The shifting balance theory and macroevolution

Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies

The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale. We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.

Endogenous network states predict gain or loss of functions for genetic mutations in hepatocellular carcinoma

Cancers have been typically characterized by genetic mutations. Patterns of such mutations have traditionally been analysed by posteriori statistical association approaches. One may ponder the possibility of a priori determination of any mutation regularity. Here by exploring biological processes implied in a mechanistic theory recently developed (the endogenous molecular-cellular network theory), we found that the features of genetic mutations in cancers may be predicted without any prior knowledge of mutation propensities. With hepatocellular carcinoma (HCC) as an example, we found that the normal hepatocyte and cancerous hepatocyte can be represented by robust stable states of one single endogenous network. These stable states, specified by distinct patterns of expressions or activities of proteins in the network, provide means to directly identify a set of most probable genetic mutations and their effects in HCC. As the key proteins and main interactions in the network are conserved through cell types in an organism, similar mutational features may also be found in other cancers. This analysis yielded straightforward and testable predictions on accumulated and preferred mutation spectra in normal tissue. The validation of predicted cancer state mutation patterns demonstrates the usefulness and potential of a causal dynamical framework to understand and predict genetic mutations in cancer.

Synergistic and compensatory effects of two point mutations conferring target-site resistance to fipronil in the insect GABA receptor RDL

Insecticide resistance can arise from a variety of mechanisms, including changes to the target site, but is often associated with substantial fitness costs to insects. Here we describe two resistance-associated target-site mutations that have synergistic and compensatory effects that combine to produce high and persistent levels of resistance to fipronil, an insecticide targeting on γ-aminobytyric acid (GABA) receptors. In Nilaparvata lugens, a major pest of rice crops in many parts of Asia, we have identified a single point mutation (A302S) in the GABA receptor RDL that has been identified previously in other species and which confers low levels of resistance to fipronil (23-fold) in N. lugans. In addition, we have identified a second resistance-associated RDL mutation (R300Q) that, in combination with A302S, is associated with much higher levels of resistance (237-fold). The R300Q mutation has not been detected in the absence of A302S in either laboratory-selected or field populations, presumably due to the high fitness cost associated with this mutation. Significantly, it appears that the A302S mutation is able to compensate for deleterious effects of R300Q mutation on fitness cost. These findings identify a novel resistance mechanism and may have important implications for the spread of insecticide resistance.

Neuronal boost to evolutionary dynamics

Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild.

Why flying dogs are rare: A general theory of luck in evolutionary transitions

There is a worry that the 'major transitions in evolution' represent an arbitrary group of events. This worry is warranted, and we show why. We argue that the transition to a new level of hierarchy necessarily involves a nonselectionist chance process. Thus any unified theory of evolutionary transitions must be more like a general theory of fortuitous luck, rather than a rigid formulation of expected events. We provide a systematic account of evolutionary transitions based on a second-order regularity of chance events, as stipulated by the ZFEL (Zero Force Evolutionary Law). And in doing so, we make evolutionary transitions explainable and predictable, and so not entirely contingent after all.

Quantifying the role of population subdivision in evolution on rugged fitness landscapes

Natural selection drives populations towards higher fitness, but crossing fitness valleys or plateaus may facilitate progress up a rugged fitness landscape involving epistasis. We investigate quantitatively the effect of subdividing an asexual population on the time it takes to cross a fitness valley or plateau. We focus on a generic and minimal model that includes only population subdivision into equivalent demes connected by global migration, and does not require significant size changes of the demes, environmental heterogeneity or specific geographic structure. We determine the optimal speedup of valley or plateau crossing that can be gained by subdivision, if the process is driven by the deme that crosses fastest. We show that isolated demes have to be in the sequential fixation regime for subdivision to significantly accelerate crossing. Using Markov chain theory, we obtain analytical expressions for the conditions under which optimal speedup is achieved: valley or plateau crossing by the subdivided population is then as fast as that of its fastest deme. We verify our analytical predictions through stochastic simulations. We demonstrate that subdivision can substantially accelerate the crossing of fitness valleys and plateaus in a wide range of parameters extending beyond the optimal window. We study the effect of varying the degree of subdivision of a population, and investigate the trade-off between the magnitude of the optimal speedup and the width of the parameter range over which it occurs. Our results, obtained for fitness valleys and plateaus, also hold for weakly beneficial intermediate mutations. Finally, we extend our work to the case of a population connected by migration to one or several smaller islands. Our results demonstrate that subdivision with migration alone can significantly accelerate the crossing of fitness valleys and plateaus, and shed light onto the quantitative conditions necessary for this to occur.

