If LGT is the cause of incongruence between concatenation and individual trees, we would have expected to see greater degrees of incongruence for more divergent prokaryotic data sets, which was not observed, although estimated rates of LGT suggest that LGT is responsible for at least some of the observed incongruence.
Pairs of identical twins with different infection statuses one was infected and the other was not had more divergent immune systems than sets of twins in which both were uninfected.
FAM62-like genes are identifiable in yeasts and fungi, but their more divergent sequences and general lack of introns set them apart from the group of metazoan FAM62 genes and I have not analysed them here.
Interestingly, the higher percentage of reciprocal expression found among the tandem duplicates in the ADA data set is partly due to the more divergent organ types, suggesting that expression patterns among the tandem duplicates may diverge more across different organ types than the WG duplicates when compared with the ARA data set.
The tolerated polymorphism rate was set to 5%, and thus sequences more divergent than 95% were separated and those more similar than 95% were grouped together.
Instructors may wish to consider introducing smaller data sets (Lents et al., 2010) or more divergent species (Young et al., 2013) to build student understanding of phylogenetics.
It was seen again that blastp missed many unannotated homologues, and setting less stringent E-values to include more divergent homologues also began incorporating non-CydX sequences.
Overall, these data show that PPARα governs a mostly divergent set of genes in mouse and human hepatocytes, although more significant overlap was observed at the pathway level.
The set of clusters based on 30% similarity threshold were more divergent; consequently, for some large clusters alignments were problematic.
The first data set consists of 26 E. coli and Shigella genomes, which are very closely related and the second data set consist of 32 Roseobacter genomes, which are far more divergent.
