Experimental Evolution Studies Research Articles

William Lawrence Tower's Beetles: Experimental Evolution and the Manipulation of Inheritance.

William Lawrence Tower's work on the evolution of the Colorado Potato Beetle (Leptinotarsa decemlineata), documenting the environmental induction of mutation and speciation, made him a leading figure in experimental genetics during the first decade of the 20th century. His research program served as a model for other experimental evolution studies seeking to demonstrate the environmental modification of inheritance. Tower enjoyed the support of influential figures in the field, despite well-known problems that plagued Tower's earlier academic career. The validity of his genetic work, and other findings reported by Tower, were later challenged. The Tower affair illustrates how questionable and possibly fraudulent scientific practices can be tolerated to explore certain experimental directions and theoretical frameworks, particularly at the frontier of expanding disciplines. When needed, those explorations can be forestalled or extinguished by exploiting conspicuous vulnerabilities of rogue practitioners. In Tower's case, both unrefuted allegations of scientific misconduct and personal problems dissolved his institutional support, leading to a swift ouster from academic science. Tower's downfall discredited soft inheritance and neo-Lamarckian conceptions in the field of experimental genetics, facilitating the discipline's embrace of a hard inheritance model that featured a hereditary material resistant to environmental modification.

Experimental and numerical study of temperature evolution and hydrogen desorption process on an amorphous alloy Mg50Ni50

In the present study, we explored the temperature evolution and hydrogen desorption properties of the Mg50Ni50 alloy through both numerical simulation and experimental analyses. Desorption kinetics characterization was carried out using the volumetric method, specifically employing a Sievert's-type apparatus to investigate solid-gas reactions. The experiments covered a temperature range from 313 K to 353 K, with an initial hydrogen pressure of 12 bar. Simultaneously, a mathematical approach was employed to numerically investigate the temperature evolution within the hydride bed. Using COMSOL Multiphysics as a simulator, a numerical simulation was conducted based on experimental data. The study examined the impact of cooling temperature on hydride temperature evolution. Results revealed that hydrogen desorption kinetics of the amorphous Mg50Ni50 alloy are more significant compared to those of Mg2Ni compounds. Moreover, the effect of the warming temperature on the equilibrium pressure can also be observed in the hydrogen desorption isotherm curves. The experimental study of the Mg50Ni50 alloy provided activation energy data, along with determination of hydride formation enthalpy and entropy. On the other hand, we showed that the hydride temperature is maximum at the hydride-hydrogen interface within the hydride center.

Numerical and experimental study of fracture evolution in layered sandstone and mudstone above the cavity

Numerical and experimental study of fracture evolution in layered sandstone and mudstone above the cavity

Coevolution and dependency influence resistance of mutualists to exploitation

A long-standing problem in the study of mutualism is to understand the effects of non-mutualistic community members that exploit the benefits of mutualism without offering commodities in exchange (i.e., ‘exploiters’). Mutualisms are continually challenged by exploiters and their persistence may depend on the costliness of exploitation or on adaptations that allow mutualists to avoid the negative effects of exploiters. Coevolution could lead to changes in mutualists and exploiters that allow mutualisms to persist. Although coevolution is considered essential for mutualism persistence and resistance to disturbance, we have yet to obtain direct experimental evidence of the role of coevolution in resistance to exploitation. Additionally, resistance to exploitation via coevolutionary processes might vary with the degree of dependency between mutualistic partners, as facultative mutualisms are thought to be under weaker coevolutionary selection than obligate mutualisms. Here, we conducted an experimental evolution study using a synthetic yeast mutualism to test how coevolution in facultative and obligate mutualisms affects their resistance to exploitation. We found that naïve facultative mutualisms were more likely to breakdown under exploitation than naïve obligate mutualisms. After 15 weeks of coevolution, both facultative and obligate evolved mutualists were more likely to survive exploitation than naïve mutualists when we reassembled mutualist communities. Additionally, coevolved exploiters were more likely to survive with mutualists, whereas naïve exploiters frequently went extinct. These results suggest that coevolution between mutualists and exploiters can lead to mutualism persistence, potentially explaining why exploitation is ubiquitous but rarely associated with mutualism breakdown.

