The evolution of reproductive leaf dimorphism in two globally distributed fern families is neither stepwise nor irreversible, unless further specialization evolves

A contemporary interpretation of Dollo's Law states that the evolution of a specialized structure is irreversible. Among land plants, reproductive specialization shows a trend toward increasing complexity without reversion, raising questions about evolutionary steps and the irreversibility of reproductive complexity. Ferns exhibit varied reproductive strategies; some are dimorphic (producing separate leaves for photosynthesis and reproduction), while others are monomorphic (where one leaf is used for both photosynthesis and spore dispersal). This diversity provides an opportunity to examine the applicability of Dollo's Law in the evolution of reproductive leaf specialization. We analyzed 118 species in Blechnaceae and Onocleaceae, applying quantitative morphometrics and phylogenetic comparative methods to test the pillars of a modernized interpretation of Dollo's Law. The evolution of dimorphism in Blechnaceae is neither stepwise nor irreversible, with direct transitions from monomorphism to dimorphism, including several reversions. In contrast, Onocleaceae exhibits an irreversibility to monomorphism only upon further specialization of fertile leaves for humidity-driven spore dispersal; this suggests that additional specialization, not dimorphism alone, may facilitate irreversibility. These results provide insight into the canalization of fertile-sterile leaf dimorphism in seed plants, where the addition of traits like heterospory and integuments lead to further specialization and potential irreversibility. These findings suggest that as new specialized traits evolve alongside preexisting ones, reversion may become increasingly unlikely.

Organ Evolution: Emergence of Multicellular Function

Instances of multicellularity across the tree of life have fostered the evolution of complex organs composed of distinct cell types that cooperate, producing emergent biological functions. How organs originate is a fundamental evolutionary problem that has eluded deep mechanistic and conceptual understanding. Here I propose a cell- to organ-level transitions framework, whereby cooperative division of labor originates and becomes entrenched between cell types through a process of functional niche creation, cell-type subfunctionalization, and irreversible ratcheting of cell interdependencies. Comprehending this transition hinges on explaining how these processes unfold molecularly in evolving populations. Recent single-cell transcriptomic studies and analyses of terminal fate specification indicate that cellular functions are conferred by modular gene expression programs. These discrete components of functional variation may be deployed or combined within cells to introduce new properties into multicellular niches, or partitioned across cells to establish division of labor. Tracing gene expression program evolution at the level of single cells in populations may reveal transitions toward organ complexity.

Nuclear phylogenomics of Asteraceae with increased sampling provides new insights into convergent morphological and molecular evolution

Convergent morphological evolution is widespread in flowering plants, and understanding this phenomenon relies on well-resolved phylogenies. Nuclear phylogenetic reconstruction using transcriptome datasets has been successful in various angiosperm groups, but it is limited to taxa with available fresh materials. Asteraceae, which are one of the two largest angiosperm families and are important for both ecosystems and human livelihood, show multiple examples of convergent evolution. Nuclear Asteraceae phylogenies have resolved relationships among most subfamilies and many tribes, but many phylogenetic and evolutionary questions regarding subtribes and genera remain, owing to limited sampling. Here, we increased the sampling for Asteraceae phylogenetic reconstruction using transcriptomes and genome-skimming datasets and produced nuclear phylogenetic trees with 706 species representing two-thirds of recognized subtribes. Ancestral character reconstruction supports multiple convergent evolutionary events in Asteraceae, with gains and losses of bilateral floral symmetry correlated with diversification of some subfamilies and smaller groups, respectively. Presence of the calyx-related pappus may have been especially important for the success of some subtribes and genera. Molecular evolutionary analyses support the likely contribution of duplications of MADS-box and TCP floral regulatory genes to innovations in floral morphology, including capitulum inflorescences and bilaterally symmetric flowers, potentially promoting the diversification of Asteraceae. Subsequent divergences and reductions in CYC2 gene expression are related to the gain and loss of zygomorphic flowers. This phylogenomic work with greater taxon sampling through inclusion of genome-skimming datasets reveals the feasibility of expanded evolutionary analyses using DNA samples for understanding convergent evolution.

De novo genome assembly and population genomics of a shrub tree Barthea barthei (Hance) krass provide insights into the adaptive color variations

Flower color is a classic example of an ecologically important trait under selection in plants. Understanding the genetic mechanisms underlying shifts in flower color can provide key insights into ecological speciation. In this study, we investigated the genetic basis of flower color divergence in Barthea barthei, a shrub tree species exhibiting natural variation in flower color. We assembled a high-quality genome assembly for B. barthei with a contig N50 of 2.39 Mb and a scaffold N50 of 16.21 Mb. The assembly was annotated with 46,430 protein-coding genes and 1,560 non-coding RNAs. Genome synteny analysis revealed two recent tetraploidization events in B. barthei, estimated to have occurred at approximately 17 and 63 million years ago. These tetraploidization events resulted in massive duplicated gene content, with over 70% of genes retained in collinear blocks. Gene family members of the core regulators of the MBW complex were significantly expanded in B. barthei compared to Arabidopsis, suggesting that these duplications may have provided raw genetic material for the evolution of novel regulatory interactions and the diversification of anthocyanin pigmentation. Transcriptome profiling of B. barthei flowers revealed differential expression of 9 transcription factors related to anthocyanin biosynthesis between the two ecotypes. Six of these differentially expressed transcription factors were identified as high-confidence candidates for adaptive evolution based on positive selection signals. This study provides insights into the genetic basis of flower color divergence and the evolutionary mechanisms underlying ecological adaptation in plants.

Comparative floral development in Mimosa (Fabaceae: Caesalpinioideae) brings new insights into merism lability in the mimosoid clade

The genus Mimosa L. (Leguminosae; Caesalpinioideae; mimosoid clade), comprising more than 500 species, is an intriguing genus because, like other members of the mimosoid clade, it presents an enormous variation in floral characteristics and high merism lability. Thus, this study aimed to elucidate the floral development and identify which ontogenetic pathways give rise to merism variation and andromonoecy in Mimosa caesalpiniifolia, M. pudica, M. bimucronata, and M. candollei. Floral buds at various stages of development and flowers were collected, fixed, and processed for surface analysis (SEM). The development of the buds is synchronous in the inflorescences. Sepals appear simultaneously as individualized primordia in M. caesalpiniifolia and in reversed unidirectional order in M. bimucronata, with union and formation of an early ring-like calyx. Petal primordia appear in unidirectional order, with a noticeably elliptical shape in M. caesalpiniifolia. The wide merism variation in Mimosa results from the absence of organs from inception in the perianth and androecium whorls: in dimerous, trimerous, or tetramerous flowers, the additional organs primordia to compose the expected pentamerous flowers are not initiated. The haplostemonous androecium of M. pudica results from the absence of antepetalous stamens from inception. In the case of intraspecific variations (instabilities), there is no initiation and subsequent abortion of organs in the events of reduction in merosity. In addition, extra primordia are initiated in supernumerary cases. On the other hand, staminate flowers originate from the abortion of the carpel. Mimosa proved to be an excellent model for studying merism variation. The lability is associated with actinomorphic and rather congested flowers in the inflorescences. Our data, in association with others of previous studies, suggest that the high lability in merism appeared in clades that diverged later in the mimosoid clade. Thus, phylogenetic reconstruction studies are needed for more robust evolutionary inferences. The present investigation of ontogenetic processes was relevant to expand our understanding of floral evolution in the genus Mimosa and shed light on the unstable merism in the mimosoid clade.

