Beware the traps of evolutionary history

When a gene in one species is similar to a gene in another species, the two genes very probably derive from a common ancestor and are thus termed ‘homologues.’ The more differences homologue genes have the further back in time is their ancestor. It is on the basis of these homologies that scientists manage little by little to reconstruct the Tree of Life. But evolutionary history can trip up anyone who tries to trace back its path. For example, it can happen that species carry similar genes which have not been directly inherited from a common ancestor. ‘It’s like the dolphin and the shark,’ compares Denis Baurain. ‘These animals superficially resemble each other because they respond to comparable functional constraints. Nonetheless, they are nothing like each other and do not share a recent common ancestor, the former being a mammal close to the hippopotami, the latter a cartilaginous fish which is 400 million years old.’ At the molecular level, this type of convergent evolution also occurs. Thus, two distant homologous genes can end up strongly similar to each other owing to a series of independent mutations. This is what is called homoplasy. Worse, some homologous genes are plagued by orthology issues, which means they exist in several copies in some genomes, or do not faithfully represent their genome because of gene transfer between sometimes very distant species (natural GMOs).

Obviously, such difficulties can confound phylogenomic analyses! To avoid being misled by these phenomena, it is thus  important to carefully check the orthology of the selected genes and to make use of models which handle homoplasy. ‘This is what we did with the two phylogenomic studies whose conclusions we had some doubts about,’ explains Denis Baurain.

After correction, the results of the three studies of the organismal evolution before the Cambrian fully agreed with each other: ‘they reveal that the evolutionary history of the first animals followed a trend of increasing complexity, from sponges to animals with bilateral symmetry, in passing through jellyfishes,’ points out Denis Baurain. ‘That may seem logical, but not all parts of the Tree of Life necessarily show the same trend,’ he continues. ‘Baker’s yeast, for example, is derived from a secondary simplification of a fungus which at the beginning was much more complex than it.’