Climate change and plant regeneration from seed

At the core of plant regeneration, temperature and water supply are critical drivers for seed dormancy (initiation, break) and germination. Hence, global climate change is altering these environmental cues and will preclude, delay, or enhance regeneration from seeds, as already documented in some cases. Along with compromised seedling emergence and vigour, shifts in germination phenology will influence population dynamics, and thus, species composition and diversity of communities. Altered seed maturation (including consequences for dispersal) and seed mass will have ramifications on life history traits of plants. Predicted changes in temperature and precipitation, and thus in soil moisture, will affect many components of seed persistence in soil, e.g. seed longevity, dormancy release and germination, and soil pathogen activity. More/less equitable climate will alter geographic distribution for species, but restricted migratory capacity in some will greatly limit their response. Seed traits for weedy species could evolve relatively quickly to keep pace with climate change enhancing their negative environmental and economic impact. Thus, increased research in understudied ecosystems, on key issues related to seed ecology, and on evolution of seed traits in nonweedy species is needed to more fully comprehend and plan for plant responses to global warming.     

Associated evolution of fruit size,fruit colour and spines in Neotropical palms

Understanding how ecological interactions have shaped the evolutionary dynamics of species traits remains a challenge in evolutionary ecology. Combining trait evolution models and phylogenies, we analysed the evolution of characters associated with seed dispersal (fruit size and colour) and herbivory (spines) in Neotropical palms to infer the role of these opposing animal–plant interactions in driving evolutionary patterns. We found that the evolution of fruit colour and fruit size was associated in Neotropical palms, supporting the adaptive interpretation of seed‐dispersal syndromes and highlighting the role of frugivores in shaping plant evolution. Furthermore, we revealed a positive association between fruit size and the presence of spines on palm leaves, bracteas and stems. We hypothesize that interactions between palms and large‐bodied frugivores/herbivores may explain the evolutionary relationship between fruit size and spines. Large‐bodied frugivores, such as extinct megafauna, besides consuming the fruits and dispersing large seeds, may also have consumed the leaves or damaged the plants, thus simultaneously favouring the evolution of large fruits and defensive structures. Our findings show how current trait patterns can be understood as the result of the interplay between antagonistic and mutualistic interactions that have happened throughout the evolutionary history of a clade.     

The role of domestication and maternal effects on seed traits of crop–wild sunflower hybrids (Helianthus annuus)

Hybridisation between crops and their wild relatives may promote the evolution of weeds. Seed germination and dormancy are the earliest life‐history traits and are highly influenced by the maternal parent. However, the ecological role of the maternal effect on seed traits in the evolution of crop–wild hybrids has received little attention. In this study, we test the relative importance of maternal and hybridisation effects on seed traits of the first generation of crop–wild sunflower hybrids (Helianthus annuus). Seed germination was tested in two wild populations with contrasting dormancy, two cultivated materials and their reciprocal crosses at four different times after harvest and three different temperatures. Seed germination at each of the four times, after ripening response and secondary dormancy were recorded along with four morphological traits. Additionally, the pericarp anatomy was analysed with light and scanning electron microscopy. We observed strong maternal effects on all seed traits. Seed germination, morphology and pericarp anatomy differed largely between the crop and wild seeds and these traits in the crop–wild hybrids resembled their female parent. Slight but significant hybridisation effects were observed in germination, mainly in seeds produced on wild plants. Crop hybridisation changed seed germination, the after ripening response and secondary dormancy in the crop direction. Morphological and anatomical traits associated with domestication strongly correlated with the observed differences in seed germination and dormancy in crop–wild sunflower hybrids. The large maternal effects along with the evolutionary divergence in seed traits were responsible for the large phenotypic differences observed in crop–wild hybrids with the same genetic composition. Wild‐like seed traits of hybrids suggest that there are no barriers to crop gene introgression at the seed level whereas crop‐like seed traits could be strongly selected against, conditioning the selection of traits expressed later in the life cycle and in the next generations.     

