Investigating evolutionary processes using ancient and historical DNA of rodent species

Abstract

The Late Quaternary has been a period of significant change for terrestrial mammals, including episodes of extinction, population sub-division and colonisation. Studying this period provides a means to improve understanding of evolutionary mechanisms, and to determine processes that have led to current distributions. For large mammals, recent work has demonstrated the utility of ancient DNA in understanding demographic change and phylogenetic relationships, largely through well-preserved specimens from permafrost and deep cave deposits. In contrast, much less ancient DNA work has been conducted on small mammals. This project focuses on the development of ancient mitochondrial DNA datasets to explore the utility of rodent ancient DNA analysis. Two studies in Europe investigate population change over millennial timescales. Arctic collared lemming (Dicrostonyx torquatus) specimens are chronologically sampled from a single cave locality, Trou Al’Wesse (Belgian Ardennes). Two end Pleistocene population extinction-recolonisation events are identified and correspond temporally with - localised disappearance of the woolly mammoth (Mammuthus primigenius). A second study examines postglacial histories of European water voles (Arvicola), revealing two temporally distinct colonisation events in the UK. Two further studies of Caribbean rodent species assess DNA recovery from more recent, yet highly degraded, material. The Hispaniolan hutia (Plagiodontia aedium), one of the few remaining endemic Caribbean land mammals, is found to represent three distinct lineages, biogeographically consistent with the island’s Cenozoic origins and geographic heterogeneity. The extinct Antillean rice rats (Oryzomyini) were once endemic throughout the Lesser Antilles. Phylogenetic analysis of zooarchaeological rice rat material recovered from across the Lesser Antillean reveals a new genus of rice rat and at least two separate colonisation events, via over water dispersal, from South America. These overall findings demonstrate the utility of ancient rodent DNA in eliciting individual response patterns across rodent species and exploring topics of wider evolutionary interest.