Environment-dependent pleiotropic effects of mutations on the maximum growth rate r and carrying capacity K of population growth

Resource presentation dictates genetic and phenotypic adaptation in yeast

BACKGROUND

Environments shape adaptive trajectories of populations, often leading to adaptive parallelism in identical, and divergence in different environments. However, how does the likelihood of these possibilities change with minute changes in the environment remain unclear.

RESULTS

In this study, we evolved Saccharomyces cerevisiae in environments which differed only in the manner in which the sugar source is presented to the population. In one set of populations, carbon was presented as a mixture of glucose-galactose, and in the other, as melibiose, a glucose-galactose disaccharide. Since the two environments differed in how the two monosaccharides are packaged, we call these environments 'synonymous'. Our results show that even subtle environmental differences can lead to differing phenotypic responses between the two sets of evolved populations. However, despite different adaptive responses, pleiotropic effects of adaptation are largely predictable. We also show that distinct genomic targets of adaptation between the two sets of evolved populations are functionally convergent.

CONCLUSION

This study highlights how subtle environmental differences dictate phenotypic and genetic adaptation of populations. Additionally, these results also suggest the predictive potential of ancestor's fitness in understanding pleiotropic responses. Our work underscores the importance of studying more such environments to understand the generality of adaptive responses in populations.

Evolution Under Competition Increases Population Production by Reducing the Density-Dependence of Net Energy Fluxes and Growth

Competition can drive rapid evolution, but forecasting how species evolve in communities remains difficult. Life history theory predicts that evolution in crowded environments should maximize population production, with intra- and inter-specific competition producing similar outcomes if species compete for similar resources. Despite its appeal, this prediction has rarely been tested in communities. To test its generality and identify its physiological basis, we used experimental evolution to maintain four species of marine phytoplankton alone or together in a community for 4.5 months. We then quantified changes in their metabolism, demography, and competitive ability at two timepoints (~60 and 120 generations) in common garden experiments. One species was outcompeted during the evolution experiment. For the other three, we found the same evolutionary outcome: species evolved greater biovolume production regardless of competition treatment but did so either by increasing max. population size or individual cell size. Biovolume production increased because of the differential evolution of photosynthesis and respiration under intense competition. These metabolic changes meant that intraspecific competition decreased, and cells maintained higher rates of net energy production and growth as populations neared the stationary phase. Overall, these results show that intra- and inter-specific competition influence physiological and population parameters similarly in species that compete for essential resources. Life history theory thus provides a valuable base for predicting how species evolve in communities, and our results show how these predictions relate to the evolution of metabolism and competitive ability.

Trait and plasticity evolution under competition and mutualism in evolving pairwise yeast communities

Although we have a good understanding of how phenotypic plasticity evolves in response to abiotic environments, we know comparatively less about responses to biotic interactions. We experimentally tested how competition and mutualism affected trait and plasticity evolution of pairwise communities of genetically modified brewer's yeast. We quantified evolutionary changes in growth rate, resource use efficiency (RUE), and their plasticity in strains evolving alone, with a competitor, and with a mutualist. Compared to their ancestors, strains evolving alone had lower RUE and RUE plasticity. There was also an evolutionary tradeoff between changes in growth rate and RUE in strains evolving alone, suggesting selection for increased growth rate at the cost of efficiency. Strains evolving with a competitive partner had higher growth rates, slightly lower RUE, and a stronger tradeoff between growth rate and efficiency. In contrast, mutualism had opposite effects on trait evolution. Strains evolving with a mutualist had slightly lower growth rates, higher RUE, and a weak evolutionary tradeoff between growth rate and RUE. Despite their different effects on trait evolution, competition and mutualism had little effect on plasticity evolution for either trait, suggesting that abiotic factors could be more important than biotic factors in generating selection for plasticity.