Reciprocal expression of MADS-box genes and DNA methylation reconfiguration initiate bisexual cones in spruce

The naturally occurring bisexual cone of gymnosperms has long been considered a possible intermediate stage in the origin of flowers, but the mechanisms governing bisexual cone formation remain largely elusive. Here, we employed transcriptomic and DNA methylomic analyses, together with hormone measurement, to investigate the molecular mechanisms underlying bisexual cone development in the conifer Picea crassifolia. Our study reveals a "bisexual" expression profile in bisexual cones, especially in expression patterns of B-class, C-class and LEAFY genes, supporting the out of male model. GGM7 could be essential for initiating bisexual cones. DNA methylation reconfiguration in bisexual cones affects the expression of key genes in cone development, including PcDAL12, PcDAL10, PcNEEDLY, and PcHDG5. Auxin likely plays an important role in the development of female structures of bisexual cones. This study unveils the potential mechanisms responsible for bisexual cone formation in conifers and may shed light on the evolution of bisexuality.

Floral Diversity and Pollination Syndromes in Agave subgenus Manfreda

The genus Agave is an ecological keystone of American deserts and both culturally and economically important in Mexico. Agave is a large genus of about 250 species. The radiation of Agave is marked by an initial adaptation to desert environments and then a secondary diversification of species associated with pollinator groups, such as hummingbirds and nocturnal moths. Phylogenetic analyses place Agave subgenus Manfreda, or the "herbaceous agaves," in a monophyletic clade that likely evolved in part as an adaptation to novel pollination vectors. Here, we present a morphological and observational study assessing the evolution of floral form in response to pollinator specialization within this understudied group. We found significant visitation by hummingbirds and nocturnal moths to several species within the Agave subgenus Manfreda. These observations also align with our morphological analyses of floral organs and support the evolution of distinct pollination syndromes. We found that not all floral morphology is consistent within a pollination syndrome, suggesting hidden diversity in the evolution of floral phenotypes in Agave. We also characterize the morphological variation between herbarium and live specimens, demonstrating that special consideration needs to be made when combining these types of data. This work identifies the potential for studying the functional evolution of diverse floral forms within Agave and demonstrates the need to further explore ecological and evolutionary relationships to understand pollinator influence on diversification in the genus.

The origin and evolution of carpels and fruits from an evo-devo perspective

The flower is an evolutionary innovation in angiosperms that drives the evolution of biodiversity. The carpel is integral to a flower and develops into fruits after fertilization, while the perianth, consisting of the calyx and corolla, is decorative to facilitate pollination and protect the internal organs, including the carpels and stamens. Therefore, the nature of flower origin is carpel and stamen origin, which represents one of the greatest and fundamental unresolved issues in plant evolutionary biology. Here, we briefly summarize the main progress and key genes identified for understanding floral development, focusing on the origin and development of the carpels. Floral ABC models have played pioneering roles in elucidating flower development, but remain insufficient for resolving flower and carpel origin. The genetic basis for carpel origin and subsequent diversification leading to fruit diversity also remains elusive. Based on current research progress and technological advances, simplified floral models and integrative evolutionary-developmental (evo-devo) strategies are proposed for elucidating the genetics of carpel origin and fruit evolution. Stepwise birth of a few master regulatory genes and subsequent functional diversification might play a pivotal role in these evolutionary processes. Among the identified transcription factors, AGAMOUS (AG) and CRABS CLAW (CRC) may be the two core regulatory genes for carpel origin as they determine carpel organ identity, determinacy, and functionality. Therefore, a comparative identification of their protein-protein interactions and downstream target genes between flowering and non-flowering plants from an evo-devo perspective may be primary projects for elucidating carpel origin and development.

Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics

Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.

Development and Evolution of Unisexual Flowers: A Review

The development of unisexual flowers has been described in a large number of taxa, sampling the diversity of floral phenotypes and sexual systems observed in extant angiosperms, in studies focusing on floral ontogeny, on the evo-devo of unisexuality, or on the genetic and chromosomal bases of unisexuality. We review here such developmental studies, aiming at characterizing the diversity of ontogenic pathways leading to functionally unisexual flowers. In addition, we present for the first time and in a two-dimensional morphospace a quantitative description of the developmental rate of the sexual organs in functionally unisexual flowers, in a non-exhaustive sampling of angiosperms with contrasted floral morphologies. Eventually, recommendations are provided to help plant evo-devo researchers and botanists addressing macroevolutionary and ecological issues to more precisely select the taxa, the biological material, or the developmental stages to be investigated.

Case not closed: the mystery of the origin of the carpel

The carpel is a fascinating structure that plays a critical role in flowering plant reproduction and contributed greatly to the evolutionary success and diversification of flowering plants. The remarkable feature of the carpel is that it is a closed structure that envelopes the ovules and after fertilization develops into the fruit which protects, helps disperse, and supports seed development into a new plant. Nearly all plant-based foods are either derived from a flowering plant or are a direct product of the carpel. Given its importance it's no surprise that plant and evolutionary biologists have been trying to explain the origin of the carpel for a long time. Before carpel evolution seeds were produced on open leaf-like structures that are exposed to the environment. When the carpel evolved in the stem lineage of flowering plants, seeds became protected within its closed structure. The evolutionary transition from that open precursor to the closed carpel remains one of the greatest mysteries of plant evolution. In recent years, we have begun to complete a picture of what the first carpels might have looked like. On the other hand, there are still many gaps in our understanding of what the precursor of the carpel looked like and what changes to its developmental mechanisms allowed for this evolutionary transition. This review aims to present an overview of existing theories of carpel evolution with a particular emphasis on those that account for the structures that preceded the carpel and/or present testable developmental hypotheses. In the second part insights from the development and evolution of diverse plant organs are gathered to build a developmental hypothesis for the evolutionary transition from a hypothesized laminar open structure to the closed structure of the carpel.

