Environmental DNA (eDNA) applications for biodiversity monitoring across countries in the Sub-Saharan African region: a systematic review

Abstract

Sub-Saharan Africa (SSA) contains highly diverse aquatic and terrestrial ecosystems but remains underrepresented in biodiversity research. Environmental DNA (eDNA) offers a non-invasive approach for biodiversity assessment, yet its application across SSA has not been comprehensively synthesized. A systematic review following PRISMA 2020 was conducted using Google Scholar and Scopus for studies published from January 2018 to April 2026. Eligible peer-reviewed English-language studies used eDNA or DNA metabarcoding to assess aquatic or terrestrial biodiversity in SSA. Data were extracted on geographic distribution, ecosystems, target taxa, markers, sequencing platforms, sampling approaches, reference databases, and reported constraints. Twenty-five studies met the inclusion criteria. Aquatic ecosystems accounted for 88% of studies, while fish were the dominant target taxon (48%). Southern Africa had the largest geographic representation. The most frequently used marker was 12S rRNA (52%), and Illumina was the dominant sequencing platform (72%). Incomplete reference databases were reported as a major limitation in 68% of studies, while terrestrial and arthropod-focused applications were markedly underrepresented. eDNA has demonstrated substantial potential for biodiversity monitoring in SSA, particularly in aquatic systems. However, incomplete reference libraries, methodological heterogeneity, logistical constraints, contamination risks, limited infrastructure, and capacity gaps constrain broader application. Future work should strengthen African reference databases, standardize methods, expand terrestrial and arthropod applications, and support SSA-led capacity development.