Quantifying the strength of viral fitness trade-offs between hosts: a meta-analysis of pleiotropic fitness effects

The range of hosts a given virus can infect is widely presumed to be limited by fitness trade-offs between alternative hosts. These fitness trade-offs may arise naturally due to antagonistic pleiotropy if mutations that increase fitness in one host tend to decrease fitness in alternate hosts. Yet there is also growing recognition that positive pleiotropy may be more common than previously appreciated. With positive pleiotropy, mutations have concordant fitness effects such that a beneficial mutation can simultaneously increase fitness in different hosts, providing a genetic mechanism by which selection can overcome fitness trade-offs. How readily evolution can overcome fitness trade-offs therefore depends on the overall distribution of mutational fitness effects between hosts, including the relative frequency of antagonistic versus positive pleiotropy. We therefore conducted a systematic meta-analysis of the pleiotropic fitness effects of viral mutations reported in different hosts. Our analysis indicates that while both antagonistic and positive pleiotropy are common, fitness effects are overall positively correlated between hosts and unconditionally beneficial mutations are not uncommon. Moreover, the relative frequency of antagonistic versus positive pleiotropy may simply reflect the underlying frequency of beneficial and deleterious mutations in individual hosts. Given a mutation is beneficial in one host, the probability that it is deleterious in another host is roughly equal to the probability that any mutation is deleterious, suggesting there is no natural tendency toward antagonistic pleiotropy. The widespread prevalence of positive pleiotropy suggests that many fitness trade-offs may be readily overcome by evolution given the right selection pressures.

Patterns and evolutionary consequences of pleiotropy

Pleiotropy refers to the phenomenon of one gene or one mutation affecting multiple phenotypic traits. While the concept of pleiotropy is as old as Mendelian genetics, functional genomics has finally allowed the first glimpses of the extent of pleiotropy for a large fraction of genes in a genome. After describing conceptual and operational difficulties in quantifying pleiotropy and the pros and cons of various methods for measuring pleiotropy, I review empirical data on pleiotropy, which generally show an L-shaped distribution of the degree of pleiotropy (i.e., the number of traits affected) with most genes having low pleiotropy. I then review the current understanding of the molecular basis of pleiotropy. The rest of the review discusses evolutionary consequences of pleiotropy, focusing on advances in topics including the cost of complexity, regulatory vs. coding evolution, environmental pleiotropy and adaptation, evolution of ageing and other seemingly harmful traits, and evolutionary resolution of pleiotropy.

Detecting natural selection in trait-trait coevolution

No phenotypic trait evolves independently of all other traits, but the cause of trait-trait coevolution is poorly understood. While the coevolution could arise simply from pleiotropic mutations that simultaneously affect the traits concerned, it could also result from multivariate natural selection favoring certain trait relationships. To gain a general mechanistic understanding of trait-trait coevolution, we examine the evolution of 220 cell morphology traits across 16 natural strains of the yeast Saccharomyces cerevisiae and the evolution of 24 wing morphology traits across 110 fly species of the family Drosophilidae, along with the variations of these traits among gene deletion or mutation accumulation lines (a.k.a. mutants). For numerous trait pairs, the phenotypic correlation among evolutionary lineages differs significantly from that among mutants. Specifically, we find hundreds of cases where the evolutionary correlation between traits is strengthened or reversed relative to the mutational correlation, which, according to our population genetic simulation, is likely caused by multivariate selection. Furthermore, we detect selection for enhanced modularity of the yeast traits analyzed. Together, these results demonstrate that trait-trait coevolution is shaped by natural selection and suggest that the pleiotropic structure of mutation is not optimal. Because the morphological traits analyzed here are chosen largely because of their measurability and thereby are not expected to be biased with regard to natural selection, our conclusion is likely general.

What Has Genomics Taught An Evolutionary Biologist?

