The effect of population structure on the rate of evolution

Ecological factors exert a range of effects on the dynamics of the evolutionary process. A particularly marked effect comes from population structure, which can affect the probability that new mutations reach fixation. Our interest is in population structures, such as those depicted by ‘star graphs’, that amplify the effects of selection by further increasing the fixation probability of advantageous mutants and decreasing the fixation probability of disadvantageous mutants. The fact that star graphs increase the fixation probability of beneficial mutations has lead to the conclusion that evolution proceeds more rapidly in star-structured populations, compared with mixed (unstructured) populations. Here, we show that the effects of population structure on the rate of evolution are more complex and subtle than previously recognized and draw attention to the importance of fixation time. By comparing population structures that amplify selection with other population structures, both analytically and numerically, we show that evolution can slow down substantially even in populations where selection is amplified.     

The scanning behavior of juncos: A game-theoretical approach

Flocking birds frequently look up or “scan” while they are feeding on the ground. High scanning rates increase the probability that the birds in a flock will see an approaching predator in time to avoid predation; however, high scanning rates also decrease the feeding rates of the scanning individuals. Since the scanning rate that maximizes the survival probability of one individual depends on how frequently other birds in the same flock are scanning, the optimal scanning behavior must be modeled as a game. We develop a realistic model of scanning behavior and use it to find two game theoretical solutions—the “co-operative” or Pareto optimum and the “selfish” or Nash optimum. The observed scanning rates do not differ significantly from the co-operative optimal scanning rate. We argue that in a game where players meet again and again such apparent co-operation may be an evolutionarily stable strategy.     

Some models of population structure and evolution

Models of population structure analyzed include: the uniform model (k populations all exchanging at a constant rate) and the multiuniform model (s clusters of k populations exchanging at different rates within and between clusters). Analogies of the latter model with trees of descent have been shown. The algorithm used allows exact solutions for the equilibrium variances and covariances in a variety of cases, including the circular stepping-stone model.Effects of multiple sources of stabilizing pressures have been shown in the multiuniform and the star model. The latter is of interest in situations of population radiation and of centripetal migration.     

Clostridium perfringens: insight into virulence evolution and population structure

Clostridium perfringens is an important pathogen in veterinary and medical fields. Diseases caused by this organism are in many cases life threatening or fatal. At the same time, it is part of the ecological community of the intestinal tract of man and animals. Virulence in this species is not fully understood and it does seem that there is erratic distribution of the toxin/enzyme genes within C. perfringens population. We used the recently developed multiple-locus variable-number tandem repeat analysis (MLVA) scheme to investigate the evolution of virulence and population structure of this species. Analysis of the phylogenetic signal indicates that acquisition of the major toxin genes as well as other plasmid-borne toxin genes is a recent evolutionary event and their maintenance is essentially a function of the selective advantage they confer in certain niches under different conditions. In addition, it indicates the ability of virulent strains to cause disease in different host species. More interestingly, there is evidence that certain normal flora strains are virulent when they gain access to a different host species. Analysis of the population structure indicates that recombination events are the major tool that shapes the population and this panmixia is interrupted by frequent clonal expansion that mostly corresponds to disease processes. The signature of positive selection was detected in alpha toxin gene, suggesting the possibility of adaptive alleles on the other chromosomally encoded determinants. Finally, C. perfringens proved to have a dynamic population and availability of more genome sequences and use of comparative proteomics and animal modeling would provide more insight into the virulence of this organism.     

The effect of a population bottleneck on the evolution of genetic variance/covariance structure

It is well known that standard population genetic theory predicts decreased additive genetic variance (V(a) ) following a population bottleneck and that theoretical models including interallelic and intergenic interactions indicate such loss may be avoided. However, few empirical data from multicellular model systems are available, especially regarding variance/covariance (V/CV) relationships. Here, we compare the V/CV structure of seventeen traits related to body size and composition between control (60 mating pairs/generation) and bottlenecked (2 mating pairs/generation; average F = 0.39) strains of mice. Although results for individual traits vary considerably, multivariate analysis indicates that V(a) in the bottlenecked populations is greater than expected. Traits with patterns and amounts of epistasis predictive of enhanced V(a) also show the largest deviations from additive expectations. Finally, the correlation structure of weekly weights is not significantly different between control and experimental lines but correlations between necropsy traits do differ, especially those involving the heart, kidney and tail length.     

