20 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…
Anja Spang, Davide Pisani
There is more than sequence data that can be extracted from genome-scale datasets. New data types with phylogenetic potential exist and include, for example, presence and absence of gene families (eg ; ; ; ; ; ; ), as well as the more recently developed chromosome fusions with mixing (). However, new data types should…
Sudip Sharma, Sudhir Kumar, Carlos Schrago
Phylogenomic data are indispensable for establishing reliable relationships needed to build a robust Tree of Life. The superalignment approach concatenates hundreds or thousands of genomic segments, providing a straightforward, computationally efficient, and effective means of inferring phylogenies. However, 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…
Jackson H Turner, Ryan D Kuster, Margaret E Staton, John K Moulton + 1 more
Phylogenomics pipelines are designed to reconstruct evolutionary relationships among groups of organisms. Existing pipelines are dependent upon reference gene sets for which target copies may be retrieved through read-mapping. This read-mapping approach is limited by the availability of reference orthologs closely…
Sudhir Kumar, Koichiro Tamura, Sudip Sharma
Long runtime, high memory demands, and reliance on high-performance computing increasingly limit the evolutionary analysis of long phylogenomic datasets. We review a scalable framework based on phylogenomic subsampling and upsampling (PSU), in which many small subsamples of sites from a long concatenated sequence…
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…
Nan Song, Xingyu Lin, Menghan He, Qingbo Tang + 2 more
Background/Objectives: Aphids are among the most economically damaging agricultural pests globally. However, the internal phylogeny of their largest subfamily, Aphidinae, remains contentious, particularly regarding intergeneric relationships, tribal boundaries, and monophyletic status. Here, we coupled refined taxon…
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…
Guanghong Zuo
The phylogenetic tree serves as a fundamental tool for depicting the evolution of species and genes[1–3]. Phylogenetic trees are typically constructed using genetic information, such as DNA sequences and amino acid sequences, to infer evolutionary relationships[4–6]. Several approaches are available for constructing…
Liang Liu, David A. Liberles
Substitution model selection is central to phylogenetic inference and is commonly treated as a problem of identifying the substitutional complexity required to describe sequence evolution along a single tree. This framework implicitly assumes a shared genealogy across all sites, an assumption that is routinely violated…
Luc Blassel, Sauvage, Noémie, Barrat-Charlaix + 4 more
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution along phylogenetic trees, by searching for the tree maximizing the likelihood…
Kerui Huang, Wenyan Zhao, Huan Li, Ningyun Zhang + 14 more
Convergent evolution provides powerful evidence for natural selection, yet its molecular basis is typically sought in protein-coding amino acid substitutions. Whether adaptive pressures can drive the convergent evolution of synonymous codon usage bias (CUB) to override phylogenetic history remains a fundamental…
Jiayang Wang, Julia A. Palacios, Claudia Solís-Lemus
Phylogenetic networks are graphs inferred from molecular sequence data that represent ancestral histories shaped by reticulate processes such as recombination, hybridization, and horizontal gene transfer. We introduce a family of distance metrics for rooted, ranked, unlabeled phylogenetic networks, extending a…
Zhuoxin Zhang, Jieyu Wang, Fengyao Zhai, Jing Wang + 4 more
Phylogenetic inference traditionally relies on aligned characters under substitution models, but this framework becomes less reliable when alignments are unstable or when evolution is dominated by insertions, deletions, repeats, and other structural changes. We adapt Ladderpath as an alignment-free distance approach…
Aleksandr Koshkarov, Nadia Tahiri
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can preserve both taxa and branch-length information. This work introduces a…
Authors not listed
Sunlight driven transformations of plastics to dissolved organic carbon (DOC) is an important fate for plastic pollution in the ocean; however, the impact on microbial communities, including their abilities to adapt and metabolize plastic photo-products, is less understood. In this study, we characterized the…
Authors not listed
The new European (EU) regulation on water reuse explicitly incorporates antimicrobial resistance (AMR) into routine monitoring and risk management, creating an urgent need to define target antibiotic resistance genes (ARGs) for reclaimed irrigation water and agricultural sludge. However, existing global data largely…
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Extreme weather events increasingly threaten coastal water quality, yet the mechanisms by which tropical cyclones impair microbial conditions remain poorly quantified. We develop a Large Language Model–Assisted Microbial Source Tracking (LAMST) framework to trace the origins of microbial threats—fecal indicator…