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## ‣ Evolutionary History of Arabidopsis thaliana Aminoacyl-tRNA Synthetase Dual-Targeted Proteins

BRANDAO, Marcelo M.; SILVA-FILHO, Marcio C.
Fonte: OXFORD UNIV PRESS Publicador: OXFORD UNIV PRESS
Tipo: Artigo de Revista Científica
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Aminoacyl-transfer RNA (tRNA) synthetases (aaRS) are key players in translation and act early in protein synthesis by mediating the attachment of amino acids to their cognate tRNA molecules. In plants, protein synthesis may occur in three subcellular compartments (cytosol, mitochondria, and chloroplasts), which requires multiple versions of the protein to be correctly delivered to its proper destination. The organellar aaRS are nuclear encoded and equipped with targeting information at the N-terminal sequence, which enables them to be specifically translocated to their final location. Most of the aaRS families present organellar proteins that are dual targeted to mitochondria and chloroplasts. Here, we examine the dual targeting behavior of aaRS from an evolutionary perspective. Our results show that Arabidopsis thaliana aaRS sequences are a result of a horizontal gene transfer event from bacteria. However, there is no evident bias indicating one single ancestor (Cyanobacteria or Proteobacteria). The dual-targeted aaRS phylogenetic relationship was characterized into two different categories (paralogs and homologs) depending on the state recovered for both dual-targeted and cytosolic proteins. Taken together, our results suggest that the dual-targeted condition is a gain-of-function derived from gene duplication. Selection may have maintained the original function in at least one of the copies as the additional copies diverged.; Conselho nacional de Desenvolvimento Cientifico e Tecnologico (CNPq)[151048/2007-0]; Conselho nacional de Desenvolvimento Cientifico e Tecnologico (CNPq)[471664/2008-1]; FAPESP Fundacao de Amparo a Pesquisa do Estado de Sao Paulo...

## ‣ Covariance structure in the skull of Catarrhini: a case of pattern stasis and magnitude evolution

OLIVEIRA, Felipe Bandoni de; PORTO, Arthur; MARROIG, Gabriel
Tipo: Artigo de Revista Científica
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The study of the genetic variance/covariance matrix (G-matrix) is a recent and fruitful approach in evolutionary biology, providing a window of investigating for the evolution of complex characters. Although G-matrix studies were originally conducted for microevolutionary timescales, they could be extrapolated to macroevolution as long as the G-matrix remains relatively constant, or proportional, along the period of interest. A promising approach to investigating the constancy of G-matrices is to compare their phenotypic counterparts (P-matrices) in a large group of related species; if significant similarity is found among several taxa, it is very likely that the underlying G-matrices are also equivalent. Here we study the similarity of covariance and correlation structure in a broad sample of Old World monkeys and apes (Catarrhini). We made phylogenetically structured comparisons of correlation and covariance matrices derived from 39 skull traits, ranging from between species to the superfamily level. We also compared the overall magnitude of integration between skull traits (r(2)) for all Catarrhim genera. Our results show that P-matrices were not strictly constant among catarrhines, but the amount of divergence observed among taxa was generally low. There was significant and positive correlation between the amount of divergence in correlation and covariance patterns among the 30 genera and their phylogenetic distances derived from a recently proposed phylogenetic hypothesis. Our data demonstrate that the P-matrices remained relatively similar along the evolutionary history of catarrhines...

## ‣ The Evolution of Modularity in the Mammalian Skull II: Evolutionary Consequences

MARROIG, Gabriel; SHIRAI, Leila T.; PORTO, Arthur; OLIVEIRA, Felipe B. de; CONTO, Valderes De
Tipo: Artigo de Revista Científica
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Changes in patterns and magnitudes of integration may influence the ability of a species to respond to selection. Consequently, modularity has often been linked to the concept of evolvability, but their relationship has rarely been tested empirically. One possible explanation is the lack of analytical tools to compare patterns and magnitudes of integration among diverse groups that explicitly relate these aspects to the quantitative genetics framework. We apply such framework here using the multivariate response to selection equation to simulate the evolutionary behavior of several mammalian orders in terms of their flexibility, evolvability and constraints in the skull. We interpreted these simulation results in light of the integration patterns and magnitudes of the same mammalian groups, described in a companion paper. We found that larger magnitudes of integration were associated with a blur of the modules in the skull and to larger portions of the total variation explained by size variation, which in turn can exert a strong evolutionary constraint, thus decreasing the evolutionary flexibility. Conversely, lower overall magnitudes of integration were associated with distinct modules in the skull, to smaller fraction of the total variation associated with size and...

