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.

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.

Who are we now? A demographic assessment of three evolution societies

Scientific societies have the potential to catalyze support for communities that have been historically excluded from science. Many of these societies have formed committees to propose and administer initiatives to promote the career and well-being of their members, with a special emphasis on racial and ethnic minorities. Yet, these societies are rarely armed with data to inform their proposals. Three of the evolution societies (American Society of Naturalists, "ASN"; Society of Systematic Biologists, "SSB"; Society for the Study of Evolution, "SSE") have also formed Diversity, Equity, and Inclusion committees in the last few years. As a first step in determining the needs of the societies, these committees collected data on the demographic characteristics of the societies' constituents by surveying the attendants of the Evolution 2019 meeting. Here, we report the proportions for different demographic groups in attendance at the meeting and compare these proportions to the demographics of recipients of Ph.D. degrees either in evolutionary biology or in the broader life sciences, as well as population demographics of the USA. Our results indicate that historically excluded groups are still underrepresented across US-based evolutionary biology professional societies. We explore whether demographic composition differs at different professional stages and find that representation for women and LGBTQ+ members decreases as the career stage progresses. We also find some evidence for heterogeneity across societies in terms of racial composition. Finally, we discuss the caveats and limitations of our procedures. Our results will serve to inform future efforts to collect demographic data at the society levels, which should in turn be used to design and implement evidence-based initiatives for inclusion and equity. This report should be a starting point for systematic efforts to characterize the ever-changing representation in evolutionary biology and to work toward the inclusion of all groups.

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.

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.

Two MYB Proteins in a Self-Organizing Activator-Inhibitor System Produce Spotted Pigmentation Patterns

Many organisms exhibit visually striking spotted or striped pigmentation patterns. Developmental models predict that such spatial patterns can form when a local autocatalytic feedback loop and a long-range inhibitory feedback loop interact. At its simplest, this self-organizing network only requires one self-activating activator that also activates a repressor, which inhibits the activator and diffuses to neighboring cells. However, the molecular activators and inhibitors fully fitting this versatile model remain elusive in pigmentation systems. Here, we characterize an R2R3-MYB activator and an R3-MYB repressor in monkeyflowers (Mimulus). Through experimental perturbation and mathematical modeling, we demonstrate that the properties of these two proteins correspond to an activator-inhibitor pair in a two-component, reaction-diffusion system, explaining the formation of dispersed anthocyanin spots in monkeyflower petals. Notably, disrupting this pattern impacts pollinator visitation. Thus, subtle changes in simple activator-inhibitor systems are likely essential contributors to the evolution of the remarkable diversity of pigmentation patterns in flowers.

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.

Plant Domestication: Wild Date Palms Illuminate a Crop's Sticky Origins

In a new study, previously unknown populations of wild date palm have been identified in remote areas of Oman. Genomic analyses indicate date palm domestication occurred in the eastern portion of the Arabian Peninsula and reveal substantial subsequent gene flow with African palm populations.

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.

Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement

Here, we report a comprehensive paleogenomic study of archaeological and ethnographic sunflower remains that provides significant new insights into the process of domestication of this important crop. DNA from both ancient and historic contexts yielded high proportions of endogenous DNA, and although archaeological DNA was found to be highly degraded, it still provided sufficient coverage to analyze genetic changes over time. Shotgun sequencing data from specimens from the Eden's Bluff archaeological site in Arkansas yielded organellar DNA sequence from specimens up to 3,100 years old. Their sequences match those of modern cultivated sunflowers and are consistent with an early domestication bottleneck in this species. Our findings also suggest that recent breeding of sunflowers has led to a loss of genetic diversity that was present only a century ago in Native American landraces. These breeding episodes also left a profound signature on the mitochondrial and plastid haplotypes in cultivars, as two types were intentionally introduced from other Helianthus species for crop improvement. These findings gained from ancient and historic sunflower specimens underscore how future in-depth gene-based analyses can advance our understanding of the pace and targets of selection during the domestication of sunflower and other crop species.

