Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus)

Phylogenomics allows us to uncover the historical signal of evolutionary processes through time and estimate phylogenetic networks accounting for these signals. Insight from genome-wide data further allows us to pinpoint the contributions to phylogenetic signal from hybridization, introgression, and ancestral polymorphism across the genome. Here, we focus on how these processes have contributed to phylogenetic discordance among rattlesnakes (genera Crotalus and Sistrurus), a group for which there are numerous conflicting phylogenetic hypotheses based on a diverse array of molecular datasets and analytical methods. We address the instability of the rattlesnake phylogeny using genomic data generated from transcriptomes sampled from nearly all known species. These genomic data, analyzed with coalescent and network-based approaches, reveal numerous instances of rapid speciation where individual gene trees conflict with the species tree. Moreover, the evolutionary history of rattlesnakes is ..., , , # Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus)

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Sequence data, individual ML gene trees, and dated species tree

## Description of the data and file structure

`Rattlesnake_final_fastas.zip` - This directory contains 3,707 fasta files used for data analysis in this paper; all fasta files end in .fasta. Loci in this directory include benchmarking universal single-copy othologs (\"BUSCOs\"; these are named like '301078at32523.fasta'), ultra-conserved loci (named for example like 'uce-7817.fasta'), anchored hybrid enrichment loci ('AHE-L223.fasta'), traditional Sanger loci (e.g. 'HLCS.fasta'), and novel orthologous transcript sequences ('OG0005327.fasta').

`All_gene_trees.zip` - this directory contains 3,707 ML gene trees from IQtree; all gene tree files end in .treefile. The gene trees are named similarly to the above locus file names and each ...