Adaptive cis-regulatory changes may involve few mutations

A long-standing debate in evo-devo research concerns the relative role of protein-coding and cis-regulatory regions in adaptation. Recent studies of genetic adaptation have revealed that the number of substitutions contributing to phenotypic variation is lower in cis-regulatory than in structural regions, which has led to the idea that cis-regulatory regions are less important in phenotypic adaptation. However, the number of substitutions is not the only important factor, the "size" of the adaptive contribution of these substitutions is important too. A geometrical reasoning predicts that, given their lesser pleiotropic effects, cis-regulatory substitutions should have a larger average adaptive contribution than protein-coding substitutions. Thus it is possible that even with a lower number of adaptive mutations, cis-regulatory regions may contribute at the same level or even more than protein-coding regions.     

Adaptive Significance of Circadian Clocks

Circadian clocks are ubiquitous and are found in organisms ranging from bacteria to mammals. This ubiquity of occurrence implies adaptive significance, but to date there has been no rigorous empirical evidence to support this. It is believed that an organism possessing circadian clocks gains fitness advantage in two ways: (i) by synchronizing its behavioral and physiological processes to cyclic environmental factors (extrinsic adaptive value); (ii) by coordinating its internal metabolic processes (intrinsic adaptive value). There is preliminary circumstantial evidence to support both. Several studies using organisms living in constant environments have shown that these organisms possess functional circadian clocks, suggesting that circadian clocks may have some intrinsic adaptive value. Studies to assess the adaptive value of circadian clocks in periodic environments suggest that organisms may have a fitness advantage in those periodic environments, which closely match their own intrinsic periodicity. Furthermore, evidence from organisms living in the wild, selection studies, and studies on latitudinal clines suggest that circadian clocks may have an extrinsic adaptive value as well. In this paper, I have presented several hypotheses for the emergence of circadian clocks and have reviewed some major empirical studies suggesting adaptive significance of circadian clocks.     

Adaptive significance of circadian clocks

Circadian clocks are ubiquitous and are found in organisms ranging from bacteria to mammals. This ubiquity of occurrence implies adaptive significance, but to date there has been no rigorous empirical evidence to support this. It is believed that an organism possessing circadian clocks gains fitness advantage in two ways: (i) by synchronizing its behavioral and physiological processes to cyclic environmental factors (extrinsic adaptive value); (ii) by coordinating its internal metabolic processes (intrinsic adaptive value). There is preliminary circumstantial evidence to support both. Several studies using organisms living in constant environments have shown that these organisms possess functional circadian clocks, suggesting that circadian clocks may have some intrinsic adaptive value. Studies to assess the adaptive value of circadian clocks in periodic environments suggest that organisms may have a fitness advantage in those periodic environments, which closely match their own intrinsic periodicity. Furthermore, evidence from organisms living in the wild, selection studies, and studies on latitudinal clines suggest that circadian clocks may have an extrinsic adaptive value as well. In this paper, I have presented several hypotheses for the emergence of circadian clocks and have reviewed some major empirical studies suggesting adaptive significance of circadian clocks.     

The development of genetics and population studies

The contribution of genetics and population studies to physical anthropology as reflected in the pages of our Journal is traced since its establishment in 1918. Major trends include the use of more genetic polymorphisms, the search for natural selection and genetic drift, the unraveling of population structure in a wide variety of ecological niches, and the recognition of the role of culture in human biology. Nonhuman primates have also been explored from the viewpoint of population genetic. Emphasis has been increasingly on process rather than classification.     

