Life History Consequences of Bioenergetic and Biomechanical Constraints on Migration

In this paper I test the hypothesis that bioenergetic and biomechanicalconstraints to migration play a pivotal role in shaping thelife history characteristics of migrants. Firstly, I examinebioenergetic constraints on the ability to migrate by activetransport and how they shape the life histories of insects andfish, and, secondly, the consequences of biomechanical constraintsto the migration by passive transport in insects and spiders. In both insects and fish the mass-specific energetic costs ofactive transport (flight and swimming, respectively) decreasewith body size, and hence selection should favor large sizein migrant species. Because their habitats are ephemeral, migrantinsects must grow rapidly. In fish, migrant species are ableto exploit resources unavailable to more sedentary species andhence should also show an enhanced rate of growth. These predictionsare supported by comparisons within populations, between populations,and among species in both groups. In contrast to the above, biomechanical factors limit the uppersize at which insects and spiders can migrate by passive transport.Theory predicts that ballooning will be most likely in spidersconsiderably less than 6 mm in length. Therefore, species thatmigrate as adults are predicted to be smaller than those thatdo not. This prediction is supported by a comparison of migratoryand non-migratory spider species from the United Kingdom. Theaverage length of species that migrate as adults, and of migratingyoung of spiders too large to balloon as adults, is about 2mm. Further, within this geographic species assemblage, thesize distribution of adult spiders is markedly peaked in the2 mm region, suggesting that biomechanical constraints on ballooningmay have a major influence on the evolution of body size inspiders.     

Bioenergetic Constraints on Primate Abundance

Explaining variation in primate population densities is central to understanding primate ecology, evolution, and conservation. Yet no researchers to date have successfully explained variation in primate population density across dietary class and phylogeny. Most previous work has focused on measures of food availability, as access to food energy likely constrains the number of individuals supported in a given area. However, energy output may provide a measure of energy constraints on population density that does not require detailed data on food availability for a given taxon. Across mammals, many studies have shown that population densities generally scale with body mass^−0.75. Because individual energy expenditures scale with body mass^0.75, population energy use (the product of population density and individual energy use) does not change with body mass, which suggests the existence of energy constraints on population density across body sizes, i.e., taxa are limited to a given amount of energy use, constraining larger taxa to lower densities. We examined population energy use and individual energy expenditure in primates and tested this energy equivalence across body mass. We also used a residual analysis to remove the effects of body mass on primate population densities and energy expenditures using basal metabolic rates (BMR; kcal/d) as a proxy for total daily energy expenditure. After taking into account phylogeny, population energy use did not significantly correlate with body mass. Larger primates, which use more energy per day, live at lower population densities than smaller primates. In addition, we found a significant negative correlation between residuals of BMR from body mass and residuals of population density from body mass after taking phylogeny into account. Thus, energy costs constrain population density across a diverse sample of primates at a given body mass, and primate species that have relatively low BMRs exist at relatively high densities. A better understanding of the determinants of primate energy costs across geography and phylogeny will ultimately help us explain and predict primate population densities.     

Bioenergetic Constraints on Microbial Hydrogen Utilization in Precambrian Deep Crustal Fracture Fluids

Precambrian Shield rocks host the oldest fracture fluids on Earth, with residence times up to a billion years or more. Water–rock reactions in these fracture systems over geological time have produced highly saline fluids, which can contain millimolar concentrations of H₂. Mixing of these ancient Precambrian fluids with meteoric or palaeo-meteoric water can occur through tectonic fracturing, providing microbial inocula and redox couples to fuel blooms of subsurface growth. Here, we present geochemical and microbiological data from a series of borehole fluids of varying ionic strength (0.6–6.4 M) from the Thompson Mine (Manitoba) within the Canadian Precambrian Shield. Thermodynamic calculations demonstrate sufficient energy for H₂-based catabolic reactions across the entire range of ionic strengths during mixing of high ionic strength fracture fluids with meteoric water, although microbial H₂ consumption and cultivable H₂-utilizing microbes were only detected in fluids of ≤1.9 M ionic strength. This pattern of microbial H₂ utilization can be explained by the higher potential bioenergetic cost of organic osmolyte synthesis at increasing ionic strengths. We propose that further research into the bioenergetics of osmolyte regulation in halophiles is warranted to better constrain the habitability zones of hydrogenotrophic ecosystems in both terrestrial subsurface, including potential future radioactive waste disposal sites, and other planetary body crustal environments, including Mars.     

