DOI: 10.5061/dryad.m1g3v
title: Data from: Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of Neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae)

description: Accurately delimiting species is fundamentally important for understanding
 species diversity and distributions and devising effective strategies to
 conserve biodiversity. However, species delimitation is problematic in
 many taxa, including ‘non-adaptive radiations’ containing morphologically
 cryptic lineages. Fortunately, coalescent-based species delimitation
 methods hold promise for objectively estimating species limits in such
 radiations, using multilocus genetic data. Using coalescent-based
 approaches, we delimit species and infer evolutionary relationships in a
 morphologically conserved group of Central American freshwater fishes, the
 Poecilia sphenops species complex. Phylogenetic analyses of multiple
 genetic markers (sequences of two mitochondrial DNA genes and five nuclear
 loci) from 10/15 species and genetic lineages recognized in the group
 support the P. sphenops species complex as monophyletic with respect to
 outgroups, with eight mitochondrial ‘major-lineages’ diverged by ≥2%
 pairwise genetic distances. From general mixed Yule-coalescent models, we
 discovered (conservatively) 10 species within our concatenated
 mitochondrial DNA dataset, 9 of which were strongly supported by
 subsequent multilocus Bayesian species delimitation and species tree
 analyses. Results suggested species-level diversity is underestimated or
 overestimated by at least ~15% in different lineages in the complex.
 Nonparametric statistics and coalescent simulations indicate genealogical
 discordance among our gene tree results has mainly derived from
 interspecific hybridization in the nuclear genome. However, mitochondrial
 DNA show little evidence for introgression, and our species delimitation
 results appear robust to effects of this process. Overall, our findings
 support the utility of combining multiple lines of genetic evidence and
 broad phylogeographical sampling to discover and validate species using
 coalescent-based methods. Our study also highlights the importance of
 testing for hybridization versus incomplete lineage sorting, which aids
 inference of not only species limits but also evolutionary processes
 influencing genetic diversity.
description: concatenated mtDNA
 datasetNEXUS file containing
 the 'concatenated mtDNA' dataset alignment, which includes 171
 mtDNA subsamples sequenced for the mitochondrial cytochrome b and/or
 cytochrome oxidase 1 genes.171_concat_mtDNA.NEX50tax_plus8out_mtDNAonlyNEXUS file containing mtDNA locus data matching samples in the 50-sample 'concatenated nDNA' dataset.concatenated nDNA dataset - LDHA alignmentNEXUS file containing the muscle-type lactate dehydrogenase (ldh-A) sequences in the concatenated nDNA dataset.50tax_plus8out_LDHAonly.NEXconcatenated nDNA dataset - RPS7 alignmentNEXUS file containing the sequences of nuclear ribosomal protein S7 (RPS7) introns and exons in the concatenated nDNA dataset.50tax_plus8out_S7only.NEXconcatenated nDNA dataset - X-src alignmentNEXUS file containing the tyrosine-kinase class X-src oncogene (X-src) sequences in the concatenated nDNA dataset.50tax_plus8out_XSRConly.NEXconcatenated nDNA dataset - X-yes alignmentNEXUS file containing the tyrosine-kinase class X-yes oncogene (X-yes) sequences in the concatenated nDNA dataset.50tax_plus8out_XYESonly.NEXconcatenated nDNA dataset - Glyt alignmentNEXUS file containing the sequences of glycosyltransferase (Glyt) sequences in the concatenated nDNA dataset.50tax_plus8out_Glytonly.NEXconcatenated mtDNA + nDNA dataset - mtDNA alignmentNEXUS file containing the mtDNA sequences in the concatenated mtDNA + nDNA dataset.80tax_mtDNAonly.NEXconcatenated mtDNA + nDNA dataset - LDHA alignmentNEXUS file containing the ldh-A sequences in the concatenated mtDNA + nDNA dataset.80tax_LDHAonly.NEXconcatenated mtDNA + nDNA dataset - RPS7 alignmentNEXUS file containing the RPS7 sequences in the concatenated mtDNA + nDNA dataset.80tax_S7only.NEXconcatenated mtDNA + nDNA dataset - X-src alignmentNEXUS file containing the X-src sequences in the concatenated mtDNA + nDNA dataset.80tax_XSRConly.NEXconcatenated mtDNA + nDNA dataset - X-yes alignmentNEXUS file containing the X-yes sequences in the concatenated mtDNA + nDNA dataset.80tax_XYESonly.NEXconcatenated mtDNA + nDNA dataset - Glyt alignmentNEXUS file containing the Glyt sequences in the concatenated mtDNA + nDNA dataset.80tax_Glytonly.NEXconcatenated mtDNA GARLI ML treeNewick format tree file of the single 'best' maximum-likelihood tree resulting from our analysis of the concatenated mtDNA dataset in GARLI.concat_mtDNA_garli_ML_newick.txtconcatenated mtDNA GARLI ML tree - alt topologyNewick format tree file containing the single 'best' maximum-likelihood tree resulting from an additional analysis of the concatenated mtDNA dataset in GARLI. This 'alternative' topology differs from the best ML topology presented in the paper, for example in recovering sample "172554" as the most basal member of clade 2.concat_mtDNA_garli_ML_alt_newick.txtconcatenated mtDNA + nDNA GARLI ML treeNewick format tree file containing the GARLI topology shown in Fig. 3A.Fig_3A_concat_mtDNA_nDNA_ML_newick.txtconcatenated nDNA GARLI ML treeNewick format tree file containing the GARLI topology shown in Fig. 3B.Fig_3B_concat_nDNA_garli_ML_newick.txtconcatenated mtDNA + nDNA *BEAST species treeNewick format tree file containing the species tree shown in whole or in part in Fig. 4 and S3B Fig.Figs_4_and_S3B_25spp_80seq_*BEAST_species_tree_newick.txtconcatenated mtDNA BEAST treeNewick format tree file containing the time tree resulting from our analysis of the concatenated mtDNA dataset in BEAST, which is shown in S3A Fig.S3A_Fig_concat_mtDNA_BEAST_newick.txtLDHA BEAST treeNewick format tree file containing the time tree resulting from our analysis of the ldh-A dataset in BEAST, which is shown in S4 Fig.S4_Fig_LDHA_BEAST_tree_newick.txtRPS7 BEAST treeNewick format tree file containing the time tree resulting from our analysis of the RPS7 dataset in BEAST, which is shown in S4 Fig.S4_Fig_S7_BEAST_tree_newick.txtXSRC BEAST treeNewick format tree file containing the time tree resulting from our analysis of the X-src dataset in BEAST, which is shown in S4 Fig.S4_Fig_XSRC_BEAST_tree_newick.txtXYES BEAST treeNewick format tree file containing the time tree resulting from our analysis of the X-yes dataset in BEAST, which is shown in S4 Fig.S4_Fig_XYES_BEAST_tree_newick.txtGLYT BEAST treeNewick format tree file containing the time tree resulting from our analysis of the Glyt dataset in BEAST, which is shown in S4 Fig.S4_Fig_GLYT_BEAST_tree_newick.txt