Genetic diversity in the male-specific SRY gene of Lepus yarkandensis

Abstract

Lepus yarkandensis, an endemic hare species in the Tarim Basin of China, has been suffering from habitat fragmentation due to desert expansion. To evaluate the effect of habitat fragmentation on its genetic diversity, the genetic diversity based on male-specific SRY gene marker is examined. A relatively low level of SRY genetic diversity is found compared to previous studies with mtDNA data, possibly due to the low SRY mutation rate and positive selection. Furthermore, one haplotype exists in eight populations along the Tarim River but not in many other relatively isolated populations, suggesting that habitat fragmentation may affect population divergence. Despite this, our pairwise Fst analysis shows no significant differentiation among populations, and this may be mainly caused by positive selection on the SRY gene in that 88 percent of individuals share the same haplotype. Finally, the phylogenetic analysis shows deep differentiation between L. yarkandensis and other two hare species (L. capensis and L. europaeus). Lepus, genetic diversity, genetic differentiation, polymorphic sites, network Citation:Wu Y H, Xia L, Zhang Q, et al. Genetic diversity in the male-specific SRY gene of Lepus yarkandensis.

Phylogeography and ecological niche modeling unravel the evolutionary history of the Yarkand hare, Lepus yarkandensis (Mammalia: Leporidae), through the Quaternary

“…We ran models with 10 cross-validated replicates by randomly assigning the presence records to training and test datasets (90 and 10%, respectively). We assessed the performance of the models by calculating classification errors using the area under the receiver operating characteristic curve (AUC), sensitivity, specificity, and true skill statistic (TSS = sensitivity + specificity - 1) for each of the 12 models that were cross-validated against the training dataset [130–133] [29, 62–64]. We used 75% of the data to calibrate the models and 25% to calculate performance efficiency.…”

“…The previous habitats of the Yarkand hare may have been more continuous than their current habitat [61]. The previous research on Yarkand hare revealed that desert features, regional aridification, broad rivers [62, 63], and habitat fragmentation of the desert landscape [61] have all been identified as major factors that influence the genetic structure and act as barriers to the dispersal of the species. There was possibly extensive gene flow among populations during the ancient geological period [61].…”

“…There was possibly extensive gene flow among populations during the ancient geological period [61]. Low SRY genetic diversity was detected in L. yarkandensis [62] and further based on Cyt b data: two divergent, geologically different subclades of Yarkand hares have already been found. One subclade was found from the eastern area of the Keriya River, and another was found from the western area of the river [61].…”

Higher Expression Levels of Aquaporin Family of Proteins in the Kidneys of Arid-Desert Living Lepus yarkandensis

“…The content of Na + is higher and Ca 2+ is lower in blood of L. yarkandensis when compared to that of O. cuniculus , suggesting a strong adjusting ability of L. yarkandensis in maintaining the body water (Gao et al, 1998). In recent years, several researchers have investigated genetic variation, population structure and phylogeography of Yarkand hare (Li et al, 2006), the matrilineal and demographical histories of Tarim Basin’s endemic Yarkand hare (Shan et al, 2011), the bidirectional introgressive hybridization between L. capensis and L. yarkandensis (Wu et al, 2011), for the presence of Leishmania in L. yarkandensis (Gao et al, 2015), and genetic diversity in male-specific SRY gene of L. yarkandensis (Wu et al, 2010). So, the body of L. yarkandensis has specialized height, and it has strong drought tolerance ability when compared with rabbits and other hares (Li, 2011; Hui and Zhao, 2013; Yu and Zhang, 2013; Zhang et al, 2015, 2016).…”

Revealing the coexistence of differentiation and communication in an endemic hare, Lepus yarkandensis (Mammalia, Leporidae) using specific-length amplified fragment sequencing

“…Resolving the phylogenetic relationships between species and different populations within a species is a very important task in evolutionary biology and conservation genetics [ 6 ]. Previous studies exploring the genetic variation and phylogenetic relationships of Yarkand hare populations have focused on mitochondrial DNA (mtDNA) genes [ 8 , 15 , 19 – 21 ], the male-specific Y-chromosomal sex-determining region ( SRY ) gene [ 21 ], and two nuclear DNA (nDNA) markers, namely, the mechano-growth factor ( MGF ) and spectrin beta non-erythrocytic 1 ( SPTBN1 ) genes [ 8 ]. Phylogenetic analysis of mtDNA sequences showed significant genetic differentiation among most Yarkand hare populations, highlighting low migration levels among populations inhabiting oases isolated by the Taklamakan Desert.…”