Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2022.10.07.511267

Genetic diversity and structure in wild Robusta coffee (Coffea canephora A. Froehner) populations in Yangambi (DR Congo) and their relation with forest disturbance

Depecker, J.·Verleysen, L.·Asimonyio, J.·Hatangi, Y.·Kambale, J.-L.·Mwanga Mwanga, I.·Tshimi, E.·Dhed'a, B.·Bawin, Y.·Staelens, A.·Stoffelen, P.·Ruttink, T.·Vandelook, F.·Honnay, O.
View original source ↗Export metadata ↓

Abstract

Degradation and regeneration of tropical forests can strongly affect gene flow in understorey species, resulting in genetic erosion and changes in genetic structure. Yet, these processes remain poorly studied in tropical Africa. Coffea canephora is an economically important species, found in the understorey of tropical rainforests of Central and West Africa, and the genetic diversity harboured in its wild populations is vital for sustainable coffee production worldwide. Here, we aimed to quantify genetic diversity, genetic structure, and pedigree relations in wild C. canephora populations, and we investigated associations between these descriptors and forest disturbance and regeneration. Therefore, we sampled 256 C. canephora individuals within 24 plots across three forest categories in Yangambi (DR Congo), and used genotyping-by-sequencing to identify 18 894 SNPs. Overall, we found high genetic diversity, and no evidence of genetic erosion in C. canephora in disturbed old-growth forest, as compared to undisturbed old-growth forest. Additionally, an overall heterozygosity excess was found in all populations, which was expected for a self-incompatible species. Genetic structure was mainly a result of isolation-by-distance, reflecting geographical location, with low to moderate relatedness at finer scales. Populations in regrowth forest had lower allelic richness than populations in old-growth forest and were characterised by a lower inter-individual relatedness and a lack of isolation-by-distance, suggesting that they originated from different neighbouring populations and were subject to founder effects. Wild Robusta coffee populations in the study area still harbour high levels of genetic diversity, yet careful monitoring of their response to ongoing forest degradation remains required.

Source connections

Explore related subjects

ecologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Depecker, J., Verleysen, L., Asimonyio, J., Hatangi, Y., Kambale, J.-L., Mwanga Mwanga, I., Tshimi, E., Dhed'a, B., Bawin, Y., Staelens, A., Stoffelen, P., Ruttink, T., Vandelook, F., Honnay, O.. 2022-10-07. Genetic diversity and structure in wild Robusta coffee (Coffea canephora A. Froehner) populations in Yangambi (DR Congo) and their relation with forest disturbance. https://doi.org/10.1101/2022.10.07.511267

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Ecological opportunity and evolutionary relatedness predict parasite sharing differently across mammalian taxonomic scales

As global change brings species into new contact, understanding the ecological and evolutionary drivers of parasite sharing is essential for anticipating and mitigating disease emergence. Yet, the relative importance of geographic proximity and evolutionary relatedness among host species in predicting parasite sharing remains unresolved. We tested whether their relative importance changes across host taxonomic scale using 30,310 recorded associations between 680 mammalian and 11,107 parasite species. Geography accounted for 86.6% importance within genera, declining to 44.7% across all mammals, shifting toward evolutionary relatedness predominating. Parasite sharing increased nonlinearly with geographic proximity and host relatedness, and the overall trend varied among parasite types. Notably, accounting for host taxonomic scale improved parasite-sharing prediction accuracy. To explore the consequences of biotic homogenization, we applied a counterfactual scenario of reducing geographic distance by 99%, which increased mean predicted parasite sharing to 13.71% within genera and 1.50% at the class level. Together, these findings suggest that ecological opportunity is especially consequential among close relatives whereas evolutionary similarity is increasingly important among geographically distant species. Accounting for evolutionary scale can therefore improve sharing predictions and help identify which new host encounters warrant surveillance for cross-species transmission and disease emergence.

ecology↗
bioRxiv2026

Host availability, climate and pupal-stage ecology shape the predicted environmental suitability of the New World screwworm across Central and South America

Background: The New World screwworm, Cochliomyia hominivorax, causes primary myiasis in warm-blooded vertebrates. Its recent resurgence in Central America has renewed the need for spatial tools that identify environmentally suitable areas and surveillance gaps. Most previous distribution models have emphasized climate and livestock, whereas ecological constraints acting during the free-living pupal stage have rarely been incorporated. Methods: We compiled 2,461 georeferenced occurrence reports from the literature across Central and South America and linked them to climate, livestock density, forest cover and superficial soil predictors. Four sequential (nested) logistic models quantified the incremental contribution of predictor blocks, compared using likelihood-ratio tests, AIC and discrimination metrics. Logistic regression and Random Forest were then compared using five-fold spatial block cross-validation, which we treat as the primary measure of generalisation, and an independent municipality-level 70:30 train-test split. Variable importance was assessed using Random Forest Mean Decrease Accuracy together with partial-dependence profiles. Because presence and pseudo-absence classes were balanced before fitting, model outputs are interpreted as relative environmental suitability rather than absolute probability of occurrence. Results: The literature database represented 2,589 infected hosts, dominated by cattle, pigs, dogs and humans. Across the sequential models, AUC increased from 0.780 for climate alone to 0.898 with livestock density, 0.908 with forest cover and 0.918 with superficial soil properties; the increment attributable to the soil block ({Delta}AUC = 0.010) was smaller than the between-fold variability observed under spatial cross-validation (SD 0.049) and is therefore reported as suggestive rather than established. Sheep and horse density and cold-quarter soil temperature showed the highest Mean Decrease Accuracy values, while silt texture ranked above cattle density and forest cover. Under spatial block cross-validation Random Forest was markedly more stable than the GLM (mean AUC 0.926 {+/-} 0.049 versus 0.814 {+/-} 0.157) and was retained as the final model. On the independent municipality-level test set it achieved AUC 0.981, TSS 0.824, sensitivity 0.850 and specificity 0.972, values we regard as optimistic relative to the spatially blocked estimates. Predicted suitability was highest across Central America and parts of northern and tropical South America. Conclusions: C. hominivorax occurrence was associated with interacting climatic, host and landscape conditions. Superficial soil variables added a small, biologically interpretable signal consistent with constraints acting during pupation, but one that lies within the uncertainty of our spatial validation and requires confirmation with independent data. The maps estimate relative environmental suitability rather than infection incidence, and are intended to identify areas where surveillance could be strengthened rather than to guide control operations directly.

ecology↗
bioRxiv2026

Phenotypic variation in divergent mitochondrial haplotypes in migratory three-spined stickleback

Mitochondria are essential components in life-sustaining organismal processes. The mitochondrial genome can be influenced by selection, and divergent mitochondrial haplotypes have substantial potential to affect interspecies variation in life-history and physiology, yet little is known about whole organism phenotypic changes that might accompany mitochondrial genomic divergence. Three-spined stickleback on the Scottish island of North Uist provide a model to study this as their populations exhibit a well-mixed nuclear genome, yet two highly diverged mitochondrial haplotypes ( trans-Atlantic and European). Three-spined stickleback were sampled from six lochs to investigate associations between mitochondrial haplotype and phenotypic traits including organ size, body size, and ovule volume/clutch size, as well as citrate synthase enzyme activity. Results showed that mitochondrial haplotype has an influence on male gonadosomatic index (GSI) and potentially citrate synthase (CS) enzyme activity. Differences in male GSI may be explained by the timing of male spermatogenesis or potentially a need for larger testes in European haplotype fish. While no other phenotypic trait showed differences between mitochondrial haplotypes, there were many differences between sexes and populations e.g. in body size and organ/muscle size.

ecology↗