Hindcasting the late Quaternary climatic influence on species distribution, abundance, and genetic diversity of northern California pocket gophers

Background/Question/Methods

Climate change has significantly influenced past species and communities, and due to the rapidly accelerating rate and magnitude of anthropogenic climate change, is likely to become an even larger driver of ecological change into the future. Much of the present conservation focus is on predicting future biodiversity patterns in a warmer world by determining the climatic variables associated with species geographic distributions and then forecasting future distributions given climate change.  However, an important component of ecological change is abundance decline, which may lead to locally rare and vulnerable populations. Here, we determine the relationship between climate and abundance in gophers (Thomomys) using multiple lines of evidence: fossils from northern California that capture a record of paleoecological change over the past 18000 years, modern and ancient genetic analyses, and paleodistribution modeling.  We take as our starting point observations of two species (T. mazama and T. bottae) in the past and determine 1) how abundance changed through time using multiple proxies (fossil relative abundance, genetic effective population size); 2) whether those changes are correlated with the modern climatic niche of the species; and 3) the mechanism underlying those abundance changes: in situdemographic expansion or range shifts.

Results/Conclusions

Fossil data, supported by aDNA identifications, document small range contractions (T. mazama) and range expansions (T. bottae), but the main changes observed were relative abundance changes.  The two species showed broadly opposing patterns of abundance change over the past 18,000 years. Thomomys mazama sharply declined starting around 17 thousand years before present (kyr BP) and became locally extirpated by 6 kyr BP.  In contrast, T. bottae was present but rare in the Pleistocene and expanded dramatically across the Pleistocene-Holocene transition, with the increase in abundance at 14 kyr BP roughly coincident with warming during the Bolling-Allerod period. Phylogeographic data for T. bottae indicate their population expansion was due primarily to in situ expansion rather than long-range shifts in the distributions of clades.  Overall, the temporal changes in abundance of T. mazama at Samwell Cave were strongly predicted by climatic changes, whereas T. bottae had a very broad climatic niche, indicating T. bottae abundance change was likely driven by declines in the relative abundance of T. mazama and the opening up of the underground niche.