Insights into the molecular evolution of fertilization mechanism in land plants

Comparative genetics and genomics among green plants, including algae, provide deep insights into the evolution of land plant sexual reproduction. Land plants have evolved successive changes during their conquest of the land and innovations in sexual reproduction have played a major role in their terrestrialization. Recent years have seen many revealing dissections of the molecular mechanisms of sexual reproduction and much new genomics data from the land plant lineage, including early diverging land plants, as well as algae. This new knowledge is being integrated to further understand how sexual reproduction in land plants evolved, identifying highly conserved factors and pathways, but also molecular changes that underpinned the emergence of new modes of sexual reproduction. Here, we review recent advances in the knowledge of land plant sexual reproduction from an evolutionary perspective and also revisit the evolution of angiosperm double fertilization.

Biosynthesis and emission of methyl hexanoate, the major constituent of floral scent of a night-blooming water lily Victoriacruziana

Among the factors that have made flowering plants the most species-rich lineage of land plants is the interaction between flower and insect pollinators, for which floral scent plays a pivotal role. Water lilies belong to the ANA (Amborellales, Nymphaeales, and Austrobaileyales) grade of basal flowering plants. In this study, Victoria cruziana was investigated as a model night-blooming water lily for floral scent biosynthesis. Four volatile compounds, including three benzenoids and one fatty acid methyl ester methyl hexanoate, were detected from the flowers of V. cruziana during their first bloom, with methyl hexanoate accounting for 45 % of total floral volatile emission. Emission rates were largely constant before significant drop starting at the end of second bloom. To understand the molecular basis of floral scent biosynthesis in V. cruziana, particularly methyl hexanoate, a transcriptome from the whole flowers at the full-bloom stage was created and analyzed. Methyl hexanoate was hypothesized to be biosynthesized by SABATH methyltransferases. From the transcriptome, three full-length SABATH genes designated VcSABATH1-3 were identified. A full-length cDNA for each of the three VcSABATH genes was expressed in Escherichia coli to produce recombinant proteins. When tested in in vitro methyltransferase enzyme assays with different fatty acids, both VcSABATH1 and VcSABATH3 exhibited highest levels of activity with hexanoic acid to produce methyl hexanoate, with the specific activity of VcSABATH1 being about 15 % of that for VcSABATH3. VcSABATH1 and VcSABATH3 showed the highest levels of expression in stamen and pistil, respectively. In phylogenetic analysis, three VcSABATH genes clustered with other water lily SABATH methyltransferase genes including the one known for making other fatty acid methyl esters, implying both a common evolutionary origin and functional divergence. Fatty acid methyl esters are not frequent constituents of floral scents of mesangiosperms, pointing to the importance for the evolution of novel fatty acid methyltransferase for making fatty acid methyl esters in the pollination biology of water lilies.

Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants

The appearance of plant organs mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes and the development of novel regulatory programmes. However, no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we generated gene expression atlases for various organs and gametes of ten plant species comprising bryophytes, vascular plants, gymnosperms and flowering plants. A comparative analysis of the atlases identified hundreds of organ- and gamete-specific orthogroups and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, our results suggest that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, which indicates that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function.

Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants

The appearance of plant organs mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes and the development of novel regulatory programmes. However, no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we generated gene expression atlases for various organs and gametes of ten plant species comprising bryophytes, vascular plants, gymnosperms and flowering plants. A comparative analysis of the atlases identified hundreds of organ- and gamete-specific orthogroups and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, our results suggest that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, which indicates that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function.

SMRT and Illumina RNA Sequencing and Characterization of a Key NAC Gene LoNAC29 during the Flower Senescence in Lilium oriental 'Siberia'

Lily (Lilium spp.) is an important cut flower around the world. Flower senescence in lilies is characterized by the wilting and abscission of tepals, which results in a decrease in flower quality and huge economic loss. However, the mechanism underlying flower senescence in lilies is largely unknown. In this study, single-molecule, real-time (SMRT) and Illumina sequencing were carried out in L. oriental ‘Siberia’. Sequencing yielded 73,218 non-redundant transcripts, with an N50 of 3792 bp. These data were further integrated with three published transcriptomes through cogent analysis, which yielded 62,960 transcripts, with an increase in N50 of 3935 bp. Analysis of differentially expressed genes showed that 319 transcription factors were highly upregulated during flower senescence. The expression of twelve NAC genes and eleven senescence-associated genes (SAGs) showed that LoNAC29 and LoSAG39 were highly expressed in senescent flowers. Transient overexpression of LoNAC29 and LoSAG39 in tepals of lily notably accelerated flower senescence, and the promoter activity of LoSAG39 was strongly induced by LoNAC29. This work supported new evidence for the molecular mechanism of flower senescence and provided better sequence data for further study in lilies.

CmNAC73 Mediates the Formation of Green Color in Chrysanthemum Flowers by Directly Activating the Expression of Chlorophyll Biosynthesis Genes HEMA1 and CRD1

Chrysanthemum is one of the most beautiful and popular flowers in the world, and the flower color is an important ornamental trait of chrysanthemum. Compared with other flower colors, green flowers are relatively rare. The formation of green flower color is attributed to the accumulation of chlorophyll; however, the regulatory mechanism of chlorophyll metabolism in chrysanthemum with green flowers remains largely unknown. In this study, we performed Illumina RNA sequencing on three chrysanthemum materials, Chrysanthemum vestitum and Chrysanthemum morifolium cultivars ‘Chunxiao’ and ‘Green anna’, which produce white, light green and dark green flowers, respectively. Based on the results of comparative transcriptome analysis, a gene encoding a novel NAC family transcription factor, CmNAC73, was found to be highly correlated to chlorophyll accumulation in the outer whorl of ray florets in chrysanthemum. The results of transient overexpression in chrysanthemum leaves showed that CmNAC73 acts as a positive regulator of chlorophyll biosynthesis. Furthermore, transactivation and yeast one-hybrid assays indicated that CmNAC73 directly binds to the promoters of chlorophyll synthesis-related genes HEMA1 and CRD1. Thus, this study uncovers the transcriptional regulation of chlorophyll synthesis-related genes HEMA1 and CRD1 by CmNAC73 and provides new insights into the development of green flower color in chrysanthemum and chlorophyll metabolism in plants.

Evolutionary lability in floral ontogeny affects pollination biology in Trimezieae

PREMISE

There is little direct evidence linking floral development and pollination biology in plants. We characterize both aspects in plain and ornamented flowers of Trimezieae (Iridaceae) to investigate how changes in floral ontogeny may affect their interactions with pollinators through time.

METHODS

We examined floral ontogeny in 11 species and documented pollination biology in five species displaying a wide range of floral morphologies. We coded and reconstructed ancestral states of flower types over the tribal phylogeny to estimate the frequency of transition between different floral types.

RESULTS

All Trimezieae flowers are similar in early floral development, but ornamented flowers have additional ontogenetic steps compared with plain flowers, indicating heterochrony. Ornamented flowers have a hinge pollination mechanism (newly described here) and attract more pollinator guilds, while plain flowers offer less variety of resources for a shorter time. Although the ornamented condition is plesiomorphic in this clade, shifts to plain flowers have occurred frequently and abruptly during the past 5 million years, with some subsequent reversals.

