Data from: Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of Neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae)

Bagley JC, Alda F, Breitman MF, Bermingham E, van den Berghe EP, Johnson JB

Date Published: April 16, 2015

DOI: http://dx.doi.org/10.5061/dryad.m1g3v

 

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Title concatenated mtDNA dataset
Downloaded 16 times
Description NEXUS file containing the 'concatenated mtDNA' dataset alignment, which includes 171 mtDNA subsamples sequenced for the mitochondrial cytochrome b and/or cytochrome oxidase 1 genes.
Download 171_concat_mtDNA.NEX (307.1 Kb)
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Title 50tax_plus8out_mtDNAonly
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Description NEXUS file containing mtDNA locus data matching samples in the 50-sample 'concatenated nDNA' dataset.
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Title concatenated nDNA dataset - LDHA alignment
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Description NEXUS file containing the muscle-type lactate dehydrogenase (ldh-A) sequences in the concatenated nDNA dataset.
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Title concatenated nDNA dataset - RPS7 alignment
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Description NEXUS file containing the sequences of nuclear ribosomal protein S7 (RPS7) introns and exons in the concatenated nDNA dataset.
Download 50tax_plus8out_S7only.NEX (68.68 Kb)
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Title concatenated nDNA dataset - X-src alignment
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Description NEXUS file containing the tyrosine-kinase class X-src oncogene (X-src) sequences in the concatenated nDNA dataset.
Download 50tax_plus8out_XSRConly.NEX (30.86 Kb)
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Title concatenated nDNA dataset - X-yes alignment
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Description NEXUS file containing the tyrosine-kinase class X-yes oncogene (X-yes) sequences in the concatenated nDNA dataset.
Download 50tax_plus8out_XYESonly.NEX (49.13 Kb)
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Title concatenated nDNA dataset - Glyt alignment
Downloaded 5 times
Description NEXUS file containing the sequences of glycosyltransferase (Glyt) sequences in the concatenated nDNA dataset.
Download 50tax_plus8out_Glytonly.NEX (53.89 Kb)
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Title concatenated mtDNA + nDNA dataset - mtDNA alignment
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Description NEXUS file containing the mtDNA sequences in the concatenated mtDNA + nDNA dataset.
Download 80tax_mtDNAonly.NEX (143.8 Kb)
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Title concatenated mtDNA + nDNA dataset - LDHA alignment
Downloaded 3 times
Description NEXUS file containing the ldh-A sequences in the concatenated mtDNA + nDNA dataset.
Download 80tax_LDHAonly.NEX (16.37 Kb)
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Title concatenated mtDNA + nDNA dataset - RPS7 alignment
Downloaded 3 times
Description NEXUS file containing the RPS7 sequences in the concatenated mtDNA + nDNA dataset.
Download 80tax_S7only.NEX (94.69 Kb)
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Title concatenated mtDNA + nDNA dataset - X-src alignment
Downloaded 3 times
Description NEXUS file containing the X-src sequences in the concatenated mtDNA + nDNA dataset.
Download 80tax_XSRConly.NEX (42.52 Kb)
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Title concatenated mtDNA + nDNA dataset - X-yes alignment
Downloaded 3 times
Description NEXUS file containing the X-yes sequences in the concatenated mtDNA + nDNA dataset.
Download 80tax_XYESonly.NEX (67.72 Kb)
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Title concatenated mtDNA + nDNA dataset - Glyt alignment
Downloaded 3 times
Description NEXUS file containing the Glyt sequences in the concatenated mtDNA + nDNA dataset.
Download 80tax_Glytonly.NEX (74.28 Kb)
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Title concatenated mtDNA GARLI ML tree
Downloaded 4 times
Description Newick format tree file of the single 'best' maximum-likelihood tree resulting from our analysis of the concatenated mtDNA dataset in GARLI.
Download concat_mtDNA_garli_ML_newick.txt (4.578 Kb)
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Title concatenated mtDNA GARLI ML tree - alt topology
Downloaded 2 times
Description Newick 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.
Download concat_mtDNA_garli_ML_alt_newick.txt (5.239 Kb)
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Title concatenated mtDNA + nDNA GARLI ML tree
Downloaded 2 times
Description Newick format tree file containing the GARLI topology shown in Fig. 3A.
Download Fig_3A_concat_mtDNA_nDNA_ML_newick.txt (2.43 Kb)
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Title concatenated nDNA GARLI ML tree
Downloaded 5 times
Description Newick format tree file containing the GARLI topology shown in Fig. 3B.
Download Fig_3B_concat_nDNA_garli_ML_newick.txt (2.405 Kb)
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Title concatenated mtDNA + nDNA *BEAST species tree
Downloaded 3 times
Description Newick format tree file containing the species tree shown in whole or in part in Fig. 4 and S3B Fig.
Download Figs_4_and_S3B_25spp_80seq_*BEAST_species...ck.txt (1.198 Kb)
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Title concatenated mtDNA BEAST tree
Downloaded 3 times
Description Newick format tree file containing the time tree resulting from our analysis of the concatenated mtDNA dataset in BEAST, which is shown in S3A Fig.
Download S3A_Fig_concat_mtDNA_BEAST_newick.txt (8.141 Kb)
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Title LDHA BEAST tree
Downloaded 2 times
Description Newick format tree file containing the time tree resulting from our analysis of the ldh-A dataset in BEAST, which is shown in S4 Fig.
Download S4_Fig_LDHA_BEAST_tree_newick.txt (2.111 Kb)
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Title RPS7 BEAST tree
Downloaded 2 times
Description Newick format tree file containing the time tree resulting from our analysis of the RPS7 dataset in BEAST, which is shown in S4 Fig.
Download S4_Fig_S7_BEAST_tree_newick.txt (2.238 Kb)
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Title XSRC BEAST tree
Downloaded 2 times
Description Newick format tree file containing the time tree resulting from our analysis of the X-src dataset in BEAST, which is shown in S4 Fig.
Download S4_Fig_XSRC_BEAST_tree_newick.txt (2.331 Kb)
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Title XYES BEAST tree
Downloaded 3 times
Description Newick format tree file containing the time tree resulting from our analysis of the X-yes dataset in BEAST, which is shown in S4 Fig.
Download S4_Fig_XYES_BEAST_tree_newick.txt (974 bytes)
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Title GLYT BEAST tree
Downloaded 3 times
Description Newick format tree file containing the time tree resulting from our analysis of the Glyt dataset in BEAST, which is shown in S4 Fig.
Download S4_Fig_GLYT_BEAST_tree_newick.txt (1.051 Kb)
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When using this data, please cite the original publication:

Bagley JC, Alda F, Breitman MF, Bermingham E, van den Berghe EP, Johnson JB (2015) Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of Neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae). PLOS ONE 10(4): e0121139. http://dx.doi.org/10.1371/journal.pone.0121139

Additionally, please cite the Dryad data package:

Bagley JC, Alda F, Breitman MF, Bermingham E, van den Berghe EP, Johnson JB (2015) Data from: Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of Neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.m1g3v
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