Abstract Madascincus is a genus of quadrupedal skinks endemic to Madagascar, with 12 recognized species described between the 19th and 21st centuries, occupying diverse habitats from humid forests to arid southern regions and even high-altitude areas. Recent field expeditions uncovered two morphologically distinct forms that did not match any known species, prompting integrative taxonomic analyses that combine multilocus phylogenetics and morphology. Results revealed that each of these forms represents a highly divergent and likely ancient lineage, as evidenced by the substantial branch lengths in both mitochondrial and nuclear phylogenetic trees. These investigations led to the formal description of two new species with restricted distribution ranges: Madascincus irery sp. nov., likely endemic to the island of Nosy Be, and Madascincus minotaurus sp. nov., apparently restricted to the Tsingy de Namoroka karst system.

Abstract The diamond frogs of the genus Rhombophryne are a poorly understood clade of morphologically diverse frogs native to the humid forests of Madagascar. We here present a monographic revision of the taxonomy and natural history of these frogs. We first provide morphological diagnoses and contents of the established species groups in Rhombophryne. We then integrate molecular phylogenetic data from mitochondrial and nuclear genetic markers, with morphometrics, bioacoustics, and micro-CT-based osteology, to describe seven new species from across Madagascar. This brings the number of species in the genus to 27. We have obtained DNA sequences from name-bearing specimens of 23 of these species, plus topotypical specimens of two further species; we used museomics methods to sequence name-bearing types of three species collected before 1976, as well as several other specimens of interest, allowing us to clarify taxonomic assignment of those individuals. In our treatments of all existing and new species, we provide new insights into their anatomy, diet, ecology, and distribution. We provide the first published key to the genus, which we hope will make their identification more straightforward. Finally, we suggest a revised conservation assessment in light of the data that we present. We estimate 24 of the 27 species to be threatened, with two species (R. kilonjy sp. nov. and R. matavy) probably worthy of being classified as ‘Critically Endangered’. Several candidate species remain taxonomically unaddressed, due to the poor representation of specimens in museum collections. We therefore emphasise the need for increased survey efforts to fill knowledge gaps in both the taxonomy and the natural history of these frogs.

We describe a new species of treefrog of the Boophis goudotii group from Ivohiboro, a sacred forest in the Southeast of Madagascar and recently established protected area. Based on a molecular phylogeny inferred from DNA sequences of the mitochondrial 16S rRNA gene, Boophis samuelsabini sp. n. is sister to the clade of B. madagascariensis and B. roseipalmatus but differs from these species by genetic distances of 4.8-6.3%. The new species has an advertisement call consisting of various note types similar to its closest relatives, B. madagascariensis and B. roseipalmatus, but is distinguished morphologically from them by smaller body size and presence of a pattern of reticulated dermal folds on the dorsum. This discovery highlights the poor state of exploration of remnant highland forests in the South East of Madagascar which can be expected to harbour additional microendemic species in need of conservation measures.

The role of regional diversification versus the effect of migration in generating local species assemblages remains poorly known. Here, we contribute to the understanding of the role of colonisation and in situ diversification by studying an assemblage of miniaturised microhylid frogs of the genus Stumpffia Boettger, 1881, of which six species have been known to occur on Montagne d’Ambre, a volcanic mountain in the north of Madagascar. These six species are distributed over different, partly overlapping elevational levels. We examined this assemblage based on molecular data (16S mtDNA and Rag1 nDNA), new data on the elevational distribution among local Stumpffia species, and differences in advertisement calls. Our results revealed several genetic lineages constituting distinct species, including another species record for the mountain, S. mamitika Rakotoarison et al., 2017, as well as the new candidate species Stumpffia sp. aff. angeluci. This brings the total number of described species known to occur on the mountain to seven, four of which are micro-endemic. Our data indicate that one clade, consisting of four species, has arisen in situ as a microendemic radiation. We discuss alternative evolutionary scenarios for the biogeographic origin of the observed Stumpffia species.

