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They can also be used to judge the phenotypic impact of genetic changes or other types of events associated with branches within the phylogeny [see, for example, Steinbrück and McHardy (2012)].
Then, to examine whether the two paralogs were subjected to different selective pressures, we applied a different model (two-ratio model) considering two branches within the phylogeny comprising either the KLK2 or KLK3 clades.
This is because bouts of selection can be localized to specific clades or even branches within the phylogeny, causing a failure to detect a signal of selection when a wide range of species are included in the analysis [ 12, 30].
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Most of the sites that substituted along the RH2aα and RH2aα post-duplication branches also substituted along other branches of the phylogeny, and such substitution patterns may not fit neatly within the site classes defined by the Branch-site models.
Many fixed allele-SNPs (i.e., not heterozygous within a line) could be attributed to mutations occurring along specific branches of the phylogeny (Table 5).
The branch-site tests, performed at both the branch and clade levels, identified one branch evolving at an elevated rate compared to other branches of the phylogeny (B1, P = 0.011) as well as three clades within the set of orthologous NAT2 sequences with evidence of positive selection (C7, P = 0.019; C8, P = 0.040; C9, P = 0.017, C8 and C9 being component clades of C7).
Generally, values are higher along terminal branches and decrease along branches deeper in the phylogeny.
As the takahe and kagu are (unexpectedly) not allies we now have two long edges (branches) within our phylogeny that have the potential to disrupt stable clades.
Spine length is depicted as squares over branches in the phylogeny, and the associated parasite prevalence is depicted in circles.
We treated branch B as the foreground branch and all other branches in the phylogeny as background branches (Figure 2A).
The 'one-ratio' model assumes the same ratio for all branches in the phylogeny.
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