Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar

We present the data from the Insect Biome Atlas project (IBA), characterizing the terrestrial arthropod faunas of Sweden and Madagascar. Over 12 months, Malaise trap samples were collected weekly (biweekly or monthly in the winter, when feasible) at 203 locations within 100 sites in Sweden and weekly at 50 locations within 33 sites in Madagascar; this was complemented by soil and litter samples from each site. The field samples comprise 4,749 Malaise trap, 192 soil and 192 litter samples from Sweden and 2,566 Malaise trap and 190 litter samples from Madagascar. Samples were processed using mild lysis or homogenization, followed by DNA metabarcoding of CO1 (418 bp). The data comprise 698,378 non-chimeric sequence variants from Sweden and 687,866 from Madagascar, representing 33,989 (33,046 Arthropoda) and 77,599 (77,380 Arthropoda) operational taxonomic units, respectively. These are the most comprehensive data presented on these faunas so far, allowing unique analyses of the size, composition, spatial turnover and seasonal dynamics of the sampled communities. They also provide an invaluable baseline against which to gauge future changes.

Mid-Holocene aridity recorded in pygmy hippo and giant tortoise bone from southwest Madagascar

Aridity can exacerbate threats to endemic biodiversity, and arid intervals during the last couple of millennia may have contributed to endemic large herbivore extinctions on Madagascar. However, regional palaeoclimate records spanning multiple millennia are limited, and the tolerance of extinct taxa to past water scarcity is poorly known. To infer changes in the diet and habitat aridity of extinct pygmy hippos and giant tortoises during approximately 6000-1000 years ago, I used carbon and nitrogen isotope (δ13C and δ15N) data from 49 directly radiocarbon-dated bones collected around Tampolove, southwest Madagascar. Fluctuations in bone δ15N values through time in both species indicate tolerance of dry habitat during intermittent drying trends, including around a dry period known as the '4.2 ka event'. However, taxon-specific differences in the covariance of bone δ13C and δ15N values suggest that the diets of pygmy hippos and giant tortoises changed in different ways during these past arid intervals. This suggests that past aridification had different effects on these taxa. Thus, I argue that hypotheses for past extinction that involve a synergy among climate drying and forest clearance, hunting and biological invasion must consider taxon-specific responses to past aridity.

Phylogenomics, historical biogeography, and diversification of leaf traits in the Malagasy-endemic genus Uncarina (Pedaliaceae)

PREMISE

Uncarina contains 14 species of woody plants endemic to Madagascar. Its occurrence across dryland biomes on the island make it an interesting system to study the diversification of the flora.

METHODS

Using samples of all species and 512 nuclear loci, we reconstructed phylogenetic trees to examine species relationships and assess their monophyly. We also studied the historical biogeography of the genus and combined leaf trait data derived from SEM photography of trichomes and geometric morphometric analysis of leaf shape to better understand its diversification across dryland biomes.

RESULTS

Uncarina is monophyletic, and major clades showed a clear biogeographical signal. Leaf traits also corroborated relationships among major clades. Although most species are monophyletic, at least one cryptic species exists. Uncarina, like many arid-adapted plant lineages in Madagascar originated in the Miocene or Pleistocene. Geographic movement has been primarily along a south-north axis, with river basins apparently acting as barriers to gene flow. The evolution of leaf traits corroborated movement from the spiny thicket to the dry forest biome.

CONCLUSIONS

As with Malagasy lemurs and other animals, riverine barriers may have been involved in the diversification of Uncarina and may apply more broadly to epizoochorous angiosperms of Madagascar. Leaf traits suggest either a loss of adaptations to extremely arid, high irradiance environments or a release from herbivores. As is likely needed in other Malagasy lineages, more thorough population-level sampling and specimen collecting is needed to fully understand the taxonomic and morphological diversity in the genus.

Effect of Land-Use on Hantavirus Infection Among Introduced and Endemic Small Mammals of Madagascar

Hantaviruses are globally distributed zoonotic pathogens capable of causing fatal disease in humans. Addressing the risk of hantavirus spillover from animal reservoirs to humans requires identifying the local reservoirs (usually rodents and other small mammals) and the predictors of infection, such as habitat characteristics and human exposure. We screened a collection of 1663 terrestrial small mammals and 227 bats for hantavirus RNA, comprised of native and non-native species from northeastern Madagascar, trapped over 5 successive years. We specifically investigated the influence of diverse habitat types: villages, agricultural fields, regrowth areas, secondary and semi-intact forests on infection with hantaviruses. We detected Hantavirus RNA closely related to the previously described Anjozorobe virus in 9.5% of Rattus rattus sampled, with an absence of detection in other species. Land-use had a complex impact on hantavirus infections: intensive land-use positively correlated with the abundance of R. rattus and the average R. rattus body size varied between habitats. Larger individuals had a higher probability of infection, regardless of sex. Thus, villages and pristine forests which host the smallest, and hence, least infected rats, represent the lowest risk for hantavirus exposure to people while flooded rice fields which were home to the largest rats, and subsequently most infected rats, represent the greatest exposure risk. These findings provide new insights into the relationship between rat ecology and the gradients of hantavirus exposure risk for farmers in northeastern Madagascar as they work in different land-use types.

