Biology subjects

Ketola, T.

Publications and source records attributed to Ketola, T..

11 recordsLinked to original sources

bioRxiv2024

The effect of population size on adaptation to fluctuating temperatures

Climate change exposes populations to more frequent periods of extreme temperatures and faster temperature fluctuations. Theoretical models suggest that different types of adaptations should occur in constant versus fluctuating environments of varying frequency. Furthermore, evolutionary adaptation to one environment may weaken the adaptations to alternative environments due to antagonistically pleiotropic alleles. However, fitness trade-offs are rarely observed in experiments and it has been hypothesized that the number and severity of trade-offs evolving in fluctuating environments might depend on population size. To evaluate whether specific types of adaptations evolve at fluctuating temperatures and how population size affects the evolution of trade-offs, we performed an evolution experiment with fission yeast (Schizosaccharomyces pombe). The small and large populations evolved for 500 generations at constant and fluctuating temperatures, after which the evolved strains competed against ancestral strains in respective selection environments and in alternative environments to detect trade-offs. We observed significant adaptation and maladaptation only to constant heat, but not to fluctuating temperatures. Overall, the population size did not have significant effects on adaptation capacity or trade-offs in alternative environments. Our results suggest that constant extreme temperatures may act as stronger selective pressures than temperature variation and that trade-offs are unlikely to constrain adaptation to fluctuating temperatures.

evolutionary biology↗

bioRxiv2024

Genome-wide association mapping for growth rate at fluctuating and extreme temperatures

Constant temperatures and fluctuations of varying frequency affect fitness differently, which has led to suggestions of distinct genetic architectures and adaptation strategies between constant and fluctuating thermal environments. However, very little is known about the possible fitness trade-offs and genetic constraints underlying thermal adaptation and how they affect species ability to confront climatic changes. We addressed this gap in knowledge by integrating quantitative genetics and genome-wide association mapping in the filamentous fungus Neurospora crassa. Growth rates were measured for 434 strains under fast and slow frequency fluctuations, at high and low temperature range with respect to the species tolerance, and at constant mean and extreme temperatures of these ranges. We found strong genetic correlations between fast and slow frequency fluctuations, and between fluctuations and their mean temperatures, but not with the highest extreme temperature. Positive correlations were supported by high heritability values, pointing that in N. crassa there are no significant trade-offs or genetic constraints in adaptation when variance in temperature increases. Altogether, our results indicated clearly polygenic basis of thermal tolerance, with most of the variation in overall performance (83 %), and clearly less in hot-cold trade-off (8 %), or heat stress tolerance (4 %). Interestingly, GWAS discovered many SNPs associated with growth rate only at constant temperatures or at fast and slow fluctuations at high and low thermal range. However, the cellular functions of the associated genes were overlapping, and no opposite allelic effects were found between treatments. Hence, large-effect loci indicated no trade-offs, but a shared physiology across temperatures, probably owing to the general stress response or individuals overall fitness.

evolutionary biology↗

bioRxiv2024

Genome-wide association for loci influencing thermal performance curves in Neurospora crassa

Temperature poses a unique challenge to ectothermic species, as it affects all biochemical reactions in the cell and causes physiological stress. The effect of temperature on an organism can be described by a thermal performance curve (TPC), which displays organismal performance, such as growth rate, as a function of temperature. Previous studies on thermal performance have revealed different amounts of genetic variation and trade-offs in TPC shape and position within species and populations. However, very little is known about the genetic architecture of TPCs on the level of individual loci and alleles. We asked what is the identity of loci contributing to genetic variation in TPCs, and do the alleles exhibit trade-offs or thermodynamic scaling across the temperature range? We used genome-wide association mapping to find loci influencing growth rate at different temperatures and TPC traits in the filamentous fungus Neurospora crassa. We also evaluated the directions and magnitudes of allelic effects to investigate possible trade-offs. We observed both unique associations at specific temperatures, as some loci affected growth rate only at low, intermediate, or high temperatures, and associations that were shared across multiple temperatures. However, only weak evidence of trade-offs was detected, indicating that the evolution of TPCs in N. crassa is not constrained by allelic effects in opposite directions at hot and cold temperatures. Our findings indicate that trade-offs contribute little to variation in TPCs.

genetics↗

bioRxiv2020

Rich resource environment of fish farms facilitates phenotypic variation and virulence in an opportunistic fish pathogen

