Genetic diversity of Indian Major Carp, Labeo calbasu (Hamilton, 1822) populations inferred from microsatellite loci

The concept of "state fishes of India": Current status, knowledge gaps, and strategic plans for conservation and sustainable utilization

The concept of "state fishes of India" highlights the importance and significance of the prioritized fish species distributed across various states within the country. This review article systematically documents the current status of state fishes from various perspectives, identifies the prevailing knowledge gaps, and also highlights the issues and strategic plans essential for the conservation and sustainable utilization of these valuable genetic resources. A total of 8357 publications were checked for the consolidated information on state fish species, and the appropriate items were selected under eight categories: biology, physiology and nutrition, aquaculture, habitat and environmental parameters, genetics and biotechnology, harvest and postharvest, fish health management, and others. The synthesized information was used to present the current status of research and development on state fish species. The knowledge gaps that are to be addressed are also depicted under the perspectives of fisheries management and conservation aquaculture. Based on the findings, strategic plans for the targeted conservation programmes are proposed and discussed under various in situ and ex situ conservation measures. Further, the departmental processes involved in the declaration, the importance of stakeholder involvement, namely, local communities and policymakers, in fostering effective conservation measures, and planning for utilization of these valuable fish genetic resources are also indicated.

Diversity and genetic structure of freshwater shark Wallago attu: an emerging species of commercial interest

Pakistan has natural freshwater resources acting as a hotspot for diverse fish fauna. However, this aquatic fauna is declining at an alarming rate due to over-exploitation, habitat degradation, water pollution, climate change, and certain anthropogenic activities. The freshwater shark, Wallago attu, is a popular edible catfish inhabiting these freshwater ecosystems. Habitat degradation, overfishing, and human activities are heavily impacting the natural population of this species. So, sound knowledge about its population structure is necessary for its proper management in natural waters. The current study involves utilizing two mtDNA markers (COI, Cytb) to assess the genetic structure and differentiation among W. attu populations of Pakistani Rivers. Genetic variability analysis indicated a high haplotype (0.343 ± 0.046-0.870 ± 0.023) and low nucleotide diversity (0.0024 ± 0.012-0.0038 ± 0.018) among single and combined gene sequences, respectively. Overall, River Indus was populated with more diverse fauna of Wallago attu as compared to River Chenab and River Ravi. Population pairwise, Fst values (0.40-0.61) were found to be significantly different (p < 0.01) among three Riverine populations based upon combined gene sequences. The gene flow for the combined gene (COI + Cytb) dataset among three populations was less than 1.0. The transition/transversion bias value R (0.58) was calculated for testing of neutral evolution, and it declared low genetic polymorphism among natural riverine populations of Wallago attu. The current study's findings would be meaningful in planning the management and conservation of this economically important catfish in future.

Genetic diversity in natural population of Notopterus notopterus evaluated through mitochondrial DNA marker ATPase 6/8 regions and cytochrome b gene

BACKGROUND

Population structure and genetic diversity of bronze featherback Notopterus notopterus, fish was not studied yet from Pakistan. So, genetic diversity and population structure of N. notopterus was analysed using two mitochondrial DNA genetic markers, ATPase 6/8 and Cytochrome b.

METHODS AND RESULTS

150 specimens were collected from five different rivers of Pakistan, resulting 56 haplotypes were detected for ATPase 6/8, Cytb and concatenated gene. Haplotype and nucleotide diversity for ATPase 6/8, Cytb and concatenated gene was observed below 1% among five natural populations of N. notopterus. ATPase 6/8 and Cytb genetic variance among populations was 6% and among and within individuals was 94%. Concatenated genetic variance among populations was 11%, among individual 5% and within individuals 84%. Fst value among all population was found 0.091 (p-value=0.02, p<0.05). The combined data set mean coefficient of genetic differentiation (F_ST) was 0.5572. The pair-wise F_ST was 0.000 (Chenab) to 0.88911 (Ravi). Maximum likelihood phylogeographic history of concatenated gene haplotypes showed four distinct diversified clusters. AMOVA, PCoA (Principal Coordinate Analysis) and maximum likelihood tree indicated that the natural populations of N. notopterus were comprised of four genetic stocks among five Pakistani rivers (Chenab, Indus, Jehlum, Ravi and Satluj).

