Accessibility, constraint, and repetition in adaptive floral evolution

Rapid genomic evolution in Brassica rapa with bumblebee selection in experimental evolution

BACKGROUND

Insect pollinators shape rapid phenotypic evolution of traits related to floral attractiveness and plant reproductive success. However, the underlying genomic changes remain largely unknown despite their importance in predicting adaptive responses to natural or to artificial selection. Based on a nine-generation experimental evolution study with fast cycling Brassica rapa plants adapting to bumblebees, we investigate the genomic evolution associated with the previously observed parallel phenotypic evolution. In this current evolve and resequencing (E&R) study, we conduct a genomic scan of the allele frequency changes along the genome in bumblebee-pollinated and hand-pollinated plants and perform a genomic principal component analysis (PCA).

RESULTS

We highlight rapid genomic evolution associated with the observed phenotypic evolution mediated by bumblebees. Controlling for genetic drift, we observe significant changes in allelic frequencies at multiple loci. However, this pattern differs according to the replicate of bumblebee-pollinated plants, suggesting putative non-parallel genomic evolution. Finally, our study underlines an increase in genomic variance implying the putative involvement of multiple loci in short-term pollinator adaptation.

CONCLUSIONS

Overall, our study enhances our understanding of the complex interactions between pollinator and plants, providing a stepping stone towards unravelling the genetic basis of plant genomic adaptation to biotic factors in the environment.

CYCLOIDEA-like genes control floral symmetry, floral orientation, and nectar guide patterning

Actinomorphic flowers usually orient vertically (relative to the horizon) and possess symmetric nectar guides, while zygomorphic flowers often face horizontally and have asymmetric nectar guides, indicating that floral symmetry, floral orientation, and nectar guide patterning are correlated. The origin of floral zygomorphy is dependent on the dorsoventrally asymmetric expression of CYCLOIDEA (CYC)-like genes. However, how horizontal orientation and asymmetric nectar guides are achieved remains poorly understood. Here, we selected Chirita pumila (Gesneriaceae) as a model plant to explore the molecular bases for these traits. By analyzing gene expression patterns, protein-DNA and protein-protein interactions, and encoded protein functions, we identified multiple roles and functional divergence of 2 CYC-like genes, i.e. CpCYC1 and CpCYC2, in controlling floral symmetry, floral orientation, and nectar guide patterning. CpCYC1 positively regulates its own expression, whereas CpCYC2 does not regulate itself. In addition, CpCYC2 upregulates CpCYC1, while CpCYC1 downregulates CpCYC2. This asymmetric auto-regulation and cross-regulation mechanism might explain the high expression levels of only 1 of these genes. We show that CpCYC1 and CpCYC2 determine asymmetric nectar guide formation, likely by directly repressing the flavonoid synthesis-related gene CpF3'5'H. We further suggest that CYC-like genes play multiple conserved roles in Gesneriaceae. These findings shed light on the repeated origins of zygomorphic flowers in angiosperms.

How broad is the selfing syndrome? Insights from convergent evolution of gene expression across species and tissues in the Capsella genus

The shift from outcrossing to selfing is one of the main evolutionary transitions in plants. It is accompanied by profound effects on reproductive traits, the so-called selfing syndrome. Because the transition to selfing also implies deep genomic and ecological changes, one also expects to observe a genomic selfing syndrome. We took advantage of the three independent transitions from outcrossing to selfing in the Capsella genus to characterize the overall impact of mating system change on RNA expression, in flowers but also in leaves and roots. We quantified the extent of both selfing and genomic syndromes, and tested whether changes in expression corresponded to adaptation to selfing or to relaxed selection on traits that were constrained in outcrossers. Mating system change affected gene expression in all three tissues but more so in flowers than in roots and leaves. Gene expression in selfing species tended to converge in flowers but diverged in the two other tissues. Hence, convergent adaptation to selfing dominates in flowers, whereas genetic drift plays a more important role in leaves and roots. The effect of mating system transition is not limited to reproductive tissues and corresponds to both adaptation to selfing and relaxed selection on previously constrained traits.

