GENETIC DIVERSITY AND POPULATION STRUCTURE IN Trichilia emetica Vahl. IN WESTERN KENYA

Abstract

Trichilia emetica Vahl. Commonly known as Natal Mahogany (Family: Meliaceae) is a multipurpose tree of high ecological and socio-economic value across sub-Saharan Africa. In Kenya, however, its genetic resources remain largely uncharacterized. Current knowledge focuses mainly on ethno medicinal uses, photochemistry, and propagation biology, with no molecular data available to describe its genetic diversity or population structure. Without molecular information, it is difficult to determine whether populations are genetically connected or isolated, whether inbreeding is occurring, or whether genetic erosion is already underway. Although T. emetica is globally classified as Least Concern, localized population declines in Kenya indicate that its genetic base may already be narrowing, reducing its adaptability to environmental change. This lack of molecular insight is a major barrier to designing evidence-based conservation, restoration, and domestication strategies. This study sought to (i) characterize phenotypic variation of T. emetica using eight quantitative morphological traits across six natural populations in western Kenya and (ii) determine the genetic diversity and population structure of six natural populations of T. emetica in western Kenya using Inter-Simple Sequence Repeat (ISSR) markers. A total of 120 leaf samples were collected from Bungoma, Kakamega, Kisumu, Siaya, Vihiga, and Nandi counties. The morphological analysis revealed substantial variation across populations, with tree height, diameter at breast height, crown diameter, flower length, seeds per fruit, seed length, and seed dry weight differing significantly (p < 0.05). Variation within populations (67.33%) exceeded that among populations (32.67%), and clustering consistently distinguished Nandi as a separate group, Bungoma–Kakamega as another, and Kisumu–Siaya–Vihiga as a third. At the molecular level, 171 fragments were amplified, 162 of which were polymorphic, corresponding to a polymorphism rate of 94.65%. Diversity indices revealed Nei’s gene diversity (H) of 0.34 and Shannon’s index (I) of 0.51, with Nandi exhibiting the highest diversity and Kisumu–Siaya the lowest. Analysis of Molecular Variance (AMOVA) indicated that 65% of the genetic variation was distributed within populations and 35% among them. Principal coordinates analysis and Nei’s genetic distance dendrograms confirmed three genetic clusters, with Nandi being genetically isolated. This study is one of the first to assess the genetic diversity of T. emetica in Kenya, demonstrates that the species maintains considerable diversity despite fragmentation. Therefore, conservation strategies should prioritize in situ protection of genetically distinct populations such as Nandi, while safeguarding all populations to preserve intra-population diversity. Ex-situ measures, including representative sampling for seed banks and nurseries, are recommended to complement in situ strategies. Future research should expand to other ecological zones and integrate adaptive trait analyses to support domestication, breeding, and sustainable utilization of this valuable species.