A test of frequency‐dependent selection in the evolution of a generalist phenotype

A solitary population of consumers frequently evolves to the middle of a resource gradient and an intermediate mean phenotype compared to a sympatric pair of competing species that diverge to either side via character displacement. The forces governing the distribution of phenotypes in these allopatric populations, however, are little investigated. Theory predicts that the intermediate mean phenotype of the generalist should be maintained by negative frequency‐dependent selection, whereby alternate extreme phenotypes are favored because they experience reduced competition for resources when rare. However, the theory makes assumptions that are not always met, and alternative explanations for an intermediate phenotype are possible. We provide a test of this prediction in a mesocosm experiment using threespine stickleback that are ecologically and phenotypically intermediate between the more specialized stickleback species that occur in pairs. We manipulated the frequency distribution of phenotypes in two treatments and then measured effects on a focal intermediate population. We found a slight frequency‐dependent effect on survival in the predicted direction but not on individual growth rates. This result suggests that frequency‐dependent selection might be a relatively weak force across the range of phenotypes within an intermediate population and we suggest several general reasons why this might be so. We propose that allopatric populations might often be maintained at an intermediate phenotype instead by stabilizing or fluctuating directional selection.     

Shifting season of fire and its interaction with fire severity: Impacts on reproductive effort in resprouting plants

Fire regimes shape plant communities but are shifting with changing climate. More frequent fires of increasing intensity are burning across a broader range of seasons. Despite this, impacts that changes in fire season have on plant populations, or how they interact with other fire regime elements, are still relatively understudied. We asked (a) how does the season of fire affect plant vigor, including vegetative growth and flowering after a fire event, and (b) do different functional resprouting groups respond differently to the effects of season of fire? We sampled a total of 887 plants across 36 sites using a space‐for‐time design to assess resprouting vigor and reproductive output for five plant species. Sites represented either a spring or autumn burn, aged one to three years old. Season of fire had the clearest impacts on flowering in Lambertia formosa with a 152% increase in the number of plants flowering and a 45% increase in number of flowers per plant after autumn compared with spring fires. There were also season × severity interactions for total flowers produced for Leptospermum polygalifolium and L. trinervium with both species producing greater flowering in autumn, but only after lower severity fires. Severity of fire was a more important driver in vegetative growth than fire season. Season of fire impacts have previously been seen as synonymous with the effects of fire severity; however, we found that fire season and severity can have clear and independent, as well as interacting, impacts on post‐fire vegetative growth and reproductive response of resprouting species. Overall, we observed that there were positive effects of autumn fires on reproductive traits, while vegetative growth was positively related to fire severity and pre‐fire plant size.     

Bigger is not always better: Viability selection on body mass varies across life stages in a hibernating mammal

Body mass is often viewed as a proxy of past access to resources and of future survival and reproductive success. Links between body mass and survival or reproduction are, however, likely to differ between age classes and sexes. Remarkably, this is rarely taken into account in selection analyses. Selection on body mass is likely to be the primary target accounting for juvenile survival until reproduction but may weaken after recruitment. Males and females also often differ in how they use resources for reproduction and survival. Using a long‐term study on body mass and annual survival in yellow‐bellied marmots (Marmota flaviventer), we show that body mass was under stabilizing viability selection in the first years of life, before recruitment, which changed to positive directional selection as age increased and animals matured. We found no evidence that viability selection across age classes on body mass differed between sexes. By investigating the link between running speed and body mass, we show that the capacity to escape predators was not consistent across age classes and followed a quadratic relationship at young ages only. Overall, our results indicate that mature age classes exhibit traditional patterns of positive viability selection on body mass, as expected in a hibernating mammal, but that mass in the first years of life is subjected to stabilizing selection which may come from additional predation pressures that negate the benefits of the largest body masses. Our study highlights the importance to disentangle selection pressures on traits across critical age (or life) classes.     

