Whole-genomes illuminate the drivers of gene tree discordance and the tempo of tinamou diversification (Aves: Tinamidae)

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 an..., , , # 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 ...,