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.

Land-use trajectories for sustainable land system transformations: Identifying leverage points in a global biodiversity hotspot.

Sustainable land-system transformations are necessary to avert biodiversity and climate collapse. However, it remains unclear where entry points for transformations exist in complex land systems. Here, we conceptualize land systems along land-use trajectories, which allows us to identify and evaluate leverage points, i.e., entry points on the trajectory where targeted interventions have particular leverage to influence land-use decisions. We apply this framework in the biodiversity hotspot Madagascar. In the northeast, smallholder agriculture results in a land-use trajectory originating in old-growth forests and spanning from forest fragments to shifting hill rice cultivation and vanilla agroforests. Integrating interdisciplinary empirical data on seven taxa, five ecosystem services, and three measures of agricultural productivity, we assess trade-offs and cobenefits of land-use decisions at three leverage points along the trajectory. These trade-offs and cobenefits differ between leverage points: Two leverage points are situated at the conversion of old-growth forests and forest fragments to shifting cultivation and agroforestry, resulting in considerable trade-offs, especially between endemic biodiversity and agricultural productivity. Here, interventions enabling smallholders to conserve forests are necessary. This is urgent since ongoing forest loss threatens to eliminate these leverage points due to path dependency. The third leverage point allows for the restoration of land under shifting cultivation through vanilla agroforests and offers cobenefits between restoration goals and agricultural productivity. The co-occurring leverage points highlight that conservation and restoration are simultaneously necessary to avert collapse of multifunctional mosaic landscapes. Methodologically, the framework highlights the importance of considering path dependency along trajectories to achieve sustainable land-system transformations.