Inferring ancestral sequences in taxon-rich phylogenies
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Publication:709172
DOI10.1016/J.MBS.2010.07.002zbMATH Open1197.92035arXiv1004.1212OpenAlexW2029474191WikidataQ44693455 ScholiaQ44693455MaRDI QIDQ709172FDOQ709172
Publication date: 15 October 2010
Published in: Mathematical Biosciences (Search for Journal in Brave)
Abstract: Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, as sequences are often of fixed length (e.g. for a gene) although we are often able to sample more taxa, it is useful to consider a dual type of statistical consistency where we increase the number of species, rather than characters. This raises some basic questions: what can we learn about the evolutionary process as we increase the number of species? In particular, does having more species allow us to infer the ancestral state of characters accurately? This question is particularly relevant when sequence site evolution varies in a complex way from character to character, as well as for reconstructing ancestral sequences. In this paper, we assemble a collection of results to analyse various approaches for inferring ancestral information with increasing accuracy as the number of taxa increases.
Full work available at URL: https://arxiv.org/abs/1004.1212
Applications of statistics to biology and medical sciences; meta analysis (62P10) Problems related to evolution (92D15)
Cites Work
- Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today.
- Broadcasting on trees and the Ising model.
- Full reconstruction of Markov models on evolutionary trees: identifiability and consistency.
- Properties of phylogenetic trees generated by Yule-type speciation models
- Links between maximum likelihood and maximum parsimony under a simple model of site substitution
- Teasing Apart Two Trees
- Analyzing the fitch method for reconstructing ancestral states on ultrametric phylogenetic trees
- Distributions on bicoloured evolutionary trees
Cited In (11)
- Ancestral state reconstruction with large numbers of sequences and edge-length estimation
- Hadamard phylogenetic methods and the \(n\)-taxon process
- Quantifying the accuracy of ancestral state prediction in a phylogenetic tree under maximum parsimony
- Pairwise sequence alignment at arbitrarily large evolutionary distance
- Majority rule has transition ratio 4 on Yule trees under a 2-state symmetric model
- Ancestral sequence reconstruction with maximum parsimony
- Necessary and sufficient conditions for consistent root reconstruction in Markov models on trees
- Sufficient condition for root reconstruction by parsimony on binary trees with general weights
- Probabilistic ancestral sequences and multiple alignments
- Statistically consistent and computationally efficient inference of ancestral DNA sequences in the TKF91 model under dense taxon sampling
- Improving divergence time estimation in phylogenetics: more taxa vs. longer sequences
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