Modular regulation of floral traits by a PRE1 homolog in Mimulus verbenaceus: implications for the role of pleiotropy in floral integration

Floral traits often show correlated variation within and among species. For species with fused petals, strong correlations among corolla tube, stamen, and pistil length are particularly prevalent, and these three traits are considered an intra-floral functional module. Pleiotropy has long been implicated in such modular integration of floral traits, but empirical evidence based on actual gene function is scarce. We tested the role of pleiotropy in the expression of intra-floral modularity in the monkeyflower species Mimulus verbenaceus by transgenic manipulation of a homolog of Arabidopsis PRE1. Downregulation of MvPRE1 by RNA interference resulted in simultaneous decreases in the lengths of corolla tube, petal lobe, stamen, and pistil, but little change in calyx and leaf lengths or organ width. Overexpression of MvPRE1 caused increased corolla tube and stamen lengths, with little effect on other floral traits. Our results suggest that genes like MvPRE1 can indeed regulate multiple floral traits in a functional module but meanwhile have little effect on other modules, and that pleiotropic effects of these genes may have played an important role in the evolution of floral integration and intra-floral modularity.

How to approach the study of syndromes in macroevolution and ecology

Syndromes, wherein multiple traits evolve convergently in response to a shared selective driver, form a central concept in ecology and evolution. Recent work has questioned the existence of some classic syndromes, such as pollination and seed dispersal syndromes. Here, we discuss some of the major issues that have afflicted research into syndromes in macroevolution and ecology. First, correlated evolution of traits and hypothesized selective drivers is often relied on as the only evidence for adaptation of those traits to those hypothesized drivers, without supporting evidence. Second, the selective driver is often inferred from a combination of traits without explicit testing. Third, researchers often measure traits that are easy for humans to observe rather than measuring traits that are suited to testing the hypothesis of adaptation. Finally, species are often chosen for study because of their striking phenotypes, which leads to the illusion of syndromes and divergence. We argue that these issues can be avoided by combining studies of trait variation across entire clades or communities with explicit tests of adaptive hypotheses and that taking this approach will lead to a better understanding of syndrome-like evolution and its drivers.

Modularity and selection of nectar traits in the evolution of the selfing syndrome in Ipomoea lacunosa (Convolvulaceae)

Although the evolution of the selfing syndrome often involves reductions in floral size, pollen and nectar, few studies of selfing syndrome divergence have examined nectar. We investigate whether nectar traits have evolved independently of other floral size traits in the selfing syndrome, whether nectar traits diverged due to drift or selection, and the extent to which quantitative trait locus (QTL) analyses predict genetic correlations. We use F5 recombinant inbred lines (RILs) generated from a cross between Ipomoea cordatotriloba and Ipomoea lacunosa. We calculate genetic correlations to identify evolutionary modules, test whether trait divergence was due to selection, identify QTLs and perform correlation analyses to evaluate how well QTL properties reflect genetic correlations. Nectar and floral size traits form separate evolutionary modules. Selection has acted to reduce nectar traits in the selfing I. lacunosa. Genetic correlations predicted from QTL properties are consistent with observed genetic correlations. Changes in floral traits associated with the selfing syndrome reflect independent evolution of at least two evolutionary modules: nectar and floral size traits. We also demonstrate directional selection on nectar traits, which is likely to be independent of selection on floral size traits. Our study also supports the expected mechanistic link between QTL properties and genetic correlations.

Phenotypic variation of floral organs in flowering crabapples and its taxonomic significance

BACKGROUND

In angiosperms, phenotypic variation of floral organs is often considered as the traditional basis for the evolutionary relationship of different taxonomic groups above the species level. However, little is known about that at or below the species level. Here, we experimentally tested the phenotypic variation of Malus floral organs using combined methods of intraspecific uniformity test, interspecific distinctness analysis, principal component analysis, Pearson correlation analysis, and Q-type cluster analysis. The ancestor-inclined distribution characteristic analysis of Malus species and cultivars floral attributes was also carried out, so as to explore its taxonomic significance.