Using an in silico data mining approach, we previously expanded the known diversity within the family Bornaviridae by identifying novel bornavirids in publicly available sequence datasets from bony and cartilaginous fish. Building on this discovery, we systematically screened numerous additional sequence datasets from fish, amphibians, reptiles, and birds in the Sequence Read Archive and a new RNA-seq dataset to further explore bornaviral diversity and evolutionary history. Our analysis identified nearly complete and partial bornaviral genomes across multiple host taxa, that represented either new viral variants, previously known viruses detected in so far unreported hosts/sources, or novel viruses. Several novel orthobornaviral genomes were identified in snake and lizard datasets. Sequences of the species Orthobornavirus alphapsittaciforme and Orthobornavirus serini were identified in avian datasets. We also found sequences of both known and possibly new species in the genus Cultervirus, which were detected in bony fish and, for the first time, in reptile and amphibian datasets. The identification of culterviruses in reptiles and amphibians suggests that this group of viruses, which was previously only known to be associated with fish, has a much wider host range. A genetically divergent bornaviral genome was discovered in the gold-striped salamander (Chioglossa lusitanica), possessing the genomic architecture of orthobornaviruses but likely representing a new genus within the family Bornaviridae. Interestingly, multiple distinct viral genomes identified in passerine birds were classified as carboviruses based on sequence similarities, but they exhibited distinct genomic features and lacked the genes that code for glycoprotein (G) and, in some cases, the accessory protein (X) and/or matrix protein (M). Subsequent screening of samples from passerine birds further confirmed these findings and showed that these carboviral sequences likely represent genuine viruses rather than endogenous bornaviral elements. Interestingly, these carboviruses appear to co-occur with enveloped viruses in potential co-infection or helper virus scenarios. These findings contribute substantially to our understanding of Bornaviridae diversity, their evolutionary adaptation as well as modes of transcriptional regulation.

Three enzymes from African frogs with close sequence homology to avian farnesyl pyrophosphate synthase (FPPS) were studied for their function. All three enzymes converted (2Z,6E)-FPP into several bisabolane sesquiterpenes, with bisabolol and anymol as main products. Experiments with FPPS from Escherichia coli confirmed the same function, suggesting that the observed activity may be of general relevance for FPP synthases. Only one of the frog enzymes showed significant activity in the biosynthesis of FPP from terpene monomers, which may point to an evolutionary process that resulted in a functional switch from an FPPS to a bisabolane synthase. The physiological relevance of these findings is supported by the identification of bisabolol/anymol in gland extracts.

We revise the molecular variation and taxonomy of an assemblage of lineages of endemic Malagasy cophyline microhylid frogs, previously considered to be allied to Platypelis tetra. Based on DNA sequences obtained from the P. tetra holotype via a museomics approach and further complementary DNA sequences of other specimens obtained by Sanger sequencing, we genetically characterize the species and reveal at least two additional genetic lineages associated to it. These differ by uncorrected pairwise distances of 4.4-5.0% in a fragment of the mitochondrial 16S rRNA gene and require taxonomic revision in future work. A further lineage previously assigned to P. tetra differs by 16S distances of 7.1-7.8% and occupies an isolated phylogenetic position. We here formally name and describe this new species from the Sorata Massif as Platypelisefatrasp. nov. and thereby increase the number of nominal Platypelis species to 18. We provide a description of its skeleton based on a micro-computed tomography scan of a paratype, which is the first detailed osteological description of a Platypelis species, and identify some possibly diagnostic osteological differences compared to P. tetra. We furthermore provide an updated advertisement call description for P. tetra from its type locality and briefly discuss the status of a divergent population from Ambodivoangy that we tentatively assign to P. tetra pending future study.

