Miralles Aurélien

Muséum National d'Histoire Naturelle · Origines et Évolution

Motivation Haplotype networks are a routine approach to visualize relationships among alleles. Such visual analysis of single-locus data is still of importance, especially in species diagnosis and delimitation, where a limited amount of sequence data usually are available and sufficient, along with other data sets in the framework of integrative ta...

DNA barcoding plays an important role in exploring undescribed biodiversity and is increasingly used to delimit lineages at the species level (see Chap. 4 by Miralles et al.). Although several approaches and programs have been developed to perform species delimitation from datasets of single-locus DNA sequences, such as DNA barcodes, most of these...

Rapid biodiversity loss sets new requirements for taxonomic research, prompting updating some long-established practices to maximize timely documentation of species before they have gone extinct. One of the crucial procedures associated with the description of new taxa in Linnean taxonomy is assigning them a diagnosis, which is an account of the sp...

Over the past two decades, DNA barcoding has become the most popular exploration approach in molecular taxonomy, whether for identification, discovery, delimitation, or description of species. The present contribution focuses on the utility of DNA barcoding for taxonomic research activities related to species delimitation, emphasizing the following...

This chapter provides a reference glossary for the protocols in this volume. We have chosen only the very basic terms in the DNA barcode lexicon to include, and provide clear and concise definitions of these terms. We hope the reader finds this glossary useful.

The overall availability of user-friendly software tools tailored to the analysis of DNA barcodes is limited. Several obvious functions such as detecting and visualizing the DNA barcode gap, the calculation of matrices of pairwise distances at the level of species, or the filtering and decontaminating of sets of sequences based on comparisons with...

An accurate species-level taxonomy is paramount for biogeographical research, and conversely, biogeographical data are of importance for species delimitation. We here review recent developments and future perspectives of taxonomy of direct relevance for biogeographers. The understanding that species are independently evolving segments of population...

The species inventory of global biodiversity is constantly revised and refined by taxonomic research, through the addition of newly discovered species and the reclassification of known species. This almost three-century-old project provides essential knowledge for humankind. In particular, knowledge of biodiversity establishes a foundation for deve...

Hybridization between the European smooth and palmate newts has recurrently been mentioned in the literature. The only two studies that attempted to quantify the frequency of hybridization and gene admixture between these two species came to strikingly opposite conclusions. According to Arntzen et al. (1998, 42 allozymes), hybrids are rare in natur...

Aim: Discontinuity in the distribution of genetic diversity (often based on mtDNA) is usually interpreted as evidence for phylogeographic breaks, underlying vicariant units. However, a misleading signal of phylogeographicbreak can arise in the absence of barrier to gene flow, under mechanisms of isolation by distance (IBD). How and under which cond...

Uncertainties on species taxonomy and distribution are major factors hampering efficient conservation planning in the current context of biodiversity erosion, even concerning widespread and abundant species in relatively well-studied regions. Species delimitation have long been based on phylogenetic analyses of a small number of standard markers, b...

The species inventory of global biodiversity is constantly revised and refined by taxonomic research, through the addition of newly discovered species. This almost three century old project provide a knowledge foundation essential for humankind, and notably to develop appropriate conservation strategies. This task relies on the study of millions of...

The Malagasy genus Gephyromantis contains 51 species of primarily terrestrial or scansorial frogs. Although many species are morphologically weakly divergent from each other, the combination of molecular and bioacoustic evi¬dence has led to a continuous flow of species discoveries in the last years. Previous works have notably shown the existence o...

Hybridization between the European smooth and palmate newts has recurrently been mentioned in the literature. The only two studies that attempted to quantify the frequency of hybridization and gene admixture between these two species came to strikingly opposite conclusions. According to Arntzen et al (1998, 42 allozymes), hybrids are rare in nature...

Aim Discontinuity in the distribution of genetic diversity (often based on mtDNA) is usually interpreted as evidence for phylogeographic breaks, underlying vicariant units. However, misleading signal of phylogeographic break can arise in the absence of barrier to gene flow, under mechanisms of isolation by distance (IBD). How and under which condit...

