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In Pakistan there exist huge potential for development of aquaculture particularly inland fisheries sector but due to couple of reasons this field could not flourished in Pakistan. Cirrhinus mrigala is extensively cultured major carp among other major carps but there is no documentation concerning the analyses of Cirrhinus mrigala from Chenab River and Indus River for stock identification and conservation purposes. Length-weight and length-length relationships, condition factor, stock structure and morphological heterogeneity of Cirrhinus mrigala from Chenab River and Indus River were studied using traditional morphometric techniques; landmark (Truss) based geometric morphometric analysis and meristic analysis. A total of 248 samples were collected, 124 samples from each river. The higher value of regression coefficient ?b? from Indus river (b = 3.130) than regression coefficient ?b? value form Chenab River (b = 2.9875) indicated that Cirrhinus mrigala in Indus River shows comparatively better growth as compared to Chenab River. Length-weight relationships of Cirrhinus mrigala are suggestive that the wild conditions in Indus River at Taunsa Barrage are much suitable for rearing and stocking purposes instead in Chenab River at Head Muhammad Wala. Fulton?s condition factor (K) for Cirrhinus mrigala in Chenab River has shown a decreasing (negative) trend, while for the Indus River it showed an increasing (positive) trend. The higher evaluated level of Fulton?s condition factor for the population of Cirrhinus mrigala in the Indus River than the Chenab River population symbolizes the superior ecological conditions, foraging conditions, health and hygienic conditions in the Indus River at Taunsa Barrage. Discriminant function analysis on 21 landmark based geometric variables and 11 traditional morphometric variables disclosed that phenotypical variations are predominantly exist as Intra-population variations rather than inter-population variations. Final classification results in Discriminant function analysis, accounts that 67.7% of original grouped cases were correctly classified and 56.5% of cross-validated grouped cases were correctly classified. The equal discriminatory power of the discriminant function I (DFI) centred on discriminant function analysis for the both populations of Cirrhinus mrigala at Chenab River and the Indus River and non-significant (H) value of Kruskal-Wallis test patently represents the absence of statistically significant meristic variations between the two populations. Discriminant functional analysis and meristic analysis are of suggestive that there exists much merger and gene flow between two populations owing to weak geographical isolation between two rivers.
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