Hidden responses to environmental variation: maternal effects reveal species niche dimensions

Species responses to fluctuating environments structure population and community dynamics in variable ecosystems. Although offspring number is commonly used to measure these responses, maternal effects on offspring quality may be an important but largely unrecognised determinant of long‐term population growth. We selected 29 species across a Mediterranean annual plant phylogeny, and grew populations of each species in wet and dry conditions to determine responses in seed number and maternal effects (seed size, seed dormancy, and seedling growth). Maternal effects were evident in over 40% of species, but only 24% responded through seed number. Despite a strong trade‐off between seed size and seed number among species, there was no consistent trade‐off within species; we observed correlations that ranged from positive to negative. Overall, species in this plant guild show a complex range of responses to environmental variation that may be underestimated when only seed number responses are considered.     

Dormancy and germination: making every seed count in restoration

From 50 to 90% of wild plant species worldwide produce seeds that are dormant upon maturity, with specific dormancy traits driven by species' occurrence geography, growth form, and genetic factors. While dormancy is a beneficial adaptation for intact natural systems, it can limit plant recruitment in restoration scenarios because seeds may take several seasons to lose dormancy and consequently show low or erratic germination. During this time, seed predation, weed competition, soil erosion, and seed viability loss can lead to plant re‐establishment failure. Understanding and considering seed dormancy and germination traits in restoration planning are thus critical to ensuring effective seed management and seed use efficiency. There are five known dormancy classes (physiological, physical, combinational, morphological, and morphophysiological), each requiring specific cues to alleviate dormancy and enable germination. The dormancy status of a seed can be determined through a series of simple steps that account for initial seed quality and assess germination across a range of environmental conditions. In this article, we outline the steps of the dormancy classification process and the various corresponding methodologies for ex situ dormancy alleviation. We also highlight the importance of record‐keeping and reporting of seed accession information (e.g. geographic coordinates of the seed collection location, cleaning and quality information, storage conditions, and dormancy testing data) to ensure that these factors are adequately considered in restoration planning.     

THE JOINT EVOLUTION OF DISPERSAL AND DORMANCY IN A METAPOPULATION WITH LOCAL EXTINCTIONS AND KIN COMPETITION

Dispersal and dormancy are two strategies that allow recolonization of empty patches and escape from kin competition. Because they presumably respond to similar evolutionary forces, it is tempting to consider that these strategies may substitute for each other. Yet in order to predict the outcome of the evolution of dispersal and dormancy, and to characterize the emerging covariation between both traits, it is necessary to consider models where dispersal and dormancy evolve jointly. Here, we analyze the evolution of dispersal and dormancy as a function of direct fitness costs, environmental variation, and competition among relatives. We consider two scenarios depending on whether the rates of dormancy for philopatric and dispersed individuals are constrained to be the same (unconditional dormancy) or allowed to be different (conditional dormancy). We show that only philopatric individuals should enter dormancy, at a rate increasing with increasing rates of local extinction and decreasing population sizes. When dormancy and dispersal evolve jointly, we observe a wide range of evolutionary outcomes. In particular, we find that the pattern of covariation between the evolutionarily stable rates of dispersal and dormancy is molded by the rate of extinction and the local population size.     

The Price equation framework to study disease within-host evolution

The evolution of infectious diseases is known to affect epidemiological dynamics, but, for some viruses and bacteria, this evolution also takes place inside a host during the course of an infection. I develop an original approach to study intrahost evolutionary dynamics of quantitative disease traits. This approach can be expressed mathematically using the ‘Price equation’ framework recently developed in evolutionary epidemiology. This framework combines population genetics and within-host population dynamics models to identify trade-offs that affect disease intrahost evolution and to predict short-term evolutionary dynamics of life-history traits. I show that this can be applied to study the evolution of viruses competing for host cells or to study the coevolution between parasites and the immune system of the host. This framework can also easily incorporate experimental data. Studying intrahost evolutionary dynamics provides insight at the within-host level, because it allows us to better understand the course of chronic infections, and at the epidemiological level, because it helps to study multi-scale evolutionary processes. This framework can be used to address important biological issues, from immune escape to disease evolutionary response to treatments.     

Temperature thresholds of physically dormant seeds and plant functional response to fire: variation among species and relative impact of climate change

Variation in dormancy thresholds among species is rarely studied but may provide a basis to better understand the mechanisms controlling population persistence. Incorporating dormancy‐breaking temperature thresholds into existing trait frameworks could improve predictions regarding seed bank persistence, and subsequently species resilience in response to fire, climate change and anthropogenic management. A key ecological strategy for many species from fire‐prone ecosystems is the possession of a long‐lived seed bank, ensuring recovery after fire. Physical dormancy is dominant in these ecosystems and maintaining this dormancy is directly linked to seed bank persistence. We identified a suite of seed‐related factors relevant to maintaining populations in fire‐prone regions for 14 co‐occurring physically dormant species. We measured variation in initial levels of dormancy and then applied experimental heating treatments, based on current seasonal temperatures and those occurring during fires, to seeds of all study species. Additionally, higher seasonal temperature treatments were applied to assess response of seeds to temperatures projected under future climate scenarios. Levels of germination response and mortality were determined to assess how tightly germination response was bound to either fire or seasonal cues. Six species were found to have dormancy cues bound to temperatures that only occur during fires (80°C and above) and were grouped as having obligate pyrogenic dormancy release. The remaining species, classified as having facultative pyrogenic dormancy, had lower temperature dormancy thresholds and committed at least 30% of seeds to germinate after summer‐temperature treatments. Evidence from this study supports including dormancy‐breaking temperature thresholds as an attribute for identifying functional types. High temperature thresholds for breaking dormancy, found in our obligate pyrogenic group, appear to be a fire‐adapted trait, while we predict that species in the facultative group are most at risk to increased seed bank decay resulting from elevated soil temperatures under projected climate change.     

Annual dormancy cycles in buried seeds of shrub species: germination ecology of Sideritis serrata (Labiatae)

The germination ecology of Sideritis serrata was investigated in order to improve ex‐situ propagation techniques and management of their habitat. Specifically, we analysed: (i) influence of temperature, light conditions and seed age on germination patterns; (ii) phenology of germination; (iii) germinative response of buried seeds to seasonal temperature changes; (iv) temperature requirements for induction and breaking of secondary dormancy; (v) ability to form persistent soil seed banks; and (vi) seed bank dynamics. Freshly matured seeds showed conditional physiological dormancy, germinating at low and cool temperatures but not at high ones (28/14 and 32/18 °C). Germination ability increased with time of dry storage, suggesting the existence of non‐deep physiological dormancy. Under unheated shade‐house conditions, germination was concentrated in the first autumn. S. serrata seeds buried and exposed to natural seasonal temperature variations in the shade‐house, exhibited an annual conditional dormancy/non‐dormancy cycle, coming out of conditional dormancy in summer and re‐entering it in winter. Non‐dormant seeds were clearly induced into dormancy when stratified at 5 or 15/4 °C for 8 weeks. Dormant seeds, stratified at 28/14 or 32/18 °C for 16 weeks, became non‐dormant if they were subsequently incubated over a temperature range from 15/4 to 32/18 °C. S. serrata is able to form small persistent soil seed banks. The maximum seed life span in the soil was 4 years, decreasing with burial depth. This is the second report of an annual conditional dormancy/non‐dormancy cycle in seeds of shrub species.     

