Low genetic diversity in a critically endangered primate: shallow evolutionary history or recent population bottleneck?

Abstract

Background Current patterns of population genetic variation may have been shaped by long-term evolutionary history and contemporary demographic processes. Understanding the underlying mechanisms that yield those patterns is crucial for informed conservation of endangered species. The critically endangered white-headed langur, Trachypithecus leucocephalus , is endemic to a narrow range in southwest China. This species shows very low genetic diversity in its 2 main relict populations, Fusui and Chongzuo. Whether this has been caused by a short evolutionary history or recent population declines is unknown. Therefore, we investigated the contributions of historical and recent population demographic changes to population genetic diversity by using 15 nuclear microsatellite markers and mitochondrial DNA (mtDNA) control region sequences. Results Using genetic data from 214 individuals we found a total of 9 mtDNA haplotypes in the Fusui population but only 1 haplotype in the Chongzuo population, and we found an overall low genetic diversity (haplotype and nucleotide diversities: h = 0.486 ± 0.036; π = 0.0028 ± 0.0003). The demographic history inferred from mtDNA and microsatellite markers revealed no evidence for historical population size fluctuations or recent population bottlenecks. Simulations of possible population divergence histories inferred by DIYABC analysis supported a recent divergence of the Chongzuo population from the Fusui population and no population bottlenecks. Conclusions Despite severe population declines caused by anthropogenic activities in the last century, the low genetic diversity of the extant white-headed langur populations is most likely primarily due to the species’ shallow evolutionary history and to a recent, local population founder event. Electronic supplementary material The online version of this article (10.1186/s12862-019-1451-y) contains supplementary material, which is available to authorized users.

The complete mitochondrial genome of Indian gaur, Bos gaurus and its phylogenetic implications

“…Also, it can be taken as a sign of population decline 40 , 42 , 43 . Genetic variation between individuals is prerequisite for evolution and adaptive changes, and has profound implications for conservation 41 , 44 – 46 . The global gaur population is anticipated to fall by 30% within next three decades 3 due to habitat loss, poaching for its meat and horns and fatal diseases.…”

“…Similar low mtDNA diversity was also observed in Malayan www.nature.com/scientificreports/ www.nature.com/scientificreports/ gaur for partial D-loop sequence 39 . Low mtDNA diversity is likely to occur in the wild population due to the presence of small number of founder females [38][39][40][41] . Also, it can be taken as a sign of population decline 40,42,43 .…”

Unusual evolution of tree frog populations in the Chernobyl exclusion zone

“…Populations exposed to pollutants often experience genetic erosion (Straalen & Timmermans, 2002 ). Two processes can be at the origin of this decreased diversity: a directional selective pressure which can be driven by the modification of the environment (De Wolf et al, 2004 ; Ungherese et al, 2010 ), and/or a demographic bottleneck involving the fixation of polymorphic alleles with neutral drift (Hughes et al, 2008 ; Murdoch & Hebert, 1994 ; Ribeiro et al, 2012 ; Wang et al, 2019 ). Numerous population genetic studies carried out in the Chernobyl area have been conducted on the bank vole, Myodes glareolus , and showed increased genetic diversity in highly radio‐contaminated areas (Baker et al, 2001 , 2017 ; Matson et al, 2000 ; Meeks et al, 2007 , 2009 ; Wickliffe et al, 2006 ).…”

Testing the Effect of the Toba Volcanic Eruption on Population Sizes in Worldwide Mammal Species

“…This feature makes the HVS region ideal for detecting sudden expansion. We understand the limitations of using modern mtDNA samples to infer population history and that it would be beneficial to combine our analysis with microsatellites or ancient DNA, however, recent studies continue to use mtDNA to evaluate demographic history [17,4,28,32].…”