CONCLUSIONS

Heterochrony has resulted in labile morphological changes during flower evolution in Trimezieae. Counterintuitively, species with plain flowers, which are endemic to the campo rupestre, are derived within the tribe and show a higher specialization than the ornamented species, with the former being visited by pollen-collecting bees only.

On the waiting time until coordinated mutations get fixed in regulatory sequences

In this paper we consider the time evolution of a population of size N with overlapping generations, in the vicinity of m genes. We assume that this population is subject to point mutations, genetic drift, and selection. More specifically, we analyze the statistical distribution of the waiting time T_m until the expression of these genes have changed for all individuals, when transcription factors recognize and attach to short DNA-sequences (binding sites) within regulatory sequences in the neighborhoods of the m genes. The evolutionary dynamics is described by a multitype Moran process, where each individual is assigned a m×L regulatory array that consists of regulatory sequences with L nucleotides for all m genes. We study how the waiting time distribution depends on the number of genes, the mutation rate, the length of the binding sites, the length of the regulatory sequences, and the way in which the targeted binding sites are coordinated for different genes in terms of selection coefficients. These selection coefficients depend on how many binding sites have appeared so far, and possibly on their order of appearance. We also allow for back mutations, whereby some acquired binding sites may be lost over time. It is further assumed that the mutation rate is small enough to warrant a fixed state population, so that all individuals have the same regulatory array, at any given time point, until the next successful mutation arrives in some individual and spreads to the rest of the population. We further incorporate stochastic tunneling, whereby successful mutations get mutated before their fixation. A crucial part of our approach is to divide the huge state space of regulatory arrays into a small number of components, assuming that the array component varies as a Markov process over time. This implies that T_m is the time until this Markov process hits an absorbing state, with a phase-type distribution. A number of interesting results can be derived from our general setup, for instance that the expected waiting time increases exponentially with m, for a selectively neutral model, when back-mutations are possible.

Reconstructing development of the earliest seed integuments raises a new hypothesis for the evolution of ancestral seed-bearing structures

How plant seeds originated remains unresolved, in part due to disconnects between fossil intermediates and developmental genetics in extant species. The Carboniferous fossil Genomosperma is considered among the most primitive known seeds, with highly lobed integument and exposed nucellus. We have used this key fossil taxon to investigate the evolutionary origins of seed development. We examined sectioned Genomosperma specimens using modern digital 3D reconstruction techniques and established population-level measurements of Genomosperma ovules for quantitative analysis. Genomosperma ovules show significant variation in integumentary lobe fusion and curvature. Our analysis suggests that this variation represents a single species with significant variations in lobe number and fusion, reminiscent of floral development in extant species. We conclude that changes in lobe flexure occurred late in development, consistent with a previously hypothesized function in pollen guidance/retention. We also identify seeds of Genomosperma within cupules for the first time. The presence of a cupule adds evidence towards the plesiomorphy of cupules within seed plants. Together with the similarities identified between the Genomosperma lobed integument and floral organs, we propose that the cupule, integument and nucellus together developed in a shoot-like fashion, potentially ancestral to extant seed plant reproductive shoots.

Pollination syndromes in the 21st century: where do we stand and where may we go?

Pollination syndromes, recurring suites of floral traits appearing in connection with specific functional pollinator groups, have served for decades to organise floral diversity under a functional-ecological perspective. Some potential caveats, such as over-simplification of complex plant-animal interactions or lack of empirical observations, have been identified and discussed in recent years. Which of these caveats do indeed cause problems, which have been solved and where do future possibilities lie? I address these questions in a review of the pollination-syndrome literature of 2010 to 2019. I show that the majority of studies was based on detailed empirical pollinator observations and could reliably predict pollinators based on a few floral traits such as colour, shape or reward. Some traits (i.e. colour) were less reliable in predicting pollinators than others (i.e. reward, corolla width), however. I stress that future studies should consider floral traits beyond those traditionally recorded to expand our understanding of mechanisms of floral evolution. I discuss statistical methods suitable for objectively analysing the interplay of system-specific evolutionary constraints, pollinator-mediated selection and adaptive trade-offs at microecological and macroecological scales. I exemplify my arguments on an empirical dataset of floral traits of a neotropical plant radiation in the family Melastomataceae.

Revisiting floral fusion: the evolution and molecular basis of a developmental innovation

Throughout the evolution of the angiosperm flower, developmental innovations have enabled the modification or elaboration of novel floral organs enabling subsequent diversification and expansion into new niches, for example the formation of novel pollinator relationships. One such developmental innovation is the fusion of various floral organs to form complex structures. Multiple types of floral fusion exist; each type may be the result of different developmental processes and is likely to have evolved multiple times independently across the angiosperm tree of life. The development of fused organs is thought to be mediated by the NAM/CUC3 subfamily of NAC transcription factors, which mediate boundary formation during meristematic development. The goal of this review is to (i) introduce the development of fused floral organs as a key 'developmental innovation', facilitated by a change in the expression of NAM/CUC3 transcription factors; (ii) provide a comprehensive overview of floral fusion phenotypes amongst the angiosperms, defining well-known fusion phenotypes and applying them to a systematic context; and (iii) summarize the current molecular knowledge of this phenomenon, highlighting the evolution of the NAM/CUC3 subfamily of transcription factors implicated in the development of fused organs. The need for a network-based analysis of fusion is discussed, and a gene regulatory network responsible for directing fusion is proposed to guide future research in this area.

Genome-Wide Association Mapping of Floral Traits in Cultivated Sunflower (Helianthus annuus)

Floral morphology and pigmentation are both charismatic and economically relevant traits associated with cultivated sunflower (Helianthus annuus L.). Recent work has linked floral morphology and pigmentation to pollinator efficiency and seed yield. Understanding the genetic architecture of such traits is essential for crop improvement, and gives insight into the role of genetic constraints in shaping floral diversity. A diversity panel of 288 sunflower genotypes was phenotyped for a variety of morphological, phenological, and color traits in both a greenhouse and a field setting. Association mapping was performed using 5788 SNP markers using a mixed linear model approach. Several dozen markers across 10 linkage groups were significantly associated with variation in morphological and color trait variation. Substantial trait plasticity was observed between greenhouse and field phenotyping, and associations differed between environments. Color traits mapped more strongly than morphology in both settings, with markers together explaining 16% of petal carotenoid content in the greenhouse, and 17% and 24% of variation in disc anthocyanin presence in the field and greenhouse, respectively. Morphological traits like disc size mapped more strongly in the field, with markers together explaining up to 19% of disc size variation. Loci identified here through association mapping within cultivated germplasm differ from those identified through biparental crosses between modern cultivated sunflower and either its wild progenitor or domesticated landraces. Several loci lie within genomic regions involved in domestication. Differences between phenotype expression under greenhouse and field conditions highlight the importance of plasticity in determining floral morphology and pigmentation.

