Can cyclone exposure explain behavioural and demographic variation among lemur species?

Madagascar has a harsh and stochastic climate because of regular natural disturbances. This history of regular cyclones has been hypothesised to have directed evolutionary changes to lemur behaviour and morphology that make them more resilient to sudden environmental change. These adaptations may include: small group sizes, high degrees of energy-conserving behaviours, generalist habitat use, small home ranges, small body size, and a limited number of frugivorous species. To date, however, no one has tested how variation in cyclone exposure across Madagascar is associated with variation in these resilience traits. In this study, we created a detailed cyclone impact map for Madagascar using Koppen-Geiger climate class, historical cyclone tracks, the Saffir Class of cyclone and hurricane intensity, and precipitation data. We also used existing literature to calculate a resilience score for 26 lemur species for which data existed on resilience traits. Our cyclone impact map was then overlaid on known geographic ranges of these species and compared to resilience score while controlling for phylogenetic non-independence and spatial autocorrelation. We found no association between cyclone impact in a lemur range and their resilience score. When assessing traits individually, however, we found that cyclone impact was positively associated with body size, suggesting that the more impacted a species is by cyclones the smaller they are. We also found cyclone impact to be negatively associated with frugivory, with species in higher impact zones eating more fruit. While unexpected, this could reflect an increased production in fruit in tree fall gaps following cyclones. While we did not find a pattern between cyclone impact and behavioural resilience in lemurs, we suggest a similar study at a global scale across all primates would allow for more taxonomic variation and reveal larger patterns key to understanding past and future vulnerability to natural disturbances in primates.

Losing lemurs: Declining populations and land cover changes over space and time.

Forest loss and degradation due to land cover changes imperil biodiversity worldwide. Subtropical and tropical ecosystems experience high deforestation rates, negatively affecting species like primates. Madagascar's endemic lemurs face exceptionally high risks of population declines and extirpation. We examined how short-term land cover changes within a fragmented landscape in southeastern Madagascar impacted the density of lemur species. Using line transects, we assessed density changes in nine lemur species across five forest fragments. Diurnal surveys were conducted monthly from 2015 to 2019 on 35 transects (total effort = 1268 km). Additionally, 21 transects were surveyed nocturnally in 2015 and 2016 (total effort = 107.5 km). To quantify forest cover changes, we generated land use/land cover (LULC) maps from Sentinel-2 imagery using supervised classification for each year. For the LULC maps, we overlayed species-specific buffers around all transects and calculated the proportion of land cover classes within them. We observed declines in the annual densities of four diurnal and cathemeral lemur species between 2015 and 2019, with species-specific declines of up to 80% (Varecia variegata). While the density of two nocturnal species decreased, one increased fivefold (Cheirogaleus major) between 2015 and 2016. By 2019, Grassland was the dominant land type (50%), while Paddy Fields had the smallest coverage (1.03%). Mature Agricultural Land increased the most (63.37%), while New Agricultural Land decreased the most (-66.36%). Unexpectedly, we did not find evidence that higher forest cover supported a higher lemur population density within sampled areas, but we found support for the negative impact of degraded land cover types on three lemur species. Our study underscores the urgent need to address land-use changes and their repercussions for primate populations in tropical ecosystems. The diverse responses of lemur species to modified habitats highlight the complexity of these impacts and emphasize the importance of targeted conservation efforts.

Morphological variability or inter-observer bias? A methodological toolkit to improve data quality of multi-researcher datasets for the analysis of morphological variation.

