Distribution of branch lengths and phylogenetic diversity under homogeneous speciation models

DOI10.1016/J.JTBI.2011.11.019zbMATH Open1336.92056arXiv1107.5926OpenAlexW2131157335WikidataQ67213658 ScholiaQ67213658MaRDI QIDQ285204FDOQ285204

Authors: Tanja Stadler, Mike Steel 

Publication date: 19 May 2016

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Abstract: The constant rate birth--death process is a popular null model for speciation and extinction. If one removes extinct and non-sampled lineages, this process induces `reconstructed trees' which describe the relationship between extant lineages. We derive the probability density of the length of a randomly chosen pendant edge in a reconstructed tree. For the special case of a pure-birth process with complete sampling, we also provide the probability density of the length of an interior edge, of the length of an edge descending from the root, and of the diversity (which is the sum of all edge lengths). We show that the results depend on whether the reconstructed trees are conditioned on the number of leaves, the age, or both.

Full work available at URL: https://arxiv.org/abs/1107.5926

Recommendations

• The conditioned reconstructed process
• Birth-death models and coalescent point processes: the shape and probability of reconstructed phylogenies
• The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events
• Probability distribution of tree age for the simple birth-death process, with applications to distributions of number of ancestral lineages and divergence times for pairs of taxa in a Yule tree
• New analytic results for speciation times in neutral models

zbMATH Keywords

phylogenetic treebirth-death processbranch lengthYule model

Mathematics Subject Classification ID

Problems related to evolution (92D15) Applications of branching processes (60J85) Population dynamics (general) (92D25)

Cites Work

• On incomplete sampling under birth-death models and connections to the sampling-based coalescent
• The conditioned reconstructed process
• A critical branching process model for biodiversity
• New analytic results for speciation times in neutral models
• Lineages-through-time plots of neutral models for speciation
• Minimal clade size and external branch length under the neutral coalescent
• Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today.
• Sampling-through-time in birth-death trees
• Distribution of phylogenetic diversity under random extinction
• Einführung in die Wahrscheinlichkeitstheorie und Statistik
• Title not available (Why is that?)
• The expected length of pendant and interior edges of a Yule tree

Cited In (25)

• The impact and interplay of long and short branches on phylogenetic information content
• Evolutionary isolation and phylogenetic diversity loss under random extinction events
• The conditioned reconstructed process
• Lineages-through-time plots of neutral models for speciation
• Exact and approximate limit behaviour of the Yule tree's cophenetic index
• Random walk Green kernels in the neutral Moran model conditioned on survivors at a random time to origin
• Quantifying the effects of anagenetic and cladogenetic evolution
• The generalized time variable reconstructed birth-death process
• Interspecies correlation for neutrally evolving traits
• Some properties of the conditioned reconstructed process with Bernoulli sampling
• The expected loss of feature diversity (versus phylogenetic diversity) following rapid extinction at the present
• The expected length of pendant and interior edges of a Yule tree
• A consistent estimator of the evolutionary rate
• Phylogenetic effective sample size
• Majority rule has transition ratio 4 on Yule trees under a 2-state symmetric model
• Conditions under which distributions of edge length ratios on phylogenetic trees can be used to order evolutionary events
• On the Distribution of Lengths of Evolutionary Trees
• Probability distribution of tree age for the simple birth-death process, with applications to distributions of number of ancestral lineages and divergence times for pairs of taxa in a Yule tree
• A phylogenetic comparative method for studying multivariate adaptation
• Bayesian-weighted triplet and quartet methods for species tree inference
• A critical branching process model for biodiversity
• Birth-death models and coalescent point processes: the shape and probability of reconstructed phylogenies
• Phylogenetic confidence intervals for the optimal trait value
• A characterisation of the reconstructed birth-death process through time rescaling
• Modeling a trait-dependent diversification process coupled with molecular evolution on a random species tree

This page was built for publication: Distribution of branch lengths and phylogenetic diversity under homogeneous speciation models

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q285204)