As the transition states of distantly related SH3 domains were previously found to be very similar, we conclude that the free energy landscape of this protein family contains deep features which are relatively insensitive to sequence variations but can be altered by changes in topology.
Class II effects are similar, but they require substitution of phylogenetic signal with the effect that a clade shares only character states with distantly related taxa.
Each of these descriptions will help people to recall knowledge that is more distantly related to the domain in which the problem is stated.
The presence of considerable sequence conservation in more distantly related isolates rather than among close relatives, combined with the observations stated above, is a pattern consistent with the potential plasmid location of these sequences.
Thus, the frequently stated view that increased taxon sampling can help MP avoid long-branch attraction problems may only be true if the added taxa are not distantly related long-branch clades themselves.
New York State's Publicist (Distantly) Hal? Hello?
The discovery of behavioral state barriers in two distantly related phyla suggests that this property of nervous systems either emerged at least twice independently or that it arose early in evolution predating the split between arthropods and chordates.
Nevertheless, the incongruence observed in a few cases indicates that homoplasy is present in recoded data and is not correctly handled by the CAT+Γ model; not surprisingly, when a profile affiliation changes, it can either revert to the ancestral state or converge toward a state independently acquired in a distantly related clade.
Thank God this can never happen in Alabama, a state in the Heart of Dixie, very distantly located from the Mexican-American border.
Substitution processes not only produce phylogenetic signal (apomorphic character states) but also chance similarities that may attract distantly related clades in a topology.
This more distantly related material shows some identical-by-state (IBS) similarity, therefore it was not unrelated in the theoretical sense of population genetics.