Experimental and Computational Study of Microhardness Evolution in the HAZ for Al–Cu–Li Alloys

The Laser Beam Welding (LBW) of aluminum alloys has attracted significant interest from industrial sectors, including the shipbuilding, automotive and aeronautics industries, as it expects to contribute to significant cost reduction associated with the production of high-quality welds. To comprehend the behavior of welded structures in regard to their damage tolerance, the application of fracture mechanics serves as the instrumental tool. However, the methods employed overlook the changes in the microstructure within the Heat-Affected Zone (HAZ), which leads to the degradation of the mechanical properties of the material. The purpose of this study is to simulate microhardness evolution in the HAZ of AA2198-T351 LBW. The material represents the latest generation of Al-Cu-Li alloys, which exhibit improved mechanical properties, enhanced damage tolerance behavior, lower density and better corrosion and fatigue crack growth resistance than conventional Al-Cu alloys. In this work, the microhardness profile of LBW AA2198 was measured, and subsequently, through isothermal heat treatments on samples, the microhardness values of the HAZ were replicated. The conditions of the heat treatments (T, t) were selected in line with the thermal cycles that each area of the HAZ experienced during welding. ThermoCalc and DICTRA were employed in order to identify the strengthening precipitates and their evolution (dissolution and coarsening) during the weld thermal cycle. The microstructure of the heat-treated samples was studied employing LOM and TEM, and the strengthening precipitates and their characteristics (volume fraction and size) were defined and correlated to the calculations and the experimental conditions employed during welding. The main conclusion of this study is that it is feasible to imitate the microstructure evolution within the HAZ through the implementation of isothermal heat treatments. This implies that it is possible to fabricate samples for fatigue crack growth tests, enabling the experimental examination of the damage tolerance behavior in welded structures.

Genotype-by-environment interactions govern fitness changes associated with adaptive mutations in two-component response systems.

Introduction: Two-component response systems (TCRS) are the main mechanism by which prokaryotes acclimate to changing environments. These systems are composed of a membrane bound histidine kinase (HK) that senses external signals and a response regulator (RR) that activates transcription of response genes. Despite their known role in acclimation, little is known about the role TCRS play in environmental adaptation. Several experimental evolution studies have shown the acquisition of mutations in TCRS during adaptation, therefore here we set out to characterize the adaptive mechanism resulting from these mutations and evaluate whether single nucleotide changes in one gene could induce variable genotype-by-environment (GxE) interactions. Methods: To do this, we assessed fitness changes and differential gene expression for four adaptive mutations in cusS, the gene that encodes the HK CusS, acquired by Escherichia coli during silver adaptation. Results: Fitness assays showed that as the environment changed, each mutant displayed a unique fitness profile with greatest fitness in the original selection environment. RNAseq then indicated that, in ± silver nitrate, each mutant induces a primary response that upregulates cusS, its RR cusR, and constitutively expresses the target response genes cusCFBA. This then induces a secondary response via differential expression of genes regulated by the CusR through TCRS crosstalk. Finally, each mutant undergoes fitness tuning through unique tertiary responses that result in gene expression patterns specific for the genotype, the environment and optimized for the original selection conditions. Discussion: This three-step response shows that different mutations in a single gene leads to individualized phenotypes governed by unique GxE interactions that not only contribute to transcriptional divergence but also to phenotypic plasticity.

The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change

Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 y, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.

An experimental evolution study deciphers differences between the life attributes of developmental variants in Propylea dissecta (Mulsant) (Coleoptera: Coccinellidae)

An experimental evolution study deciphers differences between the life attributes of developmental variants in Propylea dissecta (Mulsant) (Coleoptera: Coccinellidae)

Experimental and theoretical study of the microstructure evolution and thermal-physical properties of hypereutectic Al–Fe alloys

Experimental and theoretical study of the microstructure evolution and thermal-physical properties of hypereutectic Al–Fe alloys

Experimental Study of Entrainment and Evolution of an Entrapped Air Pocket by Flowing Water in an Inclined U-Shaped Pipe

Experimental Study of Entrainment and Evolution of an Entrapped Air Pocket by Flowing Water in an Inclined U-Shaped Pipe

Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster.