Biome conservatism prevailed in repeated long-distance colonization of Madagascar's mountains by Helichrysum (Compositae, Gnaphalieae)

Colonization and diversification processes are responsible for the distinctiveness of island biotas, with Madagascar standing out as abiodiversity hotspot exceptionally rich in species and endemism. Regardless of its significance, the evolutionary history and diversification drivers of Madagascar's flora remain understudied. Here we focus on Helichrysum (Compositae, Gnaphalieae) to investigate the evolutionary and biogeographic origins of the Malagasy flora. We inferred a highly resolved phylogeny based on target-enrichment data from 327 species (including 51 % of Malagasy endemics) and conducted ancestral range estimation analyses. Our results revealed at least six trans-oceanic dispersal events from different African regions to Madagascar during the Pliocene. In this process, biome conservatism prevailed, as evidenced by similarities between Malagasy lineages and their African relatives. The southern African grasslands, known to be the center of diversification and the main source of African Helichrysum lineages, played a key role in the colonization of Madagascar as the ancestral source area of at least three clades. The Tropical Afromontane region was revealed as the source of at least two montane Malagasy lineages that substantially radiated in-situ. Finally, a dispersal event from southwestern Africa led to a lineage represented by a single species adapted to the island's southwestern arid conditions. The main radiations of Helichrysum in Madagascar's mountains occurred within the last 2 My, coinciding with a transition towards cooler and drier conditions and the expansion of open habitats, likely driven by a combination of geographic and ecological speciation. Overall, our findings highlight the affinities between the montane floras of continental Africa and Madagascar.

Global phylogeny of the family Gomphillaceae (Ascomycota, Graphidales) sheds light on the origin, diversification and endemism in foliicolous lineages

Foliicolous lichens grow on living leaves of vascular plants. They are mostly found in tropical to subtropical or temperate rainforests. Many phenotype-based species are considered as pantropical or even sub-cosmopolitan, either attributed to old ages, having existed prior to continental breakups or long-distance dispersal. We built a much expanded, global phylogeny of Gomphillaceae, the most diverse group of leaf-dwelling lichenised fungi. Our sampling encompassed six major biodiversity hotspots: MIOI (Madagascar and the Indian Ocean Islands), the Caribbean, New Caledonia, the Colombian Chocó, Mesoamerica and the Atlantic coast of Brazil. It was based on multilocus sequence data (mtSSU rDNA, nuLSU rDNA and RPB1), including 2207 sequences of 1256 specimens. Species delimitation methods combined with a phenotype matrix identified 473 putative species. Amongst these, 104 are confirmed as described, 213 are classified as cryptic or near cryptic (hidden diversity), 100 represent new species to science (identified on the basis of phenotype) and 56 remain unidentified. Amongst the 104 species with a valid name, 40.5% are distributed across 2-5 continents (lichenogeographical regions) by applying the phenotype-based species concept. However, using the integrative approach to delineate species, this estimate is reduced to 9%. We estimate the global species richness of Gomphillaceae at 1,861-2,356 species. The timing of species-level divergences suggests that the current distribution of foliicolous lichens is shaped more by long-distance dispersal and rapid diversification than by vicariance. The origin of the family and major clades appears to be in the Neotropics, with subsequent numerous dispersal events. Our results support the separation of three major lineages, corresponding to the former families Asterothyriaceae, Gomphillaceae s.str. and Solorinellaceae, which should be recognised at the subfamily level.

Effects of protected area coverage and research on conservation status of primates globally

Conducting conservation research and establishing protected areas (PAs) based on research results are critical to biodiversity conservation. However, the effect of research and PAs on conservation of threatened species has rarely been evaluated simultaneously. We collected data on PAs from 2000 for 2021 and determined the number of publications on global primates (published from 1950 to 2021) to assess the effect of PAs, research, and biological and socioeconomic factors on the current International Union for Conservation of Nature endangered status and change in status. We used the MCMCglmm package to conduct a phylogenetic comparative analysis to control the phylogenetic relationship of primate species. The status of 24.6% (82 of 333) of species assessed at least twice declined. Only the black lion tamarin (Leontopithecus chrysopygus) had an improved status. Species with status declines mostly occurred on the south coast of West Africa and in Madagascar. PAs covered 22.1% of each species' range. Forest loss in PAs (5.5%) was significantly lower than forest loss within 5 km outside PAs (13.8%), suggesting PAs effectively mitigated forest loss. Both the median number of total publications and conservation publications on critically endangered species were higher than those of other categories. Models showed that PA coverage and number of publications or conservation-focused publications were not related to current status or change in status over time. A decline in status was not related to creation of PAs or increase of research since the last assessment. Our results suggest that current PAs and research are not reversing the extinction crisis of global primates. Doing more conservation-oriented research, strengthening management of current PAs, and expanding PAs will be needed to protect primates globally.

Redescription of Tetebius latibunus as a new senior synonym of Malgaceros boviceps (Opiliones: Laniatores: Biantidae)

The holotype of Tetebius latibunus Roewer, 1949, and the topotype material of Malgaceros boviceps Lawrence, 1959, were thoroughly examined and compared. No morphological differences were found between these specimens. Consequently, a new synonymy is herein proposed, identifying Malgaceros boviceps as a synonym of Tetebius latibunus, and subsequently, Malgaceros Lawrence, 1959, as a synonym of Tetebius Roewer, 1949. Additionally, the holotype of Tetebius latibunus is considered a minor male, whereas the junior synonym Malgaceros boviceps is considered as a major male. A revised description and detailed illustration of the species Tetebius latibunus are provided, based on a comprehensive review of the holotype and numerous specimens that were collected in Nosy Be, Madagascar, the type locality of Malgaceros boviceps. The original type locality attributed to Tetebius latibunus by Roewer (Tete, Mozambique) is now believed to be a mislabeling, and the species is considered endemic to Madagascar.

