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Chapter 88 : Sequence-Based Discovery of Ecological Diversity within Legionella
Understanding the ecological diversity within Legionella may help in identifying all environmental reservoirs that can sustain the different potential Legionella pathogens. Here the authors apply the community phylogeny method to demarcate the ecologically distinct populations within the genus Legionella, based on the sequence of the macrophage infectivity potentiator (mip) gene from 496 Legionella isolates, obtained from Rodney M. Ratcliff, representing all characterized species within Legionella, as well as many uncharacterized groups. The community phylogeny analysis evaluates different sets of parameter values for their likelihood of yielding a phylogeny consistent with the observed clade sequence diversity of the group. This chapter provides a broad overview of the maximum likelihood approach for finding the trio of parameter values best fitting the observed curve of clade sequence diversity for Legionella, given the number of sequences sampled. The community phylogeny analysis provides an objective and theory-based method for identifying sequence clusters that are likely to correspond to ecotypes with a long history of coexistence. When a putative ecotype identified by community phylogeny is shown to be ecologically distinct in nature, it will have demonstrated the attributes of species. The authors hope that a more precise taxonomy, giving names to all the long-coexisting and ecologically distinct groups within a named species, will allow ecologists and epidemiologists to better predict the properties of newly isolated strains.