Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci

Alfaro, 2006, The posterior and the prior in Bayesian phylogenetics, Annu. Rev. Ecol. Evol. Syst., 37, 19, 10.1146/annurev.ecolsys.37.091305.110021 Ane, 2007, Bayesian estimation of concordance among gene trees, Mol. Biol. Evol., 24, 412, 10.1093/molbev/msl170 Bi, 2010, Time and time again: unisexual salamanders (genus Ambystoma) are the oldest unisexual vertebrates, BMC Evol. Biol., 10, 238, 10.1186/1471-2148-10-238 Bogart, 2003, Genetics and systematics of hybrid species, 109 Camargo, 2012, Accuracy and precision of species trees: effects of locus, individual, and base pair sampling on inference of species trees in lizards of the Liolaemus darwinii Group (Squamata, Liolaemidae), Syst. Biol., 61, 272, 10.1093/sysbio/syr105 Cronn, 2002, PCR-mediated recombination in amplification products derived from polyploid cotton, Theor. Appl. Genet., 104, 482, 10.1007/s001220100741 Drummond, 2007, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evol. Biol., 7, 214, 10.1186/1471-2148-7-214 Drummond, 2006, Relaxed phylogenetics and dating with confidence, PLoS Biol., 4, e88, 10.1371/journal.pbio.0040088 Drummond, A.J.A.B., Buxton, S., Cheung, M., Cooper, A., Duran, C., Field, M., Heled, J., Kearse, M., Markowitz, S., Moir, R., Stones-Havas, S., Sturrock, S., Thierer, T., Wilson, A., 2010. Geneious v5.3. <http://www.geneious.com>. Drummond, 2012, Bayesian Phylogenetics with BEAUti and the BEAST 1.7, Mol. Biol. Evol., 29, 1969, 10.1093/molbev/mss075 Edwards, 2007, High-resolution species trees without concatenation, Proc. Natl. Acad. Sci. USA, 104, 5936, 10.1073/pnas.0607004104 Felsenstein, 1978, Cases in which parsimony or compatibility methods will be positively misleading, Syst. Zool., 27, 401, 10.2307/2412923 Felsenstein, J., 2004. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the Author. Department of Genome Sciences, University of Washington, Seattle. Fisher-Reid, 2011, What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades, BMC Evol. Biol., 11, 300, 10.1186/1471-2148-11-300 Frost, 2006, The amphibian tree of life, Bull. Am. Mus. Nat. Hist., 297, 1, 10.1206/0003-0090(2006)297[0001:TATOL]2.0.CO;2 Guindon, 2003, A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst. Biol., 52, 696, 10.1080/10635150390235520 Heled, 2010, Bayesian inference of species trees from multilocus data, Mol. Biol. Evol., 27, 570, 10.1093/molbev/msp274 Hillis, 1987, Molecular versus morphological approaches to systematics, Annu. Rev. Ecol. Syst., 18, 23, 10.1146/annurev.es.18.110187.000323 Hillis, 2005, Analysis and visualization of tree space, Syst. Biol., 54, 471, 10.1080/10635150590946961 Holman, 2006 Huang, 2010, Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods, Syst. Biol., 59, 573, 10.1093/sysbio/syq047 Jones, 1993, When theories and methodologies clash – a phylogenetic reanalysis of the North-American ambystomatid salamanders (Caudata, Ambystomatidae), Syst. Biol., 42, 92, 10.1093/sysbio/42.1.92 Kraus, 1988, An empirical-evaluation of the use of the ontogeny polarization criterion in phylogenetic inference, Syst. Zool., 37, 106, 10.2307/2992271 Kubatko, 2007, Inconsistency of phylogenetic estimates from concatenated data under coalescence, Syst. Biol., 56, 17, 10.1080/10635150601146041 Kubatko, 2009, STEM: species tree estimation using maximum likelihood for gene trees under coalescence, Bioinformatics, 25, 971, 10.1093/bioinformatics/btp079 Larget, 2010, BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis, Bioinformatics, 26, 2910, 10.1093/bioinformatics/btq539 Larson, 1991, A molecular perspective on the evolutionary relationships of the salamander families, Evol. Biol., 25, 211 Leache, 2011, The accuracy of species tree estimation under