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

Variation in leaf carbon economics, energy balance, and heat tolerance traits highlights differing timescales of adaptation and acclimation

Multivariate leaf trait correlations are hypothesized to originate from natural selection on carbon economics traits that control lifetime leaf carbon gain, and energy balance traits governing leaf temperatures, physiological rates, and heat injury. However, it is unclear whether macroevolution of leaf traits primarily reflects selection for lifetime carbon gain or energy balance, and whether photosynthetic heat tolerance is coordinated along these axes. To evaluate these hypotheses, we measured carbon economics, energy balance, and photosynthetic heat tolerance traits for 177 species (157 families) in a common garden that minimizes co-variation of taxa and climate. We observed wide variation in carbon economics, energy balance, and heat tolerance traits. Carbon economics and energy balance (but not heat tolerance) traits were phylogenetically structured, suggesting macroevolution of leaf mass per area and leaf dry matter content reflects selection on carbon gain rather than energy balance. Carbon economics and energy balance traits varied along a common axis orthogonal to heat tolerance traits. Our results highlight a fundamental mismatch in the timescales over which morphological and heat tolerance traits respond to environmental variation. Whereas carbon economics and energy balance traits are constrained by species' evolutionary histories, photosynthetic heat tolerance traits are not and can acclimate readily to leaf microclimates.

High-performing plastic clones best explain the spread of yellow monkeyflower from lowland to higher elevation areas in New Zealand

The relative contribution of adaptation and phenotypic plasticity can vary between core and edge populations, with implications for invasive success. We investigated the spread of the invasive yellow monkeyflower, Erythranthe gutatta in New Zealand, where it is spreading from lowland agricultural land into high-elevation conservation areas. We investigated the extent of phenotypic variation among clones from across the South Island, looked for adaptation and compared degrees of plasticity among lowland core versus montane range-edge populations. We grew 34 clones and measured their vegetative and floral traits in two common gardens, one in the core range at 9 m a.s.l. and one near the range-edge at 560 m a.s.l. Observed trait variation was explained by a combination of genotypic diversity (as identified through common gardens) and high phenotypic plasticity. We found a subtle signature of local adaptation to lowland habitats but all clones were plastic and able to survive and reproduce in both gardens. In the range-edge garden, above-ground biomass was on average almost double and stolon length almost half that of the same clone in the core garden. Clones from low-elevation sites showed higher plasticity on average than those from higher elevation sites. The highest performing clones in the core garden were also top performers in the range-edge garden. These results suggest some highly fit general-purpose genotypes, possibly pre-adapted to New Zealand montane conditions, best explains the spread of E. gutatta from lowland to higher elevation areas.

Demographic consequences of an extreme heat wave are mitigated by spatial heterogeneity in an annual monkeyflower

Heat waves are becoming more frequent and intense with climate change, but the demographic and evolutionary consequences of heat waves are rarely investigated in herbaceous plant species. We examine the consequences of a short but extreme heat wave in Oregon populations of the common yellow monkeyflower (Mimulus guttatus) by leveraging a common garden experiment planted with range-wide populations and observational studies of 11 local populations. In the common garden, 89% of seedlings died during the heat wave including >96% of seedlings from geographically local populations. Some populations from hotter and drier environments had higher fitness, however, others from comparable environments performed poorly. Observational studies of local natural populations drastically differed in the consequences of the heat wave-one population was completely extirpated and nearly half had a >50% decrease in fitness. However, a few populations had greater fitness during the heat wave year. Differences in mortality corresponded to the impact of the heat wave on soil moisture-retention of soil moisture throughout the heat wave led to greater survivorship. Our results suggest that not all populations experience the same intensity or degree of mortality during extreme events and such heterogeneity could be important for genetic rescue or to facilitate the distribution of adaptive variants throughout the region.

Facultative Annual Life Cycles in Seagrasses

Plant species usually have either annual or perennial life cycles, but facultative annual species have annual or perennial populations depending on their environment. In terrestrial angiosperms, facultative annual species are rare, with wild rice being one of the few examples. Our review shows that in marine angiosperms (seagrasses) facultative annual species are more common: six (of 63) seagrass species are facultative annual. It concerns Zostera marina, Z. japonica, Halophila decipiens, H. beccarii, Ruppia maritima, and R. spiralis. The annual populations generally produce five times more seeds than their conspecific perennial populations. Facultative annual seagrass species occur worldwide. Populations of seagrasses are commonly perennial, but the facultative annual species had annual populations when exposed to desiccation, anoxia-related factors, shading, or heat stress. A system-wide 'experiment' (closure of two out of three connected estuaries for large-scale coastal protection works) showed that the initial annual Z. marina population could shift to a perennial life cycle within 5 years, depending on environmental circumstances. We discuss potential mechanisms and implications for plant culture. Further exploration of flexible life histories in plant species, and seagrasses in particular, may aid in answering questions about trade-offs between vegetative and sexual reproduction, and preprogrammed senescence.

Convergent evolution of the annual life history syndrome from perennial ancestors

Despite most angiosperms being perennial, once-flowering annuals have evolved multiple times independently, making life history traits among the most labile trait syndromes in flowering plants. Much research has focused on discerning the adaptive forces driving the evolution of annual species, and in pinpointing traits that distinguish them from perennials. By contrast, little is known about how 'annual traits' evolve, and whether the same traits and genes have evolved in parallel to affect independent origins of the annual syndrome. Here, we review what is known about the distribution of annuals in both phylogenetic and environmental space and assess the evidence for parallel evolution of annuality through similar physiological, developmental, and/or genetic mechanisms. We then use temperate grasses as a case study for modeling the evolution of annuality and suggest future directions for understanding annual-perennial transitions in other groups of plants. Understanding how convergent life history traits evolve can help predict species responses to climate change and allows transfer of knowledge between model and agriculturally important species.

