Phylotranscriptomic analysis of the origin and early diversification of land plants

By N. Wickett, Siavash Mirarab, Nam-phuong Nguyen, Tandy J. Warnow, E. Carpenter, Naim Matasci, Saravanaraj N. Ayyampalayam, Michael S. Barker, J. Burleigh, Matthew A. Gitzendanner and 32 more. Proceedings of the National Academy of Sciences of the United States of America, 2014

1,136 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3920969e17109e4c99a8d6b61208bb0fc544ea04

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In Ecology, Evolution, Behavior and Systematics

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Citations in the corpus

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies (2016, methodology): “Nevertheless, the community has adopted MLBS as a standard way of estimating support using ILS-based summary methods; most biological studies using summary methods rely on site-only or site/gene MLBS (e.g., Song et al. 2012; Jarvis et al. 2014; Wickett et al. 2014; Prum et al. 2015).”
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes (2015, background): “Contact: smirarab@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.”
Fast and accurate detection of evolutionary shifts in Ornstein–Uhlenbeck models (2016, background): “The inference of evolutionary trees with thousands of taxa or thousands of genes demands complex mathematical models and computational tools (see for instance Bininda-Emonds et al. 2007; Wickett et al. 2014).”
Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. (2017, background): “Bryophyte phylogenetic relationships remain enigmatic, 288 Cell 171, 287–304, October 5, 2017 with nearly every possible topology proposed (Nishiyama et al., 2004; Qiu et al., 2006; Wickett et al., 2014).”
The timescale of early land plant evolution (2018, neutral): “topologies (14), but sequence heterogeneity makes inferring relationships among these early land plants difficult (36).”
Constructing a broadly inclusive seed plant phylogeny. (2018, positive): “…rootward nodes that identify major clades using genomic and/or transcriptomic data with sophisticated analyses that can incorporate more complex evolutionary models (Wickett et al., 2014; Yang et al., 2015; Givnish et al., 2015; McKain et al., 2016; Comer et al., 2016; Walker et al., 2017).”
TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees (2018, methodology): “Four unfiltered gene trees from a Plant dataset [23] are shown (top).”
A community‐derived classification for extant lycophytes and ferns (2016, background): “Monophyletic (Pryer et al., 2001, 2004; Qiu et al., 2007; Schneider et al., 2009; Ruhfel et al., 2014; Wickett et al., 2014; Rothfels et al., 2015).”
Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next‐gen approaches (2015, background): “Most studies published using RNASeq were exploring deep divergences (e.g., Timme et al., 2012; Wickett et al., 2014; Zeng et al., 2014), and a few also studied family-level or lower-level relationships (Wen et al., 2013; Ma et al., 2015).”