Diagnostic applicability of mitogenomics in uncovering intraspecific carangid diversifications: insights into phylogeny, divergence time, and characterization of two cryptic Selaroides leptolepis mitogenomes

• Published in: Organisms diversity & evolution Vol. 24; no. 3; pp. 417 - 434
• Main Authors: Halasan, Lorenzo C., Lin, Hsiu-Chin
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.09.2024
• Subjects: Animal Systematics/Taxonomy/Biogeography; Biodiversity; Biomedical and Life Sciences; Caranx; Decapterus; Developmental Biology; Evolutionary Biology; family; fish; Life Sciences; lifestyle; microsatellite repeats; mitochondrial genome; mitogenomics; morphometry; Neogene period; Original Article; phylogeny; Plant Systematics/Taxonomy/Biogeography; Selaroides leptolepis; Seriola lalandi; species; Trachurus trachurus; Cryptic species; Mitochondrial DNA; Divergent evolution; Yellowstripe scad; Phylogenomics
• ISSN: 1439-6092; 1618-1077
• DOI: 10.1007/s13127-024-00648-9

Carangidae is an economically important fish family comprised of 32 genera with more than 140 circumglobally distributed species. Its members exhibit vast differences in morphology and lifestyle, thus making them compelling subjects for evolutionary studies. Recently, more works on carangids have detected the presence of cryptic lineages through molecular and/or non-molecular techniques. Credited for its inherent amplification efficiency, mitophylogenomics became effective in opening avenues to further understand higher-level interrelationships in many fish groups. However, the mitophylogenomic approach has not yet been widely applied to infer evolutionary history at the lower-level interrelationships, especially on cryptic representatives. In this study, we evaluated the diagnostic applicability of mitogenomes in detecting population-level divergences within Carangidae. Using the mitogenomes, we detected intraspecific divergences on some taxa, namely Caranx melampygus , Selaroides leptolepis , Seriola lalandi , Decapterus maruadsi , and Trachurus trachurus , with divergences highly correspondent to that of their geographic origins. Additionally, a widespread Pacific arrangement was also detected for S. rivoliana . Our discoveries were highly corroborative with findings from other Carangidae studies which utilized different diagnostic markers (e.g., SNPs, microsatellites, morphometrics, parasites). Dated phylogeny also suggested that intraspecific diversifications occurred during the Late Neogene. Likewise, we characterized two mitogenomes from different cryptic lineages of Selaroides leptolepis and revealed that the two mitogenomes were K2P pairwise = 5.58% different from each other. Its genetic compositions included 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. These findings paved way for future evolutionary insights into the divergence histories of other fish populations.