Troubleshooting Molecular Phylogenetic Analyses

By Michael J. Sanderson, H. B. Shaffer. 2002

311 citations recorded by the source corpus.

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

View Paper: https://www.semanticscholar.org/paper/0a8e4fd6b34962ede4a9ff758a92f8ccb2ce0900

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In Ecology, Evolution, Behavior and Systematics

In Molecular Biology

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Citations in the corpus

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice (2012, background): “As a consequence, such merged bipartitions are then contained in all trees that contained any of the previously distinct bipartitions.”
On wings of lace: phylogeny and Bayesian divergence time estimates of Neuropterida (Insecta) based on morphological and molecular data (2010, background): “…and analysis that often accompany multigene phylogenetics, especially when sampled genes differ significantly in evolutionary rate, copy number and substitution dynamics, and when cladogenetic radiations appear both ancient and rapid (Sanderson & Schaeffer, 2002; Whitfield & Lockhart, 2007).”
Inferring phylogeny despite incomplete lineage sorting. (2006, background): “suggestion by Takahata (1989). We recognize that these methods are not ideal.”
Relationships among the major lineages of Dictyoptera: the effect of outgroup selection on dictyopteran tree topology (2008, background): “The selection of outgroup taxa is a decision that should be made with care, as outgroup taxa that are too distant may erroneously polarize characters (Maddison et al., 1984; Wheeler, 1990; Maddison et al., 1992; Smith, 1994; LyonsWeiler et al., 1998; Nylander, 2001; Sanderson & Shaffer, 2002).”
Renewing Felsenstein’s Phylogenetic Bootstrap in the Era of Big Data (2018, background): “A difference of just one taxon (highly likely with large datasets) is sufficient for the replicated branch to be counted absent while it is nearly identical to the reference branch 13,20 .”
Genome-scale approaches to resolving incongruence in molecular phylogenies (2003, background): “Perhaps surprisingly, none of the factors known or predicted to cause phylogenetic erro”
Recent Advances in the (Molecular) Phylogeny of Vertebrates (2003, background): “There is controversy surrounding both their origin(s) in the Permian, 280–248 mya (Carroll 1988), and their interrelationships (Figure 1).”
A species-level phylogenetic supertree of marsupials (2004, background): “…clades from primary character data still presents a major challenge, both because of the difficulty in obtaining sufficient homologous data for many different species (Sanderson et al., 2003), and because of analytical limitations in reconstructing large phylogenies (Sanderson & Shaffer, 2002).”
Characterisation of the cacao somatic embryogenesis receptor-like kinase (SERK) gene expressed during somatic embryogenesis (2005, unknown): “So as to ensure that our results were consistent [30], we have also constructed the tree with NJ using Kimura-2 parameters model.”
Pitfalls in supermatrix phylogenomics (2017, unknown): “The approaches used to eschew inconsistency have been reviewed several times (e.g., Olsen 1987; Felsenstein 1988; Sanderson & Shaffer 2002; Soltis et al. 2004; Philippe et al. 2005a, 2011b) and will only be succinctly discussed here.”