OBJECTIVES: The investigation of morphological variation in animals is widely used in taxonomy, ecology, and evolution. Using large datasets for meta-analyses has dramatically increased, raising concerns about dataset compatibilities and biases introduced by contributions of multiple researchers. MATERIALS AND METHODS: We compiled morphological data on 13 variables for 3073 individual mouse lemurs (Cheirogaleidae, Microcebus spp.) from 25 taxa and 153 different sampling locations, measured by 48 different researchers. We introduced and applied a filtering pipeline and quantified improvements in data quality (Shapiro-Francia statistic, skewness, and excess kurtosis). The filtered dataset was then used to test for genus-wide sexual size dimorphism and the applicability of Rensch's, Allen's, and Bergmann's rules. RESULTS: Our pipeline reduced inter-observer bias (i.e., increased normality of data distributions). Inter-observer reliability of measurements was notably variable, highlighting the need to reduce data collection biases. Although subtle, we found a consistent pattern of sexual size dimorphism across Microcebus, with females being the larger (but not heavier) sex. Sexual size dimorphism was isometric, providing no support for Rensch's rule. Variations in tail length but not in ear size were consistent with the predictions of Allen's rule. Body mass and length followed a pattern contrary to predictions of Bergmann's rule. DISCUSSION: We highlighted the usefulness of large multi-researcher datasets for testing ecological hypotheses after correcting for inter-observer biases. Using genus-wide tests, we outlined generalizable patterns of morphological variability across all mouse lemurs. This new methodological toolkit aims to facilitate future large-scale morphological comparisons for a wide range of taxa and applications.

Factors influencing terrestriality in primates of the Americas and Madagascar.

Among mammals, the order Primates is exceptional in having a high taxonomic richness in which the taxa are arboreal, semiterrestrial, or terrestrial. Although habitual terrestriality is pervasive among the apes and African and Asian monkeys (catarrhines), it is largely absent among monkeys of the Americas (platyrrhines), as well as galagos, lemurs, and lorises (strepsirrhines), which are mostly arboreal. Numerous ecological drivers and species-specific factors are suggested to set the conditions for an evolutionary shift from arboreality to terrestriality, and current environmental conditions may provide analogous scenarios to those transitional periods. Therefore, we investigated predominantly arboreal, diurnal primate genera from the Americas and Madagascar that lack fully terrestrial taxa, to determine whether ecological drivers (habitat canopy cover, predation risk, maximum temperature, precipitation, primate species richness, human population density, and distance to roads) or species-specific traits (body mass, group size, and degree of frugivory) associate with increased terrestriality. We collated 150,961 observation hours across 2,227 months from 47 species at 20 sites in Madagascar and 48 sites in the Americas. Multiple factors were associated with ground use in these otherwise arboreal species, including increased temperature, a decrease in canopy cover, a dietary shift away from frugivory, and larger group size. These factors mostly explain intraspecific differences in terrestriality. As humanity modifies habitats and causes climate change, our results suggest that species already inhabiting hot, sparsely canopied sites, and exhibiting more generalized diets, are more likely to shift toward greater ground use.

Human density modulates spatial associations among tropical forest terrestrial mammal species.

The spatial aggregation of species pairs often increases with the ecological similarity of the species involved. However, the way in which environmental conditions and anthropogenic activity affect the relationship between spatial aggregation and ecological similarity remains unknown despite the potential for spatial associations to affect species interactions, ecosystem function, and extinction risk. Given that human disturbance has been shown to both increase and decrease spatial associations among species pairs, ecological similarity may have a role in mediating these patterns. Here, we test the influences of habitat diversity, primary productivity, human population density, and species' ecological similarity based on functional traits (i.e., functional trait similarity) on spatial associations among tropical forest mammals. Large mammals are highly sensitive to anthropogenic change and therefore susceptible to changes in interspecific spatial associations. Using two-species occupancy models and camera trap data, we quantified the spatial overlap of 1216 species pairs from 13 tropical forest protected areas around the world. We found that the association between ecological similarity and interspecific species associations depended on surrounding human density. Specifically, aggregation of ecologically similar species was more than an order of magnitude stronger in landscapes with the highest human density compared to those with the lowest human density, even though all populations occurred within protected areas. Human-induced changes in interspecific spatial associations have been shown to alter top-down control by predators, increase disease transmission and increase local extinction rates. Our results indicate that anthropogenic effects on the distribution of wildlife within protected areas are already occurring and that impacts on species interactions, ecosystem functions, and extinction risk warrant further investigation.

Global importance of Indigenous Peoples, their lands, and knowledge systems for saving the world's primates from extinction.