Captive Breeding Reveals Insights Into the Ecology and Reproductive Biology of 11 Little-Known Malagasy Frog Species

Amphibians are facing an extinction crisis, with ex situ programs increasingly being used as a tool for their conservation. However, conservation efforts are often limited because we do not understand the ecological, behavioral, and life history traits of many amphibian species. Here, we report on the seasonal breeding patterns, egg-laying behavior, clutch size, and development of 11 frog species maintained at a conservation breeding facility in Andasibe, Madagascar. The frogs exhibited diverse breeding strategies aligned with life history theory. Counting the eggs in 1239 egg masses across these 11 species, we found endotrophic microhylids and terrestrial-breeding species had the smallest clutch size yet completed metamorphosis quickly, whereas species that laid eggs above or in water with exotrophic larvae had larger clutch sizes and took longer to develop. Most reproduction in captivity occurred during the warm, rainy season and followed seasonal patterns in temperature variation. Yet, Mantidactylus betsileanus bred throughout the year, and Heterixalus betsileo required additional environmental stimuli to trigger reproduction. Notably, we confirmed that Gephyromantis mitsinjo lays eggs on land with tadpoles developing terrestrially within jelly, a behavior previously theorized but which until now remained unobserved. Such observations show how captive breeding programs can be used to gain valuable data on the life history traits of species that are otherwise challenging to observe in nature. Our findings can be used to assess threats to closely related species, helping inform conservation efforts in a country harboring exceptional amphibian species richness and endemism.

Ecological and anthropogenic effects on the genomic diversity of lemurs in Madagascar

Ecological variation and anthropogenic landscape modification have had key roles in the diversification and extinction of mammals in Madagascar. Lemurs represent a radiation with more than 100 species, constituting roughly one-fifth of the primate order. Almost all species of lemurs are threatened with extinction, but little is known about their genetic diversity and demographic history. Here, we analyse high-coverage genome-wide resequencing data from 162 unique individuals comprising 50 species of Lemuriformes, including multiple individuals from most species. Genomic diversity varies widely across the infraorder and yet is broadly consistent among individuals within species. We show widespread introgression in multiple genera and generally high levels of genomic diversity likely resulting from allele sharing that occurred during periods of connectivity and fragmentation during climatic shifts. We find distinct patterns of demographic history in lemurs across the ecogeographic regions of Madagascar within the last million years. Within the past 2,000 years, lemurs underwent major declines in effective population size that corresponded to the timing of human population expansion in Madagascar. In multiple regions of the island, we identified chronological trajectories of inbreeding that are consistent across genera and species, suggesting localized effects of human activity. Our results show how the extraordinary diversity of these long-neglected, endangered primates has been influenced by ecological and anthropogenic factors.

LIFEPLAN: A worldwide biodiversity sampling design

As the technology for mass identification of species is advancing rapidly, we developed a field sampling method that takes advantage of the emerging possibilities of combining sensor-based data with automated high-throughput data processing. This article describes the five field sampling methods used by the LIFEPLAN project to collect biodiversity data in a systematic manner, all over the world. These methods are designed for use by anyone with basic biology or ecology knowledge from the higher education or university level. We present the selection and characteristics of international sampling locations for urban and natural sites, as well as the nested scale design in the Nordic countries and Madagascar. We describe the steps to collect sequences of animal images (.jpg) from infrared triggered camera traps, audio data (.WAV) of environment sounds from audio recorders, invertebrate samples in ethanol from Malaise traps for DNA metabarcoding, as well as both soil samples and 24-hour air samples obtained from cyclone samplers for fungal DNA metabarcoding. To ensure the usability and consistency of the data for future use, we pay particular attention to the metadata collected. In specifying the current sampling protocols, we note that technology will continue to improve and evolve. Hardware will also change within a short time period, with the advantage of improving the equipment used for collecting samples. Thus, we present examples of the samples collected by each current sampling method, to be used as a baseline or in comparison with different equipment models.

expowo: An R package for mining global plant diversity and distribution data

Premise

Data on plant distribution and diversity from natural history collections and taxonomic databases are increasingly becoming available online as exemplified by the Royal Botanic Gardens, Kew's Plants of the World Online (POWO) database. This growing accumulation of biodiversity information requires an advance in bioinformatic tools for accessing and processing the massive data for use in downstream science. We present herein expowo, an open-source package that facilitates extracting and using botanical data from POWO.

Methods and Results

The expowo package is implemented in R and designed to handle the entire vascular plant tree of life. It includes functions to readily distill taxonomic and distributional information about all families, genera, or species of vascular plants. It outputs a complete list of species in each genus of any plant family, with the associated original publication, synonyms, and distribution, and plots global maps of species richness at the country and botanical country levels, as well as graphs displaying species-discovery accumulation curves and nomenclatural changes over time. To demonstrate expowo's strengths in producing easy-to-handle outputs, we also show empirical examples from a set of biodiverse countries and representative species-rich and ecologically important angiosperm families.

Conclusions

By harnessing bioinformatic tools that accommodate varying levels of R programming proficiency, expowo functions assist users who have limited R programming expertise in efficiently distilling specific botanical information from online sources and producing maps and graphics for the further interpretation of biogeographic and taxonomic patterns.