Copepod reproductive effort and oxidative status as responses to warming in the marine environment

The marine ecosystems are under severe climate change‐induced stress globally. The Baltic Sea is especially vulnerable to ongoing changes, such as warming. The aim of this study was to measure eco‐physiological responses of a key copepod species to elevated temperature in an experiment, and by collecting field samples in the western Gulf of Finland. The potential trade‐off between reproductive output and oxidative balance in copepods during thermal stress was studied by incubating female Acartia sp. for reproduction rate and oxidative stress measurements in ambient and elevated temperatures. Our field observations show that the glutathione cycle had a clear response in increasing stress and possibly had an important role in preventing oxidative damage: Lipid peroxidation and ratio of reduced and oxidized glutathione were negatively correlated throughout the study. Moreover, glutathione‐s‐transferase activated in late July when the sea water temperature was exceptionally high and Acartia sp. experienced high oxidative stress. The combined effect of a heatwave, increased cyanobacteria, and decreased dinoflagellate abundance may have caused larger variability in reproductive output in the field. An increase of 7°C had a negative effect on egg production rate in the experiment. However, the effect on reproduction was relatively small, implying that Acartia sp. can tolerate warming at least within the temperature range of 9–16°C. However, our data from the experiment suggest a link between reproductive success and oxidative stress during warming, shown as a significant combined effect of temperature and catalase on egg production rate.     

Exploring the interplay between natural and intersexual selection on the evolution of a cognitive trait

There has been an increased focus on the role of natural and sexual selection in shaping cognitive abilities, but the importance of the interaction between both forces remains largely unknown. Intersexual selection through female mate choice might be an important driver of the evolution of cognitive traits, especially in monogamous species, where females may obtain direct fitness benefits by choosing mates with better cognitive abilities. However, the importance given by female to male cognitive traits might vary among species and/or populations according to their life‐history traits and ecology. To disentangle the effects of natural and sexual selection, here we use an agent‐based simulation model and compare the model''s predictions when females mate with the first randomly encountered male (i.e., under natural selection) versus when they choose among males based on their cognitive trait values (i.e., under natural and intersexual selection). Males and females are characterized, respectively, by their problem‐solving ability and assessment strategy. At each generation, agents go through (1) a choosing phase during which females assess the cognitive abilities of potential mates until eventually finding an acceptable one and (2) a reproductive phase during which all males compete for limited resources that are exploited at a rate, which depends on their cognitive abilities. Because males provide paternal care, the foraging success of mated males determines the breeding success of the pair through its effect on nestling provisioning efficiency. The model predicts that intersexual selection plays a major role in most ecological conditions, by either reinforcing or acting against the effect of natural selection. The latter case occurs under harsh environmental conditions, where intersexual selection contributes to maintaining cognitive diversity. Our findings thus demonstrate the importance of considering the interaction between both selective forces and highlight the need to build a conceptual framework to target relevant cognitive traits.     

The Latent Dirichlet Allocation model with covariates (LDAcov): A case study on the effect of fire on species composition in Amazonian forests

Understanding and predicting the effect of global change phenomena on biodiversity is challenging given that biodiversity data are highly multivariate, containing information from tens to hundreds of species in any given location and time. The Latent Dirichlet Allocation (LDA) model has been recently proposed to decompose biodiversity data into latent communities. While LDA is a very useful exploratory tool and overcomes several limitations of earlier methods, it has limited inferential and predictive skill given that covariates cannot be included in the model. We introduce a modified LDA model (called LDAcov) which allows the incorporation of covariates, enabling inference on the drivers of change of latent communities, spatial interpolation of results, and prediction based on future environmental change scenarios. We show with simulated data that our approach to fitting LDAcov is able to estimate well the number of groups and all model parameters. We illustrate LDAcov using data from two experimental studies on the long‐term effects of fire on southeastern Amazonian forests in Brazil. Our results reveal that repeated fires can have a strong impact on plant assemblages, particularly if fuel is allowed to build up between consecutive fires. The effect of fire is exacerbated as distance to the edge of the forest decreases, with small‐sized species and species with thin bark being impacted the most. These results highlight the compounding impacts of multiple fire events and fragmentation, a scenario commonly found across the southern edge of Amazon. We believe that LDAcov will be of wide interest to scientists studying the effect of global change phenomena on biodiversity using high‐dimensional datasets. Thus, we developed the R package LDAcov to enable the straightforward use of this model.     

