Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards.

By M. Brandley, A. Schmitz, T. Reeder. Systematic Biology, 2005

726 citations recorded by the source corpus.

Subfields: Genetics, Global and Planetary Change, Paleontology

View Paper: https://www.semanticscholar.org/paper/ef55bdeb7761e4c48de93e20beae6a34fa2b5b0d

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Citations in the corpus

Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration. (2010, background): “Partitioned models have been shown to improve likelihood scores considerably (Castoe et al. 2004; Brandley et al. 2005), while having a great effect on branch lengths (Marshall et al.”
Selecting optimal partitioning schemes for phylogenomic datasets (2014, background): “Choosing an appropriate model of molecular evolution (model selection) is an important part of phylogenetics, and can affect the accuracy of phylogenetic trees, divergence dates, and model parameters [1-11].”
Morphological Evolution in the Mulberry Family (Moraceae) (2009, methodology): “We tested the same hypotheses in a Bayesian framework using the 95% credible interval of trees sampled from the posterior distribution from Bayesian analyses of morphology and total evidence ( Buckley 2002 ; Brandley et al. 2005 ).”
Molecular phylogeny and historical biogeography of the cosmopolitan parasitic wasp subfamily Doryctinae (Hymenoptera:Braconidae) (2008, methodology): “A Bayesian approach (Buckley et al. 2002; Reeder 2003; Brandley et al. 2005) was used to test for alternative topologies not present in the 50% majority rule consensus trees derived from the two simultaneous analyses.”
Evidence for Gondwanan vicariance in an ancient clade of gecko lizards (2007, neutral): “That said, it is important to find the best model for each subset of data to minimize systematic error (Bull et al., 1993; Wilgenbusch & de Queiroz, 2000; Lemmon & Moriarty, 2004; Brandley et al., 2005).”
Conservation phylogenetics of the Asian box turtles (Geoemydidae, Cuora): mitochondrial introgression, numts, and inferences from multiple nuclear loci (2007, methodology): “Using the combined data partitions with mixed model analyses has the advantages of incorporating the maximum amount of information into an analysis while simultaneously accounting for the different evolutionary characteristics of the various data partitions (Brandley et al. 2005).”
Detecting the influence of climatic variables on species distributions: a test using GIS niche‐based models along a steep longitudinal environmental gradient (2008, methodology): “We chose sister species or closely related species based upon recent phylogenetic hypotheses (Cole & Hardy, 1981; Brandley et al., 2005; Hillis & Wilcox, 2005).”
Concordant molecular and phenotypic data delineate new taxonomy and conservation priorities for the endangered mountain yellow‐legged frog (2007, background): “because a single model of nucleotide substitution may not be appropriate for the ND1 and ND2 protein-coding genes and flanking and intervening tRNA genes ( Brandley, Schmitz & Reeder, 2005 ).”
A taxonomic revision of the Neotropical poison frog genus Ranitomeya (Amphibia: Dendrobatidae) (2011, background): “Values between 0 and 10 were interpreted as support for both hypotheses, and values less than 0 were interpreted as support against H A (Kass & Raftery 1995; Brandley et al. 2005; Suchard et al. 2005).”
Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. (2012, background): “Choosing an appropriate partitioning scheme is a central problem for most phylogenetic analyses (Brandley et al. 2005; Shapiro et al. 2006; McGuire et al. 2007; Li et al. 2008; Blair and Murphy 2011).”
Higher genetic diversity in introduced than in native populations of the mussel Mytella charruana: evidence of population admixture at introduction sites (2009, neutral): “The harmonic mean estimated marginal likelihood of the stationary phase samples generated by the sump command in MrBayes was used to calculate the 2 ln Bayes factors (Brandley et al., 2005).”
Improving marginal likelihood estimation for Bayesian phylogenetic model selection. (2011, background): “…the harmonic mean (HM) approach (Newton and Raftery 1994) is the most common approach for estimating marginal likelihoods, and hence BFs ( e.g., Nylander et al. 2004; Pagel and Meade 2004; Brandley et al. 2005; Bleidorn et al. 2007; Brown and Lemmon 2007; Alekseyenko et al. 2008; Praz et al. 2008).”
Evaluating the influence of connectivity and distance on biogeographical patterns in the south‐western deserts of North America (2016, methodology): “We chose to partition sequences by codon position because it has been demonstrated repeatedly that incorporating different rates of DNA evolution for each codon position outperforms single-partition strategies (Brandley et al., 2005; Fyler et al., 2005; Seago et al., 2011).”
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes (2013, background): “Similar to earlier studies, we find that the subfamily Scincinae (sensu [110]) is non-monophyletic, as Feylininae is nested within Scincinae (also found in [20,50,51,111]).”