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Sympatric and allopatric differentiation delineates population structure in free-living terrestrial bacteria

View ORCID ProfileAlexander B. Chase, Philip Arevalo, Eoin L. Brodie, Martin F. Polz, View ORCID ProfileUlas Karaoz, Jennifer B.H. Martiny
doi: https://doi.org/10.1101/644468
Alexander B. Chase
1Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
2Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
5Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, CA, USA
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  • For correspondence: abchase@uci.edu
Philip Arevalo
3Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
6Department of Ecology and Evolutionary Biology, University of Chicago, Chicago, IL, USA
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Eoin L. Brodie
2Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
4Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
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Martin F. Polz
3Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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Ulas Karaoz
2Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Jennifer B.H. Martiny
1Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
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ABSTRACT

In free-living bacteria and archaea, the equivalent of the biological species concept does not exist, creating several barriers to the study of the processes contributing to microbial diversification. As such, microorganisms are often operationally defined using conserved marker genes (i.e., 16S rRNA gene) or whole-genome measurements (i.e., ANI) to interpret intra-specific processes. However, as in eukaryotes, investigations into microbial populations must consider the potential for interacting genotypes among individuals that are subjected to similar environmental selective pressures. Therefore, we isolated 26 strains within a single bacterial ecotype (equivalent to a eukaryotic species definition) from a common habitat (leaf litter) across a regional climate gradient and asked whether the genetic diversity in a free-living soil bacterium (Curtobacterium) was consistent with patterns of allopatric or sympatric differentiation. By examining patterns of gene flow, our results indicate that microbial populations are delineated by gene flow discontinuities and exhibit evidence for population-specific adaptation. We conclude that the genetic structure within this bacterium is due to both adaptation within localized microenvironments (isolation-by-environment) as well as dispersal limitation between geographic locations (isolation-by-distance).

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  • Clarified the discussion; revised abstract

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 17, 2019.
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Sympatric and allopatric differentiation delineates population structure in free-living terrestrial bacteria
Alexander B. Chase, Philip Arevalo, Eoin L. Brodie, Martin F. Polz, Ulas Karaoz, Jennifer B.H. Martiny
bioRxiv 644468; doi: https://doi.org/10.1101/644468
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Sympatric and allopatric differentiation delineates population structure in free-living terrestrial bacteria
Alexander B. Chase, Philip Arevalo, Eoin L. Brodie, Martin F. Polz, Ulas Karaoz, Jennifer B.H. Martiny
bioRxiv 644468; doi: https://doi.org/10.1101/644468

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