The proper place of hopeful monsters in evolutionary biology

Exploring the patterns of evolution: Core thoughts and focus on the saltational model

The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.

Transgressive segregation, hopeful monsters, and phenotypic selection drove rapid genetic gains and breakthroughs in predictive breeding for quantitative resistance to Macrophomina in strawberry

Two decades have passed since the strawberry (Fragaria x ananassa) disease caused by Macrophomina phaseolina, a necrotrophic soilborne fungal pathogen, began surfacing in California, Florida, and elsewhere. This disease has since become one of the most common causes of plant death and yield losses in strawberry. The Macrophomina problem emerged and expanded in the wake of the global phase-out of soil fumigation with methyl bromide and appears to have been aggravated by an increase in climate change-associated abiotic stresses. Here we show that sources of resistance to this pathogen are rare in gene banks and that the favorable alleles they carry are phenotypically unobvious. The latter were exposed by transgressive segregation and selection in populations phenotyped for resistance to Macrophomina under heat and drought stress. The genetic gains were immediate and dramatic. The frequency of highly resistant individuals increased from 1% in selection cycle 0 to 74% in selection cycle 2. Using GWAS and survival analysis, we found that phenotypic selection had increased the frequencies of favorable alleles among 10 loci associated with resistance and that favorable alleles had to be accumulated among four or more of these loci for an individual to acquire resistance. An unexpectedly straightforward solution to the Macrophomina disease resistance breeding problem emerged from our studies, which showed that highly resistant cultivars can be developed by genomic selection per se or marker-assisted stacking of favorable alleles among a comparatively small number of large-effect loci.

Disruptive selection and the evolution of discrete color morphs in Timema stick insects

A major unresolved issue in biology is why phenotypic and genetic variation is sometimes continuous, yet other times packaged into discrete units of diversity, such as morphs, ecotypes, and species. In theory, ecological discontinuities can impose strong disruptive selection that promotes the evolution of discrete forms, but direct tests of this hypothesis are lacking. Here, we show that Timema stick insects exhibit genetically determined color morphs that range from weakly to strongly discontinuous. Color data from nature and a manipulative field experiment demonstrate that greater morph differentiation is associated with shifts from host plants exhibiting more continuous color variation to those exhibiting greater coloration distance between green leaves and brown stems, the latter of which generates strong disruptive selection. Our results show how ecological factors can promote discrete variation, and we further present results on how this can have variable effects on the genetic differentiation that promotes speciation.

Two-way exchanges between animal and plant biology, with focus on evo-devo

By definition, biology is the science of all living beings. However, horizons restricted to either plants or animals have characterized the development of life sciences well beyond the emergence of unified perspectives applying to all forms of life, such as the cell theory or the theory of evolution. Separation between botanical and zoological traditions is not destined to go extinct easily, or shortly. Disciplinary isolation is emphasized by institutional contexts such as scientific societies and their congresses, specialist journals, disciplines recognized as teaching subjects and legitimate and fundable research fields. By shaping the personal agendas of individual scientists, this has a strong impact on the development of biology. In some fields, botanical and zoological contributions have long being effectively intertwined, but in many others plant and animal biology have failed to progress beyond a marginal dialogue. Characteristically, the so-called “general biology” and the philosophy of biology are still zoocentric (and often vertebrato- or even anthropocentric). In this article, I discuss legitimacy and fruitfulness of some old lexical and conceptual exchanges between the two traditions (cell, tissue, and embryo). Finally, moving to recent developments, I compare the contributions of plant vs. animal biology to the establishment of evolutionary developmental biology. We cannot expect that stronger integration between the different strands of life sciences will soon emerge by self-organization, but highlighting this persisting imbalance between plant and animal biology will arguably foster progress.

Microevolution, speciation and macroevolution in rhizobia: Genomic mechanisms and selective patterns

Nodule bacteria (rhizobia), N₂-fixing symbionts of leguminous plants, represent an excellent model to study the fundamental issues of evolutionary biology, including the tradeoff between microevolution, speciation, and macroevolution, which remains poorly understood for free-living organisms. Taxonomically, rhizobia are extremely diverse: they are represented by nearly a dozen families of α-proteobacteria (Rhizobiales) and by some β-proteobacteria. Their genomes are composed of core parts, including house-keeping genes (hkg), and of accessory parts, including symbiotically specialized (sym) genes. In multipartite genomes of evolutionary advanced fast-growing species (Rhizobiaceae), sym genes are clustered on extra-chromosomal replicons (megaplasmids, chromids), facilitating gene transfer in plant-associated microbial communities. In this review, we demonstrate that in rhizobia, microevolution and speciation involve different genomic and ecological mechanisms: the first one is based on the diversification of sym genes occurring under the impacts of host-induced natural selection (including its disruptive, frequency-dependent and group forms); the second one-on the diversification of hkgs under the impacts of unknown factors. By contrast, macroevolution represents the polyphyletic origin of super-species taxa, which are dependent on the transfer of sym genes from rhizobia to various soil-borne bacteria. Since the expression of newly acquired sym genes on foreign genomic backgrounds is usually restricted, conversion of resulted recombinants into the novel rhizobia species involves post-transfer genetic changes. They are presumably supported by host-induced selective processes resulting in the sequential derepression of nod genes responsible for nodulation and of nif/fix genes responsible for symbiotic N₂ fixation.

A degenerative process underlying hierarchic transitions in evolution

This paper describes an evolutionary process likely involved in hierarchic transitions in biological evolution at many levels, from genetics to social organization. It is related to the evolutionary process described as contingent neutral evolution (CNE). It involves a sequence of stages initiated by the spontaneous appearance of functional redundancy. This redundancy can be the result of gene duplication, symbiosis, cell-cell interactions, environmental supports, etc. The availability of redundant sources of biological functionality relaxes purifying selection and allows degenerative changes to accumulate in one or more of the duplicates, potentially degrading or otherwise fractionating its function. This degeneration will be effectively neutral so long as another maintains functional integrity. Sexual recombination can potentially sample different combinations of these sub functional alternatives, with the result that favorable synergistic interactions between independently degenerate duplicates will have a non-negligible probability of being uncovered. The expression of such a synergistic combinatorial effect will result in the irreversible degradation of any remaining autonomous functionality, thereby initiating selection to prevent breakup of co-dependency. This becomes relevant to the evolution of hierarchic transitions when two or more organisms reciprocally duplicate functions that each other requires. If the resulting relaxation of selection reliably persists for an extended evolutionary period it will tend to produce complementary degenerative effects in each organism, leading to their irreversible codependency and purifying selection to avoid loss of integrity of their higher order functional unity. This provides a partial inversion of Darwinian logic that explains how the potential costs of the loss of organism autonomy can be mitigated, enabling the incremental transition to a synergistic higher order unit of evolution.

