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.

Herbarium specimens provide verifiable and citable evidence of the occurrence of particular plants at particular points in space and time, and are vital resources for assessing extinction risk in the tropics, where plant diversity and threats to plants are greatest. We reviewed approaches to assessing extinction risk in response to the Convention on Biological Diversity's Global Strategy for Plant Conservation Target 2: an assessment of the conservation status of all known plant species by 2020. We tested five alternative approaches, using herbarium-derived data for trees, shrubs and herbs in five different plant groups from temperate and tropical regions. All species were previously fully assessed for the IUCN Red List. We found significant variation in the accuracy with which different approaches classified species as threatened or not threatened. Accuracy was highest for the machine learning model (90%) but the least data-intensive approach also performed well (82%). Despite concerns about spatial, temporal and taxonomic biases and uncertainties in herbarium data, when specimens represent the best available evidence for particular species, their use as a basis for extinction risk assessment is appropriate, necessary and urgent. Resourcing herbaria to maintain, increase and disseminate their specimen data is essential to guide and focus conservation action. This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.

Societal Impact Statement: Trees play vital roles in many of the world's ecosystems while providing many benefits to people. New evidence indicates that a third of tree species are threatened with extinction, representing a tree extinction crisis. Here we demonstrate how tree species extinction will lead to the loss of many other plants and animals and significantly alter the world's ecosystems. We also show how tree extinction will negatively affect billions of people through loss of livelihoods and benefits. We highlight a series of urgent actions needed to avert an ecological, cultural and socio‐economic catastrophe caused by widespread extinction of tree species.Summary: Trees are of exceptional ecological importance, playing a major functional role in the world's ecosystems, while also supporting many other plants, animals and fungi. Many tree species are also of direct value to people, providing a wide range of socio‐economic benefits. Loss of tree diversity could lead to abrupt declines in biodiversity, ecosystem functions and services and ultimately ecosystem collapse. Here we provide an overview of the current knowledge regarding the number of tree species that are threatened with extinction, and the threats that affect them, based on results of the Global Tree Assessment. This evidence suggests that a third of the world's tree species are currently threatened with extinction, which represents a major ecological crisis. We then examine the potential implications of tree extinctions, in terms of the functioning of the biosphere and impacts on human well‐being. Large‐scale extinction of tree species will lead to major biodiversity losses in other species groups and substantially alter the cycling of carbon, water and nutrients in the world's ecosystems. Tree extinction will also undermine the livelihoods of the billions of people who currently depend on trees and the benefits they provide. This warning to humanity aims to raise awareness of the tree extinction crisis, which is a major environmental issue that requires urgent global attention. We also identify some priority actions that need to be taken to reduce the extinction risk of tree species and to avert the ecological and socio‐economic catastrophe that will result from large‐scale extinction of tree species.