Dataset Information

The complete mitochondrial genomes of the flapper skate Dipturus intermedius and the longnose skate Dipturus oxyrinchus.

ABSTRACT: We describe the complete mitochondrial genomes of the flapper skate Dipturus intermedius (Parnell 1837) and the longnose skate Dipturus oxyrinchus (Linnaeus 1758), which have been obtained by Sanger sequencing. We report the length of the sequences to be 16,906 and 16,911 bp, respectively. The length and structure of gene regions, containing 13 protein-coding regions, 22 tRNA genes, two rRNA genes, and two non-coding areas, resemble those of related skate species. Despite D. intermedius being considered a cryptic species with D. batis, the full mitogenomes confirm that D. intermedius and D. oxyrinchus are more genetically similar. In comparison to other Dipturus species, D. intermedius is missing a whole codon in its cytochrome oxidase subunit 2 gene. These mitogenomes will be a useful resource furthering investigation of the population genetic differences and evolutionary history of skate species.

SUBMITTER: Schwanck TN

PROVIDER: S-EPMC9176345 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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The complete mitochondrial genomes of the flapper skate Dipturus intermedius and the longnose skate Dipturus oxyrinchus.

Schwanck Tanja N TN Delaval Aurelien N AN Noble Leslie R LR Wright Peter J PJ Donnan David W DW Jones Catherine S CS

Mitochondrial DNA. Part B, Resources 20220526 5

We describe the complete mitochondrial genomes of the flapper skate Dipturus intermedius (Parnell 1837) and the longnose skate Dipturus oxyrinchus (Linnaeus 1758), which have been obtained by Sanger sequencing. We report the length of the sequences to be 16,906 and 16,911 bp, respectively. The length and structure of gene regions, containing 13 protein-coding regions, 22 tRNA genes, two rRNA genes, and two non-coding areas, resemble those of related skate species. Despite D. int ...[more]

PMID: 35692707

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Project description:Longnose skates have great economic importance in South American fisheries, and in order to preserve them, it is important to have a well-defined taxonomic status of their species. Dipturus lamillai was recently described for Malvinas Islands waters based on morphological and molecular comparisons with Zearaja chilensis. Although D. lamillai has been compared with several congeneric species, it was not properly compared with the morphologically similar Zearaja brevicaudata, the most abundant longnose skate in the Southwest Atlantic. Here, these species were compared by morphological and molecular analyses in order to evaluate their conspecificity. Linear morphometric variables of holotype and paratypes of D. lamillai and 69 specimens of Z. brevicaudata were compared and investigated using Principal Component Analysis. In addition, thorn patterns, denticle distributions, color, and clasper morphology were compared. No body proportions or other single character that could differentiate D. lamillai from Z. brevicaudata were found. Molecular analyses comprised of the comparison of the Cytochrome oxidase subunit I (COI) and the NADH dehydrogenase subunit 2. The results of the Maximum Likelihood (ML) carried out for each molecular marker showed that sequences from D. lamillai clustered together with those of Z. brevicaudata, and the molecular distance determined by Kimura two-parameter were lower than the expected for different species. Additionally, the Automatic Barcode Gap Discovery method and the Bayesian implementation of the Poisson tree processes were carried out with COI sequences to explore species limits, and their results were consistent with ML analyses. In summary, the results obtained showed that there are no morphological or molecular differences between these nominal species of the valid skate genus Zearaja, leading to the conclusion that they are conspecific. Therefore, we designated Z. brevicaudata as a senior synonym of D. lamillai.

Project description:The blue skate (Dipturus batis) has a patchy distribution across the North-East Atlantic Ocean, largely restricted to occidental seas around the British Isles following fisheries-induced population declines and extirpations. The viability of remnant populations remains uncertain and could be impacted by continued fishing and by-catch pressure, and the projected impacts of climate change. We genotyped 503 samples of D. batis, obtained opportunistically from the widest available geographic range, across 6 350 single nucleotide polymorphisms (SNPs) using a reduced-representation sequencing approach. Genotypes were used to assess the species' contemporary population structure, estimate effective population sizes and identify putative signals of selection in relation to environmental variables using a seascape genomics approach. We identified genetic discontinuities between inshore (British Isles) and offshore (Rockall and Faroe Island) populations, with differentiation most pronounced across the deep waters of the Rockall Trough. Effective population sizes were largest in the Celtic Sea and Rockall, but low enough to be of potential conservation concern among Scottish and Faroese sites. Among the 21 candidate SNPs under positive selection was one significantly correlated with environmental variables predicted to be affected by climate change, including bottom temperature, salinity and pH. The paucity of well-annotated elasmobranch genomes precluded us from identifying a putative function for this SNP. Nevertheless, our findings suggest that climate change could inflict a strong selective force upon remnant populations of D. batis, further constraining its already-restricted habitat. Furthermore, the results provide fundamental insights on the distribution, behaviour and evolutionary biology of D. batis in the North-East Atlantic that will be useful for the establishment of conservation actions for this and other critically endangered elasmobranchs.

Dataset Information

The complete mitochondrial genomes of the flapper skate Dipturus intermedius and the longnose skate Dipturus oxyrinchus.

Publications

The complete mitochondrial genomes of the flapper skate <i>Dipturus intermedius</i> and the longnose skate <i>Dipturus oxyrinchus</i>.

Similar Datasets

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