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Based on sequences of three mitochondrial and two nuclear-encoded genes, we examine genetic variation in the leaf tailed geckos Uroplatus sameiti and U. sikorae, and morphological and chromatic characteristics of the genetic clusters identified. The mitochondrial phylogeny reveals a puzzling diversity of 16 deep lineages (4 in U. sameiti and 12 in U. sikorae) differing by 2.9–9.9% uncorrected pairwise distance in a fragment of the 16S rRNA gene. Populations from Analalava in the North and Zahamena in the Northern Central East form two mitochondrial lineages clustering with U. sameiti but being deeply divergent (>8% 16S distance); however, no information on their morphology is available. In U. sikorae, the mitochondrial lineages identified form several major geographic clades, two of which (from the northernmost and southernmost populations, respectively) received substantial support in the phylogenetic analysis. No instance of sympatry of two or more mitochondrial lineages was observed, precluding an unambiguous assessment of species status under the biological species criterion without experimental approaches or detailed hybrid zone analyses. In the fragment of the nuclear encoded gene SACS we observed haplotype sharing between species and mitochondrial lineages, while in the fragment of KIAA1239 no haplotype sharing was detected although neither species nor mitochondrial lineages formed coherent phylogroups in the respective network. A screening of colour patterns from live photos, partly of the genotyped individuals, confirmed a large variation within species and populations, with a possible sexual dichromatism where a longitudinally striped phenotype is restricted to males. All individuals from populations of the U. sikorae clade from the Southern Central East and South East had an unpigmented oral mucosa just like U. sameiti, while all other U. sikorae populations are characterized by a black oral mucosa pigmentation. The extremely strong phylogeographic structure in the U. sikorae complex without obvious species-level divergences is unprecedented for large-sized squamates in Madagascar and calls for further taxonomic scrutiny using phylogenomic approaches; and it exemplifies how the loss of any major block of the remaining rainforests in Madagascar will inevitably lead to a substantial loss of genetic diversity – even if often intraspecific – in rainforest-specialized species. [ABSTRACT FROM AUTHOR]

How environmental factors shape patterns of biotic diversity in tropical ecosystems is an active field of research, but studies examining the possibility of ecological speciation in terrestrial tropical ecosystems are scarce. We use the isolated rainforest herpetofauna on the Montagne d'Ambre (Amber Mountain) massif in northern Madagascar as a model to explore elevational divergence at the level of populations and communities. Based on intensive sampling and DNA barcoding of amphibians and reptiles along a transect ranging from ca. 470–1470 m above sea level (a.s.l.), we assessed a main peak in species richness at an elevation of ca. 1000 m a.s.l. with 41 species. The proportion of local endemics was highest (about 1/3) at elevations >1100 m a.s.l. Two species of chameleons (Brookesia tuberculata, Calumma linotum) and two species of frogs (Mantidactylus bellyi, M. ambony) studied in depth by newly developed microsatellite markers showed genetic divergence up the slope of the mountain, some quite strong, others very weak, but in each case with genetic breaks between 1100 and 1270 m a.s.l. Genetic clusters were found in transect sections significantly differing in bioclimate and herpetological community composition. A decrease in body size was detected in several species with increasing elevation. The studied rainforest amphibians and reptiles show concordant population genetic differentiation across elevation along with morphological and niche differentiation. Whether this parapatric or microallopatric differentiation will suffice for the completion of speciation is, however, unclear, and available phylogeographic evidence rather suggests that a complex interplay between ecological and allopatric divergence processes is involved in generating the extraordinary species diversity of Madagascar's biota. Our study reveals concordant patterns of diversification among main elevational bands, but suggests that these adaptational processes are only part of the complex of processes leading to species formation, among which geographical isolation is probably also important. [ABSTRACT FROM AUTHOR]

The study of diamond frogs (genus Rhombophryne, endemic to Madagascar) has been historically hampered by the paucity of available specimens, because of their low detectability in the field. Over the last 10 years, 13 new taxa have been described, and 20 named species are currently recognized. Nevertheless, undescribed diversity within the genus is probably large, calling for a revision of the taxonomic identification of published records and an update of the known distribution of each lineage. Here we generate DNA sequences of the mitochondrial 16S rRNA gene of all specimens available to us, revise the genetic data from public databases, and report all deeply divergent mitochondrial lineages of Rhombophryne identifiable from these data. We also generate a multi-locus dataset (including five mitochondrial and eight nuclear markers; 9844 bp) to infer a species-level phylogenetic hypothesis for the diversification of this genus and revise the distribution of each lineage. We recognize a total of 10 candidate species, two of which are identified here for the first time. The genus Rhombophryne is here proposed to be divided into six main species groups, and phylogenetic relationships among some of them are not fully resolved. These frogs are primarily distributed in northern Madagascar, and most species are known from only few localities. A previous record of this genus from the Tsingy de Bemaraha (western Madagascar) is interpreted as probably due to a mislabelling and should not be considered further unless confirmed by new data. By generating this phylogenetic hypothesis and providing an updated distribution of each lineage, our findings will facilitate future species descriptions, pave the way for evolutionary studies, and provide valuable information for the urgent conservation of diamond frogs. [ABSTRACT FROM AUTHOR]

Traditionally considered the earliest-diverging group of snakes, scolecophidians are central to major evolutionary paradigms regarding squamate feeding mechanisms and the ecological origins of snakes. However, quantitative analyses of these phenomena remain scarce. Herein, we therefore assess skull modularity in squamates via anatomical network analysis, focusing on the interplay between 'microstomy' (small-gaped feeding), fossoriality, and miniaturization in scolecophidians. Our analyses reveal distinctive patterns of jaw connectivity across purported 'microstomatans', thus supporting a more complex scenario of jaw evolution than traditionally portrayed. We also find that fossoriality and miniaturization each define a similar region of topospace (i.e., connectivity-based morphospace), with their combined influence imposing further evolutionary constraint on skull architecture. These results ultimately indicate convergence among scolecophidians, refuting widespread perspectives of these snakes as fundamentally plesiomorphic and morphologically homogeneous. This network-based examination of skull modularity—the first of its kind for snakes, and one of the first to analyze squamates—thus provides key insights into macroevolutionary trends among squamates, with particular implications for snake origins and evolution. [ABSTRACT FROM AUTHOR]