Tests of search image and learning in the wild: Insights from sexual conflict in damselflies

Search image formation, a proximal mechanism to maintain genetic polymorphisms by negative frequency‐dependent selection, has rarely been tested under natural conditions. Females of many nonterritorial damselflies resemble either conspecific males or background vegetation. Mate‐searching males are assumed to form search images of the majority female type, sexually harassing it at rates higher than expected from its frequency, thus selectively favoring the less common morph. We tested this and how morph coloration and behavior influenced male perception and intersexual encounters by following marked Ischnura elegans and noting their reactions to conspecifics. Contrary to search image formation and associative learning hypotheses, although males encountered the minority, male‐like morph more often, sexual harassment and clutch size were similar for both morphs. Prior mating attempts or copula with morphs did not affect a male''s subsequent reaction to them; males rarely attempted matings with immature females or males. Females mated early in the day, reducing the opportunity for males to learn their identity beforehand. Once encountered, the male‐like morph was more readily noticed by males than the alternative morph, which once noticed was more likely to receive mating attempts. Flexible behavior gave morphs considerable control over their apparency to males, influencing intersexual encounters. Results suggested a more subtle proximal mechanism than male learning maintains these color polymorphisms and call for inferences of learning to be validated by behavior of wild receivers and their signalers.     

Simultaneous selection on vegetative and reproductive phenology in a perennial herb

The timing of different life‐history events is often correlated, and selection might only rarely be exerted independently on the timing of a single event. In plants, phenotypic selection has often been shown to favor earlier flowering. However, little is known about to what extent this selection acts directly versus indirectly via vegetative phenology, and if selection on the two traits is correlational. We estimated direct, indirect, and correlational phenotypic selection on vegetative and reproductive phenology over 3 years for flowering individuals of the perennial herb Lathyrus vernus. Direct selection favored earlier flowering and shorter timespans between leaf‐out and flowering in all years. However, early flowering was associated with early leaf‐out, and the direction of selection on leaf‐out day varied among years. As a result, selection on leaf‐out weakened selection for early flowering in one of the study years. We found no evidence of correlational selection. Our results highlight the importance of including temporally correlated traits when exploring selection on the phenology of seasonal events.     

Sexual selection,feather wear,and time constraints on the pre‐basic molt explain the acquisition of the pre‐alternate molt in European passerines

Avian feathers need to be replaced periodically to fulfill their functions, with natural, social, and sexual selection presumably driving the evolution of molting strategies. In temperate birds, a common pattern is to molt feathers immediately after the breeding season, the pre‐basic molt. However, some species undergo another molt in winter‐spring, the pre‐alternate molt. Using a sample of 188 European passerine species, Bayesian phylogenetic mixed models, and correlated evolution analyses, we tested whether the occurrence of the pre‐alternate molt was positively associated with proxies for sexual selection (sexual selection hypothesis) and nonsexual social selection (social selection hypothesis), and with factors related to feather wear (feather wear hypothesis) and time constraints on the pre‐basic molt (time constraints hypothesis). We found that the pre‐alternate molt was more frequent in migratory and less gregarious species inhabiting open/xeric habitats and feeding on the wing, and marginally more frequent in species with strong sexual selection and those showing a winter territorial behavior. Moreover, an increase in migratory behavior and sexual selection intensity preceded the acquisition of the pre‐alternate molt. These results provide support for the feather wear hypothesis, partial support for the sexual selection and time constraints hypotheses, and no support for the social selection hypothesis.     

Dispersal without drivers: Intrinsic and extrinsic variables have no impact on movement distances in a terrestrial amphibian

