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Northern Red Oak (Quercus rubra L.; native in North America) is regarded as an invasive species in Central Europe, where it is the most common non-indigenous broad-leafed tree species in forestry. The species’ impact on native ecosystems and thus its future management are discussed controversially. Because dispersal is an important step in an invasion process, we studied whether European Jays (Garrulus glandarius L.) and mice, both main dispersers of native oaks in Europe, mediate the dispersal of Q. rubra seeds. Morphological characteristics of Q. rubra and native Q. robur L. acorns were quantified according to their implications for dispersal. We tested experimentally whether and to what extent mice and jays collect acorns of both oak species and if their behavior depends on choice options (dual choice vs. no-choice). Acorns were offered on feeding platforms, controlled by scouting cameras. Results showed that Q. rubra acorns have a thicker pericarp, a rounder shape and a higher dry weight compared to acorns of Q. robur. In the behavioral assays jays avoided acorns of Q. rubra if they were offered together with those of Q. robur (dual choice) as well as when Q. rubra acorns were offered alone (no-choice). This selection behavior could be caused by the differences in morphological traits observed between the acorns of the two species. In contrast to jays, mice took acorns of both oak species likewise indicating that seed morphology does not affect the attractiveness of Red Oak acorns for rodents. In conclusion, Quercus rubra is collected by animals in Central Europe to a considerable amount but dispersal should be restricted to moderate distances mediated by mice, leading mainly to stabilizing and increasing existing populations rather than founding of new ones.

The hermaphroditic nematode Caenorhabditis elegans has been one of the primary model systems in biology since the 1970s, but only within the last two decades has this nematode also become a useful model for experimental evolution. Here, we outline the goals and major foci of experimental evolution with C. elegans and related species, such as C. briggsae and C. remanei, by discussing the principles of experimental design, and highlighting the strengths and limitations of Caenorhabditis as model systems. We then review three exemplars of Caenorhabditis experimental evolution studies, underlining representative evolution experiments that have addressed the: (1) maintenance of genetic variation; (2) role of natural selection during transitions from outcrossing to selfing, as well as the maintenance of mixed breeding modes during evolution; and (3) evolution of phenotypic plasticity and its role in adaptation to variable environments, including host–pathogen coevolution. We conclude by suggesting some future directions for which experimental evolution with Caenorhabditis would be particularly informative.

While native populations are often adapted to historical biotic and abiotic conditions at their home site, populations from other locations in the range may be better adapted to current conditions due to changing climates or extreme conditions in a single year. We examine whether local populations of a widespread species maintain a relative advantage over distant populations that have evolved at sites better matching the current climate. Specifically, we grew lines derived from low- and high-elevation annual populations in California and Oregon of the common monkeyflower (Erythranthe guttata) and conducted phenotypic selection analyses in low- and high-elevation common gardens in Oregon to examine relative fitness and the traits mediating relative fitness. Californian low-elevation populations have the highest relative fitness at the low-elevation site, and Californian high-elevation populations have the highest relative fitness at the high-elevation site. Relative fitness differences are mediated by selection for properly timed transitions to flowering, with selection favoring more rapid growth rates at the low-elevation site and greater vegetative biomass prior to flowering at the high-elevation site. Fitness advantages for Californian plants occur despite incurring higher herbivory at both sites than the native Oregonian plants. Our findings suggest that a lag in adaptation causes maladaptation in extreme years that may be more prevalent in future climates, but local populations still have high growth rates and thus are not yet threatened.

Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response. Humans have been making use of artificial selection for thousands of years. Much of what we eat, for example, from beef to poultry to cereals, comes from a collection of organisms with genomes that have been completely reshaped by the actions of generations of farmers and breeders. Yet, despite decades of research in evolutionary biology, it remains difficult to predict what will happen to an organism’s genes when selective pressure is applied. Traits that at first seem simple often arise from layers upon layers of complexity. It can take hundreds if not thousands of tiny changes to many genes, plus just the right alterations to a few key ones, to have a desired effect on a single trait. Also, if you consider that often the genomes of the starting population are unknown and that many traits are under simultaneous selection in wild populations, it becomes clear why many questions remain unanswered. Castro, Yancoskie, et al. have analyzed an on-going laboratory experiment dubbed “the Longshanks experiment” to explore how an animal’s genome changes under strong selection. Over five years, two independent populations of mice were selectively bred to have longer legs. In each generation, the mice were measured and those with the longest tibia – a bone in the shin – relative to their body mass were allowed to breed. Genetic data were also recorded. Now, Castro, Yancoskie, et al. have analyzed the genetic data up to the first 17 generations in the Longshanks experiment to find out what kind of genes may be relevant to the 13% increase in leg length seen in the mice so far. This analysis uncovered many genes, possibly thousands, all acting in concert to increase tibia length. But the gene with the largest effect by far was a key developmental gene called Nkx3-2. Mutations in this gene cause a disease called spondylo-megaepiphyseal-metaphyseal dysplasia in people, which can lead to long limbs and a short trunk. Although inactivating this gene completely in mice is lethal, among the founding group of mice in the Longshanks experiment was a rare copy of Nkx3-2. This copy of the gene worked perfectly in all tissues with the exception of the legs, where a genetic switch that controls it was left in the “off” state. Mice inheriting this short stretch of DNA ended up having longer tibia. In effect, these mice held the winning ticket in the genetic lottery that was the Longshanks experiment. Even in highly controlled experiments that record a great deal of information about the organisms involved, predicting how the genome will change and which genes will be involved is not a straightforward question. Finding out how the genome may change in response to selection is important because scientists can build better models to help with breeding farm animals or crops, or with predicting the consequences of climate change. As a result, experiments such as these may have broad applications in conservation, genomic medicine and agriculture.

Evolution of body size is likely to involve trade-offs between body size, growth rate and longevity. Within species, larger body size is associated with faster growth and ageing, and reduced longevity, but the cellular processes driving these relationships are poorly understood. One mechanism that might play a key role in determining optimal body size is the relationship between body size and telomere dynamics. However, we know little about how telomere length is affected when selection for larger size is imposed in natural populations. We report here on the relationship between structural body size and telomere length in wild house sparrows at the beginning and end of a selection regime for larger parent size that was imposed for 4 years in an isolated population of house sparrows. A negative relationship between fledgling size and telomere length was present at the start of the selection; this was extended when fledgling size increased under the selection regime, demonstrating a persistent covariance between structural size and telomere length. Changes in telomere dynamics, either as a correlated trait or a consequence of larger size, could reduce potential longevity and the consequent trade-offs could thereby play an important role in the evolution of optimal body size.

Characterizing differences in sequences between two conditions, such as with and without drug exposure, using high-throughput sequencing data is a prevalent problem involving quantifying changes in sequence abundances, and predicting such differences for unobserved sequences. A key shortcoming of current approaches is their extremely limited ability to share information across related but non-identical reads. Consequently, they cannot use sequencing data effectively, nor be directly applied in many settings of interest. We introduce model-based enrichment (MBE) to overcome this shortcoming. We evaluate MBE using both simulated and real data. Overall, MBE improves accuracy compared to current differential analysis methods.

A novel class of antibiotics based on the antimicrobial properties of immune peptides of multicellular organisms is attracting increasing interest as a major weapon against resistant microbes. It has been claimed that cationic antimicrobial peptides exploit fundamental features of the bacterial cell so that resistance is much less likely to evolve than in the case of conventional antibiotics. Population models of the evolutionary genetics of resistance have cast doubt on this claim. We document the experimental evolution of resistance to a cationic antimicrobial peptide through continued selection in the laboratory. In this selection experiment, 22/24 lineages of Escherichia coli and Pseudomonas fluorescens independently evolved heritable mechanisms of resistance to pexiganan, an analogue of magainin, when propagated in medium supplemented with this antimicrobial peptide for 600-700 generations.