Experimental evidence has recently been accumulating to suggest that fitness landscape ruggedness is common in a variety of organisms. Rugged landscapes arise from interactions between genetic variants, called epistasis, which can lead to fitness valleys or plateaus. The time needed to cross such fitness valleys or plateaus exhibits a rich dependence on population size, since stochastic effects have higher importance in small populations, increasing the probability of fixation of neutral or deleterious mutants. This may lead to an advantage of population subdivision, a possibility which has been strongly debated for nearly one hundred years. In this work, we quantitatively determine when, and to what extent, population subdivision accelerates valley and plateau crossing. Using the simple model of an asexual population subdivided into identical demes connected by gobal migration, we derive the conditions under which crossing by a subdivided population is driven by its fastest deme, thus giving rise to the maximal speedup. Our analytical predictions are verified using stochastic simulations. We investigate the effect of varying the degree of subdivision of a population. We generalize our results to weakly beneficial intermediates and to different population structures. We discuss the magnitude and robustness of the effect for realistic parameter values.

Growth and fluctuating asymmetry of human newborns: influence of inbreeding and parental education

Historically, medical concerns about the deleterious effects of closely inbred marriages have focused on the risk posed by recessive Mendelian disease, with much less attention to developmental instability. We studied the effects of inbreeding (first-cousin marriage) on growth and fluctuating asymmetry of 200 full-term infants (101 inbred and 99 outbred) whose parents were of similar socioeconomic status in Sivas Province, Turkey. In addition to differences in their mean inbreeding coefficients (f = 1/16 for first cousins and f < 1/1,024 for unrelated parents), the consanguineous parents were less well educated (3 years, on average for both husbands and wives). We measured weight, height, head circumference, and chest circumference of the newborns, as well as four bilateral traits (ear width, ear length, and second and fourth digit lengths). After taking education into account, none of the measures of size (weight, height, head circumference, and chest circumference) and fluctuating asymmetry differed between the inbred and outbred groups. Male children of well-educated parents, however, were larger and had less fluctuating asymmetry. Female children of well-educated parents weighed more than those of less well-educated parents, but were otherwise indistinguishable for height, head circumference, chest circumference, and fluctuating asymmetry. We conclude that inbreeding depression causes neither an increase in fluctuating asymmetry of full-term newborns, nor a decrease in body size. Unmeasured variables correlated with education appear to have an effect on fluctuating asymmetry and size of male children and only a weak effect on size (weight) of female children.

[Speciation and its mechanisms: conceptual background and recent advances]

This paper presents a historical approach on general concepts of speciation and its mechanisms, from the primordial ideas to the most recent theories that seek to elucidate the origin of biodiversity. It is common knowledge that speciation is a controversial and complex issue that encompasses virtually all the lines of research of biology, in addition to geology and paleontology. The main objective of the paper is to clarify the theoretical concepts on the origin of the animal species, in the chronological order in which they became established throughout the whole of the development of evolutionary biology as a science.

Drift load in populations of small size and low density

According to theory, drift load in randomly mating populations is determined by past population size, because enhanced genetic drift in small populations causes accumulation and fixation of recessive deleterious mutations of small effect. In contrast, segregating load due to mutations of low frequency should decline in smaller populations, at least when mutations are highly recessive and strongly deleterious. Strong local selection generally reduces both types of load. We tested these predictions in 13 isolated, outcrossing populations of Arabidopsis lyrata that varied in population size and plant density. Long-term size was estimated by expected heterozygosity at 20 microsatellite loci. Segregating load was assessed by comparing performance of offspring from selfings versus within-population crosses. Drift load was the heterosis effect created by interpopulation outbreeding. Results showed that segregating load was unrelated to long-term size. However, drift load was significantly higher in populations of small effective size and low density. Drift load was mostly expressed late in development, but started as early as germination and accumulated thereafter. The study largely confirms predictions of theory and illustrates that mutation accumulation can be a threat to natural populations.

The generation of variation and the developmental basis for evolutionary novelty

Organisms exhibit an incredible diversity of form, a fact that makes the evolution of novelty seemingly self-evident. However, despite the "obvious" case for novelty, defining this concept in evolutionary terms is highly problematic, so much so that some have suggested discarding it altogether. Approaches to this problem tend to take either an adaptation- or development-based perspective, but we argue here that an exclusive focus on either of these misses the original intent of the novelty concept and undermines its practical utility. We propose instead that for a feature to be novel, it must have evolved both by a transition between adaptive peaks on the fitness landscape and that this transition must have overcome a previous developmental constraint. This definition focuses novelty on the explanation of apparently difficult or low-probability evolutionary transitions and highlights how the integration of developmental and functional considerations are necessary to evolutionary explanation. It further reinforces that novelty is a central concern not just of evolutionary developmental biology (i.e., "evo-devo") but of evolutionary biology more generally. We explore this definition of novelty in light of four examples that range from the obvious to subtle.

On the shifting balance: the case of Staphylococcus aureus CC398

The recent study by L. Price et al. [mBio, 3(1):e00305-11, 2012] demonstrating the human origin of the livestock-associated CC398 Staphylococcus aureus provides an excellent example of how bacterial populations can explore a wide range of potential niches and acquire optimal adaptations for life in alternative hosts. The shifting balance theory proposed by Sewall Wright 80 years ago serves as a perfect model for understanding the observed facts: a possibly large CC398 population optimally positioned on the top of a fitness peak for living in a human host probably began evolving long ago by variation, drift, and migration, until it reached the low fitness edge of a neighboring alternative peak in the fitness landscape, one in a livestock host. The bacterial population then evolved again, moving uphill to reach a novel optimal "top of the peak" position in livestock. In the case of CC398, it is worrisome to think that it might readapt to human hosts without losing fitness in livestock; a double-host-adapted organism could certainly be in an optimal position for increasing its virulence and antibiotic resistance.

Population subdivision and adaptation in asexual populations of Saccharomyces cerevisiae

Population subdivision limits competition between individuals, which can have a profound effect on adaptation. Subdivided populations maintain more genetic diversity at any given time compared to well-mixed populations, and thus "explore" larger parts of the genotype space. At the same time, beneficial mutations take longer to spread in such populations, and thus subdivided populations do not "exploit" discovered mutations as efficiently as well-mixed populations. Whether subdivision inhibits or promotes adaptation in a given environment depends on the relative importance of exploration versus exploitation, which in turn depends on the structure of epistasis among beneficial mutations. Here we investigate the relative importance of exploration versus exploitation for adaptation by evolving 976 independent asexual populations of budding yeast with several degrees of geographic subdivision. We find that subdivision systematically inhibits adaptation: even the luckiest demes in subdivided populations on average fail to discover genotypes that are fitter than those discovered by well-mixed populations. Thus, exploitation of discovered mutations is more important for adaptation in our system than a thorough exploration of the mutational neighborhood, and increasing subdivision slows adaptation.

