DOI: 10.5061/dryad.cn74h
title: Data from: Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium)

description: High-throughput sequencing is helping biologists to overcome the
 difficulties of inferring the phylogenies of recently diverged taxa. The
 present study analyzes the phylogenetic signal of genomic regions with
 different inheritance patterns using genome skimming and ddRAD-seq in a
 species-rich Andean genus (Diplostephium) and its allies. We analyzed the
 complete nuclear ribosomal cistron, the complete chloroplast genome, a
 partial mitochondrial genome, and a nuclear-ddRAD matrix separately with
 phylogenetic methods. We applied several approaches to understand the
 causes of incongruence among datasets, including simulations and the
 detection of introgression using the D-statistic (ABBA-BABA test). We
 found significant incongruence among the nuclear, chloroplast, and
 mitochondrial phylogenies. The strong signal of hybridization found by
 simulations and the D-statistic among genera and inside the main clades of
 Diplostephium indicate reticulate evolution as a main cause of
 phylogenetic incongruence. Our results add evidence for a major role of
 reticulate evolution in events of rapid diversification. Hybridization and
 introgression confound chloroplast and mitochondrial phylogenies in
 relation to the species tree as a result of the uniparental inheritance of
 these genomic regions. Practical implications regarding the prevalence of
 hybridization are discussed in relation to the phylogenetic method.
description: Matrices and control
 filesHere we provide all the
 necessary files to run the analyses described in the paper. Files are
 organized by folders. dating_analysis -&gt; control files necessary to run
 the dating analysis. ddrad_data -&gt; Intermediate files from pyrad's
 steps 3 and 5, and matrices derived from the ddRAD method used for the
 phylogenetic and introgression analyses. genome_skimming_matrices -&gt;
 matrices derived from genome skimming method used in the phylogenetic
 analyses. JML_analysis -&gt; all the files used to run and visualize the
 JML analysis.matrices_and_control_files.zipread_subsets_1Files with the subsets of reads used in the study Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering). cp indicates chloroplast reads mt indicates mitochondrial reads nr indicates nuclear ribosomal readsread_subsets_2Files with the subsets of reads used in the study Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering). cp indicates chloroplast reads mt indicates mitochondrial reads nr indicates nuclear ribosomal readsread_subsets_3Files with the subsets of reads used in the study Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering). cp indicates chloroplast reads mt indicates mitochondrial reads nr indicates nuclear ribosomal readsread_subsets_4Files with the subsets of reads used in the study Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering). cp indicates chloroplast reads mt indicates mitochondrial reads nr indicates nuclear ribosomal readsread_subsets_5Files with the subsets of reads used in the study Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering). cp indicates chloroplast reads mt indicates mitochondrial reads nr indicates nuclear ribosomal readsread_subsets_6Files with the subsets of reads used in the study Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering). cp indicates chloroplast reads mt indicates mitochondrial reads nr indicates nuclear ribosomal reads