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Many of the diverse scaffolds prepared have scope for easy further diversification which may allow the discovery of novel bioactive small molecule tools.
Our data also elude to the possibility of distinct mechanisms, among different phage families, of tail fiber and tailspike diversification, which may be linked to evolution of host specificity.
The lack of a rate shift in the branch leading to the three collapsed families (Paguridae, Hapalogastridae, and Lithodidae) does not necessarily imply that subclades within that group have not experienced changes in the tempo of diversification, which may be masked by the lack of taxonomic resolution among these taxa.
While our homogenous approach may be associated with some advantages with respect to efficiency, simplicity and unstructured volatility, the heterogenous models such as Early Burst have the benefit of imposing an explicit evolutionary narrative on the process of trait diversification which may be useful for exploring and testing general hypotheses about historical processes [ 14].
In addition to ectopic duplication of genes and segments to produce heterogeneous clusters, gene conversion may also be involved in sequence diversification, which may be promoted not only by the GA microsatellites, but also by the repeats and shared element sequences within the coding region.
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The synallaxines were found to have had a particularly high diversification rate, which may be explained by their ability to build exposed vegetative nests and thus to expand into a variety of novel habitats that emerged during a period of cooling and aridification in South America.
Thereby, the genomic islands associated with the Hcp and VgrG proteins could drive functional diversification of the T6SS, which may explain the plethora of biological roles described for this secretion system.
The phylogenetic relationship between conifers and angiosperms highlights the ancient diversification of this family, which may precede the transition to terrestrial environments, as suggested by Engstrom [ 71] based on comparisons among GRAS proteins from angiosperms, bryophytes and lycophytes, but not gymnosperms.
All three settings induce the relaxation of selection pressure, which may promote diversification [3].
Many of the genes from the second group are preferentially expressed in two or more tissues, suggesting possible diversification or specialization of function, which may be accompanied with evolutionary divergence.
These results further support gene duplication in rice and Arabidopsis during evolution which may allow functional diversification by adaptive protein structures [ 77].
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