title: Large numbers of vertebrates began rapid population decline in the late 19th century.
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.
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming 650223, China.|CAS Key Laboratory of Computational Biology, CAS-Max Planck Society (CAS-MPS) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China.
authors.forename: Haipeng
authors.initials: H
authors.lastname: Li
authors.affiliation: CAS Key Laboratory of Computational Biology, CAS-Max Planck Society (CAS-MPS) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China.
authors.forename: Jinggong
authors.initials: J
authors.lastname: Xiang-Yu
authors.affiliation: CAS Key Laboratory of Computational Biology, CAS-Max Planck Society (CAS-MPS) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China.
authors.forename: Guangyi
authors.initials: G
authors.lastname: Dai
authors.affiliation: CAS Key Laboratory of Computational Biology, CAS-Max Planck Society (CAS-MPS) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China.
authors.forename: Zhili
authors.initials: Z
authors.lastname: Gu
authors.affiliation: CAS Key Laboratory of Computational Biology, CAS-Max Planck Society (CAS-MPS) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China.|University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Ming
authors.affiliation: CAS Key Laboratory of Computational Biology, CAS-Max Planck Society (CAS-MPS) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China.|University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Zongfeng
authors.initials: Z
authors.lastname: Yang
authors.affiliation: Institute for Conservation Research, San Diego Zoo Global, Escondido, CA 92027.
authors.forename: Oliver A
authors.initials: OA
authors.lastname: Ryder
authors.affiliation: Biodiversity Research Center, Academia Sinica, Taipei 11529, Republic of China; wli@uchicago.edu Yunxin.Fu@uth.tmc.edu zhangyp@mail.kiz.ac.cn.|Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637.
authors.forename: Wen-Hsiung
authors.initials: WH
authors.lastname: Li
authors.affiliation: State Key Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China; wli@uchicago.edu Yunxin.Fu@uth.tmc.edu zhangyp@mail.kiz.ac.cn.|Department of Biostatistics and Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030.
authors.forename: Yun-Xin
authors.initials: YX
authors.lastname: Fu
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming 650223, China; wli@uchicago.edu Yunxin.Fu@uth.tmc.edu zhangyp@mail.kiz.ac.cn.|University of Chinese Academy of Sciences, Beijing 100049, China.|State Key Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China.
authors.forename: Ya-Ping
authors.initials: YP
authors.lastname: Zhang
mesh_terms: D000818:Animals; D044822:Biodiversity; D003247:Conservation of Natural Resources / Q000639:trends; D017753:Ecosystem; D056727:Endangered Species / Q000639:trends; D053476:Extinction, Biological; D014644:Genetic Variation / Q000235:genetics; D005828:Genetics, Population / Q000379:methods; D049672:History, 19th Century; D010802:Phylogeny; D011156:Population Density; D011157:Population Dynamics / Q000639:trends*; D014714:Vertebrates / Q000235:genetics*
keywords: coalescent; conservation; rapid population decline; threatened species; vertebrate