## ‣ Evolutionary placement of Xanthomonadales based on conserved protein signature sequences

CUTINO-JIMENEZ, Ania M.; MARTINS-PINHEIRO, Marinalva; LIMA, Wanessa C.; MARTIN-TORNET, Alexander; MORALES, Osleidys G.; MENCK, Carlos F. M.
Tipo: Artigo de Revista Científica
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## ‣ Chromosomal evolution of neotropical cichlids: The role of repetitive DNA sequences in the organization and structure of karyotype

Schneider, Carlos Henrique; Gross, Maria Claudia; Terencio, Maria Leandra; Artoni, Roberto Ferreira; Vicari, Marcelo Ricardo; Martins, Cesar; Feldberg, Eliana
Tipo: Artigo de Revista Científica Formato: 201-214
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Cichlids are important in the aquaculture and ornamental fish trade and are considered models for evolutionary biology. However, most studies of cichlids have investigated African species, and the South American cichlids remain poorly characterized. Studies in neotropical regions have focused almost exclusively on classical cytogenetic approaches without investigating physical chromosomal mapping of specific sequences. The aim of the present study is to investigate the genomic organization of species belonging to different tribes of the subfamily Cichlinae (Cichla monoculus, Astronotus ocellatus, Geophagus proximus, Acaronia nassa, Bujurquina peregrinabunda, Hoplarchus psittacus, Hypselecara coryphaenoides, Hypselecara temporalis, Caquetaia spectabilis, Uaru amphiacanthoides, Pterophyllum leopoldi, Pterophyllum scalare, and Symphysodon discus) and reexamine the karyotypic evolutionary patterns proposed for this group. Variations in some cytogenetic markers were observed, although no trends were found in terms of the increase, decrease, or maintenance of the basal diploid chromosome number 2n = 48 in the tribes. Several species were observed to have 18S rDNA genetic duplications, as well as multiple rDNA loci. In most of the taxa analyzed...

## ‣ Unravelling the determinants of insular body size shifts

McClain, Craig R.; Durst, Paul A. P.; Boyer, Alison G.; Francis, Clinton D.
Fonte: The Royal Society Publicador: The Royal Society
Tipo: Artigo de Revista Científica
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The island rule, a pattern of size shifts on islands, is an oft-cited but little understood phenomenon of evolutionary biology. Here, we explore the evolutionary mechanisms behind the rule in 184 mammal species, testing climatic, ecological and phylogenetic hypotheses in a robust quantitative framework. Our findings confirm the importance of species’ ecological traits in determining both the strength and the direction of body size changes on islands. Although the island rule pattern appears relatively weak overall, we find strongest support for models incorporating trait, climatic and geographical factors in a phylogenetic context, lending support to the idea that the island rule is a complex phenomenon driven by interacting intrinsic and extrinsic mechanisms. Overall, we find that different clades may be evolutionarily predisposed to dwarfism or gigantism, but the magnitude of size changes depends more on adaptation to the novel island environment.

## ‣ Chromodynamics of Cooperation in Finite Populations

Nowak, Martin; Traulsen, Arne
Fonte: Public Library of Science Publicador: Public Library of Science
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Background: The basic idea of tag-based models for cooperation is that individuals recognize each other via arbitrary signals, so-called tags. If there are tags of different colors, then cooperators can always establish new signals of recognition. The resulting “chromodynamics” is a mechanism for the evolution of cooperation. Cooperators use a secret tag until they are discovered by defectors who then destroy cooperation based on this tag. Subsequently, a fraction of the population manages to establish cooperation based on a new tag. Methodology/Principal Findings: We derive a mathematical description of stochastic evolutionary dynamics of tag-based cooperation in populations of finite size. Benefit and cost of cooperation are given by b and c. We find that cooperators are more abundant than defectors if (b/c > 1+2u/v), where (u) is the mutation rate changing only the strategy and v is the mutation rate changing strategy and tag. We study specific assumptions for (u) and (v) in two genetic models and one cultural model. Conclusions/Significance: In a genetic model, tag-based cooperation only evolves if a gene encodes both strategy and tag. In a cultural model with equal mutation rates between all possible phenotypes (tags and behaviors)...

