Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations [electronic resource].

Published: Washington, D.C. : United States. Dept. of Energy. Office of Science, 2016.
Oak Ridge, Tenn. : Distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy
Physical Description: pages 1,589-1,601 : digital, PDF file
Additional Creators: United States. Department of Energy. Office of Science and United States. Department of Energy. Office of Scientific and Technical Information

Access Online

www.osti.gov

Availability

Finding items...

Restrictions on Access

Free-to-read Unrestricted online access

Summary

Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Using a 9-year metagenomic study of a freshwater lake (2005–2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. Furthermore, these patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the ‘ecotype model’ of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Finally, evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment.

Report Numbers

E 1.99:1347107

Subject(s)

Basic Biological Sciences

Note

Published through SciTech Connect.
01/08/2016.
"ismej2015241"
The ISME Journal 10 7 ISSN 1751-7362 AM
Matthew L. Bendall; Sarah L.R. Stevens; Leong-Keat Chan; Stephanie Malfatti; Patrick Schwientek; Julien Tremblay; Wendy Schackwitz; Joel Martin; Amrita Pati; Brian Bushnell; Jeff Froula; Dongwan Kang; Susannah G. Tringe; Stefan Bertilsson; Mary A. Moran; Ashley Shade; Ryan J. Newton; Katherine D. McMahon; Rex R. Malmstrom.
Dept. of Energy Joint Genome Inst., Walnut Creek, CA (United States)

Funding Information

AC02-05CH11231

View MARC record | catkey: 23498032