Dataset Information

Mitocondrial COI and 16S rDNA sequences support morphological identification and biogeography of deep-sea red crabs of the genus Chaceon (Crustacea, Decapoda, Geryonidae) in the Eastern Central and South Atlantic Ocean.

ABSTRACT: The geographical spreading of new fishing activities and the increasingly deeper locations of these activities have shown the worldwide distribution of gerionid crabs and new descriptions of Chaceon taxa. However, incomplete penetrance, variable expressivity, and phenotypic overlap make the morphometric identification of these species difficult. In this study, partial sequences of the cytochrome c oxidase subunit 1 (COI) and 16S mitochondrial ribosomal RNA (16S rRNA) genes have been analyzed in Chaceon species from the Eastern Central and South Atlantic and compared with sequences of species from Western Atlantic. Our results corroborate the proposed morphological species and highlight the significant separation of the Eastern Atlantic species and those from Atlantic coasts of South America for both markers (97% Bayesian posterior probability, BPP / 83% Bootstrap replicates, BT). Interestingly, Chaceon sanctaehelenae shows a closer relationship with the species of the American coast than with those from the Eastern Atlantic. On the other hand, while COI marker clearly separates Chaceon atopus and Chaceon erytheiae species (99 BPP / 91% BT), these species share haplotypes for the 16S rRNA marker, pointing to a recent speciation process. Moreover, a close relationship was observed between Chaceon maritae and Chaceon affinis (94% BPP / 77% BT). The topologies of the trees obtained indicate that the ancestor of this genus was closer related to those species from South America than to those from the Eastern Atlantic.

SUBMITTER: Hernandez M

PROVIDER: S-EPMC6370203 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Mitocondrial COI and 16S rDNA sequences support morphological identification and biogeography of deep-sea red crabs of the genus Chaceon (Crustacea, Decapoda, Geryonidae) in the Eastern Central and South Atlantic Ocean.

Hernández Mariano M Martín M Virginia MV Herrador-Gómez Pedro M PM Jiménez Sebastián S Hernández-González Carlos C Barreiro Santiago S Sarralde Roberto R van Zyl Barend Johannes BJ Gamatham Johny Charles JC Almeida Teresa T López-Abellán Luis J LJ

PloS one 20190211 2

The geographical spreading of new fishing activities and the increasingly deeper locations of these activities have shown the worldwide distribution of gerionid crabs and new descriptions of Chaceon taxa. However, incomplete penetrance, variable expressivity, and phenotypic overlap make the morphometric identification of these species difficult. In this study, partial sequences of the cytochrome c oxidase subunit 1 (COI) and 16S mitochondrial ribosomal RNA (16S rRNA) genes have been analyzed in ...[more]

PMID: 30742637

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Project description:BackgroundDecapods are the most recognizable of all crustaceans and comprise a dominant group of benthic invertebrates of the continental shelf and slope, including many species of economic importance. Of the 17635 morphologically described Decapoda species, only 5.4% are represented by COI barcode region sequences. It therefore remains a challenge to compile regional databases that identify and analyse the extent and patterns of decapod diversity throughout the world.Methodology/principal findingsWe contributed 101 decapod species from the North East Atlantic, the Gulf of Cadiz and the Mediterranean Sea, of which 81 species represent novel COI records. Within the newly-generated dataset, 3.6% of the species barcodes conflicted with the assigned morphological taxonomic identification, highlighting both the apparent taxonomic ambiguity among certain groups, and the need for an accelerated and independent taxonomic approach. Using the combined COI barcode projects from the Barcode of Life Database, we provide the most comprehensive COI data set so far examined for the Order (1572 sequences of 528 species, 213 genera, and 67 families). Patterns within families show a general predicted molecular hierarchy, but the scale of divergence at each taxonomic level appears to vary extensively between families. The range values of mean K2P distance observed were: within species 0.285% to 1.375%, within genus 6.376% to 20.924% and within family 11.392% to 25.617%. Nucleotide composition varied greatly across decapods, ranging from 30.8 % to 49.4 % GC content.Conclusions/significanceDecapod biological diversity was quantified by identifying putative cryptic species allowing a rapid assessment of taxon diversity in groups that have until now received limited morphological and systematic examination. We highlight taxonomic groups or species with unusual nucleotide composition or evolutionary rates. Such data are relevant to strategies for conservation of existing decapod biodiversity, as well as elucidating the mechanisms and constraints shaping the patterns observed.

Project description:BackgroundThe 5' region of cytochrome oxidase I (COI) is the standard marker for DNA barcoding. However, COI has proved to be of limited use in identifying some species, and for some taxa, the coding sequence is not efficiently amplified by PCR. These deficiencies lead to uncertainty as to whether COI is the most suitable barcoding fragment for species identification of ticks.MethodsIn this study, we directly compared the relative effectiveness of COI, 16S ribosomal DNA (rDNA), nuclear ribosomal internal transcribed spacer 2 (ITS2) and 12S rDNA for tick species identification. A total of 307 sequences from 84 specimens representing eight tick species were acquired by PCR. Besides the 1,834 published sequences of 189 tick species from GenBank and the Barcode of Life Database, 430 unpublished sequences representing 59 tick species were also successfully screened by Bayesian analyses. Thereafter, the performance of the four DNA markers to identify tick species was evaluated by identification success rates given by these markers using nearest neighbour (NN), BLASTn, liberal tree-based or liberal tree-based (+threshold) methods.ResultsGenetic divergence analyses showed that the intra-specific divergence of each marker was much lower than the inter-specific divergence. Our results indicated that the rates of correct sequence identification for all four markers (COI, 16S rDNA, ITS2, 12S rDNA) were very high (> 96%) when using the NN methodology. We also found that COI was not significantly better than the other markers in terms of its rate of correct sequence identification. Overall, BLASTn and NN methods produced higher rates of correct species identification than that produced by the liberal tree-based methods (+threshold or otherwise).ConclusionsAs the standard DNA barcode, COI should be the first choice for tick species identification, while 16S rDNA, ITS2, and 12S rDNA could be used when COI does not produce reliable results. Besides, NN and BLASTn are efficient methods for species identification of ticks.

Dataset Information

Mitocondrial COI and 16S rDNA sequences support morphological identification and biogeography of deep-sea red crabs of the genus Chaceon (Crustacea, Decapoda, Geryonidae) in the Eastern Central and South Atlantic Ocean.

Publications

Mitocondrial COI and 16S rDNA sequences support morphological identification and biogeography of deep-sea red crabs of the genus Chaceon (Crustacea, Decapoda, Geryonidae) in the Eastern Central and South Atlantic Ocean.

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