Orthologous

 1.     During evolution, it is very common for a gene to be duplicated. The copies continue to evolve separately, resulting in two (or more) similar instances of the same gene along the genome of a species. Therefore, when discussing matching genes in different species, we differentiate between orthologous matches - which means both genes are ``the same'' gene in the strong sense - they are connected directly, and not through a duplication, paralogous matches - which are the result of some duplication along the evolutionary line, and xenologs (horizontal transfers) which are genes that are transfered between organisms in other ways (e.g., by virus). Therefore, if we base our analysis on paralogs or xenologs (rather than orthologs) we are in big trouble. However, throughout this lecture we will assume there were no gene duplications. Many important patterns and processes vary across the phylogeny and depend on phylogenetic scale. Nonetheless, phylogenetic scale has never been formally conceptualized, and its potential remains largely unexplored. Here, we formalize the concept of phylogenetic scale, review how phylogenetic scale has been considered across multiple fields and provide practical guidelines for the use of phylogenetic scale to address a range of biological questions.