SEARCH · PubMed Health
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Studying microbial genomics has shown that the genomes of bacteria are extremely dynamic in evolutionary terms. Many research groups have linked the adaptation of an organism to a niche to large changes in genome size and content. A number of recent papers have underlined the degree to which the genomes of different organisms are a reflection of the opportunities and constraints imposed by their chosen niche.
Current epidemiologic models concerning the fetal origins of later health risk are evaluated from the perspectives of evolutionary and developmental biology. Claims of adaptive value for and biological status of fetal programming are critically examined. Life history theory is applied to identify key trade-offs in adaptive strategies that constrain developmental design to use information from the environment to guide ontogeny and establish cost-benefit trade-offs that weigh early survival advantage against remote or unlikely future costs. Expectable environments of evolutionary adaptedness, particularly of gestation, are characterized and their impact on human adaptive design discussed. The roles of neuroendocrine mechanisms in scaffolding life course development, negotiating ongoing cost-benefit trade-offs, and mediating their long-term impacts on function and health are reviewed in detail. Overviews of gestational biology and the postnatal physiologic, cognitive-affective, and behavioral effects of gestational stress identify a shared central role for the hypothalamic-pituitary-adrenal (HPA) axis. Rather than merely mediating stress responses, the axis emerges an agent of resource allocation that draws a common thread among conditions of gestation, postnatal environments, and functional and health-related outcomes. The preponderance of evolutionary and developmental analysis identifies environments as agents on both sides of the health risk equation, by influencing vulnerabilities and capacities established in early and later life course development, and determining exposures and demands encountered over the life course.
Examples of adaptive radiation by Darwinian evolution will always enthral, and the theory of natural selection binds the whole of biology. But is selection all-powerful? Evolutionary developmental biology is beginning to provide the background to understanding how the internal organisation of organisms can influence the tempo and direction of evolutionary change. Do the mechanisms that generate the phenotype channel, bias or limit morphological evolution? The formation of eyespots on the wings of the butterfly Bicyclus anynana is a process which is becoming comparatively well understood from the genetical, developmental and ecological perspectives. We have begun to combine this knowledge with artificial selection experiments to examine the rates at which morphological changes of a particular eyespot pattern in different directions can be achieved. Our initial selection experiment performed over twenty-five generations has shown that in contrast to predictions based on shared genetical and developmental properties, two butterfly eyespots on the same wing surface can be freely uncoupled from each other with respect to their pattern of relative sizes. This flexibility in development and in response to selection may occur because our base population is part of a lineage with a long legacy of natural selection building up genetic variation that enables independent behaviour for eyespot size, and thus it no longer reflects a tightly modular organisation of eyespots as may well have existed close to their evolutionary origin in basal Lepidoptera. Comparisons can be made between such descriptions of the potential for short-term changes in morphology in B. anynana and observed patterns of divergence among all extant species in this species-rich genus. Being able to map phenotypes onto genotypes via developmental processes provides a powerful basis for exploring genetical and developmental constraints. This will eventually lead to examples of evolutionary constraints that represent more than 'just-so' stories, and thus to a more balanced view of Darwinian evolution.
Molecular genetics teaches three lessons relevant to the nature of genetic change during evolution: (1) Genomes are organized as hierarchies of composite systems (multidomain protein-coding sequences; functional loci made up of regulatory, coding, processing, and intervening sequences; and multilocus regulons and replicons) interconnected and organized into specific "system architectures" by repetitive DNA elements. (2) Genetic change often occurs via natural genetic engineering systems (cellular biochemical functions, such as recombination complexes, topoisomerases, and mobile elements, capable of altering DNA sequence information and joining together different genomic components). (3) The activity of natural genetic systems is regulated by cellular control circuits with respect to the timing, activity levels, and specificities of DNA rearrangements (e.g., adaptive mutation, Ty element mobility, and P factor insertions). These three lessons provide plausible molecular explanations for the episodic, multiple, nonrandom DNA rearrangements needed to account for the evolution of novel genomic system architectures and complex multilocus adaptations. This molecular genetic perspective places evolutionary change in the biologically responsive context of cellular biochemistry.
