Curated VCF files of Z. mauritianus and Z. chloronothos for study of selection and species threat status - evidence from a comparative genetic time series spanning the duration of human activity

A problem of global importance is understanding why some species are threatened with extinction, while others are at comparatively little risk. The role of evolutionary history in determining which species decline in population size in response to environmental change is expected to be major, but is poorly understood. Faced with environmental change, it is well documented that species may retain differences in ecological characteristics resulting from their different evolutionary histories, and decline towards extinction due to loss of environmental conditions under which they previously survived. However, much less is known about the role of the evolutionary lability of a species’ environmental tolerance and whether differences in the degree or timing of selective responses may influence extinction risk. A major difficulty is tracking selective responses over the same timescale as major environmental changes have occurred. Here we focus on islands of the Mascarene archipelago, which had no human population until 400 years ago but have since experienced severe anthropogenic environmental changes. Two sympatric and closely-related Mascarene bird species show marked differences in abundance; Zosterops chloronothos has experienced a recent sharp demographic decline and is Critically Endangered, while Zosterops mauritianus remains common. We develop a genetic time series for both species, unique in spanning the full duration of human activity, and use it to test whether the rare species shows less evidence of post-human adaptation, or adapted later than the common one. We combined four different genome-wide selection scans to identify the timing of selection, and genes putatively under selection. Critically, spatially explicit genetic simulations enabled us to distinguish, for the rare species, the effects of natural selection from those of drift induced by major population contraction. Our results show evidence for selection in both species in genes linked to adaptation to human-modified environments, but this selection may have been staggered in time. Selection was only detected after 1800-1874 AD in the rare species, but was largely detected earlier in the common species (likely between 1598 and 1800-1874). Differences in the timescale over which such species undergo selective responses to environmental change may plausibly be an intrinsic biological factor contributing to differences in extinction risk.