Background: Phylogeographic reconstructions serve as a basis to understand the spread and evolution of pathogens. Visualization of these reconstructions often lead to complex graphical representations which are difficult to interpret.
Result: We present EvoLaps, a user-friendly web interface to visualize phylogeographic reconstructions based on the analysis of latitude/longitude coordinates with various clustering levels. EvoLaps also produces transition diagrams that provide concise and easy to interpret summaries of phylogeographic reconstructions.
Conclusion: The main contribution of EvoLaps is to assemble known numerical and graphical methods/tools into a user-friendly interface dedicated to the visualization and edition of evolutionary scenarios based on continuous phylogeographic reconstructions. EvoLaps is freely usable at www.evolaps.org .
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http://dx.doi.org/10.1186/s12859-021-04386-z | DOI Listing |
BMC Plant Biol
December 2024
Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China.
Background: The genus Lithocarpus is a species-rich dominant woody lineage in East Asian evergreen broad-leaved forests. Despite its ecological and economic significance, the plastome structure and evolutionary history of the genus remain poorly understood. In this study, we comprehensively analyzed the 34 plastomes representing 33 Lithocarpus species.
View Article and Find Full Text PDFVirus Evol
November 2024
Research Laboratory, Botswana Harvard Health Partnership, Gaborone, Private Bag BO 320, Botswana.
Botswana, like the rest of the world, has been significantly impacted by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In December 2022, we detected a monophyletic cluster of genomes comprising a sublineage of the Omicron variant of concern (VOC) designated as B.1.
View Article and Find Full Text PDFCurr Biol
December 2024
CIRAD, UMR PVBMT, La Réunion, 97410 Saint-Pierre, La Réunion, France. Electronic address:
Fossils and other preserved specimens are integral for informing timing and evolutionary history in every biological system. By isolating a plant pathogen genome from herbarium-preserved diseased grapevine material from 1906 (Herb_1906), we were able to answer questions about an enigmatic system. The emergence of Pierce's disease (PD) of grapevine has shaped viticultural production in North America; yet, there are uncertainties about the geographic origin of the pathogen (Xylella fastidiosa subsp.
View Article and Find Full Text PDFDuring last two decades, morphological and genetic studies of the microcrustaceans from the family Moinidae Goulden, 1968 (Crustacea: Branchiopoda: Cladocera) were intensified. However, species diversity within this family remains underestimated. It refers to both subtropical and tropical areas of different continents that have traditionally been less studied compared with Central Europe and some other Palaearctic regions.
View Article and Find Full Text PDFBioinformatics
November 2024
Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven 3000, Belgium.
Motivation: Bayesian phylogeographic analyses are pivotal in reconstructing the spatio-temporal dispersal histories of pathogens. However, interpreting the complex outcomes of phylogeographic reconstructions requires sophisticated visualization tools.
Results: To meet this challenge, we developed spread.
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