DOI: 10.5061/dryad.7h44j102s
title: Data from: Whole-genomes illuminate the drivers of gene tree discordance and the tempo of tinamou diversification (Aves: Tinamidae)

description: As an old group that has diversified in South America over millions of
 years, the tinamous (Palaeognathae: Tinamidae) are of high interest for
 understanding the evolution of birds and the assembly of the Neotropical
 biota. However, there are currently no complete species-level phylogenies
 of this group. Most prior work has been based on either morphological data
 or a small number of molecular markers, each of which has limited
 capability for reconstructing the tinamou phylogeny. Therefore, the
 interrelationships of most tinamou species are uncertain. We analyzed 80
 whole genomes from a mix of historical study skins and frozen tissues,
 including all 46 recognized species of tinamous, to (1) reconstruct their
 interrelationships, (2) estimate the timeframe of tinamou evolution, and
 (3) examine the effects of incomplete lineage sorting (ILS) and ancestral
 introgression on genome evolution. We compared results for coding (BUSCO)
 and ultraconserved element (UCE) loci, as well as sex-linked and autosomal
 markers, and used fossil-calibrated tip-dating to estimate divergence
 times. Tinamous diverged from their sister-group, the extinct Moas, 50-60
 mya, and their crown divergence occurred roughly 30-40 mya, followed by
 constant diversification rates until the present. Phylogenetic
 reconstructions were largely robust across methods and datasets. Only one
 clade in the genus Crypturellus displayed substantial species-tree
 discordance across the different data sets. To investigate the impacts of
 introgression on this discordance, we quantified introgression for 100kb
 non-overlapping windows across the genome and identified pervasive
 genome-wide introgression. The distribution of this introgression across
 the genome was dependent on the assumed phylogeny applied to the f-branch
 model. When assuming one of these topologies in the f-branch model,
 patterns of introgression matched theoretical predictions about genome
 architecture. Overall, we present the most complete phylogeny for tinamous
 to date, identify an unrecognized species, and provide a case study for
 species-level phylogenomic analysis using whole genomes
description: # Data from: Whole-genomes illuminate the drivers of gene tree discordance
 and the tempo of tinamou diversification (Aves: Tinamidae) This repository
 contains scripts and code for Musher et al. The main file is
 Tinamou-phylogenomics2.zip, which contains multiple folders with scripts
 and data. Folder details: ABBA-BABA-windows contains data needed to run
 and the results of the 100 kb window introgression analysis, including an
 R script to generate Figure 4B. * Abba-baba-windows.R = script for
 plotting introgression statistics * ABBABABAwindows.w100k.T1.csv = output
 from introgression analysis assuming Tree "T1" *
 ABBABABAwindows.w100k.T2.csv = output from introgression analysis assuming
 Tree "T2" * ABBABABAwindows.w100k.T3.csv = output from
 introgression analysis assuming Tree "T3" "ASTRAL"
 contains files with all collapsed gene trees in a single file for each
 dataset used as input for ASTRAL * Files ending in .trees are input gene
 trees for ASTRAL-III * Files ending in .log are output log files from
 ASTRAL-III * Files ending in .tre are output tree results from ASTRAL-III
 * File names include information about missing data (75p=75%; 100p=100%),
 dataset (e.g., UCE100=UCE's with 100 bp of flanking region)
 "phylonet" contains input and output files for phylonet, along
 with breakpoint analysis for determining the optimal m-value *
 "breakpoint_analysis.R" = R-script for finding optimal m-value *
 "model_likelihoods.xlsx" = list of likelihoods for each output
 network * Input files for phylonet analysis include ".nex"
 extension for autosomal and z-chromosome datasets of different values of m
 (migration). e.g., uce1000.cladeA.autosomes.m0.nex is the phylonet input
 for autosomal UCE dataset assuming m=0. and
 "uce1000.cladeA.chrz.m1.nex" is the input for the z-chromosome
 UCE dataset assuming m=1. - Output files from phylonet analysis include a
 ".log" extension following the same structure as the input.
 "RF.distances" contains a script for replicating several
 statistics and figures in the manuscript,
 "PIS_rf_dist_collapsed.R", output tables, and alignment/genetree
 files for each dataset. The R script also contains code for looking at
 node heights of phylogenetic triplets. * Sub-directories include gene
 trees from each of four datasets: BUSCO's (cds prefix), UCE100,
 UCE300, and UCE1000 (see supplemental materials). *
 "PIS_rf_dist_collapsed.R" is the R script used for estimating RF
 distances and modeling them against alignment attributes like GC content
 variation or parsimony-informative sites *
 "Topologies_Support.csv" contains gene concordance and bootstrap
 values for each species tree inferred from each dataset * .csv files
 contain output from the R-script, including columns for: * aln: the
 alignment name * pars.site: the number of parsimony informative sites *
 tot.sites: the alignment length * pars.site.prop: the proportion of
 parsimony informative sites * rf.dist.coll: the distance between the gene
 tree for each alignment and the inferred species tree of a given dataset.
 * gc.cont: variance in gc content for each alignment
 "MSCquartets" contains data and a script that will replicate
 quartet analyses for assessing the effect of ILS *
 "MSCquartents.R" = R-script for running MSCquartets *
 "autosomes-cladeA-100p.trees" = autosomal gene trees for clade A
 only sampling * "chrz-cladeA-100p.trees" = Z-chromosome gene
 trees for clade A only sampling "beast" contains input and
 results from the Beast analysis * Beuti_2.7_23_uces_6fossils+Moa_final.xml
 is the input file generated in Beauti. * The remaining three files are
 outputs from the beast analysis (.trees=posterior tree set, .log=posterior
 log-file, and .tre=summarized tree from treeAnnotator)
 "Filter_loci_for_beast" contains autsomal UCEs and gene trees
 for filtering prior to Beast analysis *
 "Autosomes-mafft-nexus-clean-trimmed-100p" is a directory
 containing all alignments and trees for autosomal UCEs used in the
 filtering exercise * "Filter_loci.R" is the R script used to
 filter loci * "Filtered_fastas" is the list of alignments in
 fasta format used for beast * "tinamous_27Aug24.csv" shows the
 details of the filtering exercise on all UCEs from
 "Autosomes-mafft-nexus-clean-trimmed-100p", including columns
 for * loc: alignment file used * Tre: tree-file used * seq.len: alignment
 length * var.sites: number of parsimony informative sites * var.frac:
 proportion of parsimony informative sites * lambda: the inferred value of
 lambda from the branch-length smoothing * log10lambda: log10 transformed
 lambda * LR: the likelihood ratio of the clock to the non-clock model of
 sequence evolution * RF: the RF distance between gene and species tree *
 p: the p-value of the likelihood ratio test * df: the degrees of freedom
 in the likelihood ratio test - "filtered_loci.csv": is the same
 table as above, but only including final loci after filtering
 "Trees" contains all concatenated and astral phylogenies for
 each dataset. Those with the prefix "concord" contain gene
 concordance values at all nodes. Those with the prefix "crypt"
 show only relationships for clade A. TESS contains a script,
 "TESS.R," for replicating the TESS analysis of diversification
 rates Table S1 is the supplementary table 1 referenced in the article
 text, containing a list of samples used in the study and BUSCO statistics
 for each genotype. Table S6 is a table of clade ages inferred by Beast2st2
 Tinamou_assembly_pipeline.txt is a list of commands used for bioinformatic
 assembly of tinamou whole genomes Supplemental_Materials.pdf: This PDF
 contains supplemental methods, tables, and figures supporting the studies
 of Musher et al.