Testing macro–evolutionary models using incomplete molecular phylogenies

By Oliver George Pybus, P. Harvey. Proceedings of the Royal Society of London. Series B: Biological Sciences, 2000

848 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/840faabcbcaff095406103a849f06794f6862246

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Citations in the corpus

Palaeotropical origins, boreotropical distribution and increased rates of diversification in a clade of edible ectomycorrhizal mushrooms (Amanita section Caesareae) (2015, methodology): “We also estimated the c-statistic (Pybus & Harvey, 2000) as a quantitative measure of deviation from”
Are the Northern Andes a species pump for Neotropical birds? Phylogenetics and biogeography of a clade of Neotropical tanagers (Aves: Thraupini) (2010, positive): “…framework with packages ape (Paradis et al., 2004), laser (Rabosky, 2006) and geiger (Harmon et al., 2007) was used to implement the Monte Carlo constantrates (MCCR) test following Pybus & Harvey (2000) and to create a lineage-through-time plot as a graphical representation of the ultrametric tree.”
Phylogenetic scale in ecology and evolution (2016, background): “Gamma statistic (Pybus & Harvey, 2000) laser (Rabosky, 2007) Community ecology and biogeography Community structure and phylogenetic diversity Phylometrics (NRI, NTI, MNND, MPD, PD) (Faith, 1992; Swenson, 2009; Webb et al., 2002) picante (Kembel et al., 2010), Phy-loMeasures (Tsirogiannis & Sandel,…”
Tip rates, phylogenies and diversification: What are we estimating, and how good are the estimates? (2019, background): “A related bias might arise due to incomplete taxon sampling, which disproportionately affects the length of terminal (or otherwise recent) branch lengths (Pybus & Harvey, 2000).”
APE: Analyses of Phylogenetics and Evolution in R language (2004, positive): “…are approaches such as phylogenetically independent contrasts (Felsenstein, 1985; Harvey & Pagel, 1991), ﬁtting birth–death models (Nee et al. , 1994; Pybus & Harvey, 2000), population-genetic analysis (Nee et al. , 1995; Strimmer & Pybus, 2001), non-parametric smoothing of evolutionary rates…”
A simple polytomy resolver for dated phylogenies (2011, methodology): “We simulate trees (10 000 trees for N = 10; 1000 trees for N = 100 and 500) under each method and compare the summary tree statistic, Pybus’ gamma, c (Pybus & Harvey 2000) using the program TreeStat v1.”
Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets (2013, background): “…a constant death rate (Nee et al. 1994). p<1 represents an apparent decrease in diversification rate toward the present, consistent with niche-filling models, or incomplete sampling of species within the clade (Pybus and Harvey 2000; Nee 2001; Phillimore and Price 2008; Rabosky and Lovette 2008).”
Phylogeny, ecology, and the origins of climate-richness relationships (2012, methodology): “We used the gamma statistic of Pybus and Harvey (2000) to test for diversity-dependent diversification within regions.”
Ecological opportunity and the origin of adaptive radiations (2010, positive): “The most common measure of this slowdown is the gamma statistic of Pybus & Harvey (2000), which compares observed sets of waiting times (i.e. ‘lag’ times between speciation events) to those expected under a uniform process of diversification.”
LASER: A Maximum Likelihood Toolkit for Detecting Temporal Shifts in Diversification Rates From Molecular Phylogenies (2006, methodology): “Approaches such as the gamma statistic (Pybus and Harvey, 2000) and survival analysis (Paradis, 1997), which are implemented in the R library ‘ape’ (Paradis et al.”
Early evolutionary history of the flowering plant family Annonaceae: steady diversification and boreotropical geodispersal (2011, positive): “In order to test for a constant rate of diversification under incomplete taxon sampling, null models are generally constructed (Pybus & Harvey, 2000) where a number of phylogenies are generated to a true standing species richness of the group and then pruned randomly to the number of taxa sampled.”