Finally, to assess the influence that various gene tree inference methods have on the overall inferred species tree topology, we present topologies for each of the four gene tree inference methods, constructed from clade counts that were averaged over species tree inference methods and outgroup species.
Various approaches for obtaining a single supertree from several gene trees within the same set of genomes (sometimes referred to as a "species tree" in the literature) have been proposed [ 81- 83].
Incongruence may appear among gene trees for various reasons.
Individual F. keratoplasticum gene trees indicated various levels of intralocus homoplasy, with consistency indices (CI) ranging between 0.75 in TEF to 1.0 in RPB2, 3972, and 5439 (Table 1).
In light of current genome sequencing efforts and the ease of sequencing large numbers of independent gene loci using new generation sequencing technologies, it is important to find ways to differentiate between various explanations of gene tree incongruence.
The first algorithm (Algorithm 1), which accepts the input of type 2 (a collection of gene trees inferred for various genes), is suitable for inferring either diploid or polyploidy hybridization events occurred among the observed species, or for finding recombination events occurred at the chromosome level.
The accepted species tree [ 40, 48] was generated by hand and gene trees were generated using various nucleotide and amino acid substitution models in PHYLIP [ 49].
Unrooted gene trees can be analyzed through various methods of tree-cutting, the most famous so far being the methods of quartet decomposition that can inform us about evolution without necessarily providing a grand rooted unified evolutionary scheme, or requiring the reduction to a single graph (tree-like or web-like).
The causes of incongruence among and between gene trees and species trees may be ascribed to various factors, which have been extensively reviewed previously e.g., [ 31- 33].
Estimating the complete distribution of gene trees across genomes can provide novel insights into the various processes that shaped this gene tree variability.