Comparison of seed and seedling functional traits in native Helianthus species and the crop H. annuus (sunflower)

• Seed functional traits of native Helianthus species contribute towards ecosystem services but limitations to their use in managed programmes exist. Many perennial Helianthus possess seed dormancy. The ability for germination to occur under different temperature and drought conditions, as well as the capacity of germinated seeds to convert into normal seedlings is rarely considered. Our aim was to identify and quantify these constraints through functional trait analyses.
• In five seed lots of native Helianthus (four perennial and one annual) and five genotypes of sunflower (H. annuus) for comparison, dormancy, thermal and hydro thresholds and times, morphology, mass, oil content and conversion into normal seedlings were quantified. The influence of the seed collection site environment on these traits was also explored.
• Seed dormancy of the perennial species was overcome by scarification followed by germination in 5 mm GA₃. Thermal and hydro‐time analyses revealed slower germination for the native seed lots (>1350 °Ch) in comparison to the sunflower genotypes (<829.9 °Ch). However, native seed lots had a higher capacity to convert into normal seedlings at high temperatures and low water potentials than sunflower genotypes. For the native seed lots, the average monthly temperature of the collection site was negatively correlated with thermal time.
• Variability in seed functional traits of native Helianthus and greater capacity for germinated seeds to convert into normal seedlings suggests they are better equipped to cope with high temperature and drought scenarios than sunflower. Effective dormancy alleviation is required to facilitate the use of native Helianthus species.

     

Weak seed banks influence the signature and detectability of selective sweeps

Seed banking (or dormancy) is a widespread bet-hedging strategy, generating a form of population overlap, which decreases the magnitude of genetic drift. The methodological complexity of integrating this trait implies it is ignored when developing tools to detect selective sweeps. But, as dormancy lengthens the ancestral recombination graph (ARG), increasing times to fixation, it can change the genomic signatures of selection. To detect genes under positive selection in seed banking species it is important to (1) determine whether the efficacy of selection is affected, and (2) predict the patterns of nucleotide diversity at and around positively selected alleles. We present the first tree sequence-based simulation program integrating a weak seed bank to examine the dynamics and genomic footprints of beneficial alleles in a finite population. We find that seed banking does not affect the probability of fixation and confirm expectations of increased times to fixation. We also confirm earlier findings that, for strong selection, the times to fixation are not scaled by the inbreeding effective population size in the presence of seed banks, but are shorter than would be expected. As seed banking increases the effective recombination rate, footprints of sweeps appear narrower around the selected sites and due to the scaling of the ARG are detectable for longer periods of time. The developed simulation tool can be used to predict the footprints of selection and draw statistical inference of past evolutionary events in plants, invertebrates, or fungi with seed banks.     

Ecomorphological adaptation of acorn weevils to their oviposition site

Comparisons between closely related species in different habitats provide a window into understanding how biotic factors shape evolutionary pathways. Weevils in the genus Curculio have radiated extensively across the Palearctic, where similar ecomorphs have evolved independently on different hosts. We examined ecological and morphological data for 31 Curculio species using multivariate statistics to determine which morphological traits covary and which correlate with the host seed size. A subset of 15 taxa for which phylogenetic relationships were known were used for comparative analyses and inferring historical patterns of trait evolution. The morphological analyses suggest rostrum size increased proportionately to body size in both males and females and that both rostrum and body size correlate with host seed size but that rostrum shape does not correlate with any of the seed traits used in the analyses. Host shifts from small seeds to considerably larger seeds or vice versa have occurred several times independently and historical trait evolution indicates that these host shifts were accompanied by morphological changes in rostrum size. These patterns suggest that seed size is an important selective agent for changes in rostrum length along with body size and thus may be a key factor promoting morphological differentiation in the genus Curculio.     

Eco‐evolutionary dynamics in a coevolving host–virus system

Eco‐evolutionary dynamics have been shown to be important for understanding population and community stability and their adaptive potential. However, coevolution in the framework of eco‐evolutionary theory has not been addressed directly. Combining experiments with an algal host and its viral parasite, and mathematical model analyses we show eco‐evolutionary dynamics in antagonistic coevolving populations. The interaction between antagonists initially resulted in arms race dynamics (ARD) with selective sweeps, causing oscillating host–virus population dynamics. However, ARD ended and populations stabilised after the evolution of a general resistant host, whereas a trade‐off between host resistance and growth then maintained host diversity over time (trade‐off driven dynamics). Most importantly, our study shows that the interaction between ecology and evolution had important consequences for the predictability of the mode and tempo of adaptive change and for the stability and adaptive potential of populations.     

