Inferring ancestral sequences in taxon-rich phylogenies
From MaRDI portal
Publication:709172
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.
Recommendations
- Statistically consistent and computationally efficient inference of ancestral DNA sequences in the TKF91 model under dense taxon sampling
- Ancestral state reconstruction with large numbers of sequences and edge-length estimation
- The impact and interplay of long and short branches on phylogenetic information content
- Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites
- Consistency of Bayesian inference of resolved phylogenetic trees
Cites work
- Analyzing the fitch method for reconstructing ancestral states on ultrametric phylogenetic trees
- Broadcasting on trees and the Ising model.
- Distributions on bicoloured evolutionary trees
- Full reconstruction of Markov models on evolutionary trees: identifiability and consistency.
- Links between maximum likelihood and maximum parsimony under a simple model of site substitution
- Properties of phylogenetic trees generated by Yule-type speciation models
- Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today.
- Teasing Apart Two Trees
Cited in
(12)- Improving divergence time estimation in phylogenetics: more taxa vs. longer sequences
- Pairwise sequence alignment at arbitrarily large evolutionary distance
- Ancestral sequence reconstruction with maximum parsimony
- Ancestral state reconstruction with large numbers of sequences and edge-length estimation
- The influence of taxon sampling on Bayesian divergence time inference under scenarios of rate heterogeneity among lineages
- Majority rule has transition ratio 4 on Yule trees under a 2-state symmetric model
- Sufficient condition for root reconstruction by parsimony on binary trees with general weights
- Statistically consistent and computationally efficient inference of ancestral DNA sequences in the TKF91 model under dense taxon sampling
- Probabilistic ancestral sequences and multiple alignments
- Quantifying the accuracy of ancestral state prediction in a phylogenetic tree under maximum parsimony
- Necessary and sufficient conditions for consistent root reconstruction in Markov models on trees
- Hadamard phylogenetic methods and the \(n\)-taxon process
This page was built for publication: Inferring ancestral sequences in taxon-rich phylogenies
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q709172)
