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PubMed2006

An evolutionary perspective on the regulation of carpel development.

The carpel, or female reproductive organ enclosing the ovules, is one of the major evolutionary innovations of the flowering plants. The control of carpel development has been intensively studied in the model eudicot species Arabidopsis thaliana. This review traces the evolutionary history of genes involved in carpel development by surveying orthologous genes in taxa whose lineages separated from that of A. thaliana at different levels of the phylogenetic tree of the seed plants. Some aspects of the control of female reproductive development are conserved between the flowering plants and their sister group, the gymnosperms, indicating the presence of these in the common ancestor of the extant seeds plants, some 300 million years ago. Gene duplications that took place in the pre-angiosperm lineage, before the evolution of the first flowering plants, provided novel gene clades of potential importance for the origin of the carpel. Subsequent to the appearance of the first flowering plants, further gene duplications have led to sub-functionalization events, in which pre-existing reproductive functions were shared between paralogous gene clades. In some cases, fluidity in gene function is evident, leading to similar functions in carpel development being controlled by non-orthologous genes in different taxa. In other cases, gene duplication events have created sequences that evolved novel functions by the process of neo-functionalization, thereby generating biodiversity in carpel and fruit structures.

Biological Evolution↗
PubMed1999

The future of the fossil record.

The fossil record provides a powerful basis for analyzing the controlling factors and impact of biological evolution over a wide range of temporal and spatial scales and in the context of an evolving Earth. An increasingly interdisciplinary paleontology has begun to formulate the next generation of questions, drawing on a wealth of new data, and on methodological advances ranging from high-resolution geochronology to simulation of morphological evolution. Key issues related to evolutionary biology include the biotic and physical factors that govern biodiversity dynamics, the developmental and ecological basis for the nonrandom introduction of evolutionary innovations in time and space, rules of biotic response to environmental perturbations, and the dynamic feedbacks between life and the Earth's surface processes. The sensitivity of evolutionary processes to rates, magnitudes, and spatial scales of change in the physical and biotic environment will be important in all these areas.

Animals↗
PubMed2005

Cell structure of developing barbs and barbules in downfeathers of the chick: Central role of barb ridge morphogenesis for the evolution of feathers.

The present ultrastructural study shows how cells organize to form the complex structure of downfeathers in chick embryos. The embryonic epidermis of the apical part of feather filaments folds inward forming barb ridges which extend toward the base of the feather. The stratification of epidermal cells in barb ridges is maintained but the basal layer loses most of the germinal activity. New cells for the growth of feather filaments are mainly produced in its basal part. In barb ridges only the original four epidermal layers of the embryonic epidermis remain to form feathers: 1) the external periderm, 2) three-five layers of the feather sheath and barb vane ridge cells, 3) subperiderm cells, and 4) basal or cylindrical cells. Periderm, sheath, barb vane ridge and cylindrical cells synthesize only alpha-keratin. Instead, cells of the subperiderm layer synthesize a small type of beta-keratin: feather beta-keratin. At hatching, the subperiderm layer is lost in most areas of the skin of the chick (apteric and scaled), and is replaced by cells containing alpha-keratin (interfollicular-apteric epidermis), scale beta-keratin (scales), beak beta-keratin (beak), and claw beta-keratin (claws). Only in feathers, cells of the original subperiderm layer remain and give origin to barb and barbule cells. The formation of separated chains of barb and barbule cells is allowed by the presence of barb vane ridge cells that function as spacers between merging cells of barb and barbule cells. Subperiderm cells elongate and merge into a syncitium to form barbules and barbs. While barbule and barb cells accumulate feather-keratin, barb vane and cylindrical cells accumulate lipids, vesicles and little alpha-keratin. These cells eventually degenerate by necrosis leaving empty spaces and lipids between barbules and barbs. No apoptosis is necessary to explain the process of carving out of barb and barbules in feathers after dissolution of the external sheath. In fact, the retraction of blood vessels nourishing the apical part of the feather filament determines anoxia and eventually necrosis of all cells of the feather. While sheath, barb vane and cylindrical cells degenerate, the keratinized syncitium forming barbs and barbules simply remain in place to form the ramifications of feathers. The formation of barb ridges is considered as the evolutionary innovation necessary for the origin of feathers. The evolution of the morphogenetic process of barb ridge formation within epidermal tubular outgrowths of the integument of ancient archosaurians was an evolutionary novelty, a true avian and theropod characteristic. Barb ridges morphogenesis determines the contemporary formation of barb and barbule cells as a unique and inseparable process so that intermediate forms of evolving feathers with only barbs but not barbules are unlikely. Barb ridges can merge with a large ridge (rachis) or into branched ridges, a process which was at the origin of the ramogenic process from which pennaceous feathers evolved.

