Taxonomy of rare congenital metabolic bone disorders

International audience

ENEOLITHIC, YAMNAYA, CATACOMB AND BABYNO CULTURE CEMETERIES, PIDLISIVKA, BARROW 1, YAMPIL REGION, VINNITSA OBLAST: ARCHAEOMETRY, CHRONOMETRY AND TAXONOMY

The paper presents excavation results and analytical studies concerning the taxonomic classification of a funerary site identified with the communities of the early ‘barrow cultures’ settling the north-western Black Sea Coast in the 4th/3rd-2nd millennium BC. The study focuses on the ceremonial centres of the Eneolithic, Yamnaya, Catacomb and Babyno cultures.

ENEOLITHIC, BABYNO AND NOUA CULTURE CEMETERIES, KLEMBIVKA, SITE 1, YAMPIL REGION, VINNITSA OBLAST: ARCHAEOMETRY, TAXONOMY AND TOPOGENETICS

The paper presents excavation results and analytical studies concerning the taxonomic classification of a funerary site identified with the communities of the ‘barrow cultures’ settling the north-western Black Sea Coast in the first half of the 3rd and the middle of the 2nd millennia BC . The study focuses on the ceremonial centres of the Eneolithic communities of the Babyno and Noua cultures .

TAXONOMY, MORPHOLOGY, AND RNA-SEQ TRANSCRIPTOMICS OF THE CUBOZOAN ALATINA ALATA, AN EMERGING MODEL CNIDARIAN

Cnidarians are often considered simple animals, but the more than 13,000 estimated species (e.g., corals, hydroids and jellyfish) of the early diverging phylum exhibit a broad diversity of forms, functions and behaviors, some of which are demonstrably complex. In particular, cubozoans (box jellyfish) are cnidarians that have evolved a number of distinguishing features. Some cubozoan species possess complex mating behaviors or particularly potent stings, and all possess well-developed light sensation involving image-forming eyes. Like all cnidarians, cubozoans have specialized subcellular structures called nematocysts that are used in prey capture and defense. The objective of this study is to contribute to the development of the box jellyfish Alatina alata as a model cnidarian. This cubozoan species offers numerous advantages for investigating morphological and molecular traits underlying complex processes and coordinated behavior in free-living medusozoans (i.e., jellyfish), and more broadly throughout Metazoa. First, I provide an overview of Cnidaria with an emphasis on the current understanding of genes and proteins implicated in complex biological processes in a few select cnidarians. Second, to further develop resources for A. alata, I provide a formal redescription of this cubozoan and establish a neotype specimen voucher, which serve to stabilize the taxonomy of the species. Third, I generate the first functionally annotated transcriptome of adult and larval A. alata tissue and apply preliminary differential expression analyses to identify candidate genes implicated broadly in biological processes related to prey capture and defense, vision and the phototransduction pathway and sexual reproduction and gametogenesis. Fourth, to better understand venom diversity and mechanisms controlling venom synthesis in A. alata, I use bioinformatics to investigate gene candidates with dual roles in venom and digestion, and review the biology of prey capture and digestion in cubozoans. The morphological and molecular resources presented herein contribute to understanding the evolution of cubozoan characteristics and serve to facilitate further research on this emerging cubozoan model.

Empathy in the field: towards a taxonomy of empathic communication in information gathering interviews with suspected sex offenders

Research suggests that those suspected of sexual offending might be more willing to reveal information about their crimes if interviewers display empathic behaviour. However, the literature concerning investigative empathy is in its infancy, and so as yet is not well understood. This study explores empathy in a sample of real-life interviews conducted by police officers in England with suspected sex offenders. Using qualitative methodology, the presence and type of empathic verbal behaviours displayed was examined. Resulting categories were quantitatively analysed to investigate their occurrence overall, and across interviewer gender. We identified four distinct types of empathy, some of which were used significantly more often than others. Female interviewers displayed more empathic behaviour per se by a considerable margin.

The taxonomy, zoogeography and ecology of amphibians and reptiles of Hin Nam No National Protected Area (Laos) in comparison with data from Phong Nha – Ke Bang National Park (Vietnam).

