Genomes and associated scripts for paper: Potential millennial-scale avian declines by humans in southern China

Mounting observational records demonstrate human-caused faunal decline in
recent decades, while accumulating archaeological
evidence suggests an early biodiversity impact of human
activities during the Holocene. A fundamental question arises concerning
whether modern wildlife population declines began during early human
disturbance. Here, we performed population genomic analysis of six common
forest birds in East Asia to address this question. For five of them,
demographic history inference based on 25-33 genomes of each species
revealed dramatic population declines by 4-48-fold over millennia
(two to five thousand years ago). Nevertheless, ecological niche
models predicted extensive range persistence during the Holocene and imply
limited demographic impact of historical climate change. Summary
statistics further suggest high negative correlations between these
population declines and human disturbance intensities and indicate a
potential driver of human activities. These findings provide deep-time and
large-scale insight into the recently recognized avifaunal decline and
support an early origin hypothesis of human effects on
biodiversity. Overall, our study sheds light on the current biodiversity
crisis in the context of long-term human-environment interactions and
offers a multievidential framework for quantitatively
assessing the ecological consequences of human
disturbance.