Taking quantitative genomics into the wild

We organized this special issue to highlight new work and review recent advances at the cutting edge of 'wild quantitative genomics'. In this editorial, we will present some history of wild quantitative genetic and genomic studies, before discussing the main themes in the papers published in this special issue and highlighting the future outlook of this dynamic field.

Population genomic consequences of life-history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers

Local selection can promote phenotypic divergence despite gene flow across habitat mosaics, but adaptation itself may generate substantial barriers to genetic exchange. In plants, life-history, phenology, and mating system divergence have been proposed to promote genetic differentiation in sympatry. In this study, we investigate phenotypic and genetic variation in Mimulus guttatus (yellow monkeyflowers) across a geothermal soil mosaic in Yellowstone National Park (YNP). Plants from thermal annual and nonthermal perennial habitats were heritably differentiated for life-history and mating system traits, consistent with local adaptation to the ephemeral thermal-soil growing season. However, genome-wide genetic variation primarily clustered plants by geographic region, with little variation sorting by habitat. The one exception was an extreme thermal population also isolated by a 200 m geographical gap of no intermediate habitat. Individual inbreeding coefficients (F_IS ) were higher (and predicted by trait variation) in annual plants and annual pairs showed greater isolation by distance at local (<1 km) scales. Finally, YNP adaptation does not reuse a widespread inversion that underlies M. guttatus life-history ecotypes range-wide, suggesting a novel genetic mechanism. Overall, this work suggests that life-history and mating system adaptation strong enough to shape individual mating patterns does not necessarily generate incipient speciation without geographical barriers.

Evidence linking life-form to a major shift in diversification rate in Crassula

PREMISE

Plants have evolved different ecological strategies in response to environmental challenges, and a higher lability of such strategies is more common in plant groups that adapt to various niches. Crassula (Crassulaceae), occurring in varied mesic to xeric habitats, exhibits a remarkable diversity of life-forms. However, whether any particular life-form trait has shaped species diversification in Crassula has remained unexplored. This study aims to investigate diversification patterns within Crassula and identify potential links to its life-form evolution.

METHODS

A phylogenetic tree of 140 Crassula taxa was reconstructed using plastid and nuclear loci and dated based on the nuclear DNA information only. We reconstructed ancestral life-form characters to estimate the evolutionary trends of ecophysiological change, and subsequently estimated net diversification rates. Multiple diversification models were applied to examine the association between certain life-forms and net diversification rates.

RESULTS

Our findings confirm a radiation within Crassula in the last 10 million years. A configuration of net diversification rate shifts was detected, which coincides with the emergence of a speciose lineage during the late Miocene. The results of ancestral state reconstruction demonstrate a high lability of life-forms in Crassula, and the trait-dependent diversification analyses revealed that the increased diversification is strongly associated with a compact growth form.

CONCLUSIONS

Transitions between life-forms in Crassula seem to have driven adaptation and shaped diversification of this genus across various habitats. The diversification patterns we inferred are similar to those observed in other major succulent lineages, with the most-speciose clades originating in the late Miocene.

Chromosomal fusions facilitate adaptation to divergent environments in threespine stickleback

Chromosomal fusions are hypothesized to facilitate adaptation to divergent environments, both by bringing together previously unlinked adaptive alleles and by creating regions of low recombination that facilitate the linkage of adaptive alleles; but, there is little empirical evidence to support this hypothesis. Here, we address this knowledge gap by studying threespine stickleback (Gasterosteus aculeatus), in which ancestral marine fish have repeatedly adapted to freshwater across the northern hemisphere. By comparing the threespine and ninespine stickleback (Pungitius pungitius) genomes to a de novo assembly of the fourspine stickleback (Apeltes quadracus) and an outgroup species, we find two chromosomal fusion events involving the same chromosomes have occurred independently in the threespine and ninespine stickleback lineages. On the fused chromosomes in threespine stickleback, we find an enrichment of quantitative trait loci underlying traits that contribute to marine versus freshwater adaptation. By comparing whole-genome sequences of freshwater and marine threespine stickleback populations, we also find an enrichment of regions under divergent selection on these two fused chromosomes. There is elevated genetic diversity within regions under selection in the freshwater population, consistent with a simulation study showing that gene flow can increase diversity in genomic regions associated with local adaptation and our demographic models showing gene flow between the marine and freshwater populations. Integrating our results with previous studies, we propose that these fusions created regions of low recombination that enabled the formation of adaptative clusters, thereby facilitating freshwater adaptation in the face of recurrent gene flow between marine and freshwater threespine sticklebacks.

The role of genus and life span in predicting seed and vegetative trait variation and correlation in Lathyrus, Phaseolus, and Vicia

PREMISE

Annual and perennial life history transitions are abundant among angiosperms, and understanding the phenotypic variation underlying life span shifts is a key endeavor of plant evolutionary biology. Comparative analyses of trait variation and correlation networks among annual and perennial plants is increasingly important as new herbaceous perennial crops are being developed for edible seed. However, it remains unclear how seed to vegetative growth trait relationships correlate with life span.

METHODS

To assess the relative roles of genus and life span in predicting phenotypic variation and trait correlations, we measured seed size and shape, germination proportion, and early-life-stage plant height and leaf growth over 3 mo in 29 annual and perennial, herbaceous congeneric species from three legume genera (Lathyrus, Phaseolus, and Vicia).

RESULTS

Genus was the strongest predictor of seed size and shape variation, and life span consistently predicted plant height and leaf number at single time points. Correlation networks revealed that annual species had significant associations between seed traits and vegetative traits, whereas perennials had no significant seed-vegetative associations. Each genus also differed in the extent of integration between seed and vegetative traits, as well as within-vegetative-trait correlation patterns.