Animals↗
PubMed2006

African cichlid fish: a model system in adaptive radiation research.

The African cichlid fish radiations are the most diverse extant animal radiations and provide a unique system to test predictions of speciation and adaptive radiation theory. The past few years have seen major advances in the phylogenetics, evolutionary biogeography and ecology of cichlid fish. Most of this work has concentrated on the most diverse radiations. Unfortunately, a large number of small radiations and 'non-radiations' have been overlooked, potentially limiting the contribution of the cichlid system to our understanding of speciation and adaptive radiation. I have reviewed the literature to identify 33 intralacustrine radiations and 76 failed radiations. For as many as possible I collected information on lake size, age and phylogenetic relationships. I use these data to address two questions: (i) whether the rate of speciation and the resulting species richness are related to temporal and spatial variation in ecological opportunity and (ii) whether the likelihood of undergoing adaptive radiation is similar for different African cichlid lineages. The former is a key prediction of the ecological theory of adaptive radiation that has been presumed true but remains untested for cichlid radiations. The second is based on the hypothesis that the propensity of cichlids to radiate is due to a key evolutionary innovation shared by all African cichlids. The evidence suggests that speciation rate declines through time as niches get filled up during adaptive radiation: young radiations and early stages of old radiations are characterized by high rates of speciation, whereas at least 0.5 Myr into a radiation speciation becomes a lot less frequent. The number of species in cichlid radiations increases with lake size, supporting the prediction that species diversity increases with habitat heterogeneity, but also with opportunity for isolation by distance. Finally, the data suggest that the propensity to radiate within lakes is a derived property that evolved during the evolutionary history of some African cichlids, and the appearance of which does not coincide with the appearance of proposed key innovations in morphology and life history.

Adaptation, Physiological↗
PubMed1999

Molecular domestication--more than a sporadic episode in evolution.

Transposable elements are short but complex pieces of DNA or RNA containing a streamlined minimal-genome with the capacity for its selfish replication in a foreign genomic environment. Cis-regulatory sections within the elements orchestrate tempo and mode of TE expression. Proteins encoded by TEs mainly direct their own propagation within the genome by recruitment of host-encoded factors. On the other hand, TE-encoded proteins harbor a very attractive repertoire of functional abilities for a cell. These proteins mediate excision, replication and integration of defined DNA fragments. Furthermore, some of these proteins are able to manipulate important host factors by altering their original function. Thus, if the host genome succeeds in domesticating such TE-encoded proteins by taming their 'anarchistic behavior,' such an event can be considered as an important evolutionary innovation for its own benefit. In fact, the domestication of TE-derived cis-regulatory modules and protein coding sections took place repeatedly in the course of genome evolution. We will present prominent cases that impressively demonstrate the beneficial impact of TEs on host biology over evolutionary time. Furthermore, we will propose that molecular domestication might be considered as a resumption of the same evolutionary process that drove the transition from 'primitive genomes' to 'modern' ones at the early dawn of life, that is, the adaptive integration of a short piece of autonomous DNA into a complex regulatory network.

Amino Acid Sequence↗
PubMed2006

Evolutionary complexity of MADS complexes.

Developmental programs rely on the timely and spatially correct expression of sets of interacting factors, many of which appear to be transcription factors. Examples of these can be found in the MADS-box gene family. This gene family has greatly expanded, particularly in plants, by a range of duplications that have enabled the genes to diversify in structure and function. MADS-box genes appear to have been instrumental in shaping one of the great evolutionary innovations, the true flower, which originated around 120-150 million years ago and led to the enormous radiation of the angiosperms. We propose a shift from analyzing individual gene functions towards studying MADS-box gene function at the subfamily level. This will enable us to distinguish subfunctionalization events from the evolutionary changes that defined floral morphology.