If genetic architectures of various quantitative traits are similar, as studies on model organisms suggest, comparable selection pressures should produce similar molecular patterns for various traits. To test this prediction, we used a laboratory model of vertebrate adaptive radiation to investigate the genetic basis of the response to selection for predatory behavior and compare it with evolution of aerobic capacity reported in an earlier work. After 13 generations of selection, the proportion of bank voles (Myodes [=Clethrionomys] glareolus) showing predatory behavior was five times higher in selected lines than in controls. We analyzed the hippocampus and liver transcriptomes and found repeatable changes in allele frequencies and gene expression. Genes with the largest differences between predatory and control lines are associated with hunger, aggression, biological rhythms, and functioning of the nervous system. Evolution of predatory behavior could be meaningfully compared with evolution of high aerobic capacity, because the experiments and analyses were performed in the same methodological framework. The number of genes that changed expression was much smaller in predatory lines, and allele frequencies changed repeatably in predatory but not in aerobic lines. This suggests that more variants of smaller effects underlie variation in aerobic performance, whereas fewer variants of larger effects underlie variation in predatory behavior. Our results thus contradict the view that comparable selection pressures for different quantitative traits produce similar molecular patterns. Therefore, to gain knowledge about molecular-level response to selection for complex traits, we need to investigate not only multiple replicate populations but also multiple quantitative traits.

Trade-offs between host resistance to parasites and host growth or reproduction can occur due to allocation of limited available resources between competing demands. To predict potential trade-offs arising from genetic selection for host resistance, a better understanding of the associated nutritional costs is required. Here, we studied resistance costs by using sheep from lines divergently selected on their resistance to a common blood-feeding gastro-intestinal parasite (Haemonchus contortus). First, we assessed the effects of selection for high or low host resistance on condition traits (body weight, back fat, and muscle thickness) and infection traits (parasite fecal egg excretion and loss in blood haematocrit) at various life stages, in particular during the periparturient period when resource allocation to immunity may limit host resistance. Second, we analysed the condition-infection relationship to detect a possible trade-off, in particular during the periparturient period. We experimentally infected young females in four stages over their first 2 years of life, including twice around parturition (at 1 year and at 2 years of age). Linear mixed-model analyses revealed a large and consistent between-line difference in infection traits during growth and outside of the periparturient period, whereas this difference was strongly attenuated during the periparturient period. Despite their different responses to infection, lines had similar body condition traits. Using covariance decomposition, we then found that the phenotypic relationship between infection and condition was dominated by direct infection costs arising from parasite development within the host. Accounting for these within-individual effects, a cost of resistance on body weight was detected among ewes during their first reproduction. Although this cost and the reproductive constraint on resistance are unlikely to represent a major concern for animal breeding in nutrient-rich environments, this study provides important new insights regarding the nutritional costs of parasite resistance at different lifestages and how these may affect response to selection.

Trade-offs have often been invoked to explain the evolution of ecological specialization. Phytophagous insects have been especially well studied, but there has been little evidence that resource-based trade-offs contribute to the evolution of host specialization in this group. Here, we combine experimental evolution and partial genome resequencing of replicate seed beetle selection lines to test the trade-off hypothesis and measure the repeatability of evolution. Bayesian estimates of selection coefficients suggest that rapid adaptation to a poor host (lentil) was mediated by standing genetic variation at multiple genetic loci and involved many of the same variants in replicate lines. Sublines that were then switched back to the ancestral host (mung bean) showed a more gradual and variable (less repeatable) loss of adaptation to lentil. We were able to obtain estimates of variance effective population sizes from genome-wide differences in allele frequencies within and between lines. These estimates were relatively large, which suggests that the contribution of genetic drift to the loss of adaptation following reversion was small. Instead, we find that some alleles that were favored on lentil were selected against during reversion on mung bean, consistent with the genetic trade-off hypothesis.