17 papers · ranked by Valyu relevance
Hiranya Sudasinghe, Ralf Britz, Michael Matschiner, Kevin Conway + 11 more
Cypriniformes, the most species-rich order of freshwater fishes (∼5,000 species), represents a key lineage for understanding vertebrate diversification in freshwater ecosystems. This clade includes several highly miniaturized and understudied lineages whose phylogenetic placements have long remained contentious. Here…
Xun Gu
Rapid growth of entire genome data has revolutionized the field of phylogenomics, i.e., the problem of tree of life. Substantial studies demonstrated that genome phylogeny can be inferred based upon the generalized gene content approach. Two simple types were widely-used: the first-order gene content (J=1) for the…
Sudhir Kumar, Koichiro Tamura, Sudip Sharma
Long runtimes, high memory demands, and reliance on high-performance computing impede phylogenomic analyses. We review a scalable phylogenomic subsampling with upsampling (PSU) framework, in which small subsamples of sites from a concatenated alignment are expanded by upsampling before inference, and the resulting…
Marc Tollis, John H. Neddermeyer, Simone M. Gable
Phylogenomic-scale studies of the same clades using different markers and methods often support highly confident yet different species trees, obscuring many phylogenetic relationships and hampering comparative studies. Among reptiles, the >11,000 extant species of squamates (Order Squamata: lizards, snakes, and…
James O. McInerney, Christopher J. Creevey, Mary J. O’Connell
Phylogenetic inference relies on robust measures of branch support to assess the reliability of evolutionary relationships. While bootstrap resampling and Bayesian probabilities have become the predominant support metrics in molecular phylogenetics, decay indices (also known as Bremer support) provide an alternative…
Romain Derelle, John A. Lees, Leonid Chindelevitch
Amino acid-based phylogenetics usually relies on first clustering and aligning orthologous proteins. This approach is powerful but computationally demanding. Here, we present kamino, a reference- and alignment-free method that rapidly builds amino acid phylogenomic alignments directly from proteomes. As with similar…
Nimisha Maurya, Shefali Dobhal, George Sundin, Brendan Rodoni + 2 more
The genus Erwinia comprises a diverse group of bacteria associated with plants, insects, and the environment, including several economically important phytopathogens. The genus has been revised taxonomically many times, yet a thorough and genome-wide assessment of its evolutionary relationships and genomic diversity…
Lucas Vandenabeele, Anaïs Gibert, Pascaline Salvado, Roselyne Buscail + 4 more
Ophrys orchids (or bee orchids) provide an outstanding example of a plant adaptive radiation. Over the last five million years, this genus has diversified into hundreds of taxa as a result of its unconventional pollination strategy, known as ‘sexual swindling’. However, the rapid and substantial diversification of this…
Laura E. Tibbs-Cortes, Oliva C. Haley, John Portwood, Ethalinda Cannon + 2 more
Phylostratigraphic analysis identifies the evolutionary origins and level of conservation of proteins, facilitating research in evolutionary biology and comparative genomics. We developed the MaizeGDB Phylostrata Tool, a custom web application that enables users to explore the evolutionary origins of maize proteins.…
Laurence J. Belcher, Steven Kelly
Changes in gene content through gain and loss play a key role in the adaptation and diversification of species. Accordingly, our ability to detect and accurately document the history of these changes is important for our understanding the evolutionary trajectories of life on Earth. Here we present GLADE, a tool that…
Michael G. Branstetter, Felipe V. Freitas, Ligia R. Benavides Silva, Silas Bossert + 2 more
Genome-scale data have transformed phylogenetic inference, yet most studies continue to rely on reduced-representation approaches that target a subset of loci to reduce cost and increase taxon sampling. Although effective, these methods require specialized laboratory workflows, constrain long-term data reuse, and may…
Tian-Wen Xiao, Xue-Jun Ge
Sinia rhodoleuca, the sole species of the monotypic genus Sinia (Ochnaceae), was previously transferred to Sauvagesia based mainly on morphological similarities. However, its phylogenetic position has remained unresolved because molecular data for the species were unavailable. Here, we generated genomic data for Sinia…
Kathryn Kananen, Nghi Tran, Patrick H. Bradley
In microbiome studies, associations between microbial functions and the environment are often confounded by phylogeny. While some methods explicitly account for this confounder, they require information about genome content, limiting their use in biomes where few genomes have been available. To make these methods more…
Nicola De Maio
Maximum likelihood phylogenetic methods are popular approaches for estimating evolutionary histories. These methods do not assume prior hypotheses regarding the shape of the phylogenetic tree, and this lack of prior assumptions can be useful in particular in case of idiosyncratic sampling patterns. For example, the…
Katyayni Ganesan, Elisa Billard, Tom L. Kaufmann, Cody B Strange + 4 more
Phylogenetic trees play a fundamental role in elucidating evolutionary relationships among taxa. Clustering taxa remains a major challenge across diverse biological domains such as cancer genomics, microbial systematics, and phylogenomics. Several methods partition taxa in phylogenetic trees into clusters, but these…
Tom Carruthers, William J. Baker, Wolf L. Eiserhardt, Félix Forest + 3 more
Molecular datasets for estimating phylogenetic trees increasingly include more species and gene regions. Often trees are constructed using backbone phylogenies, subtrees, and other techniques to address the challenges of large dataset size. Currently, there is no established approach to integrate these rapidly…
Niels Holtgrefe
Reticulate evolutionary processes (events in which lineages merge, such as hybridization, recombination, and horizontal gene transfer) are widespread across nature but cannot be represented by phylogenetic trees alone. Phylogenetic networks have therefore become an important modelling tool, yet existing software is…