Flower orientation influences floral temperature, pollinator visits and plant fitness.

Effective insect pollination requires appropriate responses to internal and external environmental cues in both the plant and the pollinator. Helianthus annuus, a highly outcrossing species, is marked for its uniform eastward orientation of mature pseudanthia, or capitula. Here we investigate how this orientation affects floral microclimate and the consequent effects on plant and pollinator interactions and reproductive fitness. We artificially manipulated sunflower capitulum orientation and temperature in both field and controlled conditions and assessed flower physiology, pollinator visits, seed traits and siring success. East-facing capitula were found to have earlier style elongation, pollen presentation and pollinator visits compared with capitula manipulated to face west. East-facing capitula also sired more offspring than west-facing capitula and under some conditions produced heavier and better-filled seeds. Local ambient temperature change on the capitulum was found to be a key factor regulating the timing of style elongation, pollen emergence and pollinator visits. These results indicate that eastward capitulum orientation helps to control daily rhythms in floral temperature, with direct consequences on the timing of style elongation and pollen emergence, pollinator visitation, and plant fitness.

Adaptive and nonadaptive causes of heterogeneity in genetic differentiation across the Mimulus guttatus genome.

Genetic diversity becomes structured among populations over time due to genetic drift and divergent selection. Although population structure is often treated as a uniform underlying factor, recent resequencing studies of wild populations have demonstrated that diversity in many regions of the genome may be structured quite dissimilar to the genome-wide pattern. Here, we explored the adaptive and nonadaptive causes of such genomic heterogeneity using population-level, whole genome resequencing data obtained from annual Mimulus guttatus individuals collected across a rugged environment landscape. We found substantial variation in how genetic differentiation is structured both within and between chromosomes, although, in contrast to other studies, known inversion polymorphisms appear to serve only minor roles in this heterogeneity. In addition, much of the genome can be clustered into eight among-population genetic differentiation patterns, but only two of these clusters are particularly consistent with patterns of isolation by distance. By performing genotype-environment association analysis, we also identified genomic intervals where local adaptation to specific climate factors has accentuated genetic differentiation among populations, and candidate genes in these windows indicate climate adaptation may proceed through changes affecting specialized metabolism, drought resistance, and development. Finally, by integrating our findings with previous studies, we show that multiple aspects of plant reproductive biology may be common targets of balancing selection and that variants historically involved in climate adaptation among populations have probably also fuelled rapid adaptation to microgeographic environmental variation within sites.

Population responses to a historic drought across the range of the common monkeyflower (Mimulus guttatus).

PREMISE: Due to climate change, more frequent and intense periodic droughts are predicted to increasingly pose major challenges to the persistence of plant populations. When a severe drought occurs over a broad geographical region, independent responses by individual populations provide replicated natural experiments for examining the evolution of drought resistance and the potential for evolutionary rescue. METHODS: We used a resurrection approach to examine trait evolution in populations of the common monkeyflower, Mimulus guttatus, exposed to a record drought in California from 2011 to 2017. Specifically, we compared variation in traits related to drought escape and avoidance from seeds collected from 37 populations pre- and post-drought in a common garden. In a parallel experiment, we evaluated fitness in two populations, one which thrived and one which was nearly extirpated during the drought, under well-watered and dry-down conditions. RESULTS: We observed substantial variation among populations in trait evolution. In the subset of populations where phenotypes changed significantly, divergence proceeded along trait correlations with some populations flowering rapidly with less vegetative tissue accumulation and others delaying flowering with greater vegetative tissue accumulation. The degree of trait evolution was only weakly correlated with drought intensity but strongly correlated with initial levels of standing variation. Fitness was higher in the post-drought than pre-drought accessions in both treatments for the thriving population, but lower in both treatments for the nearly extirpated population. CONCLUSIONS: Together, our results indicate that evolutionary responses to drought are context dependent and reflect the standing genetic variation and genetic correlations present within populations.

Evolutionary processes from the perspective of flowering time diversity.

Although it is well appreciated that genetic studies of flowering time regulation have led to fundamental advances in the fields of molecular and developmental biology, the ways in which genetic studies of flowering time diversity have enriched the field of evolutionary biology have received less attention despite often being equally profound. Because flowering time is a complex, environmentally responsive trait that has critical impacts on plant fitness, crop yield, and reproductive isolation, research into the genetic architecture and molecular basis of its evolution continues to yield novel insights into our understanding of domestication, adaptation, and speciation. For instance, recent studies of flowering time variation have reconstructed how, when, and where polygenic evolution of phenotypic plasticity proceeded from standing variation and de novo mutations; shown how antagonistic pleiotropy and temporally varying selection maintain polymorphisms in natural populations; and provided important case studies of how assortative mating can evolve and facilitate speciation with gene flow. In addition, functional studies have built detailed regulatory networks for this trait in diverse taxa, leading to new knowledge about how and why developmental pathways are rewired and elaborated through evolutionary time.