CONCLUSIONS

Genus and life span were important for predicting aspects of early-life-stage phenotypic variation and trait relationships. Differences in phenotypic correlation may indicate that selection on seed size traits will impact vegetative growth differently depending on life span, which has important implications for nascent perennial breeding programs.

Genomic signatures of parallel alpine adaptation in recently evolved flightless insects

Natural selection along elevational gradients has potential to drive predictable adaptations across distinct lineages, but the extent of such repeated evolution remains poorly studied for many widespread alpine taxa. We present parallel genomic analyses of two recently evolved flightless alpine insect lineages to test for molecular signatures of repeated alpine adaptation. Specifically, we compare low-elevation vs. alpine stonefly ecotypes from parallel stream populations in which flightless upland ecotypes have been independently derived. We map 67,922 polymorphic genetic markers, generated across 176 Zelandoperla fenestrata specimens from two independent alpine stream populations in New Zealand's Rock and Pillar Range, to a newly developed plecopteran reference genome. Genome-wide scans revealed 31 regions with outlier single nucleotide polymorphisms (SNPs) differentiating lowland vs. alpine ecotypes in Lug Creek, and 37 regions with outliers differentiating ecotypes in Six Mile Creek. Of these regions, 13% (8/60) yielded outlier SNPs across both within-stream ecotype comparisons, implying comparable genomic shifts contribute to this repeated alpine adaptation. Candidate genes closely linked to repeated outlier regions include several with documented roles in insect wing-development (e.g., dishevelled), suggesting that they may contribute to repeated alpine wing reduction. Additional candidate genes have been shown to influence insect fecundity (e.g., ovo) and lifespan (e.g., Mrp4), implying that they might contribute to life history differentiation between upland and lowland ecotypes. Additional outlier genes have potential roles in the evolution of reproductive isolation among ecotypes (hedgehog and Desaturase 1). These results demonstrate how replicated outlier tests across independent lineages can potentially contribute to the discovery of genes underpinning repeated adaptation.

Variation in seasonal timing traits and life history along a latitudinal transect in Mimulus ringens

Seasonal timing traits are commonly under recurrent, spatially variable selection, and are therefore predicted to exhibit clinal variation. Temperate perennial plants often require vernalization to prompt growth and reproduction; however, little is known about whether vernalization requirements change across the range of a broadly distributed species. We performed a critical vernalization duration study in Mimulus ringens, coupled with population genomic analysis. Plants from eight populations spanning the latitudinal range were exposed to varying durations of 4°C vernalization between 0 and 56 days, and flowering response was assessed. RADSeq was also performed to generate 1179 polymorphic SNPs, which were used to examine population structure. We found unexpected life history variation, with some populations lacking vernalization requirement. Population genomic analyses show that these life history variants are highly divergent from perennials, potentially revealing a cryptic species. For perennial populations, minimum vernalization time was surprisingly consistent. However, once vernalized, northern populations flowered almost 3 weeks faster than southern. Furthermore, southern populations exhibited sensitivity to vernalization times beyond flowering competency, suggesting an ability to respond adaptively to different lengths of winter. Mimulus ringens, therefore, reveals evidence of clinal variation, and provides opportunities for future studies addressing mechanistic and ecological hypotheses both within and between incipient species.

Genetic trade-offs underlie divergent life history strategies for local adaptation in white clover

Local adaptation is common in plants, yet characterization of its underlying genetic basis is rare in herbaceous perennials. Moreover, while many plant species exhibit intraspecific chemical defence polymorphisms, their importance for local adaptation remains poorly understood. We examined the genetic architecture of local adaptation in a perennial, obligately-outcrossing herbaceous legume, white clover (Trifolium repens). This widespread species displays a well-studied chemical defence polymorphism for cyanogenesis (HCN release following tissue damage) and has evolved climate-associated cyanogenesis clines throughout its range. Two biparental F₂  mapping populations, derived from three parents collected in environments spanning the U.S. latitudinal species range (Duluth, MN, St. Louis, MO and Gainesville, FL), were grown in triplicate for two years in reciprocal common garden experiments in the parental environments (6,012 total plants). Vegetative growth and reproductive fitness traits displayed trade-offs across reciprocal environments, indicating local adaptation. Genetic mapping of fitness traits revealed a genetic architecture characterized by allelic trade-offs between environments, with 100% and 80% of fitness QTL in the two mapping populations showing significant QTL×E interactions, consistent with antagonistic pleiotropy. Across the genome there were three hotspots of QTL colocalization. Unexpectedly, we found little evidence that the cyanogenesis polymorphism contributes to local adaptation. Instead, divergent life history strategies in reciprocal environments were major fitness determinants: selection favoured early investment in flowering at the cost of multiyear survival in the southernmost site versus delayed flowering and multiyear persistence in the northern environments. Our findings demonstrate that multilocus genetic trade-offs contribute to contrasting life history characteristics that allow for local adaptation in this outcrossing herbaceous perennial.

Ecological Interactions, Environmental Gradients, and Gene Flow in Local Adaptation

Despite long-standing interest in local adaptation of plants to their biotic and abiotic environment, existing theory, and many case studies, little work to date has addressed within-species evolution of concerted strategies and how these might contrast with patterns across species. Here we consider the interactions between pollinators, herbivores, and resource availability in shaping plant local adaptation, how these interactions impact plant phenotypes and gene flow, and the conditions where multiple traits align along major environmental gradients such as latitude and elevation. Continued work in emerging model systems will benefit from the melding of classic experimental approaches with novel population genetic analyses to reveal patterns and processes in plant local adaptation.

