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6 This evolutionary network apparently emerged owing to extensive gene exchange, often between widely different elements, as well as parallel acquisition of homologous genes from the hosts.
As argued elsewhere [ 73, 138, 208], such a scheme implies an extensive (gene) exchange between the members of one consortium, but not between dwellers of different, physically discrete inorganic compartments.
CRISPR spacers provide direct evidence for extensive gene exchange in archaea, especially within genera, and support the current dogma where the primary role of the CRISPR/Cas system is anti-viral and anti-plasmid defense.
A mechanism promoting prokaryotic close physical association that does not depend on highly species-specific interactions, and which thus naturally gives rise to promiscuous assemblies in which extensive gene exchange among multiple species could occur, could help explain these genetic diversities.
Phylogenetic analysis of the moumouvirus genes with closest bacterial homologs supported the origin of these genes from diverse bacteria (two examples are shown in fig. 4 C and D), in agreement with the previously noticed extensive gene exchange among symbionts and parasites of amoeba (Ogata et al. 2006; Moreira and Brochier-Armanet 2008; Boyer et al. 2009; Raoult and Boyer 2010).
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Phylogenetic analyses of some of these transporters have revealed extensive gene exchanges between VPES and Firmicutes [ 26].
These arguments provide a mechanism for the evolution of symbiotically-linked prokaryotic ecologies characterized by extensive gene interchange and coupled protein and energy exchange systems.
However, analysis of the entire complement of M. infernorum genes seems to tell a different story, namely, one of extensive horizontal gene exchange with a variety of bacteria.
Comparative-genomic analysis suggests that evolution of the M. infernorum lineage involved extensive horizontal gene exchange with a variety of bacteria.
This denotes that continuous evolution is occurring in the V. cholerae O1 population, which could be due to its ability for extensive horizontal gene exchange.
For organisms whose history includes extensive horizontal gene exchange, all individual gene phylogenies could, in principle, be different, so instead of the species tree, the dominant vertical trend of evolution can be represented by a ST.
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