Evolution of Darwin's Peloric Gloxinia (Sinningia speciosa) Is Caused by a Null Mutation in a Pleiotropic TCP Gene

Unlike most crops, which were domesticated through long periods of selection by ancient humans, horticultural plants were primarily domesticated through intentional selection over short time periods. The molecular mechanisms underlying the origin and spread of novel traits in the domestication process have remained largely unexplored in horticultural plants. Gloxinia (Sinningia speciosa), whose attractive peloric flowers influenced the thoughts of Darwin, have been cultivated since the early 19th century, but its origin and genetic basis are currently unknown. By employing multiple experimental approaches including genetic analysis, genotype-phenotype associations, gene expression analysis, and functional interrogations, we showed that a single gene encoding a TCP protein, SsCYC, controls both floral orientation and zygomorphy in gloxinia. We revealed that a causal mutation responsible for the development of peloric gloxinia lies in a 10-bp deletion in the coding sequence of SsCYC. By combining genetic inference and literature searches, we have traced the putative ancestor and reconstructed the domestication path of the peloric gloxinia, in which a 10-bp deletion in SsCYC under selection triggered its evolution from the wild progenitor. The results presented here suggest that a simple genetic change in a pleiotropic gene can promote the elaboration of floral organs under intensive selection pressure.

Reconstructing the ancestral flower of extant angiosperms: the 'war of the whorls' is heating up

The origin of the angiosperm flower is a long-standing problem of botany and evolutionary biology. One widely accepted milestone towards solving it is the reconstruction of the ancestral flower of extant angiosperms, here termed 'AFEA'. A recent approach employing novel methods gave results that were not anticipated. Most notably the reconstructed phyllotaxis of AFEA soon was criticized and sparked a heated debate in the literature. To better explain, clarify, and perhaps cool the debate, we first summarize the results of previous attempts to reconstruct AFEA and contrast them with the more recent, controversial prediction of its structure. We then outline the major arguments made by contrasting parties in the recent debate. Finally, we discuss two key topics, the molecular mechanism of phyllotaxis and the role of gene regulatory networks during flower development and evolution, that may help to clarify the issue in the intermediate future.

The role of APETALA1 in petal number robustness

Invariant floral forms are important for reproductive success and robust to natural perturbations. Petal number, for example, is invariant in Arabidopsis thaliana flowers. However, petal number varies in the closely related species Cardamine hirsuta, and the genetic basis for this difference between species is unknown. Here we show that divergence in the pleiotropic floral regulator APETALA1 (AP1) can account for the species-specific difference in petal number robustness. This large effect of AP1 is explained by epistatic interactions: A. thaliana AP1 confers robustness by masking the phenotypic expression of quantitative trait loci controlling petal number in C. hirsuta. We show that C. hirsuta AP1 fails to complement this function of A. thaliana AP1, conferring variable petal number, and that upstream regulatory regions of AP1 contribute to this divergence. Moreover, variable petal number is maintained in C. hirsuta despite sufficient standing genetic variation in natural accessions to produce plants with four-petalled flowers.

Water relations of Calycanthus flowers: Hydraulic conductance, capacitance, and embolism resistance

For most angiosperms, producing and maintaining flowers is critical to sexual reproduction, yet little is known about the physiological processes involved in maintaining flowers throughout anthesis. Among extant species, flowers of the genus Calycanthus have the highest hydraulic conductance and vein densities of species measured to date, yet they can wilt by late morning under hot conditions. Here, we combine diurnal measurements of gas exchange and water potential, pressure-volume relations, functional responses of gas exchange, and characterization of embolism formation using high resolution X-ray computed microtomography to determine drought responses of Calycanthus flowers. Transpiration from flowers frequently exceeded transpiration from leaves, and flowers were unable to limit transpiration under conditions of high vapour pressure deficit. As a result, they rely heavily on hydraulic capacitance to prevent water potential declines. Despite having high water potentials at turgor loss, flowers were very resistant to embolism formation, with no embolism apparent until tepal water potentials had declined to -2 MPa. Although Calycanthus flowers remain connected to the stem xylem and have high hydraulic capacitance, their inability to curtail transpiration leads to turgor loss. These results suggest that extreme climate events may cause flower failure, potentially preventing successful reproduction.

Changing MADS-Box Transcription Factor Protein-Protein Interactions as a Mechanism for Generating Floral Morphological Diversity

Flowers display fantastic morphological diversity. Despite extreme variability in form, floral organ identity is specified by a core set of deeply conserved proteins-the floral MADS-box transcription factors. This indicates that while core gene function has been maintained, MADS-box transcription factors have evolved to regulate different downstream genes. Thus, the evolution of gene regulation downstream of the MADS-box transcription factors is likely central to the evolution of floral form. Gene regulation is determined by the combination of transcriptional regulators present at a particular cis-regulatory element at a particular time. Therefore, the interactions between transcription factors can be of profound importance in determining patterns of gene regulation. Here, after a short primer on flowers and floral morphology, I discuss the centrality of protein-protein interactions to MADS-box transcription factor function, and review the evidence that the evolution of MADS-box protein-protein interactions is a key driver in the evolution of gene regulation downstream of the MADS-box genes.

Recent Trends in Plant Protein Complex Analysis in a Developmental Context

Because virtually all proteins interact with other proteins, studying protein-protein interactions (PPIs) is fundamental in understanding protein function. This is especially true when studying specific developmental processes, in which proteins often make developmental stage- or tissue specific interactions. However, studying these specific PPIs in planta can be challenging. One of the most widely adopted methods to study PPIs in planta is affinity purification coupled to mass spectrometry (AP/MS). Recent developments in the field of mass spectrometry have boosted applications of AP/MS in a developmental context. This review covers two main advancements in the field of affinity purification to study plant developmental processes: increasing the developmental resolution of the harvested tissues and moving from affinity purification to affinity enrichment. Furthermore, we discuss some new affinity purification approaches that have recently emerged and could have a profound impact on the future of protein interactome analysis in plants.

