Genome-Scale Assessment of Phenotypic Changes During Adaptive Evolution

2008 ◽  
pp. 183-195
Author(s):  
Stephen S. Fong
Keyword(s):  
Adaptive Evolution ◽  
Phenotypic Changes ◽  
Scale Assessment ◽  
Genome Scale

scholarly journals Description and Interpretation of Adaptive Evolution of Escherichia coli K-12 MG1655 by Using a Genome-Scale In Silico Metabolic Model

2003 ◽  
Vol 185 (21) ◽  
pp. 6400-6408 ◽  
Author(s):  
Stephen S. Fong ◽  
Jennifer Y. Marciniak ◽  
Bernhard Ø. Palsson
Keyword(s):  
Escherichia Coli ◽  
Adaptive Evolution ◽  
Growth Rates ◽  
In Silico ◽  
A Priori ◽  
E Coli ◽  
End Point ◽  
In Silico Model ◽  
Uptake Rates ◽  
Genome Scale

ABSTRACT Genome-scale in silico metabolic networks of Escherichia coli have been reconstructed. By using a constraint-based in silico model of a reconstructed network, the range of phenotypes exhibited by E. coli under different growth conditions can be computed, and optimal growth phenotypes can be predicted. We hypothesized that the end point of adaptive evolution of E. coli could be accurately described a priori by our in silico model since adaptive evolution should lead to an optimal phenotype. Adaptive evolution of E. coli during prolonged exponential growth was performed with M9 minimal medium supplemented with 2 g of α-ketoglutarate per liter, 2 g of lactate per liter, or 2 g of pyruvate per liter at both 30 and 37°C, which produced seven distinct strains. The growth rates, substrate uptake rates, oxygen uptake rates, by-product secretion patterns, and growth rates on alternative substrates were measured for each strain as a function of evolutionary time. Three major conclusions were drawn from the experimental results. First, adaptive evolution leads to a phenotype characterized by maximized growth rates that may not correspond to the highest biomass yield. Second, metabolic phenotypes resulting from adaptive evolution can be described and predicted computationally. Third, adaptive evolution on a single substrate leads to changes in growth characteristics on other substrates that could signify parallel or opposing growth objectives. Together, the results show that genome-scale in silico metabolic models can describe the end point of adaptive evolution a priori and can be used to gain insight into the adaptive evolutionary process for E. coli.

Genome scale assessment of a species translocation program

2017 ◽  
Vol 18 (5) ◽  
pp. 1191-1199 ◽  
Author(s):  
Cassie M. Dresser ◽  
R. Michael Ogle ◽  
Benjamin M. Fitzpatrick
Keyword(s):  
Scale Assessment ◽  
Species Translocation ◽  
Genome Scale

scholarly journals Phenotypic Convergence in Bacterial Adaptive Evolution to Ethanol Stress

2014 ◽  
Author(s):  
Takaaki Horinouchi ◽  
Shingo Suzuki ◽  
Takashi Hirasawa ◽  
Naoaki Ono ◽  
Tetsuya Yomo ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Ethanol Tolerance ◽  
Environmental Changes ◽  
Site Directed Mutagenesis ◽  
Genetic Mutations ◽  
Ethanol Stress ◽  
Bacterial Cells ◽  
Phenotypic Changes ◽  
Escherichia Coli Cells ◽  
Phenotypic Convergence

Bacterial cells have a remarkable ability to adapt and evolve to environmental changes, a phenomenon known as adaptive evolution. Adaptive evolution can be explained by phenotypic changes caused by genetic mutations, and by phenotypic plasticity that occur without genetic alteration, although far less is known about the contributions of the latter. In this study, we analyzed phenotypic and genotypic changes in Escherichia coli cells during adaptive evolution to ethanol stress. Phenotypic changes were quantified by transcriptome and metabolome analyses and found similar among independently evolved ethanol tolerant strains. The contribution of identified mutations in the tolerant strain was evaluated by using site-directed mutagenesis, which suggested that the fixation of these mutations cannot fully explain the observed ethanol tolerance. The phenotype of ethanol tolerance was stably maintained after an environmental change, suggesting that a mechanism of non-genetic memory contributed to at least part of the adaptation process.

scholarly journals Quantifying how constraints limit the diversity of viable routes to adaptation