New Insights on Chromosome Diversification in Malagasy Chameleons

In this work, we performed a preliminary molecular analysis and a comparative cytogenetic study on 5 different species of Malagasy chameleons of the genus Brookesia (B. superciliaris) and Furcifer (F. balteautus, F. petteri, F. major and F. minor). A DNA barcoding analysis was first carried out on the study samples using a fragment of the mitochondrial gene coding for the cytochrome oxidase subunit 1 (COI) in order to assess the taxonomic identity of the available biological material. Subsequently, we performed on the studied individuals a chromosome analysis with standard karyotyping (5% Giemsa solution at pH 7) and sequential C-banding + Giemsa, + CMA3, and + DAPI. The results obtained indicate that the studied species are characterized by a different chromosome number and a variable heterochromatin content and distribution, with or without differentiated sex chromosomes. In particular, B. superciliaris (2n = 36) and F. balteatus (2n = 34) showed a similar karyotype with 6 macro- and 12-11 microchromosome pairs, without differentiated sex chromosomes. In turn, F. petteri, F. major, and F. minor showed a karyotype with a reduced chromosome number (2n = 22-24) and a differentiated sex chromosome system with female heterogamety (ZZ/ZW). Adding our newly generated data to those available from the literature, we highlight that the remarkable chromosomal diversification of the genus Furcifer was likely driven by non-homologous chromosome fusions, including autosome-autosome, Z-autosome, and W-autosome fusions. The results of this process resulted in a progressive reduction in the chromosome number and partially homologous sex chromosomes of different shapes and sizes.

Multi-method survey rediscovers critically endangered species and strengthens Madagascar's freshwater fish conservation

Freshwater ecosystems are crucial for global biodiversity through supporting plant and animal species and providing essential resources. These ecosystems are under significant threat, particularly in island environments such as Madagascar. Our study focuses on the Amboaboa River basin, home to the rare and endemic fish species Rheocles derhami, last recorded in 2013. To assess the status of this and other threatened fish species including Ptychochromis insolitus and Paretroplus gymnopreopercularis, and to understand freshwater fish population dynamics in this biodiversity hotspot, we conducted a comprehensive survey using both environmental DNA (eDNA) and traditional fishing methods. While traditional methods effectively captured a diverse range of species, including several invasive aliens and the critically endangered endemic species that were the focus of this study, the eDNA approach detected only a fraction of these introduced species and struggled to identify some critically endangered endemics at the species level. This highlights the value of combining methods to enhance species detection. We also investigated the trade-offs associated with multi-primer assessments in eDNA analysis, focusing on three different primer combinations targeting the 12S mitochondrial gene: MiFish, Tele02, and Riaz. Additionally, we provided 12S reference barcodes for 10 species across 9 genera of fishes from the region to increase the coverage of the public reference databases. Overall, our study elucidates the current state of freshwater biodiversity in the Amboaboa River basin and underscores the value of employing multiple methods for effective conservation strategies.

Variation in nest survival of three species of tropical plovers in Madagascar with clutch size, age of nest, year and El Niño effect

A combination of life history traits and environmental conditions has been highlighted as the main drivers of avian breeding success. While drivers of breeding success are well known in some species, especially birds in northern, temperate regions; species in other parts of the world have received relatively little attention. In this study, we used a long-term dataset on breeding success of tropical plovers from south-west Madagascar to investigate whether nest survival changed over time and whether the drivers of nest survival were similar for multiple species breeding in the same arid habitat. In the 12-year period of 2009-2020, we monitored 2077 nests for three species with different breeding strategies: 1185 nests of Kittlitz's plovers (Anarhynchus pecuarius) with a flexible breeding strategy and uniparental care; and 565 nests of white-fronted plovers (A. marginatus) and 327 nests of Madagascar plovers (A. thoracicus) which both have biparental care. We found that nest survival was associated with a combination of clutch-size, age of nest and year among the three plover species. In addition, annual variation in climatic conditions associated with El Niño/La Niña events were included in the most supported survival models for Kittlitz's and white-fronted plovers, but the effects were not significant. Overall estimates of daily nest survival were similar for all three species: Kittlitz's plover: 0.950 ± 0.002 SE, Madagascar plover: 0.919 ± 0.007 SE, and white-fronted plover: 0.862 ± 0.047 SE. Estimates of nest success for the breeding season, based on increases in daily nest survival with the clutch age during the incubation periods (26 days for Kittlitz's plovers and 29 days for Madagascar and white-fronted plovers), were relatively low: Kittlitz's plover: 0.161 ± 0.056 SE, Madagascar plover: 0.287 ± 0.022 SE, and white-fronted plover: 0.228 ± 0.019 SE. All three species had a combination of factors affecting nest survival, both environmental and life history traits.

Conserving Madagascar's Amphibians and Reptiles Requires Collaboration between Scientists

Madagascar is well known for its exceptional biodiversity and striking endemicity levels, which are accompanied by high rates of deforestation and habitat alteration [...].

Towards computable taxonomic knowledge: Leveraging nanopublications for sharing new synonyms in the Madagascan genus Helictopleurus (Coleoptera, Scarabaeinae)

Background

Numerous taxonomic studies have focused on the dung beetle genus Helictopleurus d'Orbigny, 1915, endemic to Madagascar. However, this genus stilll needs a thorough revision. Semantic technologies, such as nanopublications, hold the potential to enhance taxonomy by transforming how data are published and analysed. This paper evaluates the effectiveness of nanopublications in establishing synonyms within the genus Helictopleurus.