Biological Evolution↗
PubMed2026

Tandem Duplication-Driven Neofunctionalization of UDP-Glycosyltransferases Shapes the Diversification of Triterpenoid Saponins in the Cucurbitaceae.

Tandem duplication of tailoring enzymes allows evolutionary innovation that diversifies plant specialized metabolism. Here, we present an interesting example of how tandem duplicated UDP-glycosyltransferases undergo neofunctionalization and shape the chemical diversity of triterpenoid saponins in the Cucurbitaceae family. A chromosome-level genome of Siraitia grosvenorii was assembled and aligned with multiple cucurbit genomes, revealing a specific UGT73AM tandem duplication responsible for regio-selective glycosylation (e.g. the rare 1,4-linked disaccharide) of diverse saponins such as mogrosides, ginsenosides, and momordicines. Comparative genomics depicted the evolutionary trajectory of a universal saponin-biosynthesizing UGT73 tandem arrays syntenously preserved across core eudicots, where lineage-specific UGT copies contribute to distinct metabolic phenotypes. A crystal structure of SgUGT73AM30 (mogrol 25-O-glycosyltransferase) in complex with UDP and mogrol was obtained to elucidate the molecular basis of the regio-specific decoration on vicinal diol of the substrates. Altogether, these findings provide insights into tandem duplication-driven diversification of glycosyltransferases and lay the foundation for engineered glycosylation of valuable triterpenoid saponins.

Saponins↗
PubMed1998

[Evolutionary role of sex chromosomes (a new concept)].

Sex differentiation provides for testing evolutionary innovations in the male genome before they are transferred to the female genetic system. This is possible with dichronous (asynchronous) evolution, when evolution in males precedes that in females [3-7]. Hence, along with common autosomal genes for stable characters, exclusively male and exclusively female genes must exist. The male genes are already acquired by the male genome but are not yet transferred to the female one. The female genes are already lost by the male genome but still remain in the female genome. They constitute temporary evolutionary genotypic sexual dimorphism. Common genes cannot exhibit genotypic sexual dimorphism; they show only constant phenotypic hormonal sexual dimorphism. On the basis of the interpretation of genotypic sexual dimorphism as a consequence of sex dichronism, the evolutionary role of sex chromatins is clarified and a new concept for them is suggested. According to this concept, the Y chromosome is the "conductor" of ecological information into the genome, the "place of birth" and testing of new genes, the accelerator and regulator of genotypic sexual dimorphism. By contrast, the X chromosome of the heterogametic sex provides the transportation of new genes from the Y chromosome to autosomes. This chromosome stabilizes, relaxes, and suppresses genotypic sexual dimorphism and accumulates genes that will be eliminated. This concept sheds light on many problems: the chromosomal localization of genes and their transfer to other chromosomes, the inactivation of chromosomes, mobile genes, mutation bursts, insertional mutagenesis, the association of the Y chromosome with stress, retroviruses, etc. In particular, it explains why genes "jump," why transpositions of mobile elements depend on ecological stress, why different genes mutate simultaneously, etc.

Biological Evolution↗
PubMedDate not supplied

[Evolutionary chromosomes and sex dimorphism].

In order to understand the phenomenon of sex, it is not enough to know about its reproductive role and role in recombination. In addition, knowledge of its evolutionary role is required. Sexual differentiation allows us to test evolutionary innovations in the male genome before they are transmitted to the female genome. This is possible in the framework of dichronous evolution, when the evolution of the male sex goes faster than the evolution of the female sex. This implies that there clearly should be male genes, which are already present in the male genome, but are not yet in the female genome; and vice versa, there should exist female genes, which have already been lost by the male sex, but still remain in females. Dichronicity results from different reaction norm of the sexes. This interpretation implies (1) the nomadic behavior of genes in the genome (2) the existence of evolutionary sexual dimorphism, which begins in the form of modificational changes in the female sex followed by selection-derived changes in the male sex; (3) the discovery of evolutionary roles of chromosomes and the proposition of a new concept, according to which the Y-chromosome represents a "gateway" for environment-related information coming to the genome, i.e., place of "birth" and testing of new genes, which comprise the basis of evolutionary sexual dimorphism--its initiator, accelerator, and regulator. The X-chromosome is the "transport" chromosome that transfers new genes from the Y-chromosomes into autosomes and therefore serves as a stabilizer, relaxer, and liquidator of evolutionary sexual dimorphism; it also serves as repository of the outgoing genes that await elimination. This concept provides for a new interpretation of the appearance, localization, and movement of genes along chromosomes and between them, and it sheds new light on the phenomena of chromosomal inactivation, mobile genes, association of Y-chromosome with stress, viruses, etc.