Quantitative trait locus mapping reveals an independent genetic basis for joint divergence in leaf function, life-history, and floral traits between scarlet monkeyflower (Mimulus cardinalis) populations

PREMISE

Across taxa, vegetative and floral traits that vary along a fast-slow life-history axis are often correlated with leaf functional traits arrayed along the leaf economics spectrum, suggesting a constrained set of adaptive trait combinations. Such broad-scale convergence may arise from genetic constraints imposed by pleiotropy (or tight linkage) within species, or from natural selection alone. Understanding the genetic basis of trait syndromes and their components is key to distinguishing these alternatives and predicting evolution in novel environments.

METHODS

We used a line-cross approach and quantitative trait locus (QTL) mapping to characterize the genetic basis of twenty leaf functional/physiological, life history, and floral traits in hybrids between annualized and perennial populations of scarlet monkeyflower (Mimulus cardinalis).

RESULTS

We mapped both single and multi-trait QTLs for life history, leaf function and reproductive traits, but found no evidence of genetic co-ordination across categories. A major QTL for three leaf functional traits (thickness, photosynthetic rate, and stomatal resistance) suggests that a simple shift in leaf anatomy may be key to adaptation to seasonally dry habitats.

CONCLUSIONS

Our results suggest that the co-ordination of resource-acquisitive leaf physiological traits with a fast life-history and more selfing mating system results from environmental selection rather than functional or genetic constraint. Independent assortment of distinct trait modules, as well as a simple genetic basis to leaf physiological traits associated with drought escape, may facilitate adaptation to changing climates.

The genetic architecture and evolution of life-history divergence among perennials in the Mimulus guttatus species complex

Ecological divergence is a fundamental source of phenotypic diversity between closely related species, yet the genetic architecture of most ecologically relevant traits is poorly understood. Differences in elevation can impose substantial divergent selection on both complex, correlated suites of traits (such as life-history), as well as novel adaptations. We use the Mimulus guttatus species complex to assess if the divergence in elevation is accompanied by trait divergence in a group of closely related perennials and determine the genetic architecture of this divergence. We find that divergence in elevation is associated with differences in life-history, as well as a unique trait, the production of rhizomes. The divergence between two perennials is largely explained by few mid-to-large effect quantitative trait loci (QTLs). However, the presence of QTLs with correlated, but opposing effects on multiple traits leads to some hybrids with transgressive trait combinations. Lastly, we find that the genetic architecture of the ability to produce rhizomes changes through development, wherein most hybrids produce rhizomes, but only later in development. Our results suggest that elevational differences may shape life-history divergence between perennials, but aspects of the genetic architecture of divergence may have implications for hybrid fitness in nature.

Population genomic and historical analysis suggests a global invasion by bridgehead processes in Mimulus guttatus

Imperfect historical records and complex demographic histories present challenges for reconstructing the history of biological invasions. Here, we combine historical records, extensive worldwide and genome-wide sampling, and demographic analyses to investigate the global invasion of Mimulus guttatus from North America to Europe and the Southwest Pacific. By sampling 521 plants from 158 native and introduced populations genotyped at >44,000 loci, we determined that invasive M. guttatus was first likely introduced to the British Isles from the Aleutian Islands (Alaska), followed by admixture from multiple parts of the native range. We hypothesise that populations in the British Isles then served as a bridgehead for vanguard invasions worldwide. Our results emphasise the highly admixed nature of introduced M. guttatus and demonstrate the potential of introduced populations to serve as sources of secondary admixture, producing novel hybrids. Unravelling the history of biological invasions provides a starting point to understand how invasive populations adapt to novel environments.

Vallejo-Marín et al. combine historical records, extensive worldwide and genome-wide sampling, and demographic analyses to investigate the global invasion of Mimulus guttatus from North America to Europe and the Southwest Pacific. They found that M. guttatus was first likely introduced to the British Isles from the Aleutian Islands (Alaska), followed by admixture from multiple parts of the native range, and hypothesise that populations in the British Isles then served as a bridgehead for vanguard invasions worldwide.

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.

The Evolution of Annual and Perennial Plant Life Histories: Ecological Correlates and Genetic Mechanisms

Flowering plants exhibit two principal life-history strategies: annuality (living and reproducing in one year) and perenniality (living more than one year). The advantages of either strategy depend on the relative benefits of immediate reproduction balanced against survivorship and future reproduction. This trade-off means that life-history strategies are associated with particular environments, with annuals being found more often in unpredictable habitats. Annuality and perenniality are the outcome of developmental genetic programs responding to their environment, with perennials being distinguished by their delayed competence to flower and reversion to growth after flowering. Evolutionary transitions between these strategies are frequent and have consequences for mating systems and genome evolution, with perennials being more likely to outcross with higher inbreeding depression and lower rates of molecular evolution. Integrating expectations from life-history theory with knowledge of the developmental genetics of flowering and seasonality is required to understand the mechanisms involved in the evolution of annual and perennial life histories.

Increased above-ground resource allocation is a likely precursor for independent evolutionary origins of annuality in the Pooideae grass subfamily

Semelparous annual plants flower a single time during their 1-yr life cycle, investing much of their energy into rapid reproduction. By contrast, iteroparous perennial plants flower multiple times over several years, and partition their resources between reproduction and persistence. To which extent evolutionary transitions between life-cycle strategies are internally constrained at the developmental, genetic and phylogenetic level is unknown. Here we study the evolution of life-cycle strategies in the grass subfamily Pooideae and test if transitions between them are facilitated by evolutionary precursors. We integrate ecological, life-cycle strategy and growth data in a phylogenetic framework. We investigate if growth traits are candidates for a precursor. Species in certain Pooideae clades are predisposed to evolve annuality from perenniality, potentially due to the shared inheritance of specific evolutionary precursors. Seasonal dry climates, which have been linked to annuality, were only able to select for transitions to annuality when the precursor was present. Allocation of more resources to above-ground rather than below-ground growth is a candidate for the precursor. Our findings support the hypothesis that only certain lineages can respond quickly to changing external conditions by switching their life-cycle strategy, likely due to the presence of evolutionary precursors.