Paleomimetics: A Conceptual Framework for a Biomimetic Design Inspired by Fossils and Evolutionary Processes

In biomimetic design, functional systems, principles, and processes observed in nature are used for the development of innovative technical systems. The research on functional features is often carried out without giving importance to the generative mechanism behind them: evolution. To deeply understand and evaluate the meaning of functional morphologies, integrative structures, and processes, it is imperative to not only describe, analyse, and test their behaviour, but also to understand the evolutionary history, constraints, and interactions that led to these features. The discipline of palaeontology and its approach can considerably improve the efficiency of biomimetic transfer by analogy of function; additionally, this discipline, as well as biology, can contribute to the development of new shapes, textures, structures, and functional models for productive and generative processes useful in the improvement of designs. Based on the available literature, the present review aims to exhibit the potential contribution that palaeontology can offer to biomimetic processes, integrating specific methodologies and knowledge in a typical biomimetic design approach, as well as laying the foundation for a biomimetic design inspired by extinct species and evolutionary processes: Paleomimetics. A state of the art, definition, method, and tools are provided, and fossil entities are presented as potential role models for technical transfer solutions.

Eukaryogenesis: The Rise of an Emergent Superorganism

Although it is widely taught that all modern life descended via modification from a last universal common ancestor (LUCA), this dominant paradigm is yet to provide a generally accepted explanation for the chasm in design between prokaryotic and eukaryotic cells. Counter to this dominant paradigm, the viral eukaryogenesis (VE) hypothesis proposes that the eukaryotes originated as an emergent superorganism and thus did not evolve from LUCA via descent with incremental modification. According to the VE hypothesis, the eukaryotic nucleus descends from a viral factory, the mitochondrion descends from an enslaved alpha-proteobacteria and the cytoplasm and plasma membrane descend from an archaeal host. A virus initiated the eukaryogenesis process by colonising an archaeal host to create a virocell that had its metabolism reprogrammed to support the viral factory. Subsequently, viral processes facilitated the entry of a bacterium into the archaeal cytoplasm which was also eventually reprogrammed to support the viral factory. As the viral factory increased control of the consortium, the archaeal genome was lost, the bacterial genome was greatly reduced and the viral factory eventually evolved into the nucleus. It is proposed that the interaction between these three simple components generated a superorganism whose emergent properties allowed the evolution of eukaryotic complexity. If the radical tenets of the VE hypothesis are ultimately accepted, current biological paradigms regarding viruses, cell theory, LUCA and the universal Tree of Life (ToL) should be fundamentally altered or completely abandoned.

EvoDevo: Past and Future of Continuum and Process Plant Morphology

Plants and animals are both important for studies in evolutionary developmental biology (EvoDevo). Plant morphology as a valuable discipline of EvoDevo is set for a paradigm shift. Process thinking and the continuum approach in plant morphology allow us to perceive and interpret growing plants as combinations of developmental processes rather than as assemblages of structural units (“organs”) such as roots, stems, leaves, and flowers. These dynamic philosophical perspectives were already favored by botanists and philosophers such as Agnes Arber (1879–1960) and Rolf Sattler (*1936). The acceptance of growing plants as dynamic continua inspires EvoDevo scientists such as developmental geneticists and evolutionary biologists to move towards a more holistic understanding of plants in time and space. This review will appeal to many young scientists in the plant development research fields. It covers a wide range of relevant publications from the past to present.

Spontaneous homeotic mutants and genetic control of floral organ identity in a ranunculid

The regulation of floral organ identity was investigated using a forward genetic approach in five floral homeotic mutants of Thalictrum, a noncore eudicot. We hypothesized that these mutants carry defects in the floral patterning genes. Mutant characterization comprised comparative floral morphology and organ identity gene expression at early and late developmental stages, followed by sequence analysis of coding and intronic regions to identify transcription factor binding sites and protein-protein interaction (PPI) motifs. Mutants exhibited altered expression of floral MADS-box genes, which further informed the function of paralogs arising from gene duplications not found in reference model systems. The ensuing modified BCE models for the mutants supported instances of neofunctionalization (e.g., B-class genes expressed ectopically in sepals), partial redundancy (E-class), or subfunctionalization (C-class) of paralogs. A lack of deleterious mutations in the coding regions of candidate floral MADS-box genes suggested that cis-regulatory or trans-acting mutations are at play. Consistent with this hypothesis, double-flower mutants had transposon insertions or showed signs of transposon activity in the regulatory intron of AGAMOUS (AG) orthologs. Single amino acid substitutions were also found, yet they did not fall on any of the identified DNA binding or PPI motifs. In conclusion, we present evidence suggesting that transposon activity and regulatory mutations in floral homeotic genes likely underlie the striking phenotypes of these Thalictrum floral homeotic mutants.

Into another dimension: how streptophyte algae gained morphological complexity

Land plants with elaborated three-dimensional (3D) body plans have evolved from streptophyte algae. The streptophyte algae are known to exhibit varying degrees of morphological complexity, ranging from single-celled flagellates to branched macrophytic forms exhibiting tissue-like organization. In this review, I discuss mechanisms by which, during evolution, filamentous algae may have gained 2D and eventually 3D body plans. There are, in principle, two mechanisms by which an additional dimension may be added to an existing algal filament or cell layer: first, by tip growth-mediated branching. An example of this mechanism is the emergence and polar expansion of root hairs from land plants. The second possibility is the rotation of the cell division plane. In this case, the plane of the forthcoming cell division is rotated within the parental cell wall. This type of mechanism corresponds to the formative cell division seen in meristems of land plants. This literature review shows that of the extant streptophyte algae, the Charophyceae and Coleochaetophyceae are capable of performing both mechanisms, while the Zygnematophyceae (the actual sister to land plants) show tip growth-based branching only. I finally discuss how apical cells with two or three cutting faces, as found in mosses, may have evolved from algal ancestors.