Animals↗
PubMed2002

An evolutionary treatment of the morphology and physiology of circulatory organs in insects.

An overview from an evolutionary perspective is presented on the research of the past 2 decades on insect circulatory organs. Based on various functional morphology it is clear that the flow mode of the dorsal vessel ('heart') has changed during the evolution of hexapods. In all apterygotes and mayflies the flow is bidirectional. In most pterygote insects, however, it is unidirectional. In some endopterygote insects, the direction of the flow alternates. This is achieved by heartbeat reversal, which may have various physiological functions and is a derived condition that probably occurred several times during the course of insect evolution. Special attention is given to the hemolymph flow in body appendages. In ancestral hexapods, they are supplied by arteries, whereas circulation in appendages of higher insects is accomplished by accessory pulsatile organs. These auxiliary hearts are autonomous pumps and exhibit a great diversity in their functional morphology. They represent evolutionary innovations which evolved by recruitment of building blocks from various organ systems and were assembled into new functional units. Almost all pulsatile circulatory organs in insects investigated exhibit a myogenic automatism with a superimposed neuronal control. The neuroanatomy of insect circulatory organs has been investigated only in a small number of species but in considerable detail. Numerous potential peptidergic and a few aminergic mediators could be demonstrated by immunocytochemical and biochemical methods. The cardiotropic effectiveness of these mediators may vary among species and it can be stated that there is no uniform picture of the control of the various circulatory organs in insects. A possible explanation for the differences may lie in the different evolutionary origins of the muscular components. Furthermore, insect circulatory organs may represent important neurohemal releasing sites.

Animal Structures↗
PubMed2006

Zimmermann's telome theory of megaphyll leaf evolution: a molecular and cellular critique.

Megaphyll leaf evolution was a critical event in Earth history that had major consequences for the biotic regulation of the global environment. Zimmermann's telome theory has been widely accepted for over seventy years as the leading explanation for this evolutionary innovation. According to the telome theory, megaphylls evolved from the three-dimensional lateral branches of early vascular land plants in a hypothetical series of three transformations; first, the formation of determinate lateral branches (overtopping); second, the development of 'flattened' branch systems (planation); and third, the fusion of planated branches with lateral outgrowths of photosynthetic mesophyll tissue to form the leaf blade (webbing). A critical review of the molecular and cellular evidence identifies plausible genetic, cellular and physiological mechanisms in extant higher plants for overtopping and planation but more limited evidence for the process of webbing (lateral outgrowth fusion). We highlight key outstanding questions concerning the telome theory that are likely to be resolved when gene identification and functional analysis techniques are applied to photosynthetic organisms that have different evolutionary histories.

Biological Evolution↗
PubMed2006

Hagfish and lancelet fibrillar collagens reveal that type II collagen-based cartilage evolved in stem vertebrates.

The origin of vertebrates was defined by evolution of a skeleton; however, little is known about the developmental mechanisms responsible for this landmark evolutionary innovation. In jawed vertebrates, cartilage matrix consists predominantly of type II collagen (Col2alpha1), whereas that of jawless fishes has long been thought to be noncollagenous. We recently showed that Col2alpha1 is present in lamprey cartilage, indicating that type II collagen-based cartilage evolved earlier than previously recognized. Here, we investigate the origin of vertebrate cartilage, and we report that hagfishes, the sister group to lampreys, also have Col2alpha1-based cartilage, suggesting its presence in the common ancestor of crown-group vertebrates. We go on to show that lancelets, a sister group to vertebrates, possess an ancestral clade A fibrillar collagen (ColA) gene that is expressed in the notochord. Together, these results suggest that duplication and diversification of ColA genes at the chordate-vertebrate transition may underlie the evolutionary origin of vertebrate skeletal tissues.

Animals↗
PubMed2026

Control of foreign DNA: emerging roles of xenogeneic silencers.