Adaptation via pleiotropy and linkage: Association mapping reveals a complex genetic architecture within the stickleback Eda locus

Genomic mapping of the loci associated with phenotypic evolution has revealed genomic "hotspots," or regions of the genome that control multiple phenotypic traits. This clustering of loci has important implications for the speed and maintenance of adaptation and could be due to pleiotropic effects of a single mutation or tight genetic linkage of multiple causative mutations affecting different traits. The threespine stickleback (Gasterosteus aculeatus) is a powerful model for the study of adaptive evolution because the marine ecotype has repeatedly adapted to freshwater environments across the northern hemisphere in the last 12,000 years. Freshwater ecotypes have repeatedly fixed a 16 kilobase haplotype on chromosome IV that contains Ectodysplasin (Eda), a gene known to affect multiple traits, including defensive armor plates, lateral line sensory hair cells, and schooling behavior. Many additional traits have previously been mapped to a larger region of chromosome IV that encompasses the Eda freshwater haplotype. To identify which of these traits specifically map to this adaptive haplotype, we made crosses of rare marine fish heterozygous for the freshwater haplotype in an otherwise marine genetic background. Further, we performed fine-scale association mapping in a fully interbreeding, polymorphic population of freshwater stickleback to disentangle the effects of pleiotropy and linkage on the phenotypes affected by this haplotype. Although we find evidence that linked mutations have small effects on a few phenotypes, a small 1.4-kb region within the first intron of Eda has large effects on three phenotypic traits: lateral plate count, and both the number and patterning of the posterior lateral line neuromasts. Thus, the Eda haplotype is a hotspot of adaptation in stickleback due to both a small, pleiotropic region affecting multiple traits as well as multiple linked mutations affecting additional traits.

Multi-level patterns of genetic structure and isolation by distance in the widespread plant Mimulus guttatus

An understanding of genetic structure is essential for answering many questions in population genetics. However, complex population dynamics and scale-dependent processes can make it difficult to detect if there are distinct genetic clusters present in natural populations. Inferring discrete population structure is particularly challenging in the presence of continuous genetic variation such as isolation by distance. Here, we use the plant species Mimulus guttatus as a case study for understanding genetic structure at three spatial scales. We use reduced-representation sequencing and marker-based genotyping to understand dispersal dynamics and to characterise genetic structure. Our results provide insight into the spatial scale of genetic structure in a widespread plant species, and demonstrate how dispersal affects spatial genetic variation at the local, regional, and range-wide scale. At a fine-spatial scale, we show dispersal is rampant with little evidence of spatial genetic structure within populations. At a regional-scale, we show continuous differentiation driven by isolation by distance over hundreds of kilometres, with broad geographic genetic clusters that span major barriers to dispersal. Across Western North America, we observe geographic genetic structure and the genetic signature of multiple postglacial recolonisation events, with historical gene flow linking isolated populations. Our genetic analyses show M. guttatus is highly dispersive and maintains large metapopulations with high intrapopulation variation. This high diversity and dispersal confounds the inference of genetic structure, with multi-level sampling and spatially-explicit analyses required to understand population history.

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.

Life history evolution, species differences, and phenotypic plasticity in hemiparasitic eyebrights (Euphrasia)

PREMISE

Species delimitation in parasitic organisms is challenging because traits used to identify species are often plastic and vary depending on the host. Here, we use species from a recent radiation of generalist hemiparasitic Euphrasia to investigate trait variation and trait plasticity. We tested whether Euphrasia species show reliable trait differences, investigated whether these differences correspond to life history trade-offs between growth and reproduction, and quantified plasticity in response to host species.

METHODS

Common garden experiments were used to evaluate trait differences between 11 Euphrasia taxa grown on a common host, document phenotypic plasticity when a single Euphrasia species is grown on eight different hosts, and relate observations to trait differences recorded in the wild.

RESULTS

Euphrasia exhibited variation in life history strategies; some individuals transitioned rapidly to flowering at the expense of early season growth, while others invested in vegetative growth and delayed flowering. Life history differences were present between some species, though many related taxa lacked clear trait differences. Species differences were further blurred by phenotypic plasticity-many traits were plastic and changed with host type or between environments.

CONCLUSIONS

Phenotypic plasticity in response to host and environment confounds species delimitation in Euphrasia. When grown in a common garden environment, some morphologically distinct taxa can be identified, though others represent morphologically similar shallow segregates. Trait differences present between some species and populations demonstrate the rapid evolution of distinct life history strategies in response to local ecological conditions.

Contrasting environmental factors drive local adaptation at opposite ends of an environmental gradient in the yellow monkeyflower (Mimulus guttatus)

PREMISE

Identifying the environmental factors responsible for natural selection across different habitats is crucial for understanding the process of local adaptation in plants. Despite its importance, few studies have successfully isolated the environmental factors driving local adaptation in nature. In this study, we evaluated the agents of selection responsible for local adaptation of the monkeyflower Mimulus guttatus to California's coastal and inland habitats.

METHODS

We implemented a manipulative reciprocal transplant experiment at coastal and inland sites, where we excluded aboveground stressors in an effort to elucidate their role in the evolution of local adaptation.

RESULTS

Excluding aboveground stressors, most likely a combination of salt spray and herbivory, completely rescued inland annual plant fitness when transplanted to coastal habitat. The exclosures in inland habitat provided a benefit to the performance of coastal perennial plants. However, the exclosures are unlikely to provide much fitness benefit to the coastal plants at the inland site because of their general inability to flower in time to escape from the summer drought.