Primates, represented by 521 species, are distributed across 91 countries primarily in the Neotropic, Afrotropic, and Indo-Malayan realms. Primates inhabit a wide range of habitats and play critical roles in sustaining healthy ecosystems that benefit human and nonhuman communities. Approximately 68% of primate species are threatened with extinction because of global pressures to convert their habitats for agricultural production and the extraction of natural resources. Here, we review the scientific literature and conduct a spatial analysis to assess the significance of Indigenous Peoples' lands in safeguarding primate biodiversity. We found that Indigenous Peoples' lands account for 30% of the primate range, and 71% of primate species inhabit these lands. As their range on these lands increases, primate species are less likely to be classified as threatened or have declining populations. Safeguarding Indigenous Peoples' lands, languages, and cultures represents our greatest chance to prevent the extinction of the world's primates.

Madagascar Terrestrial Camera Survey Database 2021: A collation of protected forest camera surveys from 2007-2021.

Madagascar is a threatened global biodiversity hotspot and conservation priority, yet we lack broad-scale surveys to assess biodiversity across space and time. To fill this gap, we collated camera trap surveys, capturing species occurrences within Madagascar into a single standardized database. This data set includes nine distinct protected areas of Madagascar and encompasses 13 subprojects, 38 camera arrays, and 1156 sampling units (independent camera site per survey) within two important biodiversity eco-regions: western dry deciduous forest and eastern humid rainforest. Camera surveys were conducted from June 2007 to January 2021. The final data set includes 17 unique families of mammals (Bovidae, Canidae, Cheirogaleidae, Daubentoniidae, Equidae, Eupleridae, Felidae, Hominidae, Indriidae, Lemuridae, Lepilemuridae, Muridae, Nesomyidae, Pteropodidae, Soricidae, Suidae, Tenrecidae) comprising 45 species and 27 unique families of birds (Accipitridae, Acrocephalidae, Alcedinidae, Bernieridae, Brachypteraciidae, Caprimulgidae, Cisticolidae, Columbidae, Coraciidae, Corvidae, Cuculidae, Dicruridae, Mesitornithidae, Monarchidae, Motacillidae, Muscicapidae, Numididae, Phasianidae, Rallidae, Sarothruridae, Strigidae, Sturnidae, Sulidae, Threskiornithidae, Upupidae, Vangidae, Zosteropidae) comprising 58 species. Images were processed and verified by individual project data set creators and camera operation and species tables were then collated. The final product represents the first broad-scale freely available standardized formal faunal database for Madagascar. Data are available through this publication and at DOI: 10.5281/zenodo.5801806. These data will be useful for examining species-level and community-level trends in occurrence across space or time within Madagascar and globally, evaluating native and invasive species dynamics, and will aid in determining species conservation status and planning for at-risk species. There are no copyright restrictions; please cite this paper when using the data for publication.

The gut microbiome as an indicator of habitat disturbance in a Critically Endangered lemur.

BACKGROUND: Habitat disturbance affects the biology and health of animals globally. Understanding the factors that contribute to the differential responses of animals to habitat disturbance is critical for conservation. The gut microbiota represents a potential pathway through which host responses to habitat disturbance might be mediated. However, a lack of quantitative environmental data in many gut microbiome (GM) studies of wild animals limits our ability to pinpoint mechanisms through which habitat disturbance affects the GM. Here, we examine the impact of anthropogenic habitat disturbance on the diet and GM of the Critically Endangered black-and-white ruffed lemur (Varecia variegata editorum). We collected fecal samples and behavioral data from Varecia occupying habitats qualitatively categorized as primary forest, moderately disturbed forest, and heavily disturbed forest. RESULTS: Varecia diet and GM composition differed substantially across sites. Dietary richness predicted GM richness across sites, and overall GM composition was strongly correlated to diet composition. Additionally, the consumption of three specific food items positively correlated to the relative abundances of five microbial strains and one microbial genus across sites. However, diet did not explain all of the GM variation in our dataset, and differences in the GM were detected that were not correlated with diet, as measured. CONCLUSIONS: Our data suggest that diet is an important influence on the Varecia GM across habitats and thus could be leveraged in novel conservation efforts in the future. However, other factors such as contact with humans should also be accounted for. Overall, we demonstrate that quantitative data describing host habitats must be paired with GM data to better target the specific mechanisms through which environmental change affects the GM.

