DOI: 10.5061/dryad.hn104
title: Data from: Evaluating summary statistics used to test for incomplete lineage sorting: mito-nuclear discordance in the reef sponge Callyspongia vaginalis

description: Conflicting patterns of population differentiation between the
 mitochondrial and nuclear genomes (mito-nuclear discordance) have become
 increasingly evident as multilocus datasets have become easier to
 generate. Incomplete lineage sorting (ILS) of nucDNA is often implicated
 as the cause of such discordance, stemming from the large effective
 population size of nucDNA relative to mtDNA. However, selection,
 sex-biased dispersal, and historical demography can also lead to
 mito-nuclear discordance. Here we compare patterns of genetic diversity
 and subdivision for six nuclear protein-coding gene regions to those for
 mtDNA in a common Caribbean coral reef sponge, Callyspongia vaginalis,
 along the Florida reef tract. We also evaluated a suite of summary
 statistics to determine which are effective metrics for comparing
 empirical and simulated data when testing drivers of mito-nuclear
 discordance in a statistical framework. While earlier work revealed three
 divergent and geographically subdivided mtDNA COI haplotypes separated by
 2.4% sequence divergence, nuclear alleles were admixed with respect to
 mitochondrial clade and geography. Bayesian analysis showed substitution
 rates for the nuclear loci were up to 7 times faster than for
 mitochondrial COI. Coalescent simulations and neutrality tests suggested
 that mito-nuclear discordance in C. vaginalis is not the result of ILS in
 the nucDNA or selection on the mtDNA but is more likely caused by changes
 in population size. Sperm-mediated gene flow may also influence patterns
 of population subdivision in the nucDNA.
description: CatalaseDNA sequences from Callyspongia vaginalis for the Catalase gene (partial coding sequence)CathespsinDNA sequences from Callyspongia vaginalis for the Cathepsin gene (partial coding sequence)CirhinDNA sequences from Callyspongia vaginalis for the Cirhin gene (partial coding sequence)Elongation_factor1aDNA sequences from Callyspongia vaginalis for the Elongation factor 1 alpha gene (partial coding sequence)FilaminDNA sequences from Callyspongia vaginalis for the Filamin gene (partial coding sequence)Macrophage_expressed_proteinDNA sequences from Callyspongia vaginalis for the Macrophage expressed protein gene (partial coding sequence)R script Summary StatisticsThis R script was used to calculates the summary statistics theta, nucleotide diversity, and PhiST for simulated and empirical dataR_script_SumStatsScript_to_split_infilesThis 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.Scripts_null_distributionsThis 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 vaginalisSimualted Data for ILS Null Fast RateThis 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 rateSimualted Data for ILS Null Slow RateThis 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 rateSimulated Data For SumStat TestThis 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.ENA_accession_numbers_and_sequences