Dataset Information

DNA barcodes for the fishes of the Narmada, one of India's longest rivers.

ABSTRACT: This study describes the species diversity of fishes of the Narmada River in India. A total of 820 fish specimens were collected from 17 sampling locations across the whole river basin. Fish were taxonomically classified into one of 90 possible species based on morphological characters, and then DNA barcoding was employed using COI gene sequences as a supplemental identification method. A total of 314 different COI sequences were generated, and specimens were confirmed to belong to 85 species representing 63 genera, 34 families and 10 orders. Findings of this study include the identification of five putative cryptic or sibling species and 43 species not previously known from the Narmada River basin. Five species are endemic to India and three are introduced species that had not been previously reported to occur in the Narmada River. Conversely, 43 species previously reported to occur in the Narmada were not found. Genetic diversity and distance values were generated for all of the species within genera, families and orders using Kimura's 2 parameter distance model followed by the construction of a Neighbor Joining tree. High resolution clusters generated in NJ trees aided the groupings of species corresponding to their genera and families which are in confirmation to the values generated by Automatic Barcode Gap Discovery bioinformatics platform. This aided to decide a threshold value for the discrimination of species boundary from the Narmada River. This study provides an important validation of the use of DNA barcode sequences for monitoring species diversity and changes within complex ecosystems such as the Narmada River.

SUBMITTER: Khedkar GD

PROVIDER: S-EPMC4081587 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

DNA barcodes for the fishes of the Narmada, one of India's longest rivers.

Khedkar Gulab Dattarao GD Jamdade Rahul R Naik Suresh S David Lior L Haymer David D

PloS one 20140703 7

This study describes the species diversity of fishes of the Narmada River in India. A total of 820 fish specimens were collected from 17 sampling locations across the whole river basin. Fish were taxonomically classified into one of 90 possible species based on morphological characters, and then DNA barcoding was employed using COI gene sequences as a supplemental identification method. A total of 314 different COI sequences were generated, and specimens were confirmed to belong to 85 species re ...[more]

PMID: 24991801

Similar Datasets

Project description:BackgroundDNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5' region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons.Methodology/principal findingsWe bi-directionally sequenced the standard 652 bp "barcode" region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%). Most species were represented by multiple individuals (7.6 on average), the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases). The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species.Conclusions/significanceThe present study evidenced that freshwater fish species can be efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics.

Project description:This dataset [1] quantifies the extent and rate of annual change in surface water area (SWA) across India's rivers and basins over a period of 30 years spanning 1991 to 2020. This data has been derived from the Global Surface Water Explorer, which maps historical terrestrial surface water occurrence globally using the Landsat satellite image archive since 1984, at a spatial resolution of 30 m/pixel and a temporal resolution of once a month. This monthly time-series was used to create annual composites of wet-season (October, November, December), dry-season (February, March, April), and permanent (October, November, December, February, March, April) surface water extent, which were then used to estimate annual rates of change. To estimate SWA trends for both river networks and their basins, we conducted our analysis at two spatial scales - (1) cross-sectional reaches (transects) across river networks, and (2) sub-basins within river catchments. For each reach and sub-basin (henceforth basin), temporal trends in wet-season, dry-season, and permanent SWA were estimated using the non-parametric Sen's slope estimator. For every valid reach and basin, the temporal timeseries of invalid or missing data was also computed as a fractional area to inform the level of certainty associated with reported SWA trends estimates. In addition to a Zenodo data repository, this data [1] is presented as an interactive web application (https://sites.google.com/view/surface-water-trends-india/; henceforth Website) to allow users to visualize the trends of permanent, wet-season, and dry-season water along with the extent of missing data for individual transects or basins across India. The Website provides a simple user interface to enable users to download seasonal time-series of SWA for any region of interest at the scale of the river network or basin. The Website also provides details about accessing the annual permanent, dry and wet season composites, which are stored as publicly accessible cloud assets on the Google Earth Engine platform. The spatial (basin and reach) and temporal (wet season, dry season, and permanent water scenarios) scales of information provided in this dataset yield a granular understanding of water systems in India. We envision this dataset to serve as a baseline information layer that can be used in combination with other data sources to support regional analysis of hydrologic trends, watershed-based analysis, and conservation planning. Specific applications include, but are not limited to, monitoring and identifying at-risk wetlands, visualizing and measuring changes to surface water extent before and after water infrastructure projects (such as dams and water abstraction projects), mapping drought prone regions, and mapping natural and anthropogenic changes to SWA along river networks. Intended users include, but are not limited to, students, academics, decision-makers, planners, policymakers, activists, and others interested in water-related issues.

Project description:Metacercariae of Diplostomum are important fish pathogens, but reliable data on their diversity in natural fish populations are virtually lacking. This study was conducted to explore the species diversity and host-parasite association patterns of Diplostomum spp. in a large riverine system in Europe, using molecular and morphological data.Twenty-eight species of fish of nine families were sampled in the River Danube at Nyergesújfalu in Hungary in 2012 and Štúrovo in Slovakia in 2015. Isolates of Diplostomum spp. were characterised morphologically and molecularly. Partial sequences of the 'barcode' region of the cytochrome c oxidase subunit 1 (cox1) and complete sequences of the nicotinamide adenine dinucleotide dehydrogenase subunit 3 (nad3) mitochondrial genes were amplified for 76 and 30 isolates, respectively. The partial cox1 sequences were used for molecular identification of the isolates and an assessment of haplotype diversity and possible host-associated structuring of the most prevalent parasite species. New primers were designed for amplification of the mitochondrial nad3 gene.Only lens-infecting Diplostomum spp. were recovered in 16 fish species of five families. Barcoding of representative isolates provided molecular identification for three species/species-level genetic lineages, D. spathaceum, D. pseudospathaceum and 'D. mergi Lineage 2', and three single isolates potentially representing distinct species. Molecular data helped to elucidate partially the life-cycle of 'D. mergi Lineage 2'. Many of the haplotypes of D. spathaceum (16 in total), D. pseudospathaceum (15 in total) and 'D. mergi Lineage 2' (7 in total) were shared by a number of fish hosts and there was no indication of genetic structuring associated with the second intermediate host. The most frequent Diplostomum spp. exhibited a low host-specificity, predominantly infecting a wide range of cyprinid fishes, but also species of distant fish families such as the Acipenseridae, Lotidae, Percidae and Siluridae. The nad3 gene exhibited distinctly higher levels of interspecific divergence in comparison with the cox1 gene.This first exploration of the species diversity and host ranges of Diplostomum spp., in natural fish populations in the River Danube, provided novel molecular, morphological and host-use data which will advance further ecological studies on the distribution and host ranges of these important fish parasites in Europe. Our results also indicate that the nad3 gene is a good candidate marker for multi-gene approaches to systematic estimates within the genus.

Dataset Information

DNA barcodes for the fishes of the Narmada, one of India's longest rivers.

Publications

DNA barcodes for the fishes of the Narmada, one of India's longest rivers.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets