Transgenic study of parallelism in plant morphological evolution

Brassinosteroids synthesised by CYP85A/A1 but not CYP85A2 function via a BRI1-like receptor but not via BRI1 in Picea abies

Brassinosteroids (BRs) are essential plant hormones. In angiosperms, brassinolide and castasterone, the first and second most active BRs, respectively, are synthesised by CYP85A2 and CYP85A/A1, respectively. BRs in angiosperms function through an essential receptor, BR Insensitive 1 (BRI1). In addition, some angiosperms also have non-essential BRI1-like 1/3 (BRL1/3). In conifers, BRs promote seed germination under drought stress; however, how BRs function in gymnosperms is unknown. In this study, we performed functional complementation of BR biosynthesis and receptor genes from Picea abies with respective Arabidopsis mutants. We found that P. abies possessed functional PaCYP85A and PaBRL1 but not PaCYP85A2 or PaBRI1, and this results in weak BR signaling, and both PaCYP85A and PaBRL1 were abundantly expressed. However, neither BR treatment of P. abies seedlings nor expression of PaBRL1 in the Arabidopsis Atbri1 mutant promoted plant height, despite the fact that BR-responsive genes were activated. Importantly, chimeric AtBRI1 replaced with the BR-binding domain of PaBRL1 complemented the Atbri1 phenotypes. Furthermore, PaBRL1 had less kinase activity than BRI1 in vitro. Overall, P. abies had weak but still active BR signaling, explaining aspects of its slow growth and high stress tolerance. Our study sheds light on the functional and evolutionary significance of distinct BR signaling that is independent of BRI1 and brassinolide.

Brassicaceae flowers: diversity amid uniformity

The mustard family Brassicaceae, which includes the model plant Arabidopsis thaliana, exhibits morphological stasis and significant uniformity of floral plan. Nonetheless, there is untapped diversity in almost every aspect of floral morphology in the family that lends itself to comparative study, including organ number, shape, form, and color. Studies on the genetic basis of morphological diversity, enabled by extensive genetic tools and genomic resources and the close phylogenetic distance among mustards, have revealed a mosaic of conservation and divergence in numerous floral traits. Here I review the morphological diversity of the flowers of Brassicaceae and discuss studies addressing the underlying genetic and developmental mechanisms shaping floral diversity. To put flowers in the context of the floral display, I describe diversity in inflorescence morphology and the variation that exists in the structures preceding the floral organs. Reconstructing the floral morphospace in Brassicaceae coupled with next-generation sequencing data and unbiased approaches to interrogate gene function in species throughout the mustard phylogeny offers promising ways to understand how developmental mechanisms originate and diversify.

How a growing organismal perspective is adding new depth to integrative studies of morphological evolution

Over the past half century, the field of Evolutionary Developmental Biology, or Evo-devo, has integrated diverse fields of biology into a more synthetic understanding of morphological diversity. This has resulted in numerous insights into how development can evolve and reciprocally influence morphological evolution, as well as generated several novel theoretical areas. Although comparative by default, there remains a great gap in our understanding of adaptive morphological diversification and how developmental mechanisms influence the shape and pattern of phenotypic variation. Herein we highlight areas of research that are in the process of filling this void, and areas, if investigated more fully, that will add new insights into the diversification of morphology. At the centre of our discussion is an explicit awareness of organismal biology. Here we discuss an organismal framework that is supported by three distinct pillars. First, there is a need for Evo-devo to adopt a high-resolution phylogenetic approach in the study of morphological variation and its developmental underpinnings. Secondly, we propose that to understand the dynamic nature of morphological evolution, investigators need to give more explicit attention to the processes that generate evolutionarily relevant variation at the population level. Finally, we emphasize the need to address more thoroughly the processes that structure variation at micro- and macroevolutionary scales including modularity, morphological integration, constraint, and plasticity. We illustrate the power of these three pillars using numerous examples from both invertebrates and vertebrates to emphasize that many of these approaches are already present within the field, but have yet to be formally integrated into many research programs. We feel that the most exciting new insights will come where the traditional experimental approaches to Evo-devo are integrated more thoroughly with the principles of this organismal framework.

Parallel genetic adaptation across environments differing in mode of growth or resource availability

Evolution experiments have demonstrated high levels of genetic parallelism between populations evolving in identical environments. However, natural populations evolve in complex environments that can vary in many ways, likely sharing some characteristics but not others. Here, we ask whether shared selection pressures drive parallel evolution across distinct environments. We addressed this question in experimentally evolved populations founded from a clone of the bacterium Burkholderia cenocepacia. These populations evolved for 90 days (approximately 600 generations) under all combinations of high or low carbon availability and selection for either planktonic or biofilm modes of growth. Populations that evolved in environments with shared selection pressures (either level of carbon availability or mode of growth) were more genetically similar to each other than populations from environments that shared neither characteristic. However, not all shared selection pressures led to parallel evolution. Genetic parallelism between low-carbon biofilm and low-carbon planktonic populations was very low despite shared selection for growth under low-carbon conditions, suggesting that evolution in low-carbon environments may generate stronger trade-offs between biofilm and planktonic modes of growth. For all environments, a population's fitness in a particular environment was positively correlated with the genetic similarity between that population and the populations that evolved in that particular environment. Although genetic similarity was low between low-carbon environments, overall, evolution in similar environments led to higher levels of genetic parallelism and that genetic parallelism, in turn, was correlated with fitness in a particular environment.

Parallel evolution of storage roots in morning glories (Convolvulaceae)

BACKGROUND

Storage roots are an ecologically and agriculturally important plant trait that have evolved numerous times in angiosperms. Storage roots primarily function to store carbohydrates underground as reserves for perennial species. In morning glories, storage roots are well characterized in the crop species sweetpotato, where starch accumulates in storage roots. This starch-storage tissue proliferates, and roots thicken to accommodate the additional tissue. In morning glories, storage roots have evolved numerous times. The primary goal of this study is to understand whether this was through parallel evolution, where species use a common genetic mechanism to achieve storage root formation, or through convergent evolution, where storage roots in distantly related species are formed using a different set of genes. Pairs of species where one forms storage roots and the other does not were sampled from two tribes in the morning glory family, the Ipomoeeae and Merremieae. Root anatomy in storage roots and fine roots was examined. Furthermore, we sequenced total mRNA from storage roots and fine roots in these species and analyzed differential gene expression.

RESULTS

Anatomical results reveal that storage roots of species in the Ipomoeeae tribe, such as sweetpotato, accumulate starch similar to species in the Merremieae tribe but differ in vascular tissue organization. In both storage root forming species, more genes were found to be upregulated in storage roots compared to fine roots. Further, we find that fifty-seven orthologous genes were differentially expressed between storage roots and fine roots in both storage root forming species. These genes are primarily involved in starch biosynthesis, regulation of starch biosynthesis, and transcription factor activity.

CONCLUSIONS

Taken together, these results demonstrate that storage roots of species from both morning glory tribes are anatomically different but utilize a common core set of genes in storage root formation. This is consistent with a pattern of parallel evolution, thus highlighting the importance of examining anatomy together with gene expression to understand the evolutionary origins of ecologically and economically important plant traits.

CsLFY is required for shoot meristem maintenance via interaction with WUSCHEL in cucumber (Cucumis sativus)

Cucumber (Cucumis sativus) is an agronomically important vegetable with indeterminant growth habit, in which leaves are produced from the shoot apical meristem (SAM), and unisexual flowers are generated from the leaf axils. LEAFY (LFY) and its homologs have been shown to play important roles in promoting flower development and branching. The LFY homolog gene CsLFY was cloned in cucumber. Molecular biology, developmental biology and biochemical tools were combined to explore the biological function of the LFY homologous gene CsLFY in cucumber. CsLFY was expressed in the SAM, floral meristem and floral organ primordia. Ectopic expression of CsLFY rescued the phenotype of the lfy-5 mutant in Arabidopsis. Knockdown of CsLFY by RNA interference (RNAi) led to defective shoot development and premature discontinuance of leaf initiation in cucumber. Transcription of CsWUS and putative CsLFY target genes including CsAP3 and CUM1 were significantly reduced in the CsLFY-RNAi lines. Further biochemical analyses indicated that CsLFY physically interacts with CsWUS in cucumber. These data suggested that CsLFY has a novel function in regulating shoot meristem maintenance through interaction with CsWUS, and promotes flower development via activation of CsAP3 and CUM1 in cucumber.

Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes

Convergent evolution is a process that has occurred throughout the tree of life, but the historical genetic and biochemical context promoting the repeated independent origins of a trait is rarely understood. The well-known stimulant caffeine, and its xanthine alkaloid precursors, has evolved multiple times in flowering plant history for various roles in plant defense and pollination. We have shown that convergent caffeine production, surprisingly, has evolved by two previously unknown biochemical pathways in chocolate, citrus, and guaraná plants using either caffeine synthase- or xanthine methyltransferase-like enzymes. However, the pathway and enzyme lineage used by any given plant species is not predictable from phylogenetic relatedness alone. Ancestral sequence resurrection reveals that this convergence was facilitated by co-option of genes maintained over 100 million y for alternative biochemical roles. The ancient enzymes of the Citrus lineage were exapted for reactions currently used for various steps of caffeine biosynthesis and required very few mutations to acquire modern-day enzymatic characteristics, allowing for the evolution of a complete pathway. Future studies aimed at manipulating caffeine content of plants will require the use of different approaches given the metabolic and genetic diversity revealed by this study.

AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 Induce LEAFY Expression in Response to Auxin to Promote the Onset of Flower Formation in Arabidopsis

Proper timing of the onset to flower formation is critical for reproductive success. Monocarpic plants like Arabidopsis (Arabidopsis thaliana) switch from production of branches in the axils of leaves to that of flowers once in their lifecycle, during the meristem identity transition. The plant-specific transcription factor LEAFY (LFY) is necessary and sufficient for this transition. Previously, we reported that the plant hormone auxin induces LFY expression through AUXIN RESPONSE FACTOR5/MONOPTEROS (ARF5/MP). It is not known whether MP is solely responsible for auxin-directed transcriptional activation of LFY. Here, we show that two transcription factors belonging to the AINTEGUMENTA-LIKE/PLETHORA family, AINTEGUMENTA (ANT) and AINTEGUMENTA-LIKE6/PLETHORA3 (AIL6/PLT3), act in parallel with MP to upregulate LFY in response to auxin. ant ail6 mutants display a delay in the meristem identity transition and in LFY induction. ANT and AIL6/PLT3 are expressed prior to LFY and bind to the LFY promoter to control LFY mRNA accumulation. Genetic and promoter/reporter studies suggest that ANT/AIL6 act in parallel with MP to promote LFY induction in response to auxin sensing. Our study highlights the importance of two separate auxin-controlled pathways in the meristem identity transition.

Interspecies Gene Transfer as a Method for Understanding the Genetic Basis for Evolutionary Change: Progress, Pitfalls, and Prospects

The recent revolution in high throughput sequencing and associated applications provides excellent opportunities to catalog variation in DNA sequences and gene expression between species. However, understanding the astonishing diversity of the Tree of Life requires understanding the phenotypic consequences of such variation and identification of those rare genetic changes that are causal to diversity. One way to study the genetic basis for trait diversity is to apply a transgenic approach and introduce genes of interest from a donor into a recipient species. Such interspecies gene transfer (IGT) is based on the premise that if a gene is causal to the morphological divergence of the two species, the transfer will endow the recipient with properties of the donor. Extensions of this approach further allow identifying novel loci for the diversification of form and investigating cis- and trans-contributions to morphological evolution. Here we review recent examples from both plant and animal systems that have employed IGT to provide insight into the genetic basis of evolutionary change. We outline the practice of IGT, its methodological strengths and weaknesses, and consider guidelines for its application, emphasizing the importance of phylogenetic distance, character polarity, and life history. We also discuss future perspectives for exploiting IGT in the context of expanding genomic resources in emerging experimental systems and advances in genome editing.

Evolutionary transgenomics: prospects and challenges

Many advances in our understanding of the genetic basis of species differences have arisen from transformation experiments, which allow us to study the effect of genes from one species (the donor) when placed in the genetic background of another species (the recipient). Such interspecies transformation experiments are usually focused on candidate genes - genes that, based on work in model systems, are suspected to be responsible for certain phenotypic differences between the donor and recipient species. We suggest that the high efficiency of transformation in a few plant species, most notably Arabidopsis thaliana, combined with the small size of typical plant genes and their cis-regulatory regions allow implementation of a screening strategy that does not depend upon a priori candidate gene identification. This approach, transgenomics, entails moving many large genomic inserts of a donor species into the wild type background of a recipient species and then screening for dominant phenotypic effects. As a proof of concept, we recently conducted a transgenomic screen that analyzed more than 1100 random, large genomic inserts of the Alabama gladecress Leavenworthia alabamica for dominant phenotypic effects in the A. thaliana background. This screen identified one insert that shortens fruit and decreases A. thaliana fertility. In this paper we discuss the principles of transgenomic screens and suggest methods to help minimize the frequencies of false positive and false negative results. We argue that, because transgenomics avoids committing in advance to candidate genes it has the potential to help us identify truly novel genes or cryptic functions of known genes. Given the valuable knowledge that is likely to be gained, we believe the time is ripe for the plant evolutionary community to invest in transgenomic screens, at least in the mustard family Brassicaceae where many species are amenable to efficient transformation.