Lemur paparazzi: Arboreal camera trapping and occupancy modeling as conservation tools for monitoring threatened lemur species.

Primate species face growing risks of extinction throughout the world. To better protect their populations, effective monitoring techniques are needed. The goal of this study was to evaluate the use of arboreal camera traps and occupancy modeling as conservation tools for threatened lemur species. This project aimed to (1) estimate the occupancy and detection probabilities of lemur species, (2) investigate factors potentially affecting lemur habitat use, and (3) determine whether ground or arboreal cameras are better for surveying lemur assemblages. We conducted camera trapping research in five forest fragments (total trap nights = 1770; 900 arboreal trap nights (134 photo events); 870 ground trap nights (2 photo events)) and reforestation areas (total trap nights = 608; 1 photo event) in Kianjavato, Madagascar from May to September 2019. We used arboreal trap data from fragments to estimate occupancy for five species: the red-fronted brown lemur (Eulemur rufifrons; ψ = 0.54 ± SD 0.03), Jolly's mouse lemur (Microcebus jollyae; ψ = 0.14 ± 0.17), the greater dwarf lemur (Cheirogaleus major; ψ = 0.42 ± 0.30), the red-bellied lemur (Eulemur rubriventer; ψ = 0.24 ± 0.03), and the black-and-white ruffed lemur (Varecia variegata; ψ = 0.24 ± 0.08). Tree diameter, elevation, distance to village, and canopy connectivity were important predictors of occupancy, while camera height, canopy connectivity, fragment ID, and fragment size predicted detection. Arboreal cameras recorded significantly higher species richness compared with ground cameras. We suggest expanded application of arboreal camera traps in future research, but we recommend longer trapping periods to better sample rarer species. Overall, arboreal camera trapping combined with occupancy modeling can be a highly efficient and useful approach for monitoring and predicting the occurrence of elusive lemur species and has the potential to be effective for other arboreal primates and canopy taxa across the globe.

Variation in predicted COVID-19 risk among lemurs and lorises.

The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 2 million fatalities since it first emerged in late 2019. As we write, infection rates are at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary target of SARS-CoV-2 is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predict that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results while finding additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.

Tropical mammal functional diversity increases with productivity but decreases with anthropogenic disturbance.

A variety of factors can affect the biodiversity of tropical mammal communities, but their relative importance and directionality remain uncertain. Previous global investigations of mammal functional diversity have relied on range maps instead of observational data to determine community composition. We test the effects of species pools, habitat heterogeneity, primary productivity and human disturbance on the functional diversity (dispersion and richness) of mammal communities using the largest standardized tropical forest camera trap monitoring system, the Tropical Ecology Assessment and Monitoring (TEAM) Network. We use occupancy values derived from the camera trap data to calculate occupancy-weighted functional diversity and use Bayesian generalized linear regression to determine the effects of multiple predictors. Mammal community functional dispersion increased with primary productivity, while functional richness decreased with human-induced local extinctions and was significantly lower in Madagascar than other tropical regions. The significant positive relationship between functional dispersion and productivity was evident only when functional dispersion was weighted by species' occupancies. Thus, observational data from standardized monitoring can reveal the drivers of mammal communities in ways that are not readily apparent from range map-based studies. The positive association between occupancy-weighted functional dispersion of tropical forest mammal communities and primary productivity suggests that unique functional traits may be more beneficial in more productive ecosystems and may allow species to persist at higher abundances.

Variation in predicted COVID-19 risk among lemurs and lorises.

The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 1.5 million fatalities since it first emerged in late 2019. As we write, infection rates are currently at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary viral target is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predicts that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results and finds additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and Endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.

