Explaining the apparent paradox of persistent selection for early flowering

Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplants

Crop wild relatives (CWR) provide a valuable resource for improving crops. They possess desirable traits that confer resilience to various environmental stresses. To fully utilize crop wild relatives in breeding and conservation programs, it is important to understand the genetic basis of their adaptation. Landscape genomics associates environments with genomic variation and allows for examining the genetic basis of adaptation. Our study examined the differences in allele frequency of 15,416 single nucleotide polymorphisms (SNPs) generated through genotyping by sequencing approach among 153 accessions of 15 wild eggplant relatives and two cultivated species from Africa, the principal hotspot of these wild relatives. We also explored the correlation between these variations and the bioclimatic and soil conditions at their collection sites, providing a comprehensive understanding of the genetic signals of environmental adaptation in African wild eggplant. Redundancy analysis (RDA) results showed that the environmental variation explained 6% while the geographical distances among the collection sites explained 15% of the genomic variation in the eggplant wild relative populations when controlling for population structure. Our findings indicate that even though environmental factors are not the main driver of selection in eggplant wild relatives, it is influential in shaping the genomic variation over time. The selected environmental variables and candidate SNPs effectively revealed grouping patterns according to the environmental characteristics of sampling sites. Using four genotype-environment association methods, we detected 396 candidate SNPs (2.5% of the initial SNPs) associated with eight environmental factors. Some of these SNPs signal genes involved in pathways that help adapt to environmental stresses such as drought, heat, cold, salinity, pests, and diseases. These candidate SNPs will be useful for marker-assisted improvement and characterizing the germplasm of this crop for developing climate-resilient eggplant varieties. The study provides a model for applying landscape genomics to other crops' wild relatives.

CONSTANS, a HUB for all seasons: How photoperiod pervades plant physiology regulatory circuits

How does a plant detect the changing seasons and make important developmental decisions accordingly? How do they incorporate daylength information into their routine physiological processes? Photoperiodism, or the capacity to measure the daylength, is a crucial aspect of plant development that helps plants determine the best time of the year to make vital decisions, such as flowering. The protein CONSTANS (CO) constitutes the central regulator of this sensing mechanism, not only activating florigen production in the leaves but also participating in many physiological aspects in which seasonality is important. Recent discoveries place CO in the center of a gene network that can determine the length of the day and confer seasonal input to aspects of plant development and physiology as important as senescence, seed size, or circadian rhythms. In this review, we discuss the importance of CO protein structure, function, and evolutionary mechanisms that embryophytes have developed to incorporate annual information into their physiology.

A Long-Lived Alpine Perennial Advances Flowering under Warmer Conditions but Not Enough to Maintain Reproductive Success

AbstractAssessing whether phenological shifts in response to climate change confer a fitness advantage requires investigating the relationships among phenology, fitness, and environmental drivers of selection. Despite widely documented advancements in phenology with warming climate, we lack empirical estimates of how selection on phenology varies in response to continuous climate drivers or how phenological shifts in response to warming conditions affect fitness. We leverage an unusual long-term dataset with repeated, individual measurements of phenology and reproduction in a long-lived alpine plant. We analyze phenotypic plasticity in flowering phenology in relation to two climate drivers, snowmelt timing and growing degree days (GDDs). Plants flower earlier with increased GDDs and earlier snowmelt, and directional selection also favors earlier flowering under these conditions. However, reproduction still declines with warming and early snowmelt, even when flowering is early. Furthermore, the steepness of this reproductive decline increases dramatically with warming conditions, resulting in very little fruit production regardless of flowering time once GDDs exceed approximately 225 degree days or snowmelt occurs before May 15. Even though advancing phenology confers a fitness advantage relative to stasis, these shifts are insufficient to maintain reproduction under warming, highlighting limits to the potential benefits of phenological plasticity under climate change.

Multistress Interplay: Time and Duration of Ocean Acidification Modulate the Toxicity of Mercury and Other Metals

The current understanding of multistress interplay assumes stresses occur in perfect synchrony, but this assumption is rarely met in the natural marine ecosystem. To understand the interplay between nonperfectly overlapped stresses in the ocean, we manipulated a multigenerational experiment (F0-F3) to explore how different temporal scenarios of ocean acidification will affect mercury toxicity in a marine copepod Pseudodiaptomus annandalei. We found that the scenario of past acidification aggravated mercury toxicity but current and persistent acidification mitigated its toxicity. We specifically performed a proteomics analysis for the copepods of F3. The results indicated that current and persistent acidification initiated the energy compensation for development and mercury efflux, whereas past acidification lacked the barrier of H+ and had dysfunction in the detoxification and efflux system, providing a mechanistic understanding of mercury toxicity under different acidification scenarios. Furthermore, we conducted a meta-analysis on marine animals, demonstrating that different acidification scenarios could alter the toxicity of several other metals, despite evidence from nonsynchronous scenarios remaining limited. Our study thus demonstrates that time and duration of ocean acidification modulate mercury toxicity in marine copepods and suggests that future studies should move beyond the oversimplified scenario of perfect synchrony in understanding multistress interaction.

Adaptation of perennial flowering phenology across the European range of Arabis alpina

Flowering phenology is important in the adaptation of many plants to their local environment, but its adaptive value has not been extensively studied in herbaceous perennials. We used Arabis alpina as a model system to determine the importance of flowering phenology to fitness of a herbaceous perennial with a wide geographical range. Individual plants representative of local genetic diversity (accessions) were collected across Europe, including in Spain, the Alps and Scandinavia. The flowering behaviour of these accessions was documented in controlled conditions, in common-garden experiments at native sites and in situ in natural populations. Accessions from the Alps and Scandinavia varied in whether they required exposure to cold (vernalization) to induce flowering, and in the timing and duration of flowering. By contrast, all Spanish accessions obligately required vernalization and had a short duration of flowering. Using experimental gardens at native sites, we show that an obligate requirement for vernalization increases survival in Spain. Based on our analyses of genetic diversity and flowering behaviour across Europe, we propose that in the model herbaceous perennial A. alpina, an obligate requirement for vernalization, which is correlated with short duration of flowering, is favoured by selection in Spain where the plants experience a long growing season.

Spring temperature drives phenotypic selection on plasticity of flowering time

In seasonal environments, a high responsiveness of development to increasing temperatures in spring can infer benefits in terms of a longer growing season, but also costs in terms of an increased risk of facing unfavourable weather conditions. Still, we know little about how climatic conditions influence the optimal plastic response. Using 22 years of field observations for the perennial forest herb Lathyrus vernus, we assessed phenotypic selection on among-individual variation in reaction norms of flowering time to spring temperature, and examined if among-year variation in selection on plasticity was associated with spring temperature conditions. We found significant among-individual variation in mean flowering time and flowering time plasticity, and that plants that flowered earlier also had a more plastic flowering time. Selection favoured individuals with an earlier mean flowering time and a lower thermal plasticity of flowering time. Less plastic individuals were more strongly favoured in colder springs, indicating that spring temperature influenced optimal flowering time plasticity. Our results show how selection on plasticity can be linked to climatic conditions, and illustrate how we can understand and predict evolutionary responses of organisms to changing environmental conditions.