Changes in cis-regulatory elements of a key floral regulator are associated with divergence of inflorescence architectures

Higher plant species diverged extensively with regard to the moment (flowering time) and position (inflorescence architecture) at which flowers are formed. This seems largely caused by variation in the expression patterns of conserved genes that specify floral meristem identity (FMI), rather than changes in the encoded proteins. Here, we report a functional comparison of the promoters of homologous FMI genes from Arabidopsis, petunia, tomato and Antirrhinum. Analysis of promoter-reporter constructs in petunia and Arabidopsis, as well as complementation experiments, showed that the divergent expression of leafy (LFY) and the petunia homolog aberrant leaf and flower (ALF) results from alterations in the upstream regulatory network rather than cis-regulatory changes. The divergent expression of unusual floral organs (UFO) from Arabidopsis, and the petunia homolog double top (DOT), however, is caused by the loss or gain of cis-regulatory promoter elements, which respond to trans-acting factors that are expressed in similar patterns in both species. Introduction of pUFO:UFO causes no obvious defects in Arabidopsis, but in petunia it causes the precocious and ectopic formation of flowers. This provides an example of how a change in a cis-regulatory region can account for a change in the plant body plan.

Molecular phylogenetics of tribe Eudemeae (Brassicaceae) and implications for its morphology and distribution

Tribe Eudemeae comprises a morphologically heterogeneous group of genera distributed along the Andes of South America from Colombia southward into southern Chile and Argentina. The tribe currently includes seven genera: Aschersoniodoxa, Brayopsis, Dactylocardamum, Delpinophytum, Eudema, Onuris, and Xerodraba, and exhibits a wide morphological diversification in growth habit, inflorescences, and fruits. However, little is known about the phylogenetic relationships and evolution of the tribe. We present here a molecular phylogeny of representative sampling of all genera, utilizing sequence data from the nuclear ribosomal ITS region and chloroplast regions trnL-F, trnH-psbA, and rps16. Additionally, climatic niches of the tribe and its main lineages, along with the evolution of diagnostic morphological characters, were studied. All analyses confirmed the monophyly of Eudemeae, with the exception of Delpinophytum that was included with genera of the lineage I of Brassicaceae. Eudemeae is divided into two main lineages differentiated by their geographical distribution and climatic niche: the primarily north-central Andean lineage included Aschersoniodoxa, Brayopsis, Dactylocardamum, and Eudema, and the Patagonian and southern Andean lineage included Onuris and Xerodraba. Finally, ancestral-state reconstructions in the tribe generally reveal multiple and independent gains or losses of diagnostic morphological characters, such as growth form, inflorescence reduction, and fruit type. Relevant taxonomic implications stemming from the results are also discussed.

Identification of loci that cause phenotypic variation in diverse species with the reciprocal hemizygosity test

The reciprocal hemizygosity test is a straightforward genetic test that can positively identify genes that have evolved to contribute to a phenotypic difference between strains or between species. The test involves a comparison between hybrids that are genetically identical throughout the genome except at the test locus, which is rendered hemizygous for alternative alleles from the two parental strains. If the two reciprocal hemizygotes display different phenotypes, then the two parental alleles must have evolved. New methods for targeted mutagenesis will allow application of the reciprocal hemizygosity test in many organisms. This review discusses the principles, advantages, and limitations of the test.

Arguments in the evo-devo debate: say it with flowers!

A key question in evolutionary developmental biology is how DNA sequence changes have directed the evolution of morphological diversity. The widely accepted view was that morphological changes resulted from differences in number and/or type of transcription factors, or even from small changes in the amino acid sequence of similar proteins. Research over the last two decades indicated that most of the developmental and genetic mechanisms that produce new structures involve proteins that are deeply conserved. These proteins are encoded by a type of genes known as 'toolkit' genes that control a plethora of processes essential for the correct development of the organism. Mutations in these toolkit genes produce deleterious pleiotropic effects. In contrast, alterations in regulatory regions affect their expression only at specific sites in the organism, facilitating morphological change at the tissue and organ levels. However, some examples from the animal and plant fields indicate that coding mutations also contributed to phenotypic evolution. Therefore, the main question at this point is to what extent these mechanisms have contributed to the evolution of morphological diversity. Today, an increasing amount of data, especially from the plant field, implies that changes in cis-regulatory sequences in fact played a major role in evolution.

Parallel developmental genetic features underlie stickleback gill raker evolution

Background

Convergent evolution, the repeated evolution of similar phenotypes in independent lineages, provides natural replicates to study mechanisms of evolution. Cases of convergent evolution might have the same underlying developmental and genetic bases, implying that some evolutionary trajectories might be predictable. In a classic example of convergent evolution, most freshwater populations of threespine stickleback fish have independently evolved a reduction of gill raker number to adapt to novel diets. Gill rakers are a segmentally reiterated set of dermal bones important for fish feeding. A previous large quantitative trait locus (QTL) mapping study using a marine × freshwater F2 cross identified QTL on chromosomes 4 and 20 with large effects on evolved gill raker reduction.

Results

By examining skeletal morphology in adult and developing sticklebacks, we find heritable marine/freshwater differences in gill raker number and spacing that are specified early in development. Using the expression of the Ectodysplasin receptor (Edar) gene as a marker of raker primordia, we find that the differences are present before the budding of gill rakers occurs, suggesting an early change to a lateral inhibition process controlling raker primordia spacing. Through linkage mapping in F2 fish from crosses with three independently derived freshwater populations, we find in all three crosses QTL overlapping both previously identified QTL on chromosomes 4 and 20 that control raker number. These two QTL affect the early spacing of gill raker buds.

Conclusions

Collectively, these data demonstrate that parallel developmental genetic features underlie the convergent evolution of gill raker reduction in freshwater sticklebacks, suggesting that even highly polygenic adaptive traits can have a predictable developmental genetic basis.

Molecular mechanisms involved in convergent crop domestication

Domestication has helped to understand evolution. We argue that, vice versa, novel insights into evolutionary principles could provide deeper insights into domestication. Molecular analyses have demonstrated that convergent phenotypic evolution is often based on molecular changes in orthologous genes or pathways. Recent studies have revealed that during plant domestication the causal mutations for convergent changes in key traits are likely to be located in particular genes. These insights may contribute to defining candidate genes for genetic improvement during the domestication of new plant species. Such efforts may help to increase the range of arable crops available, thus increasing crop biodiversity and food security to help meet the predicted demands of the continually growing global population under rapidly changing environmental conditions.