RESULTS

15/44 phenotypic traits (e.g., flower shape, flower type, flower diameter, ...) were highly consistent, distinguishable, and independent and could be used as the basis for Malus germplasm taxonomy. The studied 142 taxa were divided into two groups (A, B) and five sub-groups (A₁, A₂, B₁, B₂, B₃), with significantly variable floral phenotypic attributes between groups and within sub-groups. Malus natural species were relatively clustered in the same section (series) while homologous cultivars showed evidence of ancestor-inclined distribution characteristics. However, no significant correlation between the evolutionary order of sections (Sect. Docyniopsis → Sect. Chloromeles → Sect. Sorbomalus → Sect. Eumalus) and group/sub-groups (B₃ → B₂ → B₁ → A).

CONCLUSIONS

Phenotypic variation of floral organs could better explore the genetic relationship between Malus taxa. The findings improved our cognition of floral phenotypic variation taxonomic significance under the species level.

Genetic architecture of divergence: the selfing syndrome in Ipomoea lacunosa

PREMISE

Highly selfing plant species frequently display a distinctive suite of traits termed the selfing syndrome. Here we tested the hypothesis that these traits are grouped into correlated evolutionary modules and determined the degree of independence between such modules.

METHODS

We evaluated phenotypic correlations and QTL overlaps in F2 offspring of a cross between the morning glories Ipomoea lacunosa and I. cordatotriloba and investigated how traits clustered into modules at both the phenotypic and genetic level. We then compared our findings to other QTL studies of the selfing syndrome.

RESULTS

In the I. lacunosa selfing syndrome, traits grouped into modules that displayed correlated evolution within but not between modules. QTL overlap predicted phenotypic correlations, and QTLs affecting the same trait module were significantly physically clustered in the genome. The genetic architecture of the selfing syndrome varied across systems, but the pattern of stronger within- than between-module correlation was widespread.

CONCLUSIONS

The genetic architecture we observe in the selfing syndrome is consistent with a growing understanding of floral morphological integration achieved via pleiotropy in clustered traits. This view of floral evolution is consistent with resource limitation or predation driving the evolution of the selfing syndrome, but invites further research into both the selective causes of the selfing syndrome and how genetic architecture itself evolves in response to changes in mating system.

Combining biotechnology and evolution for understanding the mechanisms of pollinator attraction

Many flowering plants rely on pollinators for their reproductive success. Plant-pollinator interactions usually depend on a complex combination of traits based on a fine-tuned biosynthetic machinery, with many structural and regulatory genes involved. Yet, the physiological mechanisms in plants are the product of evolutionary processes. While evolution has been modifying flowers through millions of years, it is also a rapid process that can change plant traits within few generations. Here we discuss both mechanistic and evolutionary aspects of pollinator attraction. We also propose how latest advances in biotechnology and evolutionary studies, and their combination, will improve the elucidation of molecular mechanisms and evolutionary dynamics of pollinator attraction in changing environments.

A release from developmental bias accelerates morphological diversification in butterfly eyespots

