Background and Aims Inferring the diffusion history of many human-dispersed species is still not straightforward due to unsolved past human migrations. The centre of diversification and routes of migration of the autopolyploid and clonally propagated greater yam, Dioscorea alata, one of the oldest edible tubers is still unsolved. Here, we address yam demographic and dispersal history using a worldwide sample. Methods We characterized genome-wide patterns of genetic variation by genotyping by sequencing 643 greater yam accessions spanning four continents. First, we disentangled the polyploid and clonal components of yam diversity using alleles frequency distribution and identity by descent approaches. Then, we addressed yam geographical origin and diffusion history with a model-based coalescent inferential approach. Key Results Diploid genotypes were more frequent than triploids and tetraploids in all the continents. Genetic diversity was generally low and clonality appeared to be a main factor of diversification. The most likely evolutionary scenario supported an early divergence of mainland Southeast Asian and Pacific gene pools with continuous migration between them. Triploids and tetraploids genetic make-up suggests that they have originated from these two regions before westward yam migration. The Indian Peninsula gene pool gave origin to the African gene pool, which was later introduced in the Caribbean region. Conclusions Our results are congruent with the hypothesis of independent domestication origins of the two main Asian and Pacific gene pools. The low genetic diversity and high clonality observed suggest a strong domestication bottleneck followed by thousands of years of widespread vegetative propagation and polyploidisation. Both processes reduced the extent of diversity available for breeding, which most likely threaten future adaptation.

22Various plant species establish intimate symbioses with bacteria within their aerial organs. The 23 bacteria are contained within nodules or glands often present in distinctive patterns on the leaves in 24 what is commonly referred to as leaf nodule symbiosis. We describe here a highly specific symbiosis 25 between a wild yam species from Madagascar, Dioscorea sansibarensis and bacteria of the species 26Orrella dioscoreae. Using whole genome sequencing of plastids and bacteria from wild-collected 27 samples, we show phylogenetic patterns consistent with a dominant vertical mode of transmission of 28 the symbionts. Unique so far among leaf nodule symbioses, the bacteria can be cultured and are 29 amenable to comparative transcriptomics, revealing a potential role in complementing the host's 30 arsenal of secondary metabolites. We propose a recent establishment of a vertical mode of 31 transmission in this symbiosis which, together with a large effective population size explains the 32 cultivability and apparent lack of genome reductive evolution in O. dioscoreae. We leverage these 33 unique features to reveal pathways and functions under positive selection in these specialized 34 endophytes, highlighting the candidate mechanisms enabling a permanent association in the 35 phyllosphere. 36 37 Primulaceae (Ardisia) families, and their symbionts are members of the Burkholderiaceae family of β-47 proteobacteria. The symbionts reside in dedicated structures called leaf glands or nodules, and are 48 transmitted between generations via seeds [6]. The association is essential for both hosts and 49 symbionts: Candidatus Burkholderia (Ca. Burkholderia) species cannot be cultured outside of their host 50 and bacteria-free Psychotria kirkii and Ardisia crenata display severe growth defects [7, 8]. This co-51 dependence between host and symbiont is likely the result of co-evolution over several million years, 52 compounded by small effective population sizes and genetic drift [6]. Typical of vertically-transmitted 53 symbiotic bacteria, Ca. Burkholderia leaf nodule symbionts show extensive signs of reductive genome 54 evolution, with coding capacities ranging from 41.7% to 67.3% and an accumulation of pseudogenes 55 and insertion sequences [9][10][11]. Despite extensive genome erosion, some symbionts have been shown 56 to produce secondary metabolites, likely involved in the protection of the host from herbivory, such 57 as the insecticidal kirkamide and the depsipeptide FR900359, as well as the herbicidal streptol-58 glucoside possibly involved in allelopathic interactions [11][12][13]. Because of genomic instability and 59 evolved co-dependence, it is unclear whether secondary metabolism was present in the ancestor of 60 leaf nodule Burkholderia or acquired as a secondary trait [6]. 61We recently described a leaf nodule symbiosis in the monocot species Dioscorea sansibarensis [14]. D. 62 sansibarensis, or the Zanzibar yam, is a true yam native to Madagascar and tropical Africa [15]. This 63 fast growing vine, like many yam ...

Madagascar’s biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar’s past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique “living laboratory” for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth’s biodiversity.

Madagascar’s unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar’s terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as the most prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar.

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