Most of the unique and diverse vertebrate fauna that inhabits Madagascar derives from in situ diversification from colonisers that reached this continental island through overseas dispersal. The endemic Malagasy Scincinae lizards are amongst the most species-rich squamate groups on the island. They colonised all bioclimatic zones and display many e...

Linnaean and Wallacean shortfalls (Uncertainties on species taxonomy and distribution, respectively) are major factors hampering efficient conservation planning in the current context of biodiversity erosion. These shortfalls concern even widespread and abundant species in relatively well-studied regions such as the Mediterranean biodiversity hotsp...

The Lygodactylus madagascariensis species group, constituting the subgenus Domerguella, currently contains five valid species of inconspicuous dwarf geckos from Madagascar’s humid forests, but at least 18 deep genetic lineages have been revealed by recent molecular studies. Given the high morphological similarity of these lineages, taxonomic resolu...

The mixed quality evidence about non-front-fanged snake bites has included unsupported speculation and presumption; the possible role of atopy and/or primary hypersensitivity have often been prematurely discounted. Described is a medically insignificant bite by a captive African emerald snake, Hapsidophrys smaragdinus Schlegel, 1837 (Colubridae, Co...

Summary-Taxonomic list of the herpetofauna in the Overseas France: VI Department of La Réunion. We present an updated taxonomic checklist of the Amphibians and "Reptiles" of the French department of Reunion Island located in the Mascarene archipelago, southwestern Indian Ocean. We synthesized information from the most recent publications. In additi...

Studying collection specimens is often the only way to unravel information about recent extinctions. These can reveal knowledge on threats and life traits related to extinction, and contribute, by extrapolation, to the conservation of extant species. However, high-throughput sequencing methods have rarely been applied to extinct species to reveal i...

Being phylogenetically close involves greater empathic perceptions towards other species. To explore this phenomenon, this study investigates the influence of neurocognitive predispositions to empathy on our perceptions of other organisms. Autistic spectrum disorders (ASD) are characterized, among others, by weakened empathic skills. Our online sur...

Being phylogenetically close involves a greater empathy towards other species. To explore this phenomenon, this study investigates the influence of neurocognitive predispositions to empathy on our perceptions of other organisms’ emotions. Autistic spectrum disorders (ASD) are characterized, among others, by weakened empathic skills. Our online surv...

While powerful and user-friendly software suites exist for phylogenetics, and an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, software targeted explicitly at facilitating alpha-taxonomic work, i.e., delimiting and diagnosing species, is still in its infancy. Here we present a project to...

A wide range of data types can be used to delimit species and various computer‐based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species delimitation (SD) under different assumptions, they are not routinely used by alpha‐taxonomists. One obvious s...

Burrowing is a common behavior in vertebrates. An underground life‐style offers many advantages but also poses important challenges including the high energetic cost of burrowing. Scolecophidians are a group of morphologically derived subterranean snakes that show great diversity in form and function. Although it has been suggested that leptotyphlo...

(Abstract in english) Halfway through a process of modernization undertaken some twenty years ago, the challenges facing contemporary α-taxonomy are multiple, and are as much quantitative (accelerating the inventory of living organisms) as qualitative (having reliable species hypotheses). They consist, among others, of: appropriation of concepts...

Our knowledge of the conservation status of reptiles, the most diverse class of terrestrial vertebrates, has improved dramatically over the past decade, but still lags behind that of the other tetrapod groups. Here, we conduct the first comprehensive evaluation (~92% of the world's ~1714 described species) of the conservation 1 Joint senior authors...

While powerful and user-friendly software suites exist for phylogenetics, and an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, software specifically targeted at facilitating alpha-taxonomic work, i.e., delimiting and diagnosing species, is still in its infancy. Here we present a project...

A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of SD under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack...

The genus Scaphiophryne (Anura: Microhylidae) contains at least nine species that, together with their probable sister genus Paradoxophyla, form the Madagascar-endemic subfamily Scaphiophryninae. Scaphiophryne are robust burrowing frogs with explosive breeding behavior and are characterized by a unique larval morphology, being intermediate between...

