Mitogenome-based phylogeny and evolutionary insights into Salticidae (Araneae) with emphasis on gene order evolution and selective pressures.

Salticidae (jumping spiders) is the most species-rich family within Araneae. Despite recent advances in phylogenomic studies, mitochondrial genome (mitogenome) evolution and its contribution to understanding phylogenetic relationships in Salticidae remain poorly characterized. Here, we present a mitochondrial phylogenomic analysis of 107 salticid species representing all seven recognized subfamilies. Using newly generated and publicly available mitogenomes, we investigated phylogenetic relationships and evolutionary patterns across the family, with a particular focus on comparisons between the highly diverse Salticinae and the species-poor non-Salticinae lineages. Our results show that the salticid mitogenomes are highly conserved in overall structure, with broadly similar genome size and nucleotide composition between Salticinae and non-Salticinae lineages. Codon usage showed a pronounced A/T bias, with both mutational pressure and natural selection contributing to codon usage patterns. Phylogenetic analyses strongly supported the monophyly of Salticidae and all seven subfamilies in the maximum likelihood and Bayesian analyses. Lyssomaninae and Asemoneinae were recovered as sister groups, as were Eupoinae and Spartaeinae, while Onomastinae was sister to the clade comprising Hisponinae and Salticinae. Within Salticinae, Amycoida and Salticoida were recovered as major lineages, although relationships within Salticoida were unstable among analytical methods. Selection analyses indicated that all 13 mitochondrial protein-coding genes are predominantly under purifying selection, whereas nad2 showed the most consistent signals of positive selection in Salticinae across the branch-site, FEL and MEME analyses. Fifteen distinct gene rearrangement patterns were identified in Salticidae, including 13 novel patterns, with M5 inferred as the gene order of the most recent common ancestor of Salticidae. Gene rearrangements were more diverse in non-Salticinae, particularly within Spartaeinae. Transposition was inferred as the predominant type of mitochondrial gene rearrangements in Salticidae. Overall, this study provides mitochondrial evidence for phylogenetic relationships within Salticidae and contributes to our understanding of mitochondrial sequence evolution, selection and gene order evolution in jumping spiders.