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王海山，等 水产学报, 2025, 49(11): 119104

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[25] 冯鉴童. 蜑螺科 4 属 13 种线粒体全基因组序列分析及系统 (in Chinese).

Phylogenetic analysis of 27 species of Neritidae based on
mitochondrial genomes

1,2
1,2
2
1,2
WANG Haishan , ZHANG Jing , YE Le , LI Youming , CHEN Zhi 1,2*
1. Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, Sanya 572022, China;
2. Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Ministry of Education,
Hainan Tropical Ocean University, Sanya 572022, China

Abstract: The family Neritidae is one of the most diverse groups within the subclass Neritimorpha, attracting widespread atten-
tion for its phylogenetic relationships. This study aims to explore the evolutionary relationships, genetic distances, and selec-
tion pressures of 27 species of Neritidae through a phylogenetic analysis of their mitochondrial genomes, to provide a theoret-
ical basis for the systematic evolution and origin of Neritidae. Using bioinformatics methods, we analyzed the sequence base
composition, selection pressure on protein-coding genes, and genetic distances of 27 Neritidae species. We reconstructed the
phylogenetic tree using three different methods (Astral, Bayesian inference, and maximum likelihood) based on protein-coding
genes. Results revealed that the mitochondrial genomes of 27 Neritidae species were all double-stranded closed circular DNA
molecules, containing 37 genes (13 protein-coding genes, 2 ribosomal rRNA genes, 22 transfer RNA genes, and a non-coding
control region). There was no gene rearrangement among species. The full length of the mitochondrial genomes involved in this
study ranged from 15 261 to 15 975 bp, displaying a noticeable AT bias in base composition. The results of relative synonym-
ous codon usage (RSCU) indicated that the usage frequencies of UUA, CCU, CGA and UCU were high, while that of CCG was
the lowest. Ka/Ks analysis indicated purifying selection on mitochondrial protein-coding genes in the evolutionary process.
Among the 13 protein-coding genes, ATP8 exhibited the fastest evolutionary rate, while COX2 showed the slowest. All three
tree construction methods yielded consistent results, revealing the average genetic distances of each protein-coding gene ranged
from 0.16 to 0.29. Among them, the gene with the largest average genetic distance was ND6 and the one with the smallest aver-
age genetic distance was COX1. The 27 Neritidae species were grouped into three evolutionary branches. The first branch con-
sisted of 15 species of genus Nerita, with a distinct evolutionary relationship compared to other genera. The second branch
comprised 6 species of genus Clithon and one species of genus Vitta. Species of the genera Neritina, Neripteron and Septaria
formed the third branch. This study indicates that the mitochondrial genomes of the 27 Neritidae species exhibit high conserva-
tion in structure and gene arrangement but differ in evolutionary relationships due to variations in living environments and life-
styles. This research provides a detailed molecular biology foundation for understanding the systematic evolution of Neritidae.

Key words: Neritidae; mitochondrial genome; phylogenetic analysis; purifying selection; living environments
Corresponding author: CHEN Zhi. E-mail: change@139.com
Funding projects: Open Project of Yazhou Bay Innovation Research Institute, Hainan Tropical Ocean University
(2022CXYKFKT07); National Natural Science Foundation of China (32002389)

https://www.china-fishery.cn 中国水产学会主办 sponsored by China Society of Fisheries
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