CONCLUSIONS

Our study demonstrates that a distinct set of selective agents (aboveground vs. belowground) are responsible for local adaptation at opposite ends of an environmental gradient.

Patterns of Hybrid Seed Inviability in the Mimulus guttatus sp. Complex Reveal a Potential Role of Parental Conflict in Reproductive Isolation

Genomic conflicts may play a central role in the evolution of reproductive barriers. Theory predicts that early-onset hybrid inviability may stem from conflict between parents for resource allocation to offspring. Here, we describe M. decorus: a group of cryptic species within the M. guttatus species complex that are largely reproductively isolated by hybrid seed inviability (HSI). HSI between M. guttatus and M. decorus is common and strong, but populations of M. decorus vary in the magnitude and directionality of HSI with M. guttatus. Patterns of HSI between M. guttatus and M. decorus, as well as within M. decorus, conform to the predictions of parental conflict: first, reciprocal F1s exhibit size differences and parent-of-origin-specific endosperm defects; second, the extent of asymmetry between reciprocal F1 seed size is correlated with asymmetry in HSI; and third, inferred differences in the extent of conflict predict the extent of HSI between populations. We also find that HSI is rapidly evolving, as populations that exhibit the most HSI are each others' closest relative. Lastly, although all populations appear largely outcrossing, we find that the differences in the inferred strength of conflict scale positively with π, suggesting that demographic or life history factors other than transitions to self-fertilization may influence the rate of parental-conflict-driven evolution. Overall, these patterns suggest the rapid evolution of parent-of-origin-specific resource allocation alleles coincident with HSI within and between M. guttatus and M. decorus. Parental conflict may therefore be an important evolutionary driver of reproductive isolation.

Experimental migration upward in elevation is associated with strong selection on life history traits

One of the strongest biological impacts of climate change has been the movement of species poleward and upward in elevation. Yet, what is not clear is the extent to which the spatial distribution of locally adapted lineages and ecologically important traits may also shift with continued climate change. Here, we take advantage of a transplant experiment mimicking up-slope seed dispersal for a suite of ecologically diverse populations of yellow monkeyflower (Mimulus guttatus sensu lato) into a high-elevation common garden during an extreme drought period in the Sierra Nevada mountains, California, USA. We use a demographic approach to quantify fitness and test for selection on life history traits in local versus lower-elevation populations and in normal versus drought years to test the potential for up-slope migration and phenotypic selection to alter the distribution of key life history traits in montane environments. We find that lower-elevation populations tend to outperform local populations, confirming the potential for up-slope migration. Although selection generally favored some local montane traits, including larger flowers and larger stem size at flowering, drought conditions tended to select for earlier flowering typical of lower-elevation genotypes. Taken together, this suggests that monkeyflower lineages moving upward in elevation could experience selection for novel trait combinations, particularly under warmer and drier conditions that are predicted to occur with continued climate change.

Divergence in drought-response traits between sympatric species of Mimulus

Differential adaptation to local environmental conditions is thought to be an important driver of speciation. Plants, whose sedentary lifestyle necessitates fine-tuned adaptation to edaphic conditions such as water availability, are often distributed based on these conditions. Populations occupying water-limited habitats may employ a variety of strategies, involving numerous phenotypes, to prevent and withstand desiccation. In sympatry, two closely related Mimulus species-M. guttatus and M. nasutus-occupy distinct microhabitats that differ in seasonal water availability. In a common garden experiment, we characterized natural variation within and between sympatric M. guttatus and M. nasutus in the ability to successfully set seed under well-watered and drought conditions. We also measured key phenotypes for drought adaptation, including developmental timing, plant size, flower size, and stomatal density. Consistent with their microhabitat associations in nature, M. nasutus set seed much more successfully than M. guttatus under water-limited conditions. This divergence in reproductive output under drought was due to differences in mortality after the onset of flowering, with M. nasutus surviving at a much higher rate than M. guttatus. Higher seed set in M. nasutus was mediated, at least in part, by a plastic increase in the rate of late-stage development (i.e., fruit maturation), consistent with the ability of this species to inhabit more ephemeral habitats in the field. Our results suggest adaptation to water availability may be an important factor in species maintenance of these Mimulus taxa in sympatry.

Assortative mating by flowering time and its effect on correlated traits in variable environments

Reproductive timing is a key life-history trait that impacts the pool of available mates, the environment experienced during flowering, and the expression of other traits through genetic covariation. Selection on phenology, and its consequences on other life-history traits, has considerable implications in the context of ongoing climate change and shifting growing seasons. To test this, we grew field-collected seed from the wildflower Mimulus guttatus in a greenhouse to assess the standing genetic variation for flowering time and covariation with other traits. We then created full-sib families through phenological assortative mating and grew offspring in three photoperiod treatments representing seasonal variation in daylength. We find substantial quantitative genetic variation for the onset of flowering time, which covaried with vegetative traits. The assortatively-mated offspring varied in their critical photoperiod by over two hours, so that families differed in their probability of flowering across treatments Allocation to flowering and vegetative growth changed across the daylength treatments, with consistent direction and magnitude of covariation among flowering time and other traits. Our results suggest that future studies of flowering time evolution should consider the joint evolution of correlated traits and shifting seasonal selection to understand how environmental variation influences life histories.

Estimation of QTL heritability based on pooled sequencing data

Motivation

Bulked segregant analysis combined with next generation sequencing has proven to be a simple and efficient approach for fast mapping of quantitative trait loci (QTLs). However, how to estimate the proportion of phenotypic variance explained by a QTL (or termed QTL heritability) in such pooled QTL mapping is an unsolved problem.