Dispersive movements are often thought to be multicausal and driven by individual body size, sex, conspecific density, environmental variation, personality, and/or other variables. Yet such variables often do not account for most of the variation among dispersive movements in nature, leaving open the possibility that dispersion may be indeterministic. We assessed the amount of variation in 24 h movement distances that could be accounted for by potential drivers of displacement with a large empirical dataset of movement distances performed by Fowler''s Toads (Anaxyrus fowleri) on the northern shore of Lake Erie at Long Point, Ontario (2002–2021, incl.). These toads are easy to sample repeatedly, can be identified individually and move parallel to the shoreline as they forage at night, potentially dispersing to new refuge sites. Using a linear mixed‐effect model that incorporated random effect terms to account for sampling variance and inter‐annual variation, we found that all potential intrinsic and extrinsic drivers of movement accounted for virtually none of the variation observed among 24 h distances moved by these animals, whether over short or large spatial scales. We examined the idea of movement personality by testing variance per individual toad and found no evidence of individuality in movement distances. We conclude that deterministic variables, whether intrinsic or extrinsic, neither can be shown to nor are necessary to drive movements in this population over all spatial scales. Stochastic, short time‐scale movements, such as daily foraging movements, can instead accumulate over time to produce large spatial‐scale movements that are dispersive in nature.     

Kinship,dear enemies,and costly combat: The effects of relatedness on territorial overlap and aggression in a cooperative breeder

Many species maintain territories, but the degree of overlap between territories and the level of aggression displayed in territorial conflicts can vary widely, even within species. Greater territorial overlap may occur when neighboring territory holders are close relatives. Animals may also differentiate neighbors from strangers, with more familiar neighbors eliciting less‐aggressive responses during territorial conflicts (the “dear enemy” effect). However, research is lacking in how both kinship and overlap affect territorial conflicts, especially in group‐living species. Here, we investigate kinship, territorial overlap, and territorial conflict in a habituated wild population of group‐living cooperatively breeding birds, the southern pied babbler Turdoides bicolor. We find that close kin neighbors are beneficial. Territories overlap more when neighboring groups are close kin, and these larger overlaps with kin confer larger territories (an effect not seen for overlaps with unrelated groups). Overall, territorial conflict is costly, causing significant decreases in body mass, but conflicts with kin are shorter than those conducted with nonkin. Conflicts with more familiar unrelated neighbors are also shorter, indicating these neighbors are “dear enemies.” However, kinship modulates the “dear enemy” effect; even when kin are encountered less frequently, kin elicit less‐aggressive responses, similar to the “dear enemy” effect. Kin selection appears to be a main influence on territorial behavior in this species. Groups derive kin‐selected benefits from decreased conflicts and maintain larger territories when overlapping with kin, though not when overlapping with nonkin. More generally, it is possible that kinship extends the “dear enemy” effect in animal societies.     

Low temperature has opposite effects on sex determination in a marine fish at the larval/postlarval and juvenile stages

Temperature‐dependent sex determination (TSD) can be observed in multiple reptile and fish species. It is adaptive when varying environmental conditions advantage either males or females. A good knowledge of the thermosensitive period is key to understand how environmental changes may lead to changes in population sex ratio. Here, by manipulating temperature during development, we confirm that cold temperature (16°C) increases the proportion of fish that develop as females in European sea bass (Dicentrarchus labrax) until 56 days posthatching, but show that it has an opposite effect at later stages, with the proportion of males reaching ~90% after 230 days at 16°C. This is the first observation of opposite effects of temperature at different time periods on the sex ratio of a vertebrate. Our results highlight the potential complexity of environmental effects on sex determination.     

The forestecology R package for fitting and assessing neighborhood models of the effect of interspecific competition on the growth of trees

1. Neighborhood competition models are powerful tools to measure the effect of interspecific competition. Statistical methods to ease the application of these models are currently lacking.
2. We present the forestecology package providing methods to (a) specify neighborhood competition models, (b) evaluate the effect of competitor species identity using permutation tests, and (cs) measure model performance using spatial cross‐validation. Following Allen and Kim (PLoS One, 15, 2020, e0229930), we implement a Bayesian linear regression neighborhood competition model.
3. We demonstrate the package''s functionality using data from the Smithsonian Conservation Biology Institute''s large forest dynamics plot, part of the ForestGEO global network of research sites. Given ForestGEO’s data collection protocols and data formatting standards, the package was designed with cross‐site compatibility in mind. We highlight the importance of spatial cross‐validation when interpreting model results.
4. The package features (a) tidyverse‐like structure whereby verb‐named functions can be modularly “piped” in sequence, (b) functions with standardized inputs/outputs of simple features sf package class, and (c) an S3 object‐oriented implementation of the Bayesian linear regression model. These three facts allow for clear articulation of all the steps in the sequence of analysis and easy wrangling and visualization of the geospatial data. Furthermore, while the package only has Bayesian linear regression implemented, the package was designed with extensibility to other methods in mind.