Whole genome sequences are beginning to revolutionize our understanding of phylogenetic relationships. Yet, even whole genome sequences can fail to resolve the evolutionary history of the most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure the phylogenetic history of the group. To overcome such challenges, one emerging strategy is to integrate results across different methods. Most such approaches have been implemented on reduced representation genomic data sets, but whole genomes should provide the maximum possible evidence approach. Here, we test the ability of single nucleotide polymorphisms extracted from whole genome resequencing data, implemented in an integrative genomic approach, to resolve key nodes in the phylogeny of the mbuna, rock-dwelling cichlid fishes of Lake Malaŵi, which epitomize the phylogenetic intractability that often accompanies explosive lineage diversification. This monophyletic radiation has diversified at an unparalleled rate into several hundred species in less than 2 million years. Using an array of phylogenomic methods, we consistently recovered four major clades of mbuna, but a large basal polytomy among them. Although introgression between clades apparently contributed to the challenge of phylogenetic reconstruction, reduction of the data set to nonintrogressed sites still did not help to resolve the basal polytomy. On the other hand, relationships among six congeneric species pairs were resolved without ambiguity, even in one case where existing data led us to predict that resolution would be difficult. We conclude that the bursts of diversification at the earliest stages of the mbuna radiation may be phylogenetically unresolvable, but other regions of the tree are phylogenetically clearly supported. Integration of multiple phylogenomic approaches will continue to increase confidence in relationships inferred from these and other whole-genome data sets. [Incomplete lineage sorting; introgression; linkage disequilibrium; multispecies coalescence; rapid radiation; soft polytomy.] [ABSTRACT FROM AUTHOR]

In the processes that give rise to new species, changes first occur at the population level. But with the continuous nature of the divergence process, change in biological properties delimiting the shift from "individuals of divergent populations" towards "individuals of distinct species", as well as abiotic factors driving the change, remain largely ambivalent. Here we study diversification processes at the population level in a semi-aquatic frog, Mantidactylus (Brygoomantis) bellyi, across the diverse vegetation types of Montagne d'Ambre National Park (MANP), Madagascar. Genetic diversity was assessed with seven newly developed microsatellite markers as well as mitochondrial DNA sequences and concordance with patterns of ecological, morphological, and bioacoustic divergence evaluated. We found M. bellyi lacking mitochondrial differentiation within MANP, while microsatellite datasets partitioned them into three highly differentiated, geographically separated subpopulations (with indications for up to five subpopulations). The molecular grouping–primarily clustering individuals by geographic proximity–was coincident with differences in mean depth and width of waters, suggesting a possible role of fluvial characteristics in genetic exchange in this stream-breeding species. Genetic clustering not consistent with differences in call properties, except for dominant call frequencies under the two-subpopulations model. Morphological divergence was mostly consistent with the genetic clustering; subpopulations strongly differed by their snout-vent length, with individuals from high-elevation subpopulations smaller than those from populations below 1000 m above sea level. These results exemplify how mountains and environmental conditions might primarily shape genetic and morphological divergence in frog populations, without strongly affecting their calls. [ABSTRACT FROM AUTHOR]

Although taxonomic progress on the frogs of Madagascar is currently proceeding at an unprecedented pace, the goal of completing the amphibian inventory of this hyper-diverse island is still far off. In part this is because more new species continue to be discovered at a high rate, in some cases within well-studied areas. Here, I describe Rhombophryne ellae sp. nov., a new species of diamond frog discovered in Montagne d'Ambre National Park in northern Madagascar in 2017. This new species is highly distinctive in having orange flash-markings on its hindlimbs (not known from any described species of Rhombophryne), and large, black inguinal spots (larger than in all other described Rhombophryne species). It is separated from all named species of Rhombophryne by a substantial uncorrected pairwise distance in the 16S rRNA mitochondrial barcode marker (> 7%) and is most closely related to an undescribed candidate species from Tsaratanana in northern Madagascar. Rhombophryne ellae sp. nov. adds another taxon to the growing list of cophyline microhylids that have red to orange flash-markings, the function of which remains unknown and which has clearly evolved repeatedly in this radiation. The discovery of such a distinctive species within a comparatively well-studied park points toward the low detectability of semi-fossorial frogs and the role of inclement weather in increasing that detectability. [ABSTRACT FROM AUTHOR]

Taxonomy is the cornerstone of extinction risk assessments. Currently, the IUCN Red List treats species complexes either under a single overarching species name—resulting in an unhelpfully broad circumscription and underestimated threat assessment that does not apply to any one species lineage—or omits them altogether—resulting in the omission of species that should be assessed. We argue that taxonomic uncertainty alone, as in species complexes, should be grounds for assessment as Data Deficient (DD). Yet, use of the DD category is currently discouraged, resulting in assessments based on poor data quality and dismissal of the importance of taxonomic confidence in conservation. This policy may be leading to volatile and unwarranted assessments of hundreds of species across the world, and needs to be revised. To illustrate this point, we here present a partial taxonomic revision of torrent frogs from eastern Madagascar in the Mantidactylus subgenus Hylobatrachus. Two named species, Mantidactylus (Hylobatrachus) lugubris and M. (H.) cowanii, and several undescribed candidate species are recognised, but the application of the available names has been somewhat ambiguous. In a recent re-assessment of its conservation status, M. (H.) lugubris was assessed including all complex members except M. (H.) cowanii within its distribution, giving it a status of Least Concern and distribution over most of eastern Madagascar. After describing two of the unnamed lineages as Mantidactylus (Hylobatrachus) atsimo sp. nov. (from southeastern Madagascar) and Mantidactylus (Hylobatrachus) petakorona sp. nov. (from the Marojejy Massif in northeastern Madagascar), we show that Mantidactylus (Hylobatrachus) lugubris is restricted to the central east of Madagascar, highlighting the inaccuracy of its current Red List assessment. We propose to re-assess its status under a more restrictive definition that omits well-defined candidate species, thus representing the actual species to which its assessment refers, to the best of current knowledge. We recommend that for species complexes in general, (1) nominal lineages that can be confidently restricted should be assessed under the strict definition, (2) non-nominal species-level lineages and ambiguous names should be prioritised for taxonomic research, and (3) ambiguous names should be assessed as DD to highlight the deficiency in data on their taxonomic status, which is an impediment to their conservation. This would reduce ambiguity and underestimation of threats involved in assessing species complexes, and place the appropriate emphasis on the importance of taxonomy in anchoring conservation. [ABSTRACT FROM AUTHOR]

