Evolutionary convergence

Carotenoid cleavage enzymes evolved convergently to generate the visual chromophore

The retinal light response in animals originates from the photoisomerization of an opsin-coupled 11-cis-retinaldehyde chromophore. This visual chromophore is enzymatically produced through the action of carotenoid cleavage dioxygenases. Vertebrates require two carotenoid cleavage dioxygenases, β-carotene oxygenase 1 and retinal pigment epithelium 65 (RPE65), to form 11-cis-retinaldehyde from carotenoid substrates, whereas invertebrates such as insects use a single enzyme known as Neither Inactivation Nor Afterpotential B (NinaB). RPE65 and NinaB couple trans-cis isomerization with hydrolysis and oxygenation, respectively, but the mechanistic relationship of their isomerase activities remains unknown. Here we report the structure of NinaB, revealing details of its active site architecture and mode of membrane binding. Structure-guided mutagenesis studies identify a residue cluster deep within the NinaB substrate-binding cleft that controls its isomerization activity. Our data demonstrate that isomerization activity is mediated by distinct active site regions in NinaB and RPE65-an evolutionary convergence that deepens our understanding of visual system diversity.

Principles of cognitive biology and the concept of biocivilisations

A range of studies published in the last few decades promotes the cognitive aspects of life: all organisms, from bacteria to mammals, are capable of sensing/perception, decision-making, problem-solving, learning, and other cognitive functions, including sentience and consciousness. In this paper I present a scientific and philosophical synthesis of these studies, leading to an integrated view of cognitive biology. This view is expressed through the four principles applicable to all living systems: (1) sentience and consciousness, (2) autopoiesis, (3) free energy principle and relational biology, and (4) cognitive repertoire. The principles are circular, and they reinforce themselves. The circularity is not rigid, meaning that hierarchical and heterarchical shifts are widespread in the biosphere. The above principles emerged at the dawn of life, with the first cells, bacteria and archaea. All biogenic forms and functions that emerged since then can be traced to the first cells - indivisible units of biological agency. Following these principles, I developed the concept of biocivilisations to explain various forms of social intelligence in different kingdoms of life. The term biociviloisations draws on the human interpretation of the concept of civilisation, which searches for non-human equivalents of communication, engineering, science, medicine, art, and agriculture, in all kingdoms of life by applying the principles of cognitive biology. Potential avenues for testing the concept of biocivilisations are highlighted.

Cephalopod vision: How to build a better eye

Cephalopods' eyes superficially resemble our own, but because of their evolutionary and developmental history, the photoreceptors face forward, with the downstream neural circuitry in the brain, not the retina. Two new papers uncover molecular and developmental mechanisms underlying cephalopod visual development.

Genetic and Non-Genetic Mechanisms Underlying Cancer Evolution

Simple Summary

Our manuscript summarizes the up-to-date data on the complex and dynamic nature of adaptation mechanisms and evolutionary processes taking place during cancer initiation, development and progression. Although for decades cancer has been viewed as a process governed by genetic mechanisms, it is becoming more and more clear that non-genetic mechanisms may play an equally important role in cancer evolution. In this review, we bring together these fundamental concepts and discuss how those tightly interconnected mechanisms lead to the establishment of highly adaptive quickly evolving cancers. Furthermore, we argue that in depth understanding of cancer progression from the evolutionary perspective may allow the prediction and direction of the evolutionary path of cancer populations towards drug sensitive phenotypes and thus facilitate the development of more effective anti-cancer approaches.

Abstract

Cancer development can be defined as a process of cellular and tissular microevolution ultimately leading to malignancy. Strikingly, though this concept has prevailed in the field for more than a century, the precise mechanisms underlying evolutionary processes occurring within tumours remain largely uncharacterized and rather cryptic. Nevertheless, although our current knowledge is fragmentary, data collected to date suggest that most tumours display features compatible with a diverse array of evolutionary paths, suggesting that most of the existing macro-evolutionary models find their avatar in cancer biology. Herein, we discuss an up-to-date view of the fundamental genetic and non-genetic mechanisms underlying tumour evolution with the aim of concurring into an integrated view of the evolutionary forces at play throughout the emergence and progression of the disease and into the acquisition of resistance to diverse therapeutic paradigms. Our ultimate goal is to delve into the intricacies of genetic and non-genetic networks underlying tumour evolution to build a framework where both core concepts are considered non-negligible and equally fundamental.

