Title : Going Beyond Statistics to Understand the Weaknesses of Chloroplast Phylogenetic Analysis
Abstract:
Leptosporangiatae, as well as rosid clades of angiosperms, the malvids (rosid II), the COM and the Nitrogen-fixing lineages. 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, were able to falsify the phylogenies inferred from these data on the basis of convergent evolution of proteins, that is, functional constraints on proteins led to certain sites convergently evolving the same nucleotides in different lineages. These troublesome sites were found to have contributed to high bootstrap values at some nodes, which disappeared upon removal of the sites from the data. The matrices without these sites actually produced phylogenies that agreed with those reconstructed with mitochondrial and nuclear gene sequences as well as morphology. This study demonstrates that molecular phylogenies even with high bootstrap support should not be taken for granted as a representation of the underlying organismal phylogeny, and they should be falsified using as much external evidence as possible.
Audience Take Away:
- 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.