Characterization of the sequence and expression pattern of LFY homologues from dogwood species (Cornus) with divergent inflorescence architectures

BACKGROUND AND AIMS

LFY homologues encode transcription factors that regulate the transition from vegetative to reproductive growth in flowering plants and have been shown to control inflorescence patterning in model species. This study investigated the expression patterns of LFY homologues within the diverse inflorescence types (head-like, umbel-like and inflorescences with elongated internodes) in closely related lineages in the dogwood genus (Cornus s.l.). The study sought to determine whether LFY homologues in Cornus species are expressed during floral and inflorescence development and if the pattern of expression is consistent with a function in regulating floral development and inflorescence architectures in the genus.

METHODS

Total RNAs were extracted using the CTAB method and the first-strand cDNA was synthesized using the SuperScript III first-strand synthesis system kit (Invitrogen). Expression of CorLFY was investigated by RT-PCR and RNA in situ hybridization. Phylogenetic analyses were conducted using the maximum likelihood methods implemented in RAxML-HPC v7.2.8.

KEY RESULTS

cDNA clones of LFY homologues (designated CorLFY) were isolated from six Cornus species bearing different types of inflorescence. CorLFY cDNAs were predicted to encode proteins of approximately 375 amino acids. The detection of CorLFY expression patterns using in situ RNA hybridization demonstrated the expression of CorLFY within the inflorescence meristems, inflorescence branch meristems, floral meristems and developing floral organ primordia. PCR analyses for cDNA libraries derived from reverse transcription of total RNAs showed that CorLFY was also expressed during the late-stage development of flowers and inflorescences, as well as in bracts and developing leaves. Consistent differences in the CorLFY expression patterns were not detected among the distinct inflorescence types.

CONCLUSIONS

The results suggest a role for CorLFY genes during floral and inflorescence development in dogwoods. However, the failure to detect expression differences between the inflorescence types in the Cornus species analysed suggests that the evolutionary shift between major inflorescence types in the genus is not controlled by dramatic alterations in the levels of CorLFY gene transcript accumulation. However, due to spatial, temporal and quantitative limitations of the expression data, it cannot be ruled out that subtle differences in the level or location of CorLFY transcripts may underlie the different inflorescence architectures that are observed across these species. Alternatively, differences in CorLFY protein function or the expression or function of other regulators (e.g. TFL1 and UFO homologues) may support the divergent developmental trajectories.

Phylogeny-based comparative methods question the adaptive nature of sporophytic specializations in mosses

Adaptive evolution has often been proposed to explain correlations between habitats and certain phenotypes. In mosses, a high frequency of species with specialized sporophytic traits in exposed or epiphytic habitats was, already 100 years ago, suggested as due to adaptation. We tested this hypothesis by contrasting phylogenetic and morphological data from two moss families, Neckeraceae and Lembophyllaceae, both of which show parallel shifts to a specialized morphology and to exposed epiphytic or epilithic habitats. Phylogeny-based tests for correlated evolution revealed that evolution of four sporophytic traits is correlated with a habitat shift. For three of them, evolutionary rates of dual character-state changes suggest that habitat shifts appear prior to changes in morphology. This suggests that they could have evolved as adaptations to new habitats. Regarding the fourth correlated trait the specialized morphology had already evolved before the habitat shift. In addition, several other specialized "epiphytic" traits show no correlation with a habitat shift. Besides adaptive diversification, other processes thus also affect the match between phenotype and environment. Several potential factors such as complex genetic and developmental pathways yielding the same phenotypes, differences in strength of selection, or constraints in phenotypic evolution may lead to an inability of phylogeny-based comparative methods to detect potential adaptations.

Cyclic peptides arising by evolutionary parallelism via asparaginyl-endopeptidase-mediated biosynthesis

The cyclic miniprotein Momordica cochinchinensis Trypsin Inhibitor II (MCoTI-II) (34 amino acids) is a potent trypsin inhibitor (TI) and a favored scaffold for drug design. We have cloned the corresponding genes and determined that each precursor protein contains a tandem series of cyclic TIs terminating with the more commonly known, and potentially ancestral, acyclic TI. Expression of the precursor protein in Arabidopsis thaliana showed that production of the cyclic TIs, but not the terminal acyclic TI, depends on asparaginyl endopeptidase (AEP) for maturation. The nature of their repetitive sequences and the almost identical structures of emerging TIs suggest these cyclic peptides evolved by internal gene amplification associated with recruitment of AEP for processing between domain repeats. This is the third example of similar AEP-mediated processing of a class of cyclic peptides from unrelated precursor proteins in phylogenetically distant plant families. This suggests that production of cyclic peptides in angiosperms has evolved in parallel using AEP as a constraining evolutionary channel. We believe this is evolutionary evidence that, in addition to its known roles in proteolysis, AEP is especially suited to performing protein cyclization.

The evolution of reproductive structures in seed plants: a re-examination based on insights from developmental genetics

The study of developmental genetics is providing insights into how plant morphology can and does evolve, and into the fundamental nature of specific organs. This new understanding has the potential to revise significantly the way we think about seed plant evolution, especially with regard to reproductive structures. Here, we have sought to take a step in bridging the divide between genetic data and critical fields such as paleobotany and systematics. We discuss the evidence for several evolutionarily important interpretations, including the possibility that ovules represent meristematic axes with their own type of lateral determinate organs (integuments) and a model that considers carpels as analogs of complex leaves. In addition, we highlight the aspects of reproductive development that are likely to be highly labile and homoplastic, factors that have major implications for the understanding of seed plant relationships. Although these hypotheses may suggest that some long-standing interpretations are misleading, they also open up whole new avenues for comparative study and suggest concrete best practices for evolutionary analyses of development.

Convergent evolution of a complex fruit structure in the tribe Brassiceae (Brassicaceae)

PREMISE OF STUDY

Many angiosperms have fruit morphologies that result in seeds from the same plant having different dispersal capabilities. A prime example is found in the Brassiceae (Brassicaceae), which has many members with segmented or heteroarthrocarpic fruits. Since only 40% of the genera are heteroarthrocarpic, this tribe provides an opportunity to study the evolution of an ecologically significant novelty and its variants.

METHODS

We analyzed nuclear (PHYA) and plastid (matK) sequences from 66 accessions using maximum parsimony, maximum likelihood, and Bayesian inference approaches. The evolution of heteroarthrocarpy and its variants was evaluated using maximum parsimony and maximum likelihood ancestral state reconstructions.

KEY RESULTS

Although nuclear and plastid phylogenies are incongruent with each other, the following findings are consistent: (1) Cakile, Crambe, Vella, and Zilla lineages are monophyletic; (2) the Nigra lineage is not monophyletic; and (3) within the Cakile clade, Cakile, Didesmus, and Erucaria are paraphyletic. Despite differences in the matK and PHYA topologies at both deep and shallow nodes, similar patterns of morphological evolution emerge. Heteroarthrocarpy, a complex morphological trait, has evolved multiple times across the tribe. Moreover, there are convergent transitions in dehiscence capabilities and fruit disarticulation across the tribe.

