Phenotypic and Evolutionary Distances in Phylogenetic Tree Reconstruction

Luciano Brocchieri

doi:10.4172/2329-9002.1000e106

Luciano Brocchieri

Open Access

https://doi.org/10.4172/2329-9002.1000e106

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Abstract

Copyright: © 2013 Brocchieri L. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Advances in sequencing technology and the resulting deluge of molecular sequence data have provided vast opportunities to study the evolution of gene and protein families together with the phylogenetic relations of the species harboring them. Each family of homologous sequences can provide hundreds or thousands of characters, that is, all homologous sites making up a sequence alignment, that are a potential source of valuable information for phylogenetic tree reconstruction. Moreover, molecular sequences have other advantages over, say, morphological characters. Among these, is a natural, unambiguous definition of “evolutionary distance”, which allows estimating the amount of evolutionary divergence of sequences, represented in phylograms. This precise definition of evolutionary distance stimulated the development over the last 35 years of evolutionary models that provide means to estimate evolutionary relations and to develop theories on how molecular sequences evolve, connecting phylogenetics to evolutionary biology [1-5].

Highlights

Advances in sequencing technology and the resulting deluge of molecular sequence data have provided vast opportunities to study the evolution of gene and protein families together with the phylogenetic relations of the species harboring them
Different models of how the evolutionary process depends on site and on amino acid or nucleotide type produce different inferences on the relation between evolutionary distance and phenotypic distance, all models result in similar general properties of this relation (Figure 1A): evolutionary distance is described by an increasing convex function of phenotypic distance, with slope 1.0 at phenotypic distance p=0.0, and tending to infinity as phenotypic distance approaches an asymptotic value
The evolution of molecular sequences is most often analyzed based on a multiple sequence alignment that identifies across a set of homologous sequences all homologous positions, each represented by a column in the alignment

Summary

Introduction

Advances in sequencing technology and the resulting deluge of molecular sequence data have provided vast opportunities to study the evolution of gene and protein families together with the phylogenetic relations of the species harboring them. In molecular phylogenetics evolutionary distances are unambiguously defined but can be estimated given a measurable phenotypic distance between sequences, the sequence dissimilarity. We notice that phenotypic distance between sequences is defined using elementary evolutionary events (substitutions), as the most parsimonious evolutionary distance between sequences (the p-distance), i.e., the minimum number of elementary evolutionary operations needed to transform one sequence into the other.

Results

Conclusion