Novel duplication remnant in the first complete mitogenome of Hemitriakis japanica and the unique phylogenetic position of family Triakidae

Wang, Chen; Lai, Tinghe; Ye, Peiyuan; Yan, Yunrong; Feutry, Pierre; He, Binyuan; Huang, Zhongjian; Zhu, Ting; Wang, Junjie; Chen, Xiao

doi:10.1016/j.gene.2022.146232

Cited by 9 publications

(4 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The distinctive morphology of C. oxyrhynchus does not exclude this species from the genus Carcharhinus, however, given that the tree topology and genetic distances found in the present study emphatically support the inclusion of this species in Carcharhinus. The results are also consistent with previous findings of the paraphyletic arrangement of Carcharhinus considering C. glaucus [4,10,30,31,34,37,40,41,72], but this is the first time that it is recognized as a new combination and all fossil taxa in Prionace (Prionace antiquus (Agassiz, 1856), Prionace egertoni (Agassiz, 1843), and Prionace tenuis (Agassiz, 1843)) should also be reallocated to Carcharhinus or recognized as new combinations. The relatively large dataset employed in the present study, together with the robust phylogenetic approaches applied in the analyses, supports this conclusion.…”

Section: Discussionsupporting

confidence: 91%

“…Naylor [75] argued that the morphological similarities found between the species of each group must be the result of convergent evolution and that there is a need for further studies of the phylogenetic structure of Carcharhinus. Future reclassifications based on these subdivisions are possible considering, but even with the full mitogenome datasets of Kousteni et al [40] and Wang et al [41], these arrangements are currently uncertain.…”

Section: Discussionmentioning

confidence: 99%

“…Similarly, although other studies since then have shown paraphyly of Carcharhinus, the analyses of their studies also showed weak support [10,39] or had poor taxonomic coverage [16] and also did not make any changes to the classifications. Other recent studies using mitogenomes have also shown paraphyly of P. glauca and probably Triaenodon obesus but did not include I. oxyrhynchus and focusing on other results did not reclassify P. glauca or T. obesus [40,41].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Evolutionary History and Taxonomic Reclassification of the Critically Endangered Daggernose Shark, a Species Endemic to the Western Atlantic

Rodrigues‐Filho

Nogueira

Sodré

et al. 2023

Journal of Zoological Systematics and Evolutionary Research

View full text Add to dashboard Cite

The family Carcharhinidae includes the most typical and recognizable sharks, although its internal classification is the subject of extensive debate. In particular, the type genus, Carcharhinus Blainville, 1816, which is also the most speciose, appears to be paraphyletic in relation to a number of morphologically distinct taxa. Isogomphodon oxyrhynchus (Valenciennes, 1839) (the daggernose shark) is a carcharinid, which is endemic to a limited area of the Western Atlantic between Trinidad and Tobago and the Gulf of Maranhão in northern Brazil, one of the smallest ranges of any New World elasmobranch species. In recent decades, I. oxyrhynchus populations have been decimated by anthropogenic impacts, which has led to the classification of the species as critically endangered by the IUCN. However, there is considerable debate on both the validity of the species (I. oxyrhynchus) and the status of Isogomphodon Gill, 1862 as a distinct entity from the genus Carcharhinus. The present study is based on a molecular assessment of the genetic validity of the I. oxyrhynchus that combines mitochondrial and nuclear markers, which were used to identify the biogeographic events responsible for the emergence and dispersal of the species in northern Brazil. The genetic distance analyses and phylogenetic trees confirmed the paraphyly of the genus Carcharhinus, recovering a clade comprising Carcharhinus+I. oxyrhynchus+Prionace glauca (Linnaeus, 1758). Our results indicate not only that the daggernose shark is actually a member of the genus Carcharhinus, but that it is genetically more closely related to Carcharhinus porosus (Ranzani, 1839) than it is to the other Carcharhinus species analyzed. Given this, I. oxyrhynchus and P. glauca are therefore reclassified and recognized as Carcharhinus oxyrhynchus and Carcharhinus glaucus. The daggernose shark, Carcharhinus oxyrhynchus, diverged from C. porosus during the Miocene, when significant geomorphological processes occurred on the northern coast of South America, in particular in relation to the configuration of the Amazon River. It is closely associated with the area of the Amazon plume, and its distinctive morphological features represent autapomorphic ecological adaptations to this unique habitat and do not reflect systematic distinction from Carcharhinus.