Genetic Constraints on Protein Evolution

ABSTRACT

Evolution requires the generation and optimization of new traits (“adaptation”) and involves the selection of mutations that improve cellular function. These mutations were assumed to arise by selection of neutral mutations present at all times in the population. Here we review recent evidence that indicates that deleterious mutations are more frequent in the population than previously recognized and that these mutations play a significant role in protein evolution through continuous positive selection. Positively selected mutations include adaptive mutations, i.e. mutations that directly affect enzymatic function, and compensatory mutations, which suppress the pleiotropic effects of adaptive mutations. Compensatory mutations are by far the most frequent of the two and would allow potentially adaptive but deleterious mutations to persist long enough in the population to be positively selected during episodes of adaptation. Compensatory mutations are, by definition, context-dependent and thus constrain the paths available for evolution. This provides a mechanistic basis for the examples of highly constrained evolutionary landscapes and parallel evolution reported in natural and experimental populations. The present review article describes these recent advances in the field of protein evolution and discusses their implications for understanding the genetic basis of disease and for protein engineering in vitro.     

Evolution of the F0F1 ATP Synthase Complex in Light of the Patchy Distribution of Different Bioenergetic Pathways across Prokaryotes

Bacteria and archaea are characterized by an amazing metabolic diversity, which allows them to persist in diverse and often extreme habitats. Apart from oxygenic photosynthesis and oxidative phosphorylation, well-studied processes from chloroplasts and mitochondria of plants and animals, prokaryotes utilize various chemo- or lithotrophic modes, such as anoxygenic photosynthesis, iron oxidation and reduction, sulfate reduction, and methanogenesis. Most bioenergetic pathways have a similar general structure, with an electron transport chain composed of protein complexes acting as electron donors and acceptors, as well as a central cytochrome complex, mobile electron carriers, and an ATP synthase. While each pathway has been studied in considerable detail in isolation, not much is known about their relative evolutionary relationships. Wanting to address how this metabolic diversity evolved, we mapped the distribution of nine bioenergetic modes on a phylogenetic tree based on 16S rRNA sequences from 272 species representing the full diversity of prokaryotic lineages. This highlights the patchy distribution of many pathways across different lineages, and suggests either up to 26 independent origins or 17 horizontal gene transfer events. Next, we used comparative genomics and phylogenetic analysis of all subunits of the F₀F₁ ATP synthase, common to most bacterial lineages regardless of their bioenergetic mode. Our results indicate an ancient origin of this protein complex, and no clustering based on bioenergetic mode, which suggests that no special modifications are needed for the ATP synthase to work with different electron transport chains. Moreover, examination of the ATP synthase genetic locus indicates various gene rearrangements in the different bacterial lineages, ancient duplications of atpI and of the beta subunit of the F₀ subcomplex, as well as more recent stochastic lineage-specific and species-specific duplications of all subunits. We discuss the implications of the overall pattern of conservation and flexibility of the F₀F₁ ATP synthase genetic locus.     

Developmental Constraints on Vertebrate Genome Evolution

Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on genome evolution in vertebrates. We used gene expression data from two vertebrates: zebrafish, using a microarray experiment spanning 14 stages of development, and mouse, using EST counts for 26 stages of development. We show that, in both species, genes expressed early in development (1) have a more dramatic effect of knock-out or mutation and (2) are more likely to revert to single copy after whole genome duplication, relative to genes expressed late. This supports high constraints on early stages of vertebrate development, making them less open to innovations (gene gain or gene loss). Results are robust to different sources of data—gene expression from microarrays, ESTs, or in situ hybridizations; and mutants from directed KO, transgenic insertions, point mutations, or morpholinos. We determine the pattern of these constraints, which differs from the model used to describe vertebrate morphological conservation (“hourglass” model). While morphological constraints reach a maximum at mid-development (the “phylotypic” stage), genomic constraints appear to decrease in a monotonous manner over developmental time.     