Chromoanagenesis: a piece of the macroevolution scenario

Over the last decade, new types of massive and complex chromosomal rearrangements based on the chaotic shattering and restructuring of chromosomes have been identified in cancer cells as well as in patients with congenital diseases and healthy individuals. These unanticipated phenomena are named chromothripsis, chromoanasynthesis and chromoplexy, and are grouped under the term of chromoanagenesis. As mechanisms for rapid and profound genome modifications in germlines and early development, these processes can be regarded as credible pathways for genomic evolution and speciation process. Their discovery confirms the importance of genome-centric investigations to fully understand organismal evolution.

Because they oppose the model of progressive acquisition of driver mutations or rearrangements, these phenomena conceptually give support to the concept of macroevolution, known through the models of “Hopeful Monsters” and the “Punctuated Equilibrium”. In this review, we summarize mechanisms underlying chromoanagenesis processes and we show that numerous cases of chromosomal speciation and short-term adaptation could be correlated to chromoanagenesis-related mechanisms.

In the frame of a modern and integrative analysis of eukaryote evolutionary processes, it seems important to consider the unexpected chromoanagenesis phenomena.

Using digital organisms to study the evolutionary consequences of whole genome duplication and polyploidy

The potential role of whole genome duplication (WGD) in evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary ‘dead end’, there is growing evidence that the long-term establishment of polyploidy might be linked to environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete non-polyploids at times of environmental upheaval remain indefinable. Here, we improved our recently developed bio-inspired framework, combining an artificial genome with an agent-based system, to form a population of so-called Digital Organisms (DOs), to examine the impact of WGD on evolution under different environmental scenarios mimicking extinction events of varying strength and frequency. We found that, under stable environments, DOs with non-duplicated genomes formed the majority, if not all, of the population, whereas the numbers of DOs with duplicated genomes increased under dramatically challenging environments. After tracking the evolutionary trajectories of individual genomes in terms of sequence and encoded gene regulatory networks (GRNs), we propose that duplicated GRNs might provide polyploids with better chances to acquire the drastic changes necessary to adapt to challenging conditions, thus endowing DOs with increased adaptive potential under extinction events. In contrast, under stable environments, random mutations might easily render the GRN less well adapted to such environments, a phenomenon that is exacerbated in duplicated, more complex GRNs. We believe that our results provide some additional insights into how genome duplication and polyploidy might help organisms to compete for novel niches and survive ecological turmoil, and confirm the usefulness of our computational simulation in studying the role of WGD in evolution and adaptation, helping to overcome some of the traditional limitations of evolution experiments with model organisms.

Feather evolution exemplifies sexually selected bridges across the adaptive landscape

Over the last two decades, paleontologists have pieced together the early evolutionary history of feathers. Simple hair-like feathers served as insulating pelage, but the first feathers with complex branching structures and a plainer form evolved for the purpose of sexual display. The evolution of these complex display feathers was essential to the later evolution of flight. Feathers illustrate how sexual selection can generate complex novel phenotypes, which are then available for natural selection to modify and direct toward novel functions. In the longstanding metaphor of the adaptive landscape, sexual selection is a means by which lineages resting on one adaptive peak may gradually bridge a gap to another peak, without the landscape itself being first altered by environmental changes.

Array of MADS-Box Genes: Facilitator for Rapid Adaptation?

In a world of global warming, the question emerges whether all plants have suitable mechanisms to keep pace with the rapidly changing environment. Most previous studies have focused on either the ability of plants to rapidly acclimatize via physiological and developmental plasticity, or long-term adaptation over thousands of years. However, we wonder whether plants can also adapt to changes in the environment within only a few generations. We hypothesize that rapidly evolving clusters of tandemly duplicated developmental control genes represent a source for fast adaptation. Specifically, we propose that a tandem cluster of FLC-like MADS-box genes involved in the transition to flowering in Arabidopsis functions as a facilitator for rapid adaptation to changes in ambient temperature.

Living Organisms Author Their Read-Write Genomes in Evolution

Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.

Developmental push or environmental pull? The causes of macroevolutionary dynamics

Have the large-scale evolutionary patterns illustrated by the fossil record been driven by fluctuations in environmental opportunity, by biotic factors, or by changes in the types of phenotypic variants available for evolutionary change? Since the Modern Synthesis most evolutionary biologists have maintained that microevolutionary processes carrying on over sufficient time will generate macroevolutionary patterns, with no need for other pattern-generating mechanisms such as punctuated equilibrium or species selection. This view was challenged by paleontologists in the 1970s with proposals that the differential sorting and selection of species and clades, and the effects of biotic crises such as mass extinctions, were important extensions to traditional evolutionary theory. More recently those interested in macroevolution have debated the relative importance of abiotic and biotic factors in driving macroevolutionary patterns and have introduced comparative phylogenetic methods to analyze the rates of change in taxonomic diversity. Applying Peter Godfrey-Smith's distinction between distributional explanations and explanations focusing on the origin of variation, most macroevolutionary studies have provided distributional explanations of macroevolutionary patterns. Comparative studies of developmental evolution, however, have implicated the origin of variants as a driving macroevolution force. In particular, the repatterning of gene regulatory networks provides new insights into the origins of developmental novelties. This raises the question of whether macroevolution has been pulled by the generation of environmental opportunity, or pushed by the introduction of new morphologies. The contrast between distributional and origination scenarios has implications for understanding evolutionary novelty and innovation and how macroevolutionary process may have evolved over time.

Classifying the evolutionary and ecological features of neoplasms

Neoplasms change over time through a process of cell-level evolution, driven by genetic and epigenetic alterations. However, the ecology of the microenvironment of a neoplastic cell determines which changes provide adaptive benefits. There is widespread recognition of the importance of these evolutionary and ecological processes in cancer, but to date, no system has been proposed for drawing clinically relevant distinctions between how different tumours are evolving. On the basis of a consensus conference of experts in the fields of cancer evolution and cancer ecology, we propose a framework for classifying tumours that is based on four relevant components. These are the diversity of neoplastic cells (intratumoural heterogeneity) and changes over time in that diversity, which make up an evolutionary index (Evo-index), as well as the hazards to neoplastic cell survival and the resources available to neoplastic cells, which make up an ecological index (Eco-index). We review evidence demonstrating the importance of each of these factors and describe multiple methods that can be used to measure them. Development of this classification system holds promise for enabling clinicians to personalize optimal interventions based on the evolvability of the patient's tumour. The Evo- and Eco-indices provide a common lexicon for communicating about how neoplasms change in response to interventions, with potential implications for clinical trials, personalized medicine and basic cancer research.

