DOI: 10.5061/dryad.r1d8q
title: Data from: Phylogeography and species delimitation in convict cichlids (Cichlidae: Amatitlania): implications for taxonomy and Plio–Pleistocene evolutionary history in Central America

description: We investigate phylogeographic patterns and delimit species boundaries
 within Amatitlania, a genus of Central American cichlid fishes.
 Phylogenetic analyses of mitochondrial DNA sequences from 318 individuals
 spanning the geographical ranges of all three currently recognized
 Amatitlania species strongly supported one major clade, with a relatively
 diverged subclade corresponding to A. kanna samples from eastern Costa
 Rica and Panama. Gene trees and networks revealed marked incongruences
 between phylogeographic structure and morpho-species taxonomy as a result
 of species-level polyphyly. Bayes factor comparisons of species
 delimitation models accounting for incomplete lineage sorting under the
 multispecies coalescent decisively supported the recognition of two
 distinct species within Amatitlania corresponding to Amatitlania
 nigrofasciata and A. kanna lineages. The only clearly genetically and
 morphologically diagnosable species was A. kanna. These results strongly
 suggest that incomplete lineage sorting provides the best explanation for
 the polyphyly of A. kanna, whereas the polyphyly of A. siquia is likely a
 result of an imperfect taxonomy. Additional insights from
 coalescent-dating, network, and historical demographic analyses suggested
 that the two species of Amatitlania diversified only since the early
 Pleistocene, and that A. nigrofasciata experienced population expansions
 from approximately 200 000 years ago in the mid-late Pleistocene onward.
 We discuss implications of our results for the taxonomy and evolutionary
 history of Amatitlania and, more broadly, of Central American freshwater
 fishes.
description: full-cytb
 datasetNEXUS 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).full_cytb_n408.NEXcytb haplotype datasetNEXUS file containing the 'cytb haplotype' dataset alignment, which includes 106 ingroup cytochrome b haplotype sequences plus 86 outgroup sequences.cytb_haplotype_n192.NEXreduced-cytb datasetNEXUS 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'.reduced_cytb_n38.NEXGARLI full-cytb ML analysis input fileInput data file in NEXUS format used in maximum-likelihood (ML) analysis of the full-cytb dataset in GARLI v2.0.An_CB_408wouts_forGARLI.NEXGARLI cytb haplotype ML analysis input fileInput data file in NEXUS format used in maximum-likelihood (ML) analysis of the cytb haplotype dataset in GARLI v2.0.192_An_CB_109haps83outs.NEX*BEAST 'one-species' model input fileInput 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.38_1sp_STAR_12v3cod_ULN_3NormCalib_PSSS100.xml*BEAST 'two-species disjunct' model input fileInput 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.38_2sppnigsiq_STAR_12v3cod_ULN_3NormCalib_PSSS100.xml*BEAST 'two-species allopatric' model input fileInput 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.38_2sppnigkan_STAR_12v3cod_ULN_3NormCalib_PSSS100.xml*BEAST 'three-species' model input fileInput 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.38_3spp_STAR_12v3cod_ULN_3NormCalib_PSSS100.xmlBEAST full-cytb analysis input fileInput data file in XML format used in Bayesian divergence time analysis of the full-cytb dataset in BEAST v2.An_408wouts_BD2_ULN_HKYTrN_3NormCab.xmlBEAST cytb haplotype analysis input fileInput data file in XML format used in Bayesian divergence time analysis of the cytb haplotype dataset in BEAST v2.192_An_BD2_ULN_HKYIGGTRI_3NormCab.xmlBEAST A. nigrofasciata lineage BSP analysis input fileInput 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.An_CB_313_bycodon_strict_BSP.xmlBEAST A. kanna lineage BSP analysis input fileInput 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.Akanna_CB_5_bycodon_strict_BSP.xmlfull-cytb GARLI ML treeNewick format tree file containing the single 'best' maximum-likelihood tree resulting from analysis of the full-cytb dataset in GARLI v2.0.An_CB_408wouts_GARLI_best_newick.txtcytb haplotype GARLI ML treeNewick 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. 2.192_An_CB_GARLI_best_newick.txtreduced-cytb *BEAST species treeNEXUS 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. S4.38_2sppnigkan_MCC_species_tree.NEXfull-cytb BEAST time treeNewick 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.An_408wouts_BEAST_time_tree_newick.txtcytb haplotype BEAST time treeNewick 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. S3.192_An_BEAST_time_tree_newick.txtnuclear RPS7 intron 1 datasetNEXUS file containing the nuclear ribosomal protein S7 (RPS7) intron 1 dataset alignment, which includes 24 sequences.RPS7_intron1_n24.NEXnuclear RPS7 intron 2 datasetNEXUS file containing the nuclear ribosomal protein S7 (RPS7) intron 2 dataset alignment, which includes 53 sequences of Amatitlania samples.RPS7_intron2_n53.NEXRPS7 intron 1 GARLI ML treeNewick 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.An_RPS7_intron1_GARLI_best_newick.txtRPS7 intron 2 GARLI ML treeNewick 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.An_RPS7_intron2_GARLI_best_newick.txt*BEAST 'four-species' model input fileInput 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.38_4spp_STAR_12v3cod_ULN_3NormCalib_PSSS100.xml