UC Riverside

The development of sequencing techniques and increased availability of genome assemblies have enabled comparative studies on genome evolution in the non-model organisms to better understand genomic diversity and adaptation. Using genomic data, we investigated evolutionary questions in the kangaroo rats (genus Dipodomys), a group of New World rodents adapted to arid and semi-arid habitats, and we revealed examples of genomic signatures of their speciation and adaptive evolution. We first resolved the taxonomic issue of whether the formerly conspecific species with different karyotypes, the agile kangaroo rat (AKR, D, agilis, 2N=62) and the Dulzura kangaroo rat (DKR, D. simulans, 2N=60) are distinct species. The results supported their species level status with no evidence of sympatry or interspecific gene flow. We estimated their divergence time as ~0.7 Mya in middle Pleistocene, followed by a ~5-fold decline in the DKR’s effective population size (Ne) to ~20,000 at ~0.1 Mya, recently recovering to ~50,000, converging with that of AKR. AKR is generally distributed to higher elevations than DKR, and we investigated the inter- and intra-specific effects of elevation. The mean length of runs of homozygosity (ROHs) was negatively correlated with the elevation, suggested more structured populations at higher elevations in the two species, yet the levels of nucleotide diversity (π) were constant. AKR showed more selective sweeps than DKR, apparently associated with adaptation to high elevation, e.g., thermoregulation and response to hypoxic stress, and intraspecific comparisons among populations also revealed selective sweeps associated with local adaptation linked to elevation. The changes identified appeared to be regulatory. Finally, we employed data-driven and hypothesis-driven approaches to identify genes under positive selection in arid adapted heteromyids (kangaroo rats and mice and pocket mice) and convergently in unrelated arid adapted rodents including jerboa, gerbil, and cactus mouse. Notable among the candidate genes were those involved in energy production and hemostasis, and in response to osmotic stress.