Title : DNA barcoding as a tool for biodiversity and ecological assessment in african freshwater systems: A case study of upper section of River Mpanga, Uganda
Abstract:
Freshwater ecosystems in the sub-Saharan Africa, the hierarchically nested river networks like wadable streams, support aquatic biodiversity and ecosystem functioning. However, they are increasingly impaired by anthropogenic pressures, including land-use change, pollution, hydrological degradation due to modifications and climate variability. Moreover, the genetic consequences of these stressors on aquatic biodiversity remain poorly understood. This study explored the use DNA barcoding to examine the changes of genetic diversity along a longitudinal gradient of River Mpanga, with sampling sites from pre-selected sites from Upper section of R. Mpanga. Most common genetic diversity indices such as nucleotide diversity (π), haplotype diversity (hd), number of haplotype (h), number of mutation (Eta) and number of segregation sites (S), neutrality tests for all macroinvertebrate taxa, EPT (Ephemeroptera, Plecoptera, Trichoptera) taxa, and pollution-tolerant groups at each site and pooled site datasets were evaluated using DNAsp software. In parallel, BMWP, SASS5 scores, Average Score Per Taxon (ASPT), total taxa richness, total abundance, Percentage EPT and Percentage PR taxa of the sampled sites were used to evaluate the ecological quality of the sampled sites. The forested site (W01) exhibited higher genetic diversity (π = 0.277, h = 13, S = 235, Eta = 375) compared to the polluted site (W04), which showed lower values (π = 0.167, h = 5, S = 125, Eta = 144). Moreover, neutrality tests at the forested site (W01) yielded negative values (Tajima’s D = -0.748, Fu and Li’s D = -0.426, and Fu and Li’s F = - 0.609), indicating potential population expansion or purifying selection. In contrast, the less polluted sites showed slightly positive values (Tajima’s D = 0.085, Fu and Li’s D = 0.449, and Fu and Li’s F = 0.410), suggesting neutral evolution or balancing selection or enhanced genetic drift due to environmental stress. However, despite a notably lower haplotype number (5) at the polluted midstream site(W04), haplotype diversity remained high (1), suggesting the persistence of divergent lineages under pollution stress and possible historical bottlenecks. Moreover, the taxa richness and ASPT was reduced from forested area W01 (Taxa richness = 13, and ASPT = 6.8) and to extremely low values in the polluted sites W04 (Taxa richness = 4, and ASPT =1.8). From our findings, it’s evident that pollution not only reduces species diversity but also disrupts the genetic diversity needed for long-term ecosystem resilience and adaptability. We recommend urgent restoration of polluted sections of the River Mpanga and continued, cost-effective monitoring of lakes, rivers, and streams by integrating both morphological and DNA barcoding, metabarcoding, and environmental DNA (eDNA). Protecting the genetic diversity in these freshwater ecosystems is critical for safeguarding Uganda’s water resources plus the health and livelihoods of the communities that depend on them.