CONCLUSIONS

This study provides the higher level of genetic diversity with confirmatory proofs among genetic stocks of five natural populations of N. notopterus. The information of genetic diversity and genetic variation, from this research can be utilised to help conserve and manage the species in the wild.

Genetic and morphological assessment of a vulnerable large catfish, Silonia silondia (Hamilton, 1822), in natural populations from India

Silonia silondia is a commercially important fish distributed in Asian countries, which is under threat due to overexploitation. This study focuses on the morphological analysis and genetic variation of S. silondia individuals, through truss network and sequencing of two mitochondrial regions, respectively, from six wild populations of the Ganga and Mahanadi river systems in India. A total of 38 haplotypes was observed by analysing combined mitochondrial genes (cytochrome b + ATPase 6/8) in 247 individuals of S. silondia collected from six populations. Average haplotype and nucleotide diversities were 0.8508 and 0.00231, respectively. Genetic structure analysis showed the predominant cause of genetic variation to be within populations. The two clades were observed among the haplotypes and time of divergence from their most probable ancestor was estimated to be around 0.3949 mya. Analysis of combined mitochondrial genes in six populations of S. silondia resulted into three management units or genetic stocks. The truss network analysis was carried out by interconnecting 12 landmarks from digital images of specimens to identify phenotypic stocks. Sixty-five truss morphometric variables were analysed for geometric shape variation which revealed morphological divergence in River Son specimens. The present study presents molecular markers and genetic diversity data which can be critical input for conservation and management of differentiated populations and future monitoring of the genetic bottleneck. The morphological shape analysis clearly shows that variation in the insertion of adipose fin is an important parameter influencing the morphological discrimination.

Mitochondrial DNA markers reveal genetic connectivity among populations of Osteoglossiform fish Chitala chitala

Genetic diversity and population structure in Indian featherback fish, Chitala chitala (Hamilton, 1822) was investigated by combined analyses of two full mitochondrial genes, ATPase 6/8 and Cytochrome b. A total of 403 individuals, collected from 14 rivers yielded 61 haplotypes. Hierarchical partitioning analysis identified 19.01% variance 'among' and 80.99% variance 'within groups and populations'. The mean coefficient of genetic differentiation (F_ST) was observed to be significant 0.26 (p < 0.05). Mantel tests rejected the hypothesis that genetic and geographic distances were correlated. The patterns of genetic differentiation, AMOVA and principal coordinate analyses indicated that natural populations were sub-structured and comprised of four genetic stocks of C. chitala in Indian rivers. The results also supported the higher resolution potential of concatenated gene sequences. The knowledge of genetic variation and divergence, from this study, can be utilized for its scientific conservation and management in the wild.

Microsatellite marker set for genetic diversity assessment of primitive Chitala chitala (Hamilton, 1822) derived through SMRT sequencing technology

In present study, single molecule-real time sequencing technology was used to obtain a validated set of microsatellite markers for application in population genetics of the primitive fish, Chitala chitala. Assembly of circular consensus sequencing reads resulted into 1164 sequences which contained 2005 repetitive motifs. A total of 100 sequences were used for primer designing and amplification yielded a set of 28 validated polymorphic markers. These loci were used to genotype n = 72 samples from three distant riverine populations of India, namely Son, Satluj and Brahmaputra, for determining intraspecific genetic variation. The microsatellite loci exhibited high level of polymorphism with PIC values ranging from 0.281 to 0.901. The genetic parameters revealed that mean heterozygosity ranged from 0.6802 to 0.6826 and the populations were found to be genetically diverse (F_st 0.03-0.06). This indicated the potential application of these microsatellite marker set that can used for stock characterization of C. chitala, in the wild. These newly developed loci were assayed for cross transferability in another notopterid fish, Notopterus notopterus.

