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(Note that, throughout, all figures consider the case in which C and A retain the same duplicate. For each case there is an equivalent case in which C and B (but not A) retain the same duplicate).
In this case, it is more likely that X and C retain the same duplicate, and the expected NST internal branch length will be less than d.
For two post-duplication outgroups, the KNST branch length is e2-e1 (if both outgroups retain the same duplicate; Figure 3b,e) or 2d-e2-e1 (if different duplicates are retained; Figure 3c,d).
The total expected NST internal branch length is then equal to (i) the probability that X1 and C retain the same duplicate, 0.5(1+r2), times e1, plus (ii) the probability that X1 and C retain different duplicates, 0.5(1−r2), times the average of e2 and 2d-e2 (which is d).
Although species C represents an outgroup to species A and B, retention of the same duplicate copy in species A and C (left side) but the other copy in species B (right side) leads to a case in which the remaining copies in A and C are most closely related.
Using a post-duplication outgroup the internal branch length is either e, the time between the X/ABC and C/AB divergences (if X and C retain the same duplicate copy; Figure 1d) or 2d-e (if X and C retain different copies; Figure 1e).
Similar(43)
However, for the purposes of our experiment, which compares data fusion strategies using the same duplicated data, we do not expect this strategy to influence our recommendations for the preferred matching method.
In particular, we would like to dissect apart the molecular changes in the protein-coding region that occurred when persistent duplicates were young (an early stage of duplicate gene evolution) from those changes that occurred in the same duplicates after they became old (a later stage of duplicate gene evolution).
This analysis is not the same as a comparison of young to old duplicates, which involves comparing different genes that were duplicated at different times – instead it allows comparison of an early stage of evolution to a later stage of evolution of the same duplicates.
For "The Big Show" we used those same duplicate negatives.
Since they diverge from the same ancestor, duplicate gene pairs are expected to be more functionally related than non-duplicate pairs in the topology of biochemical networks.
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