Incongruence of Gene Trees

• Published in: Phylogenomics Vol. 1; pp. 199 - 211
• Main Authors: DeSalle, Rob, Tessler, Michael, Rosenfeld, Jeffrey
• Format: Book Chapter
• Language: English
• Published: CRC Press 2021
• Edition: 2
• Subjects: ILD; Individual Gene Trees; Data Sets; Incomplete Lineage; Strict Consensus Tree; Likelihood Ratio Test Approach; Phylogenetic Signal; Phylogenetic Analysis; DNA Barcoding Study; Incongruence Length Difference Test; DNA Databank; Incomplete Lineage Sorting; Incongruence Problem; Majority Rule Consensus Tree; Coalescent Methods; Gene Trees; KH Test; Consensus Tree; Species Tree; Hgt; Coalescent Approach; Horizontal Transfer; Sh Test; Gene Tree Topologies; Gene Partitions
• ISBN: 0367028522; 9780367028497; 0367028492; 9780367028527
• DOI: 10.1201/9780429397547-19

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. This chapter discusses some programs that infer phylogeny when problems like incomplete lineage sorting and horizontal transfer are prevalent. Relationships among microbes are difficult to address by morphology. The incongruence length difference test uses parsimony, and Shimodaira-Hasegawa and Kishino-Hasegawa likelihood ratio tests assess likelihoods to determine whether two gene partitions are incongruent. Coalescence theory was developed to examine these kinds of phenomena during the evolutionary process, and can help biologists make inferences at the level of populations. Other methods for dealing with the incongruence are consensus trees, supermatrices, and supertrees. Some programs use input from both gene trees and species trees to resolve the gene tree/species tree problem. Programs have been developed to construct nets or webs from data where researchers suspect that horizontal gene transfer has been prevalent. All are based on the premise that there is a need for a richer visualization of the results of a phylogenetic analysis than a strictly bifurcating, non-reticulate tree.