Phenotypic variation allows adaptation of opportunistic pathogens to variable conditions in the outside-host environment with strong effects on their epidemiology and pathogenicity in hosts. Here we found that the isolates of an opportunistic fish pathogen Flavobacterium columnare from fish farming environment had higher phenotypic variation between two morphotypes in growth, as compared to the isolates from the natural water environment. The rough morphotypes had higher growth rate than the rhizoid morphotypes especially in the higher resource concentrations and in the higher temperature, but only if the isolate was originating from the fish farms. Rhizoid morphotype was more virulent than the rough type regardless of their origin. However, the virulence of the rough type increased sharply with the size of the fish, and the bacterial isolates from the gills of diseased fish were rhizoid type, indicating a reversal of the rough morphotype into rhizoid in contact with the fish. The high growth rate of the rough morphotype combined with the morphotype reversibility could increase the probability of columnaris epidemics at fish farms. Our findings suggest that intensive farming imposes different selection pressures on bacterial survival in the outside-host environment and its transmission compared to the natural water environment.

microbiology↗

bioRxiv2020

Quantitative genetics of temperature performance curves of Neurospora crassa

Earths temperature is increasing due to anthropogenic CO2 emissions; and organisms need either to adapt to higher temperatures, migrate into colder areas, or face extinction. Temperature affects nearly all aspects of an organisms physiology via its influence on metabolic rate and protein structure, therefore genetic adaptation to increased temperature may be much harder to achieve compared to other abiotic stresses. There is still much to be learned about the evolutionary potential for adaptation to higher temperatures, therefore we studied the quantitative genetics of growth rates in different temperatures that make up the thermal performance curve of the fungal model system Neurospora crassa. We studied the amount of genetic variation for thermal performance curves and examined possible genetic constraints by estimating the G-matrix. We observed a substantial amount of genetic variation for growth in different temperatures, and most genetic variation was for performance curve elevation. Contrary to common theoretical assumptions, we did not find strong evidence for genetic trade-offs for growth between hotter and colder temperatures. We also simulated short term evolution of thermal performance curves of N. crassa, and suggest that they can have versatile responses to selection.

evolutionary biology↗

bioRxiv2019

Environmentally triggered evolutionary cascade across trophic levels in an experimental phage-bacteria-insect system

Viruses are key actors of ecosystems and have major impacts on global biogeochemical cycles. Prophages deserve particular attention as they are ubiquitous in bacterial genomes and can enter a lytic cycle when triggered by environmental conditions. We explored how temperature affects the interactions between prophages and other biological levels by using an opportunistic pathogen, the bacterium Serratia marcescens, that harbours several prophages and that had undergone an evolution experiment under several temperature regimes. We found that the release of one of the prophages was temperature-sensitive and malleable to evolutionary changes. We further discovered that the virulence of the bacterium in an insect model also evolved and was positively correlated with phage release rates. We determined through analysis of genetic and epigenetic data that changes in the outer cell wall structure possibly explain this phenomenon. We hypothezise that the temperature-dependent phage release rate acted as a selection pressure on S. marcescens and that it resulted in modified bacterial virulence in the insect host. Our study system illustrates how viruses can mediate the influence of abiotic environmental changes to other biological levels and thus be involved in ecosystem feedback loops.

evolutionary biology↗

bioRxiv2019

Roles of adenosine and cytosine methylation changes and genetic mutations in adaptation to different temperatures

Epigenetic modifications can contribute to adaptation, but the relative contributions of genetic and epigenetic variation are unknown. Previous studies on the role of epigenetic changes in adaptation in eukaryotes have nearly exclusively focused on cytosine methylation (m5C), while prokaryotes exhibit a richer system of methyltransferases targetting adenines (m6A) or cytosines (m4C, m5C). DNA methylation in prokaryotes has many roles, but its potential role in adaptation still needs further investigation. We collected phenotypic, genetic, and epigenetic data using single molecule real-time sequencing of clones of the bacterium Serratia marcescens that had undergone experimental evolution in contrasting temperatures to investigate the relationship between environment and genetic, epigenetic, and phenotypic changes. This data provided a detailed description of the methylation landscape of S. marcescens and allowed us to examine the potential contributions of genetic and epigenetic changes to phenotypic adaptation. The genomic distribution of GATC motifs, which are the main target for m6A methylation, and of partially methylated epiloci pointed to a link between m6A methylation and regulation of gene expression in S. marcescens. Evolved strains, while genetically homogeneous, exhibited many polymorphic m6A epiloci. There was no strong support for a genetic control of methylation changes in our experiment, and no clear evidence of parallel environmentally-induced or environmentally-selected methylation changes at specific epiloci was found. Both some genetic and epigenetic variants were associated with some phenotypic traits. Overall, our results suggest that both genetic and adenine methylation changes have potential to contribute to phenotypic adaptation in S. marcescens, but that any environmentally-induced epigenetic change occurring in our experiment would probably have been quite labile.

evolutionary biology↗

bioRxiv2019

Marked Neurospora crassa strains for competition experiments and Bayesian methods for fitness estimates

