Silent Erosion: Impact of Forest Logging on Genetic Diversity in Tropical Understorey Birds

Anthropogenic habitat disturbance can erode genetic diversity long before population declines become apparent, potentially contributing to extinction debt. However, empirical assessments of genetic erosion following anthropogenic habitat degradation remain scarce. Here, we investigated whether selective logging, the most pervasive anthropogenic disturbance in tropical forests, affects genetic diversity in tropical forest biota. We resequenced whole genomes of 99 understorey songbirds from ten forest specialist species captured in both primary and selectively logged forests of Borneo. The study species are all sedentary and weak flyers but differ in their susceptibility to forest logging. The within-species comparisons of whole genomes between primary and selectively logged forests showed reduced nucleotide diversity and higher levels of inbreeding in disturbed versus undisturbed habitat for a common understorey rainforest inhabitant, Malacocincla sepiaria. We also found a substantial amount of homozygosity in the local population of that same species as well as in another, Malacopteron cinereum, regardless of forest type, indicating reduced standing genetic diversity due to historical bottlenecks. Nine out of ten species, including those considered more sensitive to the environmental conditions of selectively logged forests, showed no reduction in genetic diversity, indicating that selectively logged forests retain substantial conservation value for many rainforest birds. Nonetheless, our findings indicate that genetic erosion can occur within a few decades of habitat disturbance even in apparently common tropical bird species, raising concerns about silent population-genetic processes that might threaten the long-term persistence of seemingly abundant species in selectively logged forests.