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As suggested above, they rather indicate mechanisms acting preferentially in specific duplicated regions, and most notably in the duplication between chromosomes 11 and 12.
One of my largest issues with FriendFeed has been the duplication between commenting on Tweets (Twitter posts) which make up nearly half of all entries on FriendFeed, when Twitter itself is a two way communications tool.
The duplication between the paralogs is more recent than the duplication between the subbarrels, so one should be aligning the same region of the structures between paralogs.
For testing the MA model, the branch between the node corresponding to the duplication between Pg11 and Pg3 and the node corresponding to the duplication between Pg11a and Pg11c (i.e. the ancestral Pg11 gene) was considered as the late branch.
Thus, any effects related to the duplication between Pg11a and Pg11c is considered only in the Pg11a/ paralogsralogs pair analysis.
The duplication between Shox and Shox2 is ancient, since chicken has a Shox gene in a syntenic position to the human gene.
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Therefore, we focused on the duplications between clades I and II and between the subclades VIA and VIB.
The third study [ 12] failed to detect the duplications between rice Os03 and Os12 as well as between Os04 and Os08 that were detected by both other studies.
We estimate that the duplications between ST8Sia II and ST8Sia IV and between ST8Sia VI and ST8Sia VII took place about 552 MYA.
The earliest node datations refer to the duplications between ST8Sia I and ST8Sia VIIT8SiandI/ST8Sia VII and between ST8Sia V and ST8Sia VIIST8Siaround around 596 and 563 MYA respectively (Table 3).
Non-allelic homologous recombination can occur between two chromosomes that both contain the duplication or between one duplicated and one non-duplicated chromosome.
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