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Genomics as a Lens into the Populati...

Stevens, Sarah L. R.

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Genomics as a Lens into the Population Structure and Evolutionary Dynamics of Freshwater Microbes.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Genomics as a Lens into the Population Structure and Evolutionary Dynamics of Freshwater Microbes./
Author:	Stevens, Sarah L. R.
Published:	Ann Arbor : ProQuest Dissertations & Theses, : 2019,
Description:	173 p.
Notes:	Source: Dissertations Abstracts International, Volume: 80-08, Section: B.
Contained By:	Dissertations Abstracts International80-08B.
Subject:	Ecology. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=13427850
ISBN:	9780438837423

Genomics as a Lens into the Population Structure and Evolutionary Dynamics of Freshwater Microbes.
Stevens, Sarah L. R.

Genomics as a Lens into the Population Structure and Evolutionary Dynamics of Freshwater Microbes. - Ann Arbor : ProQuest Dissertations & Theses, 2019 - 173 p.

Source: Dissertations Abstracts International, Volume: 80-08, Section: B.

Thesis (Ph.D.)--The University of Wisconsin - Madison, 2019.

This item must not be added to any third party search indexes.

Microorganisms are important players in the ongoing biogeochemical cycling of the environment. While studies of microbial genomes have begun to increase our understanding of these nutrient transformations, much remains to be learned about how the microbial populations performing these functions are changing through time in response to evolutionary forces. In the three studies presented in this thesis, I used single-cell amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) as references to recruit reads from time series metagenomes taken from two freshwater lakes. This allowed me to track the diversity and abundance of 'sequence-discrete' populations of microbes across the whole genome through three or more years. In the first study, I observed how each of a phylogenetically diverse group of populations was changing in Trout Bog, a dystrophic lake. I observed a genome-wide sweep in the a population of Chlorobium over the course of the time series. I also found evidence that some of the other populations I tracked had experienced gene-specific sweeps prior to the start of the time series. This suggests that co-occurring populations may be controlled by different evolutionary forces. In the second chapter, I studied populations of two very common and abundant freshwater taxa. I saw that these two taxa contained populations with very different structures. These structural differences may be explained by a recent diversification among the populations represented in one group. The abundance patterns of this same group suggest that there is still significant niche overlap between these populations. In the final chapter, I investigated how the patterns of gene abundance and diversity underlie the whole population's abundance and diversity. I observed that all of the six Polynucleobacter populations recovered were fairly persistent through time, though one was considerably more abundant. None of the six populations recovered were dominated by a single strain though there is a trend between abundance and SNV homogeneity. Additionally, I characterized the core and accessory genome based using metagenomics through time and differences in evolutionary signatures between these genes. This work provides a framework for breaking down across the levels of biological organization.

ISBN: 9780438837423Subjects--Topical Terms:

516476
Ecology.

Genomics as a Lens into the Population Structure and Evolutionary Dynamics of Freshwater Microbes.
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520 $a Microorganisms are important players in the ongoing biogeochemical cycling of the environment. While studies of microbial genomes have begun to increase our understanding of these nutrient transformations, much remains to be learned about how the microbial populations performing these functions are changing through time in response to evolutionary forces. In the three studies presented in this thesis, I used single-cell amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) as references to recruit reads from time series metagenomes taken from two freshwater lakes. This allowed me to track the diversity and abundance of 'sequence-discrete' populations of microbes across the whole genome through three or more years. In the first study, I observed how each of a phylogenetically diverse group of populations was changing in Trout Bog, a dystrophic lake. I observed a genome-wide sweep in the a population of Chlorobium over the course of the time series. I also found evidence that some of the other populations I tracked had experienced gene-specific sweeps prior to the start of the time series. This suggests that co-occurring populations may be controlled by different evolutionary forces. In the second chapter, I studied populations of two very common and abundant freshwater taxa. I saw that these two taxa contained populations with very different structures. These structural differences may be explained by a recent diversification among the populations represented in one group. The abundance patterns of this same group suggest that there is still significant niche overlap between these populations. In the final chapter, I investigated how the patterns of gene abundance and diversity underlie the whole population's abundance and diversity. I observed that all of the six Polynucleobacter populations recovered were fairly persistent through time, though one was considerably more abundant. None of the six populations recovered were dominated by a single strain though there is a trend between abundance and SNV homogeneity. Additionally, I characterized the core and accessory genome based using metagenomics through time and differences in evolutionary signatures between these genes. This work provides a framework for breaking down across the levels of biological organization.
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