Stump-toed frogs (genus Stumpffia Boettger, 1881) are a diverse group of small-bodied frogs endemic to Madagascar. Seven species of this genus occur on Marojejy, a steep massif in northeastern Madagascar. Here we examine the elevational distribution, phylogenetic position, biogeographic origin, and genetic differentiation of this Stumpffia assemblage. We show that none of these species is another's closest relative, but rather they are all independent lineages that probably colonised the Marojejy Massif through repeated immigration events. All of the lineages on Marojejy are most closely related to species south and southwest of the massif, except one lineage, formerly known as Stumpffia sp. Ca07, but here assigned to S. sorata as a deep conspecific lineage (and referred to as S. cf. sorata), which occurs also in Sorata, 90 km north of Marojejy. The species on Marojejy are typically restricted to narrow elevational ranges, but at least two species, S. cf. sorata and S. tridactyla, occur over elevations spanning 1000 metres. We assessed the genetic variability of these populations, and found considerable haplotype separation in fragments of the mitochondrial 16S rRNA and nuclear Rag-1 genes, suggesting some disruption of gene flow associated with elevation. We discuss the biogeographic implications of our findings and, based on previously published data, the evolution of non-overlapping bioacoustic parameters among the diverse assemblage of Stumpffia species on the Marojejy massif. [ABSTRACT FROM AUTHOR]

Miniaturised frogs form a fascinating but poorly understood amphibian ecomorph and have been exceptionally prone to taxonomic underestimation. The subfamily Cophylinae (family Microhylidae), endemic to Madagascar, has a particularly large diversity of miniaturised species which have historically been attributed to the single genus Stumpffia largely based on their small size. Recent phylogenetic work has revealed that several independent lineages of cophyline microhylids evolved towards highly miniaturised body sizes, achieving adult snout–vent lengths under 16 mm. Here, we describe five new species belonging to three clades that independently miniaturised and that are all genetically highly divergent from their relatives: (i) a new genus (Mini gen. nov.) with three new species from southern Madagascar, (ii) one species of Rhombophryne, and (iii) one species of Anodonthyla. Mini mum sp. nov. from Manombo in eastern Madagascar is one of the smallest frogs in the world, reaching an adult body size of 9.7 mm in males and 11.3 mm in females. Mini scule sp. nov. from Sainte Luce in southeastern Madagascar is slightly larger and has maxillary teeth. Mini ature sp. nov. from Andohahela in southeast Madagascar is larger than its congeners but is similar in build. Rhombophryne proportionalis sp. nov. from Tsaratanana in northern Madagascar is unique among Madagascar’s miniaturised frogs in being a proportional dwarf, exhibiting far less advanced signs of paedomorphism than other species of similar size. Anodonthyla eximia sp. nov. from Ranomafana in eastern Madagascar is distinctly smaller than any of its congeners and is secondarily terrestrial, providing evidence that miniaturisation and terrestriality may be evolutionarily linked. The evolution of body size in Madagascar’s microhylids has been more dynamic than previously understood, and future studies will hopefully shed light on the interplay between ecology and evolution of these remarkably diverse frogs. [ABSTRACT FROM AUTHOR]

We describe a new species of dwarf chameleon from the Brookesia minima species group. Brookesia tedi sp. n. occurs above 1300 m above sea level on the Marojejy massif in northeastern Madagascar. It is genetically sister to B. peyrierasi, a species occurring in lowlands around the Baie de Antongil, but is genetically strongly divergent from that species in both nuclear (c-mos) and mitochondrial (16S, ND2) genes, and morphologically in its smaller size and distinctly different hemipenis. It is the second species of the B. minima species group from Marojejy National Park, but is not known to occur in syntopy with the other species, B. karchei, due to elevational segregation. [ABSTRACT FROM AUTHOR]

We examine the taxonomic status of two Malagasy leaf chameleon taxa, Brookesia antakarana Raxworthy & Nussbaum, 1995 and B. ambreensis Raxworthy & Nussbaum, 1995, integrating morphological and genetic evidence. Specimens assigned to these species occur in syntopy in Montagne d'Ambre, northern Madagascar, and were originally described based on differences in the shape of their pelvic shields. We found that the shape of these shields falls on a continuous spectrum, and detected only weak differences between the two taxa in a few other morphological features, all of which were correlated with shield length. Members of the two taxa (as assigned based on pelvic shield morphology) also showed extensive haplotype sharing in one nuclear and one mitochondrial marker. We conclude that at present there is no convincing evidence that these species are distinct, and act as first revisers in the sense of the International Code of Zoological Nomenclature to place B. ambreensis into the synonymy of B. antakarana [ABSTRACT FROM AUTHOR]

We describe a large and distinctive new treefrog species with blue webbing from the west coast of the Masoala peninsula in northeastern Madagascar. Boophis masoala sp. n. is morphologically similar to the other species of the Boophis albilabris group but can be distinguished from them easily by several chromatic characters of the eyes. Despite its similar morphology, it is genetically highly differentiated (10.5-13.3% pairwise p-distance in a segment of the 16S rRNA gene) from all other species in the B. albilabris group including the morphologically most similar Boophis praedictus. Both species share the blue webbing between toes and are distributed on the Masoala peninsula, but so far were not found in close sympatry. Although we recorded the new species only from the unprotected areas near the coast, we are confident that it also occurs within the adjacent Masoala National Park. We discuss the importance of eye colouration as a predictor of specific distinctness in the genus Boophis and that of webbing colouration as taxonomic characters of large treefrogs. Based on a micro-CT scan we provide a comprehensive description of the osteology of the new species, which is the first for any Boophis species, and furthermore describe its distress call which consists of three distinct sections corresponding to (1) the starting phase with closed mouth, (2) the opening of the mouth and (3) the final section with an open mouth. [ABSTRACT FROM AUTHOR]