Perspective Research Progress in Cold Responses of Capsella bursa-pastoris

Plants respond to cold stress by modulating biochemical pathways and array of molecular events. Plant morphology is also affected by the onset of cold conditions culminating at repression in growth as well as yield reduction. As a preventive measure, cascades of complex signal transduction pathways are employed that permit plants to endure freezing or chilling periods. The signaling pathways and related events are regulated by the plant hormonal activity. Recent investigations have provided a prospective understanding about plant response to cold stress by means of developmental pathways e.g., moderate growth involved in cold tolerance. Cold acclimation assays and bioinformatics analyses have revealed the role of potential transcription factors and expression of genes like CBF, COR in response to low temperature stress. Capsella bursa-pastoris is a considerable model plant system for evolutionary and developmental studies. On different occasions it has been proved that C. bursa-pastoris is more capable of tolerating cold than A. thaliana. But, the mechanism for enhanced low or freezing temperature tolerance is still not clear and demands intensive research. Additionally, identification and validation of cold responsive genes in this candidate plant species is imperative for plant stress physiology and molecular breeding studies to improve cold tolerance in crops. We have analyzed the role of different genes and hormones in regulating plant cold resistance with special reference to C. bursa-pastoris. Review of collected data displays potential ability of Capsella as model plant for improvement in cold stress regulation. Information is summarized on cold stress signaling by hormonal control which highlights the substantial achievements and designate gaps that still happen in our understanding.

Evolution of unusual morphologies in Lentibulariaceae (bladderworts and allies) and Podostemaceae (river-weeds): a pictorial report at the interface of developmental biology and morphological diversification

BACKGROUND

Various groups of flowering plants reveal profound ('saltational') changes of their bauplans (architectural rules) as compared with related taxa. These plants are known as morphological misfits that appear as rather large morphological deviations from the norm. Some of them emerged as morphological key innovations (perhaps 'hopeful monsters') that gave rise to new evolutionary lines of organisms, based on (major) genetic changes.

SCOPE

This pictorial report places emphasis on released bauplans as typical for bladderworts (Utricularia, approx. 230 secies, Lentibulariaceae) and river-weeds (Podostemaceae, three subfamilies, approx. 54 genera, approx. 310 species). Bladderworts (Utricularia) are carnivorous, possessing sucking traps. They live as submerged aquatics (except for their flowers), as humid terrestrials or as epiphytes. Most Podostemaceae are restricted to rocks in tropical river-rapids and waterfalls. They survive as submerged haptophytes in these extreme habitats during the rainy season, emerging with their flowers afterwards. The recent scientific progress in developmental biology and evolutionary history of both Lentibulariaceae and Podostemaceae is summarized.

CONCLUSIONS

Lentibulariaceae and Podostemaceae follow structural rules that are different from but related to those of more typical flowering plants. The roots, stems and leaves - as still distinguishable in related flowering plants - are blurred ('fuzzy'). However, both families have stable floral bauplans. The developmental switches to unusual vegetative morphologies facilitated rather than prevented the evolution of species diversity in both families. The lack of one-to-one correspondence between structural categories and gene expression may have arisen from the re-use of existing genetic resources in novel contexts. Understanding what developmental patterns are followed in Lentibulariaceae and Podostemaceae is a necessary prerequisite to discover the genetic alterations that led to the evolution of these atypical plants. Future molecular genetic work on morphological misfits such as bladderworts and river-weeds will provide insight into developmental and evolutionary aspects of more typical vascular plants.

Species diversity vs. morphological disparity in the light of evolutionary developmental biology

BACKGROUND

Two indicators of a clade's success are its diversity (number of included species) and its disparity (extent of morphospace occupied by its members). Many large genera show high diversity with low disparity, while others such as Euphorbia and Drosophila are highly diverse but also exhibit high disparity. The largest genera are often characterized by key innovations that often, but not necessarily, coincide with their diagnostic apomorphies. In terms of their contribution to speciation, apomorphies are either permissive (e.g. flightlessness) or generative (e.g. nectariferous spurs).

SCOPE

Except for Drosophila, virtually no genus among those with the highest diversity or disparity includes species currently studied as model species in developmental genetics or evolutionary developmental biology (evo-devo). An evo-devo approach is, however, potentially important to understand how diversity and disparity could rapidly increase in the largest genera currently accepted by taxonomists. The most promising directions for future research and a set of key questions to be addressed are presented in this review.

CONCLUSIONS

From an evo-devo perspective, the evolution of clades with high diversity and/or disparity can be addressed from three main perspectives: (1) evolvability, in terms of release from previous constraints and of the presence of genetic or developmental conditions favouring multiple parallel occurrences of a given evolutionary transition and its reversal; (2) phenotypic plasticity as a facilitator of speciation; and (3) modularity, heterochrony and a coupling between the complexity of the life cycle and the evolution of diversity and disparity in a clade. This simple preliminary analysis suggests a set of topics that deserve priority for scrutiny, including the possible role of saltational evolution in the origination of high diversity and/or disparity, the predictability of morphological evolution following release from a former constraint, and the extent and the possible causes of a positive correlation between diversity and disparity and the complexity of the life cycle.

The making of a branching annelid: an analysis of complete mitochondrial genome and ribosomal data of Ramisyllis multicaudata

Ramisyllis multicaudata is a member of Syllidae (Annelida, Errantia, Phyllodocida) with a remarkable branching body plan. Using a next-generation sequencing approach, the complete mitochondrial genomes of R. multicaudata and Trypanobia sp. are sequenced and analysed, representing the first ones from Syllidae. The gene order in these two syllids does not follow the order proposed as the putative ground pattern in Errantia. The phylogenetic relationships of R. multicaudata are discerned using a phylogenetic approach with the nuclear 18S and the mitochondrial 16S and cox1 genes. Ramisyllis multicaudata is the sister group of a clade containing Trypanobia species. Both genera, Ramisyllis and Trypanobia, together with Parahaplosyllis, Trypanosyllis, Eurysyllis, and Xenosyllis are located in a long branched clade. The long branches are explained by an accelerated mutational rate in the 18S rRNA gene. Using a phylogenetic backbone, we propose a scenario in which the postembryonic addition of segments that occurs in most syllids, their huge diversity of reproductive modes, and their ability to regenerate lost parts, in combination, have provided an evolutionary basis to develop a new branching body pattern as realised in Ramisyllis.

