geo-genomic predictors of genetree heterogeneity explain phylogeographic and introgression history: a case study in an Amazonian bird (Thamnophilus aethiops)

Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the biogeographic history of four populations of an Amazonian antbird, Thamnophilus aethiops, whose biogeographic history was associated with the dynamic evolution of the Madei..., , , # Geo-genomic predictors of genetree heterogeneity explain phylogeographic and introgression history: a case study in an Amazonian bird (Thamnophilus aethiops)

This dataset contains R scripts for replicating analyses with chromosome length, along with output from TWISST

Key to directories:

1. treeslider: directory containing chromosome trees from astral (.tre files), output from treeslider analyses containing sliding window topologies (Thamno_aethio_50000bp_window_min5snps.tree_table.csv), and the key to scaffold names in the .csv results file (Scaffold_names.csv). \"NA\" values in \"Scaffold_names.csv\" are given for non-chromosome assembly scaffolds as these were not used in any analyses. Columns for these files can be defined as follows:
* X - The scaffold \"number\" used in the analysis, corresponds to \"scaffold\" column in \"Thamno_aethio_50000bp_window_min5snps.tree_table.csv\"
* scaffold_name - The name of the scaffold according to the reference genome used in the ipyrad assemb...