Genotype specific and microbiome effects of hypoxia in the model organism Daphnia magna.

The fitness of the host is highly influenced by the interplay between the host and its associated microbiota. The flexible nature of these microbiota enables them to respond swiftly to shifts in the environment, which plays a key role in the host's capacity to withstand environmental stresses. To understand the role of the microbiome in host tolerance to hypoxia, one of the most significant chemical changes occurring in water ecosystems due to climate change, we performed a reciprocal gut transplant experiment with the freshwater crustacean Daphnia magna. In a microbiome transplant experiment, two genotypes of germ-free recipients were inoculated with gut microbiota from Daphnia donors of their own genotype or from the other genotype, that had been either pre-exposed to normoxic or hypoxic conditions. We found that D. magna individuals had a higher survival probability in hypoxia if their microbiome had been pre-exposed to hypoxia. The bacterial communities of the recipients changed over time with a reduction in alpha diversity, which was stronger when donors were pre-exposed to a hypoxic environment. While donor genotype had no influence on the long-term survival probability in hypoxia, donor genotypes was the most influential factor of the microbial community 3 days after the transplantation. Our results indicate that microbiome influencing factors mediate host fitness in a hypoxic environment in a time depending way.

The Demographic Consequences of Adaptation: Evidence from Experimental Evolution.

AbstractThe process of adaptation toward novel environments is directly connected to the acquisition of higher fitness relative to others. Such increased fitness is obtained by changes in life history traits that may directly impact population dynamics. From a functional perspective, increased fitness can be achieved through higher resource use or more efficient resource use, each potentially having its own impact on population dynamics. In the first case, adaptation is expected to directly translate into higher population growth. In the second case, adaptation requires less energy and hence may lead to higher carrying capacity. Adaptation may thus lead to changes in ecological dynamics and vice versa. Here, by using a combination of evolutionary experiments with spider mites and a population dynamic model, we investigate how an increase in fecundity (a validated proxy for adaptation) affects a population's ecological dynamics. Our results show that adaptation can positively affect population growth rate and either positively or negatively affect carrying capacity, depending on the ecological condition leading to variation in adaptation. These findings show the importance of evolution for population dynamics in changing environments, which may ultimately affect the stability and resilience of populations.

Transient local adaptation and source-sink dynamics in experimental populations experiencing spatially heterogeneous environments.

Local adaptation is determined by the strength of selection and the level of gene flow within heterogeneous landscapes. The presence of benign habitat can act as an evolutionary stepping stone for local adaptation to challenging environments by providing the necessary genetic variation. At the same time, migration load from benign habitats will hinder adaptation. In a community context, interspecific competition is expected to select against maladapted migrants, hence reducing migration load and facilitating adaptation. As the interplay between competition and spatial heterogeneity on the joint ecological and evolutionary dynamics of populations is poorly understood, we performed an evolutionary experiment using the herbivore spider mite Tetranychus urticae as a model. We studied the species's demography and local adaptation in a challenging environment that consisted of an initial sink (pepper plants) and/or a more benign environment (cucumber plants). Half of the experimental populations were exposed to a competitor, the congeneric T. ludeni. We show that while spider mites only adapted to the challenging pepper environment when it was spatially interspersed with benign cucumber habitat, this adaptation was only temporary and disappeared when the populations in the benign cucumber environment were expanding and spilling-over to the challenging pepper environment. Although the focal species outcompeted the competitor after about two months, a negative effect of competition on the focal species's performance persisted in the benign environment. Adaptation to challenging habitat in heterogeneous landscapes thus highly depends on demography and source-sink dynamics, but also on competitive interactions with other species, even if they are only present for a short time span.

Towards evolutionary predictions: Current promises and challenges.

Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions.

Population bottleneck has only marginal effect on fitness evolution and its repeatability in dioecious Caenorhabditis elegans.

The predictability of evolution is expected to depend on the relative contribution of deterministic and stochastic processes. This ratio is modulated by effective population size. Smaller effective populations harbor less genetic diversity and stochastic processes are generally expected to play a larger role, leading to less repeatable evolutionary trajectories. Empirical insight into the relationship between effective population size and repeatability is limited and focused mostly on asexual organisms. Here, we tested whether fitness evolution was less repeatable after a population bottleneck in obligately outcrossing populations of Caenorhabditis elegans. Replicated populations founded by 500, 50, or five individuals (no/moderate/strong bottleneck) were exposed to a novel environment with a different bacterial prey. As a proxy for fitness, population size was measured after one week of growth before and after 15 weeks of evolution. Surprisingly, we found no significant differences among treatments in their fitness evolution. Even though the strong bottleneck reduced the relative contribution of selection to fitness variation, this did not translate to a significant reduction in the repeatability of fitness evolution. Thus, although a bottleneck reduced the contribution of deterministic processes, we conclude that the predictability of evolution may not universally depend on effective population size, especially in sexual organisms.

