Rate and extent of genetic diversity loss under non-equilibrium scenarios of habitat loss

Habitat loss is one of the greatest threats to biodiversity, but there is considerable debate over the interplay between the total amount of habitat lost versus the degree of habitat fragmentation. Previous studies on this topic focused on the effects of habitat loss on species richness or genetic diversity over long timescales, while neglecting shorter timescales that are of immediate conservation concern. To address this knowledge gap, we examined the rate and extent of genetic diversity loss under different non-equilibrium scenarios of habitat loss, by performing analytical calculations for a non-spatial setting and individual-based simulations for spatially explicit settings, including a real-world case study of malleefowl (Leipoa ocellata, Galliformes) populations in Australia. Our work revealed that the total amount of habitat lost had the biggest negative effect on genetic diversity via reductions in population abundance and associated genetic drift, with the degree of fragmentation having smaller but nonetheless substantial negative effects. The latter result suggested that to optimize the conservation of genetic diversity, it is better to preserve a single large reserve over several small ones. Furthermore, reductions in population abundance led to loss of genetic diversity in the population only after long time-lags, which highlights the potential for genetic rescue shortly after habitat loss. The malleefowl case study revealed how sampling uncertainty due to low sample sizes can blur the effects of habitat loss on genetic diversity, underscoring the limitations of conservation genetic studies based on small sample size and uneven spatial distribution.