The impact of interspecific competition on lineage evolution and a rapid peak shift by interdemic genetic mixing in experimental bacterial populations

Epistatic interactions between genes in the genome constrain the accessible evolutionary paths of lineages. Two factors involving epistasis that can affect the evolutionary path and fate of lineages were investigated. The first factor concerns the impact of competition with another species lineage that has different epistatic constraints. Five enteric bacterial populations were evolved by point mutation in medium containing a single limiting resource. Single-species and two-species cultures were used to determine whether different asexual lineages have different capacities for producing variants due to epistatic constraints, and whether their survival is determined by local inter-lineage competition with different species. Local inter-lineage competition quickly resulted in one successful lineage, with another lineage becoming extinct before finding a higher peak. The second factor concerns a peak-shifting process, and whether the sexual recombination between different demes can cause peak shifts was investigated. An Escherichia coli population consisting of a male (Hfr) and female strain (F(-)) was evolved in a single limiting resource and compared to evolving populations containing the male or female strain alone. The E. coli sexual lineage was successful due to its ability to escape lower peaks and reach a higher peak, not because of a rapid approach to the nearest local peak the male or female asexual lineage could reach. The data in this study demonstrate that lineage survivability can be determined by the ability to produce beneficial mutations and checked by local competition between lineages of different species. Interspecific competition may prevent a population from evolving through crossing fitness valleys or adaptive ridges if it requires many generations to achieve peak shifts. The data also show that genomic recombination between different conspecific lineages can rapidly carry the combined lineage to a higher peak.

Compensation of fitness costs and reversibility of antibiotic resistance mutations

Strains of bacterial pathogens that have acquired mutations conferring antibiotic resistance often have a lower growth rate and are less invasive or transmissible initially than their susceptible counterparts. However, fitness costs of resistance mutations can be ameliorated by secondary site mutations. These so-called compensatory mutations may restore fitness in the absence and/or presence of antimicrobials. We review literature data and show that the fitness gains in the absence and presence of antibiotic treatment need not be correlated. The aim of this study is to gain a better conceptual grasp of how compensatory mutations with different fitness gains affect evolutionary trajectories, in particular reversibility. To this end, we developed a theoretical model with which we consider both a resistance and a compensation locus. We propose an intuitively understandable parameterization for the fitness values of the four resulting genotypes (wild type, resistance mutation only, compensatory mutation only, and both mutations) in the absence and presence of treatment. The differential fitness gains, together with the turnover rate and the mutation rate, strongly affected the success of antibacterial treatment, reversibility, and long-term abundance of resistant strains. We therefore propose that experimental studies of compensatory mutations should include fitness measurements of all possible genotypes in both the absence and presence of an antibiotic.

Genetic differentiation among peripheral populations of Bombina bombina from Thrace and Anatolia: an allozyme analysis

Genetic structures of Bombina bombina populations, located as peripheral isolates in Turkish Thrace and northwestern Anatolia, were analyzed by polyacrylamide gel electrophoresis using 20 allozyme loci, to investigate the populations' current genetic variation and possible colonization history. Significant genetic variability was detected in most of the loci and all populations. Allozyme pairwise F (ST) matrices and distribution of allele frequencies indicate their very close genetic relationships and relatively recent formation. Mean genetic distance values between Thracian and Anatolian populations indicate a Middle or Upper Pleistocene lineage separation before the formation of the Bosporus as an isolating geographic barrier. All the samples show substantial heterozygosity excess, and there was statistically significant evidence of recent bottlenecks. The extent and patterns of genetic divergence indicate that the Anatolian and Thracian populations have probably experienced bottlenecks, and incipient speciation may have occurred in Anatolian populations of B. bombina.

Geographic variation, frequency-dependent selection, and the maintenance of a female-limited polymorphism

A central problem in evolutionary biology is to understand how spatial and temporal variation in selection maintain genetic variation within and among populations. Brown anole lizards (Anolis sagrei) exhibit a dorsal pattern polymorphism that is expressed only in females, which occur in "diamond,""bar," and intermediate "diamond-bar" morphs. To understand the inheritance of this polymorphism, we conducted a captive breeding study that refuted several single-locus models and supported a two-locus mode of inheritance. To describe geographic variation in morph frequencies, we surveyed 13 populations from two major islands in The Bahamas. Morph frequencies differed substantially between major islands but were highly congruent within each island. Finally, we measured viability selection on each island to test two hypotheses regarding the maintenance of the polymorphism: (1) that spatial variation in selection maintains variation in morph frequencies between islands, and (2) that temporal variation in selection across years maintains variation within islands. Although bar females had relatively lower survival where they were rare, our data do not otherwise suggest that selection varies spatially between islands. However, diamond-bar females were subject to positive frequency-dependent selection across years, and the relative fitness of bar and diamond females alternated across years. We propose that this polymorphism is maintained by temporal variation in selection coupled with the sheltering of alleles via a two-locus inheritance pattern and sex-limited expression.