Development can bias the independent evolution of traits sharing ontogenetic pathways, making certain evolutionary changes less likely. The eyespots commonly found on butterfly wings each have concentric rings of differing colors, and these serially repeated pattern elements have been a focus for evo-devo research. In the butterfly family Nymphalidae, eyespots have been shown to function in startling or deflecting predators and to be involved in sexual selection. Previous work on a model species of Mycalesina butterfly, Bicyclus anynana, has provided insights into the developmental control of the size and color composition of individual eyespots. Experimental evolution has also shown that the relative size of a pair of eyespots on the same wing surface is highly flexible, whereas they are resistant to diverging in color composition, presumably due to the underlying shared developmental process. This fixed color composition has been considered as a prime example of developmental bias with significant consequences for wing pattern evolution. Here, we test this proposal by surveying eyespots across the whole subtribe of Mycalesina butterflies and demonstrate that developmental bias shapes evolutionary diversification except in the genus Heteropsis which has gained independent control of eyespot color composition. Experimental manipulations of pupal wings reveal that the bias has been released through a novel regional response of the wing tissue to a conserved patterning signal. Our study demonstrates that development can bias the evolutionary independence of traits, but it also shows how bias can be released through developmental innovations, thus, allowing rapid morphological change, facilitating evolutionary diversification.

Implications of region-specific gene expression for development of the partially fused petunia corolla

Angiosperm petal fusion (sympetaly) has evolved multiple times independently and is associated with increased specificity between plants and their pollinators. To uncover developmental genetic changes that might have led to the evolution of sympetaly in the asterid core eudicot genus Petunia (Solanaceae), we carried out global and fine-scale gene expression analyses in different regions of the corolla. We found that, despite several similarities with the choripetalous model species Arabidopsis thaliana in the proximal-distal transcriptome, the Petunia axillaris fused and proximal corolla tube expresses several genes that in A. thaliana are associated with the distal petal region. This difference aligns with variation in petal shape and fusion across ontogeny of the two species. Moreover, differential gene expression between the unfused lobes and fused tube of P. axillaris petals revealed three strong candidate genes for sympetaly based on functional annotation in organ boundary specification. Partial silencing of one of these, the HANABA TARANU (HAN)-like gene PhGATA19, resulted in reduced fusion of Petunia hybrida petals, with silencing of both PhGATA19 and its close paralog causing premature plant senescence. Finally, detailed expression analyses for the previously characterized organ boundary gene candidate NO APICAL MERISTEM (NAM) supports the hypothesis that it establishes boundaries between most P. axillaris floral organs, with the exception of boundaries between petals.

Development and evolution of age-dependent defenses in ant-acacias

Age-dependent changes in plant defense against herbivores are widespread, but why these changes exist remains a mystery. We explored this question by examining a suite of traits required for the interaction between swollen thorn acacias (genus Vachellia) and ants of the genus Pseudomyrmex In this system, plants provide ants with refuge and food in the form of swollen stipular spines, protein-lipid-rich "Beltian" bodies, and sugar-secreting extrafloral nectaries-the "swollen thorn syndrome." We show that this syndrome develops at a predictable time in shoot development and is tightly associated with the temporal decline in the microRNAs miR156 and miR157 and a corresponding increase in their targets-the SPL transcription factors. Growth under reduced light intensity delays both the decline in miR156/157 and the development of the swollen thorn syndrome, supporting the conclusion that these traits are controlled by the miR156-SPL pathway. Production of extrafloral nectaries by Vachellia sp. that do not house ants is also correlated with a decline in miR156/157, suggesting that this syndrome evolved by co-opting a preexisting age-dependent program. Along with genetic evidence from other model systems, these findings support the hypothesis that the age-dependent development of the swollen thorn syndrome is a consequence of genetic regulation rather than a passive developmental pattern arising from developmental constraints on when these traits can develop.

Nectary size is a pollination syndrome trait in Penstemon

Evolution of complex phenotypes depends on the adaptive importance of individual traits, and the developmental changes required to modify traits. Floral syndromes are complex adaptations to pollinators that include color, nectar, and shape variation. Hummingbird-adapted flowers have evolved a remarkable number of times from bee-adapted ancestors in Penstemon, and previous work demonstrates that color over shape better distinguishes bee from hummingbird syndromes. Here, we examined the relative importance of nectar volume and nectary development in defining Penstemon pollination syndromes. We tested the evolutionary association of nectar volume and nectary area with pollination syndrome across 19 Penstemon species. In selected species, we assessed cellular-level processes shaping nectary size. Within a segregating population from an intersyndrome cross, we assessed trait correlations between nectar volume, nectary area, and the size of stamens on which nectaries develop. Nectar volume and nectary area displayed an evolutionary association with pollination syndrome. These traits were correlated within a genetic cross, suggesting a mechanistic link. Nectary area evolution involves parallel processes of cell expansion and proliferation. Our results demonstrate that changes to nectary patterning are an important contributor to pollination syndrome diversity and provide further evidence that repeated origins of hummingbird adaptation involve parallel developmental processes in Penstemon.

