Table_3_How voles adapt to subterranean lifestyle: Insights from RNA-seq.XLSX

Life under the earth surface is highly challenging and associated with a number of morphological, physiological and behavioral modifications. Subterranean niche protects animals from predators, fluctuations in environmental parameters, but is characterized by high levels of carbon dioxide and low levels of oxygen and implies high energy requirements associated with burrowing. Moreover, it lacks most of the sensory inputs available above ground. The current study describes results from RNA-seq analysis of four subterranean voles from subfamily Arvicolinae: Prometheomys schaposchnikowi, Ellobius lutescens, Terricola subterraneus, and Lasiopodomys mandarinus. Original RNA-seq data were obtained for eight species, for nine species, SRA data were downloaded from the NCBI SRA database. Additionally assembled transcriptomes of Mynomes ochrogaster and Cricetulus griseus were included in the analysis. We searched for the selection signatures and parallel amino acid substitutions in a total of 19 species. Even within this limited data set, we found significant changes of dN/dS ratio by free-ratio model analysis for subterranean Arvicolinae. Parallel substitutions were detected in genes RAD23B and PYCR2. These genes are associated with DNA repair processes and response to oxidative stress. Similar substitutions were discovered in the RAD23 genes for highly specialized subterranean Heterocephalus glaber and Fukomys damarensis. The most pronounced signatures of adaptive evolution related to subterranean niche within species of Arvicolinae subfamily were detected for Ellobius lutescens. Our results suggest that genomic adaptations can occur very quickly so far as the amount of selection signatures was found to be compliant with the degree of specialization to the subterranean niche and independent from the evolutionary age of the taxon. We found that the number of genomic signatures of selection does not depend on the age of the taxon, but is positively correlated with the degree of specialization to the subterranean niche.

地表下方的生命生存极具挑战性，且伴随诸多形态学、生理学及行为学层面的适应性改变。地下生境（subterranean niche）可帮助动物躲避天敌、规避环境参数波动，但该生境存在二氧化碳浓度偏高、氧气浓度偏低的特点，且挖掘活动需要消耗大量能量。此外，地下生境几乎缺失地表环境中可获取的绝大多数感官输入信号。

本研究针对田鼠亚科（Arvicolinae）的4种地下生活田鼠开展了RNA测序（RNA-seq）分析，受试物种分别为普罗米修斯鼹形田鼠（Prometheomys schaposchnikowi）、伊朗鼹形田鼠（Ellobius lutescens）、欧洲鼹形田鼠（Terricola subterraneus）以及东方毛足田鼠（Lasiopodomys mandarinus）。本研究获取了8个物种的原始RNA测序数据，并从NCBI SRA数据库下载了9个物种的序列读取存档（Sequence Read Archive，SRA）数据。此外，本研究还纳入了褐毛田鼠（Mynomes ochrogaster）与中国仓鼠（Cricetulus griseus）的已组装转录组用于后续分析。

我们共对19个物种开展了选择信号与平行氨基酸替换的搜寻工作。即便在这一有限的数据集内，通过自由比率模型分析，我们仍发现地下生活的田鼠亚科物种的dN/dS比值发生了显著变化。研究在RAD23B与PYCR2基因中检测到了平行替换事件，这两个基因均与DNA修复过程及氧化应激应答密切相关。针对高度特化的地下生活物种裸鼹鼠（Heterocephalus glaber）和达马拉兰鼹形鼠（Fukomys damarensis），我们在其RAD23基因中也发现了类似的氨基酸替换。

在田鼠亚科物种中，与地下生境适应相关的最显著适应性进化信号，在伊朗鼹形田鼠（Ellobius lutescens）中被检测到。我们的研究结果表明，基因组适应性演化的发生速度极快：研究发现选择信号的数量与物种对地下生境的特化程度相符，且与类群的演化年代无关。进一步分析显示，基因组选择信号的数量并不取决于类群的演化年代，而是与物种对地下生境的特化程度呈显著正相关。