The genus Lygodactylus currently contains 33 Malagasy species, all of them endemic to the region. Several of these are poorly known, and sometimes known only from their name-bearing type specimens. Molecular genetic work has revealed the existence of numerous highly divergent but not yet formally named lineages. Here, we report on the finding of L. ornatus Pasteur, 1965, a species that was previously known only from the holotype and a few field observations made in 1994. The species was observed to be relatively common in rocky areas at a location near the rural town of Mandritsara and is characterized by a conspicuous color pattern, with bright yellow throat marked with 36 mostly interrupted sharp black transversal stripes, and an orange underside of the tail. Phylogenetically, the species was found to be related to L. arnoulti, L. blancae and L. heterurus, within the L. verticillatus group, despite lacking the distinct tail whorls typical of the species belonging to this group. We discovered an additional species-level lineage of Lygodactylus in the same clade, for which we provide a formal taxonomic description. The genetically highly distinct Lygodactylus namoroka sp. nov. was collected in the Tsingy de Namoroka National Park and is characterized by a throat pattern with poorly marked dark gray longitudinal stripes, and a distinct contact between the lateral parts of the mental with the postmental scales, which appears to be unique for this species within the L. verticillatus group.

Malagasy sand-swimming skinks represent several highly specialized and previously underexplored clades within the monophyletic radiation of scincine lizards of this island. Through comprehensive phylogenomic analyses including newly collected samples, we clarify the evolutionary relationships among these taxa, delimit species boundaries, and formally describe two new species: Voeltzkowia volontany sp. nov. and Voeltzkowia shaihulud sp. nov. Our findings on the genus Voeltzkowia and the equally specialized sand-swimmer genus Grandidierina suggest that species diversity within these psammophilous skinks is underestimated and shaped by a high degree of allopatry. Intriguingly, this unexpected diversity is geographically structured along a newly identified landscape feature, for which we herein coin the name 'White Sand Belt'. It consists of an aligned series of discrete, isolated white sand patches spanning >1500 km along western Madagascar. The White Sand Belt appears to follow the contours of the western sedimentary basins of the island, and we propose the hypothesis that it represents a key environmental factor in the diversification and distribution of Malagasy sand-swimming skinks and, possibly, other psammophilous organisms.

The cophyline microhylid frog genus Anilany was established as a monotypic genus in 2016 for the miniaturised species Anilany helenae (VALLAN, 2000), from the type locality Ambohitantely, a patch of rainforest surrounded by savannah in central Madagascar. Fieldwork conducted over the past two decades identified three unexpected populations from Bemaraha, Mahajanga, and Beanka from limestone caves near sea level in arid western and northwestern Madagascar, which were assigned to the genus Anilany based on diagnostic morphological features. We generated new data for specimens of the Ambohitantely, Bemaraha, and Mahajanga populations to test if all three populations belong to one or multiple species, studying their genetic variability based on mitochondrial (16S rRNA, COI) and nuclear (BDNF, RAG-1) genes, as well as morphological and osteological data. We identify several previously unknown diagnostic characters of the skeleton of Anilany compared to its closest relatives, Rhombophryne and Stumpfa, but no skeletal features that can be used to reliably distinguish among Anilany populations. Based on concordant genetic and morphological differences, we formally describe the population from the limestone karsts of Tsingy de Bemaraha National Park, formerly considered candidate species Anilany sp. Ca14, as a new species, Anilany karsticola sp. n. It can be distinguished from other Anilany lineages by larger size and shorter relative tibia length, uncorrected p-distances in DNA sequences of the 16S gene amounting to 2.6% and a lack of allele sharing in the analysed fragments of the nuclear genes BDNF and RAG-1. More data, especially advertisement call recordings and additional specimens, are required from other locations for a more thorough assessment of the genus and the distribution of its species.

