Ancient ILS

Ancient ILSEvaluating the impact of conflicting phylogenetic signal on hypotheses of early animal evolutionFigshare repositoryCaitlin Cherryh, 2024The evolutionary relationships between the Metazoa have been particularly difficult to resolve, due to the deep evolutionary timescales and due to a rapid radiation at the root of the animal tree. Both incomplete lineage sorting and long branch attraction have been hypothesised to impact metazoan tree inference. By applying concordance factors, the topological variation at key branches within the metazoan tree can be quantified to determine the evolutionary processes involved. This repository contains output files from calculating and analysing the gene and quartet concordance factors of 12 empirical metazoan phylogenetic datasets.The caitlinch/ancient_ILS GitHub repository contains all R scripts necessary to repeat these analyses: https://github.com/caitlinch/ancient_ILS/Software programsAll trees were estimated with IQ-Tree2 v2.2.2.6Gene concordance factors calculated with IQ-Tree2 v2.2.2.6Quartet concordance factors calculated with ASTRAL v5.6.9Datareadme.txtRepository structureempirical_phylogenetic_alignments.pdfDocumentation of the 12 empirical alignments analysed in this study, including original manuscript and record of where each matrix was obtained. empirical_alignmentsMatrices and partition files used in this studAlignments have been updated to have consistent taxon names to allow alignments to be batch processed using scriptsml_trees/Maximum likelihood trees estimated from each of the 12 empirical alignments. For each alignment, we estimated one tree under a Partition model using the partition file, and one tree under a C60 modelpartition_ML_trees.zip: IQ-Tree2 output from estimating a partitioned maximum likelihood tree from each alignment, including .treefile, .log and .iqtree filesC60_ML_trees.zip: IQ-Tree2 output from estimating a maximum likelihood tree under a C60 model of substitution from each alignment, including .treefile, .log and .iqtree filesconstrained_trees/3 constrained trees were estimated from each dataset with each model of substitution, one for each hypothesis of evolution. The three hypothesis of metazoan evolution under consideration were: Ctenophora as sister to all other metazoans; Porifera as sister to all other metazoans; and a monophyletic clade consisting of Ctenophora and Porifera as sister to all other animals.This resulted in a total of 6 constrained trees for each alignment (3 Partitioned, 3 C60)partition_constrained_trees.zip: IQ-Tree2 output from estimating constrained partitioned maximum likelihood tree from each alignment, including .treefile, .log and .iqtree filesc60_constrained_trees.zip: IQ-Tree2 output from estimating constrained maximum likelihood trees under a C60 model of substitution from each alignment, including .treefile, .log and .iqtree filesgene_trees/Gene trees estimated from the 12 empirical alignments. The partition files were used to separate each alignment into individual genes. One maximum likelihood gene tree was estimated from each gene with each model of substitution.mfp_genes.zip: Maximum likelihood gene tree for each gene. Substitution model for each gene was the best substitution model as determined by ModelFinder. Models were extracted from the IQ-Tree2 output after estimating partitioned maximum likelihood trees from each alignment, from the output file best_model.nexc60_genes.zip: Gene trees estimated with C60 substitution modelgcf/Gene concordance factors, calculated using maximum likelihood trees and gene treesgcf_partition.zip: Gene concordance factors calculated from Partition model trees and gene treesgcf_c60.zip: Gene concordance factors calculated from C60 model trees and gene treesqcf/Quartet concordance factors, calculated using maximum likelihood trees and gene treesqcf_partition.zip: Quartet concordance factors calculated from Partition model trees and gene treesqcf_c60.zip: Quartet concordance factors calculated from C60 model trees and gene trees