Mark D. Scherz

Fish-scale geckos (Geckolepis), endemic to Madagascar and the Comoro Islands, are nocturnal, arboreal lizards with large, imbricate scales that can be shed and regenerated in their entirety, most likely as an antipredator mechanism. Their species-level taxonomy has remained partly unresolved because morphology alone has proven insufficient to reliably assign genetic lineages to scientific names. Here, we use a museomics approach to extract and shotgun-sequence DNA from twelve liquid-preserved historical and mostly name-bearing type specimens of six historical nomina in the genus, and assemble sequences of the mitochondrial genes for 12S rRNA, 16S rRNA, and nd4 for ten of these specimens. Despite relatively low coverage, the assembled sequences robustly placed all these type specimens in a phylogenetic tree with 113 ingroup samples collected across Madagascar. Our results demonstrate the efficiency of this approach to recover mitochondrial evidence for taxonomic purposes, but also show its failure to recover reads matching single-copy nuclear genes. We discuss the promise of a renewed focus on nuclear ribosomal genes as complementary nuclear-encoded DNA barcodes for vertebrates, as we found 18S rRNA sequences to be well-represented among the reads of the historical specimens studied here. Based on evidence from the mitochondrial tree, two nuclear-encoded genes (C-MOS, RAG-1), and morphology, we resurrect G. typica var. modesta Methuen & Hewitt, 1913 as a full species, G. modesta, from north-western Madagascar, confirm the current use of the name G. maculata Peters, 1880 for specimens from northern and eastern Madagascar, of G. polylepis Boettger, 1893 for specimens from western and north-western Madagascar, and of G. typica Grandidier, 1867 for specimens from southern and south-western Madagascar. We also recognize G. typica var. anomala Mocquard, 1902 as a subspecies, G. typica anomala, and confirm G. petiti Angel, 1942 to be a synonym of this subspecies. We also describe two new species, G. bekira sp. nov. and G. spania sp. nov. from northern Madagascar. The new classification provides a robust baseline to identify the remaining taxonomic issues in the genus and tackle them, preferably using genomic approaches which are also promising to better understand the molecular mechanisms of scarless wound healing and skin regeneration in these geckos.

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 introduce BlasTax, a standalone software tool wrapping the BLAST algorithm for finding regions of similarity between nucleotide and amino acid sequences. BlasTax is designed to serve both general users of local BLAST who seek a simple and user-friendly interface, and taxonomists engaged in phylogenomics and museomics projects. BlasTax is driven by a graphical user interface that makes various BLAST functions accessible without separately installing the BLAST+ executables. It introduces several advanced modes to retrieve matching reads from FASTQ files of high-throughput sequencing of archival DNA from recent or historical collection material, to append matching sequences to existing alignments, or to decontaminate sequence data sets from sequences of non-target taxa. The program also comprises functions for the preparation of sequence files to be used as reference or query for BLAST, as well as utilities for sequence merging based on species labels, codon trimming and codon-aware multiple sequence alignments.

Madascincus is a genus of quadrupedal skinks endemic to Madagascar, with 12 recognized species described between the 19 ^th and 21 ^st 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.

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.

For the last century, herpetologists have referred to any Nectophrynoides Noble, 1926 toad characterized by a large, robust body, with large, distinct parotoid glands, as Nectophrynoides viviparus (Tornier, 1905). Consequently, Nectophrynoides viviparus is also considered to have the broadest distribution of all its congeners, with populations ranging from the Tanzanian Southern Highlands, close to the Tanzania-Malawi border, through the Udzungwa and Mahenge Mountains in the south to Uluguru, Rubeho, and Nguru Mountains in the central part of the Eastern Arc Mountains. However, there is underappreciated morphological diversity within what is generally referred to as N. viviparus , and various populations are isolated by large distances and geographical barriers. Recent molecular studies have shown that N. viviparus from the Southern Highlands, the type locality, is genetically distinct from all other N. viviparus populations in the Eastern Arc Mountains, suggesting the existence of a species complex warranting taxonomic revision. Here, we present an integrative taxonomic assessment of southern populations by supplementing the genetic results with the analysis of morphometric and morphological data for 257 specimens assigned to N. viviparus , including museomic data for name-bearing types. Based on the results, we describe three new species from the N. viviparus species complex, covering the southern Eastern Arc Mountains populations. Together with a revised morphological key to the genus and a gazetteer of known populations, we provide Extent of Occurrence and Area of Occupancy for N. viviparus sensu stricto and the new species to investigate their conservation status compared to other members of the genus.

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 Platypelis efatra sp. 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.

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.

Booidean snakes are a diverse and widespread lineage with an intriguing evolutionary and biogeographic history. By means of cranial morphology and osteology, this study investigates the evolutionary convergence in the Neotropical genera Boa and Corallus on the one hand and the Malagasy clade comprising Acrantophis and Sanzinia on the other. We hypothesize that the mostly arboreal Corallus and Sanzinia present larger jaws and longer teeth to keep hold of the prey and resist gravity and torsional forces acting on their skull while hanging from branches, while terrestrial genera such as Acrantophis show thinner jaws with shorter teeth because they can rely on the full length of their coils to immobilize and constrict the prey together with a substrate that supports the whole of their body. Overall, we highlight how booidean snakes can serve as intriguing subjects for the study of contingency, determinism, and opportunity in the evolution of distant lineages both phylogenetically and geographically. We also provide the first complete description of the skull of Boa constrictor .

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to “leap” to the next level.