Strong selection is poorly aligned with genetic variation in Ipomoea hederacea: implications for divergence and constraint

The multivariate evolution of populations is the result of the interactions between natural selection, drift, and the underlying genetic structure of the traits involved. Covariances among traits bias responses to selection, and the multivariate axis which describes the greatest genetic variation is expected to be aligned with patterns of divergence across populations. An exception to this expectation is when selection acts on trait combinations lacking genetic variance, which limits evolutionary change. Here we used a common garden field experiment of individuals from 57 populations of Ipomoea hederacea to characterize linear and nonlinear selection on 5 quantitative traits in the field. We then formally compare patterns of selection to previous estimates of within population genetic covariance structure (the G-matrix) and population divergence in these traits. We found that selection is poorly aligned with previous estimates of genetic covariance structure and population divergence. In addition, the trait combinations favored by selection were generally lacking genetic variation, possessing approximately 15%-30% as much genetic variation as the most variable combination of traits. Our results suggest that patterns of population divergence are likely the result of the interplay between adaptive responses, correlated responses, and selection favoring traits lacking genetic variation.

Rapid, nonparallel genomic evolution of Brassica rapa (field mustard) under experimental drought

While we know that climate change can potentially cause rapid phenotypic evolution, our understanding of the genetic basis and degree of genetic parallelism of rapid evolutionary responses to climate change is limited. In this study, we combined the resurrection approach with an evolve-and-resequence design to examine genome-wide evolutionary changes following drought. We exposed genetically similar replicate populations of the annual plant Brassica rapa derived from a field population in southern California to four generations of experimental drought or watered conditions in a greenhouse. Genome-wide sequencing of ancestral and descendant population pools identified hundreds of SNPs that showed evidence of rapidly evolving in response to drought. Several of these were in stress response genes, and two were identified in a prior study of drought response in this species. However, almost all genetic changes were unique among experimental populations, indicating that the evolutionary changes were largely nonparallel, despite the fact that genetically similar replicates of the same founder population had experienced controlled and consistent selection regimes. This nonparallelism of evolution at the genetic level is potentially because of polygenetic adaptation allowing for multiple different genetic routes to similar phenotypic outcomes. Our findings help to elucidate the relationship between rapid phenotypic and genomic evolution and shed light on the degree of parallelism and predictability of genomic evolution to environmental change.

Regulation of floral senescence in Arabidopsis by coordinated action of CONSTANS and jasmonate signaling

In Arabidopsis, photoperiodic flowering is controlled by the regulatory hub gene CONSTANS (CO), whereas floral organ senescence is regulated by the jasmonates (JAs). Because these processes are chronologically ordered, it remains unknown whether there are common regulators of both processes. In this study, we discovered that CO protein accumulates in Arabidopsis flowers after floral induction, and it displays a diurnal pattern in floral organs different from that in the leaves. We observed that altered CO expression could affect flower senescence and abscission by interfering with JA response, as shown by petal-specific transcriptomic analysis as well as CO overexpression in JA synthesis and signaling mutants. We found that CO has a ZIM (ZINC-FINGER INFLORESCENCE MERISTEM) like domain that mediates its interaction with the JA response repressor JAZ3 (jasmonate ZIM-domain 3). Their interaction inhibits the repressor activity of JAZ3, resulting in activation of downstream transcription factors involved in promoting flower senescence. Furthermore, we showed that CO, JAZ3, and the E3 ubiquitin ligase COI1 (Coronatine Insensitive 1) could form a protein complex in planta, which promotes the degradation of both CO and JAZ3 in the presence of JAs. Taken together, our results indicate that CO, a key regulator of photoperiodic flowering, is also involved in promoting flower senescence and abscission by augmenting JA signaling and response. We propose that coordinated recruitment of photoperiodic and JA signaling pathways could be an efficient way for plants to chronologically order floral processes and ensure the success of offspring production.

Local adaptation: Causal agents of selection and adaptive trait divergence

Divergent selection across the landscape can favor the evolution of local adaptation in populations experiencing contrasting conditions. Local adaptation is widely observed in a diversity of taxa, yet we have a surprisingly limited understanding of the mechanisms that give rise to it. For instance, few have experimentally confirmed the biotic and abiotic variables that promote local adaptation, and fewer yet have identified the phenotypic targets of selection that mediate local adaptation. Here, we highlight critical gaps in our understanding of the process of local adaptation and discuss insights emerging from in-depth investigations of the agents of selection that drive local adaptation, the phenotypes they target, and the genetic basis of these phenotypes. We review historical and contemporary methods for assessing local adaptation, explore whether local adaptation manifests differently across life history, and evaluate constraints on local adaptation.

Water and nutrient availability exert selection on reproductive phenology

PREMISE

Global change has changed resource availability to plants, which could shift the adaptive landscape. We hypothesize that novel water and nutrient availability combinations alter patterns of natural selection on reproductive phenology in Boechera stricta (Brassicaceae) and influence the evolution of local adaptation.

METHODS

We conducted a multifactorial greenhouse study using 35 accessions of B. stricta sourced from a broad elevational gradient in the Rocky Mountains. We exposed full siblings to three soil water and two nutrient availability treatment levels, reflecting current and projected future conditions. In addition, we quantified fitness (seed count) and four phenological traits: the timing of first flowering, the duration of flowering, and height and leaf number at flowering.

RESULTS

Selection favored early flowering and longer duration of flowering, and the genetic correlation between these traits accorded with the direction of selection. In most treatments, we found selection for increased height, but selection on leaf number depended on water availability, with selection favoring more leaves in well-watered conditions and fewer leaves under severe drought. Low-elevation genotypes had the greatest fitness under drought stress, consistent with local adaptation.

CONCLUSIONS

We found evidence of strong selection on these heritable traits. Furthermore, the direction and strength of selection on size at flowering depended on the variable measured (height vs. leaf number). Finally, selection often favored both early flowering and a longer duration of flowering. Selection on these two components of phenology can be difficult to disentangle due to tight genetic correlations.

Genetic variation in reproductive timing in a long-lived herbaceous perennial

PREMISE

Reproductive fitness of individual plants depends on the timing of flowering, especially in mate-limited populations, such as those in fragmented habitats. When flowering time traits are associated with differential reproductive success, the narrow-sense heritability (h² ) of traits will determine how rapidly trait means evolve in response to selection. Heritability of flowering time is documented in many annual plants. However, estimating h² of flowering time in perennials presents additional methodological challenges, often including paternity assignment and trait expression over multiple years.

METHODS

We evaluated the h² of onset and duration of flowering using offspring-midparent regressions and restricted maximum likelihood methods in an experimental population of an iterocarpic, perennial, herbaceous plant, Echinacea angustifolia, growing in natural conditions. We assessed the flowering time of the parental cohort in 2005 and 2006; the offspring in 2014 through 2017. We also examined the effects of the paternity assignment from Cervus and MasterBayes on estimates of h² .

RESULTS

We found substantial h² for onset and duration of flowering. We also observed variation in estimates among years. The most reliable estimates for both traits fell in the range of 0.1-0.17. We found evidence of a genotype by year interaction for onset of flowering and strong evidence that genotypes are consistent in their duration of flowering across years.