Competition drives trait evolution and character displacement between Mimulus species along an environmental gradient

Closely related species may evolve to coexist stably in sympatry through niche differentiation driven by in situ competition, a process termed character displacement. Alternatively, past evolution in allopatry may have already sufficiently reduced niche overlap to permit establishment in sympatry, a process called ecological sorting. The relative importance of each process to niche differentiation is contentious even though they are not mutually exclusive and are both mediated via multivariate trait evolution. We explore how competition has impacted niche differentiation in two monkeyflowers, Mimulus alsinoides and M. guttatus, which often co-occur. Through field observations, common gardens, and competition experiments, we demonstrate that M. alsinoides is restricted to marginal habitats in sympatry and that the impacts of character displacement on niche differentiation are complex. Competition with M. guttatus alters selection gradients and has favored taller M. alsinoides with earlier seasonal flowering at low elevation and floral shape divergence at high elevation. However, no trait exhibits the pattern typically associated with character displacement, higher divergence between species in sympatry than allopatry. Thus, although character displacement was unlikely the process driving initial divergence along niche axes necessary for coexistence, we conclude that competition in sympatry has likely driven trait evolution along additional niche axes.

Changing Responses to Changing Seasons: Natural Variation in the Plasticity of Flowering Time

The mechanisms by which the environment regulates flowering time have evolved as crops and wild populations have adapted to diverse climates, and the specific variants involved are increasingly known.

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.

Circadian regulation of sunflower heliotropism, floral orientation, and pollinator visits

Young sunflower plants track the Sun from east to west during the day and then reorient during the night to face east in anticipation of dawn. In contrast, mature plants cease movement with their flower heads facing east. We show that circadian regulation of directional growth pathways accounts for both phenomena and leads to increased vegetative biomass and enhanced pollinator visits to flowers. Solar tracking movements are driven by antiphasic patterns of elongation on the east and west sides of the stem. Genes implicated in control of phototropic growth, but not clock genes, are differentially expressed on the opposite sides of solar tracking stems. Thus, interactions between environmental response pathways and the internal circadian oscillator coordinate physiological processes with predictable changes in the environment to influence growth and reproduction.

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.

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.

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

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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.

Turning heads: the biology of solar tracking in sunflower

Solar tracking in the common sunflower, Helianthus annuus, is a dramatic example of a diurnal rhythm in plants. During the day, the shoot apex continuously reorients, following the sun's relative position so that the developing heads track from east to west. At night, the reverse happens, and the heads return and face east in anticipation of dawn. This daily cycle dampens and eventually stops at anthesis, after which the sunflower head maintains an easterly orientation. Although shoot apical heliotropism has long been the subject of physiological studies in sunflower, the underlying developmental, cellular, and molecular mechanisms that drive the directional growth and curvature of the stem in response to extrinsic and perhaps intrinsic cues are not known. Furthermore, the ecological functions of solar tracking and the easterly orientation of mature heads have been the subject of significant but unresolved speculation. In this review, we discuss the current state of knowledge about this complex, dynamic trait. Candidate mechanisms that may contribute to daytime and nighttime movement are highlighted, including light signaling, hormonal action, and circadian regulation of growth pathways. The merits of the diverse hypotheses advanced to explain the adaptive significance of heliotropism in sunflower are also considered.

The timing of molecular and morphological changes underlying reproductive transitions in wild tomatoes (Solanum sect. Lycopersicon)

Molecular mechanisms underlying the transition from genetic self-incompatibility to self-compatibility are well documented, but the evolution of other reproductive trait changes that accompany shifts in reproductive strategy (mating system) remains comparatively under-investigated. A notable exception is the transition from exserted styles to styles with recessed positions relative to the anthers in wild tomatoes (Solanum Section Lycopersicon). This phenotypic change has been previously attributed to a specific mutation in the promoter of a gene that influences style length (style2.1); however, whether this specific regulatory mutation arose concurrently with the transition from long to short styles, and whether it is causally responsible for this phenotypic transition, has been poorly investigated across this group. To address this gap, we assessed 74 accessions (populations) from 13 species for quantitative genetic variation in floral and reproductive traits as well as the presence/absence of deletions at two different locations (StyleD1 and StyleD2) within the regulatory region upstream of style2.1. We confirmed that the putatively causal deletion variant (a 450-bp deletion at StyleD1) arose within self-compatible lineages. However, the variation and history of both StyleD1 and StyleD2 was more complex than previously inferred. In particular, although StyleD1 was statistically associated with differences in style length and stigma exsertion across all species, we found no evidence for this association within two species polymorphic for the StyleD1 mutation. We conclude that the previous association detected between phenotypic and molecular differences is most likely due to a phylogenetic association rather than a causal mechanistic relationship. Phenotypic variation in style length must therefore be due to other unexamined linked variants in the style2.1 regulatory region.

