Sequence length bounds for resolving a deep phylogenetic divergence

DOI10.1016/J.JTBI.2008.09.031MaRDI QIDQ1798740zbMATH OpenOpenAlexWikidataFDO

Authors Mareike Fischer, Mike Steel

Publication date 23 October 2018

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

Full work available at URL https://arxiv.org/abs/0806.2500

zbMATH Keywords

DNA sequencesMarkov processmaximum parsimonyphylogenetic tree

Mathematics Subject Classification ID

Problems related to evolution (92D15) Protein sequences, DNA sequences (92D20)

Abstract: In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary relationship accurately depends on the model of sequence evolution, the substitution rate, divergence times and the method used to infer phylogenetic history. A particularly challenging problem for phylogenetic methods arises when a rapid divergence event occurred in the distant past. We analyse an idealised form of this problem in which the terminal edges of a symmetric four--taxon tree are some factor ($p$) times the length of the interior edge. We determine an order $p^2$ lower bound on the growth rate for the sequence length required to resolve the tree (independent of any particular branch length). We also show that this rate of sequence length growth can be achieved by existing methods (including the simple `maximum parsimony' method), and compare these order $p^2$ bounds with an order $p$ growth rate for a model that describes low-homoplasy evolution. In the final section, we provide a generic bound on the sequence length requirement for a more general class of Markov processes.

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Cited in

(8)

• The impact and interplay of long and short branches on phylogenetic information content
• Fast phylogeny reconstruction through learning of ancestral sequences
• Conditions under which distributions of edge length ratios on phylogenetic trees can be used to order evolutionary events
• The optimal rate for resolving a near-polytomy in a phylogeny
• On the distribution of interspecies correlation for Markov models of character evolution on Yule trees
• Improving divergence time estimation in phylogenetics: more taxa vs. longer sequences
• Strategies for resolving cellular phylogenies from sequential lineage tracing data
• Logarithmic bounds on the posterior divergence time of two sequences

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