CONCLUSIONS

We present the first explicit analysis of fruit evolution within the Brassiceae, which exemplifies evolutionary lability. The repeated loss and gain of segment dehiscence and disarticulation suggests conservation in the genetic pathway controlling abscission with differential expression across taxa. This study provides a strong foundation for future studies of mechanisms underlying variation in dispersal capabilities of Brassiceae.

Gene loss and parallel evolution contribute to species difference in flower color

Although the importance of regulatory and functional sequence evolution in generating species differences has been studied to some extent, much less is known about the role of other types of genomic changes, such as fluctuation in gene copy number. Here, we apply analyses of gene function and expression of anthocyanin pigment pathway genes, as well as cosegregation analyses in backcross populations, to examine the genetic changes involved in the shift from blue to red flowers in Andean Iochroma (Solanaceae). We demonstrate that deletion of a gene coding for an anthocyanin pathway enzyme was necessary for the transition to red floral pigmentation. The downregulation of a second pathway gene was also necessary for the novel flower color, and this regulatory pattern parallels the genetic change in the two other red-flowered species in the sister family Convolvulaceae in which flower color change has been examined genetically. Finally, we document a shift in enzymatic function at a third locus, but the importance of this change in the transition to red flowers depends on the exact order with which the three changes occurred. This study shows that gene inactivation or loss can be involved in the origin of phenotypic differences between species, thereby restricting the possibility of reversion to the ancestral state. It also demonstrates that parallel evolution of red flowers in three different species occurs via a common developmental/regulatory change but by mutations in different genes.

Cabbage family affairs: the evolutionary history of Brassicaceae

Life without the mustard family (Brassicaceae) would be a world without many crop species and the model organism Arabidopsis (Arabidopsis thaliana) that has revolutionized our knowledge in almost every field of modern plant biology. Despite this importance, research breakthroughs in understanding family-wide evolutionary patterns and processes within this flowering plant family were not achieved until the past few years. In this review, we examine recent outcomes from diverse botanical disciplines (taxonomy, systematics, genomics, paleobotany and other fields) to synthesize for the first time a holistic view on the evolutionary history of the mustard family.

Possible contributions of TERMINAL FLOWER 1 to the evolution of rosette flowering in Leavenworthia (Brassicaceae)

Leavenworthia crassa is a rosette flowering species that differs from inflorescence flowering species, such as Arabidopsis thaliana, in having elongated pedicels and shortened interfloral internodes on the main axis. Based on previous experiments, we hypothesized that changes to the L. crassa TFL1 ortholog, LcrTFL1, were important in the evolution of rosette flowering. We isolated LcrTFL1 and introduced a genomic construct into tfl1 mutant A. thaliana plants. We also generated and analyzed EGFP-LcrTFL1 reporter-fusion lines, and LcrTFL1/LcrLFY doubly transgenic lines. The transgene rescued the mutant defects, but manifested gain-of-function phenotypes. However, LcrTFL1 lines differed from 35S:TFL1 lines in several regards. Defects in floral meristem identity establishment were observed, as was the production of flowers with extra petals. We also noted features that resemble rosette flowering: LcrTFL1 lines produced significantly shorter interfloral internodes and significantly longer pedicels than either wild-type or 35S:TFL1 plants. Our data show that there are substantive differences in the regulation and/or function of TFL1 orthologs between A. thaliana and L. crassa. These may reflect changes that occurred during the evolution of rosette flowering in Leavenworthia, but, if so, our results show that additional, as-yet-unidentified genes were involved in this instance of architectural evolution.

Genetic framework for flattened leaf blade formation in unifacial leaves of Juncus prismatocarpus

Angiosperm leaves generally develop as bifacial structures with distinct adaxial and abaxial identities. However, several monocot species, such as iris and leek, develop unifacial leaves, in which leaf blades have only abaxial identity. In bifacial leaves, adaxial-abaxial polarity is required for leaf blade flattening, whereas many unifacial leaves become flattened despite their leaf blades being abaxialized. Here, we investigate the mechanisms underlying the development and evolution of flattened leaf blades in unifacial leaves. We demonstrate that the unifacial leaf blade is abaxialized at the gene expression level and that an ortholog of the DROOPING LEAF (DL) gene may promote flattening of the unifacial leaf blade. In two closely related Juncus species, Juncus prismatocarpus, which has flattened unifacial leaves, and Juncus wallichianus, which has cylindrical unifacial leaves, DL expression levels and patterns correlate with the degree of laminar outgrowth. Genetic and expression studies using interspecific hybrids of the two species reveal that the DL locus from J. prismatocarpus flattens the unifacial leaf blade and expresses higher amounts of DL transcript than does that from J. wallichianus. We also show that leaf blade flattening is a trigger for central-marginal leaf polarity differentiation. We suggest that flattened unifacial leaf blades may have evolved via the recruitment of DL function, which plays a similar cellular but distinct phenotypic role in monocot bifacial leaves.

A conserved mechanism of bract suppression in the grass family

Suppression of inflorescence leaf, or bract, growth has evolved multiple times in diverse angiosperm lineages, including the Poaceae and Brassicaceae. Studies of Arabidopsis thaliana mutants have revealed several genes involved in bract suppression, but it is not known if these genes play a similar role in other plants with suppressed bracts. We identified maize (Zea mays) tassel sheath (tsh) mutants, characterized by the loss of bract suppression, that comprise five loci (tsh1-tsh5). We used map-based cloning to identify Tsh1 and found that it encodes a GATA zinc-finger protein, a close homolog of HANABA TARANU (HAN) of Arabidopsis. The bract suppression function of Tsh1 is conserved throughout the grass family, as we demonstrate that the rice (Oryza sativa) NECK LEAF1 (NL1) and barley (Hordeum vulgare) THIRD OUTER GLUME (TRD) genes are orthologous with Tsh1. Interestingly, NL1/Tsh1/TRD expression and function are not conserved with HAN. The existence of paralogous NL1/Tsh1/TRD-like genes in the grasses indicates that the NL1/Tsh1/TRD lineage was created by recent duplications that may have facilitated its neofunctionalization. A comparison with the Arabidopsis genes regulating bract suppression further supports the hypothesis that the convergent evolution of bract suppression in the Poaceae involved recruitment of a distinct genetic pathway.