## ‣ The One-Third Law of Evolutionary Dynamics

Ohtsuki, Hisashi; Bordalo, Pedro; Nowak, Martin A.
Tipo: Artigo de Revista Científica
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Evolutionary game dynamics in finite populations provide a new framework for studying selection of traits with frequency-dependent fitness. Recently, a “one-third law” of evolutionary dynamics has been described, which states that strategy A fixates in a B-population with selective advantage if the fitness of A is greater than that of B when A has a frequency View the MathML source. This relationship holds for all evolutionary processes examined so far, from the Moran process to games on graphs. However, the origin of the “number” View the MathML source is not understood. In this paper we provide an intuitive explanation by studying the underlying stochastic processes. We find that in one invasion attempt, an individual interacts on average with B-players twice as often as with A-players, which yields the one-third law. We also show that the one-third law implies that the average Malthusian fitness of A is positive.; Mathematics; Organismic and Evolutionary Biology

## ‣ Evolutionary Stability on Graphs

Ohtsuki, Hisashi; Nowak, Martin A.
Tipo: Artigo de Revista Científica
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Evolutionary stability is a fundamental concept in evolutionary game theory. A strategy is called an evolutionarily stable strategy (ESS), if its monomorphic population rejects the invasion of any other mutant strategy. Recent studies have revealed that population structure can considerably affect evolutionary dynamics. Here we derive the conditions of evolutionary stability for games on graphs. We obtain analytical conditions for regular graphs of degree (k > 2). Those theoretical predictions are compared with computer simulations for random regular graphs and for lattices. We study three different update rules: birth–death (BD), death–birth (DB), and imitation (IM) updating. Evolutionary stability on sparse graphs does not imply evolutionary stability in a well-mixed population, nor vice versa. We provide a geometrical interpretation of the ESS condition on graphs.; Mathematics; Organismic and Evolutionary Biology

## ‣ Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum

Balenger, Susan; Bonneaud, Camille; Ferguson-Noel, Naola; Rodrigo, Allen; Delaney, Nigel F.; Marx, Christopher J; Hill, Geoffrey E.; Tsai, Peter Tzu-shin; Edwards, Scott V.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
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Measureable rates of genome evolution are well documented in human pathogens but are less well understood in bacterial pathogens in the wild, particularly during and after host switches. (Mycoplasma) (gallisepticum) (MG) is a pathogenic bacterium that has evolved predominantly in poultry and recently jumped to wild house finches ((Carpodacus) (mexicanus)), a common North American songbird. For the first time we characterize the genome and measure rates of genome evolution in House Finch isolates of MG, as well as in poultry outgroups. Using whole-genome sequences of 12 House Finch isolates across a 13-year serial sample and an additional four newly sequenced poultry strains, we estimate a nucleotide diversity in House Finch isolates of only (sim2\%) of ancestral poultry strains and a nucleotide substitution rate of (0.8−1.2 imes10^{−5}) per site per year both in poultry and in House Finches, an exceptionally fast rate rivaling some of the highest estimates reported thus far for bacteria. We also found high diversity and complete turnover of CRISPR arrays in poultry MG strains prior to the switch to the House Finch host, but after the invasion of House Finches there is progressive loss of CRISPR repeat diversity, and recruitment of novel CRISPR repeats ceases. Recent (2007) House Finch MG strains retain only (sim50\%) of the CRISPR repertoire founding (1994–95) strains and have lost the CRISPR–associated genes required for CRISPR function. Our results suggest that genome evolution in bacterial pathogens of wild birds can be extremely rapid and in this case is accompanied by apparent functional loss of CRISPRs.; Organismic and Evolutionary Biology

## ‣ Bioinformatics of Recent Aqua- and Orthoreovirus Isolates from Fish: Evolutionary Gain or Loss of FAST and Fiber Proteins and Taxonomic Implications

