iTUPA: an online automated application to perform Topographic-Unit Parsimony Analysis.

SUMMARY: iTUPA is a free online application for automatizing the Topographic-Unit Parsimony Analysis (TUPA), which identifies areas of endemism based on topography. iTUPA generates species-occurrences matrices based on user-defined topographic units (TUs) and provides a parsimony analysis of the generated matrix. We tested iTUPA after a proposal of regionalization for the Brazilian Atlantic Forest. iTUPA can handle millions of species registers simultaneously and uses Google Earth high-definition maps to visually explore the endemism data. We believe iTUPA is a useful tool for further discussions on biodiversity conservation. AVAILABILITY AND IMPLEMENTATION: iTUPA is hosted on Google cloud and freely available at http://nuvem.ufabc.edu.br/itupa. iTUPA is implemented using R (version 3.5.1), with RStudio 1.1.453 used as the implementation IDE, Shiny 1.1.0 web framework, and Google Maps® API version 3.36.

GeX: an automated tool for generating XYD files for analysis of endemicity using VNDM.

In the last decade, a method widely used to delimit areas of endemism is the analysis of endemicity (AE), a non-hierarchical and grid-dependent algorithm implemented through the package NDM/VNDM. Its input files are based on lists of georeferenced taxa, and any mistakes in their preparation will influence the results of the analyses. We describe here a free online automated tool for generating the input files for VNDM from simple spreadsheets.

The man who loved flies: a biographical profile of Nelson Papavero .

Nelson Papavero is one of the major Brazilian zoologists. His contribution to the field began in the second half of the twentieth century, when he started publishing in the areas of entomology, systematics, biogeography, and history of science, while working at graduate courses and training teachers and students. Papavero was one of the earliest Brazilian advocates of Hennig's phylogenetic systematics. In his entomological work, his first widely recognised works were the Catalogue of South American Diptera and his essays on the history of Neotropical Dipterology. Papavero's greatest contribution however, is in his Special Courses on Zoological Systematics, as well as his numerous administrative positions during his academic career. All these were fundamental to the development of zoology and comparative biology in Brazil and other Latin American countries. Here we present a biography of Nelson Papavero, along with several personal anecdotes, and his role in the development of Brazilian biological systematics over the last 50 years. 

Harnessing the power of AI language models for taxonomy and systematics: a follow-up to "Can ChatGPT be leveraged for taxonomic investigations? Potential and limitations of a new technology" by Davinack (2023).

N/A.

Assessing Negative Welfare Measures for Wild Invertebrates: The Case for Octopuses.

Welfare metrics have been established for octopuses in the laboratory, but not for octopuses living in the wild. Wild octopuses are constantly exposed to potentially harmful situations, and the ability to assess the welfare status of wild octopuses could provide pertinent information about individuals' health and species' resilience to stressors. Here, we used underwater photos and videos to identify injuries and stress-related behaviors in wild Octopus insularis in a variety of contexts, including interacting with fishermen, interacting with other octopuses and fish, proximity to predators, in den, foraging, and in senescence. We adapted established metrics of octopus welfare from the laboratory to these wild octopuses. In addition to observing all of the stress measures, we also identified two previously unknown measures associated with decreased welfare: (1) a half white eye flash and (2) a half-and-half blotch body pattern. More than half of the individuals analyzed had arm loss, and almost half of the individuals had skin injuries. We also observed that irregular chromatophore expression and abnormal motor coordination were associated with interactions with fishermen. This is the first study to apply measures of welfare from the laboratory to wild octopuses. Our results may also aid in the identification of welfare measures for other wild invertebrates.

Realism in systematics through biogeographical consilience.

There is an overlooked gap between any phylogenetic hypothesis and the natural world shaped by historical evolutionary processes, since the main concern during phylogenetic analyses is solely the search for congruence among characters under a defined criterion. Given a scientific realistic view, however, phylogenetic hypotheses are scientific theories that try to depict the historical series of cladogenetic events among biological entities. In this sense, the challenge is to establish a form of measuring the degree of truthfulness of our phylogenetic hypotheses. Here, we advocate the use of consilient biogeographical hypotheses to recognize the biological meaning of a phylogenetic inference apart from its instrumentalist value. Our proposal is based on the assumption that robust biogeographical hypotheses allows us to be close to the real evolutionary history of taxa. © The Willi Hennig Society 2011.