Modular skeletal evolution in sticklebacks is controlled by additive and clustered quantitative trait Loci

Understanding the genetic architecture of evolutionary change remains a long-standing goal in biology. In vertebrates, skeletal evolution has contributed greatly to adaptation in body form and function in response to changing ecological variables like diet and predation. Here we use genome-wide linkage mapping in threespine stickleback fish to investigate the genetic architecture of evolved changes in many armor and trophic traits. We identify >100 quantitative trait loci (QTL) controlling the pattern of serially repeating skeletal elements, including gill rakers, teeth, branchial bones, jaws, median fin spines, and vertebrae. We use this large collection of QTL to address long-standing questions about the anatomical specificity, genetic dominance, and genomic clustering of loci controlling skeletal differences in evolving populations. We find that most QTL (76%) that influence serially repeating skeletal elements have anatomically regional effects. In addition, most QTL (71%) have at least partially additive effects, regardless of whether the QTL controls evolved loss or gain of skeletal elements. Finally, many QTL with high LOD scores cluster on chromosomes 4, 20, and 21. These results identify a modular system that can control highly specific aspects of skeletal form. Because of the general additivity and genomic clustering of major QTL, concerted changes in both protective armor and trophic traits may occur when sticklebacks inherit either marine or freshwater alleles at linked or possible "supergene" regions of the stickleback genome. Further study of these regions will help identify the molecular basis of both modular and coordinated changes in the vertebrate skeleton.

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.

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.

Connecting the sun to flowering in sunflower adaptation

Species living in seasonal environments often adaptively time their reproduction in response to photoperiod cues. We characterized the expression of genes in the flowering-time regulatory network across wild populations of the common sunflower, Helianthus annuus, that we found to be adaptively differentiated for photoperiod response. The observed clinal variation was associated with changes at multiple hierarchical levels in multiple pathways. Paralogue-specific changes in FT homologue expression and tissue-specific changes in SOC1 homologue expression were associated with loss and reversal of plasticity, respectively, suggesting that redundancy and modularity are gene network characteristics easily exploited by natural selection to produce evolutionary innovation. Distinct genetic mechanisms contribute to convergent evolution of photoperiod responses within sunflower, suggesting regulatory network architecture does not impose strong constraints on the evolution of phenotypic plasticity.

Speciation genes in plants

BACKGROUND

Analyses of speciation genes--genes that contribute to the cessation of gene flow between populations--can offer clues regarding the ecological settings, evolutionary forces and molecular mechanisms that drive the divergence of populations and species. This review discusses the identities and attributes of genes that contribute to reproductive isolation (RI) in plants, compares them with animal speciation genes and investigates what these genes can tell us about speciation.

SCOPE

Forty-one candidate speciation genes were identified in the plant literature. Of these, seven contributed to pre-pollination RI, one to post-pollination, prezygotic RI, eight to hybrid inviability, and 25 to hybrid sterility. Genes, gene families and genetic pathways that were frequently found to underlie the evolution of RI in different plant groups include the anthocyanin pathway and its regulators (pollinator isolation), S RNase-SI genes (unilateral incompatibility), disease resistance genes (hybrid necrosis), chimeric mitochondrial genes (cytoplasmic male sterility), and pentatricopeptide repeat family genes (cytoplasmic male sterility).

CONCLUSIONS

The most surprising conclusion from this review is that identities of genes underlying both prezygotic and postzygotic RI are often predictable in a broad sense from the phenotype of the reproductive barrier. Regulatory changes (both cis and trans) dominate the evolution of pre-pollination RI in plants, whereas a mix of regulatory mutations and changes in protein-coding genes underlie intrinsic postzygotic barriers. Also, loss-of-function mutations and copy number variation frequently contribute to RI. Although direct evidence of positive selection on speciation genes is surprisingly scarce in plants, analyses of gene family evolution, along with theoretical considerations, imply an important role for diversifying selection and genetic conflict in the evolution of RI. Unlike in animals, however, most candidate speciation genes in plants exhibit intraspecific polymorphism, consistent with an important role for stochastic forces and/or balancing selection in development of RI in plants.

