Cite this paper:
Lei ZHOU, Shihui HUANG, Qing WANG, Zhenhai LI, Zongyang LI, Anyou HE, Jiehu CHEN, Li LIU, Keshu ZOU. Novel evolutionary insights into nemacheilid cavefish: evidence from comparative analysis of mitochondrial genomes[J]. Journal of Oceanology and Limnology, 2022, 40(4): 1640-1653

Novel evolutionary insights into nemacheilid cavefish: evidence from comparative analysis of mitochondrial genomes

Lei ZHOU1, Shihui HUANG1, Qing WANG1, Zhenhai LI1, Zongyang LI1, Anyou HE2, Jiehu CHEN3, Li LIU1, Keshu ZOU1
1 Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China;
2 Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China;
3 Science Corporation of Gene, Guangzhou 510000, China
Cavefish can be important models for understanding the relationships among evolution, adaptation, and development in extreme environments. However, cavefish remain poorly studied, particularly at the genome level. Here, we sequenced the complete mitogenome of three cavefish in the family Nemacheilidae (Paranemachilus pingguoensis, Oreonectes polystigmus, and Heminoemacheilus longibarbatus), which were collected from karst caves in South China. The mitogenomes each contained 37 genes (13 protein coding, 22 tRNA, and two rRNA genes) and a single control region, with the same genetic arrangement and distribution as those found in vertebrates. The non-synonymous/synonymous mutation ratios (Ka/Ks) of the mitogenomes indicated that the protein-coding genes (PCGs) of the three cavefish evolved under purifying selection. The mitogenomes of the three cavefish exhibit nucleotide composition biases for PCGs, tRNAs, rRNAs, and the whole genome, indicating that the mitochondrial DNA might have been subjected to evolutionary selection in response to extreme cave environments. Divergence time and evolutionary history analyses suggested that the speciation and diversification of the cavefish coincided with the Miocene uplift of the southern Qinghai-Tibet Plateau, which greatly changed cave habitats. Overall, our study sheds light on the mitogenomes, phylogeny, and evolutionary history of nemacheilid cavefish.
Key words:    cavefish|mitochondrial genome|evolution|Nemacheilidae   
Received: 2021-02-24   Revised:
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