Madagascar velvet geckos, genus Blaesodactylus, are classified in six species distributed over low-elevation sites across most of Madagascar. Based on DNA sequences of one mitochondrial and two nuclear-encoded gene fragments obtained from numerous newly collected tissue samples, we provide an updated review of their molecular variation. Our genetic screening confirms an extended distribution of B. ambonihazo, so far only known from its type locality Ankarafantsika, now reaching northwards to the Sahamalaza Peninsula. Compared to previously available molecular data, we also verify minor range extensions of B. boivini (southeastwards to Bezavona), B. antongilensis (northwards to the Marojejy Massif), and the B. sakalava complex. Samples assigned to B. sakalava according to current taxonomy fell into two mitochondrial sister lineages differing by about 8.5% pairwise distances in the 16S rRNA gene, lack of haplotype sharing in the nuclear-encoded CMOS gene, and various subtle but consistent differences in body proportions and scalation. We conclude that the lineage occurring in the South of Madagascar, encompassing known locations south of Morombe, corresponds to B. sakalava sensu stricto based on its type locality and morphological characters of its name-bearing type; and describe the lineage occurring in the West of Madagascar north of Morombe as a new species, B. ganzhorni sp. nov.

The Lygodactylus tolampyae complex currently contains four nominal species of dwarf geckos from the North West and West of Madagascar. These four species are genetically distinct but have been flagged as morphologically cryptic, with only very subtle differences in scale counts between them. Based on new collections and extended molecular datasets, we here investigate the genetic and morphological differentiation of this species complex. We find seven deeply divergent mitochondrial lineages separated by 9.718.0% uncorrected pairwise distance in the 16S rRNA gene which correspond to the four recognized species and three further candidate species. Not a single instance of haplotype sharing between any of these lineages was found in four nuclear-encoded gene fragments, despite several of these lineages occurring in close geographic proximity or even syntopy. A Principal Component Analysis of morphometric measurements and meristic characters confirmed a wide overlap of most species in morphospace, but the new data also confirm statistically significant differences between numerous lineages in scale counts and morphometric ratios. We conclude that the three candidate species previously known only from very limited material and named Lygodactylus sp. 25, L. sp. 28 and L. sp. 29 correspond to distinct species which we formally name as L. andavambato sp. nov., L. anjajavy sp. nov., and L. arnei sp. nov. One of the new species, L. andavambato sp. nov. from the limestone karst of the Tsingy de Namoroka, has a peculiar phenotype with slender body and legs, and regular dark crossbands on the tail, differing from all other species in the L. tolampyae complex while superficially reminding L. rarus, a species from the limestone karst massif of Ankarana but belonging to another species group in Lygodactylus. The taxonomic progress, in only a few years, from a single species L. tolampyae to now seven species in this complex calls for further revisionary work, including more fieldwork to survey forest fragments and rocky outcrops across Madagascar which may host yet unknown locally endemic species of dwarf geckos.

The Gephyromantis moseri complex, classified in the mantellid subgenus Duboi mantis , currently contains one species of frog, G. moseri (Glaw & Vences, 2002) from the Andasibe area in the Northern Central East of Madagascar, as well as several genetically divergent populations from the North East that have been provisionally assigned to the species. We here analyse DNA sequences of one mitochondrial (16S rRNA) and one nuclear -encoded gene (RAG -1), morphology, and advertisement calls of newly collected material of this species complex from various localities in Madagascar. Based on this integrative evidence, in particular concordant nuclear gene differentiation between seven highly divergent (> 4 %) mitochondrial lineages, as well as differences in advertisement call structure, body size and head shape between some of these lineages, we conclude that the G. moseri complex contains several additional species of which four are formally named and described in this study: G. fuscus sp. nov., a rather small -sized species sister to G. moseri , occurring in two sites (Mahasoa and the western part of the Makira Reserve), G. ma kira sp. nov., a species known from only one available voucher specimen from eastern Makira, G. bemiray sp. nov. from eastern Makira, Masoala, and Ambolokopatrika; and G. ampondo sp. nov. from Marojejy in the North East. Two further lineages for which voucher specimens were not available in the framework of this study are considered unconfirmed candidate species G. sp. Ca19 and G. sp. Ca33, pending the collection of further material. The revision of the G. moseri complex adds to the diversity of Duboimantis and once more demonstrates the existence of secretive or genuinely rare restricted -range species among the Malagasy frogs whose inventory can only be completed by further fieldwork and integrative taxonomic research.

