Christopher J Raxworthy

• American Museum of Natural History

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

Simple Summary: The genus Mantidactylus spp. is one of the exceptionally diverse amphibian clades from Madagascar. Currently, 57 species in 6 subgenera are recognized. One subgenus, Ochthomantis, is the focus of the present study. Here, we revise this taxonomic group to recognize the presence of cryptic species through an assessment of morphologica...

The subgenus Ochthomantis is an obligate forest and stream-dwelling group of mantellid frogs, endemic to Madagascar, with six species currently recognized. However, this group suffers from ongoing taxonomic confusion due to low numbers of examined specimens, and failure to consider morphological variation from development and sexual dimorphism. Her...

Speciation rates vary substantially across the tree of life. These rates should be linked to the rate at which population structure forms if a continuum between micro and macroevolutionary patterns exists. Previous studies examining the link between speciation rates and the degree of population formation in clades have been shown to be either corre...

The subgenus Ochthomantis is an obligate forest and stream-dwelling group of Mantellid frogs, endemic to Madagascar, with six species currently recognized. However, this group suffers from ongoing taxonomic confusion due to low numbers of examined specimens, and failure to con-sider morphological variation from development and sexual dimorphism. He...

The Harmonious Protected Landscape of Ambohitr'Antsingy Montagne des Français is one of the protected area located in the extreme northern of Madagascar. An assessment of the Herpe-tofauna community were made on the eastern and western slopes regarding the forest degrada-tion level, the availability of the streams and the habitat types in the massi...

Invasion risks may be influenced either negatively or positively by climate change, depending on the species. These can be predicted with species distribution models, but projections can be strongly affected by the source of the environmental data (climate data source, Global Circulation Models GCM and Shared Socioeconomic Pathways SSP). We modelle...

A fundamental assumption of evolutionary biology is that phylogeny follows a bifurcating process. However, hybrid speciation and introgression are becoming more widely documented in many groups. Hybrid inference studies have been historically limited to small sets of taxa, while exploration of the prevalence and trends of reticulation at deep time...

The highly diverse snake superfamily Elapoidea is considered to be a classic example of ancient, rapid radiation. Such radiations are challenging to fully resolve phylogenetically, with the highly diverse Elapoidea a case in point. Previous attempts at inferring a phylogeny of elapoids produced highly incongruent estimates of their evolutionary rel...

This is the story of a winner and a loser. We predicted current and future invasion risks of Phelsuma grandis and P. laticauda at the global scale. The results presented are drawn from the article titled "Choice of climate data influences current and future global invasion risks for two Phelsuma geckos".

Invasion risks may be influenced either negatively or positively by climate change, depending on the species. These can be predicted with species distribution models, but projections can be strongly affected by input environmental data (climate data source, Global Circulation Models and Shared Socio-economic Pathways SSP). We modelled the distribut...

Invasion risks may be influenced either negatively or positively by climate change, depending on the species. These can be predicted with species distribution models, but projections can be strongly affected by input environmental data (climate data source, Global Circulation Models and Shared Socio-economic Pathways SSP). We modelled the distribut...

Aim A long history of isolation coupled with complex landscapes makes Madagascar ideal for exploring the historical factors that have shaped patterns of population diversity and endemism. Many species‐level studies have suggested Late Quaternary climate change may have influenced population dynamics in the tropics, but unique biomes and individual...

Lizards of the clade Iguanidae (sensu lato) are primarily a New World group. Thus, the remarkable presence of an endemic lineage of iguanas (family Opluridae) on the isolated Indian Ocean island of Madagascar has long been considered a biogeographic anomaly. Previous work attributed this disjunct extant distribution to: (1) vicariance at about 140-...

Although genetic patterns produced by population isolation during speciation are well documented, the biogeographic and ecological processes that trigger speciation remain poorly understood. Alternative hypotheses for the biogeography and ecology of speciation include geographic isolation combined with niche conservation (soft allopatry), or parapa...

Environmental properties, and the behavioral habits of species impact sensory cues available for foraging, predator avoidance and inter/intraspecific communication. Consequently, relationships have been discovered between the sensory ecology and brain morphology in many groups of vertebrates. However, these types of studies have remained scare on s...