Adaptive Dynamics is an approach to studying evolutionary change when fitness is density or frequency dependent. Modern papers identifying themselves as using this approach first appeared in the 1990s, and have greatly increased up to the present. However, because of the rather technical nature of many of the papers, the approach is not widely known or understood by evolutionary biologists. In this review we aim to remedy this situation by outlining the methodology and then examining its strengths and weaknesses. We carry this out by posing and answering 20 key questions on Adaptive Dynamics. We conclude that Adaptive Dynamics provides a set of useful approximations for studying various evolutionary questions. However, as with any approximate method, conclusions based on Adaptive Dynamics are valid only under some restrictions that we discuss.
In evolutionary history, several events have occurred at which mixotrophs specialized into pure autotrophs and heterotrophs. We studied the conditions under which such events take place, using the Dynamic Energy Budget (DEB) theory for physiological rules of the organisms' metabolism and Adaptive Dynamics (AD) theory for evolutionary behavior of parameter values. We modeled a population of mixotrophs that can take up dissolved inorganic nutrients by autotrophic assimilation and detritus by heterotrophic assimilation. The organisms have a certain affinity for both pathways; mutations that occur in the affinities enable the population to evolve. One of the possible evolutionary outcomes is a branching point which provides an opportunity for the mixotrophic population to split up and specialize into separate autotrophs and heterotrophs. Evolutionary branching is not a common feature of the studied system, but is found to occur only under specific conditions. These conditions depend on intrinsic properties such as the cost function, the level of the costs and the boundaries of the trait space: only at intermediate cost levels and when an explicit advantage exists to pure strategies over mixed ones may evolutionary branching occur. Usually, such an advantage (and hence evolutionary branching) can be induced by interference between the two affinities, but this result changes due to the constraints on the affinities. Now, only some of the more complicated cost functions give rise to a branching point. In contrast to the intrinsic properties, extrinsic properties such as the total nutrient content or light intensity were found to have no effect on the evolutionary outcomes at all.
Temperature directly affects the performance of fish muscle through a variety of extrinsic and intrinsic mechanisms. A common observation is that species adapted to different temperatures over evolutionary time scales, or individuals exposed to temperature change from periods ranging from minutes to months are able to adjust muscle performance so as to partially offset the effects of temperature change. The underlying mechanisms are complex, involve a variety of levels of organization (behavioural, organismic, tissue and molecular) and probably vary with the time scale of adaptation to temperature. The present essay considers the extent to which interspecific differences in the structural and functional characteristics of muscle enzymes contribute to adjustments in contractile performance at different body temperatures.
This article introduces a special issue on evolutionary innovation and morphological novelty, two interrelated themes that have received a remarkable increase of attention over the past few years. We begin with a discussion of the question of whether innovation and novelty represent distinct evolutionary problems that require a distinct conceptualization. We argue that the mechanisms of innovation and their phenotypic results--novelty--can only be properly addressed if they are distinguished from the standard evolutionary themes of variation and adaptation, and we present arguments for making such a distinction. We propose that origination, the first formation of biological structures, is another distinct problem of morphological evolution, and that together with innovation and novelty it constitutes a conceptual complex we call the innovation triad. We define a problem agenda of the triad, which separates the analysis of the initiating conditions from the mechanistic realization of innovation, and we discuss the theoretical problems that arise from treating innovation as distinct from variation. Further, we categorize the empirical approaches that address themes of the innovation triad in recognizing four major strands of research: the morphology and systematics program, the gene regulation program, the epigenetic program, and the theoretical biology program. We provide examples of each program, giving priority to contributions in the present issue. In conclusion, we observe that the innovation triad is one of the defining topics of EvoDevo research and may represent its most pertinent contribution to evolutionary theory. We point out that an inclusion of developmental systems properties into evolutionary theory represents a shift of explanatory emphasis from the external factors of natural selection to the internal dynamics of developmental systems, complementing adaptation with emergence, and contingency with inherency.