Nibert, Max L.; Duncan, Roy
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
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Family Reoviridae, subfamily Spinareovirinae, includes nine current genera. Two of these genera, Aquareovirus and Orthoreovirus, comprise members that are closely related and consistently share nine homologous proteins. Orthoreoviruses have 10 dsRNA genome segments and infect reptiles, birds, and mammals, whereas aquareoviruses have 11 dsRNA genome segments and infect fish. Recently, the first 10-segmented fish reovirus, piscine reovirus (PRV), has been identified and shown to be phylogenetically divergent from the 11-segmented viruses constituting genus Aquareovirus. We have recently extended results for PRV by showing that it does not encode a fusion-associated small transmembrane (FAST) protein, but does encode an outer-fiber protein containing a long N-terminal region of predicted α-helical coiled coil. Three recently characterized 11-segmented fish reoviruses, obtained from grass carp in China and sequenced in full, are also divergent from the viruses now constituting genus Aquareovirus, though not to the same extent as PRV. In the current study, we reexamined the sequences of these three recent isolates of grass carp reovirus (GCRV)–HZ08, GD108, and 104–for further clues to their evolution relative to other aqua- and orthoreoviruses. Structure-based fiber motifs in their encoded outer-fiber proteins were characterized...

## ‣ Por uma concepção darwiniana de economia evolucionaria : abordagens, pioneiras, conflitos teoricos e propostas ontologicas; Towards a darwinian conception of evolutionary economics : pioneer approaches, theoretical conflicts and ontological proposals

Manuel Ramon Souza Luz
Fonte: Biblioteca Digital da Unicamp Publicador: Biblioteca Digital da Unicamp
Tipo: Dissertação de Mestrado Formato: application/pdf
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Esta dissertação procura apresentar uma abordagem evolucionária para as ciências econômicas, seguindo os princípios darwinianos, - como uma alternativa factível e consistente à visão essencialista do pensamento neoclássico. A partir de uma perspectiva fundada na história das idéias evolucionárias, este trabalho procura compreender como os desenvolvimentos destas idéias influenciaram o debate econômico em determinados períodos. Denominados período de fundação, especificação e disseminação, procura-se evidenciar as repercussões desses três importantes momentos da história do pensamento evolucionário sobre o desenvolvimento das idéias econômicas. Assim, o trabalho centra seus esforços, num primeiro momento, em verificar a influência da concepção evolucionária de Charles Darwin sobre a perspectiva institucionalista de Thorstein Veblen; num segundo momento, o trabalho acompanha como os desenvolvimentos da biologia evolucionária de meados do século XX, repercutiram sobre as idéias geradas a partir de debates específicos dentro da controvérsia marginalista; e, finalmente, num terceiro momento pretende-se avaliar a recente proposta de generalização dos princípios darwinianos para a economia, seguindo a perspectiva evolucionária do trabalho de Geoffrey Hodgson; This dissertation presents an evolutionary approach to economics...

## ‣ Stochastic Evolutionary Dynamics of Direct Reciprocity

Imhof, Lorens A.; Nowak, Martin A.
Fonte: Royal Society, The Publicador: Royal Society, The
Tipo: Artigo de Revista Científica
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Evolutionary game theory is the study of frequency-dependent selection. The success of an individual depends on the frequencies of strategies that are used in the population. We propose a new model for studying evolutionary dynamics in games with a continuous strategy space. The population size is finite. All members of the population use the same strategy. A mutant strategy is chosen from some distribution over the strategy space. The fixation probability of the mutant strategy in the resident population is calculated. The new mutant takes over the population with this probability. In this case, the mutant becomes the new resident. Otherwise, the existing resident remains. Then, another mutant is generated. These dynamics lead to a stationary distribution over the entire strategy space. Our new approach generalizes classical adaptive dynamics in three ways: (i) the population size is finite; (ii) mutants can be drawn non-locally and (iii) the dynamics are stochastic. We explore reactive strategies in the repeated Prisoner's Dilemma. We perform ‘knock-out experiments’ to study how various strategies affect the evolution of cooperation. We find that ‘tit-for-tat’ is a weak catalyst for the emergence of cooperation, while ‘always cooperate’ is a strong catalyst for the emergence of defection. Our analysis leads to a new understanding of the optimal level of forgiveness that is needed for the evolution of cooperation under direct reciprocity.; Organismic and Evolutionary Biology

