For two of these 7 TD introns, regional repetitiveness enhances the probability of duplications in the CDS (FBgn0002526 and FBgn0050101).
We are interested in the probability distribution of duplication times of the reconstructed lineages (the lineages that have survived to the present time), because the phylogeny reconstructed from the sequences of contemporary species does not include the extinct lineages [ 35].
Because the probability of multiple duplication events affecting a single gene increases, the pairwise estimate of the duplication rate becomes increasingly inaccurate beyond dS = 0.3.
For example, duplication shadowing in the human genome contributes to ~10 fold increased probability of sequence duplication in specific regions compared to their distribution in other regions [ 33].
Ohnologues with a slow evolutionary rate and lower probability of further duplication were therefore predominant in slowly evolving tissues such as the ectoderm.
Genes are more likely to be co-regulated by pairs of TFs or pairs of miRNAs than by pairs of TF-miRNA, perhaps due to higher probability of evolutionary duplication events of shorter DNA sequences.
The results of models using an alternate tree topology with P. humanus more closely related to Holometabola, as inferred in [ 15, 28], were highly comparable, resulting in the same models being selected in all cases (see Additional file 1: Table S1 and S2).> -wrap-foot>> -wrap-foot> λ represents the probability of gene duplication and loss per gene per million years.
In that case, P(C r | N r )≈ P(C r, D i = 1| N r ) + P(C r, D i = 0| N r ) and the posterior probability of a duplication on that branch will be P(D i = 1| C r, N r ) = P(C r, D i = 1| N r )/ P(C r | N r ).
The duplication degeneration complementation model of gene duplication (Force et al. 1999) predicts that degenerative mutations in regulatory elements can increase (rather than reduce) the probability of duplicate gene preservation and predicts that the usual mechanism of duplicate gene preservation is the partitioning of ancestral functions rather than the evolution of new functions.