On the Adaptive Significance of Circadian Clocks for Their Owners

Circadian rhythms are believed to be an evolutionary adaptation to daily environmental cycles resulting from Earth's rotation about its axis. A trait evolved through a process of natural selection is considered as adaptation; therefore, rigorous demonstration of adaptation requires evidence suggesting evolution of a trait by natural selection. Like any other adaptive trait, circadian rhythms are believed to be advantageous to living beings through some perceived function. Circadian rhythms are thought to confer advantage to their owners through scheduling of biological functions at appropriate time of daily environmental cycle (extrinsic advantage), coordination of internal physiology (intrinsic advantage), and through their role in responses to seasonal changes. So far, the adaptive value of circadian rhythms has been tested in several studies and evidence indeed suggests that they confer advantage to their owners. In this review, we have discussed the background for development of the framework currently used to test the hypothesis of adaptive significance of circadian rhythms. Critical examination of evidence reveals that there are several lacunae in our understanding of circadian rhythms as adaptation. Although it is well known that demonstrating a given trait as adaptation (or setting the necessary criteria) is not a trivial task, here we recommend some of the basic criteria and suggest the nature of evidence required to comprehensively understand circadian rhythms as adaptation. Thus, we hope to create some awareness that may benefit future studies in this direction. (Author correspondence: vsharma@jncasr.ac.in or vksharmas@gmail.com)     

Understanding Natural Selection: Essential Concepts and Common Misconceptions

Natural selection is one of the central mechanisms of evolutionary change and is the process responsible for the evolution of adaptive features. Without a working knowledge of natural selection, it is impossible to understand how or why living things have come to exhibit their diversity and complexity. An understanding of natural selection also is becoming increasingly relevant in practical contexts, including medicine, agriculture, and resource management. Unfortunately, studies indicate that natural selection is generally very poorly understood, even among many individuals with postsecondary biological education. This paper provides an overview of the basic process of natural selection, discusses the extent and possible causes of misunderstandings of the process, and presents a review of the most common misconceptions that must be corrected before a functional understanding of natural selection and adaptive evolution can be achieved.

On the mode of selection inEscherichia coli

Competition experiments between a lac⁺ prototroph and a lac⁻ auxotroph of Escherichia coli were conducted by serial transfer procedure on four levels of sugar concentration. Changes of the relative frequencies of both genotypes were followed and the relative fitness was estimated. Fitness was proved to be density-dependent. No explicit dependence of fitness upon genotype frequencies could be detected by the simple method ofKosuda (1981).     

Testing for selection on color and pattern in a mimetic radiation

In this paper,we analyze variation in spectral reflectance and color pattern among populations to demonstrate dramatic divergence between four distinct morphs of the mimic poison frog Ranitomeya imitator.We also analyze genetic divergence in d-loop mtDNA sequences between populations.We then use coalescent-based simulations to demonstrate that the high levels of observed phenotypic divergence are not consistent with levels of genetic divergence expected under neutral drift among populations,implying an important role for selection in driving divergence between these populations.     

Evolutionary dynamics, epistatic interactions, and biological information

We investigate a definition of biological information that connects population genetics with the tools of information theory by focusing on the distribution of genotypes found in a population. Previous research has treated loci as non-interacting by making specific approximations in the calculation of information-theoretic quantities. We expand earlier mathematical forms to include epistasis, or interactions between mutations at all pairs of loci. Application of our improved measure of biological information to evolution on two-locus, two-allele fitness landscapes demonstrates that mutual information between loci reflects epistatic interaction of mutations. Finally, we consider four-locus, two-allele fitness landscapes with modular structure. As modular interactions are inherently epistatic, we demonstrate that our refined approximation provides insight into the underlying structure of these non-trivial fitness landscapes.     

The strength of genetic interactions scales weakly with mutational effects

Background

Genetic interactions pervade every aspect of biology, from evolutionary theory, where they determine the accessibility of evolutionary paths, to medicine, where they can contribute to complex genetic diseases. Until very recently, studies on epistatic interactions have been based on a handful of mutations, providing at best anecdotal evidence about the frequency and the typical strength of genetic interactions. In this study, we analyze a publicly available dataset that contains the growth rates of over five million double knockout mutants of the yeast Saccharomyces cerevisiae.

Results

We discuss a geometric definition of epistasis that reveals a simple and surprisingly weak scaling law for the characteristic strength of genetic interactions as a function of the effects of the mutations being combined. We then utilized this scaling to quantify the roughness of naturally occurring fitness landscapes. Finally, we show how the observed roughness differs from what is predicted by Fisher''s geometric model of epistasis, and discuss the consequences for evolutionary dynamics.

