Dataset Information

Identification and re-evaluation of freshwater catfishes through DNA barcoding.

ABSTRACT: Catfishes are globally demanded as human food, angling sport and aquariums keeping thus are highly exploited all over the world. North-East India possess high abundance of catfishes and are equally exploited through decades. The strategies for conservation necessitate understanding the actual species composition, which is hampered due to sporadic descriptions of the species through traditional taxonomy. Therefore, actual catfish diversity in this region is important to be studied through the combined approach of morphological and molecular technique of DNA barcoding.Altogether 75 native catfish specimens were collected from across the North-East India and their morphological features were compared with the taxonomic keys. The detailed taxonomic study identified 25 species belonging to 17 genera and 9 families. The cytochrome oxidase c subunit-I gene fragment were then sequenced from the samples in accordance with the standard DNA barcoding protocols. The sequences were compared with public databases, viz., GenBank and BOLD. Sequences developed in the current study and from databases of the same and related taxa were analyzed to calculate the congeneric and conspecific genetic divergences using Kimura 2-parameter distance model, and a Neighbor Joining tree was created using software MEGA5.1. The DNA barcoding approach delineated 21 distinct species showing 4.33 folds of difference between the nearest congeners. Four species, viz., Amblyceps apangi, Glyptothorax telchitta, G. trilineatus and Erethistes pusillus, showed high conspecific divergence; hence their identification through molecular approach remained inconclusive. On the other hand, the database sequences for three species, viz., Mystus horai, Bagarius yarrelli and Clarias batrachus, appeared mislabeled.The efficiency of DNA barcoding was reaffirmed from its success by easily identifying the major share (84%) of the studied catfish into 21 distinct species. The study contributed 27 new barcodes for 7 species and confirmed the range expansion of 2 important species in NE India.

SUBMITTER: Bhattacharjee MJ

PROVIDER: S-EPMC3499493 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Identification and re-evaluation of freshwater catfishes through DNA barcoding.

Bhattacharjee Maloyjo J MJ Laskar Boni A BA Dhar Bishal B Ghosh Sankar K SK

PloS one 20121115 11

<h4>Background</h4>Catfishes are globally demanded as human food, angling sport and aquariums keeping thus are highly exploited all over the world. North-East India possess high abundance of catfishes and are equally exploited through decades. The strategies for conservation necessitate understanding the actual species composition, which is hampered due to sporadic descriptions of the species through traditional taxonomy. Therefore, actual catfish diversity in this region is important to be stud ...[more]

PMID: 23166801

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Project description:BackgroundBiodiversity surveys have long depended on traditional methods of taxonomy to inform sampling protocols and to determine when a representative sample of a given species pool of interest has been obtained. Questions remain as to how to design appropriate sampling efforts to accurately estimate total biodiversity. Here we consider the biodiversity of freshwater ostracods (crustacean class Ostracoda) from the region of Churchill, Manitoba, Canada. Through an analysis of observed species richness and complementarity, accumulation curves, and richness estimators, we conduct an a posteriori analysis of five bioblitz-style collection strategies that differed in terms of total duration, number of sites, protocol flexibility to heterogeneous habitats, sorting of specimens for analysis, and primary purpose of collection. We used DNA barcoding to group specimens into molecular operational taxonomic units for comparison.ResultsForty-eight provisional species were identified through genetic divergences, up from the 30 species previously known and documented in literature from the Churchill region. We found differential sampling efficiency among the five strategies, with liberal sorting of specimens for molecular analysis, protocol flexibility (and particularly a focus on covering diverse microhabitats), and a taxon-specific focus to collection having strong influences on garnering more accurate species richness estimates.ConclusionsOur findings have implications for the successful design of future biodiversity surveys and citizen-science collection projects, which are becoming increasingly popular and have been shown to produce reliable results for a variety of taxa despite relying on largely untrained collectors. We propose that efficiency of biodiversity surveys can be increased by non-experts deliberately selecting diverse microhabitats; by conducting two rounds of molecular analysis, with the numbers of samples processed during round two informed by the singleton prevalence during round one; and by having sub-teams (even if all non-experts) focus on select taxa. Our study also provides new insights into subarctic diversity of freshwater Ostracoda and contributes to the broader "Barcoding Biotas" campaign at Churchill. Finally, we comment on the associated implications and future research directions for community ecology analyses and biodiversity surveys through DNA barcoding, which we show here to be an efficient technique enabling rapid biodiversity quantification in understudied taxa.

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Dataset Information

Identification and re-evaluation of freshwater catfishes through DNA barcoding.

Publications

Identification and re-evaluation of freshwater catfishes through DNA barcoding.

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