Evolution and coevolution in mutualistic networks

A major current challenge in evolutionary biology is to understand how networks of interacting species shape the coevolutionary process. We combined a model for trait evolution with data for twenty plant-animal assemblages to explore coevolution in mutualistic networks. The results revealed three fundamental aspects of coevolution in species-rich mutualisms. First, coevolution shapes species traits throughout mutualistic networks by speeding up the overall rate of evolution. Second, coevolution results in higher trait complementarity in interacting partners and trait convergence in species in the same trophic level. Third, convergence is higher in the presence of super-generalists, which are species that interact with multiple groups of species. We predict that worldwide shifts in the occurrence of super-generalists will alter how coevolution shapes webs of interacting species. Introduced species such as honeybees will favour trait convergence in invaded communities, whereas the loss of large frugivores will lead to increased trait dissimilarity in tropical ecosystems.     

Eco‐evolutionary feedback promotes Red Queen dynamics and selects for sex in predator populations

Although numerous hypotheses exist to explain the overwhelming presence of sexual reproduction across the tree of life, we still cannot explain its prevalence when considering all inherent costs involved. The Red Queen hypothesis states that sex is maintained because it can create novel genotypes with a selective advantage. This occurs when the interactions between species induce frequent environmental change. Here, we investigate whether coevolution and eco‐evolutionary feedback dynamics in a predator‐prey system allows for indirect selection and maintenance of sexual reproduction in the predator. Combining models and chemostat experiments of a rotifer‐algae system we show a continuous feedback between population and trait change along with recurrent shifts from selection by predation and competition for a limited resource. We found that a high propensity for sex was indirectly selected and was maintained in rotifer populations within environments containing these eco‐evolutionary dynamics; whereas within environments under constant conditions, predators evolved rapidly to lower levels of sex. Thus, our results indicate that the influence of eco‐evolutionary feedback dynamics on the overall evolutionary change has been underestimated.     

Germ banks affect the inference of past demographic events

Continuous progress in empirical population genetics based on the whole‐genome polymorphism data requires the theoretical analysis of refined models in order to interpret the evolutionary history of populations with adequate accuracy. Recent studies focus prevalently on the aspects of demography and adaptation, whereas age structure (for example, in plants via the maintenance of seed banks) has attracted less attention. Germ banking, that is, seed or egg dormancy, is a prevalent and important life‐history trait in plants and invertebrates, which buffers against environmental variability and modulates species extinction in fragmented habitats. Within this study, we investigate the combined effect of germ banking and time‐varying population size on the neutral coalescent and particularly derive the allele frequency spectrum under some simplifying assumptions. We then perform an ABC analysis using two simple demographic scenarios—a population expansion and an instantaneous decline. We demonstrate the appreciable influence of seed banks on the estimation of demographic parameters depending on the germination rate with biases scaled by the square of the germination rate. In the more complex case of a population bottleneck, which comprises an instantaneous decline and an expansion phase, ignoring information on the germination rate denies reliable estimates of the bottleneck parameters via the allelic spectrum. In particular, when seeds remain in the bank over several generations, recent expansions may remain invisible in the frequency spectrum, whereas ancient declines leave signatures much longer than in the absence of seed bank.     

Host‐parasite coevolution can promote the evolution of seed banking as a bet‐hedging strategy

Seed (egg) banking is a common bet‐hedging strategy maximizing the fitness of organisms facing environmental unpredictability by the delayed emergence of offspring. Yet, this condition often requires fast and drastic stochastic shifts between good and bad years. We hypothesize that the host seed banking strategy can evolve in response to coevolution with parasites because the coevolutionary cycles promote a gradually changing environment over longer times than seed persistence. We study the evolution of host germination fraction as a quantitative trait using both pairwise competition and multiple mutant competition methods, while the germination locus can be genetically linked or unlinked with the host locus under coevolution. In a gene‐for‐gene model of coevolution, hosts evolve a seed bank strategy under unstable coevolutionary cycles promoted by moderate to high costs of resistance or strong disease severity. Moreover, when assuming genetic linkage between coevolving and germination loci, the resistant genotype always evolves seed banking in contrast to susceptible hosts. Under a matching‐allele interaction, both hosts’ genotypes exhibit the same seed banking strategy irrespective of the genetic linkage between loci. We suggest host–parasite coevolution as an additional hypothesis for the evolution of seed banking as a temporal bet‐hedging strategy.     

