DOI: 10.5061/dryad.wwpzgmsvv
title: Data from: Repeated mitochondrial capture with limited genomic introgression in a lizard group

description: 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 single nucleotide polymorphism (SNP) data. We also found no
 evidence of gene flow at modern contact zones and detected only a single
 early generation hybrid. Unsurprising given these results, we found no
 evidence of transgressive, intermediate, or more variable morphological
 phenotypes in taxa with introgressed mtDNA. These findings suggest that
 hybridisation in this system has, at least in some cases, resulted in
 repeated mitochondrial introgression with little or no nuclear
 introgression. This pattern aligns with other studies showing limited
 nuDNA introgression in taxa with mitonuclear discordance, highlighting a
 potentially broader trend in animal radiations.
description: # 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 in Philip format, with loci already partitioned. #### File:
 Phylos.zip **Description:** This folder contains four phylogeny files in
 Newick format. The two mtDNA trees inferred from IQ-TREE are nd2-600.tree
 and nd2-subset-78.tree, which correspond to the respective alignments
 mentioned above. The Astral_thresh30.tree file is the ASTRAL-III phylogeny
 inferred from 1478 gene trees that had branches with bootstrap support
 less than 30 collapsed (see before for the respective gene tree file). The
 bpp-A00-1000lc.tree file is the output of phylogenetic analysis using BPP
 across all lineages. #### File: BPP.zip **Description:** There are four
 subfolders within this folder. Each folder contains a additional
 subfolders (explained below), each with a the three files needed to run
 the respective BPP analysis: a sequence alignment (1000 exons in phylip
 format), an imap file (matching samples to lineages; txt format), and a
 control (.ctl) file that specifies the settings for the respective BPP
 analysis. 1\. **all-lineages-phylo** contains a subfolder to run the A01
 analysis (phylogenetic inference) and the A00 analysis (inference of
 branch lengths [tau] and population sizes [theta]). Each contains the
 necessary Phylip alignment, iMap file, and control file. 2\.
 **MSCi_multi-NM** contains three subfolders to run the MSCi analyses
 testing unidirectional introgression from multiporosa to nanamulti
 (m-nm-uni), unidirectional introgression from nanamulti to multiporosa
 (nm-m-uni), and bidirectional introgression between these two (m-nm-bd).
 Each contains the necessary Philip alignment, iMap file, and control file.
 3\. **MSCi_multi-OR** contains three subfolders to run the MSCi analyses
 testing unidirectional introgression from multiporosa to occiOR
 (m-OR-uni), unidirectional introgression from occiOR to multiporosa
 (OR-m-uni), and bidirectional introgression between these two (m-OR-bd).
 Each contains the necessary Phylip alignment, iMap file, and control file.
 4\. **MSCi_YI-KL** contains three subfolders to run the MSCi analyses
 testing unidirectional introgression from occiYI to occiKL (YI-KL-uni),
 unidirectional introgression from occiKL to occiYI (KL-YI-uni), and
 bidirectional introgression between these two (YI-KL-bd). Each contains
 the necessary Phylip alignment, iMap file, and control file. #### File:
 Genetrees.zip **Description:** This folder contains two newick files
 containing 1478 gene trees inferred using IQ-TREE for subsequent analysis
 via ASTRAL-III. The genetrees-no-collapse.newick file contains all
 unmodified gene trees. The genetrees-30collapse.newick file contains gene
 trees that have had branches with bootstrap support values less than 30
 collapsed (the one used for ASTRAL analysis). #### File: R\_data.zip
 **Description:** This folder contains three files needed to run the R
 script (MolecEcol_2025.R; see below) that performs SNP-based analyses and
 as multivariate analyses of morphological data. 1\.
 **nana-group_dart.csv** is the full DArT SNP data. This is in the typical
 format provided by DArT, where columns represent individuals and rows
 represent variant sites. For variant sites, a 0 value indicates the sample
 is homozygous for the reference allele, a 1 value represents a
 heterozygote for that site, and a 2 value represents a heterozygote for
 that site. Data in this format can be imported and analysed in R using the
 package dartR. 2\. **nana-group-meta-2023.csv** is the metadata associated
 with the SNP data mentioned above. Columns show the sample ID, the lineage
 to which the sample belongs, and the latitude and longitude of the
 respective sample. 3\. **nana-occi_morph.csv** is the morphological data.
 All measurements are in mm. Rows represent individuals and columns
 represent: "id", the id number of the specimen; "sex",
 the sex of the specimen if it could be determined; "lineage",
 the lineage to which the sample belongs; "pop", a shortened
 version of the lineage name; "group", whether the lineage
 belongs to the "occi" group or the "nana" group;
 "SVL", snout-to-vent length; "HL", head length;
 "HD", head depth; "HW", head width; "SL",
 snout length; "OW", orbit width; "WBE", width between
 eyes; "ILL", inter-limb length; "HLL", hindlimb
 length; "FLL", forelimb length. ## Code One R script is included
 with the Zenodo files: **MolecEcol_2025.R** — This imports the SNP data
 and morphology data to perform SNP filtering, Principal Coordinates
 Analysis, New Hybrids, isolation-by-distance analysis at contact zones,
 sNMF analysis, MANOVA to test for sexual dimorphism, MANOVA to test for
 morphological divergence among lineages, Principal Components Analysis of
 morphological data, Fligner-Killeen test to assess whether body size
 variance differs among lineages.