CONCLUSIONS

Substantial heritabilities in this population imply the capacity for a response to natural selection, while also suggesting the potential for differential contributions to adaptive evolution among seasons.

Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding

Rice bean (Vigna umbellata) is an underexploited domesticated legume crop consumed for dietary protein in Asia, yet little is known about the genetic diversity of this species. Here, we present a high-quality reference genome for a rice bean landrace (FF25) built using PacBio long-read data and a Hi-C chromatin interaction map, and assess the phylogenetic position and speciation time of rice bean within the Vigna genus. We sequence 440 landraces (two core collections), and GWAS based on data for growth sites at three widely divergent latitudes reveal loci associated with flowering and yield. Loci harboring orthologs of FUL (FRUITFULL), FT (FLOWERING LOCUS T), and PRR3 (PSEUDO-RESPONSE REGULATOR 3) contribute to the adaptation of rice bean from its low latitude center of origin towards higher latitudes, and the landraces which pyramid early-flowering alleles for these loci display maximally short flowering times. We also demonstrate that copy-number-variation for VumCYP78A6 can regulate seed-yield traits. Intriguingly, 32 landraces collected from a mountainous region in South-Central China harbor a recently acquired InDel in TFL1 (TERMINAL FLOWER1) affecting stem determinacy; these materials also have exceptionally high values for multiple human-desired traits and could therefore substantially advance breeding efforts to improve rice bean.

Rice bean is an underexploited legume crop that has many desirable properties against bio and abiotic stresses. Here, the authors report the genome assembly of this species, conduct population genetics studies and reveal the genetic variations associated with adaptation and yield traits.

Mutualist- and antagonist-mediated selection contribute to trait diversification of flowers

Flowers are generally short-lived, and they all face a multidimensional challenge because they have to attract mutualists, compel them to vector pollen with minimal investment in rewards, and repel floral enemies during this short time window. Their displays are under complex selection, either consistent or conflicting, to maximize reproductive fitness under heterogeneous environments. The phenological or morphological mismatches between flowers and visitors will influence interspecific competition, resource access, mating success and, ultimately, population and community dynamics. To better understand the effects of the plant visitors on floral traits, it is necessary to determine the functional significance of specific floral traits for the visitors; how plants respond to both mutualists and antagonists through adaptive changes; and to evaluate the net fitness effects of biological mutualisms and antagonism on plants. In this review, we bring together insights from fields as diverse as floral biology, insect behavioral responses, and evolutionary biology to explain the processes and patterns of floral diversity evolution. Then, we discuss the ecological significance of plant responses to mutualists and antagonists from a community perspective, and propose a set of research questions that can guide the research field to integrate studies of plant defense and reproduction.

Three problems in the genetics of speciation by selection

Speciation is the process by which barriers to gene flow evolve between populations. Although we now know that speciation is largely driven by natural selection, knowledge of the agents of selection and the genetic and genomic mechanisms that facilitate divergence is required for a satisfactory theory of speciation. In this essay, we highlight three advances/problems in our understanding of speciation that have arisen from studies of the genes and genomic regions that underlie the evolution of reproductive isolation. First, we describe how the identification of “speciation” genes makes it possible to identify the agents of selection causing the evolution of reproductive isolation, while also noting that the link between the genetics of phenotypic divergence and intrinsic postzygotic reproductive barriers remains tenuous. Second, we discuss the important role of recombination suppressors in facilitating speciation with gene flow, but point out that the means and timing by which reproductive barriers become associated with recombination cold spots remains uncertain. Third, we establish the importance of ancient genetic variation in speciation, although we argue that the focus of speciation studies on evolutionarily young groups may bias conclusions in favor of ancient variation relative to new mutations.

2b-RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation

Plant populations distributed along broad latitudinal gradients often show patterns of clinal variation in genotype and phenotype. Differences in photoperiod and temperature cues across latitudes influence major phenological events, such as timing of flowering or seed dormancy. Here, we used an array of 4,941 SNPs derived from 2b-RAD genotyping to characterize population differentiation and levels of genetic and genotypic diversity of three populations of the seagrass Cymodocea nodosa along a latitudinal gradient extending across the Atlantic-Mediterranean boundary (i.e., Gran Canaria—Canary Islands, Faro—Portugal, and Ebro Delta—Spain). Our main goal was to search for potential outlier loci that could underlie adaptive differentiation of populations across the latitudinal distribution of the species. We hypothesized that such polymorphisms could be related to variation in photoperiod-temperature regime occurring across latitudes. The three populations were clearly differentiated and exhibited diverse levels of clonality and genetic diversity. Cymodocea nodosa from the Mediterranean displayed the highest genotypic richness, while the Portuguese population had the highest clonality values. Gran Canaria exhibited the lowest genetic diversity (as observed heterozygosity). Nine SNPs were reliably identified as outliers across the three sites by two different methods (i.e., BayeScan and pcadapt), and three SNPs could be associated to specific protein-coding genes by screening available C. nodosa transcriptomes. Two SNPs-carrying contigs encoded for transcription factors, while the other one encoded for an enzyme specifically involved in the regulation of flowering time, namely Lysine-specific histone demethylase 1 homolog 2. When analyzing biological processes enriched within the whole dataset of outlier SNPs identified by at least one method, “regulation of transcription” and “signalling” were among the most represented. Our results highlight the fundamental importance signal integration and gene-regulatory networks, as well as epigenetic regulation via DNA (de)methylation, could have for enabling adaptation of seagrass populations along environmental gradients.

Phenotypic Selection in Halenia elliptica D. Don (Gentianaceae), an Alpine Biennial with Mixed Mating System

The transition from outcrossing to selfing is a common evolutionary trend in flowering plants, and floral traits change significantly with the evolution of selfing. Whether or not plant traits are subjected to selection remains an open question in species with mixed mating systems. We examined phenotypic selection in two populations of Halenia elliptica with different selfing rates. We found that the pollen–ovule ratio, seed size, plant height, spur length, and pollinator visitation rate in the population with the higher selfing rate were lower than those in the population with the lower selfing rate. Selfing provides reproductive assurance for populations when pollinator service is low, and the floral traits that are associated with selfing syndrome are evident in populations with a higher selfing rate but are subjected to weak selection in each of the two populations with different selfing rates. Directional selection for an early flowering time indicated that late blooming flowers could experience a risk of seed development in alpine environments, and for large plants, selection indicated that seed production could be limited by the available resources. The floral traits that are associated with pollinator attraction and specialization could be subjected to weak selection at the plant level as selfing evolves, and the selective pressures that are independent of pollinators might not change significantly; highlighting the selective biotic and abiotic pressures that shape the morphological traits of plant species and their independence from the mating system.

