Exploring the endangerment mechanisms of Hipposideros pomona based on molecular phylogeographic methods

Abstract

The endangerment mechanisms of various species are a focus of studies on biodiversity and conservation biology. Hipposideros pomona is an endangered species, but the reasons behind its endangerment remain unclear. We investigated the endangerment mechanisms of H. pomona using mitochondrial DNA, nuclear DNA, and microsatellite loci markers. The results showed that the nucleotide diversity of mitochondria DNA and heterozygosity of microsatellite markers were high (π = 0.04615, H _O = 0.7115), whereas the nucleotide diversity of the nuclear genes was low (THY: π = 0.00508, SORBS2: π = 0.00677, ACOX2: π = 0.00462, COPS7A: π = 0.00679). The phylogenetic tree and median-joining network based on mitochondrial DNA sequences clustered the species into three clades, namely North Vietnam-Fujian, Myanmar-West Yunnan, and Laos-Hainan clades. However, joint analysis of nuclear genes did not exhibit clustering. Analysis of molecular variance revealed a strong population genetic structure; IMa2 analysis did not reveal significant gene flow between all groups (p > .05), and isolation-by-distance analysis revealed a significant positive correlation between genetic and geographic distances (p < .05). The mismatch distribution analysis, neutral test, and Bayesian skyline plots revealed that the H. pomona population were relatively stable and exhibited a contraction trend. The results implied that H. pomona exhibits female philopatry and male-biased dispersal. The Hengduan Mountains could have acted as a geographical barrier for gene flow between the North Vietnam-Fujian clade and the Myanmar-West Yunnan clade, whereas the Qiongzhou Strait may have limited interaction between the Hainan populations and other clades. The warm climate during the second interglacial Quaternary period (c. 0.33 Mya) could have been responsible for species differentiation, whereas the cold climate during the late Quaternary last glacial maximum (c. 10 ka BP) might have caused the overall contraction of species. The lack of significant gene flow in nuclear microsatellite loci markers among the different populations investigated reflects recent habitat fragmentation due to anthropogenic activities; thus, on-site conservation of the species and restoration of gene flow corridors among populations need immediate implementation.

Keywords: conservation; gene flow; genetic diversity; geographical isolation; quaternary climate change.

FIGURE 1

Sampling locations of Hipposideros pomona, median‐joining network and ultrametric tree based on Cytb sequences. (a) Collection sites for this survey. FJ, Fujian; GD, Guangdong; HN, Hainan; LWZ, Central Laos; MD, Myanmar; YB, Yunnanbaoshan; YC, Yunnanchuxiong; YD, Yunnandali; YNB, North Vietnam; YNZ, central Vietnam; (b) Bayesian ultrametric tree inferred based on the mitochondrial Cytb sequences. Values above the branches indicate the Bayesian posterior probabilities and maximum likelihood bootstrap support values; numbers below branches are the times to the most recent common ancestor (in Ma); (c) Median‐joining network constructed using mitochondrial haplotypes. Each circle corresponds to a haplotype whose size is proportional to its total frequency, and the color of the circles represents geographical location. The numbers in the network represent mutational steps between haplotypes.

FIGURE 2

Median‐joining network and Bayesian phylogenetic tree based on nuclear gene sequences, Bayesian clustering results from STRUCTURE based on microsatellite date of Hipposideros pomona. (a) Bayesian clustering results (K = 3); Population abbreviations are identical to those included in Figure 1; (b) Bayesian phylogenetic tree constructed using a combination of four nuclear genes. Values above the branches indicate the Bayesian posterior probabilities and maximum likelihood bootstrap support values; (c) median‐joining network composed of nuclear genes. Each circle corresponds to a haplotype whose size is proportional to its total frequency, and the color of the circles represents the geographical location. The numbers in the network represent mutational steps between haplotypes.

FIGURE 3

Mismatch distribution and Bayesian Skyline Plot based on Cytb sequences. (a) Mismatch distribution based on all Cytb sequences; (b) Mismatch distribution based on North Vietnam‐Fujian clade; (c) Mismatch distribution based on Myanmar‐West Yunnan clade; (d) Mismatch distribution based on Laos‐Hainan clade; (e) Skyline plot based on all Cytb samples; (f) Skyline plot based on North Vietnam‐Fujian clade; (g) Skyline plot based on Myanmar‐West Yunnan clade; (h) Skyline plot based on Laos‐Hainan clade.