The evolution of population stability as a by-product of life-history evolution

Proposed mechanisms for the evolution of population stability include group selection through longterm persistence, individual selection acting directly on stability determining the demographic parameters, and the evolution of stability as a by-product of life-history evolution. None of these hypotheses currently has clear empirical support. Using two sets of Drosophila melanogaster populations, we provide experimental evidence of stability evolving as a correlated response to selection on traits not directly related to demography. Four populations (FEJs) were selected for faster development and early reproduction for 125 generations, and the other four (JBs) were ancestral controls. All FEJ and JB populations have been maintained on discrete generations at moderate density, thus eliminating differential selection on stability determining demographic parameters. We derived eight small populations from each FEJ and JB population, and subjected four small populations each to either stabilizing or destabilizing food regimes. Census data on these 64 small populations over 20 generations clearly showed that the FEJ populations have significantly less temporal fluctuations in their numbers in both food regimes compared to their controls. This greater stability of the FEJ populations is probably a by-product of the evolution of reduced fecundity and pre-adult survivorship, as a correlated response to selection for rapid development.     

Local population structure and sex ratio: evolution in gynodioecious plants

Although the influence of population structure on evolution has been explored previously in a variety of theoretical studies, there are few examples of specific traits whose fitness is likely to be modified by the local structure. Here we focus on a specific trait, sex expression in gynodioecious plants, and derive a model in which the fitness of females and hermaphrodites is a function of the local sex ratio. By using the concept d genes. As a consequence, when local demes vary in sex ratio, a polymorphism for a cytoplasmic male sterility (CMS) allele can be maintained in the absence of nuclear alleles that restore male function. When of subjective frequencies, it is shown that among-deme variance in the local sex ratio reduces the average fitness of females when pollen availability limits fertility. In contrast, sex ratio variance increases the fitness of hermaphrodites from the perspective of maternally inherited genes and lessens the negative impact of pollen limitation on hermaphrodite fitness when it is measured from the perspective of biparentally inheriterestorer alleles are introduced into the model, polymorphism cannot be maintained simultaneously at both the cytoplasmic and nuclear loci. In that case, the CMS allele spreads to fixation, and the equilibrium frequency of females is an inverse function of the equilibrium frequency of the restorer allele, which increases with increased structure. The results exemplify how population structure can greatly alter the fitness and evolution of a frequency-dependent trait.     

Surnames and dialects in France: population structure and cultural evolution

To study the isonymy structure of France as related to local language variations, the surname distributions of 6.03 million telephone users registered for the year 2002 were analysed in the 21 conterminous regions, their 94 departments and in 809 towns of the Country. For regions and departments the differences among local dialects were quantified according to the dialecto-metrization of the Atlas Linguistique Fran?ais. We found that Lasker's distance between regions was correlated with geographic distance with r=0.692+/-0.040, while Euclidean (r=0.546+/-0.058) and Nei's (r=0.610+/-0.048) distances were less correlated. Slightly lower correlations were observed for departments. Also, dialectometric distance was correlated with geography (r=0.582+/-0.069 for regions and r=0.617+/-0.015 for departments). The correlations between Lasker and dialectometric matrix distances for regions and departments are r=0.625+/-0.046 and 0.544+/-0.014, respectively, indicating that the common cause generating surname and language diversity accounts for about 35% of the differentiation. Both Lasker and dialectometric distances identify very similar boundaries between Poitou, Centre, Bourgogne and Franche Comptée at the North, and Aquitaine, Limousin, Auvergne, Rh?ne-Alpes in the South. Average Fisher's alpha for France was 7877 the highest value observed for the European countries studied to date. The size of alpha in most French towns indicates considerable recent immigration.     

The evolution of cuckoo parasitism: a comparative analysis

Cuckoos (family Cuculidae) show the highest diversity of breeding strategies within one bird family (parental care, facultative and obligate brood parasites). We used independent contrasts from two phylogenies to examine how this variation was related to 13 ecological and life-history variables. The ancestral state was probably tropical, resident, forest cuckoos with parental care. The evolution of brood parasitism was correlated with a shift to more open habitats, a change in diet, increases in species breeding-range size and migration, and a decrease in egg size. Once parasitism had evolved, more elaborate parasitic strategies (more harmful to host fitness) were correlated with decreased egg size, a change in diet, increased breeding-range size and migration, a shortened breeding season and a decrease in local abundance. Establishing the most probable evolutionary pathways, using the method of Pagel, shows that changes in ecological variables (such as migration, range size and diet type) preceded the evolution of brood parasitism, which is likely to be a later adaptation to reduce the cost of reproduction. By contrast, brood parasitism evolved before changes in egg size occurred, indicating that egg size is an adaptive trait in host--parasite coevolution. Our results suggest that the evolution of cuckoo brood parasitism reflects selection from both ecological pressures and host defences.     

