The conditioned reconstructed process.

By Tanja Gernhard. Journal of Theoretical Biology, 2008

1,020 citations recorded by the source corpus.

We investigate a neutral model for speciation and extinction, the constant rate birth-death process. The process is conditioned to have n extant species today, we look at the tree distribution of the reconstructed trees--i.e. the trees without the extinct species. Whereas the tree shape distribution is well-known and actually the same as under the pure birth process, no analytic results for the speciation times were known. We provide the distribution for the speciation times and calculate the expectations analytically. This characterizes the reconstructed trees completely. We will show how the results can be used to date phylogenies.

Subfields: Ecology, Nature and Landscape Conservation, Paleontology

View Paper: https://www.semanticscholar.org/paper/87b052d3a8fb5562f7b09515e37ef9848a50df3e

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Citations in the corpus

Direct long‐distance dispersal shapes a New World amphitropical disjunction in the dispersal‐limited dung moss Tetraplodon (Bryopsida: Splachnaceae) (2014, methodology): “Strict and uncorrelated log-normal relaxed clocks (Drummond et al., 2006) were both tested, with two speciation tree models: Yule and birth–death process (Gernhard, 2008).”
Bayesian Inference of Species Trees from Multilocus Data (2009, methodology): “For the divergence times, we use the reconstructed birth–death process (Gernhard 2008), parameterized by lineage birth and death rates λ and μ:”
StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates (2016, methodology): “First, 30 species trees were simulated according to a birthdeath process (Gernhard 2008) using biopy with 21 extant species, a speciation rate of 100 and a death rate of 30.”
The fossilized birth–death process for coherent calibration of divergence-time estimates (2013, methodology): “For all analyses using calibration priors (fixed-scaled, fixed-true, and hyperprior), we assumed a constant-rate reconstructed birth-death process [39, 40] as a prior on speciation times.”
Accurate model selection of relaxed molecular clocks in bayesian phylogenetics. (2012, methodology): “…for the simulations (Yule 1924), with a diffuse normally distributed prior on the log birth rate (log = 1.0, log = 1.25); a birth–death process (Gernhard 2008) was used as a prior on the speciation process for the empirical data analyses with a diffuse lognormal prior ( = 17.5, log = 2.5),…”
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space (2012, methodology): “…prior model on clock trees has been expanded to incorporate recent progress in the understanding of the linear constant birth–death process with complete sampling (Gernhard 2008), with random incomplete sampling (Stadler 2009), or with clustered or diversified sampling (H¨ohna et al. 2011).”
The coalescent structure of continuous-time Galton–Watson trees (2017, result): “This allowed Popovic to give some very interesting results about critical processes, and similar techniques were built upon in various ways by her and other authors [3, 9, 17, 19].”