Distribution of branch lengths and phylogenetic diversity under homogeneous speciation models

DOI10.1016/J.JTBI.2011.11.019MaRDI QIDQ285204zbMATH OpenOpenAlexWikidataFDO

Authors Tanja Stadler, Mike Steel

Publication date 19 May 2016

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

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

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)

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.

Recommendations

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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
• Quantifying the effects of anagenetic and cladogenetic evolution
• Random walk Green kernels in the neutral Moran model conditioned on survivors at a random time to origin
• 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
• A consistent estimator of the evolutionary rate
• The expected length of pendant and interior edges of a Yule tree
• 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
• A phylogenetic comparative method for studying multivariate adaptation
• 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
• Bayesian-weighted triplet and quartet methods for species tree inference
• Birth-death models and coalescent point processes: the shape and probability of reconstructed phylogenies
• A critical branching process model for biodiversity
• 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

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