An examination of cetacean brain structure with a novel hypothesis correlating thermogenesis to the evolution of a big brain

This review examines aspects of cetacean brain structure related to behaviour and evolution. Major considerations include cetacean brain-body allometry, structure of the cerebral cortex, the hippocampal formation, specialisations of the cetacean brain related to vocalisations and sleep phenomenology, paleoneurology, and brain-body allometry during cetacean evolution. These data are assimilated to demonstrate that there is no neural basis for the often-asserted high intellectual abilities of cetaceans. Despite this, the cetaceans do have volumetrically large brains. A novel hypothesis regarding the evolution of large brain size in cetaceans is put forward. It is shown that a combination of an unusually high number of glial cells and unihemispheric sleep phenomenology make the cetacean brain an efficient thermogenetic organ, which is needed to counteract heat loss to the water. It is demonstrated that water temperature is the major selection pressure driving an altered scaling of brain and body size and an increased actual brain size in cetaceans. A point in the evolutionary history of cetaceans is identified as the moment in which water temperature became a significant selection pressure in cetacean brain evolution. This occurred at the Archaeoceti - modern cetacean faunal transition. The size, structure and scaling of the cetacean brain continues to be shaped by water temperature in extant cetaceans. The alterations in cetacean brain structure, function and scaling, combined with the imperative of producing offspring that can withstand the rate of heat loss experienced in water, within the genetic confines of eutherian mammal reproductive constraints, provides an explanation for the evolution of the large size of the cetacean brain. These observations provide an alternative to the widely held belief of a correlation between brain size and intelligence in cetaceans.     

Sequence diversity of Pseudomonas aeruginosa: impact on population structure and genome evolution

Comparative sequencing of Pseudomonas aeruginosa genes oriC, citS, ampC, oprI, fliC, and pilA in 19 environmental and clinical isolates revealed the sequence diversity to be about 1 order of magnitude lower than in comparable housekeeping genes of Salmonella. In contrast to the low nucleotide substitution rate, the frequency of recombination among different P. aeruginosa genotypes was high, leading to the random association of alleles. The P. aeruginosa population consists of equivalent genotypes that form a net-like population structure. However, each genotype represents a cluster of closely related strains which retain their sequence signature in the conserved gene pool and carry a set of genotype-specific DNA blocks. The codon adaptation index, a quantitative measure of synonymous codon bias of genes, was found to be consistently high in the P. aeruginosa genome irrespective of the metabolic category and the abundance of the encoded gene product. Such uniformly high codon adaptation indices of 0.55 to 0.85 fit the ubiquitous lifestyle of P. aeruginosa.     

Temporal analysis of clonal structure in a moss bdelloid population

Clonal structure of a population of Macrotrachela quadricornifera (Rotifera, Bdelloidea) from a terrestrial moss in Northern Italy, was investigated over a 16 month period. Every month, 40–60 specimens of M. quadricornifera were collected from about 0.1 m² of moss. The individual animals were homogenized and their isozyme phenotypes analyzed by electrophoresis on vertical polyacrylamide gel. One enzyme, phosphoglucose isomerase (PGI), was used as a marker to distinguish the different clones present in the sample. A few clones were established from the rotifers sampled and patterns of esterases and , and malic enzyme were studied. Nine electrophoretic patterns for PGI were seen. One was dominant, a second was almost always present, but in lesser amounts. The remainder were present occasionally.There seemed to be no seasonal replacement of the clones and the composition of the population appeared to be unaffected by variations in temperature. Relative humidity seemed to be the more important factor in regulating the number of electromorphs of the rotifer population.     

The influence of predator--prey population dynamics on the long-term evolution of food web structure

We develop a set of equations to describe the population dynamics of many interacting species in food webs. Predator-prey interactions are nonlinear, and are based on ratio-dependent functional responses. The equations account for competition for resources between members of the same species, and between members of different species. Predators divide their total hunting/foraging effort between the available prey species according to an evolutionarily stable strategy (ESS). The ESS foraging behaviour does not correspond to the predictions of optimal foraging theory. We use the population dynamics equations in simulations of the Webworld model of evolving ecosystems. New species are added to an existing food web due to speciation events, whilst species become extinct due to coevolution and competition. We study the dynamics of species-diversity in Webworld on a macro-evolutionary time-scale. Coevolutionary interactions are strong enough to cause continuous overturn of species, in contrast to our previous Webworld simulations with simpler population dynamics. Although there are significant fluctuations in species diversity because of speciation and extinction, very large-scale extinction avalanches appear to be absent from the dynamics, and we find no evidence for self-organized criticality.     

