Before the last 50,000 years, the world was full of large animals, or megafauna. Giant armadillos and ground sloths were found across the Americas while rhinoceros-sized marsupials roamed Australia. Elephants (and elephant-like animals) were far more diverse and widespread than they are today, as were rhinoceroses. In the time since, however, there have been numerous extinctions of megafauna, with only a vanishing remnant of the original variety surviving to the present day. Surviving large animals might have benefitted from lower competition, but it is also possible that they have suffered reductions as part of the same process that eventually led to the extinction of other larger animals. Climate change and human activity have been considered the main potential culprits in the megafauna extinctions, and so the question also arises of how these factors might have affected surviving species.

In answering such questions, the study of fossils has been used extensively for uncovering features of past ecosystems, the forces that shaped them and the histories of the inhabitant species. However, the level of detail that fossil records provide is often limited due to the  number of epochs with adequate data, as well as varying specimen availability for different species and localities. In recent decades, the advancement of DNA sequencing technology has resulted in the accumulation of a novel type of biological record: high-quality genomic sequence data. Each nucleotide position in a contemporary genome has its own evolutionary history that spans millions of years in the past. With three billion of such positions in an average mammalian genome, the nucleotide variation present in a genome forms a detailed and biologically maintained record of a species’ history.

Unlike the fossil record, a species’ genome represents a continuum of biological variation that is shaped by the accumulation of mutations, each occurring at a specific time in the past and during a specific evolutionary context - in our study, the context of interest is the population size of a species. Given the richness  of genomic data and methodological advancements in population genetics, it is now possible to use the distribution of nucleotide variation along the genome to reconstruct population size dynamics of a species up to several million years into the past. In an effort to characterize the history of the surviving megafaunal component of our planet, we shed light on past population size trajectories of 139 living megafauna species.

While the megafauna extinction event of the late-Quaternary might have provided competitive release to the surviving species, genome-based population size trajectories of extant megafauna show that such a scenario was never realized. On the contrary, a period between 32,000 and 76,000 years ago marks the onset of a global decline in population size for the majority of megafauna that survived to present time. The decline of extant megafauna during this period therefore mirrors the late-Quaternary extinction event, implying that megafaunal impoverishment of our biosphere was a coupled process of extinction and population size reduction of survivors.

The cause of megafauna decline has always been a source of heated scientific debate. We set out to test the two main hypotheses - climate-induced change of megafauna population sizes and the correspondence of megafauna decline with human arrival to specific landmasses. We found that megafauna decline is considerably better explained by human predictors than climatic conditions. Even when we simultaneously considered climate and human predictors, human-only models largely outperformed models that contained both predictor types. We concluded that humans have been a major driver of megafauna population sizes for at least 50,000 years.

The consequences of the late-Quaternary megafauna decline are extensive. When considering the census loss of extant and extinct megafauna, we estimate that over one billion individuals have been lost across the global megafauna community, with only 80 million individuals remaining today. As a consequence, the amount of biomass and energy contribution of megafauna species have been reduced by approximately 95% during the last 50,000 years, likely causing major restructuring of ecosystems at a global scale. Given that a large fraction of surviving megafauna are currently threatened with extinction, the opportunity to restore their ecological function is rapidly diminishing. Coordination of global efforts of species conservation and trophic rewilding are therefore urgently needed to mitigate the loss of megafauna diversity and restore the crucial ecological functions they perform throughout the biosphere.