Family Wide Molecular Adaptations to Underground Life in African Mole-Rats Revealed by Phylogenomic Analysis.
Family Wide Molecular Adaptations to Underground Life in African Mole-Rats Revealed by Phylogenomic Analysis.
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DOI：
10.1093/molbev/msv175
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发表时间：
2015-12
影响因子：
10.7
通讯作者：
Faulkes CG
中科院分区：
文献类型：
--
作者：
Davies KT;Bennett NC;Tsagkogeorga G;Rossiter SJ;Faulkes CG
在它们的进化辐射过程中，哺乳动物已经殖民了不同的栖息地。可以说，地下生态位是其中最不适合居住的，其特征是氧气减少，二氧化碳升高，缺乏光线，食物匮乏，以及挖掘的能量成本很高的基质。在所有已经过渡到地下生态位的血统中，非洲鼹鼠是最成功的之一。它们在生态上的成功在很大程度上可以归功于植物储存器官的饮食，这使它们能够在撒哈拉以南非洲气候多样的栖息地定居，并可能有助于其多样化社会制度的演变。然而，尽管它们有许多显著的表型特化，但对这些特征背后的分子适应却知之甚少。为了解决这个问题，我们对七个鼹鼠分类群的转录组进行了测序，其中包括三个单独的物种，并将新的序列与现有的基因组数据集相结合。超过13，000个蛋白质编码基因的比对首次涵盖了所有六个属以及进化枝中生态和社会变异的全部范围。我们检测到正选择的鼹鼠分支内和沿着祖先的分支在大约700个基因，包括与肿瘤发生，衰老，形态发育和社会性的基因座。通过将这些结果与基因本体注释和蛋白质-蛋白质网络相结合，我们确定了几个功能相关基因的簇。这个全家族的分子进化分析鼹鼠已经确定了一套积极选择的基因，加深了我们对这个群体所表现出的极端表型特征的理解。
During their evolutionary radiation, mammals have colonized diverse habitats. Arguably the subterranean niche is the most inhospitable of these, characterized by reduced oxygen, elevated carbon dioxide, absence of light, scarcity of food, and a substrate that is energetically costly to burrow through. Of all lineages to have transitioned to a subterranean niche, African mole-rats are one of the most successful. Much of their ecological success can be attributed to a diet of plant storage organs, which has allowed them to colonize climatically varied habitats across sub-Saharan Africa, and has probably contributed to the evolution of their diverse social systems. Yet despite their many remarkable phenotypic specializations, little is known about molecular adaptations underlying these traits. To address this, we sequenced the transcriptomes of seven mole-rat taxa, including three solitary species, and combined new sequences with existing genomic data sets. Alignments of more than 13,000 protein-coding genes encompassed, for the first time, all six genera and the full spectrum of ecological and social variation in the clade. We detected positive selection within the mole-rat clade and along ancestral branches in approximately 700 genes including loci associated with tumorigenesis, aging, morphological development, and sociality. By combining these results with gene ontology annotation and protein–protein networks, we identified several clusters of functionally related genes. This family wide analysis of molecular evolution in mole-rats has identified a suite of positively selected genes, deepening our understanding of the extreme phenotypic traits exhibited by this group.