Alice Petzold

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.

The Himalaya and Hindu Kush remain among the least scientifically explored mountain regions of Asia. Within their vertebrate fauna, pitvipers of the Gloydius himalayanus (Günther, 1864) complex have long presented taxonomic challenges due to limited sampling in remote areas and the absence of integrative analyses. Here, we present a comprehensive taxonomic revision of the G. himalayanus complex using an integrative framework that combines genetic and distributional data, external morphology, osteology, and ecological evidence. Our dataset also uniquely incorporates both newly collected material and DNA sequences obtained from 19 ^th - and early 20 ^th -century museum specimens, including one of the syntypes of G. himalayanus (BMNH 1946.1.19.64), underscoring the enduring value of historical collections in modern taxonomy. Analyses of four mitochondrial and three nuclear genes from populations across the western and central Himalaya and the Hindu Kush, many of which were genetically studied for the first time, recover five well-supported monophyletic lineages: G. himalayanus sensu stricto, G. chambensis , and three previously unrecognised lineages from the Hindu Kush of north-western Pakistan, the Hazara region of north-eastern Pakistan at the western margin of the Himalaya, and the Himalaya of western and central Nepal. Genetic distances in protein-coding mtDNA markers indicate species-level divergence among these lineages, ranging from 9.2–12.6% in cyt b and 8.1–14.1% in ND4, with additional support from partial allelic differentiation in phased nuclear markers, morphology, and osteology. Based on these results, we formally describe three new species, substantially expanding the known diversity of Gloydius along the southern Himalaya. To stabilise the nomenclature, we designate a lectotype for Halys himalayanus Günther. By integrating modern and historical data, this study demonstrates the lasting scientific relevance of natural history collections and emphasises the urgent need for conservation of these narrowly distributed and potentially regionally threatened mountain snakes.

Biodiversité actuelle et historique des girafes (Mammalia, Cetartiodactyla): En 1758, Carl von Linné proposa de classer les girafes dans l’espèce Cervus camelopardalis en s’appuyant sur des descriptions anciennes de spécimens censés provenir du Sennar (Soudan) et d’Ethiopie. En 1785, la première preuve concrète (peau et squelette) de l’existence des girafes est rapportée par François Levaillant en provenance du Cap de Bonne-Espérance. L'exploration de l'Afrique subsaharienne par les naturalistes européens aux XIXe et XXe siècles a permis d’enrichir les collections muséales. Les nombreux spécimens ramenés présentant des variations du pelage et du crâne, plusieurs espèces et sous-espèces ont été décrites au fur et à mesure des découvertes. Aujourd’hui, l’Union Internationale pour la Conservation de la Nature (UICN) ne reconnait cependant qu’une seule espèce et neuf sous-espèces, alors que des études génétiques concluent à l’existence de quatre à sept espèces au sein du genre Giraffa. Au cours de de cette thèse, la systématique des girafes a été examinée en analysant trois jeux de données moléculaires complémentaires : (1) 21 introns autosomaux disponibles dans les banques pour 137 individus ; (2) un fragment mitochondrial (couvrant le gène du cytochrome b jusqu’à la région 5’ de la région de contrôle) séquencé pour 548 individus, dont 19 spécimens historiques, notamment Zarafa et les girafes de Levaillant ; (3) quatre gènes du chromosome Y (AMELY, DDX3Y, SRY, ZFY) et leurs homologues du chromosome X, extraits à partir des génomes de six girafes, deux okapis et 11 autres ruminants. L’analyse des données autosomales par différentes méthodes de délimitation d’espèces (phylogénie, structure des populations, coalescence) indique l’existence de trois espèces : Giraffa camelopardalis (girafe du nord), G. tippelskirchi (girafe masaï d’Afrique de l’Est) et G. giraffa (girafe du sud). Cette hypothèse taxonomique est corroborée par l’analyse des gènes du chromosome Y. Les discordances observées entre les données mitochondriales et nucléaires sont expliquées, d’une part, par des introgressions mitochondriales et, d’autre part, par la philopatrie des femelles et une plus grande capacité de dispersion des mâles. L’intégration de girafes collectées aux XVIIIe et XIXe siècles dans les analyses phylogéographiques a permis de proposer une nouvelle classification du genre Giraffa, notamment une nouvelle sous-espèce, aujourd’hui éteinte, décrite à partir de spécimens du Sénégal. L’estimation moléculaire des temps de divergence suggère que les populations de girafes ont évolué en réponse aux changements climatiques du Pléistocène.

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.

We describe four new cryptic Ptychadena species from rainforest habitats in the Guinean Forests of West Africa, a renowned biodiversity hotspot. The new taxa are diagnosed based on morphological and molecular data (the mitochondrial markers 12S and 16S, and the nuclear gene RAG1), including museomic data from the types of the morphologically most similar taxon, P. aequiplicata, which was believed to range from West Africa into western Central Africa. The four new species form a clade that is sister to a clade of Ptychadena species from East, West and Central Africa that contains the type specimens of P. aequiplicata. We consequently restrict the distribution of P. aequiplicata to records from western Central Africa. The similar morphology and colour pattern of P. aequiplicata and the four new species are most likely a convergent adaptation to their habitat, leaf litter of rainforests. All four new species depend on primary forests and seem to tolerate little to no forest alteration. This habitat preference and very small ‘Areas of Occupancy’ qualify all four new species as Endangered, according to IUCN Red List criteria. The new West African Ptychadena species comprise two clades with two species each, both including an eastern and a western species that may differ in their preference of different forest environments. The four new species thus seem to be a very promising model system to investigate the forest history of West Africa. At least in parts, they have a reproductive strategy adapted to unpredictable rainfall and high air humidity, which is distinctly different from the rest of the genus. The new species confirm the assumption that West Africa is home to a unique amphibian fauna that is markedly distinct from the rest of the continent.

We describe a new species of puddle frog, genus Phrynobatrachus, from southern Ivory Coast. The new species, which we designate as Phrynobatrachus moroedeli sp. nov., exhibits striking variation in colour pattern of the ventral surface with either very few small black dots or large dark or even black blotches along the edges, and differs from all other West African species of the genus by the combination of unique morphological characters: small sized (snout–vent length of 13.9–23 mm), compact-bodied frog with a short rounded to pointed snout; rough to slightly warty dorsal skin with variable colouration; males with greyish dark, deep dark to completely black throats absence of a spiny eyelid tubercle; absence of femoral gland; presence of narrow X-shaped pair of scapular ridges; presence of light or whitish vertebral line or band; distinct black lateral band on flanks; distinct but rudimentary pedal webbing and small but distinct discs on fingers and toes; spinulae on dorsal surfaces of thighs and lower legs. It is further distinguished by mitochondrial 16S rRNA genetic distances ranging from 4.05–11.43% relative to other West African species of Phrynobatrachus, and by the absence of haplotype sharing within the analysed fragment of the nuclear RAG1 gene. Phylogenetically, the new lineage is closely related to but genealogically exclusive from Phrynobatrachus afiabirago, P. fraterculus, P. gutturosus, P. maculiventris, and P. pintoi, all of which are endemic to the Upper Guinean forest zone of West Africa. One formerly recognized distinct lineage (P. aff. gutturosus 1) may further correspond to the newly described species (mean 16S genetic distance 1.96%), but it is currently represented by a single sample from an unvouchered specimen. Additional specimens are thus needed to clarify its taxonomic identity and morphological characteristics.

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.