Structural Constraints on RNA Virus Evolution

The recently discovered hepatitis G virus (HGV) or GB virus C (GBV-C) is widely distributed in human populations, and homologues such as HGV/GBV-CCPZ and GBV-A are found in a variety of different primate species. Both epidemiological and phylogenetic analyses support the hypothesis that GB viruses coevolved with their primate hosts, although their degree of sequence similarity appears incompatible with the high rate of sequence change of HGV/GBV-C over short observation periods. Comparison of complete coding sequences (8,500 bases) of different genotypes of HGV/GBV-C showed an excess of invariant synonymous sites (at 23% of all codons) compared with the frequency expected by chance (10%). To investigate the hypothesis that RNA secondary-structure formation through internal base pairing limited sequence variability at these sites, an algorithm was developed to detect covariant sites among HGV/GBV-C sequences of different genotypes. At least 35 covariant sites that were spatially associated with potential stem-loop structures were detected, whose positions correlated with positions in the genome that showed reductions in synonymous variability. Although the functional roles of the predicted secondary structures remain unclear, the restriction of sequence change imposed by secondary-structure formation provides a mechanism for differences in net rate of accumulation of nucleotide substitutions at different sites. However, the resulting disparity between short- and long-term rates of sequence change of HGV/GBV-C violates the assumptions of the "molecular clock." This places a major restriction on the use of nucleotide or amino acid sequence comparisons to calculate times of divergence of other viruses evolving under the same structural constraints as GB viruses.     

Hominin Obstetrics and the Evolution of Constraints

Birth is significantly more complicated and dangerous in modern humans than in other great apes. This disparity is often hypothesized to be the result of evolutionary constraints on obstetric dimensions related to bipedalism and/or thermoregulation in later hominins. Previous attempts to test such hypotheses have used biomechanical methods and results have been mixed. But evolutionary constraints, restrictions or limitations on the course or outcome of evolution, are the result of an interaction between selective pressures and genetic constraints—the latter revealed in patterns of integration. Integration between traits can result in directional or stabilizing selection on one trait leading to correlated responses in other traits, which can bias and constrain evolutionary trajectories. Therefore, trait evolution may be constrained for reasons separate from those that can be estimated using biomechanical models, and to study evolutionary constraints it is necessary to understand the role genetic constraints play in morphological change. The results presented here show that genetic constraints can significantly reduce the evolutionary potential of the birth canal to evolve in humans, apes, and likely earlier hominins, but also point to an overall reduction in the level of constraints during hominin evolution. These findings suggest that divergent selection pressures for obstetric requirements and other pelvic functions in hominins reduced levels of genetic constraint on birth canal evolution, likely lowering the amount of time needed for evolutionary change, and permitting morphological evolution along a trajectory that might have previously been difficult or impossible to traverse.     

A Multivariate Analysis of Genetic Constraints to Life History Evolution in a Wild Population of Red Deer

Evolutionary theory predicts that genetic constraints should be widespread, but empirical support for their existence is surprisingly rare. Commonly applied univariate and bivariate approaches to detecting genetic constraints can underestimate their prevalence, with important aspects potentially tractable only within a multivariate framework. However, multivariate genetic analyses of data from natural populations are challenging because of modest sample sizes, incomplete pedigrees, and missing data. Here we present results from a study of a comprehensive set of life history traits (juvenile survival, age at first breeding, annual fecundity, and longevity) for both males and females in a wild, pedigreed, population of red deer (Cervus elaphus). We use factor analytic modeling of the genetic variance–covariance matrix (G) to reduce the dimensionality of the problem and take a multivariate approach to estimating genetic constraints. We consider a range of metrics designed to assess the effect of G on the deflection of a predicted response to selection away from the direction of fastest adaptation and on the evolvability of the traits. We found limited support for genetic constraint through genetic covariances between traits, both within sex and between sexes. We discuss these results with respect to other recent findings and to the problems of estimating these parameters for natural populations.     

