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Building a DNA BARCode Library for the Freshwater Fishes of Bangladesh

Md. Mizanur Rahman
University of Dhaka, Department of Zoology, Dhaka, Dhaka, 1000, Bangladesh

Michael Norén
Swedish Museum of Natural History, Department of Zoology, SE-104 05, Stockholm, Sweden

Abdur Rob Mollah
University of Dhaka, Department of Zoology, Dhaka, Dhaka, 1000, Bangladesh

Sven O. Kullander
Swedish Museum of Natural History, Department of Zoology, SE-104 05, Stockholm, Sweden

Abstract/ Executive Summary:

We sequenced the standard DNA barcode gene fragment in 694 newly collected specimens, representing 243 species-level Operational Barcode Units (OBUs) of freshwater fishes from Bangladesh. We produced coi sequences for 149 out of the 237 species already recorded from Bangladesh. Another 83 species sequenced were not previously recorded for the country, and include about 30 undescribed or potentially undescribed species. Several of the taxa that we could not sample represent erroneous records for the country, or sporadic occurrences. Species identifications were classified at confidence levels 1(best) to 3 (worst). We propose the new term Operational Barcode Unit (OBU) to simplify references to would-be DNA barcode sequences and sequence clusters. We found one case where there were two mitochondrial lineages present in the same species, several cases of cryptic species, one case of introgression, one species yielding a pseudogene to standard barcoding primers, and several cases of taxonomic uncertainty and need for taxonomic revision. Large-scale national-level DNA barcode prospecting in high diversity regions may suffer from a lack of taxonomic expertise that cripples the result. Consequently, DNA barcoding should be performed in the context of taxonomic revision, and have a defined, competent end-user.

Keywords: DNA, Barcode library, Freshwater fishes, Bangladesh

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Start Date:

End Date:

Program Area: Conservation and Biodiversity

Commodity: Fish

Objectives:

We present the results and lessons from sequencing freshwater fishes collected in markets and natural habitats in Bangladesh, 2014–2016, in a study strictly aimed at a complete coi-based DNA barcode reference library of Bangladeshi freshwater fish species, introduce a new term for species-level DNA sequence clusters interpreted as candidates for DNA barcodes: the Operational Barcode Unit (OBU).

Methodology:

Fish and fisheries play an important role in Bangladesh’s economy, nutrition and culture. With 47 609 km² of inland water bodies, it is the third inland fish-producing country in the world after China and India¹. The annual fish production from inland waters is estimated to be 3,496,958 mt, of which 1,163,606 mt comes from inland open waters. Fish is a second staple food in Bangladesh and alone supplements about 60% of animal protein in the daily dietary requirement². Open water fishery is still the primary source of food fishes for the larger population. The Hilsa (Tenualosa ilisha) capture fishery alone contributes about 12% of the fish production and provides outcome for 2.5 million people.

Bangladesh sits in between the biologically rich and diverse Indo-Burma and Eastern Himalaya regions, and is traversed by three of Asia’s largest rivers, the Ganga, Brahmaputra, and Meghna, which reach the Bay of Bengal in Bangladesh. Nonetheless, Bangladesh has one of the most incompletely known national freshwater fish faunas in Asia. As with other tropical countries, diversity estimates for Bangladeshi freshwater fishes are uncertain. Estimates of freshwater fish species vary from 237 to 247, 260, or 267, but those numbers include migrating and estuarine species; an estimate of riverine species only gives 104 species. From several books and review papers on Bangladeshi fishes, it is evident, however, that the taxonomy used is outdated and not harmonized with the taxonomy employed globally or even in neighboring countries. Apparently, considering the economic importance of inland fishery and the expected richness of the fish fauna, and in the absence of an expert-based taxonomy, DNA barcoding may be an important component in the biological conservation and management of biodiversity and fishery of Bangladeshi freshwater fishes.

DNA barcoding is a tool based on the observation and premise that each species is genetically distinct — has a unique DNA. Unique sequences of DNA from expert-identified specimens enable the construction of a library of species-specific DNA sequences, “DNA barcodes”, against which unidentified samples can be matched. DNA barcodes are useful for the identification of both fresh specimens and market products such as frozen fish. The standard barcode sequence, a fragment of the mitochondrial cytochrome c subunit I gene (coi), is also frequently used in phylogeographic and phylogenetic analyses, but concerns have also been raised that the utility of barcoding has been overstated and that dependency on single markers may lead to deficient taxonomy.

Source of Information: Sci Rep 9, 9382 (2019). https://doi.org/10.1038/s41598-019-45379-6

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Achievement/Findings:

Large scale national level DNA barcode prospecting in high diversity regions may suffer from a lack of taxonomic expertise that cripples the result. Consequently, DNA barcoding should be performed in the context of taxonomic revision, and have a defined, competent end-user.

Knowledge Management: Journal