We describe a new frog species of the genus Guibemantis, subgenus Pandanusicola, from Marojejy National Park in northeastern Madagascar. Guibemantis milingilingy, the new species, exhibits high genetic divergence from all other described species of Guibemantis based on DNA sequences of a fragment of the mitochondrial 16S rRNA gene. This new species inhabits Pandanus plants like the majority of other members of this subgenus, but is found at much higher elevations (2026 m a.s.l.). It differs from its closest relative, G. punctatus, by the lack of speckled or spotted dorsal patterns and by the presence of a distinctly dark tympanum. As a high-elevation species, it is likely to be a species sensitive to climate change, similar to other montane endemics in Madagascar. [ABSTRACT FROM AUTHOR]

We describe a new species of the genus Gephyromantis, subgenus Vatomantis (Mantellidae, Mantellinae), from moderately high elevation (1164-1394 m a.s.l.) on the Marojejy, Sorata, and Andravory Massifs in northern Madagascar. The new species, Gephyromantis (Vatomantis) lomorina sp. n. is highly distinct from all other species, and was immediately recognisable as an undescribed taxon upon its discovery. It is characterised by a granular, mottled black and green skin, reddish eyes, paired subgular vocal sacs of partly white colour, bulbous femoral glands present only in males and consisting of three large granules, white ventral spotting, and a unique, amplitude-modulated advertisement call consisting of a series of 24-29 rapid, quiet notes at a dominant frequency of 5124-5512 Hz. Genetically the species is also strongly distinct from its congeners, with uncorrected pairwise distances =10 % in a fragment of the mitochondrial 16S rRNA gene to all other nominal Gephyromantis species. A molecular phylogeny based on 16S sequences places it in a clade with species of the subgenera Laurentomantis and Vatomantis, and we assign it to the latter subgenus based on its morphological resemblance to members of Vatomantis. We discuss the biogeography of reptiles and amphibians across the massifs of northern Madagascar, the evidence for a strong link between Marojejy and Sorata, and the role of elevation in determining community sharing across this landscape. [ABSTRACT FROM AUTHOR]

Frogs assigned to the monotypic genus Madecassophryne (Anura, Microhylidae, Cophylinae), and possibly belonging to Madecassophryne truebae, were found in December 2016 in two low-altitude localities, Ambahavala and Kapilavato, in the Anosy Mountain in southeastern Madagascar. This poorly known genus was described in 1974 based on osteology, and neither verifiably identified photos of living specimens nor molecular information were available until now. We here update the available information on these enigmatic frogs and provide new data on morphology, osteology, bioacoustics and observations on their habitat, together with a preliminary molecular phylogenetic study, suggesting that Madecassophryne is highly divergent from other members of the cophyline clade. [ABSTRACT FROM AUTHOR]

A recent study clarified several aspects of microhylid phylogeny by combining DNA sequences from Sanger sequencing and anchored phylogenomics, although numerous aspects of tree topology proved highly susceptible to data partition and chosen model. Although the phylogenetic results of the study were in conflict with previous publications, the authors made several changes to the taxonomy of Madagascar’s cophyline microhylids. We re-analyzed part of their data together with our own molecular and morphological data. Based on a supermatrix of 11 loci, we propose a new phylogeny of the Cophylinae, and discuss it in the context of a newly generated osteological dataset. We found several sample misidentifications, partially explaining their deviant results, and propose to resurrect the genera Platypelis and Stumpffia from the synonymy of Cophyla and Rhombophryne , respectively. We provide support for the previous genus-level taxonomy of this subfamily, and erect a new genus, Anilany gen. nov., in order to eliminate paraphyly of Stumpffia and to account for the osteological differences observed among these groups. Deep nodes in our phylogeny remain poorly supported, and future works will certainly refine our classification, but we are confident that these will not produce large-scale rearrangements. [ABSTRACT FROM AUTHOR]

We describe two new microhylid frog species of the genus Rhombophryne from the humid forests of northeastern Madagascar: Rhombophryne botabota sp. n. and R. savaka sp. n. The former is a medium-sized species, characterised by darkened lateral sides of the head (present in only one other congener, R. laevipes) and a unique combination of morphological, osteological, and molecular characters. The latter is a rather small species, characterised by medially undivided vomerine teeth with two large lateral diastemata, and presence of inguinal spots. Rhombophryne savaka sp. n. is the first species of the genus known from Makira Natural Park, and is reported also from Marojejy National Park and Ambolokopatrika (Betaolana Forest). Although its distribution range is relatively large compared to those of congeners, its known extent of occurrence is less than 2,000 km². As deforestation and habitat degradation persist as threats despite formal legal protection, we suggest an IUCN Red List status of Vulnerable for this species. Rhombophryne savaka sp. n. is possibly endemic to the Marojejy National Park, like several other Rhombophryne species, but is unusual in being found at a relatively low altitude. As such, it is likely to be at high risk of habitat loss and decreasing range, and we propose a status of Endangered for it. We discuss the affinities of these new species and the variability of calls in this genus. [ABSTRACT FROM AUTHOR]

