DOI: 10.5061/dryad.f1vhhmh0t
title: Data from: A 4-lineage statistical suite to evaluate the support of large-scale retrotransposon insertion data to reconstruct evolutionary trees

description: Retrophylogenomics makes use of genome-wide retrotransposon
 presence/absence insertion patterns to resolve questions in phylogeny and
 population genetics. In the genomics era, evaluating high-throughput data
 requires the associated development of appropriately powerful statistical
 tools. The currently used KKSC 3-lineage statistical test for estimating
 the significance of retrophylogenomic data is limited by the number of
 possible tree topologies it can assess in one step. To improve on this, we
 have extended the analysis to simultaneously compare 4-lineages, enabling
 us to evaluate ten distinct presence/absence insertion patterns for 26
 possible tree topologies plus 129 trees with different incidences of
 hybridization or introgression. The new tool provides statistics for cases
 involving multiple ancestral hybridizations/introgressions, ancestral
 incomplete lineage sorting, bifurcation, and polytomy. The test is
 embedded in a user-friendly web R-application
 (http://retrogenomics.uni-muenster.de:3838/hammlet/) and is available for
 use by the scientific community.
description: # Data from: A 4-lineage statistical suite to evaluate the support of
 large-scale retrotransposon insertion data to reconstruct evolutionary
 trees **Appendix_1.pdf:** Detailed description of mathematical models
 **Appendix_2.csv:** Supplementary Tables S1-S7 **S1:** Comparison of the
 *stepwise* method with chi-square distribution against a 50% chi-square
 distribution with a 50% point mass 0 mixture criterion for frequency of
 correct recognition of models in the Poisson randomized sets. **S2:**
 Comparison of the *reverse* method and chi-square distribution against
 binary chi-square distribution according to degrees of freedom plus point
 mass 0 mixture and binary chi-square distribution according to degrees of
 freedom plus point mass 1 mixture criteria for frequency of correct
 recognition of models in the Poisson randomized set. **S3:** Testing the
 *reverse* method and chi-square distribution criterion for frequency of
 correct recognition of models in the Poisson randomized set. **S4:**
 Testing the *stepwise* method and chi-square distribution criterion for
 frequency of correct recognition of models in the Poisson randomized set.
 **S5:** Testing the *reverse* method and empirical distribution criterion
 (eCDF) for frequency of correct recognition of models in the Poisson
 randomized set. **S6:** Testing the *stepwise* method and empirical
 distribution criterion (eCDF) for frequency of correct recognition of
 models in the Poisson randomized set. **S7:** Testing the dependence of
 the number of user makers on the frequency of correct recognition of
 models in the Poisson randomized set.  **S2Appendix_3.csv:** Supplementary
 Tables S8-S9 **S8:** Simple conflict-free patterns. **S9:** Formulas for
 generating data for KKSC comparisons of resolved tree topologies (without
 hybridization). **Appendix_4.pdf:** Sources of genomes used and
 RepeatMasker reports