Limited introgression between rock-wallabies with extensive chromosomal rearrangements

Chromosome rearrangements can result in the rapid evolution of hybrid incompatibilities. Robertsonian fusions, particularly those with monobrachial homology, can drive reproductive isolation amongst recently diverged taxa. The recent radiation of rock-wallabies (genus Petrogale) is an important model to explore the role of Robertsonian fusions in speciation. Here we pursue that goal using an extensive sampling of populations and genomes of Petrogale from north-eastern Australia. In contrast to previous assessments using mitochondrial DNA or nuclear microsatellite loci, genomic data are able to separate the most closely related species and to resolve their divergence histories. Both phylogenetic and population genetic analyses indicate introgression between two species that differ by a single Robertsonian fusion. Based on the available data, there is also evidence for introgression between two species which share complex chromosomal rearrangements. However, the remaining results show no consistent signature of introgression amongst species pairs and where evident, indicate generally low introgression overall. X-linked loci have elevated divergence compared to autosomal loci indicating a potential role for genic evolution to produce reproductive isolation in concert with chromosome change. Our results highlight the value of genome scale data in identifying a strong role for Robertsonian fusions and structural variation in speciation.

Methods
We used the draft genome assembly for Petrogale penicillata to serve as a reference for mapping reads and calling single nucleotide polymorphisms (SNPs). We generated three datasets, two exon sequence datasets for the six species in the penicillata group and one SNP dataset for five species (excluding P. coenensis). The SNP dataset we refer to as "DArT” based on the genome reduction approach used. It genotyped 22,724 SNPs from 77 individuals with a mean of 15 per taxon (including four known F1 P. godmani x P. mareeba hybrids). The second dataset is referred to as “phased exons” because it consists of phased haplotype sequences (627,699 bp) from exon capture experiments. It resolved haplotypes at 1215 loci for 67 individuals (mean of 15 per taxon). The third dataset is referred to as “unphased exons” and is based on sequence data (843,619 bp) from exon capture experiments, and includes 1617 loci on those same individuals.

Exon data was collected using a custom in-solution exon capture approach using target sequences from a yellow-footed rock-wallaby (Petrogale xanthopus) transcriptome. Sequences were cleaned and de novo assembled using a range of scripts included here. 

SNP data was generated using Diversity Arrays technology and raw sequencing data was mapped to the reference Petrogale genome using the GATK docker (information included here as well).