Mitochondrial cytochrome b sequence data are not an improvement for species identification in Scleractinian corals
- Published
- Accepted
- Subject Areas
- Biodiversity, Evolutionary Studies, Genetics, Marine Biology, Zoology
- Keywords
- coral, barcoding, mitochondrial DNA
- Copyright
- © 2014 Wares
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2014. Mitochondrial cytochrome b sequence data are not an improvement for species identification in Scleractinian corals. PeerJ PrePrints 2:e429v1 https://doi.org/10.7287/peerj.preprints.429v1
Abstract
There are well-known difficulties in using the cytochrome oxidase I (COI) mitochondrial gene region for population genetics and DNA barcoding in corals. A recent study of species divergence in the endemic Caribbean genus Agaricia reinforced such knowledge. However, the growing availability of whole mitochondrial genomes may help indicate more promising gene regions for species delineation. I assembled the whole mitochondrial genome for Agaricia fragilis from Illumina single-end 250bp reads and compared this sequence to that of the congener A. humilis. Although these data suggest that the cytochrome b (CYB) gene region is more promising, comparison of all available Scleractinian CYB sequence data indicates that multilocus approaches are still probably necessary for phylogenetic and population genetic analysis of recently-diverged coral taxa.
Author Comment
This paper developed from concerns my lab has had with finding appropriate loci for phylogenetics and species delimitation in the Caribbean coral genus Agaricia. Upon generation of the complete mitochondrial genome sequence, I used comparison with congeneric data to see if a better gene region could be identified. This result led to further evaluation of available data; these results are presented here, unfortunately reinforcing the idea that the mitochondrial genome is often not the best target for such studies in coral taxa.
Supplemental Information
Aligned Cyt B of Scleractinian corals
Nexus formatted sequence alignment of cytochrome b reads from Scleractinian corals, obtained from Genbank. Individual accession numbers associated with each sequence.