The Canary Islands have been a focus for phylogeographic studies on the colonization and diversification of endemic angiosperm taxa. Based on phylogeographic patterns, both inter island colonization and adaptive radiation seem to be the driving forces for speciation in most taxa. Here, we investigated the diversification of Micromeria on the Canary Islands and Madeira at the inter- and infraspecific level using inter simple sequence repeat PCR (ISSR), the trnK-Intron and the trnT-trnL-spacer of the cpDNA and a low copy nuclear gene. The genus Micromeria (Lamiaceae, Mentheae) includes 16 species and 13 subspecies in Macaronesia. Most taxa are restricted endemics, or grow in similar ecological conditions on two islands. An exception is M. varia, a widespread species inhabits the lowland scrub on each island of the archipelago and could represent an ancestral taxon from which radiation started on the different islands. Our analyses support a split between the "eastern" islands Fuerteventura, Lanzarote and Gran Canaria and the "western" islands Tenerife, La Palma and El Hierro. The colonization of Madeira started from the western Islands, probably from Tenerife as indicated by the sequence data. We identified two lineages of Micromeria on Gomera but all other islands appear to be colonized by a single lineage, supporting adaptive radiation as the major evolutionary force for the diversification of Micromeria. We also discuss the possible role of gene flow between lineages of different Micromeria species on one island after multiple colonizations.
Gene duplication, arising from region-specific duplication or genome-wide polyploidization, is a prominent feature in plant genome evolution. Understanding the mechanisms generating duplicate gene copies and the subsequent dynamics among gene duplicates is vital because these investigations shed light on regional and genome-wide aspects of evolutionary forces shaping intra- and interspecific genome contents, evolutionary relationships, and interactions. This review discusses recent gene duplication analyses in plants, focusing on the molecular and evolutionary dynamics occurring at three different timescales following duplication: (1). initial establishment and persistence of cytotypes, (2). interactions among duplicate gene copies, and (3). longer term differentiation between duplicated genes. These relative time points are presented in terms of their potential adaptive significance and impact on plant evolutionary genomics research.
The rice Xa21 gene confers resistance to Xanthomonas oryzae pv oryzae in a race-specific manner. Analysis of the inheritance patterns and resistance spectra of transgenic plants carrying six Xa21 gene family members indicated that one member, designated Xa21D, displayed a resistance spectrum identical to that observed for Xa21 but conferred only partial resistance. Xa21D encodes a receptor-like protein carrying leucine-rich repeat (LRR) motifs in the presumed extracellular domain. The Xa21D transcript terminates shortly after the stop codon introduced by the retrotransposon Retrofit. Comparison of nucleotide substitutions in the LRR coding regions of Xa21 and Xa21D provided evidence of adaptive selection. Both functional and evolutionary evidence indicates that the Xa21D LRR domain controls race-specific pathogen recognition.
The impact of genome structure on adaptation is a growing focus in evolutionary biology, revealing an important role for structural variation and recombination landscapes in shaping genetic diversity across genomes and among populations. This is particularly relevant when local adaptation occurs despite gene flow, where clustering of differentiated loci can maintain locally adapted variants by reducing recombination between them. However, the limited genomic resources for nonmodel species, including reference genomes and recombination maps, have constrained our understanding of these patterns. In this study, we leverage the Atlantic silverside-a nonmodel fish with extensive local adaptation across a steep latitudinal gradient-as an ideal system to explore how genome structure influences adaptation under varying levels of gene flow, using a newly available reference genome and multiple recombination maps. Analyzing 168 genomes from four populations, we found a continuum of genome-wide differentiation increasing from south to north, reflecting higher connectivity among southern populations and reduced gene flow at northern latitudes. With increasing gene flow, the number and clustering of FST outlier loci also increased, with differentiated loci found exclusively within large haploblocks harboring inversions and smaller peaks overlapping putative centromeric regions. Notably, sequence divergence was only evident in inversions, supporting their role in adaptive divergence with gene flow, whereas centromeric regions appeared differentiated because of low recombination and diversity, with no indication of elevated divergence. Our results support the hypothesis that clustered genomic architectures evolve with high gene flow and enhance our understanding of how inversions and centromeres are linked to different evolutionary processes.