Results

In this paper, we propose a method called PQHE to estimate QTL heritability using pooled sequencing data obtained under different experimental designs. Simulation studies indicated that our method is correct and feasible. Four practical examples from rice and yeast are demonstrated, each representing a different situation.

Availability and implementation

The R scripts of our method are open source under GPLv3 license at http://genetics.fafu.edu.cn/PQHE or https://github.com/biotangweiqi/PQHE. The R scripts require the R package rootSolve.

Contact

wuwr@fafu.edu.cn.

Supplementary information

Supplementary data are available at Bioinformatics online.

Gene regulatory divergence between locally adapted ecotypes in their native habitats

Local adaptation is a key driver of ecological specialization and the formation of new species. Despite its importance, the evolution of gene regulatory divergence among locally adapted populations is poorly understood, especially how that divergence manifests in nature. Here, we evaluate gene expression divergence and allele-specific gene expression responses for locally adapted coastal perennial and inland annual accessions of the yellow monkeyflower, Mimulus guttatus, in a field reciprocal transplant experiment. Overall, 6765 (73%) of surveyed genes were differentially expressed between coastal and inland habitats, while 7213 (77%) were differentially expressed between the coastal perennial and inland annual accessions. Cis-regulatory variation was pervasive, affecting 79% (5532) of differentially expressed genes. We detected trans effects for 52% (3611) of differentially expressed genes. Expression plasticity of alleles across habitats (G × E interactions) appears to be relatively common (affecting 18% of transcripts) and could minimize fitness trade-offs at loci that contribute to local adaptation. We also found evidence that at least one chromosomal inversion may act as supergene by holding together haplotypes of differentially expressed genes, but this pattern depends on habitat context. Our results highlight multiple key patterns regarding the relationship between gene expression and the evolution of locally adapted populations.

Dissecting the role of a large chromosomal inversion in life history divergence throughout the Mimulus guttatus species complex

Chromosomal inversions can play an important role in adaptation, but the mechanism of their action in many natural populations remains unclear. An inversion could suppress recombination between locally beneficial alleles, thereby preventing maladaptive reshuffling with less-fit, migrant alleles. The recombination suppression hypothesis has gained much theoretical support but empirical tests are lacking. Here, we evaluated the evolutionary history and phenotypic effects of a chromosomal inversion which differentiates annual and perennial forms of Mimulus guttatus. We found that perennials likely possess the derived orientation of the inversion. In addition, this perennial orientation occurs in a second perennial species, M. decorus, where it is strongly associated with life history differences between co-occurring M. decorus and annual M. guttatus. One prediction of the recombination suppression hypothesis is that loci contributing to local adaptation will predate the inversion. To test whether the loci influencing perenniality pre-date this inversion, we mapped QTLs for life history traits that differ between annual M. guttatus and a more distantly related, collinear perennial species, M. tilingii. Consistent with the recombination suppression hypothesis, we found that this region is associated with life history in the absence of the inversion, and this association can be broken into at least two QTLs. However, the absolute phenotypic effect of the LG8 inversion region on life history is weaker in M. tilingii than in perennials which possess the inversion. Thus, while we find support for the recombination suppression hypothesis, the contribution of this inversion to life history divergence in this group is likely complex.

Circadian rhythms are associated with shoot architecture in natural settings

Circadian rhythms are key regulators of diverse biological processes under controlled settings. Yet, the phenotypic and fitness consequences of quantitative variation in circadian rhythms remain largely unexplored in the field. As with other pathways, phenotypic characterization of circadian outputs in the field may reveal novel clock functions. Across consecutive growing seasons, we test for associations between clock variation and flowering phenology, plant size, shoot architecture, and fruit set in clock mutants and segregating progenies of Arabidopsis thaliana expressing quantitative variation in circadian rhythms. Using structural equation modeling, we find that genotypic variation in circadian rhythms within a growing season is associated directly with branching, which in turn affects fruit production. Consistent with direct associations between the clock and branching in segregating progenies, cauline branch number is lower and rosette branch number higher in a short-period mutant relative to wild-type and long-period genotypes, independent of flowering time. Differences in branching arise from variation in meristem fate as well as leaf production rate before flowering and attendant increases in meristem number. Our results suggest that clock variation directly affects shoot architecture in the field, suggesting a novel clock function and means by which the clock affects performance.

Grow with the flow: a latitudinal cline in physiology is associated with more variable precipitation in Erythranthe cardinalis

Local adaptation is commonly observed in nature: organisms perform well in their natal environment, but poorly outside it. Correlations between traits and latitude, or latitudinal clines, are among the most common pieces of evidence for local adaptation, but identifying the traits under selection and the selective agents is challenging. Here, we investigated a latitudinal cline in growth and photosynthesis across 16 populations of the perennial herb Erythranthe cardinalis (Phrymaceae). Using machine learning methods, we identify interannual variation in precipitation as a likely selective agent: southern populations from more variable environments had higher photosynthetic rates and grew faster. We hypothesize that selection may favour a more annualized life history - grow now rather than save for next year - in environments where severe droughts occur more often. Thus, our study provides insight into how species may adapt if Mediterranean climates become more variable due to climate change.

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.

Pleiotropy, constraint, and modularity in the evolution of life histories: insights from genomic analyses

Multicellular organisms display an enormous range of life history (LH) strategies and present an evolutionary conundrum; despite strong natural selection, LH traits are characterized by high levels of genetic variation. To understand the evolution of life histories and maintenance of this variation, the specific phenotypic effects of segregating alleles and the genetic networks in which they act need to be elucidated. In particular, the extent to which LH evolution is constrained by the pleiotropy of alleles contributing to LH variation is generally unknown. Here, we review recent empirical results that shed light on this question, with an emphasis on studies employing genomic analyses. While genome-scale analyses are increasingly practical and affordable, they face limitations of genetic resolution and statistical power. We describe new research approaches that we believe can produce new insights and evaluate their promise and applicability to different kinds of organisms. Two approaches seem particularly promising: experiments that manipulate selection in multiple dimensions and measure phenotypic and genomic response and analytical approaches that take into account genome-wide associations between markers and phenotypes, rather than applying a traditional marker-by-marker approach.

