Worldwide late-Quaternary population declines in extant megafauna are due to Homo sapiens rather than climate

The worldwide loss of large animal species over the past 100,000 years is evident from the fossil record, with climate and human impact as the most likely causes of megafauna extinctions. To help distinguish between these two scenarios, we analysed whole-genome sequence data of 142 species to infer their population size histories during the Quaternary. We modelled differences in population dynamics among species using ecological factors, paleoclimate and human presence as covariates. We report a significant population decline towards the present time in more than 90% of species, with larger megafauna experiencing the strongest decline. We find that population decline became ubiquitous approximately 100,000 years ago, with the majority of species experiencing their lowest population sizes during this period. We assessed the relative impact of climate fluctuations and human presence on megafauna dynamics and found that climate has limited explanatory power for late-Quaternary shifts in megafauna population sizes, which are largely explained by Homo sapiens arrival times. As a consequence of megafauna decline, total biomass and metabolic input provided by these species has drastically reduced to less than 25% compared to 100,000 years ago. These observations imply that the worldwide expansion of H. sapiens caused a major restructuring of ecosystems at global scale.