Genetic evidence of recent population contraction in the southernmost population of giant pandas

Abstract

Anthropogenic habitat loss and fragmentation have been implicated in the endangerment and extinction of many species. Here we assess genetic variation and demographic history in the southernmost population of giant pandas (Ailuropoda melanoleuca) that continues to be threatened by habitat degradation and fragmentation, using noninvasive genetic sampling, mitochondrial control region sequence and 12 microsatellite loci. Compared to other giant panda populations, this population has medium-level genetic diversity based on the measure of both mitochondrial and nuclear markers. Mitochondrial DNA-based demographic analyses revealed that no historical population expansion or contraction has occurred, indicating a relatively stable population size. However, a Bayesian-coalescent method based on the observed allele distribution and allele frequencies of microsatellite clearly did detect, quantify and date a recent decrease in population size. Overall, the results indicate that a population contraction in the order of 95-96% has taken place over the last 910-999 years and is most likely due to anthropogenic habitat loss. These findings highlight the need for a greater focus on habitat protection and restoration for the long-term survival of this giant panda population.

Genetic consequences of historical anthropogenic and ecological events on giant pandas

“…1). For modern samples, there were two sources: our published data collected between 2001 and 2008 (Zhang et al 2007, Hu et al 2010, Zhu et al 2011, and blood samples from wild-born animals kept currently in captivity. In this study, we obtained 470 new genotypes from 379 skin samples, 41 blood samples, and the fecal samples of 50 individuals (Table 1).…”

“…In this study, we obtained 470 new genotypes from 379 skin samples, 41 blood samples, and the fecal samples of 50 individuals (Table 1). We combined these data with 399 genotypes previously published, comprising 64 skins and 335 individuals from varied sources (feces, muscle, hair, and blood) (Zhang et al 2007, Hu et al 2010, Zhu et al 2011; see details in Table 1). In total, we genotyped 869 individuals, including 443 historical samples (skins) and 426 modern samples (feces, muscle, hair, and blood).…”

“…Overall, mean genotyping error rates were less than 1% (see Hu et al 2010, Zhu et al 2011). In addition, we checked the final data set for the presence of null alleles and errors such as allele stuttering and large allele dropout, using the software Micro-Checker (Van Oosterhout et al 2004).…”

“…Specifically, based on the observed alleles and allele frequencies, we simulated loss of heterozygosity (H t /H 0 ) for the Minshan and Qionglai populations, respectively. The age at sexual maturity is around 6 years old (Schaller et al 1985), the reproduction system is polygyny (Schaller et al 1985, Pan et al 2001, and the sex ratio is not significantly different from 1:1 (Zhan et al 2006, Hu et al 2010, Zhu et al 2011. We used conservative values of 1500 and 1000 as prebottleneck census population sizes for Minshan and Qionglai, respectively, and these pre-bottleneck sizes ).…”

A review of phylogeography: biotic and abiotic factors

“…The important feature of plant dispersal biology is that flow of gene is leptokurtic, with most of the seeds and pollens scattering locally close to where genotypes are well adapted (Bradshaw, 1972). Trees have good in the environment and various other anthropogenic factors (Hu, Qi, Wang, & Wei, 2010). Numerous mathematical models are available to study the population contraction like hierarchical Bayesian model, correlative species distribution model so on and so forth.…”