## ‣ Evolutionary Game Dynamics with Non-Uniform Interaction Rates

Taylor, Christine Jiayou; Nowak, Martin A.
Tipo: Artigo de Revista Científica
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The classical setting of evolutionary game theory, the replicator equation, assumes uniform interaction rates. The rate at which individuals meet and interact is independent of their strategies. Here we extend this framework by allowing the interaction rates to depend on the strategies. This extension leads to non-linear fitness functions. We show that a strict Nash equilibrium remains uninvadable for non-uniform interaction rates, but the conditions for evolutionary stability need to be modified. We analyze all games between two strategies. If the two strategies coexist or exclude each other, then the evolutionary dynamics do not change qualitatively, only the location of the equilibrium point changes. If, however, one strategy dominates the other in the classical setting, then the introduction of non-uniform interaction rates can lead to a pair of interior equilibria. For the Prisoner's Dilemma, non-uniform interaction rates allow the coexistence between cooperators and defectors. For the snowdrift game, non-uniform interaction rates change the equilibrium frequency of cooperators.; Human Evolutionary Biology; Mathematics

## ‣ Evolutionary Games on Cycles

Ohtsuki, Hisashi; Nowak, Martin A.
Fonte: Royal Society, The Publicador: Royal Society, The
Tipo: Artigo de Revista Científica
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Traditional evolutionary game theory explores frequency-dependent selection in well-mixed populations without spatial or stochastic effects. But recently there has been much interest in studying the evolutionary game dynamics in spatial settings, on lattices and other graphs. Here, we present an analytic approach for the stochastic evolutionary game dynamics on the simplest possible graph, the cycle. For three different update rules, called ‘birth–death’ (BD), ‘death–birth’ (DB) and ‘imitation’ (IM), we derive exact conditions for natural selection to favour one strategy over another. As specific examples, we consider a coordination game and Prisoner's Dilemma. In the latter case, selection can favour cooperators over defectors for DB and IM updating. We also study the case where the replacement graph of evolutionary updating remains a cycle, but the interaction graph for playing the game is a complete graph. In this setting, all three update rules lead to identical conditions in the limit of weak selection, where we find the ‘1/3-law’ of well-mixed populations.; Mathematics; Organismic and Evolutionary Biology

## ‣ Evolutionary Trees and the Ising Model on the Bethe Lattice: a Proof of Steel's Conjecture

Daskalakis, Constantinos; Mossel, Elchanan; Roch, Sebastien
Tipo: Artigo de Revista Científica
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A major task of evolutionary biology is the reconstruction of phylogenetic trees from molecular data. The evolutionary model is given by a Markov chain on a tree. Given samples from the leaves of the Markov chain, the goal is to reconstruct the leaf-labelled tree. It is well known that in order to reconstruct a tree on $n$ leaves, sample sequences of length $\Omega(\log n)$ are needed. It was conjectured by M. Steel that for the CFN/Ising evolutionary model, if the mutation probability on all edges of the tree is less than $p^{\ast} = (\sqrt{2}-1)/2^{3/2}$, then the tree can be recovered from sequences of length $O(\log n)$. The value $p^{\ast}$ is given by the transition point for the extremality of the free Gibbs measure for the Ising model on the binary tree. Steel's conjecture was proven by the second author in the special case where the tree is "balanced." The second author also proved that if all edges have mutation probability larger than $p^{\ast}$ then the length needed is $n^{\Omega(1)}$. Here we show that Steel's conjecture holds true for general trees by giving a reconstruction algorithm that recovers the tree from $O(\log n)$-length sequences when the mutation probabilities are discretized and less than $p^\ast$. Our proof and results demonstrate that extremality of the free Gibbs measure on the infinite binary tree...