Understanding the role of floral development in the evolution of angiosperm flowers: clarifications from a historical and physico-dynamic perspective

Flower morphology results from the interaction of an established genetic program, the influence of external forces induced by pollination systems, and physical forces acting before, during and after initiation. Floral ontogeny, as the process of development from a meristem to a fully developed flower, can be approached either from a historical perspective, as a "recapitulation of the phylogeny" mainly explained as a process of genetic mutations through time, or from a physico-dynamic perspective, where time, spatial pressures, and growth processes are determining factors in creating the floral morphospace. The first (historical) perspective clarifies how flower morphology is the result of development over time, where evolutionary changes are only possible using building blocks that are available at a certain stage in the developmental history. Flowers are regulated by genetically determined constraints and development clarifies specific transitions between different floral morphs. These constraints are the result of inherent mutations or are induced by the interaction of flowers with pollinators. The second (physico-dynamic) perspective explains how changes in the physical environment of apical meristems create shifts in ontogeny and this is reflected in the morphospace of flowers. Changes in morphology are mainly induced by shifts in space, caused by the time of initiation (heterochrony), pressure of organs, and alterations of the size of the floral meristem, and these operate independently or in parallel with genetic factors. A number of examples demonstrate this interaction and its importance in the establishment of different floral forms. Both perspectives are complementary and should be considered in the understanding of factors regulating floral development. It is suggested that floral evolution is the result of alternating bursts of physical constraints and genetic stabilization processes following each other in succession. Future research needs to combine these different perspectives in understanding the evolution of floral systems and their diversification.

How to Evolve a Perianth: A Review of Cadastral Mechanisms for Perianth Identity

The flower of angiosperms is considered to be a major evolutionary innovation that impacted the whole biome. In particular, two properties of the flower are classically linked to its ecological success: bisexuality and a differentiated perianth with sepals and petals. Although the molecular basis for floral organ identity is well understood in extant species and summarized in the famous ABC model, how perianth identity appeared during evolution is still unknown. Here we propose that cadastral mechanisms that maintain reproductive organ identities to the center of the flower could have supported perianth evolution. In particular, repressing B- and C-class genes expression toward the inner whorls of the flower, is a key process to isolate domains with sepal and petal identity in the outer whorls. We review from the literature in model species the diverse regulators that repress B- and C-class genes expression to the center of the flower. This review highlights the existence of both unique and conserved repressors between species, and possible candidates to investigate further in order to shed light on perianth evolution.

The ancestral flower of angiosperms and its early diversification

Recent advances in molecular phylogenetics and a series of important palaeobotanical discoveries have revolutionized our understanding of angiosperm diversification. Yet, the origin and early evolution of their most characteristic feature, the flower, remains poorly understood. In particular, the structure of the ancestral flower of all living angiosperms is still uncertain. Here we report model-based reconstructions for ancestral flowers at the deepest nodes in the phylogeny of angiosperms, using the largest data set of floral traits ever assembled. We reconstruct the ancestral angiosperm flower as bisexual and radially symmetric, with more than two whorls of three separate perianth organs each (undifferentiated tepals), more than two whorls of three separate stamens each, and more than five spirally arranged separate carpels. Although uncertainty remains for some of the characters, our reconstruction allows us to propose a new plausible scenario for the early diversification of flowers, leading to new testable hypotheses for future research on angiosperms.

Evolving Ideas on the Origin and Evolution of Flowers: New Perspectives in the Genomic Era

The origin of the flower was a key innovation in the history of complex organisms, dramatically altering Earth's biota. Advances in phylogenetics, developmental genetics, and genomics during the past 25 years have substantially advanced our understanding of the evolution of flowers, yet crucial aspects of floral evolution remain, such as the series of genetic and morphological changes that gave rise to the first flowers; the factors enabling the origin of the pentamerous eudicot flower, which characterizes ∼70% of all extant angiosperm species; and the role of gene and genome duplications in facilitating floral innovations. A key early concept was the ABC model of floral organ specification, developed by Elliott Meyerowitz and Enrico Coen and based on two model systems,Arabidopsis thalianaandAntirrhinum majus Yet it is now clear that these model systems are highly derived species, whose molecular genetic-developmental organization must be very different from that of ancestral, as well as early, angiosperms. In this article, we will discuss how new research approaches are illuminating the early events in floral evolution and the prospects for further progress. In particular, advancing the next generation of research in floral evolution will require the development of one or more functional model systems from among the basal angiosperms and basal eudicots. More broadly, we urge the development of "model clades" for genomic and evolutionary-developmental analyses, instead of the primary use of single "model organisms." We predict that new evolutionary models will soon emerge as genetic/genomic models, providing unprecedented new insights into floral evolution.

The Evolution of COP9 Signalosome in Unicellular and Multicellular Organisms

The COP9 signalosome (CSN) is a highly conserved protein complex, recently being crystallized for human. In mammals and plants the COP9 complex consists of nine subunits, CSN 1–8 and CSNAP. The CSN regulates the activity of culling ring E3 ubiquitin and plays central roles in pleiotropy, cell cycle, and defense of pathogens. Despite the interesting and essential functions, a thorough analysis of the CSN subunits in evolutionary comparative perspective is missing. Here we compared 61 eukaryotic genomes including plants, animals, and yeasts genomes and show that the most conserved subunits of eukaryotes among the nine subunits are CSN2 and CSN5. This may indicate a strong evolutionary selection for these two subunits. Despite the strong conservation of the protein sequence, the genomic structures of the intron/exon boundaries indicate no conservation at genomic level. This suggests that the gene structure is exposed to a much less selection compared with the protein sequence. We also show the conservation of important active domains, such as PCI (proteasome lid-CSN-initiation factor) and MPN (MPR1/PAD1 amino-terminal). We identified novel exons and alternative splicing variants for all CSN subunits. This indicates another level of complexity of the CSN. Notably, most COP9-subunits were identified in all multicellular and unicellular eukaryotic organisms analyzed, but not in prokaryotes or archaeas. Thus, genes encoding CSN subunits present in all analyzed eukaryotes indicate the invention of the signalosome at the root of eukaryotes. The identification of alternative splice variants indicates possible “mini-complexes” or COP9 complexes with independent subunits containing potentially novel and not yet identified functions.

Stochastic variation in Cardamine hirsuta petal number

BACKGROUND AND AIMS

Floral development is remarkably robust in terms of the identity and number of floral organs in each whorl, whereas vegetative development can be quite plastic. This canalization of flower development prevents the phenotypic expression of cryptic genetic variation, even in fluctuating environments. A cruciform perianth with four petals is a hallmark of the Brassicaceae family, typified in the model species Arabidopsis thaliana However, variable petal loss is found in Cardamine hirsuta, a genetically tractable relative of A. thaliana Cardamine hirsuta petal number varies in response to stochastic, genetic and environmental perturbations, which makes it an interesting model to study mechanisms of decanalization and the expression of cryptic variation.

METHODS

Multitrait quantitative trait locus (QTL) analysis in recombinant inbred lines (RILs) was used to identify whether the stochastic variation found in C. hirsuta petal number had a genetic basis.

