Genetic and epigenetic changes across 20 000 years: quantifying demographic and adaptive responses of mammal populations to climate change.

Throughout the whole planet, populations are facing unprecedented rates of climate change and habitat destruction by human activities. Most of current research has investigated the genetic consequences of environmental perturbation and the underlying epigenetic changes potentially mediating the stress response. This project will fill this important gap in our knowledge by directly quantifying both the demographic and adaptive responses to global climate change within late Pleistocene and early Holocene fossil populations. We will analyse an exceptional time series of subfossil bones from three mammal species, collected in the Igue du Gral, a karstic hole in South-Western France, which acted as a wide natural trap for the fauna during at least 20,000 years. This time period experience major environmental changes, following the last glacial maximum and early Holocene global warming. All macro-fossil bone samples are stored at the Museum of Natural History of Geneva and thus readily available for DNA analyses. Our work will focus on the three most abundant species of the 20+ mammal species found at Igue du Gral, i.e., the reindeer (Rangifer tarandus), the European bison (Bison bonasus or Bison priscus), and the horse (Equus caballus). The available paleontological record will encompass 10 time points between ca 30,000 and 10,000 years ago, a time period characterized by abrupt changes in the climate of Europe, both in continental and Mediterranean areas, notably showing a drastic warming phase. Using techniques developed in our laboratory, we can reliably sequence a reduced representation of ancient genomes from such subfossils, and so analyse adaptive and neutral genetic dynamics as well as epigenetic changes in the form of DNA methylation marks (identified by specific post-mortem modifications). This project will for the first time offer sufficient samples in space and time as well as sufficient genetic markers to identify how past populations responded to environmental perturbation. By contrasting the respective evolutionary trajectories of each  individual model species, our data will help advance current models of species extinction and response to global environmental change. In particular, we will characterize the genetic and epigenetic variants conditioning the capacity of individual species to respond to climate change. Our work will provide the necessary empirical data to refine current predictive models of future demographic and adaptive potential of mammal populations. This will be essential at a time of the sixth major biodiversity crisis.

Main coordinator = N. Alvarez, Museum of Geneva.