The dark side of phylogeny: Percent homology, functional orthology, and other misunderstands
Channel: Lars Juhl Jensen
Date: 08/11/2021

A look at the dark side of phylogeny. The presentation covers how evolutionary concepts, such as homology and orthology, are commonly confused with sequence similarity and gene function, and how the lack of ground truth about evolution can result in shouting matches. You may want to watch my short introduction to the core concepts of phylogeny first: https://youtu.be/oJVa-FO0E9o

0:00 Introduction: mix-up of homologs / orthologs and how they are identified
0:24 Levels of homology: high / low / percent homology, common in literature, homology is binary, and confusion with sequence similarity
1:22 Functional orthologs: multiple orthologs, no one true / functional ortholog, and confusion of evolution, similarity, and function
2:45 Evolution is unknown: evolutionary concepts, clear definitions, limited practical use, inference methods, disagreement between methods, and lack of ground truth
3:58 What to do: keep concepts straight, sequence similarity, evolution of genes, evolutionary distance, and gene function annotation