KEY RESULTS

Stochastic variation (standard error of the average petal number) was found to be a heritable phenotype, and four QTL that influenced this trait were identified. The sensitivity to detect these QTL effects was increased by accounting for the effect of ageing on petal number variation. All QTL had significant effects on both average petal number and its standard error, indicating that these two traits share a common genetic basis. However, for some QTL, a degree of independence was found between the age of the flowers where allelic effects were significant for each trait.

CONCLUSIONS

Stochastic variation in C. hirsuta petal number has a genetic basis, and common QTL influence both average petal number and its standard error. Allelic variation at these QTL can, therefore, modify petal number in an age-specific manner via effects on the phenotypic mean and stochastic variation. These results are discussed in the context of trait evolution via a loss of robustness.

Evolutionary Dynamics of Floral Homeotic Transcription Factor Protein-Protein Interactions

Protein–protein interactions (PPIs) have widely acknowledged roles in the regulation of development, but few studies have addressed the timing and mechanism of shifting PPIs over evolutionary history. The B-class MADS-box transcription factors, PISTILLATA (PI) and APETALA3 (AP3) are key regulators of floral development. PI-like (PI^L) and AP3-like (AP3^L) proteins from a number of plants, including Arabidopsis thaliana (Arabidopsis) and the grass Zea mays (maize), bind DNA as obligate heterodimers. However, a PI^L protein from the grass relative Joinvillea can bind DNA as a homodimer. To ascertain whether Joinvillea PI^L homodimerization is an anomaly or indicative of broader trends, we characterized PI^L dimerization across the Poales and uncovered unexpected evolutionary lability. Both obligate B-class heterodimerization and PI^L homodimerization have evolved multiple times in the order, by distinct molecular mechanisms. For example, obligate B-class heterodimerization in maize evolved very recently from PI^L homodimerization. A single amino acid change, fixed during domestication, is sufficient to toggle one maize PI^L protein between homodimerization and obligate heterodimerization. We detected a signature of positive selection acting on residues preferentially clustered in predicted sites of contact between MADS-box monomers and dimers, and in motifs that mediate MADS PPI specificity in Arabidopsis. Changing one positively selected residue can alter PI^L dimerization activity. Furthermore, ectopic expression of a Joinvillea PI^L homodimer in Arabidopsis can homeotically transform sepals into petals. Our results provide a window into the evolutionary remodeling of PPIs, and show that novel interactions have the potential to alter plant form in a context-dependent manner.

A transcriptomics investigation into pine reproductive organ development

The development of reproductive structures in gymnosperms is still poorly studied because of a lack of genomic information and useful genetic tools. The hermaphroditic reproductive structure derived from unisexual gymnosperms is an even less studied aspect of seed plant evolution. To extend our understanding of the molecular mechanism of hermaphroditism and the determination of sexual identity of conifer reproductive structures in general, unisexual and bisexual cones from Pinus tabuliformis were profiled for gene expression using 60K microarrays. Expression patterns of genes during progression of sexual cone development were analysed using RNA-seq. The results showed that, overall, the transcriptomes of male structures in bisexual cones were more similar to those of female cones. However, the expression of several MADS-box genes in the bisexual cones was similar to that of male cones at the more juvenile developmental stage, while despite these expression shifts, male structures of bisexual cones and normal male cones were histologically indistinguishable and cone development was continuous. This study represents a starting point for in-depth analysis of the molecular regulation of cone development and also the origin of hermaphroditism in pine.

The genetic architecture of petal number in Cardamine hirsuta

Invariant petal number is a characteristic of most flowers and is generally robust to genetic and environmental variation. We took advantage of the natural variation found in Cardamine hirsuta petal number to investigate the genetic basis of this trait in a case where robustness was lost during evolution. We used quantitative trait locus (QTL) analysis to characterize the genetic architecture of petal number. Αverage petal number showed transgressive variation from zero to four petals in five C. hirsuta mapping populations, and this variation was highly heritable. We detected 15 QTL at which allelic variation affected petal number. The effects of these QTL were relatively small in comparison with alleles induced by mutagenesis, suggesting that natural selection may act to maintain petal number within its variable range below four. Petal number showed a temporal trend during plant ageing, as did sepal trichome number, and multi-trait QTL analysis revealed that these age-dependent traits share a common genetic basis. Our results demonstrate that petal number is determined by many genes of small effect, some of which are age-dependent, and suggests a mechanism of trait evolution via the release of cryptic variation.

Species diversity driven by morphological and ecological disparity: a case study of comparative seed morphology and anatomy across a large monocot order

Phenotypic variation can be attributed to genetic heritability as well as biotic and abiotic factors. Across Zingiberales, there is a high variation in the number of species per clade and in phenotypic diversity. Factors contributing to this phenotypic variation have never been studied in a phylogenetic or ecological context. Seeds of 166 species from all eight families in Zingiberales were analyzed for 51 characters using synchrotron based 3D X-ray tomographic microscopy to determine phylogenetically informative characters and to understand the distribution of morphological disparity within the order. All families are distinguishable based on seed characters. Non-metric multidimensional scaling analyses show Zingiberaceae occupy the largest seed morphospace relative to the other families, and environmental analyses demonstrate that Zingiberaceae inhabit both temperate and tropical regions, while other Zingiberales are almost exclusively tropical. Temperate species do not cluster in morphospace nor do they share a common suite of character states. This suggests that the diversity seen is not driven by adaptation to temperate niches; rather, the morphological disparity seen likely reflects an underlying genetic plasticity that allowed Zingiberaceae to repeatedly colonize temperate environments. The notable morphoanatomical variety in Zingiberaceae seeds may account for their extraordinary ecological success and high species diversity as compared to other Zingiberales.

Origin and evolution of Petrocosmea (Gesneriaceae) inferred from both DNA sequence and novel findings in morphology with a test of morphology-based hypotheses

BACKGROUND

Petrocosmea Oliver (Gesneriaceae) currently comprises 38 species with four non-nominate varieties, nearly all of which have been described solely from herbarium specimens. However, the dried specimens have obscured the full range of extremely diverse morphological variation that exists in the genus and has resulted in a poor subgeneric classification system that does not reflect the evolutionary history of this group. It is important to develop innovative methods to find new morphological traits and reexamine and reevaluate the traditionally used morphological data based on new hypothesis. In addition, Petrocosmea is a mid-sized genus but exhibits extreme diverse floral variants. This makes the genus of particular interest in addressing the question whether there are any key factors that is specifically associated with their evolution and diversification.

