Phylogenomics

Abstract

All life on earth shares a common ancestor, and the aim of phylogenetic systematics is to reconstruct the tree or network of life. Shortly after the availability of the first pro- tein sequences, molecular phylogenetic approaches were developed to understand the evolutionary relationships between proteins (or genes). It became clear that gene trees will also help to unravel the phylogeny of species. The introduction of Sanger sequenc- ing and polymerase chain reaction (PCR) paved the way that genetic approaches became available across the scientific community and contributed to the rise of molec- ular phylogenetics. At the end of the 1990s, results from single-gene studies challenged the century-old textbook view of evolutionary relationships of many groups (e.g. ani- mals, plants). Fierce discussions regarding the validity of these results led to important methodological advances, and, nowadays, molecular phylogenies are broadly accepted to represent organismal relationships in textbooks. In the mid-2000s, the way of sequencing has been revolutionized, leading to a huge drop in its costs, and unprece- dented amounts of sequence data became affordable for every type of study and also for non-model organisms. This development transformed the field of molecular phy- logenetics to phylogenomics, where genome-scale data (genomes, transcriptomes) can be exploited. The term phylogenomics was already coined in 1998 by Jonathan Eisen (also known under his twitter handle @phylogenomics), who outlined the importance of phylogenetic methods for the annotation of genes without relying on direct (time consuming) functional studies. This underlines how deeply embedded phylogenetic methods are in the field of genomics