Constraints in naming parts of the Tree of Life

There are now overlapping codes of nomenclature that govern some of the same names of biological taxa. The International Code of Zoological Nomenclature (ICZN) uses the non-evolutionary concept of a "type species" to fix the names of animal taxa to particular ranks in the nomenclatural hierarchy. The PhyloCode, in contrast, uses phylogenetic definitions for supraspecific taxa at any hierarchical level within the Tree of Life (without associating the names to particular ranks), but does not deal with the names of species. Thus, biologists who develop classifications of animals need to use both systems of nomenclature, or else operate without formal rules for the names of some taxa (either species or many monophyletic groups). In addition, the ICZN does not permit the unique naming of many taxa that are considered to be between the ranks of genus and species. Hillis and Wilcox [Hillis, D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Mol. Phylogenet. Evol. 34, 299-314] provided recommendations for the classification of New World true frogs that utilized the ICZN to provide names for species, and the PhyloCode to provide names for supraspecific taxa. Nonetheless, they created new taxon names that followed both sets of rules, to avoid conflicting classifications. They also recommended that established names for both species and clades be used whenever possible, to stabilize the names of both species and clades under either set of rules, and to avoid conflicting nomenclatures. Dubois [Dubois, A., 2006. Naming taxa from cladograms: a cautionary tale. Mol. Phylogenet. Evol., 42, 317-330] objected to these principles, and argued that the names provided by Hillis and Wilcox [Hillis, D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Mol. Phylogenet. Evol. 34, 299-314] are unavailable under the ICZN, and that the two nomenclatural systems are incompatible. Here, I argue that he is incorrect in these assertions, and present arguments for retaining the established names of New World true frogs, which are largely compatible under both sets of nomenclatural rules.     

Predicting the Evolution of Sex on Complex Fitness Landscapes

Most population genetic theories on the evolution of sex or recombination are based on fairly restrictive assumptions about the nature of the underlying fitness landscapes. Here we use computer simulations to study the evolution of sex on fitness landscapes with different degrees of complexity and epistasis. We evaluate predictors of the evolution of sex, which are derived from the conditions established in the population genetic literature for the evolution of sex on simpler fitness landscapes. These predictors are based on quantities such as the variance of Hamming distance, mean fitness, additive genetic variance, and epistasis. We show that for complex fitness landscapes all the predictors generally perform poorly. Interestingly, while the simplest predictor, ΔVar_HD, also suffers from a lack of accuracy, it turns out to be the most robust across different types of fitness landscapes. ΔVar_HD is based on the change in Hamming distance variance induced by recombination and thus does not require individual fitness measurements. The presence of loci that are not under selection can, however, severely diminish predictor accuracy. Our study thus highlights the difficulty of establishing reliable criteria for the evolution of sex on complex fitness landscapes and illustrates the challenge for both theoretical and experimental research on the origin and maintenance of sexual reproduction.     

Shelf Life Degradation of Bulk Heterojunction Solar Cells: Intrinsic Evolution of Charge Transfer Complex

Achievement of long‐term stability of organic photovoltaics is currently one of the major topics for this technology to reach maturity. Most of the techniques used to reveal degradation pathways are destructive and/or do not allow for real‐time measurements in operating devices. Here, three different, nondestructive techniques able to provide real‐time information, namely, film absorbance, capacitance–voltage (C–V), and impedance spectroscopy (IS), are combined over a period of 1 year using non‐accelerated intrinsic degradation conditions. It is discerned between chemical modifications in the active layer, physical processes taking place in the bulk of the blend from those at the active layer/contact interfaces. In particular, it is observed that during the ageing experiment, the main source for device performance degradation is the formation of donor–acceptor charge‐transfer complex (–) that acts as an exciton quencher. Generation of these radical species diminishes photocurrent and reduces open‐circuit voltage by the creation of electronic defect states. Conclusions extracted from absorption, C–V, and IS measurements will be further supported by a range of other techniques such as atomic force microscopy, X‐ray diffraction, and dark‐field imaging of scanning transmission electron microscopy on ultrathin cross‐sections.     