Phytochrome interacting factors 4 and 5 regulate axillary branching via bud abscisic acid and stem auxin signalling.

The ratio of red light to far-red light (R:FR) is perceived by phytochrome B (phyB) and informs plants of nearby competition. A low R:FR indicative of competition induces the shade avoidance syndrome and suppresses branching by incompletely understood mechanisms. Phytochrome interacting factors (PIFs) are transcription factors targeted by phytochromes to evoke photomorphogenic responses. PIF4 and PIF5 promote shade avoidance responses and become inactivated by direct interaction with active phyB in the nucleus. Here, genetic and physiological assays show that PIF4 and PIF5 contribute to the suppression of branching resulting from phyB loss of function and a low R:FR, although roles for other PIFs or pathways may exist. The suppression of branching is associated with PIF4/PIF5 promotion of the expression of the branching inhibitor BRANCHED 1 and abscisic acid (ABA) accumulation in axillary buds and is dependent on the function of the key ABA biosynthetic enzyme Nine-cis-epoxycarotenoid dioxygenase 3. However, PIF4/PIF5 function is not confined to a single hormonal pathway, as they also promote stem indole-3-acetic acid accumulation and stimulate systemic auxin signalling, which contribute to the suppression of bud growth when phyB is inactive.

GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity.

Understanding genomic structural variation such as inversions and translocations is a key challenge in evolutionary genetics. We develop a novel statistical approach to comparative genetic mapping to detect large-scale structural mutations from low-level sequencing data. The procedure, called Genome Order Optimization by Genetic Algorithm (GOOGA), couples a Hidden Markov Model with a Genetic Algorithm to analyze data from genetic mapping populations. We demonstrate the method using both simulated data (calibrated from experiments on Drosophila melanogaster) and real data from five distinct crosses within the flowering plant genus Mimulus. Application of GOOGA to the Mimulus data corrects numerous errors (misplaced sequences) in the M. guttatus reference genome and confirms or detects eight large inversions polymorphic within the species complex. Finally, we show how this method can be applied in genomic scans to improve the accuracy and resolution of Quantitative Trait Locus (QTL) mapping.

The Genetic Architecture of Plant Defense Trade-offs in a Common Monkeyflower.

Determining how adaptive combinations of traits arose requires understanding the prevalence and scope of genetic constraints. Frequently observed phenotypic correlations between plant growth, defenses, and/or reproductive timing have led researchers to suggest that pleiotropy or strong genetic linkage between variants affecting independent traits is pervasive. Alternatively, these correlations could arise via independent mutations in different genes for each trait and extensive correlational selection. Here we evaluate these alternatives by conducting a quantitative trait loci (QTL) mapping experiment involving a cross between 2 populations of common monkeyflower (Mimulus guttatus) that differ in growth rate as well as total concentration and arsenal composition of plant defense compounds, phenylpropanoid glycosides (PPGs). We find no evidence that pleiotropy underlies correlations between defense and growth rate. However, there is a strong genetic correlation between levels of total PPGs and flowering time that is largely attributable to a single shared QTL. While this result suggests a role for pleiotropy/close linkage, several other QTLs also contribute to variation in total PPGs. Additionally, divergent PPG arsenals are influenced by a number of smaller-effect QTLs that each underlie variation in 1 or 2 PPGs. This result indicates that chemical defense arsenals can be finely adapted to biotic environments despite sharing a common biochemical precursor. Together, our results show correlations between defense and life-history traits are influenced by pleiotropy or genetic linkage, but genetic constraints may have limited impact on future evolutionary responses, as a substantial proportion of variation in each trait is controlled by independent loci.

Lagging Adaptation to Climate Supersedes Local Adaptation to Herbivory in an Annual Monkeyflower.

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

The genetic architecture of local adaptation and reproductive isolation in sympatry within the Mimulus guttatus species complex.

