Data from: Phylogeography and species delimitation in convict cichlids (Cichlidae: Amatitlania): implications for taxonomy and Plio–Pleistocene evolutionary history in Central America

Bagley JC, Matamoros WA, McMahan CD, Tobler M, Chakrabarty P, Johnson JB

Date Published: August 2, 2016

DOI: http://dx.doi.org/10.5061/dryad.r1d8q

 

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Title full-cytb dataset
Downloaded 7 times
Description NEXUS file containing the 'full-cytb' dataset alignment, which includes 408 mtDNA sequences of the mitochondrial cytochrome b gene. This file includes sequences from 318 ingroup samples and from 90 outgroup samples (see text and Supporting information Data S1 for details).
Download full_cytb_n408.NEX (468.5 Kb)
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Title cytb haplotype dataset
Downloaded 3 times
Description NEXUS file containing the 'cytb haplotype' dataset alignment, which includes 106 ingroup cytochrome b haplotype sequences plus 86 outgroup sequences.
Download cytb_haplotype_n192.NEX (220.5 Kb)
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Title reduced-cytb dataset
Downloaded 4 times
Description NEXUS file containing the 'reduced-cytb' dataset alignment, which includes sequences of the cytochrome b gene for a subset of 20 ingroup samples and 18 outgroup samples. The ingroup samples in this file represent five samples per nominal Amatitlania species, as well as five samples from the Lago Coatepeque, El Salvador population formerly known as 'A. coatepeque'.
Download reduced_cytb_n38.NEX (43.74 Kb)
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Title GARLI full-cytb ML analysis input file
Downloaded 1 time
Description Input data file in NEXUS format used in maximum-likelihood (ML) analysis of the full-cytb dataset in GARLI v2.0.
Download An_CB_408wouts_forGARLI.NEX (468.7 Kb)
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Title GARLI cytb haplotype ML analysis input file
Downloaded 2 times
Description Input data file in NEXUS format used in maximum-likelihood (ML) analysis of the cytb haplotype dataset in GARLI v2.0.
Download 192_An_CB_109haps83outs.NEX (220.7 Kb)
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Title *BEAST 'one-species' model input file
Downloaded 4 times
Description Input data file in XML format used in *BEAST (multispecies coalescent) species tree analysis of the reduced-cytb dataset in BEAST v1.8.3 under a 'one-species' model lumping all Amatitlania samples into a single 'A. nigrofasciata' lineage. The final section of this file calls a post-run analysis estimating the log-marginal likelihood of the model using path sampling (PS) and stepping-stone (SS) sampling approaches.
Download 38_1sp_STAR_12v3cod_ULN_3NormCalib_PSSS100.xml (81.40 Kb)
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Title *BEAST 'two-species disjunct' model input file
Downloaded 2 times
Description Input data file in XML format used in *BEAST (multispecies coalescent) species tree analysis of the reduced-cytb dataset in BEAST v1.8.3 under a 'two-species disjunct' model lumping all Amatitlania samples into A. nigrofasciata or A. siquia. The final section of this file calls a post-run analysis estimating the log-marginal likelihood of the model using path sampling (PS) and stepping-stone (SS) sampling approaches.
Download 38_2sppnigsiq_STAR_12v3cod_ULN_3NormCalib...00.xml (82.15 Kb)
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Title *BEAST 'two-species allopatric' model input file
Downloaded 2 times
Description Input data file in XML format used in *BEAST (multispecies coalescent) species tree analysis of the reduced-cytb dataset in BEAST v1.8.3 under a 'two-species allopatric' model lumping all Amatitlania samples into A. kanna and A. nigrofasciata. The final section of this file calls a post-run analysis estimating the log-marginal likelihood of the model using path sampling (PS) and stepping-stone (SS) sampling approaches.
Download 38_2sppnigkan_STAR_12v3cod_ULN_3NormCalib...00.xml (82.05 Kb)
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Title *BEAST 'three-species' model input file
Downloaded 3 times
Description Input data file in XML format used in *BEAST (multispecies coalescent) species tree analysis of the reduced-cytb dataset in BEAST v1.8.3 under a 'three-species' null model grouping sequences into the corresponding three currently recognized species of Amatitlania. The final section of this file calls a post-run analysis estimating the log-marginal likelihood of the model using path sampling (PS) and stepping-stone (SS) sampling approaches.
Download 38_3spp_STAR_12v3cod_ULN_3NormCalib_PSSS100.xml (82.21 Kb)
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Title BEAST full-cytb analysis input file
Downloaded 1 time
Description Input data file in XML format used in Bayesian divergence time analysis of the full-cytb dataset in BEAST v2.
Download An_408wouts_BD2_ULN_HKYTrN_3NormCab.xml (542.7 Kb)
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Title BEAST cytb haplotype analysis input file
Downloaded 2 times
Description Input data file in XML format used in Bayesian divergence time analysis of the cytb haplotype dataset in BEAST v2.
Download 192_An_BD2_ULN_HKYIGGTRI_3NormCab.xml (270.2 Kb)
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Title BEAST A. nigrofasciata lineage BSP analysis input file
Downloaded 1 time