Genomics, an interdisciplinary field of biology on the structure, function, and evolution of genomes, has revolutionized many subdisciplines of life sciences, including my field of evolutionary biology, by supplying huge data, bringing high-throughput technologies, and offering a new approach to biology. In this review, I describe what I have learned from genomics and highlight the fundamental knowledge and mechanistic insights gained. I focus on three broad topics that are central to evolutionary biology and beyond-variation, interaction, and selection-and use primarily my own research and study subjects as examples. In the next decade or two, I expect that the most important contributions of genomics to evolutionary biology will be to provide genome sequences of nearly all known species on Earth, facilitate high-throughput phenotyping of natural variants and systematically constructed mutants for mapping genotype-phenotype-fitness landscapes, and assist the determination of causality in evolutionary processes using experimental evolution.

Complex genetics cause and constrain fungal persistence in different parts of the mammalian body

Determining how genetic polymorphisms enable certain fungi to persist in mammalian hosts can improve understanding of opportunistic fungal pathogenesis, a source of substantial human morbidity and mortality. We examined the genetic basis of fungal persistence in mice using a cross between a clinical isolate and the lab reference strain of the budding yeast Saccharomyces cerevisiae. Employing chromosomally encoded DNA barcodes, we tracked the relative abundances of 822 genotyped, haploid segregants in multiple organs over time and performed linkage mapping of their persistence in hosts. Detected loci showed a mix of general and antagonistically pleiotropic effects across organs. General loci showed similar effects across all organs, while antagonistically pleiotropic loci showed contrasting effects in the brain vs the kidneys, liver, and spleen. Persistence in an organ required both generally beneficial alleles and organ-appropriate pleiotropic alleles. This genetic architecture resulted in many segregants persisting in the brain or in nonbrain organs, but few segregants persisting in all organs. These results show complex combinations of genetic polymorphisms collectively cause and constrain fungal persistence in different parts of the mammalian body.

Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions

Early evolution of mutualism is characterized by big and predictable adaptive changes, including the specialization of interacting partners, such as through deleterious mutations in genes not required for metabolic cross-feeding. We sought to investigate whether these early mutations improve cooperativity by manifesting in synergistic epistasis between genomes of the mutually interacting species. Specifically, we have characterized evolutionary trajectories of syntrophic interactions of Desulfovibrio vulgaris (Dv) with Methanococcus maripaludis (Mm) by longitudinally monitoring mutations accumulated over 1000 generations of nine independently evolved communities with analysis of the genotypic structure of one community down to the single-cell level. We discovered extensive parallelism across communities despite considerable variance in their evolutionary trajectories and the perseverance within many evolution lines of a rare lineage of Dv that retained sulfate-respiration (SR+) capability, which is not required for metabolic cross-feeding. An in-depth investigation revealed that synergistic epistasis across pairings of Dv and Mm genotypes had enhanced cooperativity within SR- and SR+ assemblages, enabling their coexistence within the same community. Thus, our findings demonstrate that cooperativity of a mutualism can improve through synergistic epistasis between genomes of the interacting species, enabling the coexistence of mutualistic assemblages of generalists and their specialized variants.

Correlational selection in the age of genomics

Ecologists and evolutionary biologists are well aware that natural and sexual selection do not operate on traits in isolation, but instead act on combinations of traits. This long-recognized and pervasive phenomenon is known as multivariate selection, or-in the particular case where it favours correlations between interacting traits-correlational selection. Despite broad acknowledgement of correlational selection, the relevant theory has often been overlooked in genomic research. Here, we discuss theory and empirical findings from ecological, quantitative genetic and genomic research, linking key insights from different fields. Correlational selection can operate on both discrete trait combinations and quantitative characters, with profound implications for genomic architecture, linkage, pleiotropy, evolvability, modularity, phenotypic integration and phenotypic plasticity. We synthesize current knowledge and discuss promising research approaches that will enable us to understand how correlational selection shapes genomic architecture, thereby linking quantitative genetic approaches with emerging genomic methods. We suggest that research on correlational selection has great potential to integrate multiple fields in evolutionary biology, including developmental and functional biology, ecology, quantitative genetics, phenotypic polymorphisms, hybrid zones and speciation processes.