The Rhombophryne serratopalpebrosa (Guibé 1975) species complex consists of numerous cryptic narrow-mouthed frogs (Microhylidae) mostly restricted to northern Madagascar. We here provide an updated phylogeny of the genus Rhombophryne, and formally define the R. serratopalpebrosa group, characterized by the possession of small, fleshy superciliary spines. We describe two new species belonging to this group from the Tsaratanana Massif in northern Madagascar: Rhombophryne ornata sp. nov. and R. tany sp. nov. Both of the new species have fewer superciliary spines above each eye than any other member of the group (2 vs. 3-4). Rhombophryne ornata sp. nov. is unusual in having fairly elaborate dorsal markings, and is unique in having reddish thighs. In contrast, R. tany sp. nov. is a truly cryptic species characterized by a combination of characters unique within the R. serratopalpebrosa group. Micro-CT scans revealed differences between the skeletons of these species and other members of the group: the pubis is unossified in both species, and R. ornata sp. nov. lacks ossification in the epiphyses of its limb bones and in many of its small bones. We give a full osteological description of these frog species to facilitate ongoing research concerning this group. Genetic data suggest that these two syntopic species might be sister to each other, but they show a substantial genetic divergence of 3.9% and 8.4% uncorrected pairwise distance in the mitochondrial 16S rRNA and cytochrome oxidase subunit I genes, respectively. As these species have a limited extent of occurrence, and are known only from a single location in a forest that is declining in quality, we propose they be listed as Vulnerable B1ab(iii) on the International Union for Conservation of Nature Red List. [ABSTRACT FROM AUTHOR]

The Madagascar-endemic microhylid genus Rhombophryne consists of a range of partly or completely fossorial frog species. They lead a poorly known, secretive lifestyle, and may be more diverse than previously thought. We describe a new species from the high altitude forests of the Sorata massif in north Madagascar with unusual characteristics for this genus; R. longicrus sp. n. has long, slender legs, unlike most of its fossorial or semi-fossorial congeners. The new species is closely related to R. minuta, a much smaller frog from the Marojejy massif to the southeast of Sorata with similarly long legs. We discuss the morphology of these species relative to the rest of the genus, and argue that it suggests adaptation away from burrowing and toward a more saltatorial locomotion and an accordingly more terrestrial lifestyle. If this is the case, then these frogs represent yet more ecological diversity within the already diverse Cophylinae. We recommend an IUCN Red List status of Endangered B1ab(iii) for R. longicrus sp. n., because it is known only from a single site in a forested area of roughly 250 km2, which is not yet incorporated into any protected area. [ABSTRACT FROM AUTHOR]

Premise of the study: Over the past 75 Myr, successive groups of plants have entered the "oil bee pollination niche," meaning that they depend on oil-collecting bees for their pollination. The highly dissimilar numbers of plant species and bee species involved in these mutualisms imply evolutionary host switching, asymmetric mutual dependencies, and uncoupled diversification. Among the clades with the best field data on oil bee behavior is the Angelonieae, which we here investigate to better understand the evolutionary time frame of this pollination syndrome. • Methods: We generated nuclear and plastid data matrices for 56% of the Angelonieae species (plus outgroups) and used Bayesian methods of molecular clock dating, ancestral state reconstruction, and biogeographic inference. • Key results: We found that Angelonieae have two major clades, Angelonia (including Monopera) and Basistemon, and Monttea, Melosperma, and Ourisia. • Conclusions: Angelonieae date back to the Uppermost Eocene, ca. 35 (26-47) Myr ago (Ma) and diversified in dry areas of southern South America; they switched from nectar to oil as a reward four or five times over the past 25 Ma. As predicted in a previous non-clock-dated study, dispersal to Australasia dates to the Miocene/Pliocene. [ABSTRACT FROM AUTHOR]

Taxonomic progress is often hindered by intrinsic factors, such as morphologically cryptic species that require a broad suite of methods to distinguish, and extrinsic factors, such as uncertainties in the allocation of scientific names to species. These uncertainties can be due to a wide variety of factors, including old and poorly preserved type specimens (which contain only heavily degraded DNA or have lost important diagnostic characters), inappropriately chosen type specimens (e.g. juveniles without diagnostic characters) or poorly documented type specimens (with unprecise, incorrect, or missing locality data). Thanks to modern sequencing technologies it is now possible to overcome many such extrinsic factors by sequencing DNA from name-bearing type specimens of uncertain assignment and assigning these to known genetic lineages. Here, we apply this approach to frogs of the Mantidactylus ambreensis complex, which was recently shown to consist of two genetic lineages supported by concordant differentiation in mitochondrial and nuclear genes. These lineages co-occur on the Montagne dʼAmbre Massif in northern Madagascar but appear to have diverged in allopatry. We use a recently published bait set based on three mitochondrial markers from all known Malagasy frog lineages to capture DNA sequences from the 127-year-old holotype of Mantidactylus ambreensis Mocquard, 1895. With the obtained sequences we are able to assign the name M. ambreensis to the lowland lineage, which is rather widespread in the rainforests of northern Madagascar, leaving the microendemic high-elevation lineage on Montagne d'Ambre in north Madagascar in need of description. We describe this species as Mantidactylus ambony sp. nov., differing from M. ambreensis in call parameters and a smaller body size. Thus, using target enrichment to obtain DNA sequence data from this old specimen, we were able to resolve the extrinsic (nomenclatural) hindrances to taxonomic resolution of this complex. We discuss the broad-scale versatility of this 'barcode fishing' approach, which can draw on the enormous success of global DNA barcoding initiatives to quickly and efficiently assign type specimens to lineages. [ABSTRACT FROM AUTHOR]