2018 ◽  
Author(s):  
Sam Yeaman ◽  
Aleeza C. Gerstein ◽  
Kathryn A. Hodgins ◽  
Michael C. Whitlock
Keyword(s):  
Adaptive Evolution ◽  
Null Hypothesis ◽  
Hypergeometric Distribution ◽  
Simultaneous Analysis ◽  
Selection Pressures ◽  
Wide Range ◽  
Genetic Responses ◽  
Genome Scale ◽  
Pairwise Contrasts

AbstractConvergent adaptation can occur at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures. These patterns provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolution. A first step in studying such factors is to quantify the observed amount of repeatability relative to expectations under a null hypothesis. Here, we formulate a novel metric to quantify the constraints driving the observed amount of repeated adaptation in pairwise contrasts based on the hypergeometric distribution, and then generalize this for simultaneous analysis of multiple lineages. This metric is explicitly based on the probability of observing a given amount of repeatability by chance under an arbitrary null hypothesis, and is readily compared among different species and types of trait. We also formulate a metric to quantify the effective proportion of genes in the genome that have the potential to contribute to adaptation. As an example of how these metrics can be used to draw inferences, we assess the amount of repeatability observed in existing datasets on adaptation to antibiotics in yeast and climate in conifers. This approach provides a method to test a wide range of hypotheses about how different kinds of factors can facilitate or constrain the diversity of genetic responses observed during adaptive evolution.

scholarly journals A genome-scale assessment of peripheral blood B-cell molecular homeostasis in patients with rheumatoid arthritis

Rheumatology ◽  
2006 ◽  
Vol 45 (12) ◽  
pp. 1466-1476 ◽  
Author(s):  
P. Szodoray ◽  
P. Alex ◽  
M. B. Frank ◽  
M. Turner ◽  
S. Turner ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
B Cell ◽  
Peripheral Blood ◽  
Scale Assessment ◽  
A Genome ◽  
Genome Scale

scholarly journals Genome-Scale Assessment of Age-Related DNA Methylation Changes in Mouse Spermatozoa

PLoS ONE ◽  
2016 ◽  
Vol 11 (11) ◽  
pp. e0167127 ◽  
Author(s):  
Norio Kobayashi ◽  
Hiroaki Okae ◽  
Hitoshi Hiura ◽  
Hatsune Chiba ◽  
Yoshiki Shirakata ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Scale Assessment ◽  
Age Related ◽  
Genome Scale

scholarly journals Genome-Scale Phylogenetic and Population Genetic Studies Provide Insight Into Introgression and Adaptive Evolution of Takifugu Species in East Asia

2021 ◽  
Vol 12 ◽  
Author(s):  
Bo Liu ◽  
Zhixiong Zhou ◽  
Yulin Bai ◽  
Junyi Yang ◽  
Yue Shi ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Incomplete Lineage Sorting ◽  
Morphological Characteristics ◽  
Sister Group ◽  
Natural Hybridization ◽  
Takifugu Rubripes ◽  
Female Reproduction ◽  
Lineage Sorting ◽  
Group Relationships ◽  
Genome Scale

As a typical marine adaptive radiation species, most Takifugu species are widely distributed in East Asian offshore, which have diversified morphological characteristics and different ecological habits. The phylogenetic relationship and population structure of the Takifugu species was complicated because of incomplete lineage sorting, widespread hybridization and introgression. Therefore, to systematically clarify the phylogenetic relationships of Takifugu genus, explore the introgression and natural hybridization between different Takifugu species, and detect the selective signatures in the adaptive evolution of diversified traits, whole-genome resequencing was used in 122 Takifugu samples from 10 species. Phylogenetic analysis showed solid sister-group relationships between Takifugu bimaculatus and Takifugu flavidus, Takifugu oblongus, and Takifugu niphobles, Takifugu rubripes, and Takifugu obscurus, Takifugu xanthoptreus, and Takifugu ocellatus. Further admixture analysis indicated the divergence of T. obscurus population and the bidirectional gene flow between T. bimaculatus and T. flavidus. Using species-specific homozygous genetic variance sites, we detected the asymmetric introgression between T. bimaculatus and T. flavidus at China East sea and southern Taiwan Strait. By genome-scale genetic diversity scanning, we detected two copies of syt1, zar1 and tgfbr1 related to the semilunar reproduction rhythm in T. niphobles, involved in memory formation, embryo maturation and female reproduction. Furthermore, we also found lots of T. niphobles specific mutations in CDS region of circadian rhythm related genes and endocrine hormone genes. For Takifugu species, our research provides reliable genetic resources and results for the phylogeny, introgression, hybridization and adaptive evolution, and could be used as a guide for the formulation of the protection and proliferation release policies.

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