The global exploration of evolutionary trends in groupers, based on mitogenomes, is currently underway. This research extensively investigates the structure of and variations in Cephalopholis species mitogenomes, along with their phylogenetic relationships, focusing specifically on Cephalopholis taeniops from the Eastern Atlantic Ocean. The generated mitogenome spans 16,572 base pairs and exhibits a gene order analogous to that of the ancestral teleost’s, featuring 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. The mitogenome of C. taeniops displays an AT bias (54.99%), aligning with related species. The majority of PCGs in the mitogenome initiate with the start codon ATG, with the exceptions being COI (GTG) and atp6 (TTG). The relative synonymous codon usage analysis revealed the maximum abundance of leucine, proline, serine, and threonine. The nonsynonymous/synonymous ratios were <1, which indicates a strong negative selection among all PCGs of the Cephalopholis species. In C. taeniops, the prevalent transfer RNAs display conventional cloverleaf secondary structures, except for tRNA-serine (GCT), which lacks a dihydrouracil (DHU) stem. A comparative examination of conserved domains and sequence blocks across various Cephalopholis species indicates noteworthy variations in length and nucleotide diversity. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic analyses, employing the concatenated PCGs and a combination of PCGs + rRNAs, distinctly separate all Cephalopholis species, including C. taeniops. Overall, these findings deepen our understanding of evolutionary relationships among serranid groupers, emphasizing the significance of structural considerations in mitogenomic analyses.

The collective understanding of global-scale evolutionary trends in barracuda mitogenomes is presently limited. This ongoing research delves into the maternal evolutionary path of Sphyraena species, with a specific focus on the complete mitogenome of Sphyraena sphyraena, sourced from the Atlantic Ocean through advanced next-generation sequencing. This mitogenome spans 16,841 base pairs and encompasses 37 genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. Notably, the mitogenome of S. sphyraena exhibits a preference for AT-base pairs, constituting 55.06% of the composition, a trait consistent with a similar bias found in related species. Most protein-coding genes initiate with an ATG codon, with the exception of Cytochrome c oxidase I (COI), which begins with a GTG codon. Additionally, six PCGs terminate with a TAA codon, COI with AGA, while six others exhibit incomplete termination codons. In the S. sphyraena mitogenome, the majority of transfer RNAs exhibit typical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the D-loop regions of six Sphyraenidae species reveals that the CSB-I block extends to 22 base pairs, surpassing other blocks and containing highly variable sites. Both maximum-likelihood and Bayesian phylogenetic analyses, using concatenated 13 mitochondrial PCGs, distinctly separate all Sphyraenidae species. The European Barracuda, S. sphyraena, demonstrates a sister relationship with the ‘Sphyraena barracuda’ group, including S. barracuda and S. jello. In conclusion, this study advances our understanding of the evolutionary relationship and genetic diversity within barracudas. Furthermore, it recommends comprehensive exploration of mitogenomes and broader genomic data for all existing Sphyraenidae fishes, providing invaluable insights into their systematics, genetic characterization, and maternal evolutionary history within marine environments.