Genetic analysis of life-history constraint and evolution in a wild ungulate population

Trade-offs among life-history traits are central to evolutionary theory. In quantitative genetic terms, trade-offs may be manifested as negative genetic covariances relative to the direction of selection on phenotypic traits. Although the expression and selection of ecologically important phenotypic variation are fundamentally multivariate phenomena, the in situ quantification of genetic covariances is challenging. Even for life-history traits, where well-developed theory exists with which to relate phenotypic variation to fitness variation, little evidence exists from in situ studies that negative genetic covariances are an important aspect of the genetic architecture of life-history traits. In fact, the majority of reported estimates of genetic covariances among life-history traits are positive. Here we apply theory of the genetics and selection of life histories in organisms with complex life cycles to provide a framework for quantifying the contribution of multivariate genetically based relationships among traits to evolutionary constraint. We use a Bayesian framework to link pedigree-based inference of the genetic basis of variation in life-history traits to evolutionary demography theory regarding how life histories are selected. Our results suggest that genetic covariances may be acting to constrain the evolution of female life-history traits in a wild population of red deer Cervus elaphus: genetic covariances are estimated to reduce the rate of adaptation by about 40%, relative to predicted evolutionary change in the absence of genetic covariances. Furthermore, multivariate phenotypic (rather than genetic) relationships among female life-history traits do not reveal this constraint.     

AWclust: point-and-click software for non-parametric population structure analysis

Background  

Population structure analysis is important to genetic association studies and evolutionary investigations. Parametric approaches, e.g. STRUCTURE and L-POP, usually assume Hardy-Weinberg equilibrium (HWE) and linkage equilibrium among loci in sample population individuals. However, the assumptions may not hold and allele frequency estimation may not be accurate in some data sets. The improved version of STRUCTURE (version 2.1) can incorporate linkage information among loci but is still sensitive to high background linkage disequilibrium. Nowadays, large-scale single nucleotide polymorphisms (SNPs) are becoming popular in genetic studies. Therefore, it is imperative to have software that makes full use of these genetic data to generate inference even when model assumptions do not hold or allele frequency estimation suffers from high variation.     

The structure of protein evolution and the evolution of protein structure

The observed distribution of protein structures can give us important clues about the underlying evolutionary process, imposing important constraints on possible models. The availability of results from an increasing number of genome projects has made the development of these models an active area of research. Models explaining the observed distribution of structures have focused on the inherent functional capabilities and structural properties of different folds and on the evolutionary dynamics. Increasingly, these elements are being combined.     

Dietary differentiation and the evolution of population genetic structure in a highly mobile carnivore

Recent studies on highly mobile carnivores revealed cryptic population genetic structures correlated to transitions in habitat types and prey species composition. This led to the hypothesis that natal-habitat-biased dispersal may be responsible for generating population genetic structure. However, direct evidence for the concordant ecological and genetic differentiation between populations of highly mobile mammals is rare. To address this we analyzed stable isotope profiles (δ(13)C and δ(15)N values) for Eastern European wolves (Canis lupus) as a quantifiable proxy measure of diet for individuals that had been genotyped in an earlier study (showing cryptic genetic structure), to provide a quantitative assessment of the relationship between individual foraging behavior and genotype. We found a significant correlation between genetic distances and dietary differentiation (explaining 46% of the variation) in both the marginal test and crucially, when geographic distance was accounted for as a co-variable. These results, interpreted in the context of other possible mechanisms such as allopatry and isolation by distance, reinforce earlier studies suggesting that diet and associated habitat choice are influencing the structuring of populations in highly mobile carnivores.     

The evolution of the Uruguayan population

Uruguay is usually considered an immigrants' country that, unlike other South American countries, has no native population and only a slight African contribution. The perception of its identity frequently refers to this characteristic: there are no regional differences and population variability is minimal. The object of this paper is to analyze the processes that shaped the present population and the regional diversity in their historical context. For this purpose parish and civil archives of three Departments were reviewed for the period 1840–1990: Cerro Largo and Tacuarembo, in the Northeast and Montevideo, in the south. The origin of the population, individual migration distance, consanguinity and marriage age were taken into account. With the exception of age, differences were found between the capital, Montevideo, and the Northeast for the selected variables during most of the period analyzed. On the basis of these results, the importance of Montevideo as the point of entry of both immigrants and slaves, the regional homogeneity and the concept of national identity are discussed.