Low diversity, little genetic structure but no inbreeding in a high-density island endemic pit-viperGloydius shedaoensis

Abstract

Islands species and their ecosystems play an important role in global biodiversity preservation, and many vulnerable island species are conservation priorities. Although insular habitat likely facilitates the species diversification process, it may also aggravate the fragility of these species with high risk of inbreeding. The Shedao pit-viper Gloydius shedaoensis is an island endemic species with an extremely high population density, which has been categorized as vulnerable in the IUCN Red List. We collected 13,148 SNP from across its genome and examined its genetic diversity and demographic history. The Shedao pit-viper has a low genetic diversity but shows no sign of inbreeding. Furthermore, population genetic structure analysis, including the NJ tree, PCoA, clustering, and spatial autocorrelation, revealed a general lack of spatial structure. Only the IBD residues suggested a weak patchiness. Overall, the population is nearly panmictic and gene flow is evenly distributed across the island. The large number of individuals, small size of the island, and the lack of population structure likely all contribute to the lack of inbreeding in this species. We also detected signs of male-biased dispersal, which likely is another inbreeding avoidance strategy. Historical demographic analysis suggested that the historical population size and distribution of the species are much larger than their current ones. The multiple transgressive-regressive events since the Late Pleistocene are likely the main cause of the population size changes. Taken together, our results provide a basic scientific foundation for the conservation of this interesting and important species.

Genomic differentiation with isolation by distance along a latitudinal gradient in the spotted‐leg treefrogPolypedates megacephalus

“…We detected no sign of inbreeding and the average inbreeding F was negative (mean F UNI = −0.145). This is consistent with previous reports that the inbreeding is not detected within each population when the mean F UNI is negative (Wang et al 2015;Wen et al 2021). The factors affecting inbreeding usually included male-biased dispersal and strong seasonal constraints on reproduction.…”

“…2015; Wen et al. 2021). The factors affecting inbreeding usually included male‐biased dispersal and strong seasonal constraints on reproduction.…”

“…In particular, geography acts on spatial processes contributing to the variations of the genetic diversity and differentiation within and among populations (Allentoft & O'Brien 2010; Wen et al. 2021). However, although the recognition of the IBD is prevalent in many species, the geographic factors driving the degree of the genetic differentiation are largely unknown.…”

“…Email: liaobo_0_0@126.com differentiation is a key scientific question for evolutionary biologists. The resulting pattern of isolation by distance (IBD) (Wright 1943), which entails the increase in genetic differentiation within and among populations, has now been reported in a variety of nature systems (Guo et al 2016;Medina et al 2021;Wen et al 2021;Jin et al 2022). In particular, geography acts on spatial processes contributing to the variations of the genetic diversity and differentiation within and among populations (Allentoft & O'Brien 2010;Wen et al 2021).…”

“…The resulting pattern of isolation by distance (IBD) (Wright 1943), which entails the increase in genetic differentiation within and among populations, has now been reported in a variety of nature systems (Guo et al 2016;Medina et al 2021;Wen et al 2021;Jin et al 2022). In particular, geography acts on spatial processes contributing to the variations of the genetic diversity and differentiation within and among populations (Allentoft & O'Brien 2010;Wen et al 2021). However, although the recognition of the IBD is prevalent in many species, the geographic factors driving the degree of the genetic differentiation are largely unknown.…”