Ecological bistability and evolutionary reversals under asymmetrical competition

Abstract How does the process of life‐history evolution interplay with population dynamics? Almost all models that have addressed this question assume that any combination of phenotypic traits uniquely determine the ecological population state. Here we show that if multiple ecological equilibria can exist, the evolution of a trait that relates to competitive performance can undergo adaptive reversals that drive cyclic alternation between population equilibria. The occurrence of evolutionary reversals requires neither environmentally driven changes in selective forces nor the coevolution of interactions with other species. The mechanism inducing evolutionary reversals is twofold. First, there exist phenotypes near which mutants can invade and yet fail to become fixed; although these mutants are eventually eliminated, their transitory growth causes the resident population to switch to an alternative ecological equilibrium. Second, asymmetrical competition causes the direction of selection to revert between high and low density. When ecological conditions for evolutionary reversals are not satisfied, the population evolves toward a steady state of either low or high abundance, depending on the degree of competitive asymmetry and environmental parameters. A sharp evolutionary transition between evolutionary stasis and evolutionary reversals and cycling can occur in response to a smooth change in ecological parameters, and this may have implications for our understanding of size‐abundance patterns.     

Genetic variation in a female genital trait evolved by sexual coevolution

Understanding the patterns of genetic variation of traits subject to sexual selection is fundamental for explaining its evolutionary dynamics and potential for sexual coevolution. The signa of female Lepidoptera are sclerotized structures located on the inner surface of the genital receptacle that receives the spermatophore during copulation (the corpus bursae), whose main function is tearing the spermatophore envelope. Comparative data indicate that the evolution of signa has been influenced by sexually antagonistic coevolution with spermatophore envelopes. We looked for additive genetic variation in the size and shape of signa in females of the butterfly Callophrys xami (Lycaenidae) from two localities (BG and FC) in Mexico City. We also looked for genetic variation in female body size and in the size of corpus bursae. There were significant between-population differences in female body size, signa width and three signa shape traits. We found significant extranuclear maternal effects in one component of signa shape in the BG population, and in body weight, signa length and in one uniform component of signa shape in the FC population. Extranuclear maternal contributions could permit the evolution of female adaptations even if these reduce male fitness. We found additive genetic variation in signa length and width only in one population (BG); heritability estimates were high: 0.96 and 0.8, respectively. The existence of additive genetic variation in signa size could be, at least in part, a result of relaxed sexually antagonistic selection pressures due to the low level of polyandry exhibited by this species. Our results imply that there is currently potential for further sexual coevolution in this trait.     

The coevolution of long‐term pair bonds and cooperation

The evolution of social traits may not only depend on but also change the social structure of the population. In particular, the evolution of pairwise cooperation, such as biparental care, depends on the pair‐matching distribution of the population, and the latter often emerges as a collective outcome of individual pair‐bonding traits, which are also under selection. Here, we develop an analytical model and individual‐based simulations to study the coevolution of long‐term pair bonds and cooperation in parental care, where partners play a Snowdrift game in each breeding season. We illustrate that long‐term pair bonds may coevolve with cooperation when bonding cost is below a threshold. As long‐term pair bonds lead to assortative interactions through pair‐matching dynamics, they may promote the prevalence of cooperation. In addition to the pay‐off matrix of a single game, the evolutionarily stable equilibrium also depends on bonding cost and accidental divorce rate, and it is determined by a form of balancing selection because the benefit from pair‐bond maintenance diminishes as the frequency of cooperators increases. Our findings highlight the importance of ecological factors affecting social bonding cost and stability in understanding the coevolution of social behaviour and social structures, which may lead to the diversity of biological social systems.