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Four new Liberonautes species of freshwater crabs are described from material collected during an expedition to the rainforests of Sierra Leone, West Africa. Liberonautes kasonko sp. nov., L. njala sp. nov., L. schubarti sp. nov. and L. sugarloaf sp. nov. are recognized based on a combination of morphological characters including the carapace, adult male chelipeds, and first gonopods, and on genetic evidence involving analyses of partial segments of the mitochondrial genes of COI, 16S rRNA and 12S rRNA. Diagnoses, illustrations, and a tree of phylogenetic relationships based on mtDNA sequences, as well as a map showing the distributions of the new species are provided. [ABSTRACT FROM AUTHOR]

The Indo-Australian genus Caltoris has over 15 species distributed from India through south China and SE Asia into New Guinea and Solomon Islands. Based on wing colouration, characters of male genitalia, and early larval stages on the host plant Phragmites karka, a new subspecies of Caltoris bromus (Leech, 1894), C. b. sadasiva ssp. nov., is described from the coastal lakes and mangrove associated swamps of Kerala, southern India on the western slopes of the Western Ghats. This is the first record of C. bromus from Western Ghats and Peninsular India. This extends the distribution range of the species from NE India to south-western India, adding it to the butterfly fauna of the Western Ghats. [ABSTRACT FROM AUTHOR]

ABSTRACT The state of Rio Grande do Sul (RS) is located in the extreme south of Brazil, within a transition region between the tropical and subtropical zones of South America that has been frequently affected by fluctuations in climate and vegetation over the last millennia. Palynomorphs preserved in sediments have provided excellent study material for paleoenvironmental reconstitutions of this region, as they reveal the source organisms and their respective environments over geological time. The present study was conducted to provide additional palynological reference material preserved in Quaternary sediments from the RS coastal plain for paleoenvironmental reconstruction studies. Here, we present taxonomic descriptions of pollen from 29 angiosperm taxa extracted along two Quaternary sedimentary profiles: the Pirataba forest profile (29° 15’ S 49° 51’W) and the Faxinal forest profile (29° 21’ S 49° 45’ W), Torres municipality, in the extreme north of the coastal plain of RS. Ecological data and pollen photomicrographs accompany the taxonomic descriptions. This reference material, together with the other palynomorphs found in the two sedimentary profiles, was the basis for our study of paleoenvironments from the last millennia in southern Brazil, according to the dynamics of climate and vegetation.

Two new species of the genus Macrobrachium Spence Bate have been described from near Mandalay of Ayeyarwady (Irrawaddy) River, Myanmar (22°2′37″N; 96°2′37″E). Macrobrachium univmandalay sp. nov. is closely related to Macrobrachium spinosum Cai & Ng, 2002 and Macrobrachium yui Holthuis, 1950 and is characterized by the presence of 10–12 dorsal teeth of which 3–4 post-orbital, first tooth at about 1/4th of anterior carapace; second chelate legs are dissimilar in size and shape in which carpus of major leg distinctly shorter than palm, cutting edges of fingers with 2 large and 2–3 smaller denticles at proximal part and without denticles on the distal half. Minor leg in which merus longer than carpus and palm, carpus shorter than palm as well as fingers and fingers without denticles in the cutting edges. M. spinosum and M. yui differ from this species in all these characters above. Macrobrachium ayeyarwadiense sp. nov. shows close affinity with Macrobrachium horstii de Man, 1892 and M. spinosum and can be easily separated on the basis of difference in characters of rostrum, position and arrangement of teeth on upper and lower margins, position of first dorsal tooth, distance between post-orbital edge and first dorsal tooth and its relation to rostrum length, length of antennular peduncle in relation to post-orbital carapace, shape and structure of 2nd cheliped, nature, size and arrangement of spines on outer and inner margins of ischium, merus, carpus, palm and fingers and nature of denticles on cutting edges of major and minor legs. The species can at once be identified on the absence of tubercles at distal half beyond larger denticles on fingers, convex nature of merus, carpus and disposition of spines on them, swollen palm and curved nature of movable finger and crossed nature of fingers distally of major 2nd peraeopod. Nature of long stiff setae on inner side of ischium, merus and carpus of major cheliped is characteristic to the species. Minor 2nd cheliped is also species specific in which the fingers are slender and curved so that a wide gap exists when closed. A note on Macrobrachium lamarrei (H. Milne Edwards 1937) is also given in the text. [ABSTRACT FROM AUTHOR]

Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448(T), were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.