The influence of genetic architecture on responses to selection under drought in rice

Accurately predicting responses to selection is a major goal in biology and important for successful crop breeding in changing environments. However, evolutionary responses to selection can be constrained by such factors as genetic and cross‐environment correlations, linkage, and pleiotropy, and our understanding of the extent and impact of such constraints is still developing. Here, we conducted a field experiment to investigate potential constraints to selection for drought resistance in rice (Oryza sativa) using phenotypic selection analysis and quantitative genetics. We found that traits related to drought response were heritable, and some were under selection, including selection for earlier flowering, which could allow drought escape. However, patterns of selection generally were not opposite under wet and dry conditions, and we did not find individual or closely linked genes that influenced multiple traits, indicating a lack of evidence that antagonistic pleiotropy, linkage, or cross‐environment correlations would constrain selection for drought resistance. In most cases, genetic correlations had little influence on responses to selection, with direct and indirect selection largely congruent. The exception to this was seed mass under drought, which was predicted to evolve in the opposite direction of direct selection due to correlations. Because of this indirect effect on selection on seed mass, selection for drought resistance was not accompanied by a decrease in seed mass, and yield increased with fecundity. Furthermore, breeding lines with high fitness and yield under drought also had high fitness and yield under wet conditions, indicating that there was no evidence for a yield penalty on drought resistance. We found multiple genes in which expression influenced both water use efficiency (WUE) and days to first flowering, supporting a genetic basis for the trade‐off between drought escape and avoidance strategies. Together, these results can provide helpful guidance for understanding and managing evolutionary constraints and breeding stress‐resistant crops.

Adaptive significance of flowering time variation across natural seasonal environments in Arabidopsis thaliana

The relevance of flowering time variation and plasticity to climate adaptation requires a comprehensive empirical assessment. We investigated natural selection and the genetic architecture of flowering time in Arabidopsis through field experiments in Europe across multiple sites and seasons. We estimated selection for flowering time, plasticity and canalization. Loci associated with flowering time, plasticity and canalization by genome-wide association studies were tested for a geographic signature of climate adaptation. Selection favored early flowering and increased canalization, except at the northernmost site, but was rarely detected for plasticity. Genome-wide association studies revealed significant associations with flowering traits and supported a substantial polygenic inheritance. Alleles associated with late flowering, including functional FRIGIDA variants, were more common in regions experiencing high annual temperature variation. Flowering time plasticity to fall vs spring and summer environments was associated with GIGANTEA SUPPRESSOR 5, which promotes early flowering under decreasing day length and temperature. The finding that late flowering genotypes and alleles are associated with climate is evidence for past adaptation. Real-time phenotypic selection analysis, however, reveals pervasive contemporary selection for rapid flowering in agricultural settings across most of the species range. The response to this selection may involve genetic shifts in environmental cuing compared to the ancestral state.

Phenotypic and Methylome Responses to Salt Stress in Arabidopsis thaliana Natural Accessions

Salt stress threatens plant growth, development and crop yields, and has become a critical global environmental issue. Increasing evidence has suggested that the epigenetic mechanism such as DNA methylation can mediate plant response to salt stress through transcriptional regulation and transposable element (TE) silencing. However, studies exploring genome-wide methylation dynamics under salt stress remain limited, in particular, for studies on multiple genotypes. Here, we adopted four natural accessions of the model species Arabidopsis thaliana and investigated the phenotypic and genome-wide methylation responses to salt stress through whole-genome bisulfite sequencing (WGBS). We found that salt stress significantly changed plant phenotypes, including plant height, rosette diameter, fruit number, and aboveground biomass, and the change in biomass tended to depend on accessions. Methylation analysis revealed that genome-wide methylation patterns depended primarily on accessions, and salt stress caused significant methylation changes in ∼ 0.1% cytosines over the genomes. About 33.5% of these salt-induced differential methylated cytosines (DMCs) were located to transposable elements (TEs). These salt-induced DMCs were mainly hypermethylated and accession-specific. TEs annotated to have DMCs (DMC-TEs) across accessions were found mostly belonged to the superfamily of Gypsy, a type II transposon, indicating a convergent DMC dynamic on TEs across different genetic backgrounds. Moreover, 8.0% of salt-induced DMCs were located in gene bodies and their proximal regulatory regions. These DMCs were also accession-specific, and genes annotated to have DMCs (DMC-genes) appeared to be more accession-specific than DMC-TEs. Intriguingly, both accession-specific DMC-genes and DMC-genes shared by multiple accessions were enriched in similar functions, including methylation, gene silencing, chemical homeostasis, polysaccharide catabolic process, and pathways relating to shifts between vegetative growth and reproduction. These results indicate that, across different genetic backgrounds, methylation changes may have convergent functions in post-transcriptional, physiological, and phenotypic modulation under salt stress. These convergent methylation dynamics across accession may be autonomous from genetic variation or due to convergent genetic changes, which requires further exploration. Our study provides a more comprehensive picture of genome-wide methylation dynamics under salt stress, and highlights the importance of exploring stress response mechanisms from diverse genetic backgrounds.

Fire influences reproductive outcomes by modifying flowering phenology and mate-availability

A recent study posited that fire in grasslands promotes persistence of plant species by improving mating opportunities and reproductive outcomes. We devised an investigation to test these predicted mechanisms in two widespread, long-lived perennials. We expect fire to synchronize flowering, increase mating and boost seed set. We quantified individual flowering phenology and seed set of Liatris aspera and Solidago speciosa for 3 yr on a preserve in Minnesota, USA. The preserve comprises two management units burned on alternating years, allowing for comparisons between plants in burned and unburned areas within the same year, and plants in the same area across years with and without burns. Fire increased flowering synchrony and increased time between start date and peak flowering. Individuals of both species that initiated flowering later in the season had higher seed set. Fire was associated with substantially higher flowering rates and seed set in L. aspera but not S. speciosa. In L. aspera, greater synchrony was associated with increased mean seed set. Although fire affected flowering phenology in both species, reproductive success improved only in the species in which fire also synchronized among-year flowering. Our results support the hypothesis that reproduction in some grassland species benefits from fire.

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.

Plasticity, pleiotropy and fitness trade-offs in Arabidopsis genotypes with different telomere lengths

Telomere length has been implicated in the organismal response to stress, but the underlying mechanisms are unknown. Here we examine the impact of telomere length changes on the responses to three contrasting abiotic environments in Arabidopsis, and measure 32 fitness, developmental, physiological and leaf-level anatomical traits. We report that telomere length in wild-type and short-telomere mutants is resistant to abiotic stress, while the elongated telomeres in ku70 mutants are more plastic. We detected significant pleiotropic effects of telomere length on flowering time and key leaf physiological and anatomical traits. Furthermore, our data reveal a significant genotype by environment (G × E) interaction for reproductive fitness, with the benefits and costs to performance depending on the growth conditions. These results imply that life-history trade-offs between flowering time and reproductive fitness are impacted by telomere length variation. We postulate that telomere length in plants is subject to natural selection imposed by different environments.

Genome-wide association mapping of transcriptome variation in Mimulus guttatus indicates differing patterns of selection on cis- versus trans-acting mutations

We measured the floral bud transcriptome of 151 fully sequenced lines of Mimulus guttatus from one natural population. Thousands of single nucleotide polymorphisms (SNPs) are implicated as transcription regulators, but there is a striking difference in the allele frequency spectrum of cis-acting and trans-acting mutations. Cis-SNPs have intermediate frequencies (consistent with balancing selection) while trans-SNPs exhibit a rare-alleles model (consistent with purifying selection). This pattern only becomes clear when transcript variation is normalized on a gene-to-gene basis. If a global normalization is applied, as is typically in RNAseq experiments, asymmetric transcript distributions combined with "rarity disequilibrium" produce a superabundance of false positives for trans-acting SNPs. To explore the cause of purifying selection on trans-acting mutations, we identified gene expression modules as sets of coexpressed genes. The extent to which trans-acting mutations influence modules is a strong predictor of allele frequency. Mutations altering expression of genes with high "connectedness" (those that are highly predictive of the representative module expression value) have the lowest allele frequency. The expression modules can also predict whole-plant traits such as flower size. We find that a substantial portion of the genetic (co)variance among traits can be described as an emergent property of genetic effects on expression modules.

Rapid, parallel evolution of field mustard (Brassica rapa) under experimental drought

Climate change is driving evolutionary and plastic responses in populations, but predicting these responses remains challenging. Studies that combine experimental evolution with ancestor-descendant comparisons allow assessment of the causes, parallelism, and adaptive nature of evolutionary responses, although such studies remain rare, particularly in a climate change context. Here, we created experimental populations of Brassica rapa derived from the same natural population and exposed these replicated populations to experimental drought or watered conditions for four generations. We then grew ancestors and descendants concurrently, following the resurrection approach. Experimental populations under drought showed rapid evolution of earlier flowering time and increased specific leaf area, consistent with a drought escape strategy and observations in natural populations. Evolutionary shifts followed the direction of selection and increased fitness under drought, indicative of adaptive evolution. Evolution to drought also occurred largely in parallel among replicate populations. Further, traits showed phenotypic plasticity to drought, but the direction and effect size of plasticity varied. Our results demonstrate parallel evolution to experimental drought, suggesting that evolution to strong, consistent selection may be predictable. Broadly, our study demonstrates the utility of combining experimental evolution with the resurrection approach to investigate responses to climate change.

Rapid divergent evolution of an annual plant across a latitudinal gradient revealed by seed resurrection

Global change is expected to drive short-term evolution of natural populations. However, it remains unclear whether different populations are changing in unison. Here, we study contemporary evolution of growth-related and reproductive traits of three populations of Cyanus segetum facing warming and pollinator decline across a latitudinal gradient in France. We resurrected stored seeds sampled up to 24 years apart from northern, central-western, and southern populations and conducted an in situ common-garden experiment. To disentangle neutral from selection-driven differentiation, we calculated neutral genetic differentiation (F_ST ) and quantitative trait differentiation (Q_ST ) between temporal samples. We found that phenotypic evolution was divergent across populations exhibiting different trends for rosette size, date of flowering, and capitula size. By measuring seed set as a proxy of fitness, we showed that samples with larger mean capitula size outperformed samples with smaller mean capitula size in the western and southern populations. Regression of traits on seed set showed that flowering date and capitula size are the primary determinants of fitness, and Q_ST -F_ST comparisons indicated that natural selection has likely contributed to the shifts in flowering phenology and rosette size. These findings outline the potential for rescue of natural populations through contemporary evolution and emphasize the complex interplay between spatial and temporal variation in species' responses to global change.

Plant-animal interactions mediate climatic effects on selection on flowering time

Selection on flowering time in plants is often mediated by multiple agents, including climatic conditions and the intensity of mutualistic and antagonistic interactions with animals. These selective agents can have both direct and indirect effects. For example, climate might not only influence phenotypic selection on flowering time directly by affecting plant physiology, but it can also alter selection indirectly by modifying the seasonal activity and relative timing of animals interacting with plants. We used 21 yr of data to identify the drivers of selection on flowering time in the perennial herb Lathyrus vernus, and to examine if antagonistic plant-animal interactions mediate effects of climate on selection. We examined the fitness consequences of vertebrate grazing and predispersal seed predation, and how these effects varied among years and among individuals within years. Although both antagonistic plant-animal interactions had important negative effects on plant fitness, only grazing intensity was consistently related to plant phenology, being higher in early-flowering individuals. Spring temperature influenced the intensity of both plant-animal interactions, as well as the covariance between seed predation and plant phenology. However, only differences in grazing intensity among years were associated with differences in selection on flowering time; the strength of selection for early flowering being stronger in years with lower mean intensity of grazing. Our results illustrate how climatic conditions can influence plant-animal interactions that are important selective agents for plant traits. A broader implication of our findings is that both ecological and evolutionary responses to climatic changes might be indirect, and largely mediated by species interactions.

The evolution of developmental thresholds and reaction norms for age and size at maturity

Developing organisms typically mature earlier and at larger sizes in favorable growth conditions, while in rarer cases, maturity is delayed. The rarer reaction norm is easily accommodated by general life history models, whereas the common pattern is not. Theory suggests that a solution to this paradox lies in the existence of critical size thresholds at which maturation or metamorphosis can commence, and in the evolution of these threshold sizes in response to environmental variation. For example, ephemeral environments might favor the evolution of smaller thresholds, enabling earlier maturation. The threshold model makes two unique and untested predictions. First, reaction norms for age and size should steepen, and even change sign, with decreases in threshold size; second, food reductions at sizes below the threshold should delay maturation, while those occurring after the threshold should accelerate maturation. We test these predictions through food manipulations in five damselfly species that theory suggests should differ in threshold size. The results provide strong support for the threshold model's predictions. In all species, early food reductions delayed maturation, while late reductions accelerated maturation. Reaction norms were steeper, and the effect of food reductions changed from decelerating to accelerating at a much smaller size in species from ephemeral habitats. These results support the view that developmental thresholds can account for the widespread observation of negative correlations between age and size at maturity. Moreover, evolution of the threshold appears to be both predictable and central to the observed diversity of reaction norms for age and size at maturity.

The impacts of flowering phenology on the reproductive success of the narrow endemic Nouelia insignis Franch. (Asteraceae)

Nouelia insignis Franch. (Asteraceae) is a short, narrow endemic and endangered tree, growing with a natural population in the dry and hot valley of the Jinsha River in the southwest area of China. In this work, flowering phenology (time and duration), floral biology, visit frequency and behavior of pollinators, and pollination characteristics were studied based on investigation in the field and analysis in the laboratory with the help of a stereomicroscope, and the relationship between seed setting rate and reproductive traits, as well as the relationship between flowering time and rainfall before flowering, was tested using the method of general linear regression model. The results showed that natural population of N. insignis exhibited high flowering synchrony with relatively stable flowering duration, and the flowering time fluctuated greatly depending on the rainfall 5 months before flowering. The pollination of N. insignis required pollinators, and insect activities played a very important role in the pollination process. However, lack of the pollinators was not a limitation for reproductive fitness in N. insignis, although the number of pollinators was small and the frequency of visits was low. In addition, no pollen limitation was found during pollination. The average seed setting rate of N. insignis in the natural condition was only 1.52%-3.73%, and it was generally affected by changes in flowering phenology between years and had a higher seed set in early flowering year. The annual variation of seed set might be related to the annual variations of stamen and pistil functions, such as changes of pollen viability and stigma receptivity, which were closely related to flowering time. The results of this study are of value for further conservation actions on natural population of this threatened endemic plant.

