Data from: Speciation with gene flow in whiptail lizards from a Neotropical xeric biome

Oliveira EF, Gehara M, São Pedro VA, Chen X, Myers EA, Burbrink FT, Mesquita DO, Garda AA, Colli GR, Rodrigues MT, Arias FJ, Zaher H, Santos RML, Costa GC

Date Published: October 22, 2015

DOI: http://dx.doi.org/10.5061/dryad.44372

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Align_12S_62samples_substitution.rate.estimation
Downloaded 7 times
Description This file contains aligned sequences used to estimate a 12S substitution rate for Teiidae.
Download Align_12S_62samples_substitution.rate.est...on.fas (30.11 Kb)
Details View File Details
Title Align_12S_137samples.outgroup_gblock
Downloaded 6 times
Description This file contains aligned sequences used to estimate 12S gene tree.
Download Align_12S_137samples.outgroup_gblock.fas (52.29 Kb)
Details View File Details
Title Align_ATPSB_126samples.outgroup_gblock
Downloaded 3 times
Description This file contains aligned sequences used to estimate ATPSB gene tree.
Download Align_ATPSB_126samples.outgroup_gblock.fas (80.25 Kb)
Details View File Details
Title Align_NKTR_115samples.outgroup
Downloaded 5 times
Description This file contains aligned sequences used to estimate NKTR gene tree.
Download Align_NKTR_115samples.outgroup.fas (42.09 Kb)
Details View File Details
Title Align_R35_134samples.outgroup
Downloaded 8 times
Description This file contains aligned sequences used to estimate R35 gene tree.
Download Align_R35_134samples.outgroup.fas (54.66 Kb)
Details View File Details
Title Align_RP40_132samples.outgroup
Downloaded 5 times
Description This file contains aligned sequences used to estimate RP40 gene tree.
Download Align_RP40_132samples.outgroup.fas (48.27 Kb)
Details View File Details
Title Align_NE.SW_12S_398samples_gblock
Downloaded 6 times
Description This file contains 12S aligned sequences used to calculate the number of polymorphic sites (S), haplotype number (h), haplotype diversity (Hd), nucleotide diversity (π), and Tajima’s D for Northeast (NE) and Southwest (SW) lineages. This file was also used to to estimate uncorrected pairwise genetic distances between and within lineages and to investigate genetic structure with analyses of molecular variance (AMOVA).
Download Align_NE.SW_12S_398samples_gblock.fas (151.9 Kb)
Details View File Details
Title Align_NE.SW_12S_137samples_gblock
Downloaded 4 times
Description This file contains 12S aligned sequences used in most phylogeographic analyses: population assignment, haplotype genealogy, species tree estimation, migration estimate, species validation, and model based approach. Northeast (NE) and Southwest (SW) sequence clusters were used separately in historical demography analyses and phylogeographic reconstruction.
Download Align_NE.SW_12S_137samples_gblock.fas (52.59 Kb)
Details View File Details
Title Align_NE.SW_ATPSB_252.phased.sequences_gblock
Downloaded 5 times
Description This file contains ATPSB aligned sequences used in most phylogeographic analyses: population assignment, haplotype genealogy, species tree estimation, migration estimate, species validation, and model based approach. Northeast (NE) sequences cluster was used separately in phylogeographic reconstruction.
Download Align_NE.SW_ATPSB_252.phased.sequences_gblock.fas (160.4 Kb)
Details View File Details
Title Align_NE.SW_NKTR_230.phased.sequences
Downloaded 6 times
Description This file contains NKTR aligned sequences used in most phylogeographic analyses: population assignment, haplotype genealogy, species tree estimation, migration estimate, species validation, and model based approach. Northeast (NE) sequences cluster was used separately in phylogeographic reconstruction.
Download Align_NE.SW_NKTR_230.phased.sequences.fas (84.61 Kb)
Details View File Details
Title Align_NE.SW_R35_268.phased.sequeces
Downloaded 5 times
