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Robust Phylogenetic Regression
Systematic Biology, 2022 Abstract Modern comparative biology owes much to phylogenetic regression. At its conception, this technique sparked a revolution that armed biologists with phylogenetic comparative methods (PCMs) for disentangling evolutionary correlations from those arising from hierarchical phylogenetic relationships.
Richard Adams +3 more
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Phylogenetic context using phylogenetic outlines [PDF]
, 2021 A bstract Microbial studies typically involve the sequencing and assembly of draft genomes for individual microbes or whole microbiomes. Given a draft genome, one first task is to determine its phylogenetic context, that is, to place it relative to the set of related reference ...
Caner Bagci +3 more
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Distinguishing Phylogenetic Networks [PDF]
SIAM Journal on Applied Algebra and Geometry, 2018 Phylogenetic networks are becoming increasingly popular in phylogenetics since they have the ability to describe a wider range of evolutionary events than their tree counterparts. In this paper, we study Markov models on phylogenetic networks and their associated geometry.
Elizabeth Gross, Colby Long
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, 2023 Phylogenetic PCA (p-PCA) is a version of PCA for observations that are leaf nodes of a phylogenetic tree. P-PCA accounts for the fact that such observations are not independent, due to shared evolutionary history. The method works on Euclidean data, but in evolutionary biology there is a need for applying it to data on manifolds, particularly shapes ...
Morten Akhøj +2 more
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Uprooted Phylogenetic Networks [PDF]
Bulletin of Mathematical Biology, 2017 The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard model of a phylogenetic tree by also allowing for cycles and have been introduced in rooted and unrooted form.
Gambette, Philippe +2 more
openaire +6 more sources
Phylogenetic Factor Analysis [PDF]
Systematic Biology, 2017 51 pages (42 main, 9 supplemental), 9 figures (5 main, 4 supplemental), 4 tables (2 main, 2 supplemental), submitted to Systematic ...
Tolkoff, Max R. +4 more
openaire +5 more sources
Molecular Oncology, EarlyView.EXOSC10, an essential nuclear RNA exosome‐associated 3′‐5′ exoribonuclease, is inhibited by the anticancer drug 5‐fluorouracil (5‐FU), and EXOSC10 depletion increases 5‐FU sensitivity. The colon‐cancer variant EXOSC10S402T, located in a proteolysis motif, is stable and nuclear but nonfunctional in vivo.
Radhika Sain +10 more
wiley +1 more source
When monophyly is not enough: Exclusivity as the key to defining a phylogenetic species concept [PDF]
, 2009 A natural starting place for developing a phylogenetic species concept is to examine monophyletic groups of organisms. Proponents of "the" Phylogenetic Species Concept fall into one of two camps.
Velasco, Joel, Velasco, Joel D.
core
FEBS Open Bio, EarlyView.Despite frogs avoiding low temperatures, examination of four salamander species revealed that none avoided cold and all possessed cold tolerance. Functional analysis of TRPM8, a cold sensor, showed that all salamander TRPM8s had lost their cold sensitivity.
Tadahiro Sawao +3 more
wiley +1 more source
Letter: TreeAdder: a tool to assist the optimal positioning of a new leaf into an existing phylogenetic tree [PDF]
, 2007 TreeAdder is a computer application that adds a leaf in all possible positions on a phylogenetic tree. The resulting set of trees represent a dataset appropriate for maximum likelihood calculation of the optimal tree.
Gatherer, Derek
core +1 more source