Museum skins enable identification of introgression associated with cytonuclear discordance

Increased sampling of genomes and populations across closely related species has revealed that levels of genetic exchange during and after speciation are higher than previously thought. One obvious manifestation of such exchange is strong cytonuclear discordance, where the divergence in mitochondrial DNA (mtDNA) differs from that for nuclear genes more (or less) than expected from differences between mtDNA and nuclear DNA (nDNA) in population size and mutation rate. Given genome-scale datasets and coalescent modelling, we can now confidently identify cases of strong discordance and test specifically for historical or recent introgression as the cause. Using population sampling, combining exon capture data from historical museum specimens and recently collected tissues, we showcase how genomic tools can resolve complex evolutionary histories in the brachyotis group of rock-wallabies (Petrogale). In particular, applying population and phylogenomic approaches, we can assess the role of dem..., This dataset includes ~1000 nuclear loci from a custom-designed exon capture approach (SeqCap EZ Developer Library; Roche NimbleGen), designed from a yellow-footed rock-wallaby (Petrogale xanothpus) transcriptome. The raw sequencing data were processed following the workflow of Singhal (2013), and scripts for this pipeline are available from 10.5061/dryad.7c99f (see Supplementary Materials and Methods here for more detail). The dataset includes samples from both modern and historical specimens, and these were processed in different pipelines. Modern samples were assembled de novo from the cleaned sequencing reads following the workflow described in Bragg et al. (2016). The historical samples were assembled using custom scripts https://github.com/CGRL-QB3-UCBerkeley/denovoTargetCapturePhylogenomics) and published methods (Bi et al. 2012; Portik et al. 2016; refer to Supplementary Materials and Methods here for more detail). Data was finally aligned and filtered using the Eaphy (v1.2..., The files in this repository are either text, Word, Excel or PDF. Most software programs can be used to open or view these files. The sequence alignments (e.g., .phy or .fasta) can be opened in text documents., 28 June 2021

GENERAL INFORMATION

Title: Museum skins enable identification of introgression associated with cytonuclear discordance

Principal Investigator: Dr Sally Potter, School of Natural Sciences, Macquarie University, Sydney, NSW, Australia

[[e-mail]](mailto:[e-mail])

Date of data collection: 2013-2023

Geographic location of data collection: northern Australia, Kimberley region of Western Australia, Top End region of Northern Territory to just across the border into Queensland, Australia

Keywords: mito-nuclear discordance, introgression, rock-wallabies, museum skins, exon capture

Citation: Potter S, Moritz C, Piggott MP, Bragg JG, Afonso Silva AC, Bi K, McDonald-Spicer C,Turakulov R, Eldridge MDB (2023) Museum skins enable identification of introgression associated with cytonuclear discordance. Systematic Biology submitted.

DATA & FILE OVERVIEW

These data were generated to investigate the evolutionary relationships and divergence history of the...,