Interspecific hybrids show a reduced adaptive potential under DNA damaging conditions

Hybridization may increase the probability of adaptation to extreme stresses. This advantage could be caused by an increased genome plasticity in hybrids, which could accelerate the search for adaptive mutations. High ultraviolet (UV) radiation is a particular challenge in terms of adaptation because it affects the viability of organisms by directly damaging DNA, while also challenging future generations by increasing mutation rate. Here we test whether hybridization accelerates adaptive evolution in response to DNA damage, using yeast as a model. We exposed 180 populations of hybrids between species (Saccharomyces cerevisiae and Saccharomyces paradoxus) and their parental strains to UV mimetic and control conditions for approximately 100 generations. Although we found that adaptation occurs in both hybrids and parents, hybrids achieved a lower rate of adaptation, contrary to our expectations. Adaptation to DNA damage conditions comes with a large and similar cost for parents and hybrids, suggesting that this cost is not responsible for the lower adaptability of hybrids. We suggest that the lower adaptive potential of hybrids in this condition may result from the interaction between DNA damage and the inherent genetic instability of hybrids.

Variation in the life history strategy underlies functional diversity of tumors

Classical r- vs. K-selection theory describes the trade-offs between high reproductive output and competitiveness and guides research in evolutionary ecology. While its impact has waned in the recent past, cancer evolution may rekindle it. Herein, we impose r- or K-selection on cancer cell lines to obtain strongly proliferative r cells and highly competitive K cells to test ideas on life-history strategy evolution. RNA-seq indicates that the trade-offs are associated with distinct expression of genes involved in the cell cycle, adhesion, apoptosis, and contact inhibition. Both empirical observations and simulations based on an ecological competition model show that the trade-off between cell proliferation and competitiveness can evolve adaptively. When the r and K cells are mixed, they exhibit strikingly different spatial and temporal distributions. Due to this niche separation, the fitness of the entire tumor increases. The contrasting selective pressure may operate in a realistic ecological setting of actual tumors.

Effect of microplastics PAN polymer and/or Cu2+ pollution on the growth of Chlorella pyrenoidosa

Polyacrylonitrile polymer (PAN), a common representative textile material and a microplastic, has significant influence on phytoplankton algae, especially with co-exposure with other pollutants, e.g. Cu²⁺. In the present study, we carried out experiments to reveal the population size variation trends of Chlorella pyrenoidosa over time (during a whole growth cycle of 6 days) under PAN and/or Cu²⁺. The levels of pigments (chlorophyll a, b, total chlorophyll and carotenoids), chlorophyll a fluorescence parameters, and other physiological and biochemical indices, containing total protein measurements of H₂O₂, catalase (CAT), and malondialdehyde (MDA) under different treatment groups were measured to explain the physio-ecological mechanism of the effect of PAN and/or Cu²⁺ on the growth of C. pyrenoidosa. The results showed that PAN, Cu²⁺ and the combination of PAN and Cu²⁺ inhibited the growth of C. pyrenoidosa. Chlorophyll a and b decreased significantly with increasing levels of pollutants (PAN and/or Cu²⁺); however, the carotenoid levels increased with increasing levels of pollutants (PAN and/or Cu²⁺) for the first three cultivation days. The oxygen-evolving complexes (OECs) of C. pyrenoidosa had been damaged under Cu²⁺ pollution. The results also showed that CAT activity, MDA content and H₂O₂ activity of C. pyrenoidosa increased with increasing levels of pollutants (PAN and/or Cu²⁺); however, total protein content decreased with increasing levels of pollutants (PAN and/or Cu²⁺) at the first cultivation day. These results indicate that pollutants (PAN and/or Cu²⁺) are harmful to the growth of the C. pyrenoidosa population and negatively affect the levels and function of the pigments in C. pyrenoidosa by decreasing chlorophyll a and b levels, increasing carotenoid levels, and increasing antioxidant enzyme activity.