The genetic architecture of local adaptation has been of central interest to evolutionary biologists since the modern synthesis. In addition to classic theory on the effect size of adaptive mutations by Fisher, Kimura and Orr, recent theory addresses the genetic architecture of local adaptation in the face of ongoing gene flow. This theory predicts that with substantial gene flow between populations local adaptation should proceed primarily through mutations of large effect or tightly linked clusters of smaller effect loci. In this study, we investigate the genetic architecture of divergence in flowering time, mating system-related traits, and leaf shape between Mimulus laciniatus and a sympatric population of its close relative M. guttatus. These three traits are probably involved in M. laciniatus' adaptation to a dry, exposed granite outcrop environment. Flowering time and mating system differences are also reproductive isolating barriers making them 'magic traits'. Phenotypic hybrids in this population provide evidence of recent gene flow. Using next-generation sequencing, we generate dense SNP markers across the genome and map quantitative trait loci (QTLs) involved in flowering time, flower size and leaf shape. We find that interspecific divergence in all three traits is due to few QTL of large effect including a highly pleiotropic QTL on chromosome 8. This QTL region contains the pleiotropic candidate gene TCP4 and is involved in ecologically important phenotypes in other Mimulus species. Our results are consistent with theory, indicating that local adaptation and reproductive isolation with gene flow should be due to few loci with large and pleiotropic effects.

Optimal defense theory explains deviations from latitudinal herbivory defense hypothesis.

The latitudinal herbivory defense hypothesis (LHDH) postulates that the prevalence of species interactions, including herbivory, is greater at lower latitudes, leading to selection for increased levels of plant defense. While latitudinal defense clines may be caused by spatial variation in herbivore pressure, optimal defense theory predicts that clines could also be caused by ecogeographic variation in the cost of defense. For instance, allocation of resources to defense may not increase plant fitness when growing seasons are short and plants must reproduce quickly. Here we use a common garden experiment to survey genetic variation for constitutive and induced phenylpropanoid glycoside (PPG) concentrations across 35 Mimulus guttatus populations over a ~13° latitudinal transect. Our sampling regime is unique among studies of the LHDH in that it allows us to disentangle the effects of growing season length from those of latitude, temperature, and elevation. For five of the seven PPGs surveyed, we find associations between latitude and plant defense that are robust to population structure. However, contrary to the LHDH, only two PPGs were found at higher levels in low latitude populations, and total PPG concentrations were higher at higher latitudes. PPG levels are strongly correlated with growing season length, with higher levels of PPGs in plants from areas with longer growing seasons. Further, flowering time is positively correlated with the concentration of nearly all PPGs, suggesting that there may be a strong trade-off between development time and defense production. Our results reveal that ecogeographic patterns in plant defense may reflect variation in the cost of producing defense compounds in addition to variation in herbivore pressure. Thus, the biogeographic pattern predicted by the LHDH may not be accurate because the underlying factors driving variation in defense, in this case, growing season length, are not always associated with latitude in the same manner. Given these results, we conclude that LHDH cannot be interpreted without considering life history, and we recommend that future work on the LHDH move beyond solely testing the core LHDH prediction and place greater emphasis on isolating agents of selection that generate spatial variation in defense and herbivore pressure.

Replicate altitudinal clines reveal that evolutionary flexibility underlies adaptation to drought stress in annual Mimulus guttatus.

Examining how morphology, life history and physiology vary along environmental clines can reveal functional insight into adaptations to climate and thus inform predictions about evolutionary responses to global change. Widespread species occurring over latitudinal and altitudinal gradients in seasonal water availability are excellent systems for investigating multivariate adaptation to drought stress. Under common garden conditions, we characterized variation in 27 traits for 52 annual populations of Mimulus guttatus sampled from 10 altitudinal transects. We also assessed variation in the critical photoperiod for flowering and surveyed neutral genetic markers to control for demography when analyzing clinal patterns. Many drought escape (e.g. flowering time) and drought avoidance (e.g. specific leaf area, succulence) traits exhibited geographic or climatic clines, which often remained significant after accounting for population structure. Critical photoperiod and flowering time in glasshouse conditions followed distinct clinal patterns, indicating different aspects of seasonal phenology confer adaptation to unique agents of selection. Although escape and avoidance traits were negatively correlated range-wide, populations from sites with short growing seasons produced both early flowering and dehydration avoidance phenotypes. Our results highlight how abundant genetic variation in the component traits that build multivariate adaptations to drought stress provides flexibility for intraspecific adaptation to diverse climates.

The extent and genetic basis of phenotypic divergence in life history traits in Mimulus guttatus.