A Müllerian mimicry ring in Appalachian millipedes

Few biological phenomena provide such an elegant and straightforward example of evolution by natural selection as color mimicry among unrelated organisms. By mimicking the appearance of a heavily defended aposematic species, members of a second species gain protection from predators and, potentially, enhanced fitness. Mimicking a preexisting warning advertisement is economical because a potentially costly novel one can be avoided; simultaneously, the addition of more aposematic individuals enhances the overall warning effect. The better-known mimetic systems comprise tropical taxa, but here, we show a remarkable example of color mimicry in 7 species of blind, cyanide-generating millipedes endemic to the Appalachian Mountains of temperate North America. Because these millipedes lack eyes, there is no sexual selection or intraspecific signaling for coloration, providing an ideal system for mimicry studies. We document a Müllerian symbiosis where unrelated species vary in color and pattern over geographical space but appear identical where they co-occur. By using spectral color data, estimations of evolutionary history, and detailed field observations of species abundance, we test 4 predictions of Müllerian mimicry theory and begin to unravel the story of an elaborate mimetic diversification in the forests of Appalachia.

Empirical study of hybrid zone movement

Hybrid zones are 'natural laboratories' for studying the origin, maintenance and demise of species. Theory predicts that hybrid zones can move in space and time, with significant consequences for both evolutionary and conservation biology, though such movement is often perceived as rare. Here, a review of empirical studies of moving hybrid zones in animals and plants shows 23 examples with observational evidence for movement, and a further 16 where patterns of introgression in molecular markers could be interpreted as signatures of movement. The strengths and weaknesses of methods used for detecting hybrid zone movement are discussed, including long-term replicated sampling, historical surveys, museum/herbarium collections, patterns of relictual populations and introgression of genetic markers into an advancing taxon. Factors governing hybrid zone movement are assessed in the light of the empirical studies, including environmental selection, competition, asymmetric hybridization, dominance drive, hybrid fitness, human activity and climate change. Hybrid zone movement means that untested assumptions of stability in evolutionary studies on hybrid zone can lead to mistaken conclusions. Movement also means that conservation effort aimed at protecting against introgression could unwittingly favour an invading taxon. Moving hybrid zones are of wide interest as examples of evolution in action and possible indicators of environmental change. More long-term experimental studies are needed that incorporate reciprocal transplants, hybridization experiments and surveys of molecular markers and population densities on a range of scales.

Sex determination in Chlamydomonas

The sex-determination system of the unicellular green alga, Chlamydomonas reinhardtii, is governed by genes in the mating-type (MT) locus and entails additional genes located in autosomes. Gene expression is initiated by nitrogen starvation, and cells differentiate into plus or minus gametes within 6h. Reviewed is our current understanding of gametic differentiation and fertilization, initiation of zygote development, and the uniparental inheritance of organelle genomes.

Quantifying antagonistic epistasis in a multifunctional RNA secondary structure of the Rous sarcoma virus

Recent studies have suggested that antagonistic epistasis (i.e. mutations having smaller effects in combination than alone) may be common among RNA viruses, in contrast to other biological systems. Here, by re-analysing previously published data from a random viral library, selection and epistasis coefficients were estimated in the U5-IR stem and loop of theRous sarcoma virus, a region that adopts a conserved secondary structure and is involved in various essential steps of viral infection. The estimated mutational fitness effects are extremely high and genetic interactions are antagonistic on average. This pattern might be representative of RNA virus genomes, which show high compaction and frequent secondary structures. The implications for RNA virus adaptability are explored.

