Rapid genomic evolution in Brassica rapa with bumblebee selection in experimental evolution

Mapping Intimacies ◽

10.1101/2021.12.02.470896 ◽

2021 ◽

Author(s):

Léa Frachon ◽

Florian P. Schiestl

Keyword(s):

Brassica Rapa ◽

Experimental Evolution ◽

Parallel Evolution ◽

Genomic Evolution ◽

Adaptive Responses ◽

Genomic Changes ◽

Plant Reproductive Success ◽

Signature Of Selection ◽

Genomic Variance ◽

Frequency Changes

AbstractInsect pollinators shape rapid phenotypic evolution of traits related to floral attractiveness and plant reproductive success. However, the underlying genomic changes and their impact on standing genetic variation remain largely unknown despite their importance in predicting adaptive responses in nature or in crop’s artificial selection. Here, based on a previous, nine generation experimental evolution study with fast cycling Brassica rapa plants adapting to bumblebees, we document genomic evolution associated to the adaptive process. We performed a genomic scan of the allele frequency changes along the genome and estimated the nucleotide diversity and genomic variance changes. We detected signature of selection associated with rapid changes in allelic frequencies on multiple loci. During experimental evolution, we detected an increase in overall genomic variance, whereas for loci under selection, a reduced variance was apparent in both replicates suggesting a parallel evolution. Our study highlights the polygenic nature of short-term pollinator adaptation and the importance of a such genetic architecture in the maintenance of genomic variance during strong natural selection by biotic factors.

Download Full-text

Male fertility thermal limits predict vulnerability to climate warming

Nature Communications ◽

10.1038/s41467-021-22546-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Belinda van Heerwaarden ◽

Carla M. Sgrò

Keyword(s):

Climate Warming ◽

Experimental Evolution ◽

Male Fertility ◽

Extinction Risk ◽

Conservation Strategies ◽

Tropical Species ◽

Adaptive Responses ◽

Widespread Species ◽

Thermal Limits ◽

Critical Thermal Limits

AbstractForecasting which species/ecosystems are most vulnerable to climate warming is essential to guide conservation strategies to minimize extinction. Tropical/mid-latitude species are predicted to be most at risk as they live close to their upper critical thermal limits (CTLs). However, these assessments assume that upper CTL estimates, such as CTmax, are accurate predictors of vulnerability and ignore the potential for evolution to ameliorate temperature increases. Here, we use experimental evolution to assess extinction risk and adaptation in tropical and widespread Drosophila species. We find tropical species succumb to extinction before widespread species. Male fertility thermal limits, which are much lower than CTmax, are better predictors of species’ current distributions and extinction in the laboratory. We find little evidence of adaptive responses to warming in any species. These results suggest that species are living closer to their upper thermal limits than currently presumed and evolution/plasticity are unlikely to rescue populations from extinction.

Download Full-text

Experimental evolution of gallium resistance in Escherichia coli

Evolution Medicine and Public Health ◽

10.1093/emph/eoz025 ◽

2019 ◽

Vol 2019 (1) ◽

pp. 169-180

Author(s):

Joseph L Graves ◽

Akamu J Ewunkem ◽

Jason Ward ◽

Constance Staley ◽

Misty D Thomas ◽

...

Keyword(s):

Escherichia Coli ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Experimental Evolution ◽

Molecular Mechanisms ◽

Gallium Nitrate ◽

Whole Genome ◽

Mechanisms Of Resistance ◽

Genomic Changes ◽

K 12

Abstract Background and Objectives Metallic antimicrobial materials are of growing interest due to their potential to control pathogenic and multidrug-resistant bacteria. Yet we do not know if utilizing these materials can lead to genetic adaptations that produce even more dangerous bacterial varieties. Methodology Here we utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance. Results By day 10 of evolution, increased gallium resistance was evident in populations cultured in medium containing a sublethal concentration of gallium. Furthermore, these populations showed increased resistance to ionic silver and iron (III), but not iron (II) and no increase in traditional antibiotic resistance compared with controls and the ancestral strain. In contrast, the control populations showed increased resistance to rifampicin relative to the gallium-resistant and ancestral population. Genomic analysis identified hard selective sweeps of mutations in several genes in the gallium (III)-resistant lines including: fecA (iron citrate outer membrane transporter), insl1 (IS30 tranposase) one intergenic mutations arsC →/→ yhiS; (arsenate reductase/pseudogene) and in one pseudogene yedN ←; (iapH/yopM family). Two additional significant intergenic polymorphisms were found at frequencies > 0.500 in fepD ←/→ entS (iron-enterobactin transporter subunit/enterobactin exporter, iron-regulated) and yfgF ←/→ yfgG (cyclic-di-GMP phosphodiesterase, anaerobic/uncharacterized protein). The control populations displayed mutations in the rpoB gene, a gene associated with rifampicin resistance. Conclusions This study corroborates recent results observed in experiments utilizing pathogenic Pseudomonas strains that also showed that Gram-negative bacteria can rapidly evolve resistance to an atom that mimics an essential micronutrient and shows the pleiotropic consequences associated with this adaptation. Lay summary We utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance.

