DOI: 10.5061/dryad.mpg4f4r62
title: Speciation across biomes: rapid diversification with reproductive isolation in the Australian delicate mice

description: Phylogeographic studies of continental clades, especially when combined
 with palaeoclimate modelling, provide powerful insight into how
 environment drives speciation across climatic contexts. Australia, a
 continent characterized by disparate modern biomes and dynamic climate
 change, is a model system for reconstructing the impact of past and
 present environments on diversification. Here we use genomic-scale data
 (1310 exons and whole mitogenomes from n = 111 samples) to investigate
 Pleistocene diversification, cryptic diversity, and secondary contact in
 the Australian delicate mice (Hydromyini: Pseudomys), a recent radiation
 spanning almost all Australian environments. Across northern Australia, we
 find no evidence for introgression between cryptic lineages within
 Pseudomys delicatulus sensu lato, with palaeoclimate models supporting
 contraction and expansion of suitable habitat since the last glacial
 maximum. Despite multiple contact zones, we also find little evidence of
 introgression at a continental scale, with the exception of a potential
 hybrid zone in the mesic biome. In the arid zone, combined insights from
 genetic data and palaeomodels support a recent expansion in the arid
 specialist P. hermannsburgensis, and contraction in the semi-arid P.
 bolami. In the face of repeated secondary contact, differences in sperm
 morphology and chromosomal rearrangements are potential mechanisms that
 maintain species boundaries in these recently diverged species.
 Additionally, we describe the western delicate mouse as a new species and
 recommend taxonomic reinstatement of the eastern delicate mouse. Overall,
 we show that speciation in an evolutionarily young and widespread clade
 has been driven by environmental change, and potentially maintained by
 divergence in reproductive morphology and chromosome rearrangements.
description: Molecular Data Collection For frozen and ethanol preserved tissue samples,
 we extracted total genomic DNA using a standard Qiagen DNeasy Blood and Tissue Kit. For
 historical museum specimens, we used a phenol-chloroform extraction
 protocol optimised for historical DNA (Roycroft, MacDonald, et al., 2021; Roycroft,
 Moritz, et al., 2022). We
 prepared DNA libraries following a modified (Roycroft, Moussalli, et al.,
 2020) Meyer and Kircher
 (2010) protocol. Genomic libraries from historical
 specimens were treated with PreCR Repair Mix (New England BioLabs) to
 repair degraded DNA, following the manufacturer’s instructions. Samples
 were uniquely indexed with dual barcodes, and up to 96 sample libraries
 were pooled and hybridised using the custom sequence capture probe design
 for murine rodents described in Roycroft, Moussalli, et al.,
 (2020). This probe set
 targets 1.27Mb of genomic DNA (1417 exons, SeqCap EZ Developer Library;
 Roche NimbleGen). Post-capture libraries were sequenced on either an
 Illumina HiSeq 2500 or Novaseq SP platform (100 bp paired-end reads) at
 the Australian National University’s Biomolecular Resource
 Facility. Bioinformatic
 Processing Raw
 sequence data were processed using Exon Capture Pipeline for Phylogenetics (ECPP,
 https://github.com/Victaphanta/ECPP), following the settings described in Roycroft, Moussalli, et al., (2020), using the high-quality de novo mapping approach described in Roycroft, Moritz, et al., (2022). Targets were aligned using MAFFT (Katoh & Standley, 2013) and processed with BMGE (Criscuolo & Gribaldo, 2010) to remove poorly represented regions. We excluded loci with average heterozygosity &gt;3% across samples (putative paralogs) and filtered the final dataset to include only loci that were &gt;90% sample complete. The final filtered exon dataset consisted of 1310 exons, making up a combined nucleotide alignment of 1.15 Mb.  See Methods section of associated manuscript for full details and citations.
description: # Speciation across biomes: rapid diversification with reproductive
 isolation in the Australian delicate mice
 This repository contains
 final processed DNA sequence alignments (1310 nuclear exons and whole
 mitochondrial genomes) used in the manuscript Roycroft et al.
 'Speciation across biomes: rapid diversification with reproductive
 isolation in the Australian delicate mice', as well as species
 occurrence records used in niche modelling. ## Description of the data and
 file structure Files in this repository include; 1. A concatenated
 alignment of all nuclear exonic loci for all samples, in nexus format. At
 the footer of the file, there a nexus partition that defines the start and
 stop co-ordinates of all individual loci
 (**Roycroft_etal_delicates_1310exons_combined_221228154528_new_taxnames.nex**) 2. A whole mitochondrial genome alignment (filtered and trimmed to only include alignable regions) in fasta format (**Roycroft_etal_delicates_whole_mitogenome_alignment.fasta**) 3. Input alignment file for MCMCtree analysis in phylip format, partitioned by codon position, for one representative per lineage as used for molecular dating analysis (**combined_for_mcmctree.codon123.renamed.tips.phy**) ## Sharing/Access information The raw sequence reads that underlie these final processed files have been deposited at the Bioplatforms Australia Data Portal () as part of the Oz Mammals Genomics Initiative (doi:10.25953/cg5b-qd03). Link to publicly accessible location of the data: * ## Code/Software Sequence data were processed using Exon Capture Pipeline for Phylogenetics (ECPP, github.com/Victaphanta/ECPP), following the settings described in Roycroft, Moussalli, et al., (2020), using the high-quality *de novo* mapping approach described in Roycroft, Moritz, et al., (2022) - see methods section in the manuscript for full detail and citations