Repeated mitochondrial capture with limited genomic introgression in a lizard group

Mitochondrial introgression is common among animals and is often first identified through mitonuclear discordance — discrepancies between evolutionary relationships inferred from mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA). Over recent decades, genomic data have also revealed extensive nuclear introgression in many animal groups, with implications for genetic and phenotypic diversity. However, the extent to which mtDNA introgression corresponds to nuDNA introgression varies. Here, we investigated historical and recent introgression in the Gehyra nana-occidentalis clade, a complex group of Australian geckos with documented cases of mitonuclear discordance suggestive of repeated mtDNA introgression. We hypothesised that mitonuclear discordance in this clade reflects mtDNA introgression with substantial nuclear introgression. Despite evidence of repeated mtDNA introgression, however, we found little to no evidence of historical nuDNA introgression using exon capture and genome-wide s..., , , # Data from: Repeated mitochondrial capture with limited genomic introgression in a lizard group

## Description of the data and file structure

Six folders are included here, the contents of each are outlined. The R script is available via Zenodo.

### Files and variables

#### File: mtDNA.zip

**Description:** This folder simply contains two ND2 mitochondrial DNA sequence alignments in fasta format along with the respective partition file (nd2_partitions.txt). The two sequence alignments are: 1) nd2-600.fasta, which contains all 600 samples; and 2) nd2-subset-78.fasta, which is a representative subset of 78 of these 600 samples to create a phylogeny that can actually fit onto a multi-panel figure.

#### File: Exons.zip

**Description:** This folder contains three files. The concat.all.fasta file is a concatenated sequence alignment of 1478 exotic loci, with the concat.partitions.txt file being the associated partition file. The all-100lc.phy file contains the 1000 longest exotic loci ...,