Genetic identification of two species of Pleuronichthys by DNA barcoding

Chinese Journal of Oceanology and Limnology (Impact Factor: 0.58). 01/2011; 29(5):967-972. DOI: 10.1007/s00343-011-0040-8

ABSTRACT DNA barcoding is a new method for biological taxonomy, offering the ability to identify species from fragments in any life-history
stage. Pleuronichthys cornutus and P. japonicus are two morphologically similar species. Pleuronichthys japonicus has never been found previously in China. However, in this study, we identified both species using DNA barcoding (cytochrome
c oxidase subunit I (COI)), the mtDNA control region and cytochrome b. The results reveal that: 1) intraspecific variation in the DNA barcode is much less than interspecific variation; 2) the
two morphologically similar species were placed into separate clades distinguishable by high bootstrap values; 3) COI barcodes
are more powerful for identifying the two species than the other two mtDNA fragments.

–DNA barcoding–COI–CR–Cyt b

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    ABSTRACT: Near-complete collagen (I) sequences are proposed for elephantid and mammutid taxa, based upon available African elephant genomic data and supported with LC–MALDI-MS/MS and LC–ESI-MS/MS analyses of collagen digests from proboscidean bone. Collagen sequence coverage was investigated from several specimens of two extinct mammoths (Mammuthus trogontherii and Mammuthus primigenius), the extinct American mastodon (Mammut americanum), the extinct straight-tusked elephant (Elephas (Palaeoloxodon) antiquus) and extant Asian (Elephas maximus) and African (Loxodonta africana) elephants and compared between the two ionization techniques used. Two suspected mammoth fossils from the British Middle Pleistocene (Cromerian) deposits of the West Runton Forest Bed were analysed to investigate the potential use of peptide mass spectrometry for fossil identification. Despite the age of the fossils, sufficient peptides were obtained to identify these as elephantid, and sufficient sequence variation to discriminate elephantid and mammutid collagen (I). In-depth LC–MS analyses further failed to identify a peptide that could be used to reliably distinguish between the three genera of elephantids (Elephas, Loxodonta and Mammuthus), an observation consistent with predicted amino acid substitution rates between these species.
    Geochimica et Cosmochimica Acta 01/2011; · 3.88 Impact Factor