Connecting genetic variation to phenotypic clines

From early allozyme work to recent genome-wide scans, many studies have reported associations between molecular markers and latitude. These geographic patterns are tantalizing because they hint at the possibility of identifying specific mutations responsible for climatic adaptation. Unfortunately, few studies have done so because these exciting first glances often prove extremely challenging to follow up. Many difficulties can hinder connecting genetic and phenotypic variation in this context, and without such links, distinguishing the action of spatially varying selection from the other evolutionary processes capable of generating these patterns can be quite thorny. Nevertheless, two papers in this issue report excellent progress in overcoming these obstacles and provide persuasive evidence supporting the involvement of specific natural variants in clinal adaptation of Drosophila melanogaster populations (Fig. 1). In the first paper, Paaby et al. (2010) describe replicated allele frequency clines for a coding polymorphism in the Insulin-like Receptor (InR) gene on two continents, findings that strongly point to selection acting at this locus and that likely reflect life history adaptation. McKechnie et al. (2010) report compelling functional evidence that cis-regulatory variation in the Dca (drosophila cold acclimation) gene contributes to an adaptive cline in wing size. Notably, these papers employ largely alternative and complementary approaches, and together they exemplify how diverse strategies may be interwoven to draw convincing connections between genotype, phenotype, and evolutionary process.

The role of recently derived FT paralogs in sunflower domestication

Gene duplication provides an important source of genetic raw material for phenotypic diversification, but few studies have detailed the mechanisms through which duplications produce evolutionary novelty within species. Here, we investigate how a set of recently duplicated homologs of the floral inducer FLOWERING LOCUS T (FT) has contributed to sunflower domestication. We find that changes in expression of these duplicates are associated with differences in flowering behavior between wild and domesticated sunflower. In addition, we present genetic and functional evidence demonstrating that a frameshift mutation in one paralog, Helianthus annuus FT 1 (HaFT1), underlies a major QTL for flowering time and experienced a selective sweep during early domestication. Notably, this dominant-negative allele delays flowering through interference with action of another paralog, HaFT4. Together, these data reveal that changes affecting the expression, sequence, and gene interactions of HaFT paralogs have played key roles during sunflower domestication. Our findings also illustrate the important role that evolving interactions between new gene family members may play in fostering phenotypic change.

Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks

Hindlimb loss has evolved repeatedly in many different animals by means of molecular mechanisms that are still unknown. To determine the number and type of genetic changes underlying pelvic reduction in natural populations, we carried out genetic crosses between threespine stickleback fish with complete or missing pelvic structures. Genome-wide linkage mapping shows that pelvic reduction is controlled by one major and four minor chromosome regions. Pitx1 maps to the major chromosome region controlling most of the variation in pelvic size. Pelvic-reduced fish show the same left-right asymmetry seen in Pitx1 knockout mice, but do not show changes in Pitx1 protein sequence. Instead, pelvic-reduced sticklebacks show site-specific regulatory changes in Pitx1 expression, with reduced or absent expression in pelvic and caudal fin precursors. Regulatory mutations in major developmental control genes may provide a mechanism for generating rapid skeletal changes in natural populations, while preserving the essential roles of these genes in other processes.

Evidence for ecology's role in speciation

A principal challenge in testing the role of natural selection in speciation is to connect the build-up of reproductive isolation between populations to divergence of ecologically important traits. Demonstrations of 'parallel speciation', or assortative mating by selective environment, link ecology and isolation, but the phenotypic traits mediating isolation have not been confirmed. Here we show that the parallel build-up of mating incompatibilities between stickleback populations can be largely accounted for by assortative mating based on one trait, body size, which evolves predictably according to environment. In addition to documenting the influence of body size on reproductive isolation for stickleback populations spread across the Northern Hemisphere, we have confirmed its importance through a new experimental manipulation. Together, these results suggest that speciation may arise largely as a by-product of ecological differences and divergent selection on a small number of phenotypic traits.

The genetic architecture of parallel armor plate reduction in threespine sticklebacks

How many genetic changes control the evolution of new traits in natural populations? Are the same genetic changes seen in cases of parallel evolution? Despite long-standing interest in these questions, they have been difficult to address, particularly in vertebrates. We have analyzed the genetic basis of natural variation in three different aspects of the skeletal armor of threespine sticklebacks (Gasterosteus aculeatus): the pattern, number, and size of the bony lateral plates. A few chromosomal regions can account for variation in all three aspects of the lateral plates, with one major locus contributing to most of the variation in lateral plate pattern and number. Genetic mapping and allelic complementation experiments show that the same major locus is responsible for the parallel evolution of armor plate reduction in two widely separated populations. These results suggest that a small number of genetic changes can produce major skeletal alterations in natural populations and that the same major locus is used repeatedly when similar traits evolve in different locations.

In stickleback populations separated over 10,000 years ago, dramatic morphological evolution appears to result from a relatively small number of genetic changes