Multigene phylogeny, phylogenetic network, and morphological characterizations reveal four new arthropod-associated Simplicillium species and their evolutional relationship [PDF]
Frontiers in Microbiology, 2022 Simplicillium species are widely distributed and commonly found on various substrates. A minority of species are associated with arthropods. A spider-associated species Simplicillium araneae, and three insect-associated species, Simplicillium ...
Wanhao Chen +5 more
doaj +3 more sources
Phylogenetic network analysis of SARS-CoV-2 genomes. [PDF]
Proc Natl Acad Sci U S A, 2020 Significance This is a phylogenetic network of SARS-CoV-2 genomes sampled from across the world. These genomes are closely related and under evolutionary selection in their human hosts, sometimes with parallel evolution events, that is, the same virus ...
Forster P +3 more
europepmc +2 more sources
Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. [PDF]
Proc Natl Acad Sci U S A, 2020 There is obvious interest in gaining insights into the epidemiology and evolution of the virus that has recently emerged in humans as the cause of the coronavirus disease 2019 (COVID-19) pandemic. The recent paper by Forster et al.
Mavian C +35 more
europepmc +2 more sources
Reply to Sánchez-Pacheco et al., Chookajorn, and Mavian et al.: Explaining phylogenetic network analysis of SARS-CoV-2 genomes. [PDF]
Proc Natl Acad Sci U S A, 2020 We calculated a phylogenetic analysis network of the 160 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) complete genomes submitted to the international Global Initiative on Sharing Avian Influenza Data (GISAID) database by early March 2020,
Forster P +3 more
europepmc +2 more sources
A divide-and-conquer method for scalable phylogenetic network inference from multilocus data. [PDF]
Bioinformatics, 2019 Reticulate evolutionary histories, such as those arising in the presence of hybridization, are best modeled as phylogenetic networks. Recently developed methods allow for statistical inference of phylogenetic networks while also accounting for other ...
Zhu J, Liu X, Ogilvie HA, Nakhleh LK.
europepmc +2 more sources
Phylogenetic network of infectious bronchitis virus: exploring the impact of migratory birds on viral clustering, evolution, and recombination [PDF]
Veterinary QuarterlyInfectious bronchitis virus (IBV) presents a major threat to global poultry production, necessitating a thorough understanding of its evolutionary relationships for effective control measures.
Yu-Chen Tai, Geng-Ming Hu, Chi-Ming Chen
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Applicability of several rooted phylogenetic network algorithms for representing the evolutionary history of SARS-CoV-2 [PDF]
BMC Ecology and Evolution, 2021 Background Rooted phylogenetic networks are used to display complex evolutionary history involving so-called reticulation events, such as genetic recombination.
Rosanne Wallin +3 more
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On Unrooted and Root-Uncertain Variants of Several Well-Known Phylogenetic Network Problems. [PDF]
Algorithmica, 2018 The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized.
van Iersel L +4 more
europepmc +3 more sources
Phylogenetic Network Analysis Revealed the Occurrence of Horizontal Gene Transfer of 16S rRNA in the Genus Enterobacter. [PDF]
Front Microbiol, 2017 Horizontal gene transfer (HGT) is a ubiquitous genetic event in bacterial evolution, but it seldom occurs for genes involved in highly complex supramolecules (or biosystems), which consist of many gene products.
Sato M, Miyazaki K.
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Exploring the Tiers of Rooted Phylogenetic Network Space Using Tail Moves. [PDF]
Bull Math Biol, 2018 Popular methods for exploring the space of rooted phylogenetic trees use rearrangement moves such as rooted Nearest Neighbour Interchange (rNNI) and rooted Subtree Prune and Regraft (rSPR).
Janssen R +4 more
europepmc +3 more sources