simulation: a comparison of methods, Syst. Biol., 60, 126, 10.1093/sysbio/syq073 Maddison, 1997, Gene trees in species trees, Syst. Biol., 46, 523, 10.1093/sysbio/46.3.523 Maddison, 2006, Inferring phylogeny despite incomplete lineage sorting, Syst. Biol., 55, 21, 10.1080/10635150500354928 Maddison, W.P., Maddison, D.R., 2004. Mesquite: A Modular System for Evolutionary Analysis. Version 1.05. <http://mesquiteproject.org>. McCormack, 2009, Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design, Syst. Biol., 58, 501, 10.1093/sysbio/syp045 O’Neill, 2013, Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex, Mol. Ecol., 22, 111, 10.1111/mec.12049 Pauly, 2007, Phylogeographic concordance in the southeastern United States: the flatwoods salamander, Ambystoma cingulatum, as a test case, Mol. Ecol., 16, 415, 10.1111/j.1365-294X.2006.03149.x Posada, 2008, JModelTest: phylogenetic model averaging, Mol. Biol. Evol., 25, 1253, 10.1093/molbev/msn083 Putta, 2004, From biomedicine to natural history research: EST resources for ambystomatid salamanders, BMC Genom., 5, 54, 10.1186/1471-2164-5-54 Rambaut, A., Drummond, A.J., 2009. Tracer v1.5. <http://tree.bio.ed.ac.uk/software/tracer>. Robertson, 2006, An unexpected recent ancestor of unisexual Ambystoma, Mol. Ecol., 15, 3339, 10.1111/j.1365-294X.2006.03005.x Roelants, 2007, Global patterns of diversification in the history of modern amphibians, Proc. Natl. Acad. Sci. USA, 104, 887, 10.1073/pnas.0608378104 Rokas, 2005, More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy, Mol. Biol. Evol., 22, 1337, 10.1093/molbev/msi121 Ronquist, 2003, MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, 19, 1572, 10.1093/bioinformatics/btg180 Shaffer, 1993, Phylogenetics of model organisms – the laboratory axolotl, Ambystoma mexicanum, Syst. Biol., 42, 508, 10.1093/sysbio/42.4.508 Shaffer, 1996, The polytypic species revisited: genetic differentiation and molecular phylogenetics of the tiger salamander Ambystoma tigrinum (Amphibia: Caudata) complex, Evolution, 50, 417, 10.2307/2410811 Shaffer, 1991, When molecules and morphology clash – a phylogenetic analysis of the North-American ambystomatid salamanders (Caudata, Ambystomatidae), Syst. Zool., 40, 284, 10.2307/2992323 Smith, 2005, A comprehensive expressed sequence tag linkage map for tiger salamander and Mexican axolotl: enabling gene mapping and comparative genomics in Ambystoma, Genetics, 171, 1161, 10.1534/genetics.105.046433 Stanley, 2011, Between a rock and a hard polytomy: rapid radiation in the rupicolous girdled lizards (Squamata: Cordylidae), Mol. Phylogenet. Evol., 58, 53, 10.1016/j.ympev.2010.08.024 Weisrock, 2001, Molecular phylogenetics and historical biogeography among salamandrids of the “true” salamander clade: rapid branching of numerous highly divergent lineages in Mertensiella luschani associated with the rise of Anatolia, Mol. Phylogenet. Evol., 18, 434, 10.1006/mpev.2000.0905 Weisrock, 2005, Resolving deep phylogenetic relationships in salamanders: analyses of mitochondrial and nuclear genomic data, Syst. Biol., 54, 758, 10.1080/10635150500234641 Weisrock, 2012, Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics, Mol. Biol. Evol., 29, 1615, 10.1093/molbev/mss008 Wiens, 2000, War of the iguanas: conflicting molecular and morphological phylogenies and long-branch attraction in iguanid lizards, Syst. Biol., 49, 143, 10.1080/10635150050207447 Wiens, 2005, Ontogeny discombobulates phylogeny: paedomorphosis and higher-level salamander relationships, Syst. Biol., 54, 91, 10.1080/10635150590906037 Zylstra, 1998, PCR amplification of murine immunoglobulin germline V genes: strategies for minimization of recombination artefacts, Immunol. Cell Biol., 76, 395, 10.1046/j.1440-1711.1998.00772.x