Genetic Characteristics and Phylogenetic Relationships of 18 Anchovy Species Based on Mitochondrial Genomes in the Seas Around China

The anchovy family (Engraulidae) holds significant economic and ecological value in seas around China, playing a crucial role in fisheries and marine ecosystems in these regions. This study analyzed the complete mitochondrial genome data of 18 Engraulidae species from seas around China, integrating molecular evidence to systematically investigate mitochondrial genome structure, codon usage patterns, and phylogenetic relationships within the family. The mitochondrial genomes of Engraulidae exhibited a highly conserved structure, characterized by significant A + T richness and variable control region lengths. Codon usage analysis in seven <i>Thryssa</i> species revealed that base composition, particularly GC content at the third codon position (GC3s), along with purifying selection, jointly influenced codon usage patterns. Phylogenetic analyses supported the division of the 18 species into two subfamilies, Engraulinae and Coiliinae, and highlighted variability in the phylogenetic placement of <i>Setipinna</i> depending on the inclusion of third codon positions. Furthermore, the genus <i>Thryssa</i> was supported to be polyphyletic: <i>T. baelama</i> and <i>T. kammalensis</i> formed one clade, while <i>T. dussumieri</i>, <i>T. hamiltonii</i>, <i>T. setirostris</i>, <i>T. vitrirostris</i>, and <i>T. mystax</i> constituted a separate branch. These findings provide novel molecular evidence for species identification and the taxonomic classification of Engraulidae, while offering a foundation for further exploration of their evolutionary relationships and systematic taxonomy.