Organisms producing resting stages provide unique opportunities for reconstructing the genetic history of natural populations. Diapausing seeds and eggs often are preserved in large numbers, representing entire populations captured in an evolutionary inert state for decades and even centuries. Starting from a natural resting egg bank of the waterflea Daphnia, we compare the evolutionary rates of change in an adaptive quantitative trait with those in selectively neutral DNA markers, thus effectively testing whether the observed genetic changes in the quantitative trait are driven by natural selection. The population studied experienced variable and well documented levels of fish predation over the past 30 years and shows correlated genetic changes in phototactic behavior, a predator-avoidance trait that is related to diel vertical migration. The changes mainly involve an increased plasticity response upon exposure to predator kairomone, the direction of the changes being in agreement with the hypothesis of adaptive evolution. Genetic differentiation through time was an order of magnitude higher for the studied behavioral trait than for neutral markers (DNA microsatellites), providing strong evidence that natural selection was the driving force behind the observed, rapid, evolutionary changes.
The principle that mutations occur randomly with respect to the direction of evolutionary change has been challenged by the phenomenon of adaptive mutations. There is currently no entirely satisfactory theory to account for how a cell can selectively mutate certain genes in response to environmental signals. However, spontaneous mutations are initiated by quantum events such as the shift of a single proton (hydrogen atom) from one site to an adjacent one. We consider here the wave function describing the quantum state of the genome as being in a coherent linear superposition of states describing both the shifted and unshifted protons. Quantum coherence will be destroyed by the process of decoherence in which the quantum state of the genome becomes correlated (entangled) with its surroundings. Using a very simple model we estimate the decoherence times for protons within DNA and demonstrate that quantum coherence may be maintained for biological time-scales. Interaction of the coherent genome wave function with environments containing utilisable substrate will induce rapid decoherence and thereby destroy the superposition of mutant and non-mutant states. We show that this accelerated rate of decoherence may significantly increase the rate of production of the mutated state.
On the basis of evolutionary game theory, it was hypothesized that humans have an evolved cognitive specialization for reasoning about social exchange, including a subroutine for detecting cheaters. This hypothesis led to a specific prediction: Although humans are known to be poor at detecting potential violations of conditional rules in general, they should nevertheless detect them easily when the rule involves social exchange and looking for violations corresponds to looking for cheaters. This prediction was subsequently confirmed by numerous tests. Evolutionary analyses further predict that: (i) in humans, complex adaptations will be distributed in a species-typical fashion; and (ii) aspects of cognitive organization relevant to performing the evolved function of an adaptation should be more buffered against environmental and cultural variation than function-irrelevant aspects. Here we report experiments testing whether social exchange reasoning exhibits these properties of adaptations. Existing tests of conditional reasoning were adapted for nonliterate experimental subjects and were administered to Shiwiar hunter-horticulturalists of the Ecuadorian Amazon. As predicted, Shiwiar subjects were as highly proficient at cheater detection as subjects from developed nations. Indeed, the frequency of cheater-relevant choices among Shiwiar hunter-horticulturalists was indistinguishable from that of Harvard undergraduates. Also as predicted, cultural variation was confined to those aspects of reasoning that are irrelevant to social exchange algorithms functioning as an evolutionarily stable strategy. Finally, Shiwiar subjects displayed the same low performance on descriptive conditionals as subjects from developed nations. Taken together, these findings support the hypotheses that social exchange algorithms are species-typical and that their evolutionarily stable strategy (ESS)-relevant subroutines are developmentally buffered against cultural variation.