New information

In this study, we identify four new synonyms within Helictopleurus: H.rudicollis (Fairmaire, 1898) = H.hypocrita Balthasar, 1941 syn. nov.; H.vadoni Lebis, 1960 = H.perpunctatus Balthasar, 1963 syn. nov.; H.halffteri Balthasar, 1964 = H.dorbignyi Montreuil, 2005 syn. nov.; H.clouei (Harold, 1869) = H.gibbicollis (Fairmaire, 1895) syn. nov. Helictopleurus may have a significantly larger number of synonyms than currently known, indicating potentially inaccurate estimates about its recent extinction.We also publish the newly-established synonyms as nanopublications, which are machine-readable data snippets accessible online. Additionally, we explore the utility of nanopublications in taxonomy and demonstrate their practical use with an example query for data extraction.

Sequential diversification with Miocene extinction and Pliocene speciation linked to mountain uplift explains the diversity of the African rain forest clade Monodoreae (Annonaceae)

BACKGROUND AND AIMS

Throughout the Cenozoic, Africa underwent several climatic and geological changes impacting the evolution of tropical rain forests (TRFs). African TRFs are thought to have extended from east to west in a 'pan-African' TRF, followed by several events of fragmentation during drier climate periods. During the Miocene, climate cooling and mountain uplift led to the aridification of tropical Africa and open habitats expanded at the expense of TRFs, which probably experienced local extinctions. However, in plants, these drivers were previously inferred using limited taxonomic and molecular data. Here, we tested the impact of climate and geological changes on diversification within the diverse clade Monodoreae (Annonaceae) composed of 90 tree species restricted to African TRFs.

METHODS

We reconstructed a near-complete phylogenetic tree, based on 32 nuclear genes, and dated using relaxed clocks and fossil calibrations in a Bayesian framework. We inferred the biogeographical history and the diversification dynamics of the clade using multiple birth-death models.

KEY RESULTS

Monodoreae originated in East African TRFs ~25 million years ago (Ma) and expanded toward Central Africa during the Miocene. We inferred range contractions during the middle Miocene and document important connections between East and West African TRFs after 15-13 Ma. Our results indicated a sudden extinction event during the late Miocene, followed by an increase in speciation rates. Birth-death models suggested that African elevation change (orogeny) is positively linked to speciation in this clade.

CONCLUSION

East Africa is inferred as an important source of Monodoreae species, and possibly for African plant diversity in general. Our results support a 'sequential scenario of diversification' in which increased aridification triggered extinction of TRF species in Monodoreae. This was quickly followed by fragmentation of rain forests, subsequently enhancing lagged speciation resulting from vicariance and improved climate conditions. In contrast to previous ideas, the uplift of East Africa is shown to have played a positive role in Monodoreae diversification.

Patterns of Grewia (Malvaceae) diversity across geographical scales in Africa and Madagascar

BACKGROUND AND AIMS

Quantifying spatial species richness is useful to describe biodiversity patterns across broad geographical areas, especially in large, poorly known plant groups. We explore patterns and predictors of species richness across Africa in one such group, the palaeotropical genus Grewia L. (Malvaceae).

METHODS

Grewia species richness was quantified by extracting herbarium records from GBIF and Tropicos and creating geographical grids at varying spatial scales. We assessed predictors of species richness using spatial regression models with 30 environmental variables. We explored species co-occurrence in Madagascar at finer resolutions using Schoener's index and compared species range sizes and International Union for Conservation of Nature status among ecoregions. Lastly, we derived a trait matrix for a subset of species found in Madagascar to characterize morphological diversity across space.

KEY RESULTS

Grewia species occur in 50 countries in Africa, with the highest number of species in Madagascar (93, with 80 species endemic). Species richness is highest in Madagascar, with ≤23 Grewia species in a grid cell, followed by coastal Tanzania/Kenya (≤13 species) and northern South Africa and central Angola (11 species each). Across Africa, higher species richness was predicted by variables related to aridity. In Madagascar, a greater range in environmental variables best predicted species richness, consistent with geographical grid cells of highest species richness occurring near biome/ecoregion transitions. In Madagascar, we also observe increasing dissimilarity in species composition with increasing geographical distance.

CONCLUSIONS

The spatial patterns and underlying environmental predictors that we uncover in Grewia represent an important step in our understanding of plant distribution and diversity patterns across Africa. Madagascar boasts nearly twice the Grewia species richness of the second most species-rich country in Africa, which might be explained by complex topography and environmental conditions across small spatial scales.

The rise of baobab trees in Madagascar

The baobab trees (genus Adansonia) have attracted tremendous attention because of their striking shape and distinctive relationships with fauna1. These spectacular trees have also influenced human culture, inspiring innumerable arts, folklore and traditions. Here we sequenced genomes of all eight extant baobab species and argue that Madagascar should be considered the centre of origin for the extant lineages, a key issue in their evolutionary history2,3. Integrated genomic and ecological analyses revealed the reticulate evolution of baobabs, which eventually led to the species diversity seen today. Past population dynamics of Malagasy baobabs may have been influenced by both interspecific competition and the geological history of the island, especially changes in local sea levels. We propose that further attention should be paid to the conservation status of Malagasy baobabs, especially of Adansonia suarezensis and Adansonia grandidieri, and that intensive monitoring of populations of Adansonia za is required, given its propensity for negatively impacting the critically endangered Adansonia perrieri.

The effect of a political crisis on performance of community forests and protected areas in Madagascar

Understanding the effectiveness of conservation interventions during times of political instability is important given how much of the world's biodiversity is concentrated in politically fragile nations. Here, we investigate the effect of a political crisis on the relative performance of community managed forests versus protected areas in terms of reducing deforestation in Madagascar, a biodiversity hotspot. We use remotely sensed data and statistical matching within an event study design to isolate the effect of the crisis and post-crisis period on performance. Annual rates of deforestation accelerated at the end of the crisis and were higher in community forests than in protected areas. After controlling for differences in location and other confounding variables, we find no difference in performance during the crisis, but community-managed forests performed worse in post-crisis years. These findings suggest that, as a political crisis subsides and deforestation pressures intensify, community-based conservation may be less resilient than state protection.

