Total counts of duplications were also computed discarding the fraction of duplications that is expected to be more sensitive to error annotation: lineage-specific duplications with highly similar duplicates and duplications found in recently assembled genomes (see main text).
In the tree reconciliation analysis, the steep decrease in inferred ancient duplications with increasing strictness in duplicate retention likely reflects such gene loss.
We found 124 subtrees with C. hamatus lineage-specific duplications, with the number of duplicates per gene ranging from 2 to 8.
Moreover, we also excluded 1) all OGs with a very large number of duplications, 2) all duplicates with incomplete or dubious gene annotation, 3) very recent duplications (with zero or close to zero dN values), and 4) pseudogene sequences.
We detected deletions, inversions and duplications with sizes between 100 bp and 1 Mb, and translocations.
We identified only three putative Neandertal-specific duplications with no evidence of duplication among humans or any other primate (fig. S23), and none contained known genes.
In addition, CYP21A2 gene duplications with one of the copies mutated have been found to be a common event.
These two new insertions are located in the first exon and consist of genome duplications with several single-base substitutions.
Finally, scrutiny of non-representative OGs revealed high levels of split genes versus gene duplications, with both phenomena confounding gene orthology assignment.
Using high-density arrays we identified 50 deletions and duplications (with a threshold of >10 SNPs) in the large Amish pedigree segregating BPD and related mental disturbances.
Interestingly, we very often observed multiple duplications with three or four transverse HG in WS subjects, which occurs only rarely in the general population.