Ecological causes of fluctuating natural selection on habitat choice in an amphibian

We estimated natural selection targeting three traits related to habitat choice in a frog (Pseudacris maculata) breeding in pools on the rocky shores of Isle Royale, Michigan, over 16 years. Our aim was to identify the form and ecological causes of annual variation in directional and correlational selection as expressed in the survival and growth of tadpoles. We found directional selection favoring early breeding, but pool choice was under weak stabilizing selection. However, the form of stabilizing selection and the position of the optimum trait value shifted among years with the severity of disturbance and the intensity of biotic interactions. In years when wave wash and pool desiccation were severe, selection shifted to favor tadpoles in habitats where these risks were less pronounced. If predatory dragonfly larvae were abundant, selection favored tadpoles in small pools where dragonflies did not occur. When intraspecific competition was strong, selection favored early broods within a broader range of pool types. The agents of selection in this study—biotic interactions and disturbance—are common to many ecological systems and frequently exhibit temporal variation; this suggests that fluctuating selection may be widespread in natural populations.

Chronic selection for early reproductive phenology in an annual plant across a steep, elevational gradient of growing season length

Colonization along ubiquitous gradients of growing season length should require adaptation of phenological traits, driven by natural selection. Although phenology often varies with season length and genetic differentiation in phenological traits sometimes seems adaptive, few studies test whether natural selection is responsible for these patterns. The annual plant Rhinanthus minor is genetically differentiated for phenology across a 1000-m elevational gradient of growing season length in the Canadian Rocky Mountains. We estimated phenotypic selection on five phenological traits for three generations of naturally occurring individuals at 12 sites (n = 10,112), and two generations of genetically and phenotypically more variable transplanted populations at nine of these sites (n = 24,611). Selection was weak for most traits, but consistently favored early flowering across the gradient rather than only under short seasons. There was no evidence that apparent selection favoring early reproduction arose from failure to consider all components of fitness, or variation in other correlated phenological traits. Instead, selection for earlier flowering may be balanced by selection for strong cogradient phenological plasticity that indirectly favors later flowering. However, this probably does not explain the consistency of selection on flowering time across this steep, elevational gradient of growing season length.

The earlier the better? Nesting timing and reproductive success in subalpine cavity-nesting bees

Reproductive timing can affect an organism's production of offspring and its offspring's success, both of which contribute to its overall fitness. In seasonal environments, the timing of reproductive activity may be restricted to short periods of the year owing to numerous potential selective pressures such as variation in daylength, weather, food availability, predation or competition. We documented the relationships between reproductive timing and individual reproductive success (total reproductive output and offspring success) in subalpine populations of five cavity-nesting solitary bee species. We also examined the relationships between bee reproductive success and environmental variables that are likely ultimate drivers of bee phenology in subalpine environments (i.e. seasonality of floral resource abundance and temperature). Over 6 years, we recorded solitary bee nesting timing, egg production and offspring success using artificial nesting structures ('trap-nests') established at multiple study sites. We also quantified floral resources and recorded temperature throughout growing seasons. Bees nesting earlier in the season exhibited greater reproductive success. Reproductive output generally increased with floral abundance, although this relationship was weak and only significant for some bee species. Elevated temperatures were associated with increased nest construction rate, but not with greater reproductive output. These contrasting effects of temperature may have been driven by the negative relationship between temperature and bee longevity. Bees who nested for shorter durations of time (a proxy for longevity) produced fewer offspring, and individuals exhibiting the shortest nesting durations were also those that began nesting late in the season. Overall, bees who initiated nesting early and sustained activity for a long duration had the highest reproductive output. This work documents the relationship between reproductive phenology and fitness in wild insect populations and highlights the ways in which organisms can cope with the challenges of living in seasonal and highly variable environments.

Inflorescence preformation prior to winter: a surprisingly widespread strategy that drives phenology of temperate perennial herbs

Organ preformation in overwintering buds of perennial plants has been known for almost two centuries. It is hypothesized to underlie fast growth and early flowering, but its frequency, phylogenetic distribution, and ecological relevance have never been systematically examined. We microscopically observed inflorescence preformation in overwintering buds (IPB) in the autumn. We studied a phylogenetically and ecologically representative set of 330 species of temperate perennial angiosperms and linked these observations with quantitative data on species' flowering phenology, genome size, and ecology. IPB was observed in 34% of species examined (in 14% species the stamens and/or pistils were already developed). IPB is fairly phylogenetically conserved and frequent in many genera (Alchemilla, Carex, Euphorbia, Geranium, Primula, Pulmonaria) or families (Ranunculaceae, Euphorbiaceae, Violaceae, Boraginaceae). It was found in species of any genome size, although it was almost universal in those with large genomes. Compared with non-IPB species, IPB species flowered 38 d earlier on average and were more common in shaded and undisturbed habitats. IPB is a surprisingly widespread adaptation for early growth in predictable (undisturbed) conditions. It contributes to temporal niche differentiation and has important consequences for understanding plant phenology, genome size evolution, and phylogenetic structure of plant communities.

Natural selection on traits and trait plasticity in Arabidopsis thaliana varies across competitive environments

Interspecific competition reduces resource availability and can affect evolution. We quantified multivariate selection in the presence and absence of strong interspecific competition using a greenhouse experiment with 35 natural accessions of Arabidopsis thaliana. We assessed selection on nine traits representing plant phenology, growth, and architecture, as well as their plasticities. Competition reduced biomass and fitness by over 98%, and plastic responses to competition varied by genotype (significant G × E) for all traits except specific leaf area (SLA). Competitive treatments altered selection on flowering phenology and plant architecture, with significant selection on all phenology traits and most architecture traits under competition-present conditions but little indication that selection occurred in the absence of competitors. Plasticity affected fitness only in competition-present conditions, where plasticity in flowering time and early internode lengths was adaptive. The competitive environment caused changes in the trait correlation structure and surprisingly reduced phenotypic integration, which helped explain some of the observed selection patterns. Despite this overall shift in the trait correlation matrix, genotypes with delayed flowering had lower SLA (thicker, tougher leaves) regardless of the competitive environment, a pattern we have not seen previously reported in the literature. Overall, our study highlights multiple ways in which interspecific competition can alter selective regimes, contributing to our understanding of variability in selection processes over space and time.

No evidence that rapid adaptation impedes biological control of an invasive plant

Biological control is a popular tool for invasive species management, but its success in nature is difficult to predict. One risk is that invasive plants, which may have adapted to lower herbivore pressure in the introduced range, could rapidly evolve defences upon re-association with their biocontrol agent(s). Previous studies have demonstrated that populations of the invasive plant purple loosestrife (Lythrum salicaria) exposed to biocontrol exhibit traits consistent with the rapid evolution of defence. However, to date, no one has tested this hypothesis under field-natural levels of herbivory. Using seed from 17 populations of purple loosestrife growing in eastern Canada, that varied in their history of exposure to their biocontrol agent, the leaf beetle Neogalerucella spp., we transplanted 1,088 seedlings from 136 maternal families into a common garden under ambient herbivory. Over the following three and half years, we assessed plant performance in the face of biocontrol by measuring early-season plant size, defoliation, flowering, and season-end biomass. We discovered that a population history with biocontrol explained little variation in herbivory or plant performance, suggesting that adaptation is not hindering biocontrol effectiveness. Instead, plant size, subsequent defoliation, and spatio-temporal variables were the main predictors of plant growth and flowering during the study. The high individual variability we observed in plant performance underscores that flexible strategies of allocation and phenology are important contributors to the persistence of invasive plants. Our findings suggest that plant adaptation to biocontrol is unlikely to be a strong impediment to biological control in this species, however, the high survival and variable defoliation of plants in our study also indicate that biocontrol alone is unlikely to result in significant population decline. We recommend that the application of multiple forms of control simultaneously (e.g. thinning plus biocontrol) could help to prevent the existence of refuges of large, reproductive individuals.

