The evolutionary history of three Baracoffea species from western Madagascar revealed by chloroplast and nuclear genomes

The wild species of the Coffea genus present a very wide morphological, genetic, and biochemical diversity. Wild species are recognized more resistant to diseases, pests, and environmental variations than the two species currently cultivated worldwide: C. arabica (Arabica) and C. canephora (Robusta). Consequently, wild species are now considered as a crucial resource for adapting cultivated coffee trees to climate change. Within the Coffea genus, 79 wild species are native to the Indian Ocean islands of Comoros, Mayotte, Mauritius, Réunion and Madagascar, out of a total of 141 taxa worldwide. Among them, a group of 9 species called "Baracoffea" are particularly atypical in their morphology and adaptation to the sandy soils of the dry deciduous forests of western Madagascar. Here, we have attempted to shed light on the evolutionary history of three Baracoffea species: C. ambongensis, C. boinensis and C. bissetiae by analyzing their chloroplast and nuclear genomes. We assembled the complete chloroplast genomes de novo and extracted 28,800 SNP (Single Nucleotide Polymorphism) markers from the nuclear genomes. These data were used for phylogenetic analysis of Baracoffea with Coffea species from Madagascar and Africa. Our new data support the monophyletic origin of Baracoffea within the Coffea of Madagascar, but also reveal a divergence with a sister clade of four species: C. augagneurii, C. ratsimamangae, C. pervilleana and C. Mcphersonii (also called C. vohemarensis), belonging to the Subterminal botanical series and living in dry or humid forests of northern Madagascar. Based on a bioclimatic analysis, our work suggests that Baracoffea may have diverged from a group of Malagasy Coffea from northern Madagascar and adapted to the specific dry climate and low rainfall of western Madagascar. The genomic data generated in the course of this work will contribute to the understanding of the adaptation mechanisms of these particularly singular species.

Complementary ecosystem services from multiple land uses highlight the importance of tropical mosaic landscapes

Tropical agricultural landscapes often consist of a mosaic of different land uses, yet little is known about the spectrum of ecosystem service bundles and materials they provide to rural households. We interviewed 320 households on the different benefits received from prevalent land-use types in north-eastern Madagascar (old-growth forests, forest fragments, vanilla agroforests, woody fallows, herbaceous fallows, and rice paddies) in terms of ecosystem services and plant uses. Old-growth forests and forest fragments were reported as important for regulating services (e.g. water regulation), whilst fallow lands and vanilla agroforests as important for provisioning services (food, medicine, fodder). Households reported the usage of 285 plant species (56% non-endemics) and collected plants from woody fallows for varying purposes, whilst plants from forest fragments, predominantly endemics, were used for construction and weaving. Multiple land-use types are thus complementary for providing ecosystem services, with fallow lands being particularly important. Hence, balancing societal needs and conservation goals should be based on diversified and comprehensive land management.

Win-win opportunities combining high yields with high multi-taxa biodiversity in tropical agroforestry

Resolving ecological-economic trade-offs between biodiversity and yields is a key challenge when addressing the biodiversity crisis in tropical agricultural landscapes. Here, we focused on the relation between seven different taxa (trees, herbaceous plants, birds, amphibians, reptiles, butterflies, and ants) and yields in vanilla agroforests in Madagascar. Agroforests established in forests supported overall 23% fewer species and 47% fewer endemic species than old-growth forests, and 14% fewer endemic species than forest fragments. In contrast, agroforests established on fallows had overall 12% more species and 38% more endemic species than fallows. While yields increased with vanilla vine density and length, non-yield related variables largely determined biodiversity. Nonetheless, trade-offs existed between yields and butterflies as well as  reptiles. Vanilla yields were generally unrelated to richness of trees, herbaceous plants, birds, amphibians, reptiles, and ants, opening up possibilities for conservation outside of protected areas and restoring degraded land to benefit farmers and biodiversity alike.

Resolving ecological-economic trade-offs is a challenge in agriculture. Here, Wurz et al. find that in Malagasy vanilla agroforests, vanilla yield is generally not related to tree, herbaceous plant, bird, amphibian, reptile and ant biodiversity, creating opportunities for conservation outside protected areas.

Forest Fragments, Lemur Communities and Local Perception of Nature in a Protected Area of Northwestern Madagascar

Biological conservation projects conducted in inhabited areas are often based on the combination of ecological diagnostics and study of practices and use of the environment by local communities. They less frequently integrate the influence of the perception and representation of nature on these practices, while these should also be taken into account in the initiation of sustainable conservation actions. We carried out a long-term study combining biological and social science approaches in North-western Madagascar in the Antrema protected area (with dry forest/savannah/coastal ecosystems), including an analysis of the use and perception of nature by its inhabitants. Together with the study of tree diversity, forest structure and biomass in 7 forest fragments, we estimated population densities of whole communities of diurnal and nocturnal lemurs, one of which is considered sacred. We interviewed local resource users from several villages using classical methods of social anthropology supplemented with perception tests derived from sensory evaluation methods. The structure of forest fragments as well as their basal area and richness in tree species varied with human pressure on specific plants (timber extraction) or with historical changes in pasture management (forest regrowth). Lemurs were generally abundant, with a high total biomass compared to other dry forests. Although the inhabitants of Antrema (Sakalava, Tsimihety, and Betsileo) still strongly adhered to local use rights and shared deeply rooted knowledge about the forest, the use and perception of nature (e.g., regarding the sacred lemur Propithecus coronatus) have changed since the Antrema protection project in 2000. The results suggest that local communities tend to integrate traditional rules about nature with international environmental regulation, perhaps a sign of a new ecological awareness. However, in the new management mode accompanying this transition, it can also be a means of local empowerment that takes advantage of a program supporting pro-environmental management of the Antrema area.