Historical DNA (hDNA), obtained from museum and herbarium specimens, has yielded spectacular new insights into the history of organisms. This includes documenting historical genetic erosion and extinction, discovering species new to science, resolving evolutionary relationships, investigating epigenetic effects, and determining origins of infectiou...

Aim To investigate whether the frequently advocated climate-matching species distribution modeling approach could predict the well-characterized colonization of Florida by the Madagascar giant day gecko Phelsuma grandis. Location Madagascar and Florida, USA. Methods To determine the climatic conditions associated with the native range of P. grand...

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrich...

The kinetic skull is a key innovation that allowed snakes to capture, manipulate, and swallow prey exclusively using their heads using the coordinated movement of 8 bones. Despite these unique feeding behaviors, patterns of evolutionary integration and modularity within the feeding bones of snakes in a phylogenetic framework have yet to be addresse...

The kinetic skull is a key innovation that allowed snakes to capture, manipulate, and swallow prey exclusively using their heads using the coordinated movement of 8 bones. Despite these unique feeding behaviors, patterns of evolutionary integration and modularity within the feeding bones of snakes in a phylogenetic framework have yet to be addresse...

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrich...

The genus Amolops (“torrent frogs”) is one of the most species-rich genera in Ranidae, with 59 recognized species. This genus currently includes six species groups diagnosed mainly by morphology. Several recent molecular studies indicated that the classification of species groups within Amolops remains controversial, and key nodes in the phylogeny...

We present information on primary type specimens for 13,282 species and subspecies of reptiles compiled in the Reptile Database, that is, holotypes, neotypes, lectotypes, and syntypes. These represent 99.4% of all 13,361 currently recognized taxa (11,050 species and 2311 subspecies). Type specimens of 653 taxa (4.9%) are either lost or not located,...

Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards and snakes, amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a con...

Processes leading to spectacular diversity of both form and species on islands have been well-documented under island biogeography theory, where distance from source and island size are key factors determining immigration and extinction resistance. But far less understood are the processes governing in situ diversification on the world's mega islan...

Significance In humans, patterns of cranial variation mirror genetic diversity globally, implicating population history as a key driver of cranial disparity. Here, we demonstrate that the magnitude of genetic diversity within 12 extant ape taxa explains a large proportion of cranial shape variation. Taxa that are more genetically diverse tend to be...

In wide-ranging taxa with historically dynamic ranges, past allopatric isolation and range expansion can both influence the current structure of genetic diversity. Considering alternate historical scenarios involving expansion from either a single refugium or from multiple refugia can be useful in differentiating the effects of isolation and expans...

Although many wide-ranging taxa occur in Madagascar, phylogeographic studies for most of these species are still lacking. This is especially the case for snakes, where of more than 100 endemic species, the population structure of only two species has so far been examined. Here, we examine genetic population structure of one of the most common snake...

Origins of giant tortoises on the Indian Ocean’s islands have been debated, and most recently attributed to human translocation (see Wilme, Patrick, & Ganzhorn, 2017). To resolve the issue, we analyse all available molecular sequences from extinct and extant Indian Ocean’s giant tortoises, along with major clades of the family Testudinidae using ph...

Peloso et al. (2015: PELOSO) published a comprehensive phylogenetic study of the frog family Microhylidae, which resulted in the discovery that several taxa were not monophyletic. To remedy this, a series of nomenclatural changes were proposed (several generic synonymies and two new subfamilies named). A recent study published in this journal by Sc...

A six month herpetological survey was undertaken between March and September 2015 on Nosy Komba, an island off of the north-west coast of mainland Madagascar which has undergone considerable anthropogenic modification. A total of 14 species were found that have not been previously recorded on Nosy Komba, bringing the total island diversity to 52 (4...

The cat-eyed snakes of the genus Madagascarophis are among the most commonly encountered snake species in Madagascar. Yet despite their broad distribution and frequent occurrence in human-disturbed habitat, Madagascarophis still contains unrecognized species diversity. Here, we describe a new species of Malagasy cat-eyed snake from a specimen found...