## ‣ Time and Knowability in Evolutionary Processes

Sober, Elliott; Steel, Mike
Tipo: Artigo de Revista Científica
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Historical sciences like evolutionary biology reconstruct past events by using the traces that the past has bequeathed to the present. The Markov Chain Convergence Theorem and the Data Processing Inequality describe how the mutual information between present and past is affected by how much time there is in between. These two results are very general; they pertain to any process, not just to the biological processes that occur in evolution. To study the specifically biological question of how the present state of a lineage provides information about its evolutionary past, we use a Moran process framework and consider how the kind of evolutionary process (drift, and selection of various kinds) at work in a lineage affects the epistemological relation of present to past.; Comment: 22 pages, 4 figures

## ‣ Understanding Evolutionary Potential in Virtual CPU Instruction Set Architectures

Bryson, David M.; Ofria, Charles
Tipo: Artigo de Revista Científica
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We investigate fundamental decisions in the design of instruction set architectures for linear genetic programs that are used as both model systems in evolutionary biology and underlying solution representations in evolutionary computation. We subjected digital organisms with each tested architecture to seven different computational environments designed to present a range of evolutionary challenges. Our goal was to engineer a general purpose architecture that would be effective under a broad range of evolutionary conditions. We evaluated six different types of architectural features for the virtual CPUs: (1) genetic flexibility: we allowed digital organisms to more precisely modify the function of genetic instructions, (2) memory: we provided an increased number of registers in the virtual CPUs, (3) decoupled sensors and actuators: we separated input and output operations to enable greater control over data flow. We also tested a variety of methods to regulate expression: (4) explicit labels that allow programs to dynamically refer to specific genome positions, (5) position-relative search instructions, and (6) multiple new flow control instructions, including conditionals and jumps. Each of these features also adds complication to the instruction set and risks slowing evolution due to epistatic interactions. Two features (multiple argument specification and separated I/O) demonstrated substantial improvements int the majority of test environments. Some of the remaining tested modifications were detrimental...

## ‣ Investigating prostate cancer tumour-stroma interactions - clinical and biological insights from an evolutionary game

David Basanta; Jacob G. Scott; Mayer N. Fishman; Gustavo E. Ayala; Simon W. Hayward; Alexander R. A. Anderson
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
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BACKGROUND: Tumours are made up of a mixed population of different types of cells that include normal structures as well as ones associated with the malignancy, and there are multiple interactions between the malignant cells and the local microenvironment. These intercellular interactions, modulated by the microenvironment, effect tumour progression and represent a largely under appreciated therapeutic target. We use observations of primary tumor biology from prostate cancer to extrapolate a mathematical model: specifically; it has been observed that in prostate cancer three disparate cellular outcomes predominate: (i) the tumour remains well differentiated and clinically indolent - in this case the local stromal cells may act to restrain the growth of the cancer; (ii) early in its genesis the tumour acquires a highly malignant phenotype, growing rapidly and displacing the original stromal population (often referred to as small cell prostate cancer) - these less common aggressive tumours are relatively independent of the local microenvironment; and, (iii) the tumour co-opts the local stroma - taking on a classic stromagenic phenotype where interactions with the local microenvironment are critical to the cancer growth. METHODS: We present an evolutionary game theoretical construct that models the influence of tumour-stroma interactions in driving these outcomes. We consider three characteristic and distinct cellular populations: stromal cells...

## ‣ Variety in evolutionary strategies favours biodiversity in habitats of moderate productivity

Simon Pierce
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
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The mechanism whereby biodiversity varies between habitats differing in productivity is a missing link between ecological and evolutionary theory with vital implications for biodiversity conservation, management and the assessment of ecosystem services. A unimodal, humped-back relationship, with biodiversity greatest at intermediate productivities, is evident when plant, animal and microbial communities are compared across productivities in nature. However, the mechanistic, evolutionary basis of this observation remains enigmatic. We show, for natural and semi-natural plant communities across a range of bioclimatic zones, that biodiversity is greatest where communities include species with widely divergent values for phenotypic traits involved in resource economics and reproductive timing, coinciding with intermediate biomass production, whilst each productivity extreme is associated with small numbers of specialised species with similar trait values. Our data demonstrate that evolution can generate a greater range of phenotypes where large, fast-growing species are prevented from attaining dominance and extreme adaptation to a harsh abiotic environment is not a prerequisite for survival.