Download Full-text

Using seasonal genomic changes to understand historical adaptation: parallel selection on stickleback in highly-variable estuaries

10.1101/2020.11.24.396291 ◽

2020 ◽

Author(s):

Alan Garcia-Elfring ◽

Antoine Paccard ◽

Timothy J. Thurman ◽

Ben A. Wasserman ◽

Eric P. Palkovacs ◽

...

Keyword(s):

Natural Selection ◽

Allele Frequency ◽

Calcium Binding ◽

Gasterosteus Aculeatus ◽

Environmental Changes ◽

Threespine Stickleback ◽

Functional Enrichment ◽

Genomic Changes ◽

Parallel Selection ◽

Frequency Changes

AbstractParallel evolution is considered strong evidence for natural selection. However, few studies have investigated the process of parallel selection as it plays out in real time. The common approach is to study historical signatures of selection in populations already well adapted to different environments. Here, to document selection in action under natural conditions, we study six populations of threespine stickleback (Gasterosteus aculeatus) inhabiting bar-built estuaries that undergo seasonal cycles of environmental changes. Estuaries are periodically isolated from the ocean due to sandbar formation during dry summer months, with concurrent environmental shifts that resemble the long-term changes associated with postglacial colonization of freshwater habitats by marine populations. We used pooled whole-genome sequencing (Pool-WGS) to track seasonal allele frequency changes in these populations and search for signatures of natural selection. We found consistent changes in allele frequency across estuaries, suggesting a potential role for parallel selection. Functional enrichment among candidate genes included transmembrane ion transport and calcium binding, which are important for osmoregulation and ion balance. The genomic changes that occur in threespine stickleback from bar-built estuaries could provide a glimpse into the early stages of adaptation that have occurred in many historical marine to freshwater transitions.

Download Full-text

Rapid, parallel evolution of field mustard ( Brassica rapa ) under experimental drought

Evolution ◽

10.1111/evo.14413 ◽

2021 ◽

Author(s):

Stephen E. Johnson ◽

Elena Hamann ◽

Steven J Franks

Keyword(s):

Brassica Rapa ◽

Parallel Evolution

Download Full-text

Experimental Evolution of Resistance in Brassica rapa: Correlated Response of Tolerance in Lines Selected for Glucosinolate Content

Evolution ◽

10.2307/2411265 ◽

1998 ◽

Vol 52 (3) ◽

pp. 703 ◽

Cited By ~ 75

Author(s):

Kirk A. Stowe

Keyword(s):

Brassica Rapa ◽

Experimental Evolution ◽

Glucosinolate Content ◽

Correlated Response ◽

Evolution Of Resistance

Download Full-text

Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant

Genes ◽

10.3390/genes11040400 ◽

2020 ◽

Vol 11 (4) ◽

pp. 400 ◽

Cited By ~ 2

Author(s):

Alexandre Rêgo ◽

Samridhi Chaturvedi ◽

Amy Springer ◽

Alexandra M. Lish ◽

Caroline L. Barton ◽

...

Keyword(s):

Gene Expression ◽

Allele Frequency ◽

Development Time ◽

Callosobruchus Maculatus ◽

Parallel Evolution ◽

Frequency Change ◽

Multiple Traits ◽

Population Genomic ◽

Performance Traits ◽

Frequency Changes

Genes that affect adaptive traits have been identified, but our knowledge of the genetic basis of adaptation in a more general sense (across multiple traits) remains limited. We combined population-genomic analyses of evolve-and-resequence experiments, genome-wide association mapping of performance traits, and analyses of gene expression to fill this knowledge gap and shed light on the genomics of adaptation to a marginal host (lentil) by the seed beetle Callosobruchus maculatus. Using population-genomic approaches, we detected modest parallelism in allele frequency change across replicate lines during adaptation to lentil. Mapping populations derived from each lentil-adapted line revealed a polygenic basis for two host-specific performance traits (weight and development time), which had low to modest heritabilities. We found less evidence of parallelism in genotype-phenotype associations across these lines than in allele frequency changes during the experiments. Differential gene expression caused by differences in recent evolutionary history exceeded that caused by immediate rearing host. Together, the three genomic datasets suggest that genes affecting traits other than weight and development time are likely to be the main causes of parallel evolution and that detoxification genes (especially cytochrome P450s and beta-glucosidase) could be especially important for colonization of lentil by C. maculatus.