The Paroedura bastardi clade, a subgroup of the Madagascan gecko genus Paroedura, currently comprises four nominal species: P. bastardi, supposedly widely distributed in southern and western Madagascar, P. ibityensis, a montane endemic, and P. tanjaka and P. neglecta, both restricted to the central west region of the island. Previous work has shown...

The Paroedura bastardi clade, a subgroup of the Madagascan gecko genus Paroedura , currently comprises four nominal species: P. bastardi , supposedly widely distributed in southern and western Madagascar, P. ibityensis , a montane endemic, and P. tanjaka and P. neglecta , both restricted to the central west region of the island. Previous work has s...

Trade-offs are thought to be important in constraining evolutionary divergence as they may limit phenotypic diversification. The cranial system plays a vital role in many functions including defensive, territorial, predatory and feeding behaviours in addition to housing the brain and sensory systems. Consequently, the morphology of the cranial syst...

Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), 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 15-20,...

We generated an extensive morphological and multilocus molecular dataset to investigate the taxonomy of Acanthodactylus erythrurus, a widespread species across the Mediterranean and semiarid habitats of the Iberian Peninsula and the Maghreb. Our integrated analyses revealed the existence of at least five basal lineages: (i) an Ibero-Moroccan clade...

The ability to rapidly generate and share molecular, visual, and acoustic data, and to compare them with existing information, and thereby to detect and name biological entities is fundamentally changing our understanding of evolutionary relationships among organisms and is also impacting taxonomy. Harnessing taxonomic data for rapid, automated spe...

Currently the planet is inhabited by several millions of extremely diversified species. Not all of them arouse emotions of the same nature or intensity in humans. Little is known about the extent of our affective responses toward them and the factors that may explain these differences. Our online survey involved 3500 raters who had to make choices...

Motivation: Species delimitation (SD) is on the verge of becoming a fully-fledged research field in systematics, but the variety of available approaches tend to result in significant - sometimes striking - incongruences, when tested comparatively with a given taxonomic sampling. Results: We present LIMES, an automatic calculation tool which qual...

The phylogenetic relationships between the three main clades of worm snakes remain controversial. This question is, however, crucial to elucidate the origin of the successful snake radiation, as these burrowing and miniaturized wormlike organisms represent the earliest branching clades within the snake tree. The present molecular phylogenetic study...

The family Xenophidiidae is an extremely rare and little-known family of snakes that contains only two species, Xenophidion acanthognathus Günther & Manthey and X. schaeferi Günther & Manthey that are each known only from their holotypes. We report on the rediscovery of X. schaeferi from two new locations in southern Peninsular Malaysia. The new sp...

Significance Retroviral envelope gene capture and exaptation for a placental function has been demonstrated in mammals. Remarkably, placental structures have also emerged on rare occasions in nonmammalian vertebrates, resulting in related modes of reproduction. The Mabuya lizard, which emerged 25 Mya, possesses a placenta closely related to that of...

Article only available online on the website of The Conversation (no PDF) : https://theconversation.com/pourquoi-les-scientifiques-collectent-ils-des-animaux-sauvages-81809

Marine iguanas are among the most highly emblematic taxa of the Galápagos archipelago but have paradoxically received little attention from taxonomists. Amblyrhynchus is currently considered as a monotypic genus with a total of seven subspecies, A. cristatus cristatus, A. c. nanus, A. c. venustissimus, A. c. albemarlensis, A. c. hassi, A. c. merten...

Among the endemic biota of Madagascar, skinks are a diverse radiation of lizards that exhibit a striking ecomorphological variation, and could provide an interesting system to study body-form evolution in squamate reptiles. We provide a new phylogenetic hypothesis for Malagasy skinks of the subfamily Scincinae based on an extended molecular dataset...

Molecular Systematic of Guadeloupian Mabuya skinks (Squamata, Scincidae). Six new species of Mabuya endemic to the Guadeloupian archipelago have been described in the course of the last decade, mainly based on phenotypic data: Mabuya cochonae Hedges & Conn, 2012 (îlet à Cochon), M. desiradae Hedges & Conn, 2012 (La Désirade), M. grandisterrae Hedge...