Spaces of the possible: universal Darwinism and the wall between technological and biological innovation

Innovations in biological evolution and in technology have many common features. Some of them involve similar processes, such as trial and error and horizontal information transfer. Others describe analogous outcomes such as multiple independent origins of similar innovations. Yet others display similar temporal patterns such as episodic bursts of change separated by periods of stasis. We review nine such commonalities, and propose that the mathematical concept of a space of innovations, discoveries or designs can help explain them. This concept can also help demolish a persistent conceptual wall between technological and biological innovation.

Comparative study of the shell development of hard- and soft-shelled turtles

The turtle shell provides a fascinating model for the investigation of the evolutionary modifications of developmental mechanisms. Different conclusions have been put forth for its development, and it is suggested that one of the causes of the disagreement could be the differences in the species of the turtles used - the differences between hard-shelled turtles and soft-shelled turtles. To elucidate the cause of the difference, we compared the turtle shell development in the two groups of turtle. In the dorsal shell development, these two turtle groups shared the gene expression profile that is required for formation, and shared similar spatial organization of the anatomical elements during development. Thus, both turtles formed the dorsal shell through a folding of the lateral body wall, and the Wnt signaling pathway appears to have been involved in the development. The ventral portion of the shell, on the other hand, contains massive dermal bones. Although expression of HNK-1 epitope has suggested that the trunk neural crest contributed to the dermal bones in the hard-shelled turtles, it was not expressed in the initial anlage of the skeletons in either of the types of turtle. Hence, no evidence was found that would support a neural crest origin.

An APETALA3 homolog controls both petal identity and floral meristem patterning in Nigella damascena L. (Ranunculaceae)

Flower architecture mutants provide a unique opportunity to address the genetic origin of flower diversity. Here we study a naturally occurring floral dimorphism in Nigella damascena (Ranunculaceae), involving replacement of the petals by numerous sepal-like and chimeric sepal/stamen organs. We performed a comparative study of floral morphology and floral development, and characterized the expression of APETALA3 and PISTILLATA homologs in both morphs. Segregation analyses and gene silencing were used to determine the involvement of an APETALA3 paralog (NdAP3-3) in the floral dimorphism. We demonstrate that the complex floral dimorphism is controlled by a single locus, which perfectly co-segregates with the NdAP3-3 gene. This gene is not expressed in the apetalous morph and exhibits a particular expression dynamic during early floral development in the petalous morph. NdAP3-3 silencing in petalous plants perfectly phenocopies the apetalous morph. Our results show that NdAP3-3 is fully responsible for the complex N. damascena floral dimorphism, suggesting that it plays a role not only in petal identity but also in meristem patterning, possibly through regulation of perianth organ number and the perianth/stamen boundary.

Growth habit of the late Paleozoic rhizomorphic tree-lycopsid family Diaphorodendraceae: phylogenetic, evolutionary, and paleoecological significance

PREMISE OF THE STUDY

Rhizomorphic lycopsids evolved the tree habit independently of all other land plants. Newly discovered specimens allow radical revision of our understanding of the growth architectures of the extinct Paleozoic sister-genera Synchysidendron and Diaphorodendron.

METHODS

Detailed descriptions of six remarkable adpression specimens from the Pennsylvanian of the USA and three casts from the late Mississippian of Scotland are used to revise and reanalyze a previously published morphological cladistic matrix and to reinterpret their remarkable growth forms.

KEY RESULTS

Contrary to previous assertions, Synchysidendron resembled Diaphorodendron in having a distinct and relatively complex growth habit that emphasized serially homologous, closely spaced, deciduous lateral branches at the expense of reduced monocarpic crown branches. Lateral branches originated through several strongly anisotomous dichotomies before producing during extended periods large numbers of Achlamydocarpon strobili. The comparatively large diameter of abscission scars remaining on the main trunk and the emergence of branches above the horizontal plane suggest that the lateral branch systems were robust. Lateral branches were borne in two opposite rows on the main trunk and continued upward into an isotomously branched, determinate crown; their striking distichous arrangement caused preferred orientation of fallen trunks on bedding planes.

CONCLUSIONS

This discovery identifies the plagiotropic growth habit, dominated by serial lateral branches, as ubiquitous in the Diaphorodendraceae and also as unequivocally primitive within Isoetales s.l., a conclusion supported by both the revised morphological cladistic analysis and relative first appearances of taxa in the fossil record. Previously assumed complete homology between crown branching in Lepidodendraceae and that of all earlier-divergent genera requires reassessment. Saltational phenotypic transitions via modification of key developmental switches remains the most credible explanation for architectural evolution in the group. The resulting architecture allowed Diaphorodendraceae to co-dominate disturbed, clastic, equatorial wetlands from the Asbian to the Early Permian.

Evolution of the turtle bauplan: the topological relationship of the scapula relative to the ribcage

The turtle shell and the relationship of the shoulder girdle inside or 'deep' to the ribcage have puzzled neontologists and developmental biologists for more than a century. Recent developmental and fossil data indicate that the shoulder girdle indeed lies inside the shell, but anterior to the ribcage. Developmental biologists compare this orientation to that found in the model organisms mice and chickens, whose scapula lies laterally on top of the ribcage. We analyse the topological relationship of the shoulder girdle relative to the ribcage within a broader phylogenetic context and determine that the condition found in turtles is also found in amphibians, monotreme mammals and lepidosaurs. A vertical scapula anterior to the thoracic ribcage is therefore inferred to be the basal amniote condition and indicates that the condition found in therian mammals and archosaurs (which includes both developmental model organisms: chickens and mice) is derived and not appropriate for studying the developmental origin of the turtle shell. Instead, among amniotes, either monotreme mammals or lepidosaurs should be used.