Altruism, sex, and inbreeding when the genotype–phenotype map is additive

Recently published theoretical results suggest that, in a sexual population, when genotypes code for phenotypes in a complex manner, it is possible for altruistic genotypes to spread through a metapopulation (i.e. through a collection of subpopulations). This spread tends to occur during periods when the environment deteriorates throughout the metapopulation. By contrast, under asexual reproduction, non-altruistic genotypes seem to be favoured, at least when subpopulations are substantial in size. The most relevant previous study makes use of Kauffman and Levin's "NK model" as a way to relate genotypes to fitness. Unfortunately, there are both conceptual and technical problems with the application of the NK model to populations that contain many different genotypes (e.g. polymorphic diploid populations with more than a few loci under selection). The present study presents a more tractable and biologically plausible model to study the causal relationship between sexual reproduction and altruism. In particular, phenotypes are determined by additive interactions among alleles at different loci in a diploid genome, with up to 200 loci under selection. In addition, subpopulations are substantially larger than those considered in the most relevant previous work. The results show that, so long as there are multiple "fitness peaks" in "phenotype space", the additive genotype-phenotype map leads to results that are similar to those from the NK model. Various parameters are manipulated in an effort to discover the determinants of altruistic and non-altruistic outcomes. The findings should facilitate further investigations, and they should help to establish the plausibility of the suggested relationship between sexual reproduction and altruism. The results also suggest that inbreeding can lead to a similar result as asexuality. That is, inbreeding seems to enhance the probability that altruistic phenotypes will be eliminated.

Epistasis and the adaptability of an RNA virus

We have explored the patterns of fitness recovery in the vesicular stomatitis RNA virus. We show that, in our experimental setting, reversions to the wild-type genotype were rare and fitness recovery was at least partially driven by compensatory mutations. We compared compensatory adaptation for genotypes carrying (1) mutations with varying deleterious fitness effects, (2) one or two deleterious mutations, and (3) pairs of mutations showing differences in the strength and sign of epistasis. In all cases, we found that the rate of fitness recovery and the proportion of reversions were positively affected by population size. Additionally, we observed that mutations with large fitness effect were always compensated faster than mutations with small fitness effect. Similarly, compensatory evolution was faster for genotypes carrying a single deleterious mutation than for those carrying pairs of mutations. Finally, for genotypes carrying two deleterious mutations, we found evidence of a negative correlation between the epistastic effect and the rate of compensatory evolution.

The promise and peril of continuous in vitro evolution

Experimental evolution methods can be used to address and illuminate issues central to the understanding of evolutionary theory. One of the most powerful of these methods involves the in vitro evolution of nucleic acid enzymes, taking advantage of the direct relationship between the genotype of a nucleic acid sequence and the phenotype of its associated catalytic function. This review and commentary focuses on the past, present, and future potential of systems for the continuous in vitro evolution of nucleic acid enzymes as tools for modeling evolutionary processes in biology. It offers a candid appraisal of both the strengths and the limitations of these systems.

Sex causes altruism. Altruism causes sex. Maybe

This study presents a mathematical model in which the fitness of an individual depends on the individual's genotype (individual effects) and on the genotypes of other members of the individual's local group (group effects). The findings suggest that, if phenotypes are a result of complex interactions between genes at different loci, then fitness-enhancing group effects may become common in sexual populations. The spread of fitness-enhancing group effects is facilitated when environmental conditions sometimes deteriorate temporarily. This is so even if the genotypes with the highest group effects also tend to have relatively low individual effects. In this sense, the process described here can lead to the evolution of altruism. By contrast, when populations are asexual it appears that group effects are much less important in determining the outcome of evolution. Thus, in nature, asexual populations may tend to be characterized by more antagonistic interactions than those that typically prevail when reproduction is sexual. This might help to explain why asexual lineages are prone to rapid extinction.