The Malagasy stream-breeding treefrog species Boophis marojezensis contains bioacoustically and genetically highly divergent populations. Some of these populations have been defined as candidate species and emit somewhat bizarre advertisement calls consisting of multiple whistle-notes. We here enable a long-overdue taxonomic revision of this species complex by applying a museomics approach to sequence DNA from the holotype of B. marojezensis. Based on an integrative approach that combines divergence levels in mitochondrial DNA and in three nuclear-encoded genes, morphological data, and bioacoustic comparisons, we conclude that eight different species exist in this complex, seven of which are formally described herein as new. Although morphological differences between species are small and mainly separate small-sized from larger-sized species, conclusive evidence for the new species comes from their sympatric and sometimes syntopic occurrence without haplotype sharing in three nuclear genes and under maintenance of bioacoustic differences. Uncorrected genetic divergences in the mitochondrial 16S rRNA gene are >3% in almost all cases, and in some cases up to 8%. In reference to the otherworldly sounds by which these frogs fill Malagasy rainforests, some known only from unprotected sites and require adequate conservation management.

ABSTRACT The genomes of 21 Pedobacter strains isolated from the European salamander Salamandra salamandra and different Madagascan frog species were sequenced using Illumina sequencing. Here, we report their draft genome sequences (~4.7–7.2 Mbp in size) to allow comparative genomics and taxonomic assignment of these strains.

The area around the Malagasy village of Andasibe, which includes Analamazaotra-Mantadia National Park as well as other protected areas, is characterized by very species-rich and well-studied communities of animals and plants, but new species are still regularly discovered. Three species of phytotelmic frogs of the subgenus Pandanusicola in the genus Guibemantis are known from this area, G. flavobrunneus, G. liber, and G. pulcher. Further Pandanusicola frogs from this area have been provisionally assigned to G. bicalcaratus or G. albolineatus, pending detailed taxonomic review. During preliminary exploration of the ecology of these specialized frogs that live and reproduce in the leaf axils of Pandanus screw pines, we noticed the syntopic presence of two differently colored and differently sized Pandanusicola in Andasibe that could not be unambiguously assigned to any known species. A genetic screening revealed that these correspond to yet two further species in the area. Based on our data, seven species of Pandanusicola occur in Andasibe and nearby forests: (1) G. liber, the only non-phytotelmic species of the subgenus in the region; (2) G. flavobrunneus which is the largest species and characterized by a diagnostic yellowish brown dorsal pattern; (3) G. pulcher, characterized by translucent-green color with purplish brown spotting not observed in any other species in the area; (4) G. methueni, a brownish species usually lacking contrasted dorsolateral bands that differs from the other species in the area by emitting a characteristic trill-like advertisement call series (rather than clicks or chirps) and according to our data is widespread along Madagascars east coast; as well as three new species: (5) G. ambakoana sp. nov., a brownish species, typically with contrasted incomplete light dorsolateral bands and with single click-like advertisement calls; (6) G. vakoa sp. nov., a species that is equally brownish but lacks contrasted light dorsolateral bands and that has single click-like advertisement calls of very short duration; and (7) G. rianasoa sp. nov., a species that is smaller sized and has less distinct femoral glands than all the others, and emits a short series of soft chirp-like advertisement calls. All these species are genetically highly distinct, with >5% uncorrected pairwise distances in the mitochondrial 16S rRNA gene, and lack of haplotype sharing in two nuclear-encoded genes. The co-occurrence of seven Pandanusicola frogs in a relatively small geographic area is unprecedented in Madagascar and calls for in-depth studies of a possible differentiation in habitat use and life history.

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

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.