RESULTS

Here we present the first phylogenetic analyses of the genus based on dense taxonomic sampling and multiple genes combined with a comprehensive morphological investigation. Maximum-parsimony, maximum likelihood and Bayesian analyses of molecular data from two nuclear DNA and six cpDNA regions support the monophyly of Petrocosmea and recover five major clades within the genus, which is strongly corroborated by the reconstruction of ancestral states for twelve new morphological characters directly observed from living material. Ancestral area reconstruction shows that its most common ancestor was likely located east and southeast of the Himalaya-Tibetan plateau. The origin of Petrocosmea from a potentially Raphiocarpus-like ancestor might have involved a series of morphological modifications from caulescent to acaulescent habit as well as from a tetrandrous flower with a long corolla-tube to a diandrous flower with a short corolla-tube, also evident in the vestigial caulescent habit and transitional floral form in clade A that is sister to the remainder of the genus. Among the five clades in Petrocosmea, the patterns of floral morphological differentiation are consistent with discontinuous lineage-associated morphotypes as a repeated adaptive response to alternative environments.

CONCLUSION

Our results suggest that the lineage-specific morphological differentiations reflected in the upper lip, a functional organ for insect pollination, are likely adaptive responses to pollinator shifts. We further recognize that the floral morphological diversification in Petrocosmea involves several evolutionary phenomena, i.e. evolutionary successive specialization, reversals, parallel evolution, and convergent evolution, which are probably associated with adaptation to pollination against the background of heterogeneous abiotic and biotic environments in the eastern wing regions of Himalaya-Tibetan plateau.

Inferring directions of evolution from patterns of variation: the legacy of Sergei Meyen

In the era of the extended evolutionary synthesis, which no longer considers natural selection as the only leading factor of evolution, it is meaningful to revisit the legacy of biologists who discussed the role of alternative factors. Here we analyze the evolutionary views of Sergei Meyen (1935-1987), a paleobotanist who argued that the theory of evolution should incorporate a "nomothetical" approach which infers the laws of morphogenesis (i.e., form generation) from the observed patterns of variation in living organisms and in the fossil records. Meyen developed a theory of "repeated polymorphic sets" (RPSs), which he applied consistently to describe inter-organism variation in populations, intra-organism variation of metameric organs, variation of abnormalities, heterotopy, changes during embryo development, and inter-species variation within evolutionary lineages. The notion of RPS assumes the active nature of organisms that possess hidden morphogenic and behavioral capacities. Meyen's theory is compatible with Darwin's natural selection; however, Meyen emphasized the importance of other forms of selection (e.g., selection of developmental trajectories, habitats, and behaviors) in choosing specific elements from the RPS. Finally, Meyen developed a new typological concept of time, where time represents variability (i.e., change) of real objects such as living organisms or geological formations.

Dioecy is associated with higher diversification rates in flowering plants

In angiosperms, dioecious clades tend to have fewer species than their nondioecious sister clades. This departure from the expected equal species richness in the standard sister clade test has been interpreted as implying that dioecious clades diversify less and has initiated a series of studies suggesting that dioecy might be an 'evolutionary dead end'. However, two of us recently showed that the 'equal species richness' null hypothesis is not valid in the case of derived char acters, such as dioecy, and proposed a new test for sister clade comparisons; preliminary results, using a data set available in the litterature, indicated that dioecious clades migth diversify more than expected. However, it is crucial for this new test to distinguish between ancestral and derived cases of dioecy, a criterion that was not taken into account in the available data set. Here, we present a new data set that was obtained by searching the phylogenetic literature on more than 600 completely dioecious angiosperm genera and identifying 115 sister clade pairs for which dioecy is likely to be derived (including > 50% of the dioecious species). Applying the new sister clade test to this new dataset, we confirm the preliminary result that dioecy is associated with an increased diversification rate, a result that does not support the idea that dioecy is an evolutionary dead end in angiosperms. The traits usually associated with dioecy, that is, an arborescent growth form, abiotic pollination, fleshy fruits or a tropical distribution, do not influence the diversification rate. Rather than a low diversification rate, the observed species richness patterns of dioecious clades seem to be better explained by a low transition rate to dioecy and frequent losses.

Meristem identity and phyllotaxis in inflorescence development

Inflorescence morphology is incredibly diverse. This diversity of form has been a fruitful source of inquiry for plant morphologists for more than a century. Work in the grasses (Poaceae), the tomato family (Solanaceae), and Arabidopsis thaliana (Brassicaceae) has led to a richer understanding of the molecular genetics underlying this diversity. The character of individual meristems, a combination of the number (determinacy) and nature (identity) of the products a meristem produces, is key in the development of plant form. A framework that describes inflorescence development in terms of shifting meristem identities has emerged and garnered empirical support in a number of model systems. We discuss this framework and highlight one important aspect of meristem identity that is often considered in isolation, phyllotaxis. Phyllotaxis refers to the arrangement of lateral organs around a central axis. The development and evolution of phyllotaxis in the inflorescence remains underexplored, but recent work analyzing early inflorescence development in the grasses identified an evolutionary shift in primary branch phyllotaxis in the Pooideae. We discuss the evidence for an intimate connection between meristem identity and phyllotaxis in both the inflorescence and vegetative shoot, and touch on what is known about the establishment of phyllotactic patterns in the meristem. Localized auxin maxima are instrumental in determining the position of lateral primordia. Upstream factors that regulate the position of these maxima remain unclear, and how phyllotactic patterns change over the course of a plant's lifetime and evolutionary time, is largely unknown. A more complete understanding of the molecular underpinnings of phyllotaxis and architectural diversity in inflorescences will require capitalizing on the extensive resources available in existing genetic systems, and developing new model systems that more fully represent the diversity of plant morphology.

Combining phylogenetic and syntenic analyses for understanding the evolution of TCP ECE genes in eudicots

TCP ECE genes encode transcription factors which have received much attention for their repeated recruitment in the control of floral symmetry in core eudicots, and more recently in monocots. Major duplications of TCP ECE genes have been described in core eudicots, but the evolutionary history of this gene family is unknown in basal eudicots. Reconstructing the phylogeny of ECE genes in basal eudicots will help set a framework for understanding the functional evolution of these genes. TCP ECE genes were sequenced in all major lineages of basal eudicots and Gunnera which belongs to the sister clade to all other core eudicots. We show that in these lineages they have a complex evolutionary history with repeated duplications. We estimate the timing of the two major duplications already identified in the core eudicots within a timeframe before the divergence of Gunnera and after the divergence of Proteales. We also use a synteny-based approach to examine the extent to which the expansion of TCP ECE genes in diverse eudicot lineages may be due to genome-wide duplications. The three major core-eudicot specific clades share a number of collinear genes, and their common evolutionary history may have originated at the γ event. Genomic comparisons in Arabidopsis thaliana and Solanumlycopersicum highlight their separate polyploid origin, with syntenic fragments with and without TCP ECE genes showing differential gene loss and genomic rearrangements. Comparison between recently available genomes from two basal eudicots Aquilegiacoerulea and Nelumbonucifera suggests that the two TCP ECE paralogs in these species are also derived from large-scale duplications. TCP ECE loci from basal eudicots share many features with the three main core eudicot loci, and allow us to infer the makeup of the ancestral eudicot locus.