     

Application of T‐cell receptor repertoire as a novel monitor in dynamic tracking and assessment: A cohort‐study based on RA patients

T‐cell receptor repertoire (TCRR) sequencing has been widely applied in many fields as a novel tool. This study explored characteristics of TCRR in detail with a cohort of 598 rheumatoid arthritis (RA) patients before and after anti‐rheumatic treatments. We highlighted the abnormal TCRR distribution in RA characterized by decreased diversity and increased proportion of hyperexpanded clones (HECs), which was potentially attributed to skewed usage of global V/J segments but not a few certain ones. Enriched motifs analysis in RA community demonstrated the huge heterogeneity of CDR3 sequences, so that individual factors are strongly recommended to be taken into consideration when it comes to clinical application of TCRR. Disease‐modifying antirheumatic drugs (DMARDs) can regulate immune system through recovery of TCRR richness to relieve symptoms. Remarkably, sensitive gene profile and advantageous gene profile were identified in this study as new biomarkers for different DMARDs regimens.     

The effect of carbamazepine on bone structure and strength in control and osteogenesis imperfecta (Col1a2 +/p.G610C ) mice

The inherited brittle bone disease osteogenesis imperfecta (OI) is commonly caused by COL1A1 and COL1A2 mutations that disrupt the collagen I triple helix. This causes intracellular endoplasmic reticulum (ER) retention of the misfolded collagen and can result in a pathological ER stress response. A therapeutic approach to reduce this toxic mutant load could be to stimulate mutant collagen degradation by manipulating autophagy and/or ER‐associated degradation. Since carbamazepine (CBZ) both stimulates autophagy of misfolded collagen X and improves skeletal pathology in a metaphyseal chondrodysplasia model, we tested the effect of CBZ on bone structure and strength in 3‐week‐old male OI Col1a2 ^+/p.G610C and control mice. Treatment for 3 or 6 weeks with CBZ, at the dose effective in metaphyseal chondrodysplasia, provided no therapeutic benefit to Col1a2 ^+/p.G610C mouse bone structure, strength or composition, measured by micro‐computed tomography, three point bending tests and Fourier‐transform infrared microspectroscopy. In control mice, however, CBZ treatment for 6 weeks impaired femur growth and led to lower femoral cortical and trabecular bone mass. These data, showing the negative impact of CBZ treatment on the developing mouse bones, raise important issues which must be considered in any human clinical applications of CBZ in growing individuals.     

Epigenetic regulation of the placental HSD11B2 barrier and its role as a critical regulator of fetal development

“Fetal programming” is a term used to describe how early-life experience influences fetal development and later disease risk. In humans, prenatal stress-induced fetal programming is associated with increased risk of preterm birth, and a heightened risk of metabolic and neurological diseases later in life. A critical determinant of this is the regulation of fetal exposure to glucocorticoids by the placenta. Glucocorticoids are the mediators through which maternal stress influences fetal development. Excessive fetal glucocorticoid exposure during pregnancy results in low birth weight and abnormalities in a number of tissues. The amount of fetal exposure to maternal glucocorticoids depends on the expression of HSD11B2, an enzyme predominantly produced by the syncytiotrophoblast in the placenta. This protects the fetus by converting active glucocorticoids into inactive forms. In this review we examine recent findings regarding placental HSD11B2 that suggest that its epigenetic regulation may mechanistically link maternal stress and long-term health consequences in affected offspring.     

