干旱区生态环境知识资源中心(Arid): Revealing the coexistence of differentiation and communication in an endemic hare, Lepus yarkandensis (Mammalia, Leporidae) using specific-length amplified fragment sequencing

Arid

DOI	10.1186/s12983-021-00432-x
	Revealing the coexistence of differentiation and communication in an endemic hare, Lepus yarkandensis (Mammalia, Leporidae) using specific-length amplified fragment sequencing
	Ababaikeri, Buweihailiqiemu; Zhang, Yucong; Dai, Huiying; Shan, Wenjuan
通讯作者	Shan, WJ (corresponding author), Xinjiang Univ, Coll Life Sci & Technol, Xinjiang Key Lab Biol Resources & Genet Engn, Urumqi 830046, Peoples R China.
来源期刊	FRONTIERS IN ZOOLOGY
ISSN	1742-9994
出版年	2021
卷号	18 期号:1
英文摘要	Background The Yarkand hare (Lepus yarkandensis Gunther, 1875) is endemic to oasis and desert areas around the Tarim Basin in the Xinjiang Uyghur Autonomous Region of northwest China; however, genome-wide information for this species remains limited. Moreover, the genetic variation, genetic structure, and phylogenetic relationships of Yarkand hare from the plateau mountain regions have not been reported. Thus, we used specific-length amplified fragment sequencing (SLAF-seq) technology to evaluate the genetic diversity of 76 Yarkand hares from seven geographic populations in the northern and southwestern parts of the Tarim Basin to investigate single-nucleotide polymorphism (SNP) marker-based population differentiation and evolutionary processes. Selective sweep analysis was conducted to identify genetic differences between populations. Results Using SLAF-seq, a total of 1,835,504 SNPs were initially obtained, of which 308,942 high-confidence SNPs were selected for further analysis. Yarkand hares exhibited a relatively high degree of genetic diversity at the SNP level. Based on pairwise F-ST estimates, the north and southwest groups showed a moderate level of genetic differentiation. Phylogenetic tree and population structure analyses demonstrated evident systematic phylogeographical structure patterns consistent with the geographical distribution of the hares. Hierarchical analysis of molecular variation further indicated that genetic variation was mainly observed within populations. Low to moderate genetic differentiation also occurred among populations despite a common genomic background, likely due to geographical barriers, genetic drift, and differential selection pressure of distinct environments. Nevertheless, the observed lineage-mixing pattern, as indicated by the evolutionary tree, principal component analysis, population structure, and TreeMix analyses, suggests a certain degree of gene flow between the north and southwest groups. This may be related to the migration of hares to high-altitude water sources southwest of the basin during glacial climatic oscillations, as well as river re-diffusion and oasis restoration in the basin following the glacial period. We also identified candidate genes, and their associated gene ontology terms and pathways, related to the adaptation of Yarkand hares to different environmental habitats. Conclusions The identified genome-wide SNPs, genetic diversity, and population structure of Yarkand hares expand our understanding of the genetic background of this endemic species and provide valuable insights into its environmental adaptation, allowing for further exploration of the underlying mechanisms.
英文关键词	Yarkand hare Specific-length amplified fragment sequencing (SLAF-seq) Genetic differentiation Genetic diversity Gene flow Adaptation Tarim Basin
类型	Article
语种	英语
开放获取类型	Green Published, gold
收录类别	SCI-E
WOS记录号	WOS:000699897000001
WOS关键词	POPULATION GENETIC DIFFERENTIATION ; TARIM BASIN ; HABITAT FRAGMENTATION ; EAST-ASIA ; GENOME ; DIVERSITY ; ADAPTATION ; HISTORY ; CLIMATE ; TREE
WOS类目	Zoology
WOS研究方向	Zoology
来源机构	新疆大学
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/363363
作者单位	[Ababaikeri, Buweihailiqiemu; Zhang, Yucong; Dai, Huiying; Shan, Wenjuan] Xinjiang Univ, Coll Life Sci & Technol, Xinjiang Key Lab Biol Resources & Genet Engn, Urumqi 830046, Peoples R China; [Ababaikeri, Buweihailiqiemu] Coll Xinjiang Uyghur Med, Hoten 848000, Xinjiang, Peoples R China
推荐引用方式 GB/T 7714	Ababaikeri, Buweihailiqiemu,Zhang, Yucong,Dai, Huiying,et al. Revealing the coexistence of differentiation and communication in an endemic hare, Lepus yarkandensis (Mammalia, Leporidae) using specific-length amplified fragment sequencing[J]. 新疆大学,2021,18(1).
APA	Ababaikeri, Buweihailiqiemu,Zhang, Yucong,Dai, Huiying,&Shan, Wenjuan.(2021).Revealing the coexistence of differentiation and communication in an endemic hare, Lepus yarkandensis (Mammalia, Leporidae) using specific-length amplified fragment sequencing.FRONTIERS IN ZOOLOGY,18(1).
MLA	Ababaikeri, Buweihailiqiemu,et al."Revealing the coexistence of differentiation and communication in an endemic hare, Lepus yarkandensis (Mammalia, Leporidae) using specific-length amplified fragment sequencing".FRONTIERS IN ZOOLOGY 18.1(2021).