show abstract

Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Evolutionary History and Taxonomic Reclassification of the Critically Endangered Daggernose Shark, a Species Endemic to the Western Atlantic

Rodrigues‐Filho

Nogueira

Sodré

et al. 2023

Journal of Zoological Systematics and Evolutionary Research

View full text Add to dashboard Cite

show abstract

“…Between trnE and trnF , the secondary structure of the sequence could be predicted. The large non-coding region in trnE-trnF was considered DmTTF and had a similar structure to that of other insect species ( Roberti et al, 2003 ; Beckenbach, 2012 ; Yuan et al, 2016 ; Wang et al, 2022a ). Other insect groups also had the trnE-trnF IGR and other structural features consistent with repeat regions ( Wu et al, 2012 ; Zhang et al, 2014 ; Chen et al, 2020a ).…”

Section: Discussionmentioning

confidence: 99%

Comparative mitogenomic and evolutionary analysis of Lycaenidae (Insecta: Lepidoptera): Potential association with high-altitude adaptation

Chen

et al. 2023

Front. Genet.

View full text Add to dashboard Cite

Harsh environments (e.g., hypoxia and cold temperatures) of the Qinghai–Tibetan Plateau have a substantial influence on adaptive evolution in various species. Some species in Lycaenidae, a large and widely distributed family of butterflies, are adapted to the Qinghai–Tibetan Plateau. Here, we sequenced four mitogenomes of two lycaenid species in the Qinghai–Tibetan Plateau and performed a detailed comparative mitogenomic analysis including nine other lycaenid mitogenomes (nine species) to explore the molecular basis of high-altitude adaptation. Based on mitogenomic data, Bayesian inference, and maximum likelihood methods, we recovered a lycaenid phylogeny of [Curetinae + (Aphnaeinae + (Lycaeninae + (Theclinae + Polyommatinae)))]. The gene content, gene arrangement, base composition, codon usage, and transfer RNA genes (sequence and structure) were highly conserved within Lycaenidae. TrnS1 not only lacked the dihydrouridine arm but also showed anticodon and copy number diversity. The ratios of non-synonymous substitutions to synonymous substitutions of 13 protein-coding genes (PCGs) were less than 1.0, indicating that all PCGs evolved under purifying selection. However, signals of positive selection were detected in cox1 in the two Qinghai–Tibetan Plateau lycaenid species, indicating that this gene may be associated with high-altitude adaptation. Three large non-coding regions, i.e., rrnS-trnM (control region), trnQ-nad2, and trnS2-nad1, were found in the mitogenomes of all lycaenid species. Conserved motifs in three non-coding regions (trnE-trnF, trnS1-trnE, and trnP-nad6) and long sequences in two non-coding regions (nad6-cob and cob-trnS2) were detected in the Qinghai-Tibetan Plateau lycaenid species, suggesting that these non-coding regions were involved in high-altitude adaptation. In addition to the characterization of Lycaenidae mitogenomes, this study highlights the importance of both PCGs and non-coding regions in high-altitude adaptation.

show abstract

Comparative analysis of the mitochondrial genomes of Smoothhound sharks provide insight into the phylogenetic relationships within the family Triakidae

Kiser,

Skufca,

Bemis

et al. 2024

Gene Reports

View full text Add to dashboard Cite

Novel duplication remnant in the first complete mitogenome of Hemitriakis japanica and the unique phylogenetic position of family Triakidae

Cited by 9 publications

References 76 publications

Evolutionary History and Taxonomic Reclassification of the Critically Endangered Daggernose Shark, a Species Endemic to the Western Atlantic

Evolutionary History and Taxonomic Reclassification of the Critically Endangered Daggernose Shark, a Species Endemic to the Western Atlantic

Comparative mitogenomic and evolutionary analysis of Lycaenidae (Insecta: Lepidoptera): Potential association with high-altitude adaptation

Comparative analysis of the mitochondrial genomes of Smoothhound sharks provide insight into the phylogenetic relationships within the family Triakidae

Contact Info

Product

Resources

About