Parallel evolution at multiple levels in the origin of hummingbird pollinated flowers in Ipomoea

A transition in flower color accompanying a shift in pollinator guilds is a prominent and repeated adaptation in angiosperms. In many cases, shifts to similar pollinators are associated with similar flower-color transitions. The extent to which this parallelism at the phenotypic level results from parallel changes at the biochemical, developmental, and genetic levels, however, remains an open question. There have been few attempts to determine whether parallelism at these lower levels results from mutation bias or fixation bias of different classes of mutation. We address these issues by examining the biochemical, developmental, and genetic changes that have occurred in red-flowering species of the Mina lineage of morning glories (Ipomoea) and compare these to the changes reported for I. horsfalliae, which has independently evolved red flowers. Using transgenic techniques, we demonstrate that the transition from blue to red flowers in Mina species is due primarily to down-regulation of the enzyme flavonol-3'-hydroxylase (F3'H) in flowers but not in vegetative tissues, and that this down-regulation is at least partly due to cis-regulatory change in the gene for F3'H. These changes are similar to those exhibited by I. horsfalliae, indicating parallelism at the biochemical and developmental levels, and possibly at the genetic level.

Evolutionary and developmental studies of unifacial leaves in monocots: Juncus as a model system

An important objective in evolutionary developmental biology is to understand the molecular genetic mechanisms that have given rise to morphological diversity. Leaves in angiosperms generally develop as a flattened structure with clear adaxial-abaxial polarity. In monocots, however, a unifacial leaf has evolved in a number of divergent species, in which leaf blades consist of only the abaxial identity. The mechanism of unifacial leaf development has long been a matter of debate for comparative morphologists. However, the underlying molecular genetic mechanism remains unknown. Unifacial leaves would be useful materials for developmental studies of leaf-polarity specification. Moreover, these leaves offer unique opportunities to investigate important phenomena in evolutionary biology, such as repeated evolution or convergent evolution of similar morphological traits. Here we describe the potential of unifacial leaves for evolutionary developmental studies and present our recent approaches to understanding the mechanisms of unifacial leaf development and evolution using Juncus as a model system.

The key role of morphology in modelling inflorescence architecture

Emerging evidence suggests that certain key genes control the branching patterns of flower-bearing axes (i.e. inflorescences) in angiosperms. However, the terminology surrounding inflorescence architecture is heavily typological and suffers from radically divergent definitions of terms that together reduce the value of some recent predictive models. We attempt to resolve the paradox of conflicting definitions of the same terms and clarify the assumptions surrounding this complex subject. We argue in favour of uniform terminology and against over-simplification. The valid conceptual platforms for modelling should be clearly defined and should adequately reflect observed structural diversity.

Co-ordinated regulation of flowering time, plant architecture and growth by FASCICULATE: the pepper orthologue of SELF PRUNING

Wild peppers (Capsicum spp.) are either annual or perennial in their native habitat and their shoot architecture is dictated by their sympodial growth habit. To study shoot architecture in pepper, sympodial development is described in wild type and in the classical recessive fasciculate (fa) mutation. The basic sympodial unit in wild-type pepper comprises two leaves and a single terminal flower. fasciculate plants are characterized by the formation of floral clusters separated by short internodes and miniature leaves and by early flowering. Developmental analysis of these clusters revealed shorter sympodial units and, often, precocious termination prior to sympodial leaf formation. fa was mapped to pepper chromosome 6, in a region corresponding to the tomato SELF-PRUNING (SP) locus, the homologue of TFL1 of Arabidopsis. Sequence comparison between wild-type and fa plants revealed a duplication of the second exon in the mutants' orthologue of SP, leading to the formation of a premature stop codon. Ectopic expression of FASCICULATE complemented the Arabidopsis tfl1 mutant plants and as expected, stimulated late flowering. In agreement with the major effect of FASCICULATE imposed on sympodial development, the gene transcripts were localized to the centre of sympodial shoots but could not be detected in the primary shoot. The wide range of pleiotropic effects on plant architecture mediated by a single 'flowering' gene, suggests that it is used to co-ordinate many developmental events, and thus may underlie some of the widespread variation in the Solanaceae shoot architecture.

Chapter 4. New model systems for the study of developmental evolution in plants

The number of genetically tractable plant model systems is rapidly increasing, thanks to the decreasing cost of sequencing and the wide amenability of plants to stable transformation and other functional approaches. In this chapter, I discuss emerging model systems from throughout the land plant phylogeny and consider how their unique attributes are contributing to our understanding of development, evolution, and ecology. These new models are being developed using two distinct strategies: in some cases, they are selected because of their close relationship to the established models, while in others, they are chosen with the explicit intention of exploring distantly related plant lineages. Such complementary approaches are yielding exciting new results that shed light on both micro- and macroevolutionary processes in the context of developmental evolution.

Lepidium as a model system for studying the evolution of fruit development in Brassicaceae

Fruits represent a key innovation of the flowering plants that facilitates seed dispersal. In many species of the plant family Brassicaceae dehiscent fruits develop in which seed dispersal occurs through a process termed 'pod-shatter'. In the case of dehiscence, the fruit opens during fruit maturation. Phylogeny reconstructions using molecular markers indicate that the development of dehiscent fruits is the ancestral condition within the genus Lepidium s.l., but that indehiscent fruits evolved independently several times from dehiscent fruits. With Lepidium campestre and Cardaria pubescens (also known as Lepidium appelianum), very closely related taxa with dehiscent and indehiscent fruits, respectively, were identified which constitute a well-suited model system to determine the molecular genetic basis of evolutionary changes in fruit dehiscence. Following the rationale of evolutionary developmental biology ('evo-devo') phylomimicking mutants with indehiscent fruits of the close relative Arabidopsis have been used to define the candidate genes ALC, FUL, IND, RPL, and SHP1/2 which might be involved in the origin of indehiscent fruits in Cardaria. Comparative expression studies in L. campestre and C. pubescens are used to identify differentially expressed genes and thus to narrow down the number of candidate genes. Reciprocal heterologous transformation experiments may help us to distinguish direct from indirect developmental genetic causes of fruit indehiscence, and to assess the contribution of cis- and trans-regulatory changes.

Control of compound leaf development by FLORICAULA/LEAFY ortholog SINGLE LEAFLET1 in Medicago truncatula

Molecular genetic studies suggest that FLORICAULA (FLO)/LEAFY (LFY) orthologs function to control compound leaf development in some legume species. However, loss-of-function mutations in the FLO/LFY orthologs result in reduction of leaf complexity to different degrees in Pisum sativum and Lotus japonicus. To further understand the role of FLO/LFY orthologs in compound leaf development in legumes, we studied compound leaf developmental processes and characterized a leaf development mutant, single leaflet1 (sgl1), from the model legume Medicago truncatula. The sgl1 mutants exhibited strong defects in compound leaf development; all adult leaves in sgl1 mutants are simple due to failure in initiating lateral leaflet primordia. In addition, the sgl1 mutants are also defective in floral development, producing inflorescence-like structures. Molecular cloning of SGL1 revealed that it encodes the M. truncatula FLO/LFY ortholog. When properly expressed, LFY rescued both floral and compound leaf defects of sgl1 mutants, indicating that LFY can functionally substitute SGL1 in compound leaf and floral organ development in M. truncatula. We show that SGL1 and LFY differed in their promoter activities. Although the SGL1 genomic sequence completely rescued floral defects of lfy mutants, it failed to alter the simple leaf structure of the Arabidopsis thaliana plants. Collectively, our data strongly suggest that initiation of lateral leaflet primordia required for compound leaf development involves regulatory processes mediated by the SGL1 function in M. truncatula.

