ABSTRACT
Relationships among microbes are difficult to address by morphology. Instead, sequences from ribosomal RNA can be used as a tool for understanding the phylogeny of microbes because the “stem” portions are highly conserved, even among divergent organisms. To look at very closely related taxa, the mitochondrial genome was exploited as a phylogenetic tool. Particular regions of the mitochondrial genome change very rapidly, such that even closely related individuals within species will show variation. Out of necessity, the tools for dealing with incongruence of trees obtained from different sources have grown since the explosion of genome-level data. This is because, as more and more genes were sequenced, the incongruence of inferences made from these genes became evident. There are two major strategies when faced with multiple gene partitions: to combine (concatenate) or not. The subject of whether to concatenate or not is complicated. Statistical methods assess incongruence to decide whether information should be concatenated. The incongruence length difference test uses parsimony, and SH and KH likelihood ratio tests assess likelihoods to determine whether two gene partitions are incongruent. Not all gene trees reflect the species tree, owing to the genes having different evolutionary histories. This is known as the gene tree/species tree problem, and it can arise from natural selection, horizontal gene transfer, and/or lineage sorting. Coalescence offers a partial solution to the gene tree/species tree problem. Coalescence programs such as MP-ESTm BUCKy, ASTRAL, and BEST use both gene trees and species trees as input and attempt to take the coalescent into consideration when constructing phylogenetic trees.