Virus evolution is strongly affected by antagonistic co-evolution of virus and host. Host immunity positively selects for viruses that evade the immune response, which in turn may drive counter-adaptations in host immune genes. We investigated how host immune pressure shapes virus populations, using the fruit fly Drosophila melanogaster and its natural pathogen Drosophila C virus (DCV), as a model. We performed an experimental evolution study in which DCV was serially passaged for ten generations in three fly genotypes differing in their antiviral RNAi response: wild-type flies and flies in which the endonuclease gene Dicer-2 was either overexpressed or inactivated. All evolved virus populations replicated more efficiently in vivo and were more virulent than the parental stock. The number of polymorphisms increased in all three host genotypes with passage number, which was most pronounced in Dicer-2 knockout flies. Mutational analysis showed strong parallel evolution, as mutations accumulated in a specific region of the VP3 capsid protein in every lineage in a host genotype-independent manner. The parental tyrosine at position ninety-five of VP3 was substituted with either one of five different amino acids in fourteen out of fifteen lineages. However, no consistent amino acid changes were observed in the viral RNAi suppressor gene 1A, nor elsewhere in the genome in any of the host backgrounds. Our study indicates that the RNAi response restricts the sequence space that can be explored by viral populations. Moreover, our study illustrates how evolution towards higher virulence can be a highly reproducible, yet unpredictable process.

Experimental studies of cavitation evolution through a butterfly valve at different regulation conditions

Experimental studies of cavitation evolution through a butterfly valve at different regulation conditions

Unraveling the Molecular Basis of Stabilizing Selection by Experimental Evolution

Abstract Stabilizing selection provides a challenge to molecular population genetics. Although stabilizing selection is ubiquitous, its genomic signature is difficult to distinguish from demographic signals. Experimental evolution provides a promising approach to characterize genomic regions exposed to stabilizing selection. A recent experimental evolution study of Aedes aegypti populations evolving either with or without sexual selection found a pattern of genetic differentiation suggestive of relaxed stabilizing selection. I argue that this study could not have detected the signal of relaxed stabilizing selection. I highlight why incorrect statistical methods resulted in a high number of false positive candidate single nucleotide polymorphism (SNPs) and discuss the fallacy of functional validation of candidate SNPs for polygenic traits by RNA-mediated knockdown.

Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut

Probiotics often acquire potentially adaptive mutations in vivo, gaining new functional traits through gut selection. While both the host and microbiome can contribute to probiotics’ genetic evolution, separating the microbiome and the host’s contribution to such selective pressures remains challenging. Here, we introduced germ-free (GF) and specific pathogen-free (SPF) mouse models to track how probiotic strains, i.e., Lactiplantibacillus plantarum HNU082 (Lp082) and Bifidobacterium animalis subsp. lactis V9 (BV9), genetically evolved under selection pressures derived from host factors alone and both host and microbial ecological factors. Notably, compared to the genome of a probiotic strain before consumption, the host only elicited <15 probiotic mutations in probiotic genomes that emerged in the luminal environment of GF mice, while a total of 840 mutations in Lp082 mutants and 21,579 mutations in BV9 were found in SPF mice, <0.25% of those derived from both factors that were never captured by other experimental evolution studies, indicating that keen microbial competitions exhibited the predominant evolutionary force in shaping probiotic genetic composition (>99.75%). For a given probiotic, functional genes occurring in potentially adaptive mutations induced by hosts (GF mice) were all shared with those found in mutants of SPF mice. Collectively, the native microbiome consistently drove a more rapid and divergent genetic evolution of probiotic strains in seven days of colonization than host factors did. Our study further laid a theoretical foundation for genetically engineering probiotics for better gut adaptation through in vitro artificial gut ecosystems without the selection pressures derived from host factors.

Linking temperature dependence of fitness effects of mutations to thermal niche adaptation.

