Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria

Persistent Link:
http://hdl.handle.net/10150/610043
Title:
Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria
Author:
Kuo, Chih-Horng; Ochman, Howard
Affiliation:
Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA
Issue Date:
2009
Publisher:
BioMed Central
Citation:
Biology Direct 2009, 4:35 doi:10.1186/1745-6150-4-35
Journal:
Biology Direct
Rights:
© 2009 Kuo and Ochman; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:Because bacteria do not have a robust fossil record, attempts to infer the timing of events in their evolutionary history requires comparisons of molecular sequences. This use of molecular clocks is based on the assumptions that substitution rates for homologous genes or sites are fairly constant through time and across taxa. Violation of these conditions can lead to erroneous inferences and result in estimates that are off by orders of magnitude. In this study, we examine the consistency of substitution rates among a set of conserved genes in diverse bacterial lineages, and address the questions regarding the validity of molecular dating.RESULTS:By examining the evolution of 16S rRNA gene in obligate endosymbionts, which can be calibrated by the fossil record of their hosts, we found that the rates are consistent within a clade but varied widely across different bacterial lineages. Genome-wide estimates of nonsynonymous and synonymous substitutions suggest that these two measures are highly variable in their rates across bacterial taxa. Genetic drift plays a fundamental role in determining the accumulation of substitutions in 16S rRNA genes and at nonsynonymous sites. Moreover, divergence estimates based on a set of universally conserved protein-coding genes also exhibit low correspondence to those based on 16S rRNA genes.CONCLUSION:Our results document a wide range of substitution rates across genes and bacterial taxa. This high level of variation cautions against the assumption of a universal molecular clock for inferring divergence times in bacteria. However, by applying relative-rate tests to homologous genes, it is possible to derive reliable local clocks that can be used to calibrate bacterial evolution.REVIEWERS:This article was reviewed by Adam Eyre-Walker, Simonetta Gribaldo and Tal Pupko (nominated by Dan Graur).
EISSN:
1745-6150
DOI:
10.1186/1745-6150-4-35
Version:
Final published version
Additional Links:
http://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-4-35

Full metadata record

DC FieldValue Language
dc.contributor.authorKuo, Chih-Horngen
dc.contributor.authorOchman, Howarden
dc.date.accessioned2016-05-20T08:57:15Z-
dc.date.available2016-05-20T08:57:15Z-
dc.date.issued2009en
dc.identifier.citationBiology Direct 2009, 4:35 doi:10.1186/1745-6150-4-35en
dc.identifier.doi10.1186/1745-6150-4-35en
dc.identifier.urihttp://hdl.handle.net/10150/610043-
dc.description.abstractBACKGROUND:Because bacteria do not have a robust fossil record, attempts to infer the timing of events in their evolutionary history requires comparisons of molecular sequences. This use of molecular clocks is based on the assumptions that substitution rates for homologous genes or sites are fairly constant through time and across taxa. Violation of these conditions can lead to erroneous inferences and result in estimates that are off by orders of magnitude. In this study, we examine the consistency of substitution rates among a set of conserved genes in diverse bacterial lineages, and address the questions regarding the validity of molecular dating.RESULTS:By examining the evolution of 16S rRNA gene in obligate endosymbionts, which can be calibrated by the fossil record of their hosts, we found that the rates are consistent within a clade but varied widely across different bacterial lineages. Genome-wide estimates of nonsynonymous and synonymous substitutions suggest that these two measures are highly variable in their rates across bacterial taxa. Genetic drift plays a fundamental role in determining the accumulation of substitutions in 16S rRNA genes and at nonsynonymous sites. Moreover, divergence estimates based on a set of universally conserved protein-coding genes also exhibit low correspondence to those based on 16S rRNA genes.CONCLUSION:Our results document a wide range of substitution rates across genes and bacterial taxa. This high level of variation cautions against the assumption of a universal molecular clock for inferring divergence times in bacteria. However, by applying relative-rate tests to homologous genes, it is possible to derive reliable local clocks that can be used to calibrate bacterial evolution.REVIEWERS:This article was reviewed by Adam Eyre-Walker, Simonetta Gribaldo and Tal Pupko (nominated by Dan Graur).en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-4-35en
dc.rights© 2009 Kuo and Ochman; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleInferring clocks when lacking rocks: the variable rates of molecular evolution in bacteriaen
dc.typeArticleen
dc.identifier.eissn1745-6150en
dc.contributor.departmentDepartment of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USAen
dc.identifier.journalBiology Directen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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