Environmental DNA analysis reveals the distribution pattern of a Himalayan hill stream fish

• Published in: Environmental biology of fishes Vol. 105; no. 11; pp. 1575 - 1587
• Main Authors: Laxmi, Rishikesh Krishan, Sehgal, Neeta, Rawat, Varunendra Singh
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01-11-2022; Springer Nature B.V
• Subjects: Analysis; Animal Systematics/Taxonomy/Biogeography; Biomedical and Life Sciences; COI protein; Conservation; Deoxyribonucleic acid; Detection; Distribution; Distribution patterns; DNA; DNA barcoding; Endangered species; Environment; Environmental DNA; Fish; Freshwater & Marine Ecology; Gene sequencing; Geographical distribution; Life Sciences; Meristic counts; Morphometry; Nature Conservation; Nucleotide sequence; PCR; Polymerase chain reaction; Primers; Rare species; Rivers; Sampling; Schizothorax; Specificity; Threatened species; Tributaries; Wildlife conservation; Zoology; Environmental DNA (eDNA); Quantitative real-time PCR; Freshwater; DNA barcoding; Conservation
• ISSN: 0378-1909; 1573-5133
• DOI: 10.1007/s10641-022-01350-5

Assessment of distribution pattern of species with small populations is a prerequisite for conservation efforts. In our investigation, we evaluated the use of environmental DNA (eDNA) in assessing the presence and distribution pattern of a vulnerable fish species in Pranmati hill stream, a tributary of Pinder river in Chamoli, Uttarakhand. Fish specimens caught at one of the sites were classified as
Schizothorax richardsonii
after morphometric and meristic analysis. DNA isolated from these individuals was subjected to PCR for barcoding. DNA barcode confirmed that the sampled individuals belonged to
S. richardsonii
. We developed a real-time quantitative polymerase chain reaction (qPCR) assay to target 112 bp sequence of
S. richardsonii
COI gene
.
The primers on in silico analysis showed specificity for COI gene of
Schizothorax
spp. qPCR was employed to quantify the
Schizothorax
spp
.
DNA in eDNA samples collected from the four sampling sites on the Pranmati stream.
Schizothorax
spp
.
DNA was found in three out of four sites. Detection of
Schizothorax
spp
.
DNA at sites where fish specimens were neither visible nor caught, reinforces the importance of use of eDNA in sampling for rare and endangered species. This study demonstrates the efficacy of eDNA detection method for determining the distribution pattern of thinly populated fish species and can be employed to detect their presence at sites where it is difficult to locate or catch them, and can be made use of, while devising conservation strategies.