Loss of deeply conserved C-class floral homeotic gene function and C- and E-class protein interaction in a double-flowered ranunculid mutant

In the model plant Arabidopsis thaliana, a core eudicot, the floral homeotic C-class gene AGAMOUS (AG) has a dual role specifying reproductive organ identity and floral meristem determinacy. We conduct a functional analysis of the putative AG ortholog ThtAG1 from the ranunculid Thalictrum thalictroides, a representative of the sister lineage to all other eudicots. Down-regulation of ThtAG1 by virus-induced gene silencing resulted in homeotic conversion of stamens and carpels into sepaloid organs and loss of flower determinacy. Moreover, flowers exhibiting strong silencing of ThtAG1 phenocopied the double-flower ornamental cultivar T. thalictroides 'Double White.' Molecular analysis of 'Double White' ThtAG1 alleles revealed the insertion of a retrotransposon causing either nonsense-mediated decay of transcripts or alternative splicing that results in mutant proteins with K-domain deletions. Biochemical analysis demonstrated that the mutation abolishes protein-protein interactions with the putative E-class protein ThtSEP3. C- and E-class protein heterodimerization is predicted by the floral quartet model, but evidence for the functional importance of this interaction is scarce outside the core eudicots. Our findings therefore corroborate the importance and conservation of the interactions between C- and E-class proteins. This study provides a functional description of a full C-class mutant in a noncore ("basal") eudicot, an ornamental double flower, affecting both organ identity and meristem determinacy. Using complementary forward and reverse genetic approaches, this study demonstrates deep conservation of the dual C-class gene function and of the interactions between C- and E-class proteins predicted by the floral quartet model.

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

BACKGROUND

The morphological peculiarities of turtles have, for a long time, impeded their accurate placement in the phylogeny of amniotes. Molecular data used to address this major evolutionary question have so far been limited to a handful of markers and/or taxa. These studies have supported conflicting topologies, positioning turtles as either the sister group to all other reptiles, to lepidosaurs (tuatara, lizards and snakes), to archosaurs (birds and crocodiles), or to crocodilians. Genome-scale data have been shown to be useful in resolving other debated phylogenies, but no such adequate dataset is yet available for amniotes.

RESULTS

In this study, we used next-generation sequencing to obtain seven new transcriptomes from the blood, liver, or jaws of four turtles, a caiman, a lizard, and a lungfish. We used a phylogenomic dataset based on 248 nuclear genes (187,026 nucleotide sites) for 16 vertebrate taxa to resolve the origins of turtles. Maximum likelihood and Bayesian concatenation analyses and species tree approaches performed under the most realistic models of the nucleotide and amino acid substitution processes unambiguously support turtles as a sister group to birds and crocodiles. The use of more simplistic models of nucleotide substitution for both concatenation and species tree reconstruction methods leads to the artefactual grouping of turtles and crocodiles, most likely because of substitution saturation at third codon positions. Relaxed molecular clock methods estimate the divergence between turtles and archosaurs around 255 million years ago. The most recent common ancestor of living turtles, corresponding to the split between Pleurodira and Cryptodira, is estimated to have occurred around 157 million years ago, in the Upper Jurassic period. This is a more recent estimate than previously reported, and questions the interpretation of controversial Lower Jurassic fossils as being part of the extant turtles radiation.

CONCLUSIONS

These results provide a phylogenetic framework and timescale with which to interpret the evolution of the peculiar morphological, developmental, and molecular features of turtles within the amniotes.

Environmentally induced epigenetic transgenerational inheritance of phenotype and disease

Environmental epigenetics has an important role in regulating phenotype formation or disease etiology. The ability of environmental factors and exposures early in life to alter somatic cell epigenomes and subsequent development is a critical factor in how environment affects biology. Environmental epigenetics provides a molecular mechanism to explain long term effects of environment on the development of altered phenotypes and "emergent" properties, which the "genetic determinism" paradigm cannot. When environmental factors permanently alter the germ line epigenome, then epigenetic transgenerational inheritance of these environmentally altered phenotypes and diseases can occur. This environmental epigenetic transgenerational inheritance of phenotype and disease is reviewed with a systems biology perspective.

Darwin without borders? Looking at 'generalised Darwinism' through the prism of the 'hourglass model'

This article critically analyzes the arguments of the 'generalized Darwinism' recently proposed for the analysis of social-economical systems. We argue that 'generalized Darwinism' is both restrictive and empty. It is restrictive because it excludes alternative (non-selectionist) evolutionary mechanisms such as orthogenesis, saltationism and mutationism without any examination of their suitability for modeling socio-economic processes and ignoring their important roles in the development of contemporary evolutionary theory. It is empty, because it reduces Darwinism to an abstract triple-principle scheme (variation, selection and inheritance) thus ignoring the actual structure of Darwinism as a complex and dynamic theoretical structure inseparable from a very detailed system of theoretical constraints. Arguing against 'generalised Darwinism' we present our vision of the history of evolutionary biology with the help of the 'hourglass model' reflecting the internal dynamic of competing theories of evolution.

A double-flowered variety of lesser periwinkle (Vinca minor fl. pl.) that has persisted in the wild for more than 160 years

BACKGROUND AND AIMS

Homeotic transitions are usually dismissed by population geneticists as credible modes of evolution due to their assumed negative impact on fitness. However, several lines of evidence suggest that such changes in organ identity have played an important role during the origin and subsequent evolution of the angiosperm flower. Better understanding of the performance of wild populations of floral homeotic varieties should help to clarify the evolutionary potential of homeotic mutants. Wild populations of plants with changes in floral symmetry, or with reproductive organs replacing perianth organs or sepals replacing petals have already been documented. However, although double-flowered varieties are quite popular as ornamental and garden plants, they are rarely found in the wild and, if they are, usually occur only as rare mutant individuals, probably because of their low fitness relative to the wild-type. We therefore investigated a double-flowered variety of lesser periwinkle, Vinca minor flore pleno (fl. pl.), that is reported to have existed in the wild for at least 160 years. To assess the merits of this plant as a new model system for investigations on the evolutionary potential of double-flowered varieties we explored the morphological details and distribution of the mutant phenotype.

