Data from: Explicit tests of paleodrainage connections of southeastern North America and the historical biogeography of Orangethroat Darters (Percidae: Etheostoma: Ceasia)

Bossu CM, Beaulieu JM, Ceas PA, Near TJ

Date Published: August 5, 2013

DOI: http://dx.doi.org/10.5061/dryad.51s8p

 

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Title lagrange_analysis_files
Downloaded 14 times
Description We applied the DEC model implemented in lagrange (Ree & Smith 2008) to obtain reconstructed ancestral areas at all internal nodes and infer probable dispersal scenarios over a distribution of dated mitonuclear phylogenies and dated nuclear species trees. The files implemented in lagrange include the geographic data for the mitonuclear data set and the nuclear species tree data set (.data files), the rate matrices for each time period within each paleodrainage hypothesis (.rm files), the distribution of mitonuclear phylogenies and species trees (.trees files) and the scripts to call each (.lg files).
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Title BEAST and *BEAST analyses
Downloaded 11 times
Description We utilized a Bayesian strategy that relied on external fossil calibrations in the perciform fish clade Centrarchidae to time-calibrate the mtDNA phylogeny, individual gene trees inferred from each of the ten nuclear genes and a phylogeny inferred from the concatenation of ten nuclear genes, and a phylogeny inferred from the concatenation of ten nuclear and two mitochondrial genes in BEAST. We also calibrated divergence times on a nuclear species tree using *BEAST, excluding the mitochondrial genes to avoid incongruence among gene trees resulting from mitochondrial replacement via introgressive hybridization that is common among species of Ceasia. The xml files were generated in BEAUti, however the species tree divergence time xml file were also changed by hand. All samples were collected in the field and accession numbers for each gene accompany this dryad submission
Download dating_analyses_files.zip (272.8 Kb)
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Title Specimen_Genbank
Downloaded 20 times
Description A tab-delimited spread sheet of the specimens and genbank accession numbers generated in this study. The first column is the species identity, second column is the clode code identifier, and the remaining column are the gene names. The ten nuclear genes are placed above the two mitochondrial genes.
Download Specimen_Genbank.txt (17.08 Kb)
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Title spectabmtDNA_phyloParsed71911
Downloaded 7 times
Description Partitioned Bayesian analyses were used to infer sets of posterior phylogenetic trees from the densely sampled mtDNA dataset, these analyses were applied in BEAST and MrBayes. We sampled the Ceasia clade much more extensively, however centrarchid fossil calibration priors were not used to conduct divergence time analyses on the larger data set. The xml file was created in BEAUti. All samples were collected in the field and accession numbers for each gene accompany this dryad submission.
Download spectabmtDNA_2phyloParsed71911.xml (668.5 Kb)
Download spectabDNA_phyloParsed1.bay.unsafe (645.1 Kb)
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When using this data, please cite the original publication:

Bossu CM, Beaulieu JM, Ceas PA, Near TJ (2013) Explicit tests of paleodrainage connections of southeastern North America and the historical biogeography of Orangethroat Darters (Percidae: Etheostoma: Ceasia). Molecular Ecology 22(21): 5397–5417. http://dx.doi.org/10.1111/mec.12485

Additionally, please cite the Dryad data package:

Bossu CM, Beaulieu JM, Ceas PA, Near TJ (2013) Data from: Explicit tests of paleodrainage connections of southeastern North America and the historical biogeography of Orangethroat Darters (Percidae: Etheostoma: Ceasia). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.51s8p
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