Comparative phylogeography reveals deep lineages and regional evolutionary hotspots in the <scp>M</scp>ojave and <scp>S</scp>onoran Deserts

Abstract

Abstract Aim We explored lineage diversification within desert‐dwelling fauna. Our goals were (1) to determine whether phylogenetic lineages and population expansions were consistent with younger P leistocene climate fluctuation hypotheses or much older events predicted by pre‐ P leistocene vicariance hypotheses, (2) to assess concordance in spatial patterns of genetic divergence and diversity among species and (3) to identify regional evolutionary hotspots of divergence and diversity and assess their conservation status. Location Mojave, C olorado, and S onoran D eserts, USA . Methods We analysed previously published gene sequence data for twelve species. We used B ayesian gene tree methods to estimate lineages and divergence times. Within each lineage, we tested for population expansion and age of expansion using coalescent approaches. We mapped interpopulation genetic divergence and intra‐population genetic diversity in a GIS to identify hotspots of highest genetic divergence and diversity and to assess whether protected lands overlapped with evolutionary hotspots. Results In seven of the 12 species, lineage divergence substantially predated the P leistocene. Historical population expansion was found in eight species, but expansion events postdated the L ast G lacial M aximum ( LGM ) in only four. For all species assessed, six hotspots of high genetic divergence and diversity were concentrated in the C olorado D esert, along the C olorado R iver and in the M ojave/ S onoran ecotone. At least some proportion of the land within each recovered hotspot was categorized as protected, yet four of the six also overlapped with major areas of human development. Main conclusions Most of the species studied here diversified into distinct M ojave and S onoran lineages prior to the LGM – supporting older diversification hypotheses. Several evolutionary hotspots were recovered but are not strategically paired with areas of protected land. Long‐term preservation of species‐level biodiversity would entail selecting areas for protection in M ojave and S onoran D eserts to retain divergent genetic diversity and ensure connectedness across environmental gradients.