An Evo-Devo Perspective on Analogy in Biology

To explain the amazing morphological and biomechanical analogy between two distantly related vertebrates as are a dolphin and a shark, an explanation exclusively framed in terms of adaptation (i.e., in terms of the Darwinian survival of the fittest) is far from satisfactory. The same is true, of course, of any other comparison between structurally similar, but phylogenetically unrelated organisms. A purely evolutionary argument does not throw any light on how the developmental processes of their ancestors could eventually evolve in such a way as to eventually produce these peculiar phenotypes (the arrival of the fittest). How does Nature play with animal and plant form? To address the issue of the evolution of possible forms, we cannot ignore that these are products of development. This invites adopting the integrated perspective, currently known as evolutionary developmental biology, or evo-devo. Paths through the maze of living forms are not satisfactorily explained in terms of pure geometrical transformations or of the adaptive value of the phenotypes eventually produced. The emergence of form is largely dependent on the intrinsic evolvability of the developmental processes that translate the genotype into phenotypes. As a consequence, development makes analogous structures more likely to evolve than a pure adaptationist argument would ever suggest.

Stomatal and non-stomatal limitations in savanna trees and C4 grasses grown at low, ambient and high atmospheric CO2

By the end of the century, atmospheric CO₂ concentration ([CO₂]_a) could reach 800 ppm, having risen from ∼200 ppm ∼24 Myr ago. Carbon dioxide enters plant leaves through stomata that limit CO₂ diffusion and assimilation, imposing stomatal limitation (L_S). Other factors limiting assimilation are collectively called non-stomatal limitations (L_NS). C₄ photosynthesis concentrates CO₂ around Rubisco, typically reducing L_S. C₄-dominated savanna grasslands expanded under low [CO₂]_a and are metastable ecosystems where the response of trees and C₄ grasses to rising [CO₂]_a will determine shifting vegetation patterns. How L_S and L_NS differ between savanna trees and C₄ grasses under different [CO₂]_a will govern the responses of CO₂ fixation and plant cover to [CO₂]_a - but quantitative comparisons are lacking. We measured assimilation, within soil wetting-drying cycles, of three C₃ trees and three C₄ grasses grown at 200, 400 or 800 ppm [CO₂]_a. Using assimilation-response curves, we resolved L_S and L_NS and show that rising [CO₂]_a alleviated L_S, particularly for the C₃ trees, but L_NS was unaffected and remained substantially higher for the grasses across all [CO₂]_a treatments. Because L_NS incurs higher metabolic costs and recovery compared with L_S, our findings indicate that C₄ grasses will be comparatively disadvantaged as [CO₂]_a rises.

Learning by Association in Plants

In complex and ever-changing environments, resources such as food are often scarce and unevenly distributed in space and time. Therefore, utilizing external cues to locate and remember high-quality sources allows more efficient foraging, thus increasing chances for survival. Associations between environmental cues and food are readily formed because of the tangible benefits they confer. While examples of the key role they play in shaping foraging behaviours are widespread in the animal world, the possibility that plants are also able to acquire learned associations to guide their foraging behaviour has never been demonstrated. Here we show that this type of learning occurs in the garden pea, Pisum sativum. By using a Y-maze task, we show that the position of a neutral cue, predicting the location of a light source, affected the direction of plant growth. This learned behaviour prevailed over innate phototropism. Notably, learning was successful only when it occurred during the subjective day, suggesting that behavioural performance is regulated by metabolic demands. Our results show that associative learning is an essential component of plant behaviour. We conclude that associative learning represents a universal adaptive mechanism shared by both animals and 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.