• Two deep genetic lineages detected in the Malagasy frog, Mantidactylus ambreensis. • Co-occurrence without admixture confirms separate species status of these lineages. • The lineages are segregated by elevation. • Phylogeography suggests this co-occurrence originated by secondary contact. • No evidence for sympatric or parapatric speciation. Madagascar's biota is characterized by a high degree of microendemism at different taxonomic levels, but how colonization and in-situ speciation contribute to the assembly of local species communities has rarely been studied on this island. Here we analyze the phylogenetic relationships of riparian frogs of the Mantidactylus ambreensis species complex, which is distributed in the north of Madagascar and was originally described from Montagne d'Ambre, an isolated mountain of volcanic origin, currently protected within Montagne d'Ambre National Park (MANP). Data from mitochondrial DNA, and phylogenomic data from FrogCap, a sequence capture method, independently confirm that this species complex is monophyletic within the subgenus Ochthomantis , and identify two main clades within it. These two clades are separated by 5.6–6.8% pairwise distance in the mitochondrial 16S rRNA gene and co-occur in MANP, with one distributed at high elevations (940–1375 m a.s.l.) and the other at lower elevations (535–1010 m a.s.l.), but show almost no haplotype sharing in the nuclear RAG1 gene. This occurrence in syntopy without admixture confirms them as independent evolutionary lineages that merit recognition as separate species, and we here refer to them as high-elevation (HE) and low-elevation (LE) lineage; they will warrant taxonomic assessment to confidently assign the name ambreensis to one or the other. Populations of the M. ambreensis complex from elsewhere in northern Madagascar all belong to the LE lineage, although they do occur over a larger elevational range than in Montagne d'Ambre (285–1040 m a.s.l.). Within LE there are several phylogroups (LE1–LE4) of moderately deep divergence (1.5–2.8% in 16S), but phylogroup LE4 that occurs in MANP has a deeply nested phylogenetic position, as recovered separately by mitochondrial and sequence capture datasets. This suggests that HE and LE did not diverge by a local fission of lower and upper populations, but instead arose through a more complex biogeographic scenario. The branching pattern of phylogroups LE1–LE4 shows a clear south-to-north phylogeographic pattern. We derive from these results a testable hypothesis of vicariant speciation that restricted the HE lineage to MANP and the LE candidate species to a climatic refugium further south, with subsequent northwards range expansion and secondary colonization of MANP by LE. These results provide an example for complex assembly of local microendemic amphibian faunas on Madagascar. [ABSTRACT FROM AUTHOR]

The subgenus Mantidactylus is a group of frogs endemic to Madagascar, including the largest anuran species on the island. Although these frogs are common and widely distributed, their taxonomy remains unclear. Two species are currently recognised, M. grandidieri and M. guttulatus, with another available name, Rana pigra, considered to be a synonym of M. grandidieri. However, molecular studies have suggested the presence of several cryptic species within the group. Additionally, due to the lack of prominent morphological features, allocating the available names to evolutionary lineages has proven challenging. In the present study, we take a first step towards solving these problems by using fragments of the 16S mitochondrial gene and RAG1 nuclear gene from all over the range of the subgenus to describe its genetic diversity. We also use a newly designed target enrichment laboratory protocol to sequence three mitochondrial fragments from five name-holding museum specimens (as old as 120 years) in order to determine to which lineages the existing names should be applied. The study of the 16S mitochondrial gene revealed 7 geographically separated lineages, distinct enough to be considered candidate species. Out of the five museum specimens analysed, four successfully yielded DNA sequences and could be attributed to one of the aforementioned lineages. Therefore, the name Mantidactylus grandidieri should be applied to the populations from North-Eastern Madagascar, while M. guttulatus refers to populations from inland localities along the Eastern coast of the island. On the other hand, the holotype of Rana pigra did not yield enough genetic material to allow definitive identification. While our data were not sufficient to assess the status of the four lineages distributed along the Eastern coast, the populations from North-Western Madagascar were highly distinct on both the mitochondrial and nuclear markers. We thus describe them as a new species, M. radaka sp. nov. [ABSTRACT FROM AUTHOR]

Phelsuma guttata and Paroedura gracilis are two species of geckos endemic to lowland and mid-elevation rainforests of the northern half of Madagascar's rainforest band. To test for concordant phylogeographic patterns in the two species and to assess intraspecific phylogeny and genetic diversity, we sequenced DNA from two mitochondrial genes (16S and ND4) and three nuclear genes (CMOS, PDC, RAG1). The mtDNA trees of both species suggest a strong phylogeographic split between phylogroups from the North East and Northern Central East biogeographic regions of Madagascar. However, this pattern is not mirrored in the nuclear gene dataset, where common alleles can be found across the two biogeographic regions. Private alleles characterize some of the northernmost and southernmost populations, especially the Montagne d'Ambre population of P. gracilis. In this species the two main mitochondrial clades agree with two distinct dorsal colour pattern phenotypes - striped versus cross-banded - separated at the junction of North East and Northern Central East. As no obvious geographic barrier to gene flow is apparent, the observed concordant phylogeographic pattern indicates that the border between these two regions might represent an area of secondary contact after divergence in refugia. Both nuclear and mitochondrial DNA reveal a higher genetic divergence among lineages of P. gracilis as compared to Ph. guttata, calling for a more detailed taxonomic assessment of the former species. [ABSTRACT FROM AUTHOR]

We describe a large new species of leaf-tailed gecko endemic to northern Madagascar. Uroplatus garamaso sp. n. is the sister species of U. henkeli but differs by a genetic divergence > 8% in the mitochondrial 16S rRNA gene, by the absence of haplotype sharing in four nuclear-encoded genes analyzed, a smaller body size, slightly narrower tail, a more pronounced yellowish/reddish iris colour in most individuals, and lack of black pigmentation on the tip of the tongue. The new species also appears to consistently differ from U. henkeli in genital morphology, with the apex of the hemipenis ending in two terminal elements consisting of 4-5 rotulae and longitudinal rows of calyces (versus an apex with irregularly distributed calyces and ending in two symmetrical structures consisting of two broader serrated fleshy elements in U. henkeli). We genetically confirm the occurrence of U. henkeli over a rather wide area, ranging from Tsingy de Bemaraha in the West to Nosy Be in the Sambirano region of northern Madagascar. Both, U. henkeli and the new species contain several deep mitochondrial lineages that are considered as conspecific due to extensive haplotype sharing and lack of obvious morphological differences among them. [ABSTRACT FROM AUTHOR]

We describe the new gecko species Paroedura neglecta sp. n. from the Tsingy de Bemaraha National Park in western Madagascar, belonging to the P. bastardi/tanjaka clade. The species in this clade are characterized by three light dorsal crossbands on the dorsum of juveniles and subadults whereas all other Paroedura species have four such bands. The new species differs from all species in the P. bastardi complex in having the nostril in contact with the rostral scale. It is most similar to the sympatric P. tanjaka, from which it differs by the presence of prominent dorsal tubercles arranged in regular longitudinal rows (versus rather irregular rows of dorsal tubercles), smaller size, details of the dorsal colour pattern and strong genetic divergence. [ABSTRACT FROM AUTHOR]

