The un-annotated sequences may still be valid genes, but may have undergone a large amount of sequence divergence or be short fragments of genes.
In addition, when there is a large amount of sequence divergence between two nodes in a tree (site saturation) the accuracy of d S, and to a lesser extent d N, is greatly reduced.
The findings suggest that it may have been difficult to find a large number of miRNAs in this analysis, due to the possibility of a large amount of sequence divergence between S. mansoni and its closest relative in miRBase is S. mediterranea.
With the high support for these subclades and the large amount of sequence divergence between them, invoking the Phylogenetic Species criterion under the Evolutionary Species Concept as an overriding concept [ 76], we recognize this lineage as an undescribed species, St . Johnssubclade).
In addition to the large amount of amino acid divergence among the more divergent GOT1 paralogs, there are also a number of structural differences at these loci.
The large amount of CooS sequence divergence observed both in microbial species and in inventories collected in this study likely reflects functional differences among CODH types.
We also observed a large amount of within-clade sequence divergence wherein the two most distantly related OTUs from clade A, B, and C share only 57 %, 62, and 63% andno acid similarity, respectively.
There is a large amount of behavioral and morphological divergence between different cichlid species in the East African lakes.
An alternate course involving large amount of duplications followed by divergence producing a wide range of functions in selected classes might have been favorable.
Simulation studies have demonstrated that PAML is able to remain informative even with large amounts of sequence divergence, especially when the phylogenetic tree contains many branches [ 54, 55].