Molecular and morphological evidences resolve taxonomic ambiguity between Systomus sarana sarana (Hamilton, 1822) and S. sarana subnasutus (Valenciennes) and suggest elevating them into distinct species

Taxonomic ambiguity exists in genus Systomus and recently many new species were described under this genus. Systomus sarana subnasutus is considered a valid subspecies of S. sarana sarana although revisions have been done by some researchers. We employed a combination of morpho-meristics and molecular tools (Cytochrome c oxidase I, 16S and Cytochrome b genes of mitochondrial genome) to resolve the two species. Three morpho-meristic characters, head length/maxillary barbel length (HL/MxBL), Lateral Line Scales (LLSs) as well as two truss-based characters, had discernible variation between the two taxa. The sequence analysis (2353 nucleotides) depicted a separate clad of S. sarana subnasutus with high bootstrap support. The findings from combined use of morphology, meristics and mitogenes were concordant. The corroborative results suggest the possibility of two different species. The results suggest to adopt suitable management measures, accordingly.

The complete mitochondrial genome of olive barb, Systomus sarana sarana (Hamilton, 1822) and its phylogenetic status

Systomus sarana sarana, commonly known as olive barb, is an important food and ornamental fish species with wide distribution in South Asia. Here, the complete mitogenome was sequenced on HiSeq 2500. With 16,590 nucleotides, the base composition was 32.9% (A), 26% (C), 15.4% (G) and 25.7% (T), comparable with other carps. The clustering pattern depicted the monophyly of S. sarana sarana with sister cyprinids.

Characterization of mitochondrial ATPase 6/8 genes in wild Labeo calbasu (Hamilton, 1822) and mapping of natural genetic diversity

We characterized mitochondrial ATP synthase (ATPase) 6 and 8 genes in Labeo calbasu (Hamilton, 1822) and determined genetic variation in wild populations across the natural distribution in Indian rivers. A total of 206 individuals were sampled from 11 riverine sites belonging to distinct geographical locations covering five major river basins. Sequencing of 842 base pairs of ATPase 6/8 revealed 21 haplotypes with haplotype diversity ranging from 0.1250 (River Satluj) to 0.8846 (River Bhagirathi). Analysis of molecular variance (AMOVA) of mitochondrial DNA (mtDNA) data revealed significant genetic differentiation among sites (FST = 0.192, p < 0.0001) which was indicative of moderate level of genetic structuring in the wild L. calbasu populations. The patterns of genetic divergence and haplotype network of mtDNA revealed distinct clades present in Indian rivers. The analysis of data demonstrated the potential of ATPase 6/8 genes in determining the genetic diversity and indicated considerable sub-structuring in wild calbasu populations present in different rivers.

Cross-priming of microsatellite loci in subfamily cyprininae (family Cyprinidae): their utility in finding markers for population genetic analysis in three Indian major carps

This study is aimed to identify polymorphic microsatellite markers and establish their potential for population genetics studies in three carp (family cyprinidae; subfamily cyprininae) species, Labeo rohita, Catla catla and Cirrhinus mrigala through use of cyprinid primers. These species have high commercial value and knowledge of genetic variation is important for management of farmed and wild populations. We tested 108 microsatellite primers from 11 species belonging to three different cyprinid subfamilies, Cyprininae, Barbinae and Leuciscinae out of which 63 primers (58.33%) successfully amplified orthologous loci in three focal species. Forty-two loci generated from 29 primers were polymorphic in these three carp species. Sequencing of amplified product confirmed the presence of SSRs in these 42 loci and orthologous nature of the loci. To validate potential of these 42 polymorphic loci in determining the genetic variation, we analyzed 486 samples of three focal species collected from Indus, Ganges and Brahmaputra river systems. Results indicated significant genetic variation, with mean number of alleles per locus ranging from 6.80 to 14.40 and observed heterozygosity ranging from 0.50 to 0.74 in the three focal species. Highly significant (P < 0.00001) allelic homogeneity values revealed that the identified loci can be efficiently used in population genetics analysis of these carp species. Further, thirty-two loci from 19 primers were useful for genotyping in more than one species. The data from the present study was compiled with cross-species amplification data from previous results on eight species of subfamily cyprininae to compare cross-transferability of microsatellite loci. It was revealed that out of 226 heterologous loci amplified, 152 loci that originated from 77 loci exhibited polymorphism and 45 primers were of multispecies utility, common for 2-7 species.