Freshwater fish fauna of Koyna River, northern Western Ghats, India

Unveiling population structure and selection signatures of riverine and genetically improved rohu, Labeo rohita using genome wide SNPs

BACKGROUND

Captive breeding, along with artificial selection can significantly impact population structure by influencing allele frequencies and driving populations towards specific adaptation. Selective sweeps are powerful forces in shaping genetic variation within populations and can drive rapid spread of beneficial alleles while simultaneously reducing genetic diversity in localized regions of the genome. The present work was undertaken to assess the genetic structure and consequences of artificial selection in 10th generation of genetically improved rohu by comparing with wild populations.

METHODS AND RESULTS

The present study used 11,022 high-quality genome wide SNPs to compare the population genetic structure and signatures of selection between Jayanti rohu population and its wild counterpart. Outlier analysis revealed presence of 14 adaptive SNPs, out of which 5 were classified to be under decisive selection pressure. Notably, Jayanti rohu (JR) displayed 297 private alleles exclusive to its population. Chromosomes 7 and 16 emerged as potential hotspots containing a majority of the identified SNPs. Structure and principal component analysis revealed two distinct clusters, effectively distinguishing the JR and wild rohu populations. Phylogenetic analysis indicated a separate cluster of JR population distant from wild groups.

CONCLUSION

The results of present study shall help in elucidating patterns of genetic variation and characterizing selection signatures associated with captive bred and natural populations of rohu. The genomic resources generated through this work shall be helpful in improving the traceability of selectively bred germplasm for developing future strategies of genetic management.

Genetic diversity and genome-scale population structure of wild Indian major carp, Labeo catla (Hamilton, 1822), revealed by genotyping-by-sequencing

Labeo catla (catla) is the second most commercially important and widely cultured Indian major carp (IMC). It is indigenous to the Indo-Gangetic riverine system of India and the rivers of Bangladesh, Nepal, Myanmar, and Pakistan. Despite the availability of substantial genomic resources in this important species, detailed information on the genome-scale population structure using SNP markers is yet to be reported. In the present study, the identification of genome-wide single nucleotide polymorphisms (SNPs) and population genomics of catla was undertaken by re-sequencing six catla populations of riverine origin from distinct geographical regions. DNA isolated from 100 samples was used to perform genotyping-by-sequencing (GBS). A published catla genome with 95% genome coverage was used as the reference for mapping reads using BWA software. From a total of 472 million paired-end (150 × 2 bp) raw reads generated in this study, we identified 10,485 high-quality polymorphic SNPs using the STACKS pipeline. Expected heterozygosity (He) across the populations ranged from 0.162 to 0.20, whereas observed heterozygosity (Ho) ranged between 0.053 and 0.06. The nucleotide diversity (π) was the lowest (0.168) in the Ganga population. The within-population variation was found to be higher (95.32%) than the among-population (4.68%) variation. However, genetic differentiation was observed to be low to moderate, with F_st values ranging from 0.020 to 0.084, and the highest between Brahmani and Krishna populations. Bayesian and multivariate techniques were used to further evaluate the population structure and supposed ancestry in the studied populations using the structure and discriminant analysis of principal components (DAPC), respectively. Both analyses revealed the existence of two separate genomic clusters. The maximum number of private alleles was observed in the Ganga population. The findings of this study will contribute to a deeper understanding of the population structure and genetic diversity of wild populations of catla for future research in fish population genomics.

Indigenous Freshwater Ichthyofauna in the Dhanu River and Surrounding Wetlands of Bangladesh: Species Diversity, Availability, and Conservation Perspectives

A checklist of the native fishes of the Dhanu River and adjacent waters at Mithamain Upazila under the Kishoreganj district of Bangladesh is prepared with details on their availability, conservation status, habitat preferences, population trends, and threats. Data were collected monthly by field survey, focus group discussions, and personal interviews by using a semi-structured questionnaire and a pictorial check list of fish species. A total of 91 indigenous fish species of 59 genera belonging to 29 families under 11 orders were documented where 17.6%, 27.5%, 31.9%, and 23.1% species were abundantly available, commonly available, moderately available, and rarely available, respectively. Among those, 24 fish species (26.4%) were under the threatened category (3 critically endangered, 11 endangered, and 10 vulnerable) according to the IUCN Bangladesh. Notably, the globally threatened Cirrhinus cirrhosus, Channa orientalis, and Wallago attu were available in the study area. Fish population trends of 24.2% and 59.3% of the entire fish species were found in decreasing trends at the global and national level, respectively. The leading threats to the fish diversity were indiscriminate overfishing followed by fishing by dewatering of wetlands, the katha fishing method, the use of deprecated fishing gears, etc. Minimizing anthropogenic impacts, enacting fishing laws, installing and managing fish sanctuaries, and raising public awareness can be effective for the conservation of existing fisheries resources.

On the freshwater fish fauna of Krishna River, Sangli District, Maharashtra, India

Freshwater fish fauna of Krishna River, Sangli district was studied from 2013 to 2017. A total of 73 species belonging to 10 orders, 22 families, and 49 genera were recorded, of which, 29 species are endemic to the Western Ghats and 11 species endemic to the Krishna River system. Labeo kontius, an endemic barb of the Cauvery River System was recorded for the first time from the Krishna River, Maharashtra. As per the IUCN Red List of Threatened Species, 54 species are assessed as ‘Least Concern’, four species as ‘Near Threatened’, three species as ‘Vulnerable’, five as ‘Endangered’, and two as ‘Data Deficient’. The conservation status of two species has not yet been assessed. Fish fauna of the Krishna River within the study area is threatened as a result of alien species, and several anthropogenic stressors such as pollution from industrial as well as agricultural sources, human settlements, and overfishing.  Since, this small study area harbours 28 endemic and eight threatened species, their conservation should be given high priority.