The family Notopteridae is distributed across Africa and Asia and plays an important role in ecological functioning, local economies, and conservation initiatives. However, mitogenomic data for notopterids from the Sundaland hotspot remain scarce, limiting comprehensive understanding of their genetic architecture and matrilineal evolutionary history. To address this knowledge gap, the present study reports the first complete mitochondrial genome of Chitala borneensis and re‐sequences the mitogenome of Chitala lopis , two sympatric species endemic to Sundaland. Both Chitala mitogenomes exhibit the canonical teleost mitochondrial organization, comprising 37 genes and an AT‐rich control region, with C. borneensis (16,943 bp) representing the longest mitogenome reported within the genus to date. The codon usage analyses revealed a bias toward arginine, leucine, and serine, while nonsynonymous‐to‐synonymous substitution rate estimates indicated that most protein‐coding genes are evolving under purifying selection. The phylogenetic analyses recovered well‐supported African and Asian notopterid clades, with C. borneensis resolved as the sister lineage to C. lopis . Nevertheless, mitogenomic‐ and COI‐based phylogenetic frameworks inferred using Bayesian inference and maximum‐likelihood approaches supported multiple hypotheses regarding the systematic positions of mainland and island Chitala species in Southeast Asia. The divergence time estimates were congruent with historical biogeographic reconstructions, suggesting that Miocene tectonic events played a major role in the diversification of Chitala from other Asian notopterids. Furthermore, paleodrainage reorganization during the Last Glacial Maximum appears to have been critical in shaping the contemporary population structure of Chitala across the insular landscapes of this region. Collectively, this study provides new insights into the matrilineal evolutionary history of African and Asian notopterids, with particular emphasis on Sundaic Chitala species. The findings underscore the need for expanded taxon sampling and additional molecular data to improve population monitoring, inform conservation genetics, and ensure the long‐term persistence of these freshwater fishes within this biodiversity hotspot.

Butidae is a family of teleost fishes with diverse morphological and ecological adaptations, including the marbled goby (Oxyeleotris marmorata), a large species of high economic value in Southeast and East Asia. The previous mitogenomic studies on cultured populations of O. marmorata from non-native habitats have provided limited insights into genetic divergence, structural variation, and evolutionary relationships. Hence, this study presented the complete mitochondrial genome of O. marmorata from its native habitat in Indonesia, providing structural characterization, assessment of genetic diversity, and matrilineal phylogenetic analysis. The circular mitogenome was 16,525 bp, comprising 37 genes and a non-coding control region (CR). The gene organization and strand distribution were conserved among Oxyeleotris species, with 28 genes on the heavy strand and nine on the light strand, and a pronounced A+T compositional bias. The comparative analyses of O. marmorata (from both native and cultured habitats) and Oxyeleotris lineolata mitogenomes revealed minor variations in intergenic spacers, gene overlaps, protein-coding gene (PCGs) lengths, and codon usage patterns. Conversely, the nonsynonymous and synonymous substitution ratios observed in species of the family Butidae and its closest related family (Eleotridae) indicate strong purifying selection in the present dataset. Notably, the ATG was the predominant start codon, whereas the COI gene utilized GTG, and amino acid composition analysis demonstrated high frequencies of arginine, leucine, and serine. Most transfer RNAs retained the canonical cloverleaf secondary structure except for trnS1, which lacked a functional dihydrouridine arm, whereas the CR contained four conserved sequence blocks with variable nucleotide motifs and no detectable tandem repeats. The haplotype analysis of native (Indonesia) and introduced populations (China) highlighted three haplotypes with high diversity (Hd = 1.0000) and substantial nucleotide variation (π = 0.6667). The genetic divergence across 13 PCGs was gene-specific, with COI and ND5 showing the highest variation, while ND4L and ATP8 were highly conserved. The phylogenetic analyses based on concatenated 13 PCGs using both Bayesian Inference and Maximum Likelihood methods revealed that Oxyeleotris forms a monophyletic clade and is closely related to Bostrychus sinensis. In addition, the broader phylogenetic framework inferred the matrilineal relationships within the family Butidae and its closest related family, Eleotridae. This study also recommends expanding analyses to include the mitogenomes of the remaining 17 Oxyeleotris species, together with comprehensive genomic data, to further elucidate their genetic architecture, evolutionary history, and ecological adaptability across diverse aquatic ecosystems.

