Plastid gene sequences have been used commonly to resolve phylogenetic relationships of different groups of land plants. These relationships include the 1) basal monilophytes Equisetum, Ophioglossaceae, Psilotaceae, Marattiaceae, and Leptosporangiatae relationship, as well as the 2) rosid clades of angiosperms, the malvids (rosid II), the COM and the Nitrogen-fixing lineages relationship.
However, the plastid phylogenies are sometimes contradicted by those inferred from mitochondrial and nuclear genes and morphology. Close examination of the plastid genomic data, specifically the fast- evolving genes and certain nucleotide sites (points of interest), allowed us to falsify the phylogenies inferred from plastid sequences on the basis of convergent evolution of certain proteins. These troublesome sites or points of interest were found to have contributed to high bootstrap values at some nodes, which disappeared upon our removal of the sites from the data. The matrices without these sites produced phylogenies that agreed with those constructed with mitochondrial and nuclear gene sequences. We conclude that functional constraints on proteins led to certain sites convergently evolving the same nucleotides in the genome of different lineages. We attribute this effect to the relatively smaller size of the chloroplast genome as well as its faster evolving nature. This study demonstrates that molecular phylogenies even with high bootstrap support should not always be taken for granted as a representation of the underlying organismal phylogeny.
Audience Take Away Notes:
- The audience will learn about the convergent nature of plastid genomes.
- The audience will learn why certain plant phylogeny relationships exist when they are based off of plastid genomes.
- The audience will learn how to track points of interest (aka certain nucleotides) in a fast- evolving genome that can be removed to possibly remove the effect of convergence.