An exploration of LEAFY expression in independent evolutionary origins of rosette flowering in Brassicaceae

Whereas most Brassicaceae produce flowers on an elongated inflorescence, a few lineages produce flowers directly from the vegetative rosette on elongated pedicels. Knowing the extent to which independent origins of rosette flowering involve the same developmental and genetic mechanisms could clarify the constraints acting on plant architectural evolution. Prior work in Idahoa, Ionopsidium, and Leavenworthia suggested that changes in the activity or expression of the flower meristem identity gene, LEAFY (LFY), played a role in all three origins of rosette flowering. Here we studied the developmental morphology of L. crassa and immunolocalization of LFY protein in Leavenworthia and Ionopsidium to further compare independent origins of rosette flowering. Leavenworthia crassa differs from Ionopsidium and Idahoa in producing ebracteate flowers. Flowers are, however, associated with "squamules," here interpreted as stipules of a cryptic bract. LFY was detected in L. crassa flower primordia but not in inflorescence meristems. In contrast, the rosette flowering Io. acaule accumulated LFY protein in the inflorescence meristem, whereas its inflorescence-flowering close relative, Io. prolongoi, did not. Thus, although different cases of rosette flowering likely entailed modifications of the same meristem identity program, distinct developmental genetic mechanisms appear to be involved in each case.

Germline transformation of Shepherd's purse (Capsella bursa-pastoris) by the 'floral dip' method as a tool for evolutionary and developmental biology

Capsella bursa-pastoris is an attractive model system for evolutionary and developmental biology. To facilitate future studies on gene function, the 'floral dip' method was adapted to achieve germline transformation of C. bursa-pastoris. The GFP and BASTA-resistance (BAR (r)) genes were used as markers for screening or selecting, respectively, putative transgenic C. bursa-pastoris plants and the beta-glucuronidase (GUS) gene as well as the GFP gene for monitoring transgene expression level. We tested two Agrobacterium strains, LBA4404 and GV3101, for their ability to transform C. bursa-pastoris. In contrast to Arabidopsis thaliana, for which both strains were able to transform different ecotypes, only GV3101 gave satisfactory transformation rates with C. bursa-pastoris. Furthermore, we evaluated the effects of different concentrations of sucrose and the surfactant Silwet L-77 on the efficiency to generate transgenic C. bursa-pastoris plants and identified an efficient medium containing 10% (w/v) sucrose and 0.02-0.05% (v/v) Silwet L-77. Using Southern hybridisation, we confirmed the integration of the marker gene in the plant genome and the stable heredity of the introduced genes in the next generation.

Compound leaf development and evolution in the legumes

Across vascular plants, Class 1 KNOTTED1-like (KNOX1) genes appear to play a critical role in the development of compound leaves. An exception to this trend is found in the Fabaceae, where pea (Pisum sativum) uses UNIFOLIATA, an ortholog of the floral regulators FLORICAULA (FLO) and LEAFY (LFY), in place of KNOX1 genes to regulate compound leaf development. To assess the phylogenetic distribution of KNOX1-independent compound leaf development, a survey of KNOX1 protein expression across the Fabaceae was undertaken. The majority of compound-leafed Fabaceae have expression of KNOX1 proteins associated with developing compound leaves. However, in a large subclade of the Fabaceae, the inverted repeat-lacking clade (IRLC), of which pea is a member, KNOX1 expression is not associated with compound leaves. These data suggest that the FLO/LFY gene may function in place of KNOX1 genes in generating compound leaves throughout the IRLC. The contribution of FLO/LFY to leaf complexity in a member of the Fabaceae outside of the IRLC was examined by reducing expression of FLO/LFY orthologs in transgenic soybean (Glycine max). Transgenic plants with reduced FLO/LFY expression showed only slight reductions in leaflet number. Overexpression of a KNOX1 gene in alfalfa (Medicago sativa), a member of the IRLC, resulted in an increase in leaflet number. This implies that KNOX1 targets, which promote compound leaf development, are present in alfalfa and are still sensitive to KNOX1 regulation. These data suggest that KNOX1 genes and the FLO/LFY gene may have played partially overlapping roles in compound leaf development in ancestral Fabaceae but that the FLO/LFY gene took over this role in the IRLC.

Floral initiation and inflorescence architecture: a comparative view

BACKGROUND

A huge variety of plant forms can be found in nature. This is particularly noticeable for inflorescences, the region of the plant that contains the flowers. The architecture of the inflorescence depends on its branching pattern and on the relative position where flowers are formed. In model species such as Arabidopsis thaliana or Antirrhinum majus the key genes that regulate the initiation of flowers have been studied in detail and much is known about how they work. Studies being carried out in other species of higher plants indicate that the homologues of these genes are also key regulators of the development of their reproductive structures. Further, changes in these gene expression patterns and/or function play a crucial role in the generation of different plant architectures.

SCOPE

In this review we aim to present a summarized view on what is known about floral initiation genes in different plants, particularly dicotyledonous species, and aim to emphasize their contribution to plant architecture.

Morphological evolution through multiple cis-regulatory mutations at a single gene

One central, and yet unsolved, question in evolutionary biology is the relationship between the genetic variants segregating within species and the causes of morphological differences between species. The classic neo-darwinian view postulates that species differences result from the accumulation of small-effect changes at multiple loci. However, many examples support the possible role of larger abrupt changes in the expression of developmental genes in morphological evolution. Although this evidence might be considered a challenge to a neo-darwinian micromutationist view of evolution, there are currently few examples of the actual genes causing morphological differences between species. Here we examine the genetic basis of a trichome pattern difference between Drosophila species, previously shown to result from the evolution of a single gene, shavenbaby (svb), probably through cis-regulatory changes. We first identified three distinct svb enhancers from D. melanogaster driving reporter gene expression in partly overlapping patterns that together recapitulate endogenous svb expression. All three homologous enhancers from D. sechellia drive expression in modified patterns, in a direction consistent with the evolved svb expression pattern. To test the influence of these enhancers on the actual phenotypic difference, we conducted interspecific genetic mapping at a resolution sufficient to recover multiple intragenic recombinants. This functional analysis revealed that independent genetic regions upstream of svb that overlap the three identified enhancers are collectively required to generate the D. sechellia trichome pattern. Our results demonstrate that the accumulation of multiple small-effect changes at a single locus underlies the evolution of a morphological difference between species. These data support the view that alleles of large effect that distinguish species may sometimes reflect the accumulation of multiple mutations of small effect at select genes.