The Malagasy giant chameleons (Furcifer oustaleti and Furcifer verrucosus) are sister species that are both broadly distributed in Madagascar, and also endemic to the island. These species are also morphologically similar and, because of this, have been frequently misidentified in the field. Previous studies have suggested that cryptic species are...

Maximum likelihood (raxML) tree recovered using both mitochondrial and nuclear data. Full sample names are provided. The tree topology is congruent with the one found using mitochondrial data alone (see Fig 1 and S1 Fig). (TIF)

Species tree analysis with divergence dating using ND2 rate of 0.65%. All divergence times are indicated with an arrow; posterior support values are below branches. (TIF)

Localities, sample numbers, coordinates, and Genbank accession numbers for all samples included in this study. (XLSX)

Species tree analysis with divergences, when both the fossil and the biogeographic calibrations are applied. Divergence times are indicated with an arrow, and poster support values are below branches. Note that divergence dates do not vary with respect to those in Fig 2, in regards to the geologic period when diversification occurred. (TIF)

The results of the niche background test implemented in ENMTools. Each excel tab showing comparisons made in Fig 3. Same labels as in S2 Table. (XLSX)

Morphological results for all specimen examined in this study. (XLSX)

Phylogenetic relationships between the Furcifer verrucosus complex, the Furcifer oustaleti complex, and near outgroups using partial fragments of the mitochondrial genes ND2 and ND4, reconstructed in the ML tree. (TIF)

The results of the niche identity test implemented in ENMTools. Each excel tab showing comparisons made in Fig 3 (a vs. b = Furcifer verrucosus; c vs. d = Furcifer oustaleti; and verr vs. oust. = Furcifer oustaleti and Furcifer oustaleti.) (XLSX)

Despite renewed interest in the biogeography and evolutionary history of Old World tree frogs (Rhacophoridae), this family still includes enigmatic frogs with ambiguous phylogenetic placement. During fieldwork in four northeastern states of India, we discovered several populations of tree hole breeding frogs with oophagous tadpoles. We used molecul...

Lectotype of Polypedates jerdonii (= Frankixalus jerdonii), NHM 1947.2.7.84 (ex BMNH 1872.4.17.189). (A) dorsal view, (B) ventral view, (C) lateral view of head, (D) ventral view of hand, (E) ventral view of foot, (F) schematic illustration of webbing on foot. (PDF)

Snout shapes of Frankixalus and Kurixalus eiffingeri. A–C, K. eiffingeri (AMNH A14498, an adult female from Taiwan). (A) rounded in dorsal view, (B) rounded and protruding in ventral view, (C) rounded in lateral view; D–F, Frankixalus jerdonii (SDBDU 2009.1163). (D) truncate in dorsal view, (E) non-protruding semi-circular in ventral view, (F) vert...

Abbreviations. (A) Material and methods adult morphology, (B) Material and methods larval morphology, (C) Museum and people. (DOC)

Description of the lectotype of Polypedates jerdonii (= Frankixalus jerdonii), NMH 1947.2.7.84 (ex BMNH 1872.4.17.189), and additional specimens of F. jerdonii examined. (A) Description of lectotype (all measurements in mm), (B) Specimens of Frankixalus jerdonii examined. (DOC)

List of taxa and DNA sequences included in this study. (DOC)

Bayesian consensus phylogram of the total dataset showing phylogenetic relationships among 86 taxa representing all known rhacophorid genera and one outgroup species. Numbers above and below the branches represent Bayesian Posterior Probabilities obtained for the nuclear and mitochondrial datasets, respectively. (PDF)

Morphometric measurements (in mm) of the specimens used in this study. Status of specimens is given after the Museum number: LT- Lectotype, PL-Paralectotype, RS- Referred specimens. (DOC)

Phelsuma masohoala is a cryptically patterned day gecko endemic to Madagascar, and is one of the rarest geckos known on the island. It is currently known from only four museum specimens and has not been reliably seen in the wild since 1994, despite recent attempts to find it at the type locality. Here we report the rediscovery of P. masohoala at Ma...

Chameleons, lizards often synonymous with camouflage for their color-changing abilities, possess a variety of permanent coloration patterns whose evolutionary significance remains largely unknown. In this study, we explore the potential for white ventral line markings in species across the genus Chamaeleonidae to function as a camouflage pattern ag...