Description This file contains R35 aligned sequences used in most phylogeographic analyses: population assignment, haplotype genealogy, species tree estimation, migration estimate, species validation, and model based approach. Northeast (NE) sequences cluster was used separately in phylogeographic reconstruction.
Download Align_NE.SW_R35_268.phased.sequeces.fas (109.8 Kb)
Details View File Details
Title Align_NE.SW_RP40_264.phased.sequences
Downloaded 5 times
Description This file contains RP40 aligned sequences used in most phylogeographic analyses: population assignment, haplotype genealogy, species tree estimation, migration estimate, species validation, and model based approach. Northeast (NE) sequences cluster was used separately in phylogeographic reconstruction.
Download Align_NE.SW_RP40_264.phased.sequences.fas (97.12 Kb)
Details View File Details
Title Tree_12S_62samples_substitution.rate
Downloaded 5 times
Download Tree_12S_62samples_substitution.rate.estimation (84.41 Kb)
Details View File Details
Title Tree_12S_137samples.outgroup_gblock
Downloaded 4 times
Download Tree_12S_137samples.outgroup_gblock (153.1 Kb)
Details View File Details
Title Tree_ATPSB_126samples.outgroup_gblock
Downloaded 4 times
Download Tree_ATPSB_126samples.outgroup_gblock (100.1 Kb)
Details View File Details
Title Tree_NKTR_115samples.outgroup
Downloaded 7 times
Download Tree_NKTR_115samples.outgroup (88.86 Kb)
Details View File Details
Title Tree_R35_134samples.outgroup
Downloaded 5 times
Download Tree_R35_134samples.outgroup (99.94 Kb)
Details View File Details
Title Tree_RP40_132samples.outgroup
Downloaded 7 times
Download Tree_RP40_132samples.outgroup (100.5 Kb)
Details View File Details
Title Geneland_137samples_code
Downloaded 16 times
Description Sample codes used in Geneland analyses.
Download Geneland_137samples_code.txt (1.259 Kb)
Details View File Details
Title Geneland_137samples_4nuDNA_input
Downloaded 12 times
Description Geneland input file based on four nuclear genes.
Download Geneland_137samples_4nuDNA_input.txt (2.713 Kb)
Details View File Details
Title Geneland_137samples_mtDNA_input
Downloaded 9 times
Description Geneland input file based on mitochondrial gene (12S).
Download Geneland_137samples_mtDNA_input.txt (524 bytes)
Details View File Details
Title Geneland_137samples_LongLat_input
Downloaded 14 times
Description Geneland input file based on geographic coordinates (longitute and latitude) of each sample.
Download Geneland_137samples_LongLat_input.txt (2.503 Kb)
Details View File Details
Title Structure_137samples_4nuDNA_input
Downloaded 9 times
Description Structure input file based on four nuclear genes (fasta format).
Download Structure_137samples_4nuDNA_input.fas (485.1 Kb)
Details View File Details
Title Structure_137samples_4nuDNA_input
Downloaded 7 times
Description Structure input file (genotype matrix format) obtained from xmfas2struct program; -9 is used for missing data.
Download Structure_137samples_4nuDNA_input.txt (74.81 Kb)
Details View File Details
Title IMa2_137samples_5genes_input
Downloaded 16 times
Description IMa2 input file based on five genes.
Download IMa2_137samples_5genes_input.txt (501.5 Kb)
Details View File Details

When using this data, please cite the original publication:

Oliveira EF, Gehara M, São Pedro VA, Chen X, Myers EA, Burbrink FT, Mesquita DO, Garda AA, Colli GR, Rodrigues MT, Arias FJ, Zaher H, Santos RML, Costa GC (2015) Speciation with gene flow in whiptail lizards from a Neotropical xeric biome. Molecular Ecology 24(23): 5957–5975. http://dx.doi.org/10.1111/mec.13433

Additionally, please cite the Dryad data package:

Oliveira EF, Gehara M, São Pedro VA, Chen X, Myers EA, Burbrink FT, Mesquita DO, Garda AA, Colli GR, Rodrigues MT, Arias FJ, Zaher H, Santos RML, Costa GC (2015) Data from: Speciation with gene flow in whiptail lizards from a Neotropical xeric biome. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.44372
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: