Joint identifiability of ancestral sequence, phylogeny and mutation rates under the TKF91 model

2024/10/12 by Xue, Alex, Brandon Legried, Legried, Brandon +2
Biochemistry, Genetics and Molecular Biology · Medicine · #Cancer Genomics and Diagnostics #FOS: Biological sciences #FOS: Mathematics #Genetic factors in colorectal cancer #Genomics and Rare Diseases #Populations and Evolution (q-bio.PE) #Probability (math.PR) #Statistics Theory (math.ST)

paper · pdf · doi:10.48550/arxiv.2410.09620

openalex publication_date 2024/10/12 · openalex created_date 2024/10/20 · openalex updated_date 2026/07/28

Abstract

We consider the problem of identifying jointly the ancestral sequence, the phylogeny and the parameters in models of DNA sequence evolution with insertion and deletion (indel). Under the classical TKF91 model of sequence evolution, we obtained explicit formulas for the root sequence, the pairwise distances of leaf sequences, as well as the scaled rates of indel and substitution in terms of the distribution of the leaf sequences of an arbitrary phylogeny. These explicit formulas not only strengthen existing invertibility results and work for phylogeny that are not necessarily ultrametric, but also lead to new estimators with less assumption compared with the existing literature. Our simulation study demonstrates that these estimators are statistically consistent as the number of independent samples tends to infinity.

Related

• Statistically consistent and computationally efficient inference of\n ancestral DNA sequences in the TKF91 model under dense taxon sampling
• Identifiability and inference of non-parametric rates-across-sites\n models on large-scale phylogenies
• Identifiability of phylogenetic parameters from k-mer data under the coalescent
• Global Alignment of Molecular Sequences via Ancestral State Reconstruction
• Optimal Sequence Length Requirements for Phylogenetic Tree Reconstruction with Indels