[A life among insects and books: an interview with Nelson Papavero]. / Uma vida entre insetos e livros: entrevista com Nelson Papavero.

Nelson Papavero is one of the top representatives of Brazilian zoology. His decisive contributions to this science began in the second half of the twentieth century, when he started publishing in the areas of zoology, systematics, biogeography, and the history of science while also working at graduate courses and training teachers and students. He was key to the introduction of Hennig's phylogenetic systematics in Brazil and its chief advocate. His active participation in the creation of the Special Courses on Zoological Systematics within the National Council for Scientific and Technological Development and his work at numerous administrative posts which he held during his academic career were vital to the development of zoology and comparative biology in Brazil. His endeavors also reached into other Latin American countries, like Mexico and Argentina.

Comparing Phylogenetic Trees Side by Side Through iPhyloC, a New Interactive Web-Based Framework.

Current frameworks of side-by-side phylogenetic trees comparison face two issues: (1) accepting mainly binary trees as input and (2) assuming input trees having identical or highly overlapping taxa. However, cladistic comparative studies often lead with multiple nontotally resolved trees with nonidentical sets of taxa. We tackle these issues in this study, presenting the iPhyloC, an interactive web-based framework for comparing phylogenetic trees side by side. iPhyloC supports automatic identification of the common taxa in the input trees, comparison options between them, intuitive design, high usability, scalability to large trees, and cross-platform support. iPhyloC was tested using different trees and a supertree depicting the phylogenetic relationships within the insect order Diptera as examples.

A worldwide catalog of the Vermileonidae (Diptera: Brachycera).

The genera and species of worldwide wormlions (Diptera: Rhagionidae) are listed, with annotated references to nomenclature, synonymies and generic combinations, type localities, primary type depositories, distribution, and citations for the most recent revisions. The most diverse genera of the family are Vermileo Macquart, Vermipardus Stuckenberg and Lampromyia Macquart, with 13 described species each. The bulk of Vermileonidae diversity, with nearly half of the valid species, remains in the Afrotropical region.

BuM 2.0: Software for online generation of matrices for Brooks Parsimony Analysis.

Brooks Parsimony Analysis is a cladistic biogeographic method that aims to extract biogeographic information from phylogenetic trees, depicting from a group of cladograms a general pattern of relationships among the areas the taxa inhabit. We present here BuM 2.0, an online framework to automatically create matrices for Brooks Parsimony Analysis (BPA) using Baum Ragans algorithm for Matrix Representation with Parsimony.

A sketch-based system for modeling 3D objects: Applications to taxonomy.

We present a sketch-based system for modeling 3D objects with multiple contours as overlaid structures, allowing users to infer perceivable symmetries and occluded parts of the model prior to its automatic 3D reconstruction. Many approaches for sketch-based interfaces and modeling focus on the final drawing and 3D reconstruction of solid objects, exploring, as inputs, contours; however, when the subject consists of multiple drawings as overlaid structures, as usual in species descriptions, these approaches have to roughly infer or discard occluded parts. Unlike previous sketch-based techniques, we explore a set of 2D visual effects to enhance the visual perception of users while sketching multiple overlaid objects in single-view. The proposed system was applied to general simple zoological and botanical sketches as well as to published descriptions of species of Diptera, demonstrating its usefulness for taxonomy.

A catalog of Rhagionidae (Diptera: Brachycera) from Chile.

The genera and species of Chilean rhagionids (Diptera: Rhagionidae) are listed, with annotated references to nomenclature, synonymies and generic combinations, type localities, the primary type depositories, distribution, and citations for the most recent revisions. The genus Atherimorpha White is the richest genus in Chile, with 15 described species. Only Leptis basalis Philippi, 1865 is kept as incertae sedis in the family.

Endemism within endemism: a new species of Austroleptis Hardy, 1920 (Diptera: Austroleptidae) from the Brazilian Atlantic Forest highlands.