Bacteria continuously acquire foreign DNA through horizontal gene transfer, yet its successful integration depends on regulatory mechanisms that balance genome protection with evolutionary innovation. Xenogeneic silencers are central to this process: they preferentially bind AT-rich DNA, a common feature of many horizontally acquired genetic elements, and repress its transcription. Recent studies, however, reveal a much broader regulatory repertoire. Beyond transcriptional repression, these proteins contribute to chromosome organization by forming higher-order nucleoprotein complexes and phase-separated condensates that shape bacterial nucleoid architecture. Furthermore, they play roles in regulating bacteriophage infection cycles, including mechanisms by which phages hijack host silencing activities for their own benefit. Their extensive regulatory reach, spanning virulence genes, biofilm formation, specialized metabolite production, and mobile genetic elements (MGEs), underscores their central role in connecting environmental signals, including fluctuations in the second messenger c-di-GMP, with gene expression, and genome organization. The diversification of xenogeneic silencers across bacterial chromosomes, plasmids, phages, and other MGEs highlights their evolutionary significance. Together, these recent findings position xenogeneic silencers as dynamic regulatory modules that shape the fate of foreign DNA across the horizontal gene transfer network.

Gene Transfer, Horizontal↗
PubMed2006

Precraniate origin of cranial motoneurons.

The craniate head is innervated by cranial sensory and motor neurons. Cranial sensory neurons stem from the neurogenic placodes and neural crest and are seen as evolutionary innovations crucial in fulfilling the feeding and respiratory needs of the craniate "new head." In contrast, cranial motoneurons that are located in the hindbrain and motorize the head have an unclear phylogenetic status. Here we show that these motoneurons are in fact homologous to the motoneurons of the sessile postmetamorphic form of ascidians. The motoneurons of adult Ciona intestinalis, located in the cerebral ganglion and innervating muscles associated with the huge "branchial basket," express the transcription factors CiPhox2 and CiTbx20, whose vertebrate orthologues collectively define cranial motoneurons of the branchiovisceral class. Moreover, Ciona's postmetamorphic motoneurons arise from a hindbrain set aside during larval life and defined as such by its position (caudal to the prosensephalic sensory vesicle) and coexpression of CiPhox2 and CiHox1, whose orthologues collectively mark the vertebrate hindbrain. These data unveil that the postmetamorphic ascidian brain, assumed to be a derived feature, in fact corresponds to the vertebrate hindbrain and push back the evolutionary origin of cranial nerves to before the origin of craniates.

Animals↗
PubMed2005

Methods for genome-wide analysis of gene expression changes in polyploids.

Polyploidy is an evolutionary innovation, providing extra sets of genetic material for phenotypic variation and adaptation. It is predicted that changes of gene expression by genetic and epigenetic mechanisms are responsible for novel variation in nascent and established polyploids (Liu and Wendel, 2002; Osborn et al., 2003; Pikaard, 2001). Studying gene expression changes in allopolyploids is more complicated than in autopolyploids, because allopolyploids contain more than two sets of genomes originating from divergent, but related, species. Here we describe two methods that are applicable to the genome-wide analysis of gene expression differences resulting from genome duplication in autopolyploids or interactions between homoeologous genomes in allopolyploids. First, we describe an amplified fragment length polymorphism (AFLP)--complementary DNA (cDNA) display method that allows the discrimination of homoeologous loci based on restriction polymorphisms between the progenitors. Second, we describe microarray analyses that can be used to compare gene expression differences between the allopolyploids and respective progenitors using appropriate experimental design and statistical analysis. We demonstrate the utility of these two complementary methods and discuss the pros and cons of using the methods to analyze gene expression changes in autopolyploids and allopolyploids. Furthermore, we describe these methods in general terms to be of wider applicability for comparative gene expression in a variety of evolutionary, genetic, biological, and physiological contexts.

Arabidopsis↗
PubMed2026

The genomic alchemist's arsenal: A comprehensive review of gene recruitment, regulatory rewiring, and the evolutionary arms race in snake envenomation.