METHODS

The floral morphology of the double-flowered variety and of a nearby population of wild-type plants was investigated by means of visual inspection and light microscopy of flowers, the latter involving dissected or sectioned floral organs.

KEY RESULTS

The double-flowered variety was found in several patches covering dozens of square metres in a forest within the city limits of Jena (Germany). It appears to produce fewer flowers than the wild-type, and its flowers are purple rather than blue. Most sepals in the first floral whorl resemble those in the wild-type, although occasionally one sepal is broadened and twisted. The structure of second-whorl petals is very similar to that of the wild-type, but their number per flower is more variable. The double-flowered character is due to partial or complete transformation of stamens in the third whorl into petaloid organs. Occasionally, 'flowers within flowers' also develop on elongated pedicels in the double-flowered variety.

CONCLUSIONS

The flowers of V. minor fl. pl. show meristic as well as homeotic changes, and occasionally other developmental abnormalities such as mis-shaped sepals or loss of floral determinacy. V. minor fl. pl. thus adds to a growing list of natural floral homeotic varieties that have established persistent populations in the wild. Our case study documents that even mutant varieties that have reproductive organs partially transformed into perianth organs can persist in the wild for centuries. This finding makes it at least conceivable that even double-flowered varieties have the potential to establish new evolutionary lineages, and hence may contribute to macroevolutionary transitions and cladogenesis.

Microarray analysis of a salamander hopeful monster reveals transcriptional signatures of paedomorphic brain development

Background

The Mexican axolotl (Ambystoma mexicanum) is considered a hopeful monster because it exhibits an adaptive and derived mode of development - paedomorphosis - that has evolved rapidly and independently among tiger salamanders. Unlike related tiger salamanders that undergo metamorphosis, axolotls retain larval morphological traits into adulthood and thus present an adult body plan that differs dramatically from the ancestral (metamorphic) form. The basis of paedomorphic development was investigated by comparing temporal patterns of gene transcription between axolotl and tiger salamander larvae (Ambystoma tigrinum tigrinum) that typically undergo a metamorphosis.

Results

Transcript abundances from whole brain and pituitary were estimated via microarray analysis on four different days post hatching (42, 56, 70, 84 dph) and regression modeling was used to independently identify genes that were differentially expressed as a function of time in both species. Collectively, more differentially expressed genes (DEGs) were identified as unique to the axolotl (n = 76) and tiger salamander (n = 292) than were identified as shared (n = 108). All but two of the shared DEGs exhibited the same temporal pattern of expression and the unique genes tended to show greater changes later in the larval period when tiger salamander larvae were undergoing anatomical metamorphosis. A second, complementary analysis that directly compared the expression of 1320 genes between the species identified 409 genes that differed as a function of species or the interaction between time and species. Of these 409 DEGs, 84% exhibited higher abundances in tiger salamander larvae at all sampling times.

Conclusions

Many of the unique tiger salamander transcriptional responses are probably associated with metamorphic biological processes. However, the axolotl also showed unique patterns of transcription early in development. In particular, the axolotl showed a genome-wide reduction in mRNA abundance across loci, including genes that regulate hypothalamic-pituitary activities. This suggests that an axolotls failure to undergo anatomical metamorphosis late in the larval period is indirectly associated with a mechanism(s) that acts earlier in development to broadly program transcription. The axolotl hopeful monster provides a model to identify mechanisms of early brain development that proximally and ultimately affect the expression of adult phenotypes.

Punctuated equilibrium and species selection: what does it mean for one theory to suggest another?

McMullin (In: Cohen et al. (eds.) Essays in memory of Imre Lakatos, 1976, In: Leplin (ed.) Scientific realism, 1984) argues that fertility is a theoretical virtue. He thinks of a fertile theory as one whose central metaphors suggest new directions for theoretical development, where those new developments help solve previous problems and anomalies. Nolan (Br J Philos Sci 50:265-282, 1999) argues that fertility in this sense is not a distinctive theoretical virtue in its own right. Rather, Nolan thinks that fertility is reducible to predictive novelty. This article explores the relationship between punctuated equilibrium (PE) and species selection in the light of this philosophical debate about the nature of theoretical fertility, or suggestiveness. I argue that (1) PE suggests, but does not imply, that species selection is a mechanism of evolution; (2) the suggestiveness in this case is not reducible to predictive novelty; (3) species selection is not a metaphorical extension of PE; and (4) getting clear about the way in which PE suggests species selection can help solve a puzzle about punctuated equilibrium. The puzzle is that Eldredge and Gould's initial presentation of PE seems to presuppose a minimalist or extrapolationist view of macroevolution, even though many scientists take PE to challenge that minimalist view.

Developmental morphology of seedling and shoot and phylogenetic relationship of Diplobryum koyamae (Podostemaceae)

We demonstrated that saltational evolution was recurrent in the body plans of seedlings of the aquatic angiosperm Podostemaceae, in contrast to other angiosperms with seedlings having almost common body plans. Diplobryum koyamae, transferred to the genus Hydrodiscus described in this paper, has long-floating shoots with an anchoring disk-like base and is rootless. Such a body plan is distinct from other members of Asian Podostemoideae comprising reduced or moderate shoots borne on the root. Here, our molecular phylogenetic analysis revealed that H. koyamae is sister to a crustose-rooted group of Hanseniella, Hydrobryum and Thawatchaia within Asian Podostemoideae. The germinating embryo was devoid of plumule and radicle, and comprised a single cotyledon and a short hypocotyl, which produced an adventitious shoot endogenously. The leaves are formed in the absence of the shoot apical meristem, accompanying the separation of lightly stained cells. Comparison with other species of Asian Podostemoideae having the plumule and the adventitious root in the seedling, along with their phylogenetic relationship, suggests that saltational evolution occurred in the seedling body plan of H. koyamae leading to the extraordinary adult body plan, as in the separate clade of Dalzellia, Indodalzellia, and Indotristicha of the subfamily Tristichoideae.