Differential natural selection acting on populations in contrasting environments often results in adaptive divergence in multivariate phenotypes. Multivariate trait divergence across populations could be caused by selection on pleiotropic alleles or through many independent loci with trait-specific effects. Here, we assess patterns of association between a suite of traits contributing to life history divergence in the common monkey flower, Mimulus guttatus, and examine the genetic architecture underlying these correlations. A common garden survey of 74 populations representing annual and perennial strategies from across the native range revealed strong correlations between vegetative and reproductive traits. To determine whether these multitrait patterns arise from pleiotropic or independent loci, we mapped QTLs using an approach combining high-throughput sequencing with bulk segregant analysis on a cross between populations with divergent life histories. We find extensive pleiotropy for QTLs related to flowering time and stolon production, a key feature of the perennial strategy. Candidate genes related to axillary meristem development colocalize with the QTLs in a manner consistent with either pleiotropic or independent QTL effects. Further, these results are analogous to previous work showing pleiotropy-mediated genetic correlations within a single population of M. guttatus experiencing heterogeneous selection. Our findings of strong multivariate trait associations and pleiotropic QTLs suggest that patterns of genetic variation may determine the trajectory of adaptive divergence.

Leaf shape evolution has a similar genetic architecture in three edaphic specialists within the Mimulus guttatus species complex.

BACKGROUND AND AIMS: The genetic basis of leaf shape has long interested botanists because leaf shape varies extensively across the plant kingdom and this variation is probably adaptive. However, knowledge of the genetic architecture of leaf shape variation in natural populations remains limited. This study examined the genetic architecture of leaf shape diversification among three edaphic specialists in the Mimulus guttatus species complex. Lobed and narrow leaves have evolved from the entire, round leaves of M. guttatus in M. laciniatus, M. nudatus and a polymorphic serpentine M. guttatus population (M2L). METHODS: Bulk segregant analysis and next-generation sequencing were used to map quantitative trait loci (QTLs) that underlie leaf shape in an M. laciniatus × M. guttatus F2 population. To determine whether the same QTLs contribute to leaf shape variation in M. nudatus and M2L, F2s from M. guttatus × M. nudatus and lobed M2L × unlobed M. guttatus crosses were genotyped at QTLs from the bulk segregant analysis. KEY RESULTS: Narrow and lobed leaf shapes in M. laciniatus, M. nudatus and M. guttatus are controlled by overlapping genetic regions. Several promising leaf shape candidate genes were found under each QTL. CONCLUSIONS: The evolution of divergent leaf shape has taken place multiple times in the M. guttatus species complex and is associated with the occupation of dry, rocky environments. The genetic architecture of elongated and lobed leaves is similar across three species in this group. This may indicate that parallel genetic evolution from standing variation or new mutations is responsible for the putatively adaptive leaf shape variation in Mimulus.

Transitions in photoperiodic flowering are common and involve few loci in wild sunflowers (Helianthus; Asteraceae).

UNLABELLED: • PREMISE OF THE STUDY: Evolutionary changes in how flowering time responds to photoperiod cues have been instrumental in expanding the geographic range of agricultural production for many crop species. Locally adaptive natural variation in photoperiod response present in wild relatives of crop plants could be leveraged to further improve the present and future climatic ranges of cultivation or to increase region-specific yields. Previous work has demonstrated ample variability in photoperiod response among wild populations of the common sunflower, Helianthus annuus. Here, we characterize patterns of photoperiod response variation throughout the genus and examine the genetic architecture of intraspecific divergence.• METHODS: The requirement of short day lengths for floral induction was characterized for a phylogenetically dispersed sample of Helianthus species. In addition, flowering time was assessed under short days and long days for a population of F3 individuals derived from crosses between day-neutral and short-day, wild H. annuus parents.• KEY RESULTS: An obligate requirement for short-day induced flowering has evolved repeatedly in Helianthus, and this character was correlated with geographic ranges restricted to the southern United States. Parental flowering times under long days were recovered in high proportion in the F3 generation.• CONCLUSIONS: Together, these findings (1) reveal that substantial variation in the nature of flowering time responses to photoperiod cues has arisen during the evolution of wild sunflowers and (2) suggest these transitions may be largely characterized by simple genetic architectures. Thus, introgression of wild alleles may be a tractable means of genetically tailoring sunflower cultivars for climate-specific production.

Sunflower domestication alleles support single domestication center in eastern North America.