Microbiome Heritability and Its Role in Adaptation of Hosts to Novel Resources.

Microbiomes are involved in most vital processes, such as immune response, detoxification, and digestion and are thereby elementary to organismal functioning and ultimately the host's fitness. In turn, the microbiome may be influenced by the host and by the host's environment. To understand microbiome dynamics during the process of adaptation to new resources, we performed an evolutionary experiment with the two-spotted spider mite, Tetranychus urticae. We generated genetically depleted strains of the two-spotted spider mite and reared them on their ancestral host plant and two novel host plants for approximately 12 generations. The use of genetically depleted strains reduced the magnitude of genetic adaptation of the spider mite host to the new resource and, hence, allowed for better detection of signals of adaptation via the microbiome. During the course of adaptation, we tested spider mite performance (number of eggs laid and longevity) and characterized the bacterial component of its microbiome (16S rRNA gene sequencing) to determine: (1) whether the bacterial communities were shaped by mite ancestry or plant environment and (2) whether the spider mites' performance and microbiome composition were related. We found that spider mite performance on the novel host plants was clearly correlated with microbiome composition. Because our results show that only little of the total variation in the microbiome can be explained by the properties of the host (spider mite) and the environment (plant species) we studied, we argue that the bacterial community within hosts could be valuable for understanding a species' performance on multiple resources.

Substrate thermal properties influence ventral brightness evolution in ectotherms.

The thermal environment can affect the evolution of morpho-behavioral adaptations of ectotherms. Heat is transferred from substrates to organisms by conduction and reflected radiation. Because brightness influences the degree of heat absorption, substrates could affect the evolution of integumentary optical properties. Here, we show that vipers (Squamata:Viperidae) inhabiting hot, highly radiative and superficially conductive substrates have evolved bright ventra for efficient heat transfer. We analyzed the brightness of 4161 publicly available images from 126 species, and we found that substrate type, alongside latitude and body mass, strongly influences ventral brightness. Substrate type also significantly affects dorsal brightness, but this is associated with different selective forces: activity-pattern and altitude. Ancestral estimation analysis suggests that the ancestral ventral condition was likely moderately bright and, following divergence events, some species convergently increased their brightness. Vipers diversified during the Miocene and the enhancement of ventral brightness may have facilitated the exploitation of arid grounds. We provide evidence that integument brightness can impact the behavioral ecology of ectotherms.

Microbiome and environment explain the absence of correlations between consumers and their diet in Bornean microsnails.

Classical ecological theory posits that species partition resources such that each species occupies a unique resource niche. In general, the availability of more resources allows more species to co-occur. Thus, a strong relationship between communities of consumers and their resources is expected. However, correlations may be influenced by other layers in the food web, or by the environment. Here we show, by studying the relationship between communities of consumers (land snails) and individual diets (from seed plants), that there is in fact no direct, or at most a weak but negative, relationship. However, we found that the diversity of the individual microbiome positively correlates with both consumer community diversity and individual diet diversity in three target species. Moreover, these correlations were affected by various environmental variables, such as anthropogenic activity, habitat island size, and a possibly important nutrient source, guano runoff from nearby caves. Our results suggest that the microbiome and the environment explain the absence of correlations between diet and consumer community diversity. Hence, we advocate that microbiome inventories are routinely added to any community dietary analysis, which our study shows can be done with relatively little extra effort. Our approach presents the tools to quickly obtain an overview of the relationships between consumers and their resources. We anticipate our approach to be useful for ecologists and environmentalists studying different communities in a local food web.

Performance in a novel environment subject to ghost competition.

BACKGROUND: A central tenet of the evolutionary theory of communities is that competition impacts evolutionary processes such as local adaptation. Species in a community exert a selection pressure on other species and may drive them to extinction. We know, however, very little about the influence of unsuccessful or ghost species on the evolutionary dynamics within the community. METHODS: Here we report the long-term influence of a ghost competitor on the performance of a more successful species using experimental evolution. We transferred the spider mite Tetranychus urticae onto a novel host plant under initial presence or absence of a competing species, the congeneric mite T. ludeni. RESULTS: The competitor species, T. ludeni, unintentionally went extinct soon after the start of the experiment, but we nevertheless completed the experiment and found that the early competitive pressure of this ghost competitor positively affected the performance (i.e., fecundity) of the surviving species, T. urticae. This effect on T. urticae lasted for at least 25 generations. DISCUSSION: Our study suggests that early experienced selection pressures can exert a persistent evolutionary signal on species' performance in novel environments.