Whole-Genome Analyses Reveal the Distinct Taxonomic Status of the Hainan Population of Endangered Rucervus eldii and Its Conservation Implications

IF 3.5 2区 生物学 Q1 EVOLUTIONARY BIOLOGY
Chenqing Zheng, Qing Chen, Michelle Hang Gi Wong, Nick Marx, Thananh Khotpathoom, Hesheng Wang, Feng Yang, Xiaodong Rao, Bosco Pui Lok Chan, Yang Liu
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Abstract

Eld's deer Rucervus eldii (McClelland, 1842) is an ungulate that lives in tropical lowland forests in several countries of Indochina and Hainan Island of China. Its remaining population is small and scattered, and the species is listed as an Endangered species on the IUCN Red List. The debate over the taxonomic status of the Hainan population has persisted for over a century—as an island-endemic subspecies R. e. hainanus, or an insular population of the subspecies R. e. siamensis, would have significant conservation implications. And, given the Hainan population had experienced both population bottleneck and multiple translocations in the past, conservation genomics would be a powerful tool to evaluate the genetic impacts of these events. In this study, we used conservation genomics assessment to study population differentiation and genetic diversity of R. e. siamensis in Cambodia and three Eld's deer subpopulations on Hainan Island. Based on the unique genetic profile and demographic analysis, this study corroborated previous studies using genetic markers that the Hainan Eld's deer warrants the taxonomic status of a distinct subspecies. The Hainan population exhibits a reduction in genetic diversity and an increase in the level of inbreeding when compared to the population of Cambodia. The signs of purifying selection were found against homozygous loss-of-function mutations to decrease the deleterious burden in the Hainan population. However, there was an accumulation of more deleterious missense mutations. Furthermore, significant differences in genetic diversity and level of inbreeding found among the three Hainan subpopulations indicated population isolation and suboptimal translocation strategies, which calls for urgent, coordinated, and science-based genetic management to ensure the long-term viability of the endemic subspecies hainanus. This study provides guidance for the conservation and management of Eld's deer.

Abstract Image

全基因组分析揭示了海南濒危麋鹿种群的独特分类地位及其保护意义
埃尔德鹿 Rucervus eldii (McClelland, 1842) 是一种生活在印度支那几个国家和中国海南岛热带低地森林中的有蹄类动物。该物种在世界自然保护联盟红色名录中被列为濒危物种。一个多世纪以来,关于海南种群分类地位的争论一直没有停止过--是海南岛特有亚种R.e. hainanus,还是暹罗亚种R.e. siamensis的岛屿种群,都会对保护工作产生重大影响。鉴于海南种群在过去经历了种群瓶颈和多次迁移,保护基因组学将成为评估这些事件对遗传影响的有力工具。在本研究中,我们利用保护基因组学评估方法研究了柬埔寨暹罗鹿和海南岛三个坡鹿亚群的种群分化和遗传多样性。基于独特的遗传特征和人口学分析,本研究证实了之前利用遗传标记进行的研究,即海南坡鹿在分类学上应该是一个独特的亚种。与柬埔寨种群相比,海南种群的遗传多样性降低,近亲繁殖水平上升。在海南种群中,发现了针对同源功能缺失突变的纯化选择迹象,从而降低了海南种群的有害负荷。然而,更多有害的错义突变却在海南种群中积累。此外,海南三个亚种群在遗传多样性和近亲繁殖水平上存在显著差异,表明种群隔离和迁移策略不理想,这就要求进行紧急、协调和科学的遗传管理,以确保海南特有亚种的长期生存。这项研究为保护和管理坡鹿提供了指导。
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来源期刊
Evolutionary Applications
Evolutionary Applications 生物-进化生物学
CiteScore
8.50
自引率
7.30%
发文量
175
审稿时长
6 months
期刊介绍: Evolutionary Applications is a fully peer reviewed open access journal. It publishes papers that utilize concepts from evolutionary biology to address biological questions of health, social and economic relevance. Papers are expected to employ evolutionary concepts or methods to make contributions to areas such as (but not limited to): medicine, agriculture, forestry, exploitation and management (fisheries and wildlife), aquaculture, conservation biology, environmental sciences (including climate change and invasion biology), microbiology, and toxicology. All taxonomic groups are covered from microbes, fungi, plants and animals. In order to better serve the community, we also now strongly encourage submissions of papers making use of modern molecular and genetic methods (population and functional genomics, transcriptomics, proteomics, epigenetics, quantitative genetics, association and linkage mapping) to address important questions in any of these disciplines and in an applied evolutionary framework. Theoretical, empirical, synthesis or perspective papers are welcome.
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