On the use of cartographic projections in visualizing phylo-genetic tree space

Phylogenetic analysis is becoming an increasingly important tool for biological research. Applications include epidemiological studies, drug development, and evolutionary analysis. Phylogenetic search is a known NP-Hard problem. The size of the data sets which can be analyzed is limited by the exponential growth in the number of trees that must be considered as the problem size increases. A better understanding of the problem space could lead to better methods, which in turn could lead to the feasible analysis of more data sets. We present a definition of phylogenetic tree space and a visualization of this space that shows significant exploitable structure. This structure can be used to develop search methods capable of handling much larger data sets

Phylogenetic search through partial tree mixing.

BACKGROUND: Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques. RESULTS: When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at http://dna.cs.byu.edu/psoda CONCLUSIONS: The use of Partial Tree Mixing in a partition based tree space allows the algorithm to quickly converge on near optimal tree regions. These regions can then be searched in a methodical way to determine the overall optimal phylogenetic solution

LIPIcs, Volume 277, GIScience 2023, Complete Volume

LIPIcs, Volume 277, GIScience 2023, Complete Volum

The Integration Of Morphology, Variation, And Phylogenetics To Better Understand Fossil Taxa And Their Modern Relatives

Morphology, or shapes, particularly of bones, is important for understanding how animals vary and, therefore, for understanding diversity. Comparison of morphology in animals can be used to make inferences on fossil organisms. At its base, fossil specimens are described and compared with other fossil and modern specimens, often to determine if they represent a new and distinct species, thereby increasing observed biodiversity through time. Dromaeosaurids (family Dromaeosauridae) are a group of dynamic, swift predatory dinosaurs, that have a sparse fossil record, particularly at the time of their extinction near the Cretaceous-Paleogene boundary. A recently recovered specimen from the latest Cretaceous of New Mexico represents a new genus and species and is the first diagnostic dromaeosaurid from the Maastrichtian of the southern United States (southern Laramidia). The specimen also reveals aspects of this dinosaurs behavior, including potential wounds or injuries consistent with an active predatory lifestyle, features that would have made it agile, and the presence of feathers on its forelimbs. The evolutionary relationships of this dinosaur were explored through phylogenetic analysis and shows multiple lineages of these dinosaurs at the end of the Cretaceous in North America. Additionally, the Maastrichtian members of these dinosaurs would have also been living in the same environments as the largest terrestrial predators known, the tyrannosaurids, with different species in the north and south living alongside different tyrannosaurid species, creating complex ecosystems with different sized predators presumably utilizing different predatory methods. Emydids (family Emydidae) are the most diverse and widespread family of turtles in the New World. Their fossil record is relatively well known, but more complete fossils are less common and little work has been done to understand the relationships of potential fossil members. New species within both subfamilies (Deirochelyinae and Emydinae) from approximately 5 million years ago increase our knowledge of the past biodiversity of the group. A new painted turtle helps show how Chrysemys has migrated through time and part of these biogeographic changes are controlled by temperature and climate conditions. A new species of Emydoidea represents the southern-most occurrence of the genus and suggests the physiological requirements of the species have changed through time. A new species of Terrapene shows features consistent with an aquatic or semi-aquatic lifestyle, and its position basally within the genus lends further credence to the hypothesis that the genus evolved from aquatic or semi-aquatic ancestors and has evolved to become more terrestrial through time. The new species also help researchers better understand previously known fossil species. Several fossil species considered to represent Chrysemys are found to be basally within the subfamily and potentially outside Chrysemys. Emydoidea lies phylogenetically close to Emys and is part of a clade of emydine turtles that can at least partially close their shells. Features of stem Terrapene species suggest features of T. ornata are basal and further suggests terrestrially has evolved multiple times in the genus or that there have been multiple reinvasions of the water. These studies look at morphological variation to determine the distinct nature of several new fossil species and use phylogenetic analyses to hypothesize evolutionary relationships. This information can be used to make inferences of the direct groups studied and closely related groups, but also can be used to investigate ancient ecosystems and local and regional habitats and climates, along with more generalized larger-scale conditions. These continue to add to our knowledge of biodiversity and increases the information and data we have to use toward further future studies as well

