Exact(6)
CAFE infers an expansion at a given node if the number of genes in a gene family augmented compared to its number in a previous ancestral time point.
Similarly, a contraction is a reduction in the number of genes in a gene family compared its number in the previous ancestral time point.
A gain of a gene family can be considered as a particular case of an expansion for which the gene family was not present in the previous ancestral time point.
An e-node is terminated if it cannot be lengthened by the extension operation, if its extension score plus the scores of two previous ancestral extensions exceeds a threshold, or if a specified maximum depth is reached.
In contrast, the more consistent divergence time estimate inferred from the Y-chromosome data (t~2000 years; Table 4) may be related to the erasure of previous ancestral variation that seems to have caused the current predominance of haplogroup E3a-M2, leading to a better fitting of the Y-chromosome data to the model.
In previous ancestral sequence reconstruction studies, mutations of large effect are in fact usually loss-of-function rather than gain-of-function (e.g., RNaseA [ Jermann et al., 1995], chymase [ Wouters et al., 2003], and glucocorticoid receptors [ Bridgham et al., 2006; Ortlund et al., 2007; Carroll et al., 2008, 2011]).
Similar(54)
We do not know how individual mothers experienced the war, what was their previous or ancestral response to stress, or whether they were injured or bereaved in June 1967 and might have been medicated; and we do not yet know whether the risk of schizophrenia in the offspring might have been modified by events in post-natal life.
Also previous studies of ancestral state reconstruction have shown inconsistent ancestral states for the sword, depending on both how the sword was scored and which reconstruction methods were used [ 25- 27].
As with human GWA studies, we assumed no previous knowledge of ancestral haplotypes in the founder population, which precludes inference-based linkage analysis methods.
This criterion will miss enhancers such as those described in the previous paragraph: the ancestral function of these enhancers has been conserved but their sequences have become unalignable [ 18].
Contrary to our previous speculation, an ancestral urea amidolyase gene likely arose in bacteria and then appeared in the fungal lineage before the divergence of the subphyla Pezizomycotina and Saccharomycotina by prokaryote-to-eukaryote horizontal gene transfer.
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