Pakistan's Rich Freshwater Fish Fauna

Pakistan has varied water resources, comprising dams, rivers, streams, and canals. The Indus River System is the largest river system in Pakistan.

Pakistan's Rich Freshwater Fish Fauna

Pakistan has varied water resources, comprising dams, rivers, streams, and canals. The Indus River System is the largest river system in Pakistan. These water tributaries have a very rich and expanded fauna of freshwater fish.

The reason for this rich variety in fish fauna might be attributed to the geographical location of Pakistan, as it is an interim zone of zoogeographical regions, i.e., between the Oriental region, the Ethiopian region, and the Palearctic region. Numerous studies conducted on freshwater fauna gave us information that there are about one hundred and eighty-three reported freshwater fish species in Pakistan.

Cyprinidae is one of the largest families. It has the biggest number of genera and species. Approximately 74 species represent this family in Pakistan. The family Cyprinidae consists of highly important freshwater fish of commercial significance that have a chief role in aquaculture and fish farming.

Sixteen species of this family have major economic importance among the local freshwater fish fauna. Moreover, there are almost thirty freshwater fish of economic and commercial importance. However, the diversity of commercially and comically important fish is diminishing.

As compared to other animals, fish have a high protein content. Moreover, fat content in fish meat is also low in comparison to other animals, where a high amount of fat causes obesity and heart problems, whereas fish fats and oils have health benefits as they prevent diseases, improve the immune system, and prevent many diseases.

Moreover, fish are environmentally friendly because of their low carbon emissions. The identification of the species of any animal is one of the most difficult tasks of taxonomy. For identification purposes, taxonomists use morphological keys to identify fish or any other animal, and they are based solely on the visible characters and features.

In the present age, processed and ready-made fish and their products are the main focus and centre of attention for fish traders. These ready-made fish products are more susceptible to mislabelling and fraud and can be replaced by some low-quality fish.

Our research

Pakistan has the richest fish fauna. The family Cyprinidae is a freshwater fish family with 74 reported species. This vast and diversified fauna compensates for the increasing demands on food for the growing population of the country. However, fish trading has been disputed by fish scams. DNA barcoding has the potential to resolve such issues.

DNA barcoding is a taxonomic method that uses small genetic markers in organisms mitochondrial DNA (mtDNA) for identification of particular species. It uses sequence diversity in a 658-base pair fragment near the 5′ end of the mitochondrial cytochrome c oxidase subunit I (COI) gene as a tool for species identification.

It is a more accurate and reliable method as compared to morphological identification. It is equally useful in juveniles as well as adult stages of fishes. The present study was conducted to identify two fish species from Pakistan (Cyprinus carpio and Hypophthalmichthys molitrix).


Samples are collected and stored at -20 ºC. Muscle fin is isolated and stored at -20. DNA extraction was done using phenol chloroform.

Quantification of DNA

The quantity of isolated DNA was checked through 0.8% agarose gel electrophoresis incorporated in IX TAE buffer.


The isolated DNA cytochrome oxidase gene was amplified by polymerase chain reaction using the thermal cycler BIO_RAD under optimized conditions. After sequencing, the obtained sequences were examined by the bioinformatics tools. Sequence homology was checked by using BLAST.MEGA 3.0 software to develop a polygenetic tree.


DNA barcoding works on a molecular level by using specific fragments of DNA. The purpose of DNA barcoding is identification. The subunit of the cytochrome oxidase gene COI was used to develop the barcode.

The maximum elution efficiency was achieved between pH 7.0 and 8.5. Purified DNA was analysed on a gel, adding one volume of loading dye and five volumes of purified DNA. Identified the dyes according to migration distance and optimization the agarose gel run time. By using statistical software, we can find authentic data.