Orthology: definitions, inference, and impact on species phylogeny inference

Orthology is a central concept in evolutionary and comparative genomics, used to relate corresponding genes in different species. In particular, orthologs are needed to infer species trees. In this chapter, we introduce the fundamental concepts of orthology relationships and orthologous groups, including some non-trivial (and thus commonly misunderstood) implications. Next, we review some of the main methods and resources used to identify orthologs. The final part of the chapter discusses the impact of orthology methods on species phylogeny inference, drawing lessons from several recent comparative studies.