The role of two LEAFY paralogs from Idahoa scapigera (Brassicaceae) in the evolution of a derived plant architecture

Idahoa scapigera produces solitary flowers in the axils of rosette leaves without elongation of the shoot axis, a rosette-flowering architecture. Previous work with one of the two I. scapigera LFY paralogs, IscLFY1, showed that this gene caused aerial flowering rosettes in Arabidopsis thaliana. In this paper, we report that after three generations IscLFY1 transgenic lines are phenotypically indistinguishable from wild-type Arabidopsis, indicating that IscLFY1 protein is able to replace normal LFY function. Additionally, we found that ectopic LFY expression late in development can phenocopy aspects of the aerial rosette phenotype, suggesting that shoot compression caused by IscLFY1 could be caused by localized overexpression of a functional IscLFY protein. We also characterized the expression and function of the second I. scapigera LFY paralog, IscLFY2, in A. thaliana. In contrast to IscLFY1, this paralog was expressed in floral meristems and the shoot apical meristem (SAM). In I. scapigera, LFY-specific antibodies detected high protein levels in developing flowers but not in the apex, suggesting trans-regulatory differences between I. scapigera and A. thaliana. Most IscLFY2 transgenic A. thaliana plants were indistinguishable from wild type, but in a minority of lines the SAM was converted to a terminal flower as would be expected from the reporter-expression pattern. Taken together these results show that both I. scapigera paralogs have conserved LFY function, both proteins can rescue lfy and both can modify inflorescence architecture in an A. thaliana background: either by affecting internode elongation (IscLFY1) or by causing homeotic conversion of shoots into flowers (IscLFY2).

The genetic architecture of shoot branching in Arabidopsis thaliana: a comparative assessment of candidate gene associations vs. quantitative trait locus mapping

Association mapping focused on 36 genes involved in branch development was used to identify candidate genes for variation in shoot branching in Arabidopsis thaliana. The associations between four branching traits and moderate-frequency haplogroups at the studied genes were tested in a panel of 96 accessions from a restricted geographic range in Central Europe. Using a mixed-model association-mapping method, we identified three loci--MORE AXILLARY GROWTH 2 (MAX2), MORE AXILLARY GROWTH 3 (MAX3), and SUPERSHOOT 1 (SPS1)--that were significantly associated with branching variation. On the basis of a more extensive examination of the MAX2 and MAX3 genomic regions, we find that linkage disequilibrium in these regions decays within approximately 10 kb and trait associations localize to the candidate genes in these regions. When the significant associations are compared to relevant quantitative trait loci (QTL) from previous Ler x Col and Cvi x Ler recombinant inbred line (RIL) mapping studies, no additive QTL overlapping these candidate genes are observed, although epistatic QTL for branching, including one that spans the SPS1, are found. These results suggest that epistasis is prevalent in determining branching variation in A. thaliana and may need to be considered in linkage disequilibrium mapping studies of genetically diverse accessions.

Variation and constraint in plant evolution and development

The goal of this short review is to consider the interrelated phenomena of phenotypic variation and genetic constraint with respect to plant diversity. The unique aspects of plants, including sessile habit, modular growth and diverse developmental programs expressed at the phytomer level, merit a specific examination of the genetic basis of their phenotypic variation, and how they experience and escape genetic constraint. Numerous QTL studies with wild and domesticated plants reveal that most phenotypic traits are polygenic but vary in the number and effect of the loci contributing, from a few loci of large effects to many with small effects. Further, somatic mutations, developmental plasticity and epigenetic variation, especially gene methylation, can contribute to increases in phenotypic variation. The flip side of these processes, genetic constraint, can similarly be the result of many factors, including pleiotropy, canalization and genetic redundancy. Genetic constraint is not only a mechanism to prevent change, however, it can also serve to direct evolution along certain paths. Ultimately, genetic constraint often comes full circle and is released through events such as hybridization, genome duplication and epigenetic remodeling. We are just beginning to understand how these processes can operate simultaneously during the evolution of ecologically important traits in plants.

Developmental morphology of branching flowers in Nymphaea prolifera

Nymphaea and Nuphar (Nymphaeaceae) share an extra-axillary mode of floral inception in the shoot apical meristem (SAM). Some leaf sites along the ontogenetic spiral are occupied by floral primordia lacking a subtending bract. This pattern of flower initiation in leaf sites is repeated inside branching flowers of Nymphaea prolifera (Central and South America). Instead of fertile flowers this species usually produces sterile tuberiferous flowers that act as vegetative propagules. N. prolifera changes the meristem identity from reproductive to vegetative or vice versa repeatedly. Each branching flower first produces some perianth-like leaves, then it switches back to the vegetative meristem identity of the SAM with the formation of foliage leaves and another set of branching flowers. This process is repeated up to three times giving rise to more than 100 vegetative propagules. The developmental morphology of the branching flowers of N. prolifera is described using both microtome sections and scanning electron microscopy.

Evolutionary divergence of LFY function in the mustards Arabidopsis thaliana and Leavenworthia crassa

LEAFY (LFY), a transcription factor involved in the regulation of flower development in Arabidopsis thaliana, has been identified as a candidate gene in the diversification of plant architecture in Brassicaceae. Previous research with Leavenworthia crassa, which produces solitary flowers in the axils of rosette leaves, has shown that the L. crassa LFY ortholog, LcrLFY, rescues most aspects of flower development in A. thaliana but showed two novel traits: flowers produced additional petals and inflorescences produced terminal flowers. In this paper, we explore the molecular mechanisms responsible for these novel phenotypes. We used microarray hybridizations to identify 32 genes differentially expressed between a transgenic LcrLFY line and a control transgenic LFY line. Of particular interest, TERMINAL FLOWER 1 (TFL1) transcripts were found at elevated levels in LcrLFY lines. To distinguish regulatory versus functional changes within the LcrLFY locus, reciprocal chimeric transgenes between LcrLFY and LFY were constructed. These lines implicate divergence of LcrLFY cis-regulation as the primary cause of both novel transgenic phenotypes but implicate divergence of LcrLFY protein function as the primary cause of elevated TFL1 levels. Taken together these results show that LcrLFY has diverged from A. thaliana in both the cis-regulatory and protein-coding regions and imply that molecular coevolution of LcrLFY and the L. crassa TFL1 ortholog, LcrTFL1, contributed to the evolution of rosette flowering.