Adaptation to the deleterious effects of antimicrobial drug resistance mutations by compensatory evolution

Compensatory mutations, due to their ability to mask the deleterious effects of another mutation, are important for the adaptation and evolution of most organisms. Resistance to antibiotics, antivirals, antifungals, herbicides and insecticides is usually associated with a fitness cost. As a result of compensatory evolution, the initial fitness costs conferred by resistance mutations (or other deleterious mutations) can often be rapidly and efficiently reduced. Such compensatory evolution is potentially of importance for (i) the long-term persistence of drug resistance, (ii) reducing the rate of fitness loss associated with the accumulation of deleterious mutations in small asexual populations, and (iii) the evolution of complexity of cellular processes.

Comment on "Epigenetics and the renaissance of heresy"

Lamarckian inheritance (i.e., inheritance of acquired character) and Richard Golschmidt's concept of "systemic mutations" and their role in macroevolution have been two of the most controversial topics in the history of evolutionary biology. The concept of Lamarckian inheritance was put to rest first by Weismann's germplasm theory and experiment and later by the discovery of Mendelian inheritance. Goldschmidt's theory of macroevolution by systemic mutations was put to rest by the discovery of DNA's structure and subsequent demonstration showing allelic variation as the basis for genetic and phenotypic differences observed among organisms. Some authors are using recent demonstrations of epigenetic inheritance in higher organisms to support Lamarckian inheritance and Golschmidt's theory of macroevolution by systemic mutations. In this paper, I show that the recent discoveries related to mutations, such as the so called "directed" mutations in bacteria, and epigenetic inheritance in higher organisms are basically an extension of the notion of "mutation" and thus of the concept of "heritable variation" required for evolution. While the new discoveries of the laws of developmental transformations are enriching our knowledge of the intricate relationship between genotype and phenotype, the findings of epigenetic inheritance do not challenge the basic tenets of the neo-Darwinian theory of evolution, as other than producing new variation no new processes of evolutionary change have been added to the ones we already know — mutation, migration, selection, and drift.Key words: neo-Darwinian theory of evolution, epigenetics, Lamarckian inheritance, systemic mutations, speciation, macroevolution.

PERSPECTIVE: MODELS OF SPECIATION: WHAT HAVE WE LEARNED IN 40 YEARS?

Theoretical studies of speciation have been dominated by numerical simulations aiming to demonstrate that speciation in a certain scenario may occur. What is needed now is a shift in focus to identifying more general rules and patterns in the dynamics of speciation. The crucial step in achieving this goal is the development of simple and general dynamical models that can be studied not only numerically but analytically as well. I review some of the existing analytical results on speciation. I first show why the classical theories of speciation by peak shifts across adaptive valleys driven by random genetic drift run into trouble (and into what kind of trouble). Then I describe the Bateson-Dobzhansky-Muller (BDM) model of speciation that does not require overcoming selection. I describe exactly how the probability of speciation, the average waiting time to speciation, and the average duration of speciation depend on the mutation and migration rates, population size, and selection for local adaptation. The BDM model postulates a rather specific genetic architecture of reproductive isolation. I then show exactly why the genetic architecture required by the BDM model should be common in general. Next I consider the multilocus generalizations of the BDM model again concentrating on the qualitative characteristics of speciation such as the average waiting time to speciation and the average duration of speciation. Finally, I consider two models of sympatric speciation in which the conditions for sympatric speciation were found analytically. A number of important conclusions have emerged from analytical studies. Unless the population size is small and the adaptive valley is shallow, the waiting time to a stochastic transition between the adaptive peaks is extremely long. However, if transition does happen, it is very quick. Speciation can occur by mutation and random drift alone with no contribution from selection as different populations accumulate incompatible genes. The importance of mutations and drift in speciation is augmented by the general structure of adaptive landscapes. Speciation can be understood as the divergence along nearly neutral networks and holey adaptive landscapes (driven by mutation, drift, and selection for adaptation to a local biotic and/or abiotic environment) accompanied by the accumulation of reproductive isolation as a by-product. The waiting time to speciation driven by mutation and drift is typically very long. Selection for local adaptation (either acting directly on the loci underlying reproductive isolation via their pleiotropic effects or acting indirectly via establishing a genetic barrier to gene flow) can significantly decrease the waiting time to speciation. In the parapatric case the average actual duration of speciation is much shorter than the average waiting time to speciation. Speciation is expected to be triggered by changes in the environment. Once genetic changes underlying speciation start, they go to completion very rapidly. Sympatric speciation is possible if disruptive selection and/or assortativeness in mating are strong enough. Sympatric speciation is promoted if costs of being choosy are small (or absent) and if linkage between the loci experiencing disruptive selection and those controlling assortative mating is strong.

