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The results from this study indicate that the bead-based liquid suspension array will provide a reliable, analytically sensitive and specific platform to simultaneously interrogate ruminant respiratory samples for multiple Mycoplasma species, including M. mycoides cluster organisms that are exotic to the United States.
SAR202 cluster organisms occur throughout the mesopelagic zone underlying the photic zone; the photic zone being rich in cyanobacteria and their phage [16].
In addition, we conducted pairwise comparisons to cluster organisms based on their domain composition.
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The coexistence between cyanophages and cyanobacteria suggests that some cyanophages, either historically or currently, were able to utilise both bacterial genera as a host and this may have led to the horizontal transfer of the mazG gene from a C. aurantiacus relative, most-likely a SAR202 cluster organism, to a Synechococcus phage.
Clustering organisms into discrete species is often problematic (b).
We present a novel computational method for clustering organisms according to their protein domain distribution and demonstrate, both quantitatively and qualitatively, that the resulting niche map correlates to the concept of ecological niche [8] better than a phylogenetic map.
The effect of plasticity on the hierarchical clustering of orthologs is illustrated in Figure 2. Figure 2A predicts a common set of genes at each internal node (possibly ancestral genes), and the order of clustered organisms is in reasonable agreement with established phylogeny.
The α-proteobacteria group clusters organisms with widely different lifestyles.
I like the idea of clustering organisms based on the physical properties of proteins in gene families.
We investigate the clustering of organisms, where clusters are defined as reproductively isolated groups and serve as an analogue of species, as a function of maximum mutation size.
The latter form "clades" that, rather than representing the history of speciation, mostly reflect the significantly greater rates of HGT within such clusters of organisms than between clusters.
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