Phylogenetic analyses of genes with demonstrated involvement in evolutionary transitions can be an important means of resolving conflicting hypotheses about evolutionary history or process. In sunflower, two genes have previously been shown to have experienced selective sweeps during its early domestication. In the present study, we identified a third candidate early domestication gene and conducted haplotype analyses of all three genes to address a recent, controversial hypothesis about the origin of cultivated sunflower. Although the scientific consensus had long been that sunflower was domesticated once in eastern North America, the discovery of pre-Columbian sunflower remains at archaeological sites in Mexico led to the proposal of a second domestication center in southern Mexico. Previous molecular studies with neutral markers were consistent with the former hypothesis. However, only two indigenous Mexican cultivars were included in these studies, and their provenance and genetic purity have been questioned. Therefore, we sequenced regions of the three candidate domestication genes containing SNPs diagnostic for domestication from large, newly collected samples of Mexican sunflower landraces and Mexican wild populations from a broad geographic range. The new germplasm also was genotyped for 12 microsatellite loci. Our evidence from multiple evolutionarily important loci and from neutral markers supports a single domestication event for extant cultivated sunflower in eastern North America.

The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements.

Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (Helianthus annuus L.), especially given its large genome size (∼3.5 Gb) and the well-documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain-containing Gypsy LTR retrotransposons ('chromoviruses'), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole.

Interacting duplications, fluctuating selection, and convergence: the complex dynamics of flowering time evolution during sunflower domestication.

Changes in flowering time and its regulation by environmental signals have played crucial roles in the evolutionary origin and spread of many cultivated plants. Recent investigations into the genetics of flowering time evolution in the common sunflower, Helianthus annuus, have provided insight into the historical and mechanistic dynamics of this process. Genetic mapping studies have confirmed phenotypic observations that selection on flowering time fluctuated in direction over sunflower's multistage history of early domestication and modern improvement. The FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1) gene family appears to have been a major contributor in these adaptive shifts. Evolutionary and functional investigations of this family in sunflower provide some of the first empirical evidence that new competitive interactions between recent gene duplications can contribute to evolutionary innovation. Notably, similar results in additional systems that validate this hypothesis are now being discovered. With a sunflower genome sequence now on its way, further research into the evolution of flowering time and its regulation by environmental signals during sunflower domestication is poised to lead to additional, equally important contributions.

Genetic basis and dual adaptive role of floral pigmentation in sunflowers.

Variation in floral displays, both between and within species, has been long known to be shaped by the mutualistic interactions that plants establish with their pollinators. However, increasing evidence suggests that abiotic selection pressures influence floral diversity as well. Here, we analyse the genetic and environmental factors that underlie patterns of floral pigmentation in wild sunflowers. While sunflower inflorescences appear invariably yellow to the human eye, they display extreme diversity for patterns of ultraviolet pigmentation, which are visible to most pollinators. We show that this diversity is largely controlled by cis-regulatory variation affecting a single MYB transcription factor, HaMYB111, through accumulation of ultraviolet (UV)-absorbing flavonol glycosides in ligules (the 'petals' of sunflower inflorescences). Different patterns of ultraviolet pigments in flowers are strongly correlated with pollinator preferences. Furthermore, variation for floral ultraviolet patterns is associated with environmental variables, especially relative humidity, across populations of wild sunflowers. Ligules with larger ultraviolet patterns, which are found in drier environments, show increased resistance to desiccation, suggesting a role in reducing water loss. The dual role of floral UV patterns in pollinator attraction and abiotic response reveals the complex adaptive balance underlying the evolution of floral traits.

Flowers are an important part of how many plants reproduce. Their distinctive colours, shapes and patterns attract specific pollinators, but they can also help to protect the plant from predators and environmental stresses. Many flowers contain pigments that absorb ultraviolet (UV) light to display distinct UV patterns ­ although invisible to the human eye, most pollinators are able to see them. For example, when seen in UV, sunflowers feature a 'bullseye' with a dark centre surrounded by a reflective outer ring. The sizes and thicknesses of these rings vary a lot within and between flower species, and so far, it has been unclear what causes this variation and how it affects the plants. To find out more, Todesco et al. studied the UV patterns in various wild sunflowers across North America by considering the ecology and molecular biology of different plants. This revealed great variation between the UV patterns of the different sunflower populations. Moreover, Todesco et al. found that a gene called HaMYB111 is responsible for the diverse UV patterns in the sunflowers. This gene controls how plants make chemicals called flavonols that absorb UV light. Flavonols also help to protect plants from damage caused by droughts and extreme temperatures. Todesco et al. showed that plants with larger bullseyes had more flavonols, attracted more pollinators, and were better at conserving water. Accordingly, these plants were found in drier locations. This study suggests that, at least in sunflowers, UV patterns help both to attract pollinators and to control water loss. These insights could help to improve pollination ­ and consequently yield ­ in cultivated plants, and to develop plants with better resistance to extreme weather. This work also highlights the importance of combining biology on small and large scales to understand complex processes, such as adaptation and evolution.