A Comparison of Methods to Measure Fitness in Escherichia coli
In order to characterize the dynamics of adaptation, it is important to be able to quantify how a population’s mean fitness changes over time. Such measurements are especially important in experimental studies of evolution using microbes. The Long-Term Evolution Experiment (LTEE) with Escherichia co...
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| Format: | Online |
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Public Library of Science
2015
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4427439/ |
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pubmed-4427439 |
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pubmed-44274392015-05-21 A Comparison of Methods to Measure Fitness in Escherichia coli Wiser, Michael J. Lenski, Richard E. Research Article In order to characterize the dynamics of adaptation, it is important to be able to quantify how a population’s mean fitness changes over time. Such measurements are especially important in experimental studies of evolution using microbes. The Long-Term Evolution Experiment (LTEE) with Escherichia coli provides one such system in which mean fitness has been measured by competing derived and ancestral populations. The traditional method used to measure fitness in the LTEE and many similar experiments, though, is subject to a potential limitation. As the relative fitness of the two competitors diverges, the measurement error increases because the less-fit population becomes increasingly small and cannot be enumerated as precisely. Here, we present and employ two alternatives to the traditional method. One is based on reducing the fitness differential between the competitors by using a common reference competitor from an intermediate generation that has intermediate fitness; the other alternative increases the initial population size of the less-fit, ancestral competitor. We performed a total of 480 competitions to compare the statistical properties of estimates obtained using these alternative methods with those obtained using the traditional method for samples taken over 50,000 generations from one of the LTEE populations. On balance, neither alternative method yielded measurements that were more precise than the traditional method. Public Library of Science 2015-05-11 /pmc/articles/PMC4427439/ /pubmed/25961572 http://dx.doi.org/10.1371/journal.pone.0126210 Text en © 2015 Wiser, Lenski http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Wiser, Michael J. Lenski, Richard E. |
| spellingShingle |
Wiser, Michael J. Lenski, Richard E. A Comparison of Methods to Measure Fitness in Escherichia coli |
| author_facet |
Wiser, Michael J. Lenski, Richard E. |
| author_sort |
Wiser, Michael J. |
| title |
A Comparison of Methods to Measure Fitness in Escherichia coli
|
| title_short |
A Comparison of Methods to Measure Fitness in Escherichia coli
|
| title_full |
A Comparison of Methods to Measure Fitness in Escherichia coli
|
| title_fullStr |
A Comparison of Methods to Measure Fitness in Escherichia coli
|
| title_full_unstemmed |
A Comparison of Methods to Measure Fitness in Escherichia coli
|
| title_sort |
comparison of methods to measure fitness in escherichia coli |
| description |
In order to characterize the dynamics of adaptation, it is important to be able to quantify how a population’s mean fitness changes over time. Such measurements are especially important in experimental studies of evolution using microbes. The Long-Term Evolution Experiment (LTEE) with Escherichia coli provides one such system in which mean fitness has been measured by competing derived and ancestral populations. The traditional method used to measure fitness in the LTEE and many similar experiments, though, is subject to a potential limitation. As the relative fitness of the two competitors diverges, the measurement error increases because the less-fit population becomes increasingly small and cannot be enumerated as precisely. Here, we present and employ two alternatives to the traditional method. One is based on reducing the fitness differential between the competitors by using a common reference competitor from an intermediate generation that has intermediate fitness; the other alternative increases the initial population size of the less-fit, ancestral competitor. We performed a total of 480 competitions to compare the statistical properties of estimates obtained using these alternative methods with those obtained using the traditional method for samples taken over 50,000 generations from one of the LTEE populations. On balance, neither alternative method yielded measurements that were more precise than the traditional method. |
| publisher |
Public Library of Science |
| publishDate |
2015 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4427439/ |
| _version_ |
1613221894672089088 |