In this thesis the mostly unknown herpetofauna in Hin Nam No National Protected Area Laos in the northern Truong Son Range was for the first time intensively investigated, and its diversity was compared to the bordering, and well-investigated Phong Nha - Ke Bang National Park in Vietnam. Twelve new vertebrate species were described comprising 11 geckonids (Cyrtodactylus bansocensis, C. calamei, C. hinnamnoensis, C. jaegeri, C. rufford, C. sommerladi, C. soudthichaki, Gekko boehmei, G. bonkowskii, G. sengchanthavongi, G. thakhekensis, Lycodon banksi and one colubrid snake (Lycodon banksi). Seven species were discovered for the first time in Laos including three frogs (Gracixalus quyeti, G. supercornutus, Rhacophorus maximus), two geckos (Cyrtodactylus cryptus, C. pseudoquadrivirgatus) and two snakes (Lycodon futsingensis, L. ruhstrati abditus). The main hypothesis that the Truong Son Range acted as a biogeographic barrier for the distribution of amphibians and reptiles could be confirmed at least for karst adapted gekkonids. Compared to other herpetofaunal groups the number of gekkonids in karst formations was particularly high (seven bent-toed geckos, four true geckos). By comparing the relative amounts of shared species in Hin Nam No and Phong Nha - Ke Bang, it is interesting to note that fewer reptile species (38%) than amphibian species (66%) were shared between both regions. This might indicate that the Truong Son Range acts as a stronger biogeographical barrier for reptiles than for amphibians. Two pairs of karst-adapted cryptic gecko species (i.e. species with distinct genetic differences, but a similar phenotype) occurred on both sides of the Truong Son Range. Only in one case these were sibling species (Crytodactylus sommerladi in Laos versus C. roesleri in Vietnam), but not in the other (C. hinnamnoensis in Laos versus C. phongnhakebangensis in Vietnam). On the Laotian side, nine gecko species (Cyrtodactylus bansocensis, C. calamei, C. darevskii, C. hinnamnoensis, C. khammouanensis, C. multiporus, C. sommerladi, G. boehmei, G. sengchanthavongi) currently have to be regarded as endemic to the Hin Nam No region. On the Vietnamese side, seven species including two bent-toed geckos (Cyrtodactylus phongnhakebangensis and C. roesleri), three skinks (Lygosoma boehmei, Sphenomorphus tetradactylus and Tropidophorus noggei), and two snakes (Hebius andreae and Boiga bourreti) are currently only known from Phong Nha - Ke Bang and adjacent regions. These high numbers of potential endemic species together with the cryptic species complex in Cyrtodactylus provide strong evidence that the karst formations in the northern Truong Son Range represent a hot spot of reptile diversity and of speciation in Crytodactylus in particular. Correct species identification is a fundamental requirement for conservation measures. The discovery of cryptic species complexes poses a challenge for alpha taxonomy and species conservation, because the true distribution ranges of the species are in fact much smaller than previously assumed. Species conservation in this area of Laos is facing a number of further problems. New and potentially endemic species were discovered in highly populated and disturbed areas. Conversion of the Ho Chi Minh Trail into a highway provided easy access for farmers and still continues to accelerate the destruction of remote forest areas. Southern Hin Nam No with its high diversity of endemic species was identified as the first priority area for conservation. Also Ban Soc, an area isolated from Hin Nam No, should be among the conservation priorities because this region houses a so far overlooked population of the critically endangered Siamese crocodile. Efforts to establish a legal conservation status for this habitat are in progress.

Toward a Taxonomy of Harmin Knowledge Organization Systems

A starting point for contributing to the greater good is to examine and interrogate existing knowledge organization practices that do harm, whether that harm is intentional or accidental, or an inherent and unavoidable evil. As part of the transition movement, the authors propose to inventory the manifestations and implications of the production of suffering by knowledge organization systems through constructing a taxonomy of harm. Theoretical underpinnings guide ontological commitment, as well as the recognition of the problem of harm in knowledge organization systems. The taxonomy of harm will be organized around three main questions: what hap- pens?, who participates?, and who is affected and how? The aim is to heighten awareness of the violence that classifications and naming practices carry, to unearth some of the social conditions and motivations that contribute to and are reinforced by knowledge organization systems, and to advocate for intentional and ethical knowledge organization practices to achieve a minimal level of harm.

