Results and Discussion
The taxonomic classification of Mahseer species has often led to
ambiguity; sequencing of the COI gene region of Tor torwill provide valuable genetic information that can be used to solve the
ambiguity. Mitochondrial DNA (mtDNA), owing to its unique attributes
such as uniparental inheritance, exclusive presence of displacement
loop, lack of recombination, high mutation rate, small size, and
constant gene content, has recently come to the foreground in the filed
of evolutionary genomics. Furthermore, Kraytsberg et al. (2004) stated
that mtDNA recombinants fall into two structural classes: class 1, with
a short paternal sequence inserted into a mostly maternal molecule, and
class 2, with a maternal sequence flanked by paternal sequences.
Therefore, mitochondrial DNA can play a pivotal role in exploring
population structure and phylogenetic relationship within Tor
tor , which could be of great assistance in species identification and
conservation.
It was observed that of the 32 specimens collected, nine specimens from
two sites exhibited close association and the other 23 specimens
collected from the other six sites exhibited similar mitochondrial DNA
sequences, based on the COI gene sequence analysis for species
identification and phylogenetic relationship. Analysis of the alignedCOI gene sequences identified 3 haplotypes (Hap_1 to Hap_3);
the 3 haplotypes were shown in all of the populations collected from
eight sites. Number of specimens belonging to each haplotype is shown in
table 1. Specimens from five sites, Chambal river (CR), Rana Pratap
Sagar (RPS), Bassi dam (BD), Kali Sindh river (KSR), and Parwan river
(PR), exhibited Hap_1; Hap_2 was observed only in specimens obtained
from Badi lake; Hap_3 was observed in specimens obtained from Daya dam
and Madar tank. Haplotype network analysis (Fig. 2) shows three distinct
clades originating from a common ancestral haplotype. They were named as
group I, group II and group III, which correlate to Hap_1, Hap_2, and
hap_3, respectively. Group I and group II sequences were found to be
closely associated. Group III sequences showed divergence from group I
and group II sequences. This is also depicted graphically in figure 3,
which shows evolutionary divergence over sequence pairs within groups.
Haplotype/nucleotide diversity parameters are depicted in Fig.4.
Phylogenetic analysis shows that the fish population collected from
Madar tank showed distinct genetic diversity compared to the fish
populations collected from the other six sites.
Phylogenetic analysis of the mitochondrial sequences using the
Neighbour-Joining (NJ) method strongly supported the reciprocally
monophyletic status between Tor tor populations. The
Neighbour-joining tree constructed using COI gene data showed
that the sequences were clustered into two major clades. Different
environmental conditions can lead to the emergence of the same species
in different geographic locations with different genetic variations.
Present-day climate change issues have widespread effects on organisms
(Rocha et al., 2017; Wu et al., 2017).
Evolutionary relationship of the sequenced COI genes of the
specimens is shown in Fig. 5. The phylogenetic tree was constructed
using the UPGMA method and the optimal tree with the sum of branch
length (0.02044436). The highest genetic distance was observed between
specimens from Bassi Dam and Chambal River (0.0202-2.02%) followed by
that between MT and RPS (0.0199–1.99%). The lowest genetic distance
was observed between specimens from Bassi Dam and Badi Lake
(0.0026-0.26%). The Daya Dam has the “closest” genetic distance from
Badi Lake as compared to Chambal river, Rana Pratap Sagar Dam, Kali
Sindh River, Bassi Dam and Parwan River. This Comparison clearly
indicates that fish population of Daya Dam and Madar tank are
genetically different from the other six groups. Most of the specimens
from different sites were clustered together, which reflects the earlier
morphology-based taxonomic assignment.