A third species of the southern temperate tabanomorph genus Austroleptis Hardy, 1920 (Diptera: Austroleptidae)-A. camposgerais sp. nov.-from the Brazilian Atlantic Forest is described and illustrated. A key for the species of the genus in Brazil is provided. Shared derived features indicate a sister group relationship between the new species and A. longirostris Fachin et al., 2018. Whatever the relationships among the species of this clade, however, there is a process of endemism within endemism in the Atlantic Forest: species at higher altitudes undergo vicariance process that do not affect lowland species distributed around the mountain chains. The low number of specimens known from highland species and the very restricted geographic distribution of each species strongly indicate the urgency to protect the natural environments at higher altitudes in Brazil.

Building combined MRP-matrices with BuM, an automated web-tool.

The most common methods for combining different phylogenetic trees with uneven but overlapping taxon sampling are the Matrix Representation with Parsimony (MRP) and consensus tree methods. Although straightforward, some steps of MRP are time-consuming and risky when manually performed, especially the preparation of the matrix representations from the original topologies, and the creation of the single matrix containing all the information of the individual trees. Here we present Building MRP-Matrices (BuM), a free online tool for generating a combined matrix, following Baum and Ragan coding scheme, from files containing phylogenetic trees in parenthetical format.

Primary hypotheses of global areas of endemism based on the distribution of Tabanomorpha (Diptera, Brachycera).

Areas of endemism, or worthy for conservation, are mainly determined based on large data sets of vertebrates and plants. Herein, we investigated the global distribution at the species-level of the infraorder Tabanomorpha (Diptera, Brachycera), identifying areas of endemism for the group. We performed an endemicity analysis through a grid-based method-NDM/VNDM-using 1,385 species (6,392 geographical records) of Tabanomorpha. The grid size of the analysis was 7º and we applied the loose consensus rule (31%) in the recovered areas. Our results revealed 479 total areas of endemism and 18 consensus areas: the whole Neotropical region, six areas in the Nearctic region, two in the Palearctic region, and three areas in each the Oriental, Australian, and African regions. There are parallels among our results and previously proposed bioregionalisation schemes established by other taxa, showing a way forward for using insects to determine global patterns of endemism.

Functional morphology and paleoecology of Pilosa (Xenarthra, Mammalia) based on a two-dimensional geometric Morphometrics study of the Humerus.

The relationship between humerus shape and the modes of exploring substrate among extinct and extant Pilosa (especially anteaters and ground sloths) were investigated here. We used geometric morphometrics and discriminant analyses to relate morphological patterns and their possible ecological categories. Our results suggest that plesiomorphic taxa such as Nothrotheriidae, most Megalonychidae and basal Megatheriidae tend to have more slender humerus, associated to generalist habitus (climbing, swimming and digging activities), and while Mylodontidae developed specialized digging habitus. Additionally, we inferred ground sloths which inhabited the Brazilian territory during the Quaternary likely occupied at least four different niches. Mammals display morphofunctional adaptations on the limbs which are reflected on their modes of substrate exploration. Herein, we analyzed the humerus morphology of ground sloths and anteaters. Our results suggest that most of the Pleistocene Mylodonts were fossorial taxa, while most of the Santacrucian sloths plus extant anteaters were semiarboreal or semiaquatic taxa. The Pleistocene Megatheriidae should be ambulatory.

First two species of Austroleptis Hardy (Diptera: Brachycera: Austroleptidae) from Brazil.

Two new species of the genus Austroleptis Hardy, so far known only from Australia and Chile, are described from the Brazilian Atlantic Forest-A. longirostris nov. sp. and A. papaveroi nov. sp. The species share clear apomorphic features of the genus, as the subdivision of female tergite 8. Both new species share a distinctive wing pattern, and a flagellomere 1 that is as wide as the more distal flagellomeres, features that clearly differentiate them from the Chilean and Australian species. It is likely that the Brazilian species compose a small clade apart from the Chilean species of the genus. A. longirostris nov. sp. has a particular long proboscis, even for the standards of non-tabanid tabanomorphs, while A. papaveroi nov. sp. has a stump on M3. The scutum coloration also helps to discriminate between both species. This is an additional example of a group in southern Brazil with southern temperate connections, i.e., involving southern Chile and Argentina and either Australia, New Zealand or both. Additional records and illustrations of Austroleptis atriceps Malloch and           A. penai Nagatomi Nagatomi from Chile are provided.