Diet and primate evolution.
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Adaptation, Physiological↗
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Genetics. Can organisms speed their own evolution?
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Adaptation, Physiological↗
[Infections as catalysts of the evolution].
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Adaptation, Physiological↗
Molecular adaptation in plant hemoglobin, a duplicated gene involved in plant-bacteria symbiosis.
The evolutionary history of the hemoglobin gene family in angiosperms is unusual in that it involves two mechanisms known for potentially generating molecular adaptation: gene duplication and among-species interaction. In plants able to achieve symbiosis with nitrogen-fixing bacteria, class 2 hemoglobin is expressed at high concentrations in nodules and appears to be a key factor for the achievement and regulation of the symbiotic exchange. In this study, we make use of codon models of DNA sequence evolution with the goal of determining the nature of the selective forces which have driven the evolution of this gene. Our results suggest that adaptive evolution occurred during the period of time following the duplication event (functional divergence) and that a change in the selective pressures arose in class 2 hemoglobin in relation to the acquisition of a symbiotic function.
Adaptation, Biological↗
'Cooking as a biological trait'.
No human foragers have been recorded as living without cooking, and people who choose a 'raw-foodist' life-style experience low energy and impaired reproductive function. This suggests that cooking may be obligatory for humans. The possibility that cooking is obligatory is supported by calculations suggesting that a diet of raw food could not supply sufficient calories for a normal hunter-gatherer lifestyle. In particular, many plant foods are too fiber-rich when raw, while most raw meat appears too tough to allow easy chewing. If cooking is indeed obligatory for humans but not for other apes, this means that human biology must have adapted to the ingestion of cooked food (i.e. food that is tender and low in fiber) in ways that no longer allow efficient processing of raw foods. Cooking has been practiced for ample time to allow the evolution of such adaptations. Digestive adaptations have not been investigated in detail but may include small teeth, small hind-guts, large small intestines, a fast gut passage rate, and possibly reduced ability to detoxify. The adoption of cooking can also be expected to have had far-reaching effects on such aspects of human biology as life-history, social behavior, and evolutionary psychology. Since dietary adaptations are central to understanding species evolution, cooking appears to have been a key feature of the environment of human evolutionary adaptedness. Further investigation is therefore needed of the ways in which human digestive physiology is constrained by the need for food of relatively high caloric density compared to other great apes.
Animals↗
Adapting to a changing world: RAG genomics and evolution.
The origin of the recombination-activating genes (RAGs) is considered to be a foundation hallmark for adaptive immunity, characterised by the presence of antigen receptor genes that provide the ability to recognise and respond to specific peptide antigens. In vertebrates, a diverse repertoire of antigen-specific receptors, T cell receptors and immunoglobulins is generated by V(D)J recombination performed by the RAG-1 and RAG-2 protein complex. RAG homologues were identified in many jawed vertebrates. Despite their crucial importance, no homologues have been found in jawless vertebrates and invertebrates. This paper focuses on the RAG homologues in humans and other vertebrates for which the genome is completely sequenced, and also discusses the main contribution of the use of RAG homologues in phylogenetics and vertebrate evolution. Since mutations in both genes cause a spectrum of severe combined immunodeficiencies, including the Omenn syndrome (OS), these topics are discussed in detail. Finally, the relevance to genomic diversity and implications to immunomics are addressed. The search for homologues could enlighten us about the evolutionary processes that shaped the adaptive immune system. Understanding the diversity of the adaptive immune system is crucially important for the design and development of new therapies to modulate the immune responses in humans and/or animal models.
Acclimatization↗
Gene flow and the geographic structure of natural populations.
There is abundant geographic variation in both morphology and gene frequency in most species. The extent of geographic variation results from a balance of forces tending to produce local genetic differentiation and forces tending to produce genetic homogeneity. Mutation, genetic drift due to finite population size, and natural selection favoring adaptations to local environmental conditions will all lead to the genetic differentiation of local populations, and the movement of gametes, individuals, and even entire populations--collectively called gene flow--will oppose that differentiation. Gene flow may either constrain evolution by preventing adaptation to local conditions or promote evolution by spreading new genes and combinations of genes throughout a species' range. Several methods are available for estimating the amount of gene flow. Direct methods monitor ongoing gene flow, and indirect methods use spatial distributions of gene frequencies to infer past gene flow. Applications of these methods show that species differ widely in the gene flow that they experience. Of particular interest are those species for which direct methods indicate little current gene flow but indirect methods indicate much higher levels of gene flow in the recent past. Such species probably have undergone large-scale demographic changes relatively frequently.
Animals↗
Evolution of the lectin-complement pathway and its role in innate immunity.
Discrimination between self and non-self by lectins (carbohydrate-binding proteins) is a strategy of innate immunity that is found in both vertebrates and invertebrates. In vertebrates, immune recognition mediated by ficolins (lectins that consist of a fibrinogen-like and a collagen-like domain), as well as by mannose-binding lectins, triggers the activation of the complement system, which results in the activation of novel serine proteases. The presence of a similar lectin-based complement system in ascidians, our closest invertebrate relatives, indicates that the complement system probably had a pivotal role in innate immunity before the evolution of an adaptive immune system in jawed vertebrates.
Animals↗
Patterns of human genetic diversity: implications for human evolutionary history and disease.
Since the completion of the human genome sequencing project, the discovery and characterization of human genetic variation is a principal focus for future research. Comparative studies across ethnically diverse human populations and across human and nonhuman primate species is important for reconstructing human evolutionary history and for understanding the genetic basis of human disease. In this review, we summarize data on patterns of human genetic diversity and the evolutionary forces (mutation, genetic drift, migration, and selection) that have shaped these patterns of variation across both human populations and the genome. African population samples typically have higher levels of genetic diversity, a complex population substructure, and low levels of linkage disequilibrium (LD) relative to non-African populations. We discuss these differences and their implications for mapping disease genes and for understanding how population and genomic diversity have been important in the evolution, differentiation, and adaptation of humans.
Biological Evolution↗
[Evolution and auto-regulation].
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Acclimatization↗
Phenotypic divergence along lines of genetic variance.
Natural populations inhabiting the same environment often independently evolve the same phenotype. Is this replicated evolution a result of genetic constraints imposed by patterns of genetic covariation? We looked for associations between directions of morphological divergence and the orientation of the genetic variance-covariance matrix (G) by using an experimental system of morphological evolution in two allopatric nonsister species of rainbow fish. Replicate populations of both Melanotaenia eachamensis and Melanotaenia duboulayi have independently adapted to lake versus stream hydrodynamic environments. The major axis of divergence (z) among all eight study populations was closely associated with the direction of greatest genetic variance (gmax), suggesting directional genetic constraint on evolution. However, the direction of hydrodynamic adaptation was strongly associated with vectors of G describing relatively small proportions of the total genetic variance, and was only weakly associated with gmax. In contrast, divergence between replicate populations within each habitat was approximately proportional to the level of genetic variance, a result consistent with theoretical predictions for neutral phenotypic divergence. Divergence between the two species was also primarily along major eigenvectors of G. Our results therefore suggest that hydrodynamic adaptation in rainbow fish was not directionally constrained by the dominant eigenvector of G. Without partitioning divergence as a consequence of the adaptation of interest (here, hydrodynamic adaptation) from divergence due to other processes, empirical studies are likely to overestimate the potential for the major eigenvectors of G to directionally constrain adaptive evolution.
Adaptation, Biological↗
Construction of a bacterial artificial chromosome library from the inshore hagfish, Eptatretus burgeri: A resource for the analysis of the agnathan genome.
The jawless fish occupy an important phylogenetic position for understanding the evolution of body plans, the origin of adaptive immunity and genome evolution in chordates. We describe here the construction of a large-insert bacterial artificial chromosome (BAC) library from the inshore hagfish, Eptatretus burgeri. The BAC library contains 93,978 clones with an average insert size of 100 kb and is estimated to represent threefold genome-equivalent coverage. The library was organized in three-dimensional pools to facilitate screening by PCR. We have screened this library by PCR and isolated several BAC clones; the average number of positive clones was compatible with the estimated genome coverage of the library. This BAC library, constructed for the first time from the jawless fish, should serve as a useful resource for the scientific community.
Animals↗
Evolution of feeding niches in New World monkeys.
