Phylogenetics PG_D0001

Title : Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome
Author : Carolin Kosiol, Lee Bofkin, Simon Whelan
Year : 2005
Place of publish :Elsevier
Abstract :

Molecular evolutionary studies provide a means of investigating how cells function and how organisms adapt to their environment.
The products of evolutionary studies provide medically important insights to the source of major diseases, such as HIV, and hold the key
to understand the developing immunity of pathogenic bacteria to antibiotics. They have also helped mankind understand its place in
nature, casting light on the selective forces and environmental conditions that resulted in modern humans. The use of likelihood as a
framework for statistical modeling in phylogenetics has played a fundamental role in studying molecular evolution, enabling rigorous
and robust conclusions to be drawn from sequence data. The first half of this article is a general introduction to the likelihood method
for inferring phylogenies, the properties of the models used, and how it can be used for statistical testing. The latter half of the article
focuses on the emerging new generation of phylogenetic models that describe heterogeneity in the evolutionary process along sequences,
including the recoding of protein coding sequence data to amino acids and codons, and various approaches for describing dependencies
between sites in a sequence. We conclude with a detailed case study examining how modern modeling approaches have been successfully
employed to identify adaptive evolution in proteins.
2005 Elsevier Inc. All rights reserved.