Developmental Bias and Evolution: A Regulatory Network Perspective

Phenotypic variation is generated by the processes of development, with some variants arising more readily than others-a phenomenon known as "developmental bias." Developmental bias and natural selection have often been portrayed as alternative explanations, but this is a false dichotomy: developmental bias can evolve through natural selection, and bias and selection jointly influence phenotypic evolution. Here, we briefly review the evidence for developmental bias and illustrate how it is studied empirically. We describe recent theory on regulatory networks that explains why the influence of genetic and environmental perturbation on phenotypes is typically not uniform, and may even be biased toward adaptive phenotypic variation. We show how bias produced by developmental processes constitutes an evolving property able to impose direction on adaptive evolution and influence patterns of taxonomic and phenotypic diversity. Taking these considerations together, we argue that it is not sufficient to accommodate developmental bias into evolutionary theory merely as a constraint on evolutionary adaptation. The influence of natural selection in shaping developmental bias, and conversely, the influence of developmental bias in shaping subsequent opportunities for adaptation, requires mechanistic models of development to be expanded and incorporated into evolutionary theory. A regulatory network perspective on phenotypic evolution thus helps to integrate the generation of phenotypic variation with natural selection, leaving evolutionary biology better placed to explain how organisms adapt and diversify.

Natural history of the narrow endemics Ipomoea cavalcantei and I. marabaensis from Amazon Canga savannahs

Amazon comprises a vast variety of ecosystems, including savannah-like Canga barrens that evolved on iron-lateritic rock plateaus of the Carajás Mountain range. Individual Cangas are enclosed by the rain forest, indicating insular isolation that enables speciation and plant community differentiation. To establish a framework for the research on natural history and conservation management of endemic Canga species, seven chloroplast DNA loci and an ITS2 nuclear DNA locus were used to study natural molecular variation of the red flowered Ipomoea cavalcantei and the lilac flowered I. marabaensis. Partitioning of the nuclear and chloroplast gene alleles strongly suggested that the species share the most recent common ancestor, pointing a new independent event of the red flower origin in the genus. Chloroplast gene allele analysis showed strong genetic differentiation between Canga populations, implying a limited role of seed dispersal in exchange of individuals between Cangas. Closed haplotype network topology indicated a requirement for the paternal inheritance in generation of cytoplasmic genetic variation. Tenfold higher nucleotide diversity in the nuclear ITS2 sequences distinguished I. cavalcantei from I. marabaensis, implying a different pace of evolutionary changes. Thus, Canga ecosystems offer powerful venues for the study of speciation, multitrait adaptation and the origins of genetic variation.

Breaking the mold: understanding the evolution and development of lateral organs in diverse plant models

The formation of complex three-dimensional shape differs significantly between plants and animals due to the presence of the cell wall in the former, which prevents all cell migration. Instead, in lateral plant organs such as leaves or petals, shape is controlled by a series of developmental phases in which the organ acquires polarity, cells undergo proliferation, and, lastly, cells expand to their final shape and size. Although these processes were first described based on mutagenesis approaches in major model systems like Arabidopsis thaliana, further insight into their complexity is best provided by studies of natural variation in organ shape in alternative model systems that sample a broader range of plant form. Weaving together work from both forward and evolutionary genetics, this review focuses on how modification in polarity establishment, cell proliferation and cell expansion drives modifications in the fundamental lateral organ developmental program to create diversity in shape.