Competition × drought interactions change phenotypic plasticity and the direction of selection on Arabidopsis traits

Populations often exhibit genetic diversity in traits involved in responses to abiotic stressors, but what maintains this diversity is unclear. Arabidopsis thaliana exhibits high within-population variation in drought response. One hypothesis is that competition, varying at small scales, promotes diversity in resource use strategies. However, little is known about natural variation in competition effects on Arabidopsis physiology. We imposed drought and competition treatments on diverse genotypes. We measured resource economics traits, physiology, and fitness to characterize plasticity and selection in response to treatments. Plastic responses to competition differed depending on moisture availability. We observed genotype-drought-competition interactions for relative fitness: competition had little effect on relative fitness under well-watered conditions, whereas competition caused rank changes in fitness under drought. Early flowering was always selected. Higher δ¹³ C was selected only in the harshest treatment (drought and competition). Competitive context significantly changed the direction of selection on aboveground biomass and inflorescence height in well-watered environments. Our results highlight how local biotic conditions modify abiotic selection, in some cases promoting diversity in abiotic stress response. The ability of populations to adapt to environmental change may thus depend on small-scale biotic heterogeneity.

Evolutionary and plastic changes in a native annual plant after a historic drought

Severe droughts are forecast to increase with global change. Approaches that enable the study of contemporary evolution, such as resurrection studies, are valuable for providing insights into the responses of populations to global change. In this study, we used a resurrection approach to study the evolution of the California native Leptosiphon bicolor (true babystars, Polemoniaceae) across populations differing in precipitation in response to the state's recent prolonged drought (2011-2017). In the Mediterranean climate region in which L. bicolor grows, this historic drought effectively shortened its growing season. We used seeds collected both before and after this drought from three populations found along a moisture availability gradient to assess contemporary evolution in a common garden greenhouse study. We coupled this with a drought experiment to examine plasticity. We found evolution toward earlier flowering after the historic drought in the wettest of the three populations, while plasticity to experimental drought was observed across all three. We also observed trade-offs associated with earlier flowering. In the driest population, plants that flowered earlier had lower intrinsic water-use efficiency than those flowering later, which was an expected pattern. Unexpectedly, earlier flowering plants had larger flowers. Two populations exhibited evolution and plasticity toward smaller flowers with drought. The third exhibited evolution toward larger flowers, but displayed no plasticity. Our results provide valuable insights into differences among native plant populations in response to drought.

CONSTANS-FKBP12 interaction contributes to modulation of photoperiodic flowering in Arabidopsis

Flowering time is a key process in plant development. Photoperiodic signals play a crucial role in the floral transition in Arabidopsis thaliana, and the protein CONSTANS (CO) has a central regulatory function that is tightly regulated at the transcriptional and post-translational levels. The stability of CO protein depends on a light-driven proteasome process that optimizes its accumulation in the evening to promote the production of the florigen FLOWERING LOCUS T (FT) and induce seasonal flowering. To further investigate the post-translational regulation of CO protein we have dissected its interactome network employing in vivo and in vitro assays and molecular genetics approaches. The immunophilin FKBP12 has been identified in Arabidopsis as a CO interactor that regulates its accumulation and activity. FKBP12 and CO interact through the CCT domain, affecting the stability and function of CO. fkbp12 insertion mutants show a delay in flowering time, while FKBP12 overexpression accelerates flowering, and these phenotypes can be directly related to a change in accumulation of FT protein. The interaction is conserved between the Chlamydomonas algal orthologs CrCO-CrFKBP12, revealing an ancient regulatory step in photoperiod regulation of plant development.

Environmental heterogeneity generates intrapopulation variation in life-history traits in an annual plant

Environmental variation affects a plant's life cycle by influencing the timing of germination and flowering, and the duration of the growing season. Yet we know little information about how environmental heterogeneity generates variation in germination schedules and the consequences for growth and fecundity through genetic and plastic responses. We use an annual population of Mimulus guttatus in which, in nature, seeds germinate in both fall and spring. We investigate whether there is a genetic basis to the timing of germination, the effect of germination timing on fecundity, and if growth and flowering respond plastically to compensate for different season lengths. Using sibling families grown in simulated seasonal conditions, we find that families do not differ in their propensity to germinate between seasons. However, the germination season affects subsequent growth and flowering time, with significant genotype-by-environment interactions (G × E). Most G × E is due to unequal variance between seasons, because the spring cohort harbours little genetic variance. Despite their different season lengths, the cohorts do not differ in flower number (fecundity). Heterogeneous environments with unpredictable risks may maintain promiscuous germination, which then affects flowering time. Therefore, if selection at particular life stages changes with climate change, there may be consequences for the entire life cycle.

Interannual variation in season length is linked to strong co-gradient plasticity of phenology in a montane annual plant

Species are commonly distributed along latitudinal and elevational gradients of growing season length to which they might respond via phenotypic plasticity and/or adaptive genetic differentiation. However, the relative contribution of these processes and whether plasticity, if it occurs, facilitates expansion along season-length gradients remain unclear, but are important for predicting species fates during anthropogenic change. We quantified phenological trait variation in the montane annual Rhinanthus minor for three generations at 12 sites across 900 m of elevation in the Canadian Rocky Mountains and conducted a reciprocal transplant experiment for two generations among nine sites. We compared clines and interannual variation of phenological traits between natural and transplanted individuals. Season length declined by c. 37% along our elevational gradient and, as expected, plants emerged, reached first flower and made their first seed in c. 41% fewer growing degree days under shorter growing seasons. Although reciprocal transplants revealed modest genetic differentiation across elevation, trait clines primarily were due to striking co-gradient plasticity that paralleled genetic differentiation. Co-gradient plasticity likely evolved in response to considerable interannual variation in season length across our elevational transect, and should prepare R. minor to make adaptive changes to phenology in response to ongoing climate change predicted for montane environments.

How does timing of flowering affect competition for pollinators, flower visitation and seed set in an early spring grassland plant?

Knowledge on how the timing of flowering is related to plant fitness and species interactions is crucial to understand consequences of phenological shifts as they occur under climate change. Early flowering plants may face advantages of low competition for pollinators and disadvantages of low pollinator abundances and unfavourable weather conditions. However, it is unknown how this trade-off changes over the season and how the timing affects reproductive success. On eight grasslands we recorded intra-seasonal changes in pollinators, co-flowering plants, weather conditions, flower visitation rates, floral longevity and seed set of Pulsatilla vulgaris. Although bee abundances and the number of pollinator-suitable hours were low at the beginning of the season, early flowers of P. vulgaris received higher flower visitation rates and estimated total number of bee visits than later flowers, which was positively related to seed set. Flower visitation rates decreased over time and with increasing number of co-flowering plants, which competed with P. vulgaris for pollinators. Low interspecific competition for pollinators seems to be a major driver for early flowering dates. Thus, non-synchronous temporal shifts of co-flowering plants as they may occur under climate warming can be expected to strongly affect plant-pollinator interactions and the fitness of the involved plants.