Helicobacter pylori tissue tropism: mouse-colonizing strains can target different gastric niches

Studies with the mouse-adapted Helicobacter pylori strain SS1 had supported an idea that infections by this pathogen start in the gastric antrum and spread to the corpus after extensive mucosal damage. This paper shows that the unrelated strain X47 colonizes the corpus preferentially. Differences between strains in preferred gastric region were detected by co-inoculating mice with a mixture of SS1 and X47, and genotyping H. pylori recovered after 2-8 weeks of infection by vacA s allele PCR and RAPD fingerprinting. Mixed infections were found in each of 59 co-inoculated young C57BL/6J mice. On average, however, SS1 was fourfold more abundant than X47 in the antrum and X47 was threefold more abundant than SS1 in the corpus. Similar results were obtained in mice inoculated first with one strain and then the other strain 2 weeks later. SS1 was even more abundant in the antrum of elderly (>1 year old) mice (97 % of isolates). Qualitatively similar SS1 and X47 tissue distributions were seen using unrelated mouse lines (AKR/J, A/J, DBA/2J, BALB/cJ, LG/J, SM/J), but with significantly different SS1 : X47 ratios in some cases. These results suggest the existence of at least two distinct gastric niches whose characteristics may be affected by host genotype and age (physiology), and indicate that strains differ in how effectively they colonize each niche. Differences among gastric regions and the mixed infections that these allow may contribute to H. pylori diversity and genome evolution.

The fdxA ferredoxin gene can down-regulate frxA nitroreductase gene expression and is essential in many strains of Helicobacter pylori

Very few examples of metabolic regulation are known in the gastric pathogen Helicobacter pylori. An unanticipated case was suggested, however, upon finding two types of metronidazole (Mtz)-susceptible strains: type I, in which frxA (which encodes a nitroreductase that contributes to Mtz susceptibility) is quiescent, and type II, in which frxA is well expressed. Here we report that inactivation of the fdxA ferredoxin gene (hp277) in type I strains resulted in high-level frxA expression (in effect, making them type II). However, fdxA null derivatives were obtained from only 6 of 32 type I strains tested that were readily transformed with an frxA::aphA marker. This suggested that fdxA is often essential. This essentiality was overcome in 4 of 20 strains by inactivating frxA, which suggested both that frxA overexpression is potentially deleterious and also that fdxA has additional, often vital roles. With type II strains, in contrast, fdxA null derivatives were obtained in 20 of 23 cases tested. Thus, fdxA is dispensable in most strains that normally exhibit (and tolerate) strong frxA expression. We propose that restraint of frxA expression helps maintain balanced metabolic networks in most type I strains, that other homeostatic mechanisms predominate in type II strains, and that these complex results constitute a phenotypic manifestation of H. pylori's great genetic diversity.

Near-neutrality in evolution of genes and gene regulation

The nearly neutral theory contends that the interaction of drift and selection is important and occurs at various levels, including synonymous and nonsynonymous substitutions in protein coding regions and sequence turnover of regulatory elements. Recent progress of the theory is reviewed, and the interaction between drift and selection is suggested to differ at these different levels. Weak selective force on synonymous changes is stable, whereas its consequence on nonsynonymous changes depends on environmental factors. Selection on differentiation of regulatory elements is even more dependent on environmental factors than on amino acid changes. Of particular significance is the role of drift in the evolution of gene regulation that directly participates in morphological evolution. The range of near neutrality depends on the effective size of the population that is influenced by selected linked loci. In addition to the effective population size, molecular chaperones such as heat shock protein 90 have significant effects on the range of near neutrality.