An approximately unbiased test of phylogenetic tree selection.

By Hidetoshi Shimodaira. Systematic Biology, 2002

2,735 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/155a6901d8ad1ddd64bbe65af86328faed519658

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Citations in the corpus

A preliminary multi gene phylogeny of the diatoms (Bacillariophyta): Challenges for future research (2010, methodology): “We chose the Approximately Unbiased test (Shimodaira 2002), which tends to produce a smaller confidence set and also corrects well for multiple comparisons.”
New insights into the phylogeny, systematics and DNA barcoding of Nemertea (2014, methodology): “Likelihood-based Shimodaira-Hasegawa (SH; Shimodaira and Hasegawa 1999) and approximately unbiased tests (AU; Shimodaira 2002) were carried out to assess statistical differences between a posteriori topological hypotheses of the completely unconstrained (i.”
Systematics of the Gracilariales (Rhodophyta) including new subfamilies, tribes, subgenera, and two new genera, Agarophyton gen. nov. and Crassa gen. nov. (2018, background): “…placed strong emphasis on two molecular results: the paraphyletic position of a single species, H. rangiferina (note: not the generitype), in relation to all other species of Gracilarieae in their concatenated phylogenetic tree, and results from the approximate unbiased test of Shimodaira (2002).”
Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade (2022, positive): “Each of the 10 phylogenies inferred under LG+R10 failed rejection by the approximately unbiased (AU) test ( Shimodaira, 2002 ) conducted to 10,000 replicates (lowest p-value = 0.283), including those whose branch supports failed to converge.”
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary (2008, positive): “framework using the approximately unbiased test (AU) [ 64 ] in CONSEL [65], along with a”
Comparative phylogeography of pitvipers suggests a consensus of ancient Middle American highland biogeography (2009, methodology): “…placement of Bothriechis lateralis as the sister lineage to Bothriechis bicolor (Crother et al., 1992) using the Shimodaira–Hasegawa (SH) test (Shimodaira & Hasegawa, 1999) and the approximately unbiased (AU) test (Shimodaira, 2002) implemented in the program consel (Shimodaira & Hasegawa, 2001).”
Congruent evidence from α-tubulin and β-tubulin gene phylogenies for a zygomycete origin of microsporidia (2003, methodology): “To more directly test whether microsporidia really do branch within the fungi, as opposed to branching as sister group to the fungi, alternative topologies of the individual genes and the combined data were tested using the Approximately Unbiased (AU) test (Shimodaira, 2002).”
Towards a phylogenetic classification of the Myxomycetes (2019, background): “An Approximately Unbiased test (AU) (Shimodaira 2002) of competing phylogenetic hypotheses was carried out.”
A Phylogeny and Timescale for Marsupial Evolution Based on Sequences for Five Nuclear Genes (2008, methodology): “KH tests can place overconfidence in the wrong tree; SH tests can be over conservative; and the AU tests compensate for these tree selection biases although it is only approximately unbiased (Shimodaira 2002).”
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era (2019, methodology): “…tests IQ-TREE 2 also provides fast and parallel implementations of existing tree topology tests including the Shimodaira-Hasegawa test (Shimodaira and Hasegawa 1999), the approximately unbiased (AU) test (Shimodaira 2002), and the expected likelihood weight (ELW) (Strimmer and Rambaut 2002).”
Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA (2006, methodology): “More sophisticated bootstrap techniques are available to correct for this bias (e.g., Efron et al. 1996, Shimodaira 2002); unfortunately, these are rarely implemented to measure nodal support.”
Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets (2017, background): “6; supplementary table S10, Supplementary Material online) (Shimodaira 2002).”
Higher-level phylogeny of the insect order Hemiptera: is Auchenorrhyncha really paraphyletic? (2011, methodology): “Site log likelihoods for the best-constrained trees and the optimal unpartitioned ML tree were computed in paup*: these values were used to compute the approximately unbiased (AU) statistical test of topologies (Shimodaira, 2002) with the program consel (Shimodaira & Hasegawa, 2001).”
Higher level molecular phylogeny of darkling beetles (Coleoptera: Tenebrionidae) (2014, methodology): “Whenever families, subfamilies or tribes were recovered as paraphyletic, we used the approximately unbiased test (AU-test; Shimodaira, 2002) to assess whether there was statistical support for their nonmonophyly.”
Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi) (2011, methodology): “To test tree robustness around regionally rearranged, questionable branches, we performed the Shimodaira approximately unbiased (au) test (Shimodaira, 2002) and the Kishino-Hasegawa (KH) test (Kishino & Hasegawa, 1989) using CONSEL, and RELL regional bootstrap probability (RBP) calculation with 10…”