Taxonomy, phylogeography and myrmecophily of the spider genus Mastigusa (Araneae, Cybaeidae)

The genus Mastigusa Menge, 1854 includes small entelegyne spiders represented by extant and fossil species presenting characteristic features in male and female genitalia. The genus has a palearctic distribution, being present in Europe, North Africa, and the Near East, and shows ecological plasticity, with free-living, cave- dwelling and myrmecophile populations. The taxonomic history of the genus has been problematic, both regarding its phylogenetic placement and the delimitation of the species it includes. Three extant species are currently recognized, but the characters used to discriminate them have been inconsistent, leading to confusion about their identification and distribution. In the present thesis we addressed the taxonomic issues regarding Mastigusa by combining molecular and morphological data in an integrative taxonomy approach. For the first time, we included the genus in a molecular phylogenetic matrix solving a long going debate regarding its familiar placement, obtaining a well-supported placement in the family Cybaeidae. We used multi-locus molecular phylogenetic and DNA barcoding techniques as a starting point for identifying divergent lineages within the genus and revise the taxonomic status of the three known Mastigusa species, identifying a new species from the Iberian Peninsula, Algeria and the United Kingdom: M. raimondi sp. n. This taxonomic revision allowed a phylogeographic and ecological study of Mastigusa across its distribution range, carried out using phylogenetics and ecological niche modelling techniques, aiming at a comparison of the lifestyles and ecological requirements of the different species on a geographic scale. The Italian Alps were finally used as a testing ground for investigating the ecology and host preference of myrmecophile Mastigusa arietina populations living in association with ant species belonging to the Formica rufa species group. Spiders were found in association with five different Formica species, demonstrating little specificity and the tendency of associating with the locally present host species.

A Metabolomic Protocol For Plant Systematics By Matrix-assisted Laser-desorption/ionization Time-of Flight Mass Spectrometry.

Matrix-assisted laser desorption/ionization time-of flight mass spectrometry (MALDI-TOF MS) has been widely used for the identification and classification of microorganisms based on their proteomic fingerprints. However, the use of MALDI-TOF MS in plant research has been very limited. In the present study, a first protocol is proposed for metabolic fingerprinting by MALDI-TOF MS using three different MALDI matrices with subsequent multivariate data analysis by in-house algorithms implemented in the R environment for the taxonomic classification of plants from different genera, families and orders. By merging the data acquired with different matrices, different ionization modes and using careful algorithms and parameter selection, we demonstrate that a close taxonomic classification can be achieved based on plant metabolic fingerprints, with 92% similarity to the taxonomic classifications found in literature. The present work therefore highlights the great potential of applying MALDI-TOF MS for the taxonomic classification of plants and, furthermore, provides a preliminary foundation for future research.

Phenotypic Polymorphism Of Chrysomya Albiceps (wiedemann) (diptera: Calliphoridae) May Lead To Species Misidentification.

Species identification is an essential step in the progress and completion of work in several areas of biological knowledge, but it is not a simple process. Due to the close phylogenetic relationship of certain species, morphological characters are not always sufficiently distinguishable. As a result, it is necessary to combine several methods of analysis that contribute to a distinct categorization of taxa. This study aimed to raise diagnostic characters, both morphological and molecular, for the correct identification of species of the genus Chrysomya (Diptera: Calliphoridae) recorded in the New World, which has continuously generated discussion about its taxonomic position over the last century. A clear example of this situation was the first record of Chrysomya rufifacies in Brazilian territory in 2012. However, the morphological polymorphism and genetic variability of Chrysomya albiceps studied here show that both species (C. rufifacies and C. albiceps) share very similar character states, leading to misidentification and subsequent registration error of species present in our territory. This conclusion is demonstrated by the authors, based on a review of the material deposited in major scientific collections in Brazil and subsequent molecular and phylogenetic analysis of these samples. Additionally, we have proposed a new taxonomic key to separate the species of Chrysomya found on the American continent, taking into account a larger number of characters beyond those available in current literature.

