Data from: Evaluating summary statistics used to test for incomplete lineage sorting: mito-nuclear discordance in the reef sponge Callyspongia vaginalis

 

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Title Catalase
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Description DNA sequences from Callyspongia vaginalis for the Catalase gene (partial coding sequence)
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Title Cathespsin
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Description DNA sequences from Callyspongia vaginalis for the Cathepsin gene (partial coding sequence)
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Title Cirhin
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Description DNA sequences from Callyspongia vaginalis for the Cirhin gene (partial coding sequence)
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Title Elongation_factor1a
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Description DNA sequences from Callyspongia vaginalis for the Elongation factor 1 alpha gene (partial coding sequence)
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Title Filamin
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Description DNA sequences from Callyspongia vaginalis for the Filamin gene (partial coding sequence)
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Title Macrophage_expressed_protein
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Description DNA sequences from Callyspongia vaginalis for the Macrophage expressed protein gene (partial coding sequence)
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Title R script Summary Statistics
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Description This R script was used to calculates the summary statistics theta, nucleotide diversity, and PhiST for simulated and empirical data
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Title Script_to_split_infiles
Downloaded 12 times
Description This python script was used to split one file with 1000 simulated datasets into 1000 files with one dataset each. This script was used after simulating data in ms and seqgen and before summary statistics were calculated using the R script.
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Title Scripts_null_distributions
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Description This file contains the ms and seqgen commands used to simulate the data used to create the null distributions in the hypothesis testing for incomplete lineage sorting in Callyspongia vaginalis
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Title Simualted Data for ILS Null Fast Rate
Downloaded 36 times
Description This file contains the simulated data used to create the null distributions for the test of incomplete lineage sorting in Callyspongia vaginalis based on the fast substitution rate
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Title Simualted Data for ILS Null Slow Rate
Downloaded 35 times
Description This file contains the simulated data used to create the null distributions for the test of incomplete lineage sorting in Callyspongia vaginalis based on the slow substitution rate
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Title Simulated Data For SumStat Test
Downloaded 47 times
Description This file contains the data simulated to test the performance of different summary statistics to detect incomplete lineage sorting. The name of each file indicates the age of the population divergence under which the data were simulated.
Download Simulated Data For SumStat Test.zip (5.646 Mb)
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Title ENA_accession_numbers_and_sequences
Downloaded 57 times
Download ENA_accession_numbers_and_sequences.xlsx (64.18 Kb)
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When using this data, please cite the original publication:

DeBiasse MB, Nelson BJ, Hellberg ME (2014) Evaluating summary statistics used to test for incomplete lineage sorting: mito-nuclear discordance in the reef sponge Callyspongia vaginalis. Molecular Ecology 23(1): 225-238. http://dx.doi.org/10.1111/mec.12584

Additionally, please cite the Dryad data package:

DeBiasse MB, Nelson BJ, Hellberg ME (2013) Data from: Evaluating summary statistics used to test for incomplete lineage sorting: mito-nuclear discordance in the reef sponge Callyspongia vaginalis. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.hn104
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