Phylogenetic Genomics and Genomic Phylogenetics - Session Introduction

Phylogenetics has a long history, with many contributions to the field actually predating Darwin. Genomics, in contrast, is barely a decade old. While these two fields may be disparate in their ages, each has much to contribute to the further development of the other. Phylogenetics provides a rich source of methodologies able to facilitate and enhance genomic research. Genome structure and function analyses can be strengthened through examining evolutionary history, whereby patterns and rates of genomic evolution can be inferred. The analysis of evolutionary history is similarly empowered by a genomic perspective, providing both a wealth of characters ideally suited for phylogenetic analysis as well as interesting subject matter in the form of comparative genomics. This session includes three examples of research that address issues important to both phylogenetics and genomics. Zilversmit et al. provide a case study where high throughput sequencing enables phylogenetics at a genomic scale. Wang et al. propose novel phylogenetic algorithms and compare their performance to other phylogenetic algorithms designed to analyze gene order. Page and Cotton address the problem in genomic evolution imposed by gene duplication. Together, these studies address several important areas in the new field of phylogenomics. The genomic revolution has been both enabled and defined by high throughput DNA sequencing. Advances in DNA sequencing technologies have allowed for the generation of extremely large DNA sequence data sets, many including entire genomes. Zilversmit et al. demonstrate how high throughput sequencing efforts can be applied to phylogenetic questions, using the insect family Drosophilidae as an example. They outline a method that can be applied to other non-model organisms, enabling other researchers to apply high throughput techniques to phylogenetics. They discuss how the size of data sets affects the results of phylogenetic analyses, particularly as data sets grow to include many regions from throughout the genome. In this way, Zilversmit et al. present a study that is truly phylogenetic and genomic. Wang et al. present a novel phylogenetic method designed for gene order data, allowing researchers to conduct phylogenetic analyses using gene order data from whole or partial genomes. Gene order represents an attractive alternative to DNA sequence data, particularly when rates of DNA sequence evolution are high, or when divergence time is great. While DNA sequence data have provided an important source of characters for phylogenetic analyses in recent years, limitations associated with high rates of evolution together with the limited number of character …