Levantamento e características ecológicas de orchidacea e da mata ciliar do rio dourados, Dourados-MS

The Orchidaceae is one of the largest flowering plants family and with a great importance to conservation. However, no survey on orchid flowers can be found in Mato Grosso do Sul. Thus, the objective of this work was to make a survey of the Orchidaceae species and of its ecology features in a riparian forest in a fragment of Floresta Estacional Semi-Decidual that belongs to the riparian forest of the Dourados River. The inventory was made by using a sweeping method for collection, and in addition to this the vertical and horizontal position of epiphytes were assessed on the hosts. For characterization of microclimate, it was used a thermohygrometer and luximeter. It was identified 17 species of 13 genera. Of the listed genera, the most abundant ones were: Acianthera, Macradenia and Capanemia. It was also noted a vertical and horizontal distribution of the Orchidaceae in relation to inverse gradient of water and light availability. Some species tended to be sensitive to height level categorization, whereas others seemed to occur with similar frequency along the host. In relation to the cardinal orientation, the apparent preferential response for south and east directions was associated to the low sampling effort and lower water availability, which could occur because the north face is opposed to the water body.

Estrutura de um curso de taxonomia de campo: o modelo aplicado em Ubatuba, São Paulo

The field activities are essential for the education of a good taxonomist. The most common problems found in field activities are: a) large number of students, b) heterogeneous educational background and unlevelled knowledge of the participants, c) repetitions and tendency of collecting the more evidents life-forms. The causes and consequences of such problems are discussed herein. The proposed solution is a methodology, based on many years of experience in field courses for undergraduate and graduate courses. Topics about the ideal number of participants, area of coverage, period of activity, division of work and the necessary material and equipment are discussed. According to the number of species collected at the same place, this methodology may result in a list of local species with precise information about the life-forms, habitat, common names, frequency, uses, phenology and further information in this kind of work. The results of the aplication of this metodology in a field course held in the region of Ubatuba-SP are presented.

Notas sobre duas espécies de Thelypteris Schmidel (Thelypteridaceae - Pterophyta) do Brasil

During the taxonomic study of the Thelypteridaceae from southeastern Brazil was founded Thelypteris polypodioides (Raddi) C. F. Reed and Thelypteris villosa (Link) C. F. Reed, two rare and poorly known species. The taxonomic position of these species is uncertain. This study presents key, descriptions, illustrations, data on geographical distribution, and comments for both species, as well as comments on taxonomic affinity between the two species and Thelypteris subgenera.

Revisão taxonômica de Myrocarpus Allemão (Leguminosae, Papilionoideae, Sophoreae)

In Myrocarpus, an exclusively South American genus, five species are recognised: Myrocarpus frondosus Allemão, M. leprosus Pickel, M. venezuelensis Rudd, M. fastigiatus Allemãoand M. emarginatus A.L.B. Sartori & A.M.G. Azevedo. Morphologic data, habitat information and geographic distribution of each taxon are discussed. Petal morphology and ornamentation of seed chamber are an important character for species identification, though not shown previously. Key to the species, descriptions, illustrations, distribution, and new registers are presented.

Taxonomia do gênero Heliotropium L. (Heliotropiaceae) no Brasil

The taxonomy of the genus Heliotropium L. in Brazil was studied, revealing nine species and two varieties: H. amplexicaule Vahl, H. angiospermum Murray, H. curassavicum L., H. curassavicum var. argentinum I.M. Johnst., H. elongatum (Lehm.) I.M. Johnst., H. elongatum var. burchellii I.M. Johnst., H. indicum L., H. leiocarpum Morong, H. nicotianaefolium Poir., H. phylicoides Cham. and H. transalpinum Vell. Descriptions, illustrations, comments on relationships based on morphology and data on species distribution are presented.