, Northeastern Brazil, Biota Neotrop., 14, 1, 10.1590/S1676-06020140039 Ree, 2008, Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis, Syst. Biol., 57, 4, 10.1080/10635150701883881 Ribeiro, 2013, Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian Amazonian palaeoplateau in the area of the present day Pantanal Wetland, Neotrop. Ichthyol., 11, 319, 10.1590/S1679-62252013000200010 Riccomini, 1991, Estratigrafia e ambientes de sedimentação da porção central da Bacia de Taubaté, Congresso Brasileiro de Paleontologia, 12, 1 Smith, 2007, Fish, Sorocaba river sub-basin, state of São Paulo, Brazil, Check List, 3, 282, 10.15560/3.3.282 Soares, P.C., Assine, M.L., Rabelo, L., 1998. The Pantanal Basin: Recent tectonics, relationships to the Transbrasiliano Lineament. Anais IX Simpósio Brasileiro de Sensoriamento Remoto, Santos: INPE, pp. 459–469. Soria, 1989, Nuevos restos de mamiferos de la Cuenca de Taubaté, Estado de São Paulo, Brasil, An. Acad. Brasil. Cienc., 61, 157 Stamatakis, 2006, RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, 22, 2688, 10.1093/bioinformatics/btl446 Stamatakis, 2008, A rapid bootstrap algorithm for the RAxML web servers, Syst. Biol., 57, 758, 10.1080/10635150802429642 Tamura, 2011, MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol. Biol. Evol., 28, 2731, 10.1093/molbev/msr121 Tavaré, 1986, Some probabilistic and statistical problems in the analysis of DNA sequences, Lect. Math. Life Sci., 17, 57 Vari, 1988, The Curimatidae, a lowland Neotropical fish family (Pisces: Characiformes); distribution, endemism, and phylogenetic biogeography, 343 Vari, 1989, Systematics of the Neotropical characiform genus Psectrogaster Eigenmann and Eigenmann (Pisces, Characiformes), Smithsonian Contribut. Zool., 481, 1 Vari, 1998, Neotropical ichthyology: an overview, 1 Weitzman, 1954, The osteology and relationships of the South American characoid fishes of the subfamily Gasteropelecinae, Stanford Ichthyol. Bull., 4, 213 Xia, 2009, Assessing substitution saturation with DAMBE, 615 Xia, 2001, DAMBE: Data analysis in molecular biology and evolution, J. Heredity, 92, 371, 10.1093/jhered/92.4.371 Xia, 2003, An index of substitution saturation and its application, Mol. Phyl. Evol., 26, 1, 10.1016/S1055-7903(02)00326-3