Fitness effects of mutations may generally depend on temperature that influences all rate-limiting biophysical and biochemical processes. Earlier studies suggested that high temperatures may increase the availability of beneficial mutations ('more beneficial mutations'), or allow beneficial mutations to show stronger fitness effects ('stronger beneficial mutation effects'). The 'more beneficial mutations' scenario would inevitably be associated with increased proportion of conditionally beneficial mutations at higher temperatures. This in turn predicts that populations in warm environments show faster evolutionary adaptation but suffer fitness loss when faced with cold conditions, and those evolving in cold environments become thermal-niche generalists ('hotter is narrower'). Under the 'stronger beneficial mutation effects' scenario, populations evolving in warm environments would show faster adaptation without fitness costs in cold environments, leading to a 'hotter is (universally) better' pattern in thermal niche adaptation. We tested predictions of the two competing hypotheses using an experimental evolution study in which populations of two model bacterial species, Escherichia coli and Pseudomonas fluorescens, evolved for 2400 generations at three experimental temperatures. Results of reciprocal transplant experiments with our P. fluorescens populations were largely consistent with the 'hotter is narrower' prediction. Results from the E. coli populations clearly suggested stronger beneficial mutation effects at higher assay temperatures, but failed to detect faster adaptation in populations evolving in warmer experimental environments (presumably because of limitation in the supply of genetic variation). Our results suggest that the influence of temperature on mutational effects may provide insight into the patterns of thermal niche adaptation and population diversification across thermal conditions.

Species and condition shape the mutational spectrum in experimentally evolved biofilms.

Laboratory experimental evolution provides a powerful tool for studying microbial adaptation to different environments. To understand the differences and similarities of the dynamic evolutionary landscapes of two model species from the Bacillus genus as they adapt to abiotic and biotic surfaces, we revived the archived population samples from our four previous experimental evolution studies and performed longitudinal whole-population genome sequencing. Surprisingly, higher number of mutations, higher genotypic diversity, and higher evolvability were detected in the biotic conditions with smaller population size. Different adaptation strategies were observed in different environments within each species, with more diversified mutational spectrum detected in biotic conditions. The insertion sequences of Bacillus thuringiensis are critical for its adaptation to the plastic bead-attached biofilm environment, but insertion sequence mobility was a general phenomenon in this species independent of the selection condition. Additionally, certain parallel evolution has been observed across species and environments, particularly when two species adapt to the same environment at the same time. Furthermore, our results suggest that the population size might be an important driver of evolution. Together, these results provide the first comprehensive mutational landscape of two bacterial species' biofilms that is adapted to an abiotic and biotic surface. IMPORTANCE Biofilm formation is a vital factor for the survival and adaptation of bacteria in diverse environmental niches. Experimental evolution combined with the advancement of whole-population genome sequencing provides us a powerful tool to understand the genomic dynamic of evolutionary adaptation to different environments, such as during biofilm development. Previous studies described the genetic and phenotypic changes of selected clones from experimentally evolved Bacillus thuringiensis and Bacillus subtilis that were adapted under abiotic and biotic biofilm conditions. However, the full understanding of the dynamic evolutionary landscapes was lacking. Furthermore, the differences and similarities of adaptive mechanisms in B. thuringiensis and B. subtilis were not identified. To overcome these limitations, we performed longitudinal whole-population genome sequencing to study the underlying genetic dynamics at high resolution. Our study provides the first comprehensive mutational landscape of two bacterial species' biofilms that is adapted to an abiotic and biotic surface.

Topological characteristics of grain boundary networks during severe plastic deformations of copper alloys

The grain boundary character distribution strongly affects the properties of polycrystalline materials. Grain boundaries of similar characters form networks, whose topological invariants can be considered as distribution descriptors. Understanding the evolution of such descriptors during severe plastic deformations (SPD) can elucidate the evolution of properties and underpin the design of processing routes for target behaviour. For topological analysis of grain boundary networks, polycrystalline materials are considered here as polyhedral complexes with grain boundaries classified into two types — low-angle and high-angle. Changes of grain boundary types are calculated using sub-grain rotations, which reflects the physical mechanism of microstructure evolution during SPD. A non-physical approach, by direct conversions of low-angle to high-angle boundaries, is also explored as a reference to demonstrate the impact of the physical constraint imposed by rotations. Reported is the discovery of topological phase transitions in the grain boundary networks which might take place during severe plastic deformations of different copper alloys. Depending on the evolution approach, the transitions correspond to zeros of the Euler characteristic, or of the logarithm of the inverse connectivity, of the grain boundary network. The relations between these transitions and the fraction of high-angle grain boundaries, and between the fraction of high-angle grain boundaries and plastic strain obtainable experimentally, provide new perspectives for grain boundary engineering and network design. Determining the dominant evolution mechanism and critical accumulated strain for a given material and processing route requires further experimental studies of triple junction evolution.

