Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences

By J. Regier, J. Shultz, A. Zwick, April Hussey, Bernard Ball, R. Wetzer, Joel W. Martin, C. Cunningham. Nature, 2010

939 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics

View Paper: https://www.semanticscholar.org/paper/0d2f145f7be6abbb4c4fa69d20723687dbc8f7ae

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In Ecology, Evolution, Behavior and Systematics

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Citations in the corpus

PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. (2013, methodology): “15,andeffectivesample CATand10daysunderCAT–GTR.Asfornucleotides, Page:613 611–615 Philippeetal.2009, ,2011b).”
A systematic monograph of the Recent Pentastomida, with a compilation of their hosts (2013, background): “…Edgecombe, 2010: 72 (total evidence cladistic analysis with fossil Yicaris, total evidence for sistergroup relationship Raillietiella – Argulus); Regier et al., 2010: 1079 (arthropod relationships based on nuclear protein-coding sequences; mystacocarids included in Oligostraca); Poore,…”
A molecular phylogeny for the pyraloid moths (Lepidoptera: Pyraloidea) and its implications for higher‐level classification (2012, methodology): “Second, we used the ‘degen-1’ coding of Regier et al. (2010), which in effect excludes synonymous change (only) entirely.”
Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data (2011, background): “They concluded that Table 5 Information criteria of nonpartitioned, proportional and separate models at the data of Regier et al. (2010)”
Increased gene sampling yields robust support for higher‐level clades within Bombycoidea (Lepidoptera) (2011, methodology): “In a separate attempt to analyse nonsynonymous change but without excluding entire characters, a ‘degen1 analysis’ was performed on characters in which all nt1 and nt3 characters that could possibly undergo synonymous change based on the ‘universal’ genetic code were fully degenerated, using standar”
Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae) (2018, background): “…the paraphyletic vs monophyletic Cerambycinae in the NT and AA © 2017 The Royal Entomological Society, Systematic Entomology, 43, 68–89 trees, respectively), there is clearly some incongruity in support and topology between the AA and NT analyses, which is not uncommon (e.g. Regier et al., 2010).”
FOSSIL CALIBRATIONS FOR THE ARTHROPOD TREE OF LIFE (2016, methodology): “Monophyly is established based on phylogenetic analysis of nuclear protein-coding genes (Regier et al., 2010, 2005; Sasaki et al., 2013), transcriptomes (Misof et al., 2014; Simon et al., 2012), and morphology (Legg et al., 2013).”
BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics (2011, methodology): “This dataset was a subset of a larger arthropod dataset (Regier et al. 2010).”
The new systematics of scleractinia: Integrating molecular and morphological evidence (2016, positive): “Although coral molecular phylogenetic studies generally focus heavily on few mitochondrial or ribosomal markers, and whilst these have greatly improved our understanding of scleractinian phylogenetic relationships, it is now clear that to achieve higher resolution and to be able to investigate all t”
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes (2012, background): “Twenty-six were selected based on their inclusion in broad-scale eukaryotic phylogenetic studies (21, 39) and other projects (40, 41).”
The genome of Tetranychus urticae reveals herbivorous pest adaptations (2011, neutral): “At each time point (grey circles), the number of gains (1) and losses (2) of gene families is indicated as inferred by DOLLOP (black) and CAFÉ (red) programs.”
Revised systematics of Palaeozoic ‘horseshoe crabs’ and the myth of monophyletic Xiphosura (2013, methodology): “For this analysis pycnogonids were treated as ingroup taxa, contra the Cormogonida hypothesis, as supported by a number of recent molecular analyses (Regier et al., 2010; Rota-Stabelli et al., 2011).”