In a previous study, Miralles & Vences (2013) compared seven different methods of species delimitation applied to the genus Madascincus. While focusing on methodological aspects their study involved an extensive data set of multilocus DNA sequences and of comparative morphology. On this basis they emphasized the need of revising the taxonomy of Mad...

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009;...

This plot is not part of the published stance but derives from it. The plot shows the number of authors by geographic region (courtesy of Dr. Diego Astua).

In this study, we provide an extended multilocus phylogenetic analysis combining mitochondrial and nuclear DNA of a group of fossorial and miniaturized legless lizards (genus Paracontias) from Madagascar, including the description of two species new to science, P. ampijoroensis sp. nov. and P. mahamavo sp. nov. Our analyses revealed the existence o...

We provide an updated molecular phylogenetic analysis of global diversity of typhlopid and xenotyphlopid blindsnakes, adding a set of Madagascan samples and sequences of an additional mitochondrial gene to an existing supermatrix of nuclear and mitochondrial gene segments. Our data suggest monophyly of Madagascan typhlopids, exclusive of introduced...

We describe a new leaf-tailed gecko species of the Uroplatus ebenaui group from the eastern central rainforests of Madagascar, which had previously been considered as a confirmed candidate species. Our description of Uroplatus fiera sp. nov. relies on integrating evidence from molecular and morphological characters and is based on newly collected m...

Understanding the phylogenetic and geographical history of Neotropical lineages requires having adequate geographic and taxonomic sampling across the region. However, Colombia has remained a geographical gap in many studies of Neotropical diversity. Here we present a study of Neotropical skinks of the genus Mabuya, reptiles that are difficult to id...

Scincine lizards in Madagascar form an endemic clade of about 60 species exhibiting a variety of ecomorphological adaptations. Several subclades have adapted to burrowing and convergently regressed their limbs and eyes, resulting in a variety of partial and completely limbless morphologies among extant taxa. However, patterns of limb regression in...

A new species of the hitherto monotypic genus Chalarodon is described from southern Madagascar and a lectotype (ZMB 4360) is designated for C. madagascariensis Peters, 1854. The new species of terrestrial iguana, Chalarodon steinkampi sp. nov., is defined by several morphological characters and by concordant differentiation in mitochondrial and nuc...

We provide new morphological and genetic data on a poorly studied genus of geckos from Madagascar (Paragehyra) previously thought to be distributed only in the southeast and southwest of the island and discuss the biogeography and evolution of this genus. Two species (Paragehyra petiti and Paragehyra gabriellae) were formerly included in this genus...

The following chapter is a review of the female reproductive anatomy of lizards. We limit our discussions to the anatomy of the cloacae, oviducts, and sperm storage receptacles in female lizards, as other chapters focus attention toward topics such as ovarian development/ovarian cycle (Ramirez-Pinilla et al. Chapter 8, this volume and placental mor...

Novel ventrally positioned extra-cloacal glands were discovered through examination of cloacal histology of female thamnophiine snakes. The glands discovered, termed ventral urodeal glands, are paired and empty into the caudal extremity of the urodeum, lateral to the opening of the urodeal sphincter, through primary ducts that resemble folds of the...

Polydactyly is described ona specimen of marine iguana (Amblyrhynchus cristatus) from the Galápagos conserved in the MNHN Paris Natural History Museum collections.

A preliminary assessment of morphological differentiation between two common Malagasy skink species, Trachylepis elegans and T. gravenhorstii Note: This is after Schmidt et al. (2008), Randrianiaina et al. (2009), Vences et al. (2012), and Eckhardt et al. (2012) the fifth of a series of short notes produced within the yearly «Vertebrate morphology»...

Trachylepis elegans and T. gravenhorstii are two of the most widespread reptiles in Madagascar, inhabiting a wide variety of habitats. Previous studies have indicated a considerable mitochondrial DNA (mtDNA) variation within these species, but the geographic distribution of the major haplotype lineages is poorly known. Herein we analyse the phyloge...