Using molecular data generated by high throughput next generation sequencing (NGS) platforms to infer phylogeny is becoming common as costs go down and the ability to capture loci from across the genome goes up. While there is a general consensus that greater numbers of independent loci should result in more robust phylogenetic estimates, few studi...

A recent paper by Kolby et al. [1], surveying for Batrachochytrium dendrobatidis (Bd) and ranavirus in Madagascar, presents results for 508 amphibian specimens and 68 water bodies sampled during a 2-month period of the 2013-14 wet season. Kolby et al. [1] did not detect Bd in any of the samples, presenting evidence that add to our understanding of...

There are insufficient resources available to manage the world's existing protected area portfolio effectively, so the most important sites should be prioritised in investment decision-making. Sophisticated conservation planning and assessment tools developed to identify locations for new protected areas can provide an evidence base for such priori...

Despite considerable progress in unravelling the phylogenetic relationships of microhylid frogs, relationships among subfamilies remain largely unstable and many genera are not demonstrably monophyletic. Here, we used five alternative combinations of DNA sequence data (ranging from seven loci for 48 taxa to up to 73 loci for as many as 142 taxa) ge...

The conservation of Madagascar amphibians has become object of study and application in the last twenty years, and concomitant to the presence and action of several herpetologists, who take this discipline to Madagascar, and highlighted the importance of preparing a serious action plan. Until then, taxonomy and survey works were the main activities...

Amphibian chytridiomycosis, an emerging infectious disease caused by the fungus Batrachochytrium dendrobatidis (Bd), has been a significant driver of amphibian declines. While globally widespread, Bd had not yet been reported from within Madagascar. We document surveys conducted across the country between 2005 and 2014, showing Bd 's first record i...

We describe a new arboreal and diminutive species of the genus Platypelis from the Réserve Naturelle Intégrale N. 1 de Betampona, one of the last low-altitude rainforest fragments of eastern Madagascar. P. karenae sp. nov. is a phytotelmic species, living among leaves of Pandanus spp. and those of a herbaceous plant of the genus Crinum. Amongst spe...

BACKGROUND: An understanding of the conservation status of Madagascar's endemic reptile species is needed to underpin conservation planning and priority setting in this global biodiversity hotspot, and to complement existing information on the island's mammals, birds and amphibians. We report here on the first systematic assessment of the extinctio...

A new species of Scaphiophryne is described from north-eastern Madagascar. The new toadlet species is probably at least partly fossorial as can be judged from its large and sharp metatarsal tubercle, and seems to lead a secretive or strictly seasonal life since very few adult specimens were collected despite intensive field surveys in the region. T...

There is an urgent need to develop effective vulnerability assessments for evaluating the conservation status of species in a changing climate. Several new assessment approaches have been proposed for evaluating the vulnerability of species to climate change based on the expectation that established assessments such as the IUCN Red List need revisi...

Guibemantis bicalcaratus (Boettger, 1913) has been considered as a widespread member of the subgenus Pandanusicola of largely phytotelmic-breeding Malagasy frogs. Based on new collections from its type locality, the Malagasy island Nosy Boraha, and several other localities on Madagascar's east coast, we revise the status of G. bicalcaratus using mo...

Understanding ecological niche evolution over evolutionary timescales is crucial to elucidating the biogeographic history of organisms. Here, we used, for the first time, climate-based ecological niche models (ENMs) to test hypotheses about ecological divergence and speciation processes between sister species pairs of lemurs (genus Eulemur) in Mada...

Phylogenetic relationships and taxonomy of the short-necked turtles of the genera Elseya, Myuchelys, and Emydura in Australia and New Guinea have long been debated as a result of conflicting hypotheses supported by different data sets and phylogenetic analyses. To resolve this contentious issue, we analyzed sequences from two mitochondrial genes (c...

Effective and targeted conservation action requires detailed information about species, their distribution, systematics and ecology as well as the distribution of threat processes which affect them. Knowledge of reptilian diversity remains surprisingly disparate, and innovative means of gaining rapid insight into the status of reptiles are needed i...