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Chapter 88 : Sequence-Based Discovery of Ecological Diversity within

Authors: Frederick M. Cohan1, Alexander Koeppel2, Daniel Krizanc3
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Affiliations: 1: Department of Biology, Wesleyan University, Middletown, CT 06459; 2: Department of Biology, Wesleyan University, Middletown, CT 06459; 3: Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT 06459
Content Type: Monograph
Publication Year: 2006

Category: Bacterial Pathogenesis

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Sequence-Based Discovery of Ecological Diversity within , Page 1 of 2

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Abstract:

Understanding the ecological diversity within may help in identifying all environmental reservoirs that can sustain the different potential pathogens. Here the authors apply the community phylogeny method to demarcate the ecologically distinct populations within the genus , based on the sequence of the macrophage infectivity potentiator () gene from 496 isolates, obtained from Rodney M. Ratcliff, representing all characterized species within , 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 , 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.

Citation: M. Cohan F, Koeppel A, Krizanc D. 2006. Sequence-Based Discovery of Ecological Diversity within , p 367-376. In Cianciotto N, Kwaik Y, Edelstein P, Fields B, Geary D, Harrison T, Joseph C, Ratcliff R, Stout J, Swanson M (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555815660.ch88

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Sequence-Based Discovery of Ecological Diversity within Legionella
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Citation: M. Cohan F, Koeppel A, Krizanc D. 2006. Sequence-Based Discovery of Ecological Diversity within , p 367-376. In Cianciotto N, Kwaik Y, Edelstein P, Fields B, Geary D, Harrison T, Joseph C, Ratcliff R, Stout J, Swanson M (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555815660.ch88
/content/10.1128/9781555815660.ch88.ch88fig01
FIGURE 1
The clade sequence diversity pattern for the genus based on the gene. The observed pattern and the pattern predicted by the model’s optimal rates of ecotype formation and periodic selection, as well as the optimal number of extant ecotypes, are indicated. The number of bins (or sequence clusters) at a given level of sequence identity indicate the number of lineages, surviving to this day that existed at some point in the past. The steep rise in the number of bins, from 60 to 80% identity, suggests an adaptive radiation early in the history of The log-linear increase from 80% until 99% indicates a constant rate of ecotype formation over the time period represented. Because the community phylogeny analysis assumes a constant rate of ecotype formation, the analysis was applied only for sequence identity levels ≥80%. The sharp increase in the number of bins at 99% identity reflects the facile sequence divergence within ecotypes.
10.1128/9781555815660/f0368-01_thmb.gif
10.1128/9781555815660/f0368-01.gif
Image of FIGURE 1
FIGURE 1

The clade sequence diversity pattern for the genus based on the gene. The observed pattern and the pattern predicted by the model’s optimal rates of ecotype formation and periodic selection, as well as the optimal number of extant ecotypes, are indicated. The number of bins (or sequence clusters) at a given level of sequence identity indicate the number of lineages, surviving to this day that existed at some point in the past. The steep rise in the number of bins, from 60 to 80% identity, suggests an adaptive radiation early in the history of The log-linear increase from 80% until 99% indicates a constant rate of ecotype formation over the time period represented. Because the community phylogeny analysis assumes a constant rate of ecotype formation, the analysis was applied only for sequence identity levels ≥80%. The sharp increase in the number of bins at 99% identity reflects the facile sequence divergence within ecotypes.

Citation: M. Cohan F, Koeppel A, Krizanc D. 2006. Sequence-Based Discovery of Ecological Diversity within , p 367-376. In Cianciotto N, Kwaik Y, Edelstein P, Fields B, Geary D, Harrison T, Joseph C, Ratcliff R, Stout J, Swanson M (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555815660.ch88
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/content/10.1128/9781555815660.ch88.ch88fig02
FIGURE 2
Neighbor joining tree for the genus , with as an outgroup. The genus was divided into 10 clades, plus some additional strains that did not fit clearly within these clades. Each of the clades was tested for whether the Ω and σ rates estimated for the whole genus apply to the clade. A sample of eight orphan groups that are not closely related to any characterized species are labeled. Each of these groups was tested for consistency with being a single ecotype and for distinctness as a separate ecotype from the most closely related, characterized species.
10.1128/9781555815660/f0370-01_thmb.gif
10.1128/9781555815660/f0370-01.gif
Image of FIGURE 2
FIGURE 2

Neighbor joining tree for the genus , with as an outgroup. The genus was divided into 10 clades, plus some additional strains that did not fit clearly within these clades. Each of the clades was tested for whether the Ω and σ rates estimated for the whole genus apply to the clade. A sample of eight orphan groups that are not closely related to any characterized species are labeled. Each of these groups was tested for consistency with being a single ecotype and for distinctness as a separate ecotype from the most closely related, characterized species.

Citation: M. Cohan F, Koeppel A, Krizanc D. 2006. Sequence-Based Discovery of Ecological Diversity within , p 367-376. In Cianciotto N, Kwaik Y, Edelstein P, Fields B, Geary D, Harrison T, Joseph C, Ratcliff R, Stout J, Swanson M (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555815660.ch88
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/content/10.1128/9781555815660.ch88.ch88fig03
FIGURE 3
Neighbor joining tree of . Eleven putative ecotypes, labeled A to K, were demarcated by the community phylogeny method. The sequences in bold, supplied by J. Amemura-Maekawa, were not included in the community phylogeny analysis because they are shorter. Two strains previously identified as members of subsp. are labeled.
10.1128/9781555815660/f0372-01_thmb.gif
10.1128/9781555815660/f0372-01.gif
Image of FIGURE 3
FIGURE 3

Neighbor joining tree of . Eleven putative ecotypes, labeled A to K, were demarcated by the community phylogeny method. The sequences in bold, supplied by J. Amemura-Maekawa, were not included in the community phylogeny analysis because they are shorter. Two strains previously identified as members of subsp. are labeled.

Citation: M. Cohan F, Koeppel A, Krizanc D. 2006. Sequence-Based Discovery of Ecological Diversity within , p 367-376. In Cianciotto N, Kwaik Y, Edelstein P, Fields B, Geary D, Harrison T, Joseph C, Ratcliff R, Stout J, Swanson M (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555815660.ch88
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/content/10.1128/9781555815660.ch88.ch88fig04
FIGURE 4
(A) Clade sequence diversity for group E within (B) The likelihood values for various numbers of ecotypes using the -specific rates of Ω and σ. The confidence interval is based on the threshold line indicated (where the likelihood ratio is 6.83). In this case, n = 2 yields the maximum likelihood of a fit to the observed clade sequence diversity for group E, but the confidence interval ranges from 1 to 6.
10.1128/9781555815660/f0373-01_thmb.gif
10.1128/9781555815660/f0373-01.gif
Image of FIGURE 4
FIGURE 4

(A) Clade sequence diversity for group E within (B) The likelihood values for various numbers of ecotypes using the -specific rates of Ω and σ. The confidence interval is based on the threshold line indicated (where the likelihood ratio is 6.83). In this case, n = 2 yields the maximum likelihood of a fit to the observed clade sequence diversity for group E, but the confidence interval ranges from 1 to 6.

Citation: M. Cohan F, Koeppel A, Krizanc D. 2006. Sequence-Based Discovery of Ecological Diversity within , p 367-376. In Cianciotto N, Kwaik Y, Edelstein P, Fields B, Geary D, Harrison T, Joseph C, Ratcliff R, Stout J, Swanson M (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555815660.ch88
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References

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