Corrigendum: A Severe Lack of Evidence Limits Effective Conservation of the World's Primates.

[This corrects the article DOI: 10.1093/biosci/biaa082.].

A Severe Lack of Evidence Limits Effective Conservation of the World's Primates.

Threats to biodiversity are well documented. However, to effectively conserve species and their habitats, we need to know which conservation interventions do (or do not) work. Evidence-based conservation evaluates interventions within a scientific framework. The Conservation Evidence project has summarized thousands of studies testing conservation interventions and compiled these as synopses for various habitats and taxa. In the present article, we analyzed the interventions assessed in the primate synopsis and compared these with other taxa. We found that despite intensive efforts to study primates and the extensive threats they face, less than 1% of primate studies evaluated conservation effectiveness. The studies often lacked quantitative data, failed to undertake postimplementation monitoring of populations or individuals, or implemented several interventions at once. Furthermore, the studies were biased toward specific taxa, geographic regions, and interventions. We describe barriers for testing primate conservation interventions and propose actions to improve the conservation evidence base to protect this endangered and globally important taxon.

Anthropogenic pressures drive population genetic structuring across a Critically Endangered lemur species range.

In recent decades Madagascar has experienced significant habitat loss and modification, with minimal understanding of how human land use practices have impacted the evolution of its flora and fauna. In light of ongoing and intensifying anthropogenic pressures, we seek new insight into mechanisms driving genetic variability on this island, using a Critically Endangered lemur species, the black-and-white ruffed lemur (Varecia variegata), as a test case. Here, we examine the relative influence of natural and anthropogenic landscape features that we predict will impose barriers to dispersal and promote genetic structuring across the species range. Using circuit theory, we model functional connectivity among 18 sampling localities using population-based genetic distance (FST). We optimized resistance surfaces using genetic algorithms and assessed their performance using maximum-likelihood population-effects mixed models. The best supported resistance model was a composite surface that included two anthropogenic features, habitat cover and distance to villages, suggesting that rapid land cover modification by humans has driven change in the genetic structure of wild lemurs. Primary conservation priority should be placed on mitigating further forest loss and connecting regions identified as having low dispersal potential to prevent further loss of genetic diversity and promote the survival of other moist forest specialists.

An environmental DNA sampling method for aye-ayes from their feeding traces.

Noninvasive sampling is an important development in population genetic monitoring of wild animals. Particularly, the collection of environmental DNA (eDNA) which can be collected without needing to encounter the target animal facilitates the genetic analysis of endangered species. One method that has been applied to these sample types is target capture and enrichment which overcomes the issue of high proportions of exogenous (nonhost) DNA from these lower quality samples. We tested whether target capture of mitochondrial DNA from sampled feeding traces of the aye-aye, an endangered lemur species would yield mitochondrial DNA sequences for population genetic monitoring. We sampled gnawed wood where aye-ayes excavate wood-boring insect larvae from trees. We designed RNA probes complementary to the aye-aye's mitochondrial genome and used these to isolate aye-aye DNA from other nontarget DNA in these samples. We successfully retrieved six near-complete mitochondrial genomes from two sites within the aye-aye's geographic range that had not been sampled previously. Our method demonstrates the application of next-generation molecular techniques to species of conservation concern. This method can likely be applied to alternative foraged remains to sample endangered species other than aye-ayes.

Primates in peril: the significance of Brazil, Madagascar, Indonesia and the Democratic Republic of the Congo for global primate conservation.