The adaptive radiation of modern New World monkeys unfolded as the major lineages diversified within different dietary-adaptive zones predicated upon a fundamentally frugivorous habit. The broad outlines of this pattern can be seen in the fossil record, beginning in the early Miocene. Cebids are obligate frugivorous predators. The smallest forms (Cebuella, Callithrix) are specialized exudativores, and the largest (cebines) are seasonally flexible omnivores, feeding particularly on insects (Saimiri) or "hard" foods, such as pith and palm nuts (Cebus), when resources are scarce. The smaller-bodied atelids (Callicebus, Aotus) may use insects or leaves opportunistically, but pitheciins (saki-uakaris) specialize on seeds as their major protein source. The larger atelines (Alouatta, Brachyteles) depend on leaves or on ripe fruit (Ateles). Locomotion, body size, and dietary adaptations are linked: claws and small body size opened the canopy-subcanopy niche to callitrichines; climbing and hanging, the fine-branch setting to the atelines; large size and strength, semiprehensile tails, and grasping thumbs, the extractive insectivory of Cebus; deliberate quadrupedalism, the energy-saving transport of folivorous Alouatta. Body size increases and decreases occurred often and in parallel within guilds and lineages. Conventional dietary categories, particularly frugivory, are inadequate for organizing the behavioral and anatomical evidence pertinent to evolutionary adaptation. Related models of morphological evolution based on feeding frequencies tend to obfuscate the selective importance of "critical functions," responses to the biomechanically challenging components of diet that may be determined by a numerically small, or seasonal, dietary fraction. For fossils, body size is an unreliable indicator of diet in the absence of detailed morphological information. More attention needs to be given to developing techniques for identifying and quantifying mechanically significant aspects of dental form, the physical properties of primate foods, their mode of access, and the cycles of availability and nutritional value.
Adaptation, Physiological↗
Source-sink dynamics between transgenic and non-transgenic habitats and their role in the evolution of resistance.
The interaction of population dynamics and movement among two habitat types (toxic transgenic fields and nontoxic refuge fields) on the evolution of insecticide resistance was examined in two different simulation models. The two models were developed to test the hypothesis that increasing habitat grain from fine-grained to coarse-grained, and the resultant increase in nonrandom mating, would increase the rate of local adaptation, here the evolution of resistance. The first model, a complex, stochastic spatially explicit model, altered habitat grain by varying adult dispersal rates between habitat patches. In contrast to the expectation that increasing patch isolation and increasing the coarseness of the habitats would increase the rate of resistance evolution, intermediate levels of dispersal actually delayed resistance by as much as fivefold over the range of dispersal levels observed. Source-sink dynamics related to ovipositional patterns and the related population dynamics appear to explain the results. A simple deterministic model was developed to abstract out the separate impacts of mating and ovipositional behaviors. This model showed qualitatively the same results, although under similar assumptions it predicted much longer delays in resistance evolution. In this model, nonrandom mating alone always increased the rate at which insects adapted to transgenic crops, but nonrandom mating in combination with nonrandom oviposition could significantly delay resistance evolution. Differences between the two models may be due to the population regulation incorporated in the spatially explicit model. The models clearly suggest that resistance management programs using untreated refuges should not over-emphasize random mating at the cost of making the habitat too fine-grained.
Animals↗
Molecular biology and immunology for clinicians 21: The innate immune system: an introduction.
The human (mammalian) immune response includes two interrelated but separable components: the innate immune system and an adaptive immune response. The former constitutes the sole immune defense strategy of invertebrates. It is only with vertebrate evolution that an adaptive immune response, first cellular, then later humoral, develops. Recent studies and a reconsideration of the innate system allow a fuller appreciation of its complexities, unique qualities, and irreplaceable value. In the early days of an infection, long before an effective adaptive immune response can be mounted, the innate system puts up an effective defense. Innate systems provide the costimulatory signal needed to unleash the adaptive immune response. Future contributions to this series will provide details about some of the specific innate immune systems. This article serves as an introduction to this underappreciated (until recently) aspect of human immune defenses.
Journal Article↗
Adaptations to high hydrostatic pressure.