It takes great effort to manually or semi-automatically convert free-text phenotype narratives (e.g., morphological descriptions in taxonomic works) to a computable format before they can be used in large-scale analyses. We argue that neither a manual curation approach nor an information extraction approach based on machine learning is a sustainable solution to produce computable phenotypic data that are FAIR (Findable, Accessible, Interoperable, Reusable) (Wilkinson et al. 2016). This is because these approaches do not scale to all biodiversity, and they do not stop the publication of free-text phenotypes that would need post-publication curation. In addition, both manual and machine learning approaches face great challenges: the problem of inter-curator variation (curators interpret/convert a phenotype differently from each other) in manual curation, and keywords to ontology concept translation in automated information extraction, make it difficult for either approach to produce data that are truly FAIR. Our empirical studies show that inter-curator variation in translating phenotype characters to Entity-Quality statements (Mabee et al. 2007) is as high as 40% even within a single project. With this level of variation, curated data integrated from multiple curation projects may still not be FAIR. The key causes of this variation have been identified as semantic vagueness in original phenotype descriptions and difficulties in using standardized vocabularies (ontologies). We argue that the authors describing characters are the key to the solution. Given the right tools and appropriate attribution, the authors should be in charge of developing a project's semantics and ontology. This will speed up ontology development and improve the semantic clarity of the descriptions from the moment of publication. In this presentation, we will introduce the Platform for Author-Driven Computable Data and Ontology Production for Taxonomists, which consists of three components: 1. a web-based, ontology-aware software application called 'Character Recorder,' which features a spreadsheet as the data entry platform and provides authors with the flexibility of using their preferred terminology in recording characters for a set of specimens (this application also facilitates semantic clarity and consistency across species descriptions); 2. a set of services that produce RDF graph data, collects terms added by authors, detects potential conflicts between terms, dispatches conflicts to the third component and updates the ontology with resolutions; and 3. an Android mobile application, 'Conflict Resolver,' which displays ontological conflicts and accepts solutions proposed by multiple experts. The presentation will consist of: 1. a report on the findings from a recent survey of 90+ participants on the need for a tool like Character Recorder; 2. a methods section that describes how we provide semantics to an existing vocabulary of quantitative characters through a set of properties that explain where and how a measurement (e.g., length of perigynium beak) is taken. We also report on how a custom color palette of RGB values obtained from real specimens or high-quality specimen images, can be used to help authors choose standardized color descriptions for plant specimens; and 3. a software demonstration, where we show how Character Recorder and Conflict Resolver can work together to construct both human-readable descriptions and RDF graphs using morphological data derived from species in the plant genus Carex (sedges). The key difference of this system from other ontology-aware systems is that authors can directly add needed terms to the ontology as they wish and can update their data according to ontology updates. The software modules currently incorporated in Character Recorder and Conflict Resolver have undergone formal usability studies. We are actively recruiting Carex experts to participate in a 3-day usability study of the entire system of the Platform for Author-Driven Computable Data and Ontology Production for Taxonomists. Participants will use the platform to record 100 characters about one Carex species. In addition to usability data, we will collect the terms that participants submit to the underlying ontology and the data related to conflict resolution. Such data allow us to examine the types and the quantities of logical conflicts that may result from the terms added by the users and to use Discrete Event Simulation models to understand if and how term additions and conflict resolutions converge. We look forward to a discussion on how the tools (Character Recorder is online at http://shark.sbs.arizona.edu/chrecorder/public) described in our presentation can contribute to producing and publishing FAIR data in taxonomic studies. [ABSTRACT FROM AUTHOR]