Primates occur in 90 countries, but four-Brazil, Madagascar, Indonesia, and the Democratic Republic of the Congo (DRC)-harbor 65% of the world's primate species (439) and 60% of these primates are Threatened, Endangered, or Critically Endangered (IUCN Red List of Threatened Species 2017-3). Considering their importance for global primate conservation, we examine the anthropogenic pressures each country is facing that place their primate populations at risk. Habitat loss and fragmentation are main threats to primates in Brazil, Madagascar, and Indonesia. However, in DRC hunting for the commercial bushmeat trade is the primary threat. Encroachment on primate habitats driven by local and global market demands for food and non-food commodities hunting, illegal trade, the proliferation of invasive species, and human and domestic-animal borne infectious diseases cause habitat loss, population declines, and extirpation. Modeling agricultural expansion in the 21st century for the four countries under a worst-case-scenario, showed a primate range contraction of 78% for Brazil, 72% for Indonesia, 62% for Madagascar, and 32% for DRC. These pressures unfold in the context of expanding human populations with low levels of development. Weak governance across these four countries may limit effective primate conservation planning. We examine landscape and local approaches to effective primate conservation policies and assess the distribution of protected areas and primates in each country. Primates in Brazil and Madagascar have 38% of their range inside protected areas, 17% in Indonesia and 14% in DRC, suggesting that the great majority of primate populations remain vulnerable. We list the key challenges faced by the four countries to avert primate extinctions now and in the future. In the short term, effective law enforcement to stop illegal hunting and illegal forest destruction is absolutely key. Long-term success can only be achieved by focusing local and global public awareness, and actively engaging with international organizations, multinational businesses and consumer nations to reduce unsustainable demands on the environment. Finally, the four primate range countries need to ensure that integrated, sustainable land-use planning for economic development includes the maintenance of biodiversity and intact, functional natural ecosystems.

Phylogenomic Reconstruction of Sportive Lemurs (genus Lepilemur) Recovered from Mitogenomes with Inferences for Madagascar Biogeography.

The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently described. The cryptic morphological differences confounded taxonomy until recent molecular studies; however, some species' boundaries remain uncertain. To better understand the genus Lepilemur, we analyzed 35 complete mitochondrial genomes representing all recognized 26 sportive lemur taxa and estimated divergence dates. With our dataset we recovered 25 reciprocally monophyletic lineages, as well as an admixed clade containing Lepilemur mittermeieri and Lepilemur dorsalis. Using modern distribution data, an ancestral area reconstruction and an ecological vicariance analysis were performed to trace the history of diversification and to test biogeographic hypotheses. We estimated the initial split between the eastern and western Lepilemur clades to have occurred in the Miocene. Divergence of most species occurred from the Pliocene to the Pleistocene. The biogeographic patterns recovered in this study were better addressed with a combinatorial approach including climate, watersheds, and rivers. Generally, current climate and watershed hypotheses performed better for western and eastern clades, while speciation of northern clades was not adequately supported using the ecological factors incorporated in this study. Thus, multiple mechanisms likely contributed to the speciation and distribution patterns in Lepilemur.

Predicting plant diversity patterns in Madagascar: understanding the effects of climate and land cover change in a biodiversity hotspot.

Climate and land cover change are driving a major reorganization of terrestrial biotic communities in tropical ecosystems. In an effort to understand how biodiversity patterns in the tropics will respond to individual and combined effects of these two drivers of environmental change, we use species distribution models (SDMs) calibrated for recent climate and land cover variables and projected to future scenarios to predict changes in diversity patterns in Madagascar. We collected occurrence records for 828 plant genera and 2186 plant species. We developed three scenarios, (i.e., climate only, land cover only and combined climate-land cover) based on recent and future climate and land cover variables. We used this modelling framework to investigate how the impacts of changes to climate and land cover influenced biodiversity across ecoregions and elevation bands. There were large-scale climate- and land cover-driven changes in plant biodiversity across Madagascar, including both losses and gains in diversity. The sharpest declines in biodiversity were projected for the eastern escarpment and high elevation ecosystems. Sharp declines in diversity were driven by the combined climate-land cover scenarios; however, there were subtle, region-specific differences in model outputs for each scenario, where certain regions experienced relatively higher species loss under climate or land cover only models. We strongly caution that predicted future gains in plant diversity will depend on the development and maintenance of dispersal pathways that connect current and future suitable habitats. The forecast for Madagascar's plant diversity in the face of future environmental change is worrying: regional diversity will continue to decrease in response to the combined effects of climate and land cover change, with habitats such as ericoid thickets and eastern lowland and sub-humid forests particularly vulnerable into the future.