Spatial heterogeneity of neo- and paleo-endemism for plants in Madagascar

Madagascar is a biogeographically unique island with a remarkably high level of endemism. However, endemic taxa in Madagascar are massively threatened due to unprecedented pressures from anthropogenic habitat modification and climate change. A comprehensive phylogeny-based biodiversity evaluation of the island remains lacking. Here, we identify hotspots of taxonomic and phylogenetic plant diversity and neo- and paleo-endemism by generating a novel dated tree of life for the island. The tree is based on unprecedented sampling of 3,950 species (33% of the total known species) and 1,621 genera (93% of the total known genera and 69% of endemic genera) of Malagasy vascular plants. We find that island-endemic genera are concentrated in multiple lineages combining high taxonomic and phylogenetic diversity. Integrating phylogenetic and geographic distribution data, our results reveal that taxon richness and endemism are concentrated in the northern, eastern, and southeastern humid forests. Paleo-endemism centers are concentrated in humid eastern and central regions, whereas neo-endemism centers are concentrated in the dry and spiny forests in western and southern Madagascar. Our statistical analysis of endemic genera in each vegetation region supports a higher proportion of ancient endemic genera in the east but a higher proportion of recent endemic genera in the south and west. Overlaying centers of phylogenetic endemism with protected areas, we identify conservation gaps concentrated in western and southern Madagascar. These gaps should be incorporated into conservation strategies to aid the protection of multiple facets of biodiversity and their benefits to the Malagasy people.

Madagascar's burned area from Sentinel-2 imagery (2016-2022): Four times higher than from lower resolution sensors

Madagascar is one of the most burned regions in the world, to the point that it has been called the 'Isle of fire' or the 'Burning Island'. An accurate characterization of the burned area (BA) is crucial for understanding the true situation and impacts of fires on this island, where there is an active scientific debate on how fire affects multiple environmental and socioeconomic aspects, and how fire regimes should be in a complex context with differing interests. Despite this, recent advances have revealed that BA in Madagascar is poorly characterised by the currently available global BA products. In this work, we present, validate, and explore a BA database at 20 m spatial resolution for Madagascar covering the period 2016-2022. The database was built based on 75,010 Sentinel-2 images using a two-phase BA detection algorithm. The validation with independent long-term reference units showed Dice coefficients ≥79 %, omission errors ≤24 %, commission errors ≤18 %, and a relative bias ≥ - 8 %. An intercomparison with other available global BA products (GABAM, FireCCI51, C3SBA11, or MCD64) demonstrated that our product (i) exhibits temporal consistency, (ii) represents a significant accuracy improvement, as it reduces BA underestimations by about eightfold, (iii) yields BA estimates four times higher, and (iv) shows enhanced capability in detecting fires of all sizes. The observed BA spatial patterns were heterogeneous across the island, with 32 % of the grasslands burning annually, in contrast to other land cover types such as the dense tropical forest where <2 % burned every year. We conclude that the BA characterization in Madagascar must be addressed using imagery at spatial resolution higher than MODIS or Sentinel-3 (≥250 m), and temporal resolution higher than Landsat (16 days) to deal with cloudiness, the rapid attenuation of burn scars signals, and small fire patches.

Discovering unknown Madagascar biodiversity: integrative taxonomy of raft spiders (Pisauridae: Dolomedes)

Madagascar is a global biodiversity hotspot, but its biodiversity continues to be underestimated and understudied. Of raft spiders, genus Dolomedes Latreille, 1804, literature only reports two species on Madagascar. Our single expedition to humid forests of eastern and northern Madagascar, however, yielded a series of Dolomedes exemplars representing both sexes of five morphospecies. To avoid only using morphological diagnostics, we devised and tested an integrative taxonomic model for Dolomedes based on the unified species concept. The model first determines morphospecies within a morphometrics framework, then tests their validity via species delimitation using COI. It then incorporates habitat preferences, geological barriers, and dispersal related traits to form hypotheses about gene flow limitations. Our results reveal four new Dolomedes species that we describe from both sexes as Dolomedes gregoric sp. nov., D. bedjanic sp. nov., D. hydatostella sp. nov., and D. rotundus sp. nov. The range of D. kalanoro Silva & Griswold, 2013, now also known from both sexes, is expanded to eastern Madagascar. By increasing the known raft spider diversity from one valid species to five, our results merely scratch the surface of the true Dolomedes species diversity on Madagascar. Our integrative taxonomic model provides the framework for future revisions of raft spiders anywhere.