Population structure and local selection yield high genomic variation in Mimulus guttatus

Across western North America, Mimulus guttatus exists as many local populations adapted to site-specific environmental challenges. Gene flow between locally adapted populations will affect genetic diversity both within demes and across the larger metapopulation. Here, we analyse 34 whole-genome sequences from the intensively studied Iron Mountain population (IM) in conjunction with sequences from 22 Mimulus individuals sampled from across western North America. Three striking features of these data address hypotheses about migration and selection in a locally adapted population. First, we find very high levels of intrapopulation polymorphism (synonymous π = 0.033). Variation outside of genes is likely even higher but difficult to estimate because excessive divergence reduces the efficiency of read mapping. Second, IM exhibits a significantly positive genomewide average for Tajima's D. This indicates allele frequencies are typically more intermediate than expected from neutrality, opposite the pattern observed in many other species. Third, IM exhibits a distinctive haplotype structure with a genomewide excess of positive associations between rarer alleles at linked loci. This suggests an important effect of gene flow from other Mimulus populations, although a residual effect of population founding might also contribute. The combination of multiple analyses, including a novel tree-based analytic method, illustrates how the balance of local selection, limited dispersal and metapopulation dynamics manifests across the genome. The overall genomic pattern of sequence diversity suggests successful gene flow of divergent immigrant genotypes into IM. However, many loci show patterns indicative of local adaptation, particularly at SNPs associated with chromosomal inversions.

Outcrossing and photosynthetic rates vary independently within two Clarkia species: implications for the joint evolution of drought escape physiology and mating system

Background and Aims Mating systems of plants are diverse and evolutionarily labile. Abiotic environmental factors, such as seasonal drought, may impose selection on physiological traits that could lead to transitions in mating system if physiological traits are genetically correlated with traits that influence mating system. Within Clarkia, self-fertilizing taxa have higher photosynthetic rates, earlier flowering phenology, faster individual floral development and more compressed flowering periods than their outcrossing sister taxa, potentially reducing the selfing taxa's exposure to drought. In theory, this contrast in trait combinations between sister taxa could have arisen via correlated evolution due to pleiotropy or genetic linkage. Alternatively, each trait may evolve independently as part of a life history that is adaptive in seasonally dry environments. Methods To evaluate these hypotheses, we examined relationships between photosynthetic rates (adjusted for plant height and leaf node position) and outcrossing rates (estimated by allozyme variation in progeny arrays) during two consecutive years in multiple wild populations of two mixed-mating Clarkia taxa, each of which is sister to a derived selfing taxon. If the negative association between photosynthetic rate and outcrossing previously observed between sister taxa reflects correlated evolution due to a strong negative genetic correlation between these traits, then a similarly negative relationship would be observed within populations of each taxon. By contrast, if the combination of elevated photosynthetic rates and reduced outcrossing evolved independently within taxa, we predicted no consistent relationship between photosynthetic rate and outcrossing rate. Key Results We found no significant difference in outcrossing rates within populations between groups of plants with high versus low photosynthetic rates. Conclusions Overall, these results provide support for the hypothesis that the joint divergence in photosynthetic rate and mating system observed between Clarkia sister taxa is the result of independent evolutionary transitions.

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.

The scale of local adaptation in Mimulus guttatus: comparing life history races, ecotypes, and populations

Fitness trade-offs between environments are central to the evolution of biodiversity. Although transplant studies often document fitness trade-offs consistent with local adaptation (LA), many have also found an advantage of foreign genotypes (foreign advantage (FA)). Understanding the mechanisms driving the magnitude and distribution of fitness variation requires comparative approaches that test the ecological scales at which these different patterns emerge. We used a common garden transplant experiment to compare the relative fitnesses of native vs foreign genotypes at three nested ecological scales within Mimulus guttatus: annual vs perennial life history races, perennial ecotypes across an elevational range, and populations within perennial elevational ecotypes. We integrated fitness across the life-cycle and decomposed LA vs FA into contributions from different fitness components. We found LA, measured as home-site advantage, between annual and perennial races and a trend towards LA among populations within montane habitats. Conversely, we found strong FA of low-elevation perennials in a montane environment. LA between life history races reflects the fitness advantages of adult survival and vegetative growth in a mesic environment. Within the perennial race, recent climate conditions or nonselective processes, such as dispersal limitation or mutational load, could explain FA of low-elevation perennials in a montane environment.

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.

Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversion

Organisms exhibit an incredible diversity of life history strategies as adaptive responses to environmental variation. The establishment of novel life history strategies involves multilocus polymorphisms, which will be challenging to establish in the face of gene flow and recombination. Theory predicts that adaptive allelic combinations may be maintained and spread if they occur in genomic regions of reduced recombination, such as chromosomal inversion polymorphisms, yet empirical support for this prediction is lacking. Here, we use genomic data to investigate the evolution of divergent adaptive ecotypes of the yellow monkey flower Mimulus guttatus. We show that a large chromosomal inversion polymorphism is the major region of divergence between geographically widespread annual and perennial ecotypes. In contrast, ∼40,000 single nucleotide polymorphisms in collinear regions of the genome show no signal of life history, revealing genomic patterns of diversity have been shaped by localized homogenizing gene flow and large-scale Pleistocene range expansion. Our results provide evidence for an inversion capturing and protecting loci involved in local adaptation, while also explaining how adaptive divergence can occur with gene flow.