Temperature effects on dissociation constants (Kd), binding enthalpies and apparent Michaelis constants (Km) for NADH, plus Arrhenius activation energies (Ea), substrate turnover numbers (kcat), and NADH 'on' constants (k1) were measured or calculated for M4-lactate dehydrogenase homologs from deep-sea, midwater, shallow-water temperate, and shallow-water tropical teleost fishes, and a mammal. At any single measurement temperature, Km and kcat values were significantly higher for groups adapted to lower temperatures. This pattern of Km values and temperature illustrates a strong evolutionary conservation of Km of NADH. When determined at the average body temperature of each species, the Km values are very similar, resulting in the preservation of the catalytic capacity and regulatory properties of these enzyme homologs at their in situ temperatures. In contrast, Kd values, while varying considerably among species, are not significantly different among the different groups at any one temperature. The ratio of Km to Kd tends to follow a phylogenetic pattern rather than a pattern of environmental adaptation. Thus, evolutionary adjustments in Km are not directly the result of changes in cofactor binding. All the rate constants involved in determining the Km and Kd of NADH (kcat, k1 and k-1) can be modified.
Phytophagous insects have evolved sophisticated detoxification systems to overcome the antiherbivore chemical defenses produced by many plants. However, how these biotransformation systems differ in generalist and specialist insect species and their role in determining insect host plant range remains an open question. Here, we show that UDP-glucosyltransferases (UGTs) play a key role in determining the host range of insect species within the Spodoptera genus. Comparative genomic analyses of Spodoptera species that differ in host plant breadth identified a relatively conserved number of UGT genes in generalist species but high levels of UGT gene pseudogenization in the specialist Spodoptera picta. CRISPR-Cas9 knockouts of the three main UGT gene clusters of Spodoptera frugiperda revealed that UGT33 genes play an important role in allowing this species to utilize the poaceous plants maize, wheat, and rice, while UGT40 genes facilitate utilization of cotton. Further functional analyses in vivo and in vitro identified the UGT SfUGT33F32 as the key mechanism that allows generalist S. frugiperda to detoxify the benzoxazinoid DIMBOA (2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one), a potent insecticidal phytotoxin produced by poaceous plants. However, while this detoxification capacity is conserved in several generalist Spodoptera species, Spodoptera picta, which specializes on Crinum plants, is unable to detoxify DIMBOA due to a nonfunctionalizing mutation in SpUGT33F34. Collectively, these findings provide insight into the role of insect UGTs in host plant adaptation, the mechanistic basis of evolutionary transitions between generalism and specialism and offer molecular targets for controlling a group of notorious insect pests.
Climatic oscillations during the Pleistocene epoch had a dramatic impact on the distribution of biota in the northern hemisphere. In order to trace glacial refugia and postglacial colonization routes on a global scale, we studied mitochondrial DNA sequence variation in a freshwater fish (burbot, Lota lota; Teleostei, Gadidae) with a circumpolar distribution. The subdivision of burbot in the subspecies Lota lota lota (Eurasia and Alaska) and Lota lota maculosa (North America, south of the Great Slave Lake) was reflected in two distinct mitochondrial lineages (average genetic distance is 2.08%). The lota form was characterized by 30 closely related haplotypes and a large part of its range (from Central Europe to Beringia) was characterized by two widespread ancestral haplotypes, implying that transcontinental exchange/migration was possible for cold-adapted freshwater taxa in recent evolutionary time. However, the derived mitochondrial variants observed in peripheral populations point to a recent separation from the core group and postglacial recolonization from distinct refugia. Beringia served as refuge from where L. l. lota dispersed southward into North America after the last glacial maximum. Genetic variation in the maculosa form consisted of three mitochondrial clades, which were linked to at least three southern refugia in North America. Two mitochondrial clades east of the Continental Divide (Mississippian and Missourian clades) had a distinct geographical distribution in the southern refuge zones but intergraded in the previously glaciated area. The third clade (Pacific) was exclusively found west of the Continental Divide.