Sika deer is indigenous to East Asia. Currently the species is extinct or are nearing the verge of extinction, in numerous places. Reduced population size is sensitive to climate change and has poor adaptation as a result of inbreeding. In this study genome-wide Single nucleotide polymorphisms (SNPs) were identified using double-digest restriction site associated digestion (ddRAD) approach and annotated further to identify genes related to fitness. A total 85,001 SNPs were retained following the quality control. Composite Likelihood Ratio (CLR) statistics found 13 stronger selective sweeps, identified sweeps overlapped with genes related to adaptation, reproduction, cellular functions. Average heterozygosity and nucleotide diversity were 0.27 and 0.29 respectively. Admixture analysis furnished a single cluster indicating no further sub-divergence of Sika deer. These findings would help fabricate appropriate genetic improvement programs by inclusion in the SNP chips, in order to get deeper insights into deer genetics, evolution, domestication and conservation.

Graphical Abstract

Bioinformatic analysis for unravelling genomic variants and selective sweep regions in Cervus nippon

中文翻译：

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使用简化表示测序在日本鹿基因组中追踪适应的进化印记

梅花鹿原产于东亚。目前，该物种在许多地方已经灭绝或接近灭绝的边缘。种群规模的减少对气候变化很敏感，并且由于近亲繁殖而适应能力差。在这项研究中，使用双酶切限制性位点相关消化（ddRAD）方法鉴定了全基因组单核苷酸多态性（SNP），并进一步注释以鉴定与健康相关的基因。质量控制后总共保留了 85,001 个 SNP。复合似然比 (CLR) 统计发现 13 个更强的选择性扫描，识别出与适应、繁殖、细胞功能相关的基因重叠的扫描。平均杂合度和核苷酸多样性分别为0.27和0.29。混合分析提供了一个单一簇，表明梅花鹿没有进一步的亚分化。这些发现将有助于通过纳入 SNP 芯片来制定适当的遗传改良计划，以便更深入地了解鹿的遗传学、进化、驯化和保护。

图形概要

生物信息学分析揭示日本鹿基因组变异和选择性扫描区域