Biology subjects

Fredrick Onyango, O.

Publications and source records attributed to Fredrick Onyango, O..

2 recordsLinked to original sources

bioRxiv2026

State of mangrove biodiversity assessment in Kenya and the prospect of environmental DNA in strengthening surveys

Assessing and monitoring biodiversity in mangrove ecosystems remains challenging, with most studies relying on proxy indicators to infer biodiversity status. This limit understanding of biodiversity dynamics and constrains evidence-based mangrove management. In the Western Indian Ocean region, biodiversity assessments in mangrove forests remain scanty, with no clear information on spatiotemporal and taxonomic coverage. Addressing these gaps requires examining existing biodiversity records and exploring complementary approaches that can broaden the scope and efficiency of biodiversity monitoring. This study assessed the current state of biodiversity assessments in mangrove forests in Kenya and evaluated the feasibility of environmental DNA (eDNA) as a complementary biodiversity monitoring tool. A systematic literature review was conducted by retrieving published sources from major academic databases using defined search terms to extract and compile taxonomic information. In addition, a snapshot eDNA survey was carried out in selected mangrove forests, where sediment and water samples were collected, processed, and analyzed using established molecular and bioinformatics pipelines. The literature review identified 26 sources documenting biodiversity across 15 mangrove forest areas, with 68% of the studies concentrated in four sites representing about 6% of mangrove cover in Kenya. A total of 1,044 unique taxa belonging to 255 families were identified, with the classes Teleostei, Aves, Chromadorea, and Malacostraca accounting for 84.5% of documented taxa. The eDNA survey detected heterogeneous taxa from multiple ecosystems, including 502 taxa belonging to 305 families. Only 67 families were common to both datasets, highlighting the complementarity of literature-based inventories and eDNA detection. While eDNA showed considerable potential to expand biodiversity detection, its application is constrained by a number of factors. Integrating eDNA as a core biodiversity monitoring tool in mangroves will require combining conventional surveys with molecular tools, developing curated regional DNA reference databases, and adopting standardized analytical frameworks.

molecular biology↗

bioRxiv2026

Complete chloroplast genome of African Baobab (Adansonia digitata L.): structural characterization, comparative genomics, and phylogenetic placement within Malvaceae

Chloroplast genomes are invaluable resources for plant genomic research, providing insights into genome evolution and molecular adaptation. With the growing scientific and economic interest in Adansonia digitata, a comprehensive characterization of its chloroplast is timely and necessary. A complete chloroplast genome of A. digitata was assembled, annotated, and characterized. Comparative structural analysis was conducted against other Adansonia species, and the assembly was validated through phylogenetic placement within Malvaceae. The assembled genome exhibits the canonical quadripartite organization, spanning 160,061 bp with a GC content of 36.88%, 79 protein-coding genes, 32 tRNAs, and 4 rRNAs. Repeat analysis identified 100 simple sequence repeat motifs, predominantly A/T-rich mononucleotide types (76%), alongside 50 long sequence repeats dominated by forward (26) and palindromic (17) repeats. Comparative analysis with other Adansonia species revealed conserved genome structure, with minor IR boundary shifts involving the ndhF gene, and ycf1 duplication in A. gregorii and A. grandidieri. Average nucleotide identity exceeded 99% across all Adansonia species, with near-complete similarity (ANI {approx} 99.96%) observed with the putative A. kilima. All predicted RNA editing events were nonsynonymous, dominated by C[->]U conversions (55.02%). Codon usage showed non-random synonymous preferences biased toward A/U-ending codons, driven primarily by mutational pressure with detectable gene-specific translational selection. Nucleotide diversity ({pi}) was higher in intergenic spacers (0.00490 {+/-} 0.00574) than in coding regions (0.00167 {+/-} 0.00199), with the majority of genomic regions showing no sequence variation ({pi} = 0). Substitution patterns indicated pervasive purifying selection, with relatively high but insignificant signals in matK, ycf1, accD, and rpoB. Phylogenomic analyses placed the assembled A. digitata chloroplast genome within the Adansonia lineage, consistent with its established systematic position. This study provides detailed insight into the chloroplast genome of A. digitata, and the findings will contribute towards advancing its genomic research.

genomics↗