Inferring past refugia and range dynamics through the integration of fossil, niche modelling and genomic data

Abstract

Aim Reconstructing species' glacial refugial history and demographic changes over time has greatly relied on comparing inferences from multiple methods while not sufficiently acknowledging their limitations. Here, we aim to integrate as fully as possible complementary methods in ecology, genomics and palaeobiology to improve the reconstruction of species biogeographical history.

Location South-western Europe.

Taxon Cabrera vole (Microtus cabrerae).

Methods We compiled and mapped the raw fossil data of the Cabrera vole for the Last Glacial Maximum (LGM) and Mid-Holocene (MH). Alongside, we projected the calibrated ecological niche model (ENM) of the species' current distribution for the LGM, the Younger Dryas and the MH. Complementarily, we used previously obtained Genotyping-by-Sequencing data to evaluate the demographic history and range expansion patterns of all four Evolutionarily Significant Units of the species, in an integrative framework.

Results ENM-inferred refugial areas and genomic modelling consistently supported northern Iberian glacial refugia for the Cabrera vole. This contrasted with the higher fossil abundance of the species in southern and eastern Iberia and southern France from the LGM to the MH. Our results suggest that populations in areas with high fossil abundance went extinct, and were later replaced by northern Iberian populations such that they did not contribute significantly to the current gene pool.

Main conclusions Our integrative approach indicates how the range of the Cabrera vole fluctuated in response to environmental change during and following the LGM. Despite methodological limitations, the ENM and genomic approaches produced generally congruent results. Instead, the fossil record may misrepresent the ancestral distribution of this species and should be considered cautiously for ancestral distribution reconstruction, considering that it also reflects the fossilization conditions. Overall, our study supports the idea that integrative approaches are essential to provide an accurate and well-supported picture of historical refugial areas and range dynamics.