To verify an accumulation of proteins in a given ancestor term, we also compared the ratio of proteins annotated to a given GO term to the total number of proteins available from the GOA database, which was used as an unbiased standard dataset (Table S3 in additional file 5).
Recent approaches for context-dependent evolutionary modelling assume that the evolution of a given site depends upon its ancestor and that ancestor's immediate flanking sites.
As tandems of zinc-finger domains (ZFs) evolve quickly under duplications and deletions, it is not possible to determine whether the ancestor of a given tandem belonged to a KRAB-containing TF or not.
The absence of eukaryotic core components from the replication machinery of the ancestor of a given archaeal lineage would exclude the emergence of eukaryotes from one of its members (unless invoking an extremely unparsimonious scenario where the component was independently lost in all members of the lineage but only kept in the one that would have given rise to eukaryotes).
However, multiple direct ancestors of a given term may have child-parent relationships of their own.
In other words, all individuals of a given species share more common ancestors than they do with those of a closely related species.
However, most duplication-based heuristics try to duplicate all possible ancestor nodes of a given join node, in order to reduce the earliest start time (EST) of the join node, even though these ancestor nodes have already been allocated in previous steps.
Very dissimilar forms can evolve from a given type of ancestor, and similar-appearing forms can evolve entirely independently from unrelated ancestors.
Genealogical reconstruction, meaning comprehension of the total scope of ancestor-descendant relationships for a given set of individuals within a population or between different species, has reached its unprecedented resolution with introduction of modern sequencing techniques [ 1- 3].
The important point in calculating relatedness is not the number of intervening nodes along a given branch but the number of shared ancestors.
