Data from: Cryptic speciation reversal in the Etheostoma zonale (Teleostei: Percidae) species group, with an examination of the effect of recombination and introgression on species tree inference

 

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 Cytochrome b matrices
Downloaded 39 times
Description zonalecytballindividuals.nex gives the cytochrome b sequence for each individual in the study. zonalecytbmatrix.nex gives the sequence of each cytochrome b haplotype in the study, and is the matrix used to produce Figure 3.
Download cytochromebmatrices.zip (18.45 Kb)
Details View File Details
Title Nuclear Loci - Matrices with sequences for all individuals
Downloaded 36 times
Description Sequence matrices for each of the seven nuclear loci in the study. Each matrix includes the full length of each locus sequenced, prior to any removal of portions of the locus due to positive tests for recombination, and also prior to any removal of gaps. Each matrix contains the sequence for both alleles found in each individual which was sequenced at that locus. The name of each sequence is the name of the individual specimen which was sequenced.
Download nuclearlociallindividualsmatrices.zip (25.95 Kb)
Details View File Details
Title Nuclear Loci - Matrices with sequences for each distinct allele, prior to removal of gaps and tests for recombination
Downloaded 32 times
Description Sequence matrices for each of the seven nuclear loci in the study. Each matrix includes the full length of each locus sequenced, prior to any removal of portions of the locus due to positive tests for recombination, and also prior to any removal of gaps. Each matrix contains the sequence of each distinct allele found at that locus. The name of each sequence is the name of the allele that sequence represents.
Download nuclearlociinitialmatrices.zip (19.34 Kb)
Details View File Details
Title Nuclear Loci - Matrices with sequences for each distinct allele, after removal of gaps and tests for recombination
Downloaded 34 times
Description Sequence matrices for each of the seven nuclear loci in the study. Each matrix includes only that part of the locus remaining after removing any portions which resulted in positive tests of recombination, and also after removing gaps found in more than half of all alleles. Each matrix contains the sequence of each distinct allele found at that locus. The name of each sequence is the name of the allele that sequence represents. These matrices are the ones used to create the trees in Figure 4 and Figure S1. zonalenedd4lfinalmatrixsmallerportion.nex is the matrix used to produce Figure S3.
Download nuclearlocifinalmatrices.zip (14.75 Kb)
Details View File Details
Title Starbeast XML input files for species tree analyses
Downloaded 23 times
Description These are the XML files used to produce, in *BEAST, the seven species trees seen in Figure 5 and Figure S2. Figure 5a was produced using the file zonalestarbeastfullintrons30.xml; Figure 5b with zonalestarbeast30.xml, Figure 5c with zonalestarbeastnuclear30.xml, Figure S2a with zonalestarbeasthalfintrons30.xml, Figure S2b with zonalestarbeastdnasp30.xml, Figure S2c with zonalestarbeastcytbcfzonale.xml, and Figure S2d with zonalestarbeastdnaspnuclear30.xml. The codes used to designate individuals in these files may be converted to the names of each individual listed in Appendices S2, S4 and S5 using the files tableofcytochromebsequences.xlsx and tableofnuclearsequences.xlsx.
Download Starbeastxmlfiles.zip (282.6 Kb)
Details View File Details
Title Beast XML input files for EBSP analyses
Downloaded 42 times
Description The XML input files for the Extended Bayesian Skyline Plots presented in Figure 6. ebspuppertennessee.xml is the input file for Figure 6a, ebspuppertennesseenuclear.xml is the input file for Figure 6b, ebspsfholston.xml is the input file for Figure 6c, and ebspclinch.xml is the input file for Figure 6d. The codes used to designate individuals in these files may be converted to the names of each individual listed in Appendices S2, S4 and S5 using the files tableofcytochromebsequences.xlsx and tableofnuclearsequences.xlsx.
Download ebspxmlfiles.zip (29.96 Kb)
Details View File Details
Title Table of Cytochrome b Sequences
Downloaded 40 times
Description A table listing the name of each individual sequenced for cytochrome b, its collection number, tissue collection code, collection locality, haplotype, the Genbank accession number of its cytochrome b sequence, and the code for that individual's cytochrome b sequence used in the *BEAST and EBSP xml files.
Download tableofcytochromebsequences.xlsx (64.71 Kb)
Details View File Details
Title Table of Nuclear Locus Sequences
Downloaded 41 times
Description A table listing the name of each individual sequenced for any of the seven nuclear loci, its collection number, tissue collection code, collection locality, haplotype of each of nuclear locus sequenced for that individual, the Genbank accession number of each nuclear locus sequenced for that individual, and the codes for that individual's nuclear locus sequences used in the *BEAST and EBSP xml files.
Download tableofnuclearsequences.xlsx (82.68 Kb)
Details View File Details

When using this data, please cite the original publication:

Halas D, Simons AM (2014) Cryptic speciation reversal in the Etheostoma zonale (Teleostei: Percidae) species group, with an examination of the effect of recombination and introgression on species tree inference. Molecular Phylogenetics and Evolution 70: 13-28. http://dx.doi.org/10.1016/j.ympev.2013.08.014

Additionally, please cite the Dryad data package:

Halas D, Simons AM (2013) Data from: Cryptic speciation reversal in the Etheostoma zonale (Teleostei: Percidae) species group, with an examination of the effect of recombination and introgression on species tree inference. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.n7j8q
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: