However, it has been argued that such methods have shortcomings when applied to distantly related organisms [ 38].
In reference to the draft genome sequences of the Pacific bluefin tuna (Thunnus orientalis), 12 primer pairs expected to amplify introns of the bluefin tuna with lengths of 500 1000 bp were selected and applied to six distantly related fish species belonging to the Orders Clupeiformes, Tetraodontiformes, Pleuronectiformes, Perciformes, Scorpaeniformes, and Anguilliformes.
Future analyses of modularity's influence on morphological evolution should continue to test the relationship between modularity and disparity to establish whether the patterns shared by Primates and Carnivora can be applied to more distantly related clades.
It seems therefore best to apply kmacs to distantly related sequence sets, while methods such as K r and ACS may be preferred on evolutionarily more closely related sequences.
When applied to comparisons of two distantly related proteins, near-optimal alignments reveal that the most conserved regions among the near-optimal alignments are the highly structured regions in the proteins.
Genome sequence data make it possible to predict proteins that are targeted to the plastid, but current in silico prediction methods are limited in their utility, particularly when applied to organisms that are distantly related to the species whose protein sequences have been used to "train" the prediction algorithms (Foth et al. 2003; Patron and Waller 2007).
However, it had not been extensively explored whether the sequence divergence could affect the efficiency of hybridization-based capture systems designed based on a reference genome (C57BL/6 J) when applied in the study of distantly-related strains.
We applied them to arcellinids belonging to distantly related genera (Arcella, Difflugia, Netzelia and Hyalosphenia) and to Arcellinid-rich environmental samples to obtain additional Amoebozoa sequences.
To reduce false positives caused by hits corresponding to distantly related sequences, we applied a best reciprocal hit criterion i.e. orthology was assumed only if two genes in each different genome are each other's best hit [ 25].
So far, a number of Aspergillus strains belonging to phylogenetically distantly related species have been successfully applied in industrial production of organic acids due to their excellent capabilities of secreting high amounts of desired organic acids.
Sequences from distantly related taxa are not generally applied as outgroups, as phylogenetic distance can lead to degraded alignments [ 43].