Convergent evolution in locomotory patterns of flying and swimming animals

Locomotion is one of the major energetic costs faced by animals and various strategies have evolved to reduce its cost. Birds use interspersed periods of flapping and gliding to reduce the mechanical requirements of level flight while undergoing cyclical changes in flight altitude, known as undulating flight. Here we equipped free-ranging marine vertebrates with accelerometers and demonstrate that gait patterns resembling undulating flight occur in four marine vertebrate species comprising sharks and pinnipeds. Both sharks and pinnipeds display intermittent gliding interspersed with powered locomotion. We suggest, that the convergent use of similar gait patterns by distinct groups of animals points to universal physical and physiological principles that operate beyond taxonomic limits and shape common solutions to increase energetic efficiency. Energetically expensive large-scale migrations performed by many vertebrates provide common selection pressure for efficient locomotion, with potential for the convergence of locomotory strategies by a wide variety of species.

Different roles for homologous interneurons in species exhibiting similar rhythmic behaviors

It is often assumed that similar behaviors in related species are produced by similar neural mechanisms. To test this, we examined the neuronal basis of a simple swimming behavior in two nudibranchs (Mollusca, Opisthobranchia), Melibe leonina and Dendronotus iris. The side-to-side swimming movements of Dendronotus [1] strongly resemble those of Melibe [2, 3]. In Melibe, it was previously shown that the central pattern generator (CPG) for swimming is composed of two bilaterally symmetric pairs of identified interneurons, swim interneuron 1 (Si1) and swim interneuron 2 (Si2), which are electrically coupled ipsilaterally and mutually inhibit both contralateral counterparts [2, 4]. We identified homologs of Si1 and Si2 in Dendronotus. (Henceforth, homologous neurons in each species will be distinguished by the subscripts (Den) and (Mel).) We found that Si2(Den) and Si2(Mel) play similar roles in generating the swim motor pattern. However, unlike Si1(Mel), Si1(Den) was not part of the swim CPG, was not strongly coupled to the ipsilateral Si2(Den), and did not inhibit the contralateral neurons. Thus, species differences exist in the neuronal organization of the swim CPGs despite the similarity of the behaviors. Therefore, similarity in species-typical behavior is not necessarily predictive of common neural mechanisms, even for homologous neurons in closely related species.

Molecular phylogenies disprove a hypothesized C4 reversion in Eragrostis walteri (Poaceae)

BACKGROUND AND AIMS

The main assemblage of the grass subfamily Chloridoideae is the largest known clade of C(4) plant species, with the notable exception of Eragrostis walteri Pilg., whose leaf anatomy has been described as typical of C(3) plants. Eragrostis walteri is therefore classically hypothesized to represent an exceptional example of evolutionary reversion from C(4) to C(3) photosynthesis. Here this hypothesis is tested by verifying the photosynthetic type of E. walteri and its classification.

METHODS

Carbon isotope analyses were used to determine the photosynthetic pathway of several E. walteri accessions, and phylogenetic analyses of plastid rbcL and ndhF and nuclear internal transcribed spacer DNA sequences were used to establish the phylogenetic position of the species.

RESULTS

Carbon isotope analyses confirmed that E. walteri is a C(3) plant. However, phylogenetic analyses demonstrate that this species has been misclassified, showing that E. walteri is positioned outside Chloridoideae in Arundinoideae, a subfamily comprised entirely of C(3) species.

CONCLUSIONS

The long-standing hypothesis of C(4) to C(3) reversion in E. walteri is rejected, and the classification of this species needs to be re-evaluated.

Mosaic, self-similarity logic, and biological attraction principles: three explanatory instruments in biology

From a structural standpoint, living organisms are organized like a nest of Russian matryoshka dolls, in which structures are buried within one another. From a temporal point of view, this type of organization is the result of a history comprised of a set of time backcloths which have accompanied the passage of living matter from its origins up to the present day. The aim of the present paper is to indicate a possible course of this 'passage through time, and suggest how today's complexity has been reached by living organisms. This investigation will employ three conceptual tools, namely the Mosaic, Self-Similarity Logic, and the Biological Attraction principles. Self-Similarity Logic indicates the self-consistency by which elements of a living system interact, irrespective of the spatiotemporal level under consideration. The term Mosaic indicates how, from the same set of elements assembled according to different patterns, it is possible to arrive at completely different constructions: hence, each system becomes endowed with different emergent properties. The Biological Attraction principle states that there is an inherent drive for association and merging of compatible elements at all levels of biological complexity. By analogy with the gravitation law in physics, biological attraction is based on the evidence that each living organism creates an attractive field around itself. This field acts as a sphere of influence that actively attracts similar fields of other biological systems, thereby modifying salient features of the interacting organisms. Three specific organizational levels of living matter, namely the molecular, cellular, and supracellular levels, have been considered in order to analyse and illustrate the interpretative as well as the predictive roles of each of these three explanatory principles.

Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function

Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine definitions of EC sub-subclasses for improved discrimination in their classification of enzyme reactions. The results also indicate that mechanistic convergence of reaction steps is widespread, suggesting that quantitative measurement of mechanistic similarity can inform approaches for functional annotation.

Two independent C4 origins in Aristidoideae (Poaceae) revealed by the recruitment of distinct phosphoenolpyruvate carboxylase genes

Determining the number of evolutions of an adaptive novelty is primordial to understand its evolutionary significance. C(4) photosynthesis, an adaptation to low CO(2) atmospheric concentration and high temperature, evolved multiple times, but the number of convergent evolutions is still debated. In Poaceae phylogeny, numerous C(4) groups are separated by C(3) taxa, but whether these correspond to independent C(4) origins or a few C(4) evolutions followed by reversals is controversial. The Aristidoideae subfamily is formed by two C(4) genera, Aristida and Stipagrostis, separated by the C(3) genus Sartidia. In the current study, we investigated the evolutionary history of genes encoding phosphoenolpyruvate carboxylases (PEPC) to shed light on the photosynthetic transitions that occurred in Aristidoideae. We identified six distinct PEPC gene lineages that appeared through several rounds of gene duplications before or early during grass diversification. The gene lineage encoding the C(4) PEPC of Stipagrostis differs from those of the other C(4) grasses, including Aristida. These distinct origins of C(4) PEPC genes from these two Aristidoideae genera unequivocally indicate that they integrated the C(4) pathway independently. This highlights the importance of candidate-gene studies when inferring the evolutionary history of a character such as C(4) photosynthesis, one of the greatest evolutionary successes in plant history.

Multiple convergent evolution of arboreal life in oribatid mites indicates the primacy of ecology

Frequent convergent evolution in phylogenetically unrelated taxa points to the importance of ecological factors during evolution, whereas convergent evolution in closely related taxa indicates the importance of favourable pre-existing characters (pre-adaptations). We investigated the transitions to arboreal life in oribatid mites (Oribatida, Acari), a group of mostly soil-living arthropods. We evaluated which general force-ecological factors, historical constraints or chance-was dominant in the evolution of arboreal life in oribatid mites. A phylogenetic study of 51 oribatid mite species and four outgroup taxa, using the ribosomal 18S rDNA region, indicates that arboreal life evolved at least 15 times independently. Arboreal oribatid mite species are not randomly distributed in the phylogenetic tree, but are concentrated among strongly sclerotized, sexual and evolutionary younger taxa. They convergently evolved a capitate sensillus, an anemoreceptor that either precludes overstimulation in the exposed bark habitat or functions as a gravity receptor. Sexual reproduction and strong sclerotization were important pre-adaptations for colonizing the bark of trees that facilitated the exploitation of living resources (e.g. lichens) and served as predator defence, respectively. Overall, our results indicate that ecological factors are most important for the observed pattern of convergent evolution of arboreal life in oribatid mites, supporting an adaptationist view of evolution.

Plant neurobiology as a paradigm shift not only in the plant sciences

Plants are complex living beings, extremely sensitive to environmental factors, continuously adapting to the ever changing environment. Emerging research document that plants sense, memorize, and process experiences and use this information for their adaptive behavior and evolution. As any other living and evolving systems, plants act as knowledge accumulating systems. Neuronal informational systems are behind this concept of organisms as knowledge accumulating systems because they allow the most rapid and efficient adaptive responses to changes in environment. Therefore, it should not be surprising that neuronal computation is not limited to animal brains but is used also by bacteria and plants. The journal, Plant Signaling & Behavior, was launched as a platform for exchanging information and fostering research on plant neurobiology in order to allow our understanding of plants in their whole integrated, communicative, and behavioral complexity.I always go by official statistics because they are very carefully compounded and, even if they are false, we have no others ... approximately Jaroslav Hasek, 1911.