Download Full-text

Distinct Patterns of Selective Sweep and Polygenic Adaptation in Evolve and Resequence Studies

Genome Biology and Evolution ◽

10.1093/gbe/evaa073 ◽

2020 ◽

Vol 12 (6) ◽

pp. 890-904 ◽

Cited By ~ 4

Author(s):

Neda Barghi ◽

Christian Schlötterer

Keyword(s):

Experimental Evolution ◽

Selective Sweep ◽

Time Series Data ◽

Empirical Studies ◽

Series Data ◽

Stabilizing Selection ◽

Selection Signatures ◽

Polygenic Adaptation ◽

Frequency Changes ◽

Optimum Model

Abstract In molecular population genetics, adaptation is typically thought to occur via selective sweeps, where targets of selection have independent effects on the phenotype and rise to fixation, whereas in quantitative genetics, many loci contribute to the phenotype and subtle frequency changes occur at many loci during polygenic adaptation. The sweep model makes specific predictions about frequency changes of beneficial alleles and many test statistics have been developed to detect such selection signatures. Despite polygenic adaptation is probably the prevalent mode of adaptation, because of the traditional focus on the phenotype, we are lacking a solid understanding of the similarities and differences of selection signatures under the two models. Recent theoretical and empirical studies have shown that both selective sweep and polygenic adaptation models could result in a sweep-like genomic signature; therefore, additional criteria are needed to distinguish the two models. With replicated populations and time series data, experimental evolution studies have the potential to identify the underlying model of adaptation. Using the framework of experimental evolution, we performed computer simulations to study the pattern of selected alleles for two models: 1) adaptation of a trait via independent beneficial mutations that are conditioned for fixation, that is, selective sweep model and 2) trait optimum model (polygenic adaptation), that is adaptation of a quantitative trait under stabilizing selection after a sudden shift in trait optimum. We identify several distinct patterns of selective sweep and trait optimum models in populations of different sizes. These features could provide the foundation for development of quantitative approaches to differentiate the two models.

Download Full-text

Highly parallel genomic selection response in replicated Drosophila melanogaster populations with reduced genetic variation

10.1101/2021.04.06.438598 ◽

2021 ◽

Author(s):

Claire Burny ◽

Viola Nolte ◽

Marlies Dolezal ◽

Christian Schl&oumltterer

Keyword(s):

Drosophila Melanogaster ◽

Experimental Evolution ◽

Selection Response ◽

Adaptive Responses ◽

Genetic Redundancy ◽

Powerful Approach ◽

Polygenic Adaptation ◽

Parallel Selection ◽

Sufficient Variation ◽

Genomic Regions

Many adaptive traits are polygenic and frequently more loci contributing to the phenotype than needed are segregating in populations to express a phenotypic optimum. Experimental evolution provides a powerful approach to study polygenic adaptation using replicated populations adapting to a new controlled environment. Since genetic redundancy often results in non-parallel selection responses among replicates, we propose a modified Evolve and Resequencing (E&R) design that maximizes the similarity among replicates. Rather than starting from many founders, we only use two inbred Drosophila melanogaster strains and expose them to a very extreme, hot temperature environment (29°C). After 20 generations, we detect many genomic regions with a strong, highly parallel selection response in 10 evolved replicates. The X chromosome has a more pronounced selection response than the autosomes, which may be attributed to dominance effects. Furthermore, we find that the median selection coefficient for all chromosomes is higher in our two-genotype experiment than in classic E&R studies. Since two random genomes harbor sufficient variation for adaptive responses, we propose that this approach is particularly well-suited for the analysis of polygenic adaptation.

Download Full-text

The distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii inferred using frequency changes under experimental evolution

10.1101/2021.09.29.462298 ◽

2021 ◽

Author(s):

Katharina B. Böndel ◽

Toby Samuels ◽

Rory J. Craig ◽

Rob W. Ness ◽

Nick Colegrave ◽

...

Keyword(s):

Chlamydomonas Reinhardtii ◽

Experimental Evolution ◽

Spontaneous Mutations ◽

Negative Effects ◽

Serial Transfer ◽

Fitness Effects ◽

Markov Chain Method ◽

Bayesian Monte Carlo ◽

High Fraction ◽

Frequency Changes

The distribution of fitness effects (DFE) for new mutations is fundamental for many aspects of population and quantitative genetics. In this study, we have inferred the DFE in the single-celled alga Chlamydomonas reinhardtii by estimating changes in the frequencies of 254 spontaneous mutations under experimental evolution and equating the frequency changes of linked mutations with their selection coefficients. We generated seven populations of recombinant haplotypes by crossing seven independently derived mutation accumulation lines carrying an average of 36 mutations in the homozygous state to a mutation-free strain of the same genotype. We then allowed the populations to evolve under natural selection in the laboratory by serial transfer in liquid culture. We observed substantial and repeatable changes in the frequencies of many groups of linked mutations, and, surprisingly, as many mutations were observed to increase as decrease in frequency. We developed a Bayesian Monte Carlo Markov Chain method to infer the DFE. This computes the likelihood of the observed distribution of changes of frequency, and obtains the posterior distribution of the selective effects of individual mutations, while assuming a two-sided gamma distribution of effects. We infer that the DFE is a highly leptokurtic distribution, and that approximately equal proportions of mutations have positive and negative effects on fitness. This result is consistent with what we have observed in previous work on a different C. reinhardtii strain, and suggests that a high fraction of new spontaneously arisen mutations are advantageous in a simple laboratory environment.

Download Full-text