Conclusions

Although epistatic interactions between specific genes remain largely unpredictable, the statistical properties of an ensemble of interactions can display conspicuous regularities and be described by simple mathematical laws. By exploiting the amount of data produced by modern high-throughput techniques, it is now possible to thoroughly test the predictions of theoretical models of genetic interactions and to build informed computational models of evolution on realistic fitness landscapes.     

A simple model of co-evolutionary dynamics caused by epistatic selection

Epistasis is the dependency of the effect of a mutation on the genetic background in which it occurs. Epistasis has been widely documented and implicated in the evolution of species barriers and the evolution of genetic architecture. Here we propose a simple model to formalize the idea that epistasis can also lead to co-evolutionary patterns in molecular evolution of interacting genes. This model epistasis is represented by the influence of one gene substitution on the fitness rank of the resident allele at another locus. We assume that increasing or decreasing fitness rank occur equally likely. In simulations we show that this form of epistasis leads to co-evolution in the sense that the length of an adaptive walk between interacting loci is highly correlated. This effect is caused by episodes of elevated rate of evolution in both loci simultaneously. We find that the influence of epistasis on these measures of co-evolutionary dynamics is relatively robust to the details of the model. The main factor influencing the correlation in evolutionary rates is the probability that a substitution will have an epistatic effect, but the strength of epistasis or the asymmetry of the initial fitness ranks of the alleles have only a minor effect. We suggest that covariance in rates of evolution among loci could be used to detect epistasis among loci.     

Laboratory selection for resistance to sulfoxaflor and fitness costs in the green peach aphid Myzus persicae

Sulfoxaflor is a newly released fourth-generation neonicotinoid insecticide for management of sap-feeding pests that have developed resistance to established insecticide groups. The risk of resistance developing to this pesticide in target pests is unclear. We selected a strain of the green peach aphid, Myzus persicae (Sulzer) (Hemiptera: Aphididae), for resistance to sulfoxaflor in the laboratory, which showed 199-fold resistance after 45 generations compared to the starting population. Life table analysis showed that the resistant strain had a fitness of 0.83 compared to the susceptible strain. Adult longevity of the resistant strain was reduced by 9.55% compared to the susceptible strain. The period when adults of the resistant strain produced offspring was reduced by 17.19%, while the mean fecundity of the resistant strain was reduced by 15%. These findings suggest that M. persicae can develop a high level of resistance to sulfoxaflor, but fitness costs may result in a recovery of sensitivity when field populations are no longer exposed to sulfoxaflor.     

Epistatic contributions to quantitative traits in Tribolium castaneum

Summary Triple-testcross experiments were used to analyze epistatic contributions to % hatchability of eggs, age of pupation, number of eggs laid in 24-hour period, and survival from hatching to day 35. Seven diverse inbred lines and the F₁ produced by crossing the two tester lines were examined for the presence of epistasis. There was evidence of epistasis for each of the 4 traits in at least one of the 8 lines tested. Epistasis was a major source of variation in survival in all of the lines tested.     

Simultaneous modelling of distributional patterns in a guild of eastern-Australian cicadas

Summary The distributions, with respect to habitat structure, of nine species of eastern-Australian cicadas have been shown to be non-random. The most striking consequence of this non-randomness is a marked inverse relationship between habitat breadth and habitat position (terms defined in text). Eight basic models and 12 derived models were used in conjunction with a canonical space to try to account for the ways in which the species of cicadas were distributed with respect to habitat. Several models produced results that were in reasonable agreement with the observed data. The most parsimonious of these corresponds to analytical results of other workers, such as Diamond's (1975) incidence curves, occurrence sequences (Schoener and Schoener 1983), and probability functions (Adler and Wilson 1985). The distributions of cicadas can be modelled by assuming that the species occupy sites independently of one another. These species of cicadas are unlikely to engage in interspecific competition, which is consistent with independence of distributions.     

A graphical model of disruptive selection on offspring size and a possible case of speciation in freshwater gobies characterized by egg-size difference

The graphical technique devised bySmith andFretwell (1974) to construct a model of the optimal offspring size was applied to the case where disruptive selection might work on offspring size. On this basis, a possible case of speciation in freshwater gobies characterized by egg-size difference was discussed.