The current rate of species extinction is ∼1,000 times the background rate of extinction and is attributable to human impact, ecological and demographic fluctuations, and inbreeding due to small population sizes. The rate and the initiation date of rapid population decline (RPD) can provide important clues about the driving forces of population decline in threatened species, but they are generally unknown. We analyzed the genetic diversity data in 2,764 vertebrate species. Our population genetics modeling suggests that in many threatened vertebrate species the RPD on average began in the late 19th century, and the mean current size of threatened vertebrates is only 5% of their ancestral size. We estimated a ∼25% population decline every 10 y in threatened vertebrate species.

Abstract

Accelerated losses of biodiversity are a hallmark of the current era. Large declines of population size have been widely observed and currently 22,176 species are threatened by extinction. The time at which a threatened species began rapid population decline (RPD) and the rate of RPD provide important clues about the driving forces of population decline and anticipated extinction time. However, these parameters remain unknown for the vast majority of threatened species. Here we analyzed the genetic diversity data of nuclear and mitochondrial loci of 2,764 vertebrate species and found that the mean genetic diversity is lower in threatened species than in related nonthreatened species. Our coalescence-based modeling suggests that in many threatened species the RPD began ∼123 y ago (a 95% confidence interval of 20–260 y). This estimated date coincides with widespread industrialization and a profound change in global living ecosystems over the past two centuries. On average the population size declined by ∼25% every 10 y in a threatened species, and the population size was reduced to ∼5% of its ancestral size. Moreover, the ancestral size of threatened species was, on average, ∼22% smaller than that of nonthreatened species. Because the time period of RPD is short, the cumulative effect of RPD on genetic diversity is still not strong, so that the smaller ancestral size of threatened species may be the major cause of their reduced genetic diversity; RPD explains 24.1–37.5% of the difference in genetic diversity between threatened and nonthreatened species.