Snake venom represents a striking example of evolutionary innovation, in which ancestral physiological gene networks have been co-opted into potent biochemical weapons. Advances in multi-omics, single-cell genomics, and structural bioinformatics have catalyzed a conceptual shift from descriptive toxin cataloging to a systems-level understanding of venom evolution, regulation, and function. This Review integrates genomic, cellular, and structural perspectives to delineate the molecular architecture underpinning venom diversification and target-site co-evolution. Emphasis is placed on regulatory mechanisms driving rapid expression plasticity, including super-enhancer activity, transposable element insertion, spatial heterogeneity within the venom gland, and non-coding RNA-mediated modulation. At the protein level, the review examines how hypervariable toxins engage in structural arms races with prey targets, and how multi-toxin complex formation, functional synergy, and molecular dynamics simulations inform models of lethality and resistance. A comparative framework is provided by contrasting high-potency predatory snake venoms with low-potency defensive venoms of hymenopterans such as bees and wasps, revealing how ecological selective pressures shape toxin potency, composition, and target specificity across taxa. Finally, current translational strategies are evaluated, with a focus on the relative merits of recombinant human monoclonal antibodies versus catalytic-site small-molecule inhibitors as deployable interventions for snakebite. By synthesizing evolutionary genomics, structural biology, comparative toxinology, and synthetic antivenomics, this Review outlines a predictive framework for anticipating venom evolutionary trajectories and for designing broad-spectrum, next-generation therapeutics.

Animals↗
PubMed2006

Approaches to defining the ancestral eukaryotic protein complexome.

In this paper, we integrate and summarize the currently available information on the ancestral eukaryotic protein complexome, which is defined as the set of protein complexes that extant eukaryotes inherited from their last common ancestor. From the literature, we compiled lists of complexes with three or more distinct protein components from well-studied eukaryotic model organisms. Combinatorial complexes of membrane-associated signalling proteins and specific transcription factors were disregarded. A stringent but sensitive novel orthology detection algorithm, complemented with manual sequence similarity searches and with published data on whole genome or segmental and tandem gene duplications, enabled us to map the vast majority of these complexes to a virtual primitive eukaryote termed Eukaryotic Virtual Ancestor (EVA). EVA is intended to resemble the last common eukaryotic ancestor and to emulate the biological common denominator of the major extent eukaryotic lineages at the molecular level. The dataset was then used for the functional and domain annotation of the ancestral eukaryotic complexome. Furthermore, we illustrate its usefulness for inferring complexes of poorly studied eukaryotes and for the recognition of highly divergent orthologs. We also discuss the evolution of the circa 1,400 complex-associated ancestral proteins. As about 90% of these proteins have been conserved in all thirteen studied free-living eukaryotes, the evolutionary reduction and loss of complexes seems minimal. Moreover, the available data suggest that, in general, the acquisition of stable complexes of novel design occurs too slowly to be a major contributor to evolutionary innovation. Finally, given the stability of the ancestral eukarotic complexome we propose its use in the formulation of the mathematical systems that aim to simulate biological processes. Our data suggest that these simplified formulations can apply to most free-living model eukaryotes.

Animals↗
PubMed2004

Evo-devo aspects of classical and molecular data in a historical perspective.

We discuss the interplay between evolution and development as reflected in data and concepts since about 1800. Darwin and his "continental apostle" Haeckel put the striking similarity between early vertebrate embryos in an evolutionary context. Haeckel's partly illicit generalizations discredited evolutionary thinking among early experimental embryologists who moreover noted riddles incompatible with contemporary concepts of homology and evolution. Relevant solutions were suggested by the more recent concept of ontogenetic networks that embody complex regulatory properties and genes with partly overlapping functions. Molecular data on development increasingly reveal evolutionary opportunism, for instance when a widespread signaling chain involved in primitive immune defense was apparently recruited later on for dorso-ventral axis determination in some evolutionarily advanced insect groups. Recently, Rickettsia-related bacteria colonizing many arthropod species were found to "manipulate" the first steps of host development to the advantage of their own propagation, but by ways that could also promote host speciation. Molecular genetics can now document evolutionary steps in ontogenetic networks. In the fruit fly for instance, the novel bicoid gene has superseded a crucial patterning function within a pre-existing network--a case of "molecular caenogenesis." The expression patterns of conserved genes that antagonistically determine dorso-ventral polarity support a literal revolution envisioned almost 200 years ago. This is the dorso-ventral inversion of the body plan in some metazoans--ascribed then to the Articulata, now to the Chordata. The final section posits that the opportunistic character of evolutionary innovations is detrimental to parsimony in development.

Animals↗