The filamentous fungus Neurospora crassa, a model microbial eukaryote, has a life cycle with many features that make it suitable for studying experimental evolution. However, it has lacked a general tool for estimating relative fitness of different strains in competition experiments. To remedy this need, we constructed N. crassa strains that contain a modified csr-1 locus and developed an assay for detecting the proportion of the marked strain using a post PCR high resolution melting assay. DNA extraction from spore samples can be performed on 96-well plates, followed by a PCR step, which allows many samples to be processed with ease. Furthermore, we suggest a Bayesian approach for estimating relative fitness from competition experiments that takes into account the uncertainty in measured strain proportions. We show that there is a fitness effect of the mating type locus, as mating type mat a has a higher competitive fitness than mat A. The csr-1* marker also has a small fitness effect, but is still a suitable marker for competition experiments. As a proof of concept, we estimate the fitness effect of the qde-2 mutation, a gene in the RNA interference pathway, and show that its competitive fitness is lower than what would be expected from its mycelial growth rate alone.

genetics↗

bioRxiv2017

Effects of acclimation time and epigenetic mechanisms on growth of Neurospora in fluctuating environments

Reaction norms or tolerance curves have often been used to predict how organisms deal with fluctuating environments. A potential drawback is that reaction norms measured in different constant environments may not capture all aspects of organismal responses to fluctuating environments. We examined growth of the filamentous fungus Neurospora crassa in fluctuating temperatures and tested if growth in fluctuating temperatures can be explained simply by growth in different constant temperatures or if more complex models are needed. In addition, as previous studies on fluctuating environments have revealed that past temperatures that organisms have experienced can affect their response to current temperature, we tested the roles of different epigenetic mechanisms in response to fluctuating environments using different mutants. We found that growth of Neurospora can be predicted in fluctuating temperatures to some extent if acclimation times are taken into account in the model. Interestingly, while fluctuating environments have been linked with epigenetic responses we found only some evidence of involvement of epigenetic mechanisms on tolerating fluctuating temperatures. Mutants which lacked H3K4 or H3K36 methylation had slightly impaired response to temperature fluctuations, in addition the H3K4 methylation mutant and a mutant in the RNA interference pathway had altered acclimation times.

genetics↗

bioRxiv2017

Thermal Tolerance is linked with Virulence in a Fish Pathogen

Although increase in temperatures may boost the number of pathogens, a complex process involving the interaction of a susceptible host, a virulent strain, and environmental factors would influence disease virulence in unpredictable ways. Here we explored if the virulence of an environmentally growing opportunistic fish pathogen, Flavobacterium columnare, would be malleable to evolutionary changes via correlated selection on thermal tolerance. Virulence among the strains increased over years, but tolerance to higher temperatures was associated with reduced virulence. Our results suggest that observed increase in frequency of columnaris epidemics over the last decade is most likely associated with increased length of growing season, or other time dependent change in environment, rather than increased regional average temperatures. Our results also indicate that most virulent bacteria had weaker ability to tolerate outside host environments, which suggest trade-off between more obligate pathogen behaviour and ability to grow outside host.

evolutionary biology↗

bioRxiv2017

Invasion triple trouble: Environmental fluctuations, fluctuation-adapted invaders and fluctuation-mal-adapted communities all govern invasion success

It has been suggested that climate change will lead to increased environmental fluctuations, which will undoubtedly have evolutionary consequences for all biota. For instance, fluctuations can directly increase the risk of invasions of alien species into new areas, as these species have repeatedly been proposed to benefit from disturbances. At the same time increased environmental fluctuations may also select for better invaders. However, selection by fluctuations may also influence the resistance of communities to invasions, which has rarely been tested. We tested eco-evolutionary dynamics of invasion with bacterial clones, evolved either in constant or fluctuating temperatures, and conducted experimental invasions in both conditions. We found clear evidence that ecological fluctuations, as well as adaptation to fluctuations by both the invader and community, all affected invasions, but played different roles at different stages of invasion. Ecological fluctuations clearly promoted invasions, especially into fluctuation mal-adapted communities. The evolutionary background of the invader clearly played a smaller role, and only at the later stages of invasion in the fluctuating environments. Our results indicate that climate change associated disturbances can directly increase the risk of invasions by altering ecological conditions during invasions, as well as via the evolution of both the invader and communities. Our experiment provides novel information on the complex consequences of climate change on invasions in general, and also charts risk factors associated with the spread of environmentally growing opportunistic pathogens.\n\nData AccessibilityUpon acceptance the data will be made publicly available.\n\nStatement of authorshipAuthors planned the questions and experiment together. KS conducted the laboratory work and wrote the first draft of the manuscript. TK conducted statistical analyses. All authors wrote the final version of the manuscript.

ecology↗