There is a wealth of information about the characteristics (traits) of organisms within collections of taxonomic descriptions of plants and animals called a 'Flora' or 'Fauna' of a region. However, such knowledge is usually encoded as text paragraphs, and is thus unavailable for immediate analysis. In order to make use of the knowledge embedded in taxon descriptions, text must be organised into standardised, queryable datasets. Despite the recent development of natural language processing (NPL) tools to analyse taxonomic descriptions to extract trait values, the complexity and specificity of these methods currently limits broad application. Accessible and flexible methods for extracting traits across large numbers of taxonomic descriptions are therefore needed. Here we present such an R-based workflow, which can be adapted for use on any organismal group using a language familiar to researchers in the biological sciences. We document a way to (1) assemble tens of thousands of taxonomic descriptions into a standardised format, (2) split the taxon descriptions into different topics, (3) extract trait values as defined by the user, and (4) assign traits described at the genus and family level to lower level taxa to maximise trait coverage. As a case study, we apply the workflow to a collection of taxonomic descriptions drawn from Australia's state and national floras and describe useful techniques for creating workflows and thereby research-grade trait datasets. Using this method, we were able to extract 615,812 trait values from 38 different plant traits. Trait data collated using this method are freely available as part of the AusTraits trait database and have already contributed to analyses in several scientific publications. [ABSTRACT FROM AUTHOR]

Premise of the Study: Phenotypic data sets are necessary to elucidate the genealogy of life, but assembling phenotypic data for taxa across the tree of life can be technically challenging and prohibitively time consuming. We describe a semi‐automated protocol to facilitate and expedite the assembly of phenotypic character matrices of plants from formal taxonomic descriptions. This pipeline uses new natural language processing (NLP) techniques and a glossary of over 9000 botanical terms. Methods and Results: Our protocol includes the Explorer of Taxon Concepts (ETC), an online application that assembles taxon‐by‐character matrices from taxonomic descriptions, and MatrixConverter, a Java application that enables users to evaluate and discretize the characters extracted by ETC. We demonstrate this protocol using descriptions from Araucariaceae. Conclusions: The NLP pipeline unlocks the phenotypic data found in taxonomic descriptions and makes them usable for evolutionary analyses. [ABSTRACT FROM AUTHOR]

Taxonomic descriptions contain valuable phenotypic data that is often not directly accessible for modern evolutionary, ecological, or biodiversity analyses. We describe a process for building a consensus-based controlled vocabulary from taxonomic descriptions for plants, which also can be applied for building controlled vocabularies for other taxon groups. Controlled vocabularies are useful as lexicons for text mining algorithms, as source of candidate terms for ontologies, and as guides to help future authors use domain vocabulary more appropriately and consistently. We extracted phenotypedescribing phrases terms from descriptions of 30 volumes of the Flora of North America and Flora of China and merged these with terms from the Categorical Glossary of the Flora of North America. Seven contributors placed the terms into a set of categories until there was an agreement among two or more categorizations per term. Term categorization makes the meaning of a term more explicit for the subsequent users of the glossary. The resulting "Plant Glossary" (terms and categorization of terms) contains 9228 terms grouped in 53 categories. Differences in term categorization represented 49% of the categorization effort, and the many differences among individual classifications can be attributed to individual interpretation of terms and to the fluid nature of descriptive language used in Floras. The difficulties experienced while classifying the terms allowed us to explore cases where the use of language can hinder the accurate and detailed annotation of taxonomic descriptions. The Plant Glossary represents a significant step towards creating and enriching formal ontologies for plant phenotypes as the semantic phenomena found through this exercise is useful background information for building ontologies. The glossary has been used by new software to parse and annotate plant taxonomic descriptions, and over 6000 new terms are available for creating ontologies. [ABSTRACT FROM AUTHOR]

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"Classical α-taxonomy" has different interpretations. Therefore, within the framework of an integrated taxonomic approach it is not relevant to divide taxonomy in different components, each being allocated a different weight of importance. Preferably, taxonomy should be seen in a holistic way, including the act of delimiting and describing taxa, based on different features and available methods, and taxonomy can not be interpreted without looking at evolutionary relationships. The concept of diversity itself is quite diverse as is the measure of diversity. Taxonomic descriptions of free-living aquatic nematodes are very valuable as they provide basic phenotypic information that is necessary for the functional ecological, behavioral, and evolutionary interpretation of data gathered from molecular analyses and of the organism as a whole. In general, molecular taxonomic analyses have the advantage of being much faster and of being able to deal with a larger number of specimens but also possess the important advantage of dealing with a huge amount of features compared to the morphology-based approach. However, just as morphological studies, molecular analyses deal only with partial of an organism.

Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448(T), were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.