Description Input data file in XML format used in Bayesian skyline plot (BSP) historical demographical analysis of the cytb dataset corresponding to the A. nigrofasciata lineage (supported by BFD species delimitation analyses; see Results) in BEAST v1.8.3. Results from one run of this datafile, as summarized in Tracer, are presented in Fig. 4A.
Download An_CB_313_bycodon_strict_BSP.xml (422.6 Kb)
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Title BEAST A. kanna lineage BSP analysis input file
Downloaded 3 times
Description Input data file in XML format used in Bayesian skyline plot (BSP) historical demographical analysis of the cytb dataset corresponding to the A. kanna lineage (supported by BFD species delimitation analyses; see Results) in BEAST v1.8.3. Results from one run of this datafile, as summarized in Tracer, are presented in Fig. 4B.
Download Akanna_CB_5_bycodon_strict_BSP.xml (19.99 Kb)
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Title full-cytb GARLI ML tree
Downloaded 1 time
Description Newick format tree file containing the single 'best' maximum-likelihood tree resulting from analysis of the full-cytb dataset in GARLI v2.0.
Download An_CB_408wouts_GARLI_best_newick.txt (11.89 Kb)
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Title cytb haplotype GARLI ML tree
Downloaded 2 times
Description Newick format tree file containing the single 'best' maximum-likelihood tree resulting from analysis of the cytb haplotype dataset in GARLI v2.0. A portion of this tree is shown in Fig. 2.
Download 192_An_CB_GARLI_best_newick.txt (6.119 Kb)
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Title reduced-cytb *BEAST species tree
Downloaded 4 times
Description NEXUS format tree file containing the species tree inferred in the best-supported species delimitation model identified during Bayes factor delimitation, the 'two-species allopatric' model. This file is readable in FigTree v1.4.0, and the species tree within it is shown in Fig. S4.
Download 38_2sppnigkan_MCC_species_tree.NEX (33.56 Kb)
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Title full-cytb BEAST time tree
Downloaded 1 time
Description Newick format tree file containing the relaxed-clock time tree (gene tree) inferred in the BEAST analysis of the full-cytb dataset. This tree is shown in Fig. S2.
Download An_408wouts_BEAST_time_tree_newick.txt (21.41 Kb)
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Title cytb haplotype BEAST time tree
Downloaded 4 times
Description Newick format tree file containing the relaxed-clock time tree (gene tree) inferred in the BEAST analysis of the cytb haplotype dataset. This tree is shown in Fig. S3.
Download 192_An_BEAST_time_tree_newick.txt (9.276 Kb)
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Title nuclear RPS7 intron 1 dataset
Downloaded 2 times
Description NEXUS file containing the nuclear ribosomal protein S7 (RPS7) intron 1 dataset alignment, which includes 24 sequences.
Download RPS7_intron1_n24.NEX (15.59 Kb)
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Title nuclear RPS7 intron 2 dataset
Downloaded 1 time
Description NEXUS file containing the nuclear ribosomal protein S7 (RPS7) intron 2 dataset alignment, which includes 53 sequences of Amatitlania samples.
Download RPS7_intron2_n53.NEX (9.232 Kb)
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Title RPS7 intron 1 GARLI ML tree
Downloaded 2 times
Description Newick format tree file containing the single 'best' maximum-likelihood tree resulting from analysis of the ribosomal protein S7 (RPS7) intron 1 dataset in GARLI v2.0. This tree is shown at the top of Fig. S1.
Download An_RPS7_intron1_GARLI_best_newick.txt (626 bytes)
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Title RPS7 intron 2 GARLI ML tree
Downloaded 1 time
Description Newick format tree file containing the single 'best' maximum-likelihood tree resulting from analysis of the ribosomal protein S7 (RPS7) intron 2 dataset in GARLI v2.0. This tree is shown at the bottom of Fig. S1.
Download An_RPS7_intron2_GARLI_best_newick.txt (1.243 Kb)
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Title *BEAST 'four-species' model input file
Downloaded 3 times
Description Input data file in XML format used in *BEAST (multispecies coalescent) species tree analysis of the reduced-cytb dataset in BEAST v1.8.3 under a 'four-species' model grouping sequences into the corresponding three currently recognized species of Amatitlania, as well as A. nigrofasciata samples from Lago Coatepeque formerly known as 'A. coatepeque'. The final section of this file calls a post-run analysis estimating the log-marginal likelihood of the model using path sampling (PS) and stepping-stone (SS) sampling approaches.
Download 38_4spp_STAR_12v3cod_ULN_3NormCalib_PSSS100.xml (82.46 Kb)
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When using this data, please cite the original publication:

Bagley JC, Matamoros WA, McMahan CD, Tobler M, Chakrabarty P, Johnson JB (2016) Phylogeography and species delimitation in convict cichlids (Cichlidae:Amatitlania): implications for taxonomy and Plio-Pleistocene evolutionary history in Central America. Biological Journal of the Linnean Society, online in advance of print. http://dx.doi.org/10.1111/bij.12845

Additionally, please cite the Dryad data package:

Bagley JC, Matamoros WA, McMahan CD, Tobler M, Chakrabarty P, Johnson JB (2016) Data from: Phylogeography and species delimitation in convict cichlids (Cichlidae: Amatitlania): implications for taxonomy and Plio–Pleistocene evolutionary history in Central America. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.r1d8q
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