Investigating the impact of chromosomal rearrangements on the evolutionary history of rodents leading to Mus musculus

One of the long-standing arguments in the area of evolutionary biology is the extent to which chromosomal rearrangements contribute to the process of speciation. The mammalian order Rodentia was used as a model to investigate the effects of chromosomal rearrangements on gene expression, using newly developed computational methods. Predicted ancestral karyotypes for 7 ancestors across 73 million years leading from the overarching Rodentia ancestor to mouse were reconstructed, which were then used to trace the number and type of rearrangements back through the lineage. Rodentia was found to be a highly rearranged order, with an average of 6.6 rearrangements per million years, higher than that seen in similar studies in birds and Eutherians. The ancestral reconstructions were also found to be highly fragmented, producing diploid numbers often double that in comparable cytogenetic predictions, suggesting that the reconstructions need further refinement to be representative. The effect of chromosomal rearrangements on gene expression was investigated using RNA-Seq data from liver and tissue, and the inversions identified from the ancestral reconstructions, due to their link to recombination suppression. Gene expression correlation was compared between species for gene orthologues found within inversions between mouse and the Muridae ancestor, compared to those not in inversions. A reduction of gene expression was seen in genes present in inversions, however this was found to be statistically insignificant. The results of this work do not indicate that speciation is driven by inversions in Rodentia, however it is believed that future work on the reconstructions, and greater understanding of the implication of the wider genome architecture on gene expression, may lead to a more complete picture. There are still many avenues for future work to investigate before chromosomal speciation can be ruled out in this instance.