Experimental and Numerical Study of the Nonlinear Evolution of Regular Waves over a Permeable Submerged Breakwater

The permeable submerged breakwater has gained popularity in recent days due to its merits of reducing incident wave energy without negatively impacting the aesthetics of the ocean view and allowing for water exchange. However, the effect of porosity on wave nonlinearity and turbulence motion close to the water/structure interface is not well resolved in the literature. This paper presents an experimental and numerical study of regular wave propagation over a permeable submerged breakwater with a wide top width. The laboratory experiments were conducted in a wave flume and included 45 test cases. The numerical simulations were performed utilizing validated olaFoam. The results show that the nonlinearity of the waves on the permeable submerged breakwater is weak, which can effectively suppress and reduce the second harmonic waves. A large amount of turbulent kinetic energy exists at the interface between the permeable submerged breakwater and the water body, which helps to dissipate wave energy. For the wider permeable submerged breakwater in this paper, the wave dissipation capacity is greatest when the porosity is between 0.2 and 0.3, and as the length of the breakwater increases, the energy transmission coefficient decreases, and the energy dissipation coefficient increases. Better wave attenuation is achieved when the permeable submerged breakwater has a certain porosity and a large width.

Prevalence of Cyprinid herpesvirus 3 and ORF150 genomic variations in carp populations of Indonesia

Cyprinid herpesvirus-3 (CyHV-3) is the etiological agent of koi herpesvirus disease (KHVD) in common and koi carp farming. This highly contagious pathogen has a 295-kb genome that harbours 156 open reading frames. Recent in vitro experimental evolution studies highlighted strong dynamics of genomic structural variations (SVs), in particular in the region of ORF150, an ORF potentially involved in virus multiplication and host inflammatory response. Among these SVs, a 1363-bp deletion could be associated with a loss of virulence. The present study aimed at investigating the genomic variations in the ORF150 region, and especially the deletion, in viruses isolated from carp populations of Indonesia. A screening of 236 fish from 43 different farms revealed a high prevalence of CyHV-3 (nearly 70%), both in symptomatic and asymptomatic common carp. However, in contrast with the results obtained in vitro, long read sequencing of the ORF150 region revealed a low level of genetic variations and the absence of the 1363-pb deletion. The complex interactions between the virus, the environment and the host, particularly the immune system, probably play an important role in this reduced variability.

Trade-off between local replication and long-distance dissemination during experimental evolution of a satellite RNA.

Satellite RNAs (satRNAs) are molecular parasites that depend on their non-homologous helper viruses (HVs) for essential biological functions. While there are multiple molecular and phylogenetic studies on satRNAs, there is no experimental evolution study on how satRNAs may evolve in common infection conditions. In this study, we serially passaged the Bamboo mosaic virus (BaMV) associated-satRNA (satBaMV) under conditions in which satBaMV either coinfects an uninfected host plant, Nicotiana benthamiana, with BaMV or superinfects a transgenic N. benthamiana expressing the full-length BaMV genome. Single-nucleotide polymorphisms (SNPs) of satBaMV populations were analyzed by deep sequencing. Forty-eight SNPs were identified across four different experimental treatments. Most SNPs are treatment-specific, and some are also ephemeral. However, mutations at positions 30, 34, 63, and 82, all located at the 5' untranslated region (UTR), are universal in all treatments. These universal SNPs are configured into several haplotypes and follow different population dynamics. We constructed isogenic satBaMV strains only differing at positions 30 and 82 and conducted competition experiments in protoplasts and host plants. We found that the haplotype that reached high frequency in protoplasts and inoculation leaves also exhibited poor dissemination to systemic leaves and vice versa, thus suggesting an apparent trade-off between local replication and long-distance dissemination. We posit that the trade-off is likely caused by antagonistic pleiotropy at the 5' UTR. Our findings revealed a hitherto under-explored connection between satRNA genome replication and movement within a host plant. The significance of such a connection during satRNA evolution warrants a more thorough investigation.