Roughly 18,000 species are described annually as new to science, while estimated extinction rates are comparable to or even exceeding these new discoveries. Considering the estimates of up to 15 million extant eukaryotic species on Earth, of which only about 2 million have been described so far, there has been a recent 'boom' of new potential approaches to more quickly discover and describe the millions of unknown species. This deficit is particularly noted in hyperdiverse taxa, as the current rate of species discovery is considered too slow. Recently, a 'minimalist' alpha taxonomic approach was proposed, relying solely on DNA barcoding and a habitus photograph, in a claimed effort to expedite the naming of new species to combat the so-called taxonomic impediment. In this paper, we point to limitations of minimalist taxonomy, present arguments in favour of the integrative approach, and finally explore a number of potential solutions to combat the taxonomic impediment in hyperdiverse taxa without sacrificing utility and quality for apparent speed and quantity. [ABSTRACT FROM AUTHOR]

Earth's biodiversity is still so poorly known that only about two million (Bánki et al., 2021) of the estimated nine million or more eukaryotic species (Larsen et al., 2017; Mora et al., 2011) have been described. Meierotto et al. (2019), when first proposing the minimalist approach, failed to merge their new DNA barcode-based species with existing species for which barcodes are not available. COI BARCODES ARE NOT SUITABLE ON THEIR OWN The default assumption of Sharkey, Janzen, et al. (2021) is that COI barcode clusters (Barcode Index Numbers [or BINs] computed by BOLD systems) equate to species. [Extracted from the article]

The Madagascan endemic subfamily Cophylinae in the family Microhylidae, is an example of a taxonomic group for which much is still to be discovered. Indeed, the cophyline frogs present a large portion of Madagascar’s cryptic and microendemic amphibian diversity, yet they remain understudied. A new redbellied species of the microhylid frog genus Stumpffia is described from the central plateau of Madagascar. Visual encounter surveys in Ambohitantely and Anjozorobe in 2019 and 2020 identified this previously unknown Stumpffia species, which closely resembles Stumpffia kibomena known from Andasibe in the east. Stumpffia lynnae sp. nov. adds another species to the red-bellied species complex, differing from S. kibomena by genetic differentiation in the mitochondrial 16S rRNA gene (3.6–3.9%) and distinct nuclear RAG1 haplotypes, as well as strongly by its advertisement call. The new species is known from across Ambohitantely Special Reserve and Anjozorobe Angavo protected area, but is known only from one complete specimen and eight individual tissue samples. Based on the rarity of the species, the small number of locations in which it has been found, and its disappearing forest habitat, its IUCN Red List classification is suggested as “Endangered”. This species is the first Stumpffia described from Madagascar’s central plateau, highlighting the importance of conserving the remnant forest fragments in this area and the ongoing need to survey and protect this threatened habitat type. [ABSTRACT FROM AUTHOR]

[Display omitted] • Multigene phylogeny of 56 Lygodactylus species reveals four well supported clades. • TIME calibrated analysis indicates multiple dispersal events between Madagascar and Continental Africa. • Morphological characters fail to reflect molecular phylogenetic results. • 15 New potential candidate sub-/species unveiled by this study double the number of undescribed Lygodactylus species. The 71 currently known species of dwarf geckos of the genus Lygodactylus are a clade of biogeographic interest due to their occurrence in continental Africa, Madagascar, and South America. Furthermore, because many species are morphologically cryptic, our knowledge of species-level diversity within this genus is incomplete, as indicated by numerous unnamed genetic lineages revealed in previous molecular studies. Here we provide an extensive multigene phylogeny covering 56 of the named Lygodactylus species, four named subspecies, and 34 candidate species of which 19 are newly identified in this study. Phylogenetic analyses, based on ∼10.1 kbp concatenated sequences of eight nuclear-encoded and five mitochondrial gene fragments, confirm the monophyly of 14 Lygodactylus species groups, arranged in four major clades. We recover two clades splitting from basal nodes, one comprising exclusively Malagasy species groups, and the other containing three clades. In the latter, there is a clade with only Madagascar species, which is followed by a clade containing three African and one South American species groups, and its sister clade containing six African and two Malagasy species groups. Relationships among species groups within these latter clades remain weakly supported. We reconstruct a Lygodactylus timetree based on a novel fossil-dated phylotranscriptomic tree of squamates, in which we included data from two newly sequenced Lygodactylus transcriptomes. We estimate the crown diversification of Lygodactylus started at 46 mya, and the dispersal of Lygodactylus among the main landmasses in the Oligocene and Miocene, 35–22 mya, but emphasize the wide confidence intervals of these estimates. The phylogeny suggests an initial out-of-Madagascar dispersal as most parsimonious, but accounting for poorly resolved nodes, an out-of-Africa scenario may only require one extra dispersal step. More accurate inferences into the biogeographic history of these geckos will likely require broader sampling of related genera and phylogenomic approaches to provide better topological support. A survey of morphological characters revealed that most of the major clades and species groups within Lygodactylus cannot be unambiguously characterized by external morphology alone, neither by unique character states nor by a diagnostic combination of character states. Thus, any future taxonomic work will likely benefit from integrative, phylogenomic approaches. [ABSTRACT FROM AUTHOR]