Maternal effects and ecological divergence in aquatic plants: a case study in natural reciprocal hybrids between Potamogeton perfoliatus and P. wrightii

When parental taxa are adapted to different habitats, hybrid genotypes are often highly heterogeneous, such that habitat or ecological factors influence hybrid fate and ecological performance. Trait expression in hybrids is not always intermediate between the parents, but may instead be either parental‐like or extreme (transgressive) depending on genetic control of the phenotypes. Maternal effects arising from interspecific interaction between cytoplasmic and nuclear genomes are widely recognized as playing a role in character expression of natural hybrids. Such interaction often leads to hybrid sterility or inviability. When hybrids are viable, however, cytonuclear interaction may contribute to hybrid persistence through its influence on trait expression. To date, maternal influence on hybrid performance has been examined primarily in experimentally produced hybrids, or in natural hybrids without identification of the cross direction owing to difficulty in obtaining species‐specific molecular markers. In aquatic plants, many hybrids persist by extensive clonal growth and are important components of aquatic communities. Many such hybrids are known in Potamogeton (pondweeds), the largest aquatic genus. Because Potamogeton species are ecologically highly diverse and maternal lineages are readily distinguished using molecular markers, natural hybrids of Potamogeton are well‐suited for studies of maternal effects, especially those affecting vegetative performance. As a case study, we have focused on maternal effects on drought tolerance and depth distribution in the natural hybrid P. × anguillanus derived from the closely related species P. perfoliatus and P. wrightii.     

Restoration of species‐rich grasslands by transfer of local plant material and its impact on species diversity and genetic variation—Findings of a practical restoration project in southeastern Germany

Restoration of species‐rich grasslands is a key issue of conservation. The transfer of seed‐containing local plant material is a proven technique to restore species‐rich grassland, since it potentially allows to establish genetically variable and locally adapted populations. In our study, we tested how the transfer of local plant material affected the species diversity and composition of restored grasslands and the genetic variation of the typical grassland plant species Knautia arvensis and Plantago lanceolata.For our study, we selected fifteen study sites in southeastern Germany. We analyzed species diversity and composition and used molecular markers to investigate genetic variation within and among populations of the study species from grasslands that served as source sites for restoration and grasslands, which were restored by transfer of green hay and threshed local plant material.The results revealed no significant differences in species diversity and composition between grasslands at source and restoration sites. Levels of genetic variation within populations of the study species Knautia arvensis and Plantago lanceolata were comparable at source and restoration sites and genetic variation among populations at source and their corresponding restoration sites were only marginal different.Our study suggests that the transfer of local plant material is a restoration approach highly suited to preserve the composition of species‐rich grasslands and the natural genetic pattern of typical grassland plant species.     

Evidence for a synergistic effect of post‐translational modifications and genomic composition of eEF‐1α on the adaptation of Phytophthora infestans

Genetic variation plays a fundamental role in pathogen''s adaptation to environmental stresses. Pathogens with low genetic variation tend to survive and proliferate more poorly due to their lack of genotypic/phenotypic polymorphisms in responding to fluctuating environments. Evolutionary theory hypothesizes that the adaptive disadvantage of genes with low genomic variation can be compensated for structural diversity of proteins through post‐translation modification (PTM) but this theory is rarely tested experimentally and its implication to sustainable disease management is hardly discussed. In this study, we analyzed nucleotide characteristics of eukaryotic translation elongation factor‐1α (eEF‐lα) gene from 165 Phytophthora infestans isolates and the physical and chemical properties of its derived proteins. We found a low sequence variation of eEF‐lα protein, possibly attributable to purifying selection and a lack of intra‐genic recombination rather than reduced mutation. In the only two isoforms detected by the study, the major one accounted for >95% of the pathogen collection and displayed a significantly higher fitness than the minor one. High lysine representation enhances the opportunity of the eEF‐1α protein to be methylated and the absence of disulfide bonds is consistent with the structural prediction showing that many disordered regions are existed in the protein. Methylation, structural disordering, and possibly other PTMs ensure the ability of the protein to modify its functions during biological, cellular and biochemical processes, and compensate for its adaptive disadvantage caused by sequence conservation. Our results indicate that PTMs may function synergistically with nucleotide codes to regulate the adaptive landscape of eEF‐1α, possibly as well as other housekeeping genes, in P. infestans. Compensatory evolution between pre‐ and post‐translational phase in eEF‐1α could enable pathogens quickly adapting to disease management strategies while efficiently maintaining critical roles of the protein playing in biological, cellular, and biochemical activities. Implications of these results to sustainable plant disease management are discussed.