Non fire-adapted dry forest of Northwestern Madagascar: Escalating and devastating trends revealed by Landsat timeseries and GEDI lidar data

Ankarafantsika National Park (ANP), the last significant remnant of Northwestern Madagascar's tropical dry forests, is facing rapid degradation due to increased incidences of fire. This poses severe threats to biodiversity, local livelihoods, and vital ecosystem services. Our study, conducted on 3,052-ha of ANP's pristine forests, employed advanced remote-sensing techniques to assess fire impacts during the past 37 years. Our aims were to understand historical fire patterns and evaluate forest recovery and susceptibility to repeated fires following initial burns. Using data from multiple Landsat satellite sensors, we constructed a time series of fire events since 1985, which revealed no fire activity before 2014. The Global Ecosystem Dynamics Investigation (GEDI) lidar sensor data were used to observe forest structure in both post-fire areas and undisturbed zones for comparison. We recorded six fire incidents from 2014-2021, during which the fire-affected area exponentially grew. A significant fire incident in October 2021 impacted 1,052 hectares, 59% of which had experienced at least one fire in two-to-four years prior, with 60% experiencing two preceding incidents: one in 2017 and another in 2019. The initial fire drastically reduced plant cover and tree height, with subsequent fires causing minor additional loss. Post-fire recovery was negligible within the initial four years, even in patches without recurrent fires. The likelihood for an initial burn to trigger subsequent fires within a few years was high, leading to larger, more severe fires. We conclude that ANP's dry forests exhibit high vulnerability and low resilience to anthropogenic fires. Prompt preventive measures are essential to halt further fire spread and conserve the park's unique and invaluable biodiversity.

Escarpment evolution drives the diversification of the Madagascar flora

Madagascar exhibits high endemic biodiversity that has evolved with sustained and stable rates of speciation over the past several tens of millions of years. The topography of Madagascar is dominated by a mountainous continental rift escarpment, with the highest plant diversity and rarity found along the steep, eastern side of this geographic feature. Using a process-explicit model, we show that precipitation-driven erosion and landward retreat of this high-relief topography creates transient habitat organization through multiple mechanisms, including catchment expansion, isolation of highland remnants, and formation of topographic barriers. Habitat isolation and reconnection on a million-year timescale serves as an allopatric speciation pump creating the observed biodiversity.

A conservation planning strategy applied to the evolutionary history of the mantellid frogs of Madagascar

Phylogenetic diversity is an increasingly applied metric used to maximize the representation of evolutionary history in spatial conservation planning. When following this approach, researchers commonly overlook sites with a relatively higher proportion of recently diverged endemic species, also known as centers of neo-endemism. Here we aim to demonstrate how targeting the conservation of different facets of diversity (taxonomic diversity, phylogenetic diversity and centers of endemism) can provide more cost-effective solutions to the conservation of the all evolutionary spectrum of biodiversity. We do so by using the mantellid frogs of Madagascar as a case study. Our results confirm that areas with high concentrations of neo-endemism can be effectively identified as conservation planning priorities only if we specifically target them. Neglecting areas that are poor in phylogenetic diversity may therefore compromise the maintenance of diversification processes, particularly when lesser proportions of the landscape are protected. This approach can be of particular interest to island ecosystems, since they often harbor unique and restricted evolutionary radiations.

Another step through the crux: a new microendemic rock-dwelling Paroedura (Squamata, Gekkonidae) from south-central Madagascar

Using an integrative taxonomic approach including genetic and morphological data, we formally describe a new microendemic gecko species belonging to the Paroedurabastardi clade, previously referred to as P.bastardi D. We name this taxon currently known from Anja Reserve and Tsaranoro Valley Forest (south-central Madagascar), as P.manongavatosp. nov. The new species differs from other species of the P.bastardi clade by ≥ 12.4% uncorrected p-distance at the mitochondrial 16S rRNA gene and it forms a monophyletic group in the COI mtDNA phylogenetic tree. It lacks haplotype sharing at the nuclear KIAA1239 and CMOS genes with the other species of the same complex, including the syntopic P.rennerae. Given its limited extent of occurrence and high levels of habitat fragmentation linked to forest clearances and fires, we propose the IUCN Red List Category of Critically Endangered, based on the B1ab(iii) criterion. The conservation value of Anja Reserve and Tsaranoro Valley Forest is remarkable. Preserving the remaining deciduous forest habitat is of paramount importance to protect these narrow-range reptile species.

The colonisation of Madagascar by land-bound vertebrates

Despite discussions extending back almost 160 years, the means by which Madagascar's iconic land vertebrates arrived on the island remains the focus of active debate. Three options have been considered: vicariance, range expansion across land bridges, and dispersal over water. The first assumes that a group (clade/lineage) occupied the island when it was connected with the other Gondwana landmasses in the Mesozoic. Causeways to Africa do not exist today, but have been proposed by some researchers for various times in the Cenozoic. Over-water dispersal could be from rafting on floating vegetation (flotsam) or by swimming/drifting. A recent appraisal of the geological data supported the idea of vicariance, but found nothing to justify the notion of past causeways. Here we review the biological evidence for the mechanisms that explain the origins of 28 of Madagascar's land vertebrate clades [two other lineages (the geckos Geckolepis and Paragehyra) could not be included in the analysis due to phylogenetic uncertainties]. The podocnemid turtles and typhlopoid snakes are conspicuous for they appear to have arisen through a deep-time vicariance event. The two options for the remaining 26 (16 reptile, five land-bound-mammal, and five amphibian), which arrived between the latest Cretaceous and the present, are dispersal across land bridges or over water. As these would produce very different temporal influx patterns, we assembled and analysed published arrival times for each of the groups. For all, a 'colonisation interval' was generated that was bracketed by its 'stem-old' and 'crown-young' tree-node ages; in two instances, the ranges were refined using palaeontological data. The synthesis of these intervals for all clades, which we term a colonisation profile, has a distinctive shape that can be compared, statistically, to various models, including those that assume the arrivals were focused in time. The analysis leads us to reject the various land bridge models (which would show temporal concentrations) and instead supports the idea of dispersal over water (temporally random). Therefore, the biological evidence is now in agreement with the geological evidence, as well as the filtered taxonomic composition of the fauna, in supporting over-water dispersal as the mechanism that explains all but two of Madagascar's land-vertebrate groups.