Evolutionary reduction of adult body size (miniaturization) has profound consequences for organismal biology and is an important subject of evolutionary research. Based on two individuals we describe a new, extremely miniaturized chameleon, which may be the world's smallest reptile species. The male holotype of Brookesia nana sp. nov. has a snout–vent length of 13.5 mm (total length 21.6 mm) and has large, apparently fully developed hemipenes, making it apparently the smallest mature male amniote ever recorded. The female paratype measures 19.2 mm snout–vent length (total length 28.9 mm) and a micro-CT scan revealed developing eggs in the body cavity, likewise indicating sexual maturity. The new chameleon is only known from a degraded montane rainforest in northern Madagascar and might be threatened by extinction. Molecular phylogenetic analyses place it as sister to B. karchei, the largest species in the clade of miniaturized Brookesia species, for which we resurrect Evoluticauda Angel, 1942 as subgenus name. The genetic divergence of B. nana sp. nov. is rather strong (9.9‒14.9% to all other Evoluticauda species in the 16S rRNA gene). A comparative study of genital length in Malagasy chameleons revealed a tendency for the smallest chameleons to have the relatively largest hemipenes, which might be a consequence of a reversed sexual size dimorphism with males substantially smaller than females in the smallest species. The miniaturized males may need larger hemipenes to enable a better mechanical fit with female genitals during copulation. Comprehensive studies of female genitalia are needed to test this hypothesis and to better understand the evolution of genitalia in reptiles. [ABSTRACT FROM AUTHOR]

Biofluorescence is widespread in the natural world, but only recently discovered in terrestrial vertebrates. Here, we report on the discovery of iridophore-based, neon-green flourescence in the gecko Pachydactylus rangei, localised to the skin around the eyes and along the flanks. The maximum emission of the fluorescence is at a wavelength of 516 nm in the green spectrum (excitation maximum 465 nm, blue) with another, smaller peak at 430 nm. The fluorescent regions of the skin show large numbers of iridophores, which are lacking in the non-fluorescent parts. Two types of iridophores are recognized, fluorescent iridophores and basal, non-fluorescent iridophores, the latter of which might function as a mirror, amplifying the omnidirectional fluorescence. The strong intensity of the fluorescence (quantum yield of 12.5%) indicates this to be a highly effective mechanism, unique among tetrapods. Although the fluorescence is associated with iridophores, the spectra of emission and excitation as well as the small Stokes shifts argue against guanine crystals as its source, but rather a rigid pair of fluorophores. Further studies are necessary to identify their morphology and chemical structures. We hypothesise that this nocturnal gecko uses the neon-green fluorescence, excited by moonlight, for intraspecific signalling in its open desert habitat. [ABSTRACT FROM AUTHOR]

The omission of critical data in the pursuit of "revolutionary" methods to accelerate the description of species However, the latter authors failed to diagnose their 15 new I Zelomorpha i Ashmead, 1900 species from 51 out of 52 previously known species (only the type species was used in the analysis) and their three new I Hemichoma i Enderlein, 1920 species from any of the five previously known species. (2004) proposed to recognize ten species of skipper butterflies (genus I Astraptes i ) based on DNA characters and ecology and some morphological characters, but the species were not formally named until Brower (2010) described them based exclusively on unique mutations in the DNA barcode region. DNA barcoding is a rapid means to sort specimens into clusters, identify species and discover new ones (when a library of the relevant named species is already available), but does not overcome the bottleneck of the description process itself. [Extracted from the article]

Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000–20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term—ideally perpetual—data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach—linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated |$ \le $| 2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000–40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.] [ABSTRACT FROM AUTHOR]

The emerging picture of non‐monophyly of scolecophidian snakes is increasingly indicative that fossorial lifestyle, myrmecophagous diet, and miniaturisation are powerful drivers of morphological evolution in squamate skulls. We provide a detailed description of the skull of Xenotyphlops grandidieri, with reference to the skulls of other scolecophidian snakes. The skull, which shows dramatic ventral inflection of the snout complex, is remarkably bizarre, and the mouth opening is more ventrally oriented than in other typhlopoids. The eyes are strongly reduced, and the enlarged and rather flat anterior head shield is covered in numerous sensillae. We put forward several potential explanations for the evolution of these unusual modifications. On the other hand, Xenotyphlops shares numerous synapomorphies with other typhlopoid snakes, including the highly specialized jaw mechanism. We argue that the key differences between the jaw mechanisms of Leptotyphlopidae, Anomalepididae, and Typhlopoidea provide compelling evidence for a strong role of convergence in the evolution of the scolecophidian bauplan, and these clades therefore cannot be interpreted as representative of ancestral anatomy or ecology among snakes. [ABSTRACT FROM AUTHOR]

Basic ecological data are missing from the majority of Madagascar's snakes. We here report seven dietary records from two species of the genus Compsophis and one record from Alluaudina bellyi. Among these are the first records of reptile predation by the former genus, suggesting they are not as strictly anurophagous as heretofore thought. We also report the consumption of a poison frog (Mantella) by a Compsophis, the second reported instance of predation of a member of this genus by a snake, and discuss possible implications for resistance to their alkaloid toxins. The consumption of a small leaf-litter dwelling frog (Stumpffia sp.) by A. bellyi is the first ever diet record for any Alluaudina. We discuss the possible role of niche partitioning between terrestrial and arboreal prey as one of the primary axes of initial divergence between the sister genera Alluaudina and Compsophis, and suggest that differences in their diet may be evident from their dentition, warranting further study. [ABSTRACT FROM AUTHOR]

Based on recent discoveries and an integrative study including external morphology, osteology and molecular genetics, we continue to revise the Madagascar-endemic chameleons of the Calumma boettgeri complex (within the Calumma nasutum species group). We describe three new species of these small-sized, occipital-lobed chameleons. Calumma uetzi sp. nov. is a species from the Sorata and Marojejy massifs (northern Madagascar), with a spectacular display coloration in males, clearly notched occipital lobes, and females with a dorsal crest. Calumma lefona sp. nov. is described based on a male specimen from Tsaratanana (northern Madagascar), with widely notched occipital lobes, a long and pointed rostral appendage, a dorsal crest, and a frontoparietal fenestra in the skull roof. This last character also occurs in six other Calumma species, and its presence and width are correlated with the elevational distribution of the species. Calumma juliae sp. nov. is known only from a small, isolated forest fragment near Moramanga in eastern Madagascar, and only females have been found so far. It is a relatively large member of the C. nasutum group, with a distinct dorsal crest and numerous infralabial scales. Two of the new species are known exclusively from their type localities, and we recommend protection of the habitats of all three as soon as possible. [ABSTRACT FROM AUTHOR]