Bioenergetic Aspects of Halophilism

Examinination of microbial diversity in environments of increasing salt concentrations indicates that certain types of dissimilatory metabolism do not occur at the highest salinities. Examples are methanogenesis for H₂ + CO₂ or from acetate, dissimilatory sulfate reduction with oxidation of acetate, and autotrophic nitrification. Occurrence of the different metabolic types is correlated with the free-energy change associated with the dissimilatory reactions. Life at high salt concentrations is energetically expensive. Most bacteria and also the methanogenic archaea produce high intracellular concentrations of organic osmotic solutes at a high energetic cost. All halophilic microorganisms expend large amounts of energy to maintain steep gradients of NA⁺ and K⁺ concentrations across their cytoplasmic membrane. The energetic cost of salt adaptation probably dictates what types of metabolism can support life at the highest salt concentrations. Use of KCl as an intracellular solute, while requiring far-reaching adaptations of the intracellular machinery, is energetically more favorable than production of organic-compatible solutes. This may explain why the anaerobic halophilic fermentative bacteria (order Haloanaerobiales) use this strategy and also why halophilic homoacetogenic bacteria that produce acetate from H₂ + CO₂ exist whereas methanogens that use the same substrates in a reaction with a similar free-energy yield do not.     

Constraints on the Evolution of Reciprocity: An Experimental Test with Zebra Finches

Reciprocity is apparently uncommon in animal societies because it requires, to evolve, specialized cognitive abilities that most species would not possess. In particular, memory would be important because cooperation can emerge and be maintained only if the same opponents interact repeatedly and adjust their decisions to their opponent’s previous move. To investigate how these constraints influence reciprocity, we first conducted a preliminary foraging experiment with zebra finches (Taeniapygia guttata) to insure that corticosterone elevations impaired the birds’ event memory capabilities. Then, we performed a reciprocity experiment with established pairs that were tested in a two‐choice apparatus under two different conditions: once with an empty implant and once with an implant of corticosterone. We found that the birds were capable of sustained cooperation in the Prisoner’s Dilemma treatment but only when they had an empty implant. Thus, our results support the hypothesis that limitations in event memory constraint the frequency of reciprocity and hence would make this form of cooperation difficult for non‐human animals. In addition, as levels of stress hormones can differ greatly among individuals, our findings might also contribute explaining individual variation in the propensity to cooperate.     

Hormonal Mechanisms as Potential Constraints on Evolution: Examples from the Anura

Developmental constraints are limitations on phenotypic variabilityresulting from developmental mechanisms that produce biasesin phenotypic variants and hence evolution. These constraintsultimately limit the available phenotypes on which selectioncan act. Because hormones play important roles in many developmentalprocesses, there is a great potential for hormonal mechanismsto produce (or act as) developmental constraints. In the currentstudy, I present two examples to show how hormones may producedevelopmental constraints on evolution in the Anura. One example(a universal constraint in the Anura), examines evidence thatthyroid hormones are required for sex differentiation and reproductionin frogs. The thyroid hormone requirement for these processesmay prevent the evolution of neoteny in anurans. The secondexample (a local constraint) examines the mechanisms underlyingsexual dichromatism in the genus Hyperolius (Hyperoliidae) andshows how the evolution of sexual dichromatism is limited bythe hormonal mechanisms regulating pigmentation     

The Evolution of Complex Organs

The origin of complex biological structures has long been a subject of interest and debate. Two centuries ago, natural explanations for their occurrence were considered inconceivable. However, 150 years of scientific investigation have yielded a conceptual framework, abundant data, and a range of analytical tools capable of addressing this question. This article reviews the various direct and indirect evolutionary processes that contribute to the origins of complex organs. The evolution of eyes is used as a case study to illustrate these concepts, and several of the most common misconceptions about complex organ evolution are discussed.

Evolution of Rotifer Life Histories

When compared to most other multicellular animals, rotifers are all relatively small, short-lived and fast-reproducing organisms. However among and within different rotifer species there is a large variation in life history patterns. This review accounts for such variation in rotifers, with a strong focus on monogonont rotifers. As the life cycle of monogonont rotifers involves both asexual and sexual reproduction, life history patterns can be examined on the level of the genetic individual, which includes all asexual females, sexual females and males that originated from one resting egg. This concept has been applied successfully in many areas, for example in predicting optimal levels of mictic reproduction or sex allocation theory. The benefits and implications of the view of the genetic individual are discussed in detail. Rotifer life histories can also be viewed on the level of physiological individuals. A large part of this review deals with the life histories of individual amictic females and addresses life history traits like body size, egg size and resource allocation patterns. It asks which trade-offs exist among those traits, how these traits change under the influence of environmental factors like food availability or temperature, and whether these changes can be interpreted as adaptive.