Diversity and distribution of Orchidaceae in one of the world's most threatened plant hotspots (Madagascar)

INTRODUCTION

In recent decades, Madagascar has become one of the most important plant hotspots in the world. The country's remaining forests and vegetation are disappearing at an alarming rate, while dozens of new species are discovered each year. Amongst the plant families that have long been studied, Orchidaceae appear as one of the most charismatic, diverse and of high conservation concern. Based on a reviewed, comprehensive herbarium dataset, we have compiled a curated checklist of all orchid species occurring in Madagascar. Based on this complete dataset, we then compiled sampling effort, species diversity distribution and some general statistics on their ecology and IUCN conservation status.

METHODS

We compiled and standardised a global dataset using five public databases as the main data sources, supplemented by the most recent publications. The database contains ~ 10,000 geolocated records collected between 1816 and 2021. We used GIS software and rarefaction methods to examine sampling and diversity patterns.

RESULTS

According to our dataset, there are currently 913 orchid species collected in Madagascar, of which 759 orchid species (83.1%) are endemic. Doubling the sampling effort could lead to the discovery of around 100 more species, bringing the total estimated number of orchid species in Madagascar to between 986 and 1048. About one-third (297 species) of all orchid species are known only by type specimens (189 species) or have not been collected in Madagascar for more than 50 years (214 species). Although the raw data show that the Andasibe-Moramanga area would have the highest orchid species concentration, our analysis of the data, adjusted for bias, shows that the centres of orchid diversity in Madagascar are in the Tsaratanàna Strict Nature Reserve and the Ranomafana National Park. Life-form statistics show that 55.0% of orchid species are strict epiphytes. The main flowering period of orchids in Madagascar is between November and March. To date, 84% of the 226 Malagasy orchid species listed in the IUCN Red List are threatened with extinction (CR, EN or VU).

CONCLUSION

Despite geographically uneven coverage, the biodiversity of Malagasy orchids appears to be already well documented. We provide maps corrected for sampling bias that indicate priority areas for future surveys. Upcoming efforts should also focus on rediscovery and conservation of rare and/or threatened species and ensure that the protected area network is well aligned with the distribution of priority species for conservation. Finally, the conservation status of 75% of the orchid species found in Madagascar is not yet known and the inclusion of these species must be a top priority in the coming years.

Schistosomiasis elimination in Madagascar: challenges and opportunities for implementing the new WHO guidelines

Madagascar is one of the countries with the highest burden of schistosomiasis worldwide. The release from the WHO of the new 2021-2030 neglected tropical disease (NTD) roadmap alongside with the schistosomiasis guidelines sets the ambitious goal of eliminating schistosomiasis as a public health problem worldwide. In Madagascar, implementation barriers exist. This paper has the objective of identifying strengths, weaknesses, opportunities and threats in order to build on their basis practices and policies that can help the country to align with the international global health agenda and reach the ambitious goal set by the WHO.

Long forgotten record of a freshwater leech on Madagascar indicates a host-associated dispersal event from continental Africa

Madagascar houses a peculiar and largely endemic biota, having ancient Gondwanan affinities. However, the faunal composite of many invertebrate groups on the island is poorly known. For a long time, it was believed that the freshwater leech fauna of Madagascar contains a salifid species (Salifidae) only. Here, we report on a historical record of Placobdelloides multistriatus (Johansson, 1909) (Glossiphoniidae), a widespread African species, from Andrahomana, Southern Madagascar. Franz Sikora (1863-1902), an Austrian traveler and collector, who visited Andrahomana in 1899 to excavate fossils from a cave, collected the leech sample. The two specimens were obtained from an unspecified turtle species. We assume that P. multistriatus may have arrived to Madagascar relatively recently (i.e., in the Late Pleistocene or Holocene) via a long-distance dispersal event from continental Africa with its reptilian hosts such as the Nile crocodile and marsh terrapin. Based on a review of the body of available literature, two more freshwater leech species are known to occur on Madagascar: Linta be Westergren & Siddall, 2004 (Salifidae) and Alboglossiphonia sp. (Glossiphoniidae). Our findings indicate that Madagascar houses at least three freshwater leech species and that some additional taxa may have been overlooked there due to the scarcity of sampling efforts in the island’s freshwater bodies.

Spatial ecology of the invasive Asian common toad in Madagascar and its implications for invasion dynamics

Invasion dynamics are determined, among other aspects, by the spatial behaviour of invasive populations. The invasive toad Duttaphrynus melanostictus is spreading inland from the eastern coast of Madagascar, causing considerable ecological impacts. Understanding the basic factors determining the spread dynamics can inform management strategies and provide insights into spatial evolutionary processes. We radio-tracked 91 adult toads in three localities along the invasion gradient to determine whether spatial sorting of dispersive phenotypes is occurring, and investigate intrinsic and extrinsic determinants of spatial behaviour. Overall, toads in our study appeared as habitat generalists, and their sheltering behaviour was tied to water proximity, with toads changing shelter more frequently closer to waterbodies. Toads showed low displacement rates (mean = 4.12 m/day) and quite a philopatric behaviour but were able to perform daily movements of over 50 m. We did not detect any spatial sorting of dispersal-relevant traits nor sex- or size-biased dispersal. Our results suggest that toads are more likely to expand their range during the wet season, and that the range expansion is probably dominated by short-distance dispersal at this stage of the invasion, although a future increase in invasion speed is expected, due to the capacity for long-distance movements of this species.

Madagascar’s extraordinary biodiversity: Threats and opportunities

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.