Riedl's burden and the body plan: selection, constraint, and deep time

Rupert Riedl's concept of burden forms a causal hypothesis on organismic integration and evolutionary constraints. Defined as the hierarchically nested interdependence of characters within the organism, burden was seen as (1) defining and conserving body plans and (2) constraining and directing evolutionary trajectories. A review of the components of the burden concept reveals important consistencies with the modern tenets of evo-devo. This concept differs from the current consensus of evolutionary theory in that it (1) grants evolution less options for changing tightly integrated, "locked-in" characters and (2) in deducing from this an ever decreasing freedom for evolution, with cyclism and typostrophism as resulting macroevolutionary phenomena. Despite these differences, I show that the burden concept was consistent with most major tenets of the Modern Synthesis, and Riedl attempted to explain patterns of large-scale evolutionary trends exclusively by microevolutionary (gradualistic) processes. The burden concept is fruitful and unique in its focus on hierarchically nested constraints and resembles the hierarchical architecture of gene regulatory networks. However, such networks are more high-dimensional and most of their components appear to be easier to evolve than Riedl's burden. Yet in combination with evolvability, a modified concept of burden might contribute substantially to the understanding of organismic integration and the long-term evolution of body plans.

The naked and the dead: the ABCs of gymnosperm reproduction and the origin of the angiosperm flower

20 years after establishment of the ABC model many of the molecular mechanisms underlying development of the angiosperm flower are relatively well understood. Central players in the gene regulatory network controlling flower development are SQUA-like, DEF/GLO-like, AG-like and AGL6/SEP1-like MIKC-type MADS-domain transcription factors. These provide class A, class B, class C and the more recently defined class E floral homeotic functions, respectively. There is evidence that the floral homeotic proteins recognize the DNA of target genes in an organ-specific way as multimeric protein complexes, thus constituting 'floral quartets'. In contrast to the detailed insights into flower development, how the flower originated during evolution has remained enigmatic. However, while orthologues of all classes of floral homeotic genes appear to be absent from all non-seed plants, DEF/GLO-like, AG-like, and AGL6-like genes have been found in diverse extant gymnosperms, the closest relatives of the angiosperms. While SQUA-like and SEP1-like MADS-box genes appear to be absent from extant gymnosperms, reconstruction of MADS-box gene phylogeny surprisingly suggests that the most recent common ancestor of gymnosperms and angiosperms possessed representatives of both genes, but that these have been lost in the lineage that led to extant gymnosperms. Expression studies and genetic complementation experiments indicate that both angiosperm and gymnosperm AG-like and DEF/GLO-like genes have conserved functions in the specification of reproductive organs and in distinguishing male from female organs, respectively. Based on these findings novel models about the molecular basis of flower origin, involving changes in the expression patterns of DEF/GLO-like or AGL6/SEP1/SQUA-like genes in reproductive structures, were developed. While in angiosperms SEP1-like proteins play an important role in floral quartet formation, preliminary evidence suggests that gymnosperm DEF/GLO-like and AG-like proteins alone can already form floral quartet-like complexes, further corroborating the view that the formation of floral quartet-like complexes predated flower origin during evolution.

Floral visitation and reproductive traits of Stamenoid petals, a naturally occurring floral homeotic variant of Capsella bursa-pastoris (Brassicaceae)

Homeotic changes played a considerable role during the evolution of flowers, but how floral homeotic mutants initially survive in nature has remained enigmatic. To better understand the evolutionary potential of floral homeotic mutants, we established as a model system Stamenoid petals (Spe), a natural variant of Capsella bursa-pastoris (Brassicaceae). In the flowers of Spe plants, petals are transformed into stamens, whereas all other floral organs are unaffected. In contrast with most other homeotic mutants, the Spe variant occurs in relatively stable populations in the wild. In order to determine how the profound change in floral architecture influences plant performance in the wild, we performed common garden experiments running over 3 years. Here, we show that Spe and wild-type plants attract the same assemblage of floral visitors: mainly hoverflies, wild bees and thrips. However, floral visitation is about twice as frequent in wild-type plants as in Spe plants. Nevertheless, the numbers of seeds per fruit were about the same in both variants. Wild-type plants produced more flowers, fruits and seeds per plant than Spe plants, whereas the germination capacity of Spe seeds was higher than that of the wild-type. Determination of volatile composition revealed monoterpenes and 3,4-dimethylbenzaldehyde, which were detected only in wild-type flowers, presumably because they are produced only by petals. Our data indicate that the similar fitness of Spe and wild-type C. bursa-pastoris in the field results from complex compensation between plant architecture and germination capacity. In contrast, flower structure and floral visitation are only of minor importance, possibly because C. bursa-pastoris is mainly self-pollinating.

Saltational evolution of trunk segment number in centipedes

Saltational changes in segment numbers have likely occurred in arthropod evolution, especially if mechanisms of segment formation involve a multiplicative phase, as recently suggested in the evo-devo literature. Here we provide for the first time evidence of major phenotypic saltation in the evolution of segment number in a lineage of centipedes, with a newly discovered species of scolopender having segment numbers duplicated with respect to its closest relatives, and to all the remaining 700+ species of Scolopendromorpha known to date.

Why are orchid flowers so diverse? Reduction of evolutionary constraints by paralogues of class B floral homeotic genes

BACKGROUND

The nearly 30 000 species of orchids produce flowers of unprecedented diversity. However, whether specific genetic mechanisms contributed to this diversity is a neglected topic and remains speculative. We recently published a theory, the 'orchid code', maintaining that the identity of the different perianth organs is specified by the combinatorial interaction of four DEF-like MADS-box genes with other floral homeotic genes.

SCOPE

Here the developmental and evolutionary implications of our theory are explored. Specifically, it is shown that all frequent floral terata, including all peloric types, can be explained by monogenic gain- or-loss-of-function mutants, changing either expression of a DEF-like or CYC-like gene. Supposed dominance or recessiveness of mutant alleles is correlated with the frequency of terata in both cultivation and nature. Our findings suggest that changes in DEF- and CYC-like genes not only underlie terata but also the natural diversity of orchid species. We argue, however, that true changes in organ identity are rare events in the evolution of orchid flowers, even though we review some likely cases.

CONCLUSIONS

The four DEF paralogues shaped floral diversity in orchids in a dramatic way by modularizing the floral perianth based on a complex series of sub- and neo-functionalization events. These genes may have eliminated constraints, so that different kinds of perianth organs could then evolve individually and thus often in dramatically different ways in response to selection by pollinators or by genetic drift. We therefore argue that floral diversity in orchids may be the result of an unprecedented developmental genetic predisposition that originated early in orchid evolution.