Inferring ancestral sequences in taxon-rich phylogenies

TL;DR

This paper explores how increasing the number of species in phylogenetic studies can improve the accuracy of ancestral sequence inference, especially when sequence evolution varies across characters.

Contribution

It provides a collection of results analyzing the potential for more accurate ancestral sequence inference as the number of taxa grows.

Findings

More taxa can improve ancestral state reconstruction accuracy.

Complex variation in sequence evolution affects inference methods.

Increasing species number enhances understanding of evolutionary processes.

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.