Despite its ecological and economic importance, Hampala macrolepidota (Cyprinidae: Smiliogastrinae) remains taxonomically debated, having undergone historical reclassifications across multiple taxonomic ranks. These challenges highlight the urgent need for integrative genomic analyses to resolve its phylogeny and assess genome-wide diversity, establishing a baseline for effective management and conservation. In this study, the newly assembled mitogenome of H. macrolepidota from within its native range in Lake Dibawah, West Sumatra, Indonesia, was sequenced. The mitogenome spanned 17,104 bp, encoded 37 genes and a control region, and exhibited a nucleotide composition biased toward adenine and thymine. The protein-coding genes (PCGs) predominantly utilized ATG as the initiation codon and showed a higher proportion of hydrophobic compared to hydrophilic amino acids. The nonsynonymous (Ka) and synonymous (Ks) substitution ratios were below ‘1’, which indicates negative selection on most of the PCGs within Hampala and other Smiliogastrinae species. Mitogenome-wide analysis revealed overall high intraspecific genetic diversity (≥2.7%) in the native Indonesian population compared to mainland populations in Southeast Asia. The Bayesian and maximum-likelihood phylogenetic analyses elucidated matrilineal evolutionary relationships within the subfamily Smiliogastrinae, with the Hampala species forming a monophyletic cluster. The present mitogenome-based phylogenetic topologies also supported the taxonomic placement of several species in the revised classification, which previously were classified under the genera Puntius and Barbus, respectively. Additionally, the investigation of partial mitochondrial COI and Cytb genes further elucidated the population genetic structure of H. macrolepidota across Southeast and East Asia. The observed genetic divergence (0–4.2% in COI and 0–4.5% in Cytb), together with well-resolved phylogenetic clustering and the presence of both shared and distinct haplotypes among Indonesian samples, provides strong evidence for long-term population isolation and local adaptation. These patterns are most plausibly driven by historical hydrological dynamics, paleo-drainage connectivity, and persistent geographic barriers that have structured population divergence over time. In addition, this study emphasizes the need to generate mitogenomes of seven additional Hampala species from Southeast Asia to better understand their evolutionary patterns. Further, broader sampling of wild H. macrolepidota populations across their biogeographical range will be essential to strengthen understanding of their genetic diversity and guide effective conservation strategies.

Prior to this study, knowledge on the evolutionary lineage of Garra remained inadequate, as previous phylogenetic investigations were primarily based on partial gene sequences. Although several mitogenomes of Garra species have been reported, their structural organization and comprehensive genomic characteristics have not been thoroughly evaluated. In this study, Garra manipurensis, endemic to the Indo-Burma biodiversity hotspot, was identified based on its detailed morphology and meristic counts. The circular mitogenome of G. manipurensis is 16,776 bp in length and contains the canonical set of 37 genes, along with duplicated control regions separated by tRNA-Proline. The comparative assessments across Garra species indicate predominantly conserved GTG start codons, occasional alternative ATA initiation codons, and incomplete stop codons. The selection pressure examinations within Garrini taxa reveal a purifying selection across all protein-coding genes. The control region comprises four conserved sequence blocks and species-specific tandem repeats, reflecting a balance between functional constraint and lineage-dependent evolutionary dynamics. The phylogenetic inference supports the monophyly of Garra and places G. manipurensis in close affinity with Garra flavatra, which is native to the western slope of Rakhine Yoma in Myanmar and Mizoram State in northeastern India. The genetic diversity analyses revealed haplotype differentiation, with shallow intraspecific genetic distances (0.000–0.011) observed samples between two distinct drainage systems in Manipur and Mizoram, northeastern India. The observed pattern of haplotype divergence in G. manipurensis may reflect the historical or seasonal hydrological connectivity among the western-slope drainages of the Chin Hills, with the subsequent geographic isolation potentially contributing to the emergence of distinct genetic lineages. Nevertheless, the extent and evolutionary significance of this differentiation remain uncertain and warrant further investigation through expanded geographic sampling and the incorporation of additional molecular data. Collectively, these findings provide in-depth insights into the mitogenomic architecture, comparative gene arrangements, phylogenetic patterns, and matrilineal evolutionary history of G. manipurensis and other congeners, thereby improving our understanding of the systematics and genetic diversity of this important cyprinid fish lineage.