Généralisation de modèles métaboliques par connaissances

Genome-scale metabolic models describe the relationships between thousands of reactions and biochemical molecules, and are used to improve our understanding of organism’s metabolism. They found applications in pharmaceutical, chemical and bioremediation industries.The complexity of metabolic models hampers many tasks that are important during the process of model inference, such as model comparison, analysis, curation and refinement by human experts. The abundance of details in large-scale networks can mask errors and important organism-specific adaptations. It is therefore important to find the right levels of abstraction that are comfortable for human experts. These abstract levels should highlight the essential model structure and the divergences from it, such as alternative paths or missing reactions, while hiding inessential details.To address this issue, we defined a knowledge-based generalization that allows for production of higher-level abstract views of metabolic network models. We developed a theoretical method that groups similar metabolites and reactions based on the network structure and the knowledge extracted from metabolite ontologies, and then compresses the network based on this grouping. We implemented our method as a python library, that is available for download from metamogen.gforge.inria.fr.To validate our method we applied it to 1 286 metabolic models from the Path2Model project, and showed that it helps to detect organism-, and domain-specific adaptations, as well as to compare models.Based on discussions with users about their ways of navigation in metabolic networks, we defined a 3-level representation of metabolic networks: the full-model level, the generalized level, the compartment level. We combined our model generalization method with the zooming user interface (ZUI) paradigm and developed Mimoza, a user-centric tool for zoomable navigation and knowledgebased exploration of metabolic networks that produces this 3-level representation. Mimoza is available both as an on-line tool and for download atmimoza.bordeaux.inria.fr.Les réseaux métaboliques à l’échelle génomique décrivent les relations entre milliers de réactions et molécules biochimiques pour améliorer notre compréhension du métabolisme. Ils trouvent des applications dans les domaines chimiques, pharmaceutiques, et dans la biorestauration.La complexité de modèles métaboliques mets des obstacles á l’inférence des modèles, à la comparaison entre eux, ainsi que leur analyse, curation et amélioration par des experts humains. Parce que l’abondance des détailles dans les réseaux à grande échelle peut cacher des erreurs et des adaptations importantes de l’espèce qui est étudié, c’est important de trouver les correct niveaux d’abstraction qui sont confortables pour les experts humains : on doit mettre en évidence la structure essentiel du modèle ainsi que les divergences de celle-là (par exemple les chemins alternatives et les réactions manquantes), tout en masquant les détails non significatifs.Pour répondre a cette demande nous avons défini une généralisation des modèles métaboliques, fondée sur les connaissances, qui permet la création des vues abstraites de réseaux métaboliques. Nous avons développé une méthode théorétique qui regroupe les métabolites en classes d’équivalence et factorise les réactions reliant ces classes d’équivalence. Nous avons réalisé cette méthode comme une bibliothèque Python qui peut être téléchargée depuis metamogen.gforge.inria.fr.Pour valider l’intérêt de notre méthode, nous l’avons appliquée à 1 286 modèles métaboliques que nous avons extraits de la ressource Path2Model. Nous avons montré que notre méthode aide l’expert humain à relever de façon automatique les adaptations spécifiques de certains espèces et à comparer les modèles entre eux.Après en avoir discuté avec des utilisateurs, nous avons décidé de définir trois niveaux hiérarchiques de représentation de réseaux métaboliques : les compartiments, les modules et les réactions détaillées. Nous avons combiné notre méthode de généralisation et le paradigme des interfaces zoomables pour développer Mimoza, un système de navigation dans les réseaux métaboliques qui crée et visualise ces trois niveaux. Mimoza est accessible en ligne et pour le téléchargement depuis le site mimoza.bordeaux.inria.fr

12th International Conference on Geographic Information Science: GIScience 2023, September 12–15, 2023, Leeds, UK

No abstract available

The development and use of bioinformatic web applications for infectious disease microbiology

The ever-increasing generation and submission of DNA sequences, and associated biological data, to publicly available databases demands software for the analysis of the biological meanings held within. The web provides a common platform for the provision of tools enabling the concurrent deposition, visualisation and analysis of data collected by many users from many different locations. Open programmatic web standards allow the development of applications addressing diverse biological questions and, more recently, are providing methods enabling functionality more traditionally associated with desktop software to be provided via the internet. In this work I detail the development and use of web applications addressing different, but not exclusive, areas of infectious disease microbiology. Firstly, an application utilised by a group of researchers (including myself) to undertake a comparative genetic analysis of the capsular biosynthetic locus from serotypes of the pathogen Streptococcus pneumoniae is detailed. Secondly, an application widely used by communities of researchers and public health laboratories for the assignment of microbial isolates to strains via the internet: mlst.net is described. Thirdly, I describe a generic electronic taxonomy application for assigning strains to bacterial species, exemplified using sequences from the viridans group streptococci, the taxonomy of which is notoriously difficult to define. Lastly, I describe the use of web mapping tools for molecular epidemiological databases, such as mlst.net, and further detail their application to the European distribution of genotypes of Staphylococcus aureus, to catalogue the global distribution of the emerging amphibian fungal pathogen Batrachochytrium dendrobatidis and to provide geocoding tools to encourage users to submit and explore their own data in the geographical context they were collected. Each application has been designed with generality in mind and through reference to user workflows and biological examples, I demonstrate the extensibility and general applicability of current web development methodologies to enable the provision of applications addressing a diversity of biological questions

LIPIcs, Volume 244, ESA 2022, Complete Volume

LIPIcs, Volume 244, ESA 2022, Complete Volum

Dynamics of Religion

RGVV(History of Religion: Essays and Preliminary Studies) brings together the mutually constitutive aspects of the study of religion(s)—contextualized data, theory, and disciplinary positioning—and engages them from a critical historical perspective. The series publishes monographs and thematically focused edited volumes on specific topics and cases as well as comparative work across historical periods from the ancient world to the modern era