The importance of adaptation to high pressure has long been implicit in the findings of studies in which 1 atm-adapted species were subjected to elevated pressures. Recent comparative studies have shown that pressure sensitivities of enzymes, structural proteins, and membrane-based systems differ markedly between shallow- and deep-living species. These studies allow operational definition of what constitutes high pressures for different biological structures and processes. These are the habitat (adaptation) pressures at which a given type of system first exhibits reduced perturbation by pressure. These threshold pressures vary among physiological systems, but are similar for a given system among different species. Dehydrogenase enzymes and adenylyl cyclases exhibit threshold perturbation pressures of only 50-100 atm; the Na(+)-K(+)-ATPase of teleost gills appears to have a pressure perturbation threshold near 200 atm, and a similar threshold was found for actin self-assembly. Even this limited sample of physiological processes indicates that the terms deep and high pressure begin to apply at depths of only 500 m or less--and processes yet to be examined in comparative analysis may yield even lower pressure thresholds. The differences in sensitivity to pressure of homologous systems in shallow- and deep-living organisms have implications at several levels of biological organization. The vertical distribution patterns of species in aquatic habitats may be established, in part, by interspecific differences in resistance to pressure. High pressures may restrict the depths to which shallow-living species can penetrate, and the obligately barophilic systems found in deep-living organisms may limit their upper distribution limits. The similarities noted among the adaptations of deep-sea species with different shallow-water ancestors reflect a high degree of convergent evolution in pressure adaptation. It will be interesting to learn if the similarities in pressure-resistance of function among diverse deep-sea species are the result of similar or identical changes at the molecular level, e.g. in protein sequence. Acclimation to pressure may be of widespread occurrence among species that undergo large changes in depth, e.g. during ontogeny. Pressure acclimation may require pressure-regulation of gene expression. Lastly, comparisons of species from the cold deep sea with those from hydrothermal vents have shown that adaptations to both temperature and pressure play critical roles in determining the distribution patterns of deep-living species.
Adaptation, Physiological↗
The case for an error minimizing standard genetic code.
Since discovering the pattern by which amino acids are assigned to codons within the standard genetic code, investigators have explored the idea that natural selection placed biochemically similar amino acids near to one another in coding space so as to minimize the impact of mutations and/or mistranslations. The analytical evidence to support this theory has grown in sophistication and strength over the years, and counterclaims questioning its plausibility and quantitative support have yet to transcend some significant weaknesses in their approach. These weaknesses are illustrated here by means of a simple simulation model for adaptive genetic code evolution. There remain ill explored facets of the 'error minimizing' code hypothesis, however, including the mechanism and pathway by which an adaptive pattern of codon assignments emerged, the extent to which natural selection created synonym redundancy, its role in shaping the amino acid and nucleotide languages, and even the correct interpretation of the adaptive codon assignment pattern: these represent fertile areas for future research.
Amino Acids↗
The evolution of alloimmunity and the genesis of adaptive immunity.
Infectious agents select for host immune responses that destroy infectious nonself yet maintain tolerance to self. Here we propose that retroviruses and other host-antigen associated pathogens (HAAPs) select for the genetic, biochemical, and cell biological properties of alloimmunity, also known as the histocompatibility or tissue rejection response. This hypothesis predicts the major observations regarding histocompatibility responses, including: (i) their existence in animals as diverse as sponges and humans; (ii) extreme polymorphism and balanced allele frequencies at histocompatibility loci, including the human MHC and blood group loci; (iii) the frequency dependent selection of histocompatibility alleles; (iv) the ancient age of many alloantigenic polymorphisms; (v) the high ratio of nonsynonymous mutations to synonymous mutations at histocompatibility loci; (vi) disassortative mating based on MHC alleles; (vii) the inability to explain the existence and continuing selection of histocompatibility alleles by other more conventional biochemical and genetic paradigms; and (viii) the susceptibility of HAAPs, particularly retroviruses such as HIV (human immunodeficiency virus), to histocompatibility reactions. In addition, the hypothesis that HAAPs select the forms and molecules of alloimmunity offers simple explanations for the evolution of histocompatibility systems over time, the initial selection of hypervariable immune mechanisms, and the genesis of adaptive immunity.
Alleles↗