Understanding Maladaptation by Uniting Ecological and Evolutionary Perspectives

Evolutionary biologists have long trained their sights on adaptation, focusing on the power of natural selection to produce relative fitness advantages while often ignoring changes in absolute fitness. Ecologists generally have taken a different tack, focusing on changes in abundance and ranges that reflect absolute fitness while often ignoring relative fitness. Uniting these perspectives, we articulate various causes of relative and absolute maladaptation and review numerous examples of their occurrence. This review indicates that maladaptation is reasonably common from both perspectives, yet often in contrasting ways. That is, maladaptation can appear strong from a relative fitness perspective, yet populations can be growing in abundance. Conversely, resident individuals can appear locally adapted (relative to nonresident individuals) yet be declining in abundance. Understanding and interpreting these disconnects between relative and absolute maladaptation, as well as the cases of agreement, is increasingly critical in the face of accelerating human-mediated environmental change. We therefore present a framework for studying maladaptation, focusing in particular on the relationship between absolute and relative fitness, thereby drawing together evolutionary and ecological perspectives. The unification of these ecological and evolutionary perspectives has the potential to bring together previously disjunct research areas while addressing key conceptual issues and specific practical problems.

Transgenerational effects benefit offspring across diverse environments: a meta-analysis in plants and animals

The adaptive value of transgenerational effects (the ancestor environmental effects on offspring) in changing environments has received much attention in recent years, but the related empirical evidence remains equivocal. Here, we conducted a meta-analysis summarising 139 experimental studies in plants and animals with 1170 effect sizes to investigate the generality of transgenerational effects across taxa, traits, and environmental contexts. It was found that transgenerational effects generally enhanced offspring performance in response to both stressful and benign conditions. The strongest effects are in annual plants and invertebrates, whereas vertebrates appear to benefit mostly under benign conditions, and perennial plants show hardly any transgenerational responses at all. These differences among taxonomic/life-history groups possibly reflect that vertebrates can avoid stressful conditions through their mobility, and longer-lived plants have alternative strategies. In addition to environmental contexts and taxonomic/life-history groups, transgenerational effects also varied among traits and developmental stages of ancestors and offspring, but the effects were similarly strong across three generations of offspring. By way of a more comprehensive data set and a different effect size, our results differ from those of a recent meta-analysis, suggesting that transgenerational effects are widespread, strong and persistent and can substantially impact the responses of plants and animals to changing environments.

The fitness benefits of genetic variation in circadian clock regulation

Functional circadian clocks are essential for fitness in diverse ecosystems, facilitating detection of predictable light-dark and temperature cycles. The molecular basis of endogenous clocks is variable across the tree of life, but it has one omnipresent attribute: natural genetic diversity that manifests as variation for instance in circadian period length around the hypothesised optimum of 24 hours. Latitudinal variation in photoperiod alone is unlikely to account for the vast diversity documented in varied organisms, but we have yet to achieve a solid understanding of the interplay between clock variability and natural selection. Recent circadian studies sampling populations have drawn attention to the hierarchical structure of genetic diversity in the wild, unveiling pronounced genetic variation even on a scale of metres.

Accelerated flowering time reduces lifetime water use without penalizing reproductive performance in Arabidopsis

Natural selection driven by water availability has resulted in considerable variation for traits associated with drought tolerance and leaf-level water-use efficiency (WUE). In Arabidopsis, little is known about the variation of whole-plant water use (PWU) and whole-plant WUE (transpiration efficiency). To investigate the genetic basis of PWU, we developed a novel proxy trait by combining flowering time and rosette water use to estimate lifetime PWU. We validated its usefulness for large-scale screening of mapping populations in a subset of ecotypes. This parameter subsequently facilitated the screening of water use and drought tolerance traits in a recombinant inbred line population derived from two Arabidopsis accessions with distinct water-use strategies, namely, C24 (low PWU) and Col-0 (high PWU). Subsequent quantitative trait loci mapping and validation through near-isogenic lines identified two causal quantitative trait loci, which showed that a combination of weak and nonfunctional alleles of the FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) genes substantially reduced plant water use due to their control of flowering time. Crucially, we observed that reducing flowering time and consequently water use did not penalize reproductive performance, as such water productivity (seed produced per unit of water transpired) improved. Natural polymorphisms of FRI and FLC have previously been elucidated as key determinants of natural variation in intrinsic WUE (δ13 C). However, in the genetic backgrounds tested here, drought tolerance traits, stomatal conductance, δ13 C. and rosette water use were independent of allelic variation at FRI and FLC, suggesting that flowering is critical in determining lifetime PWU but not always leaf-level traits.

A natural heating experiment: Phenotypic and genotypic responses of plant phenology to geothermal soil warming

Under global warming, the survival of many populations of sedentary organisms in seasonal environments will largely depend on their ability to cope with warming in situ by means of phenotypic plasticity or adaptive evolution. This is particularly true in high-latitude environments, where current growing seasons are short, and expected temperature increases large. In such short-growing season environments, the timing of growth and reproduction is critical to survival. Here, we use the unique setting provided by a natural geothermal soil warming gradient (Hengill geothermal area, Iceland) to study the response of Cerastium fontanum flowering phenology to temperature. We hypothesized that trait expression and phenotypic selection on flowering phenology are related to soil temperature, and tested the hypothesis that temperature-driven differences in selection on phenology have resulted in genetic differentiation using a common garden experiment. In the field, phenology was related to soil temperature, with plants in warmer microsites flowering earlier than plants at colder microsites. In the common garden, plants responded to spring warming in a counter-gradient fashion; plants originating from warmer microsites flowered relatively later than those originating from colder microsites. A likely explanation for this pattern is that plants from colder microsites have been selected to compensate for the shorter growing season by starting development at lower temperatures. However, in our study we did not find evidence of variation in phenotypic selection on phenology in relation to temperature, but selection consistently favoured early flowering. Our results show that soil temperature influences trait expression and suggest the existence of genetically based variation in flowering phenology leading to counter-gradient local adaptation along a gradient of soil temperatures. An important implication of our results is that observed phenotypic responses of phenology to global warming might often be a combination of short-term plastic responses and long-term evolutionary responses, acting in different directions.

Linking genes with ecological strategies in Arabidopsis thaliana

Arabidopsis thaliana is the most prominent model system in plant molecular biology and genetics. Although its ecology was initially neglected, collections of various genotypes revealed a complex population structure, with high levels of genetic diversity and substantial levels of phenotypic variation. This helped identify the genes and gene pathways mediating phenotypic change. Population genetics studies further demonstrated that this variation generally contributes to local adaptation. Here, we review evidence showing that traits affecting plant life history, growth rate, and stress reactions are not only locally adapted, they also often co-vary. Co-variation between these traits indicates that they evolve as trait syndromes, and reveals the ecological diversification that took place within A. thaliana. We argue that examining traits and the gene that control them within the context of global summary schemes that describe major ecological strategies will contribute to resolve important questions in both molecular biology and ecology.