When does the incongruence length difference test fail?

This paper examines the efficiency of the incongruence length difference test (ILD) proposed by Farris et al. (1994) for assessing the incongruence between sets of characters. DNA sequences were simulated under various evolutionary conditions: (1) following symmetric or asymmetric trees, (2) with various mutation rates, (3) with constant or variable evolutionary rates along the branches, and (4) with different among-site substitution rates. We first compared two sets of sequences generated along the same tree and under the same evolutionary conditions. The probability of a Type-I error (wrongly rejecting the true hypothesis of congruence) was substantially below the standard 5% level of significance given by the ILD test; this finding indicates that the choice of the 5% level is rather conservative in this case. We then compared two data sets, still generated along the same tree, but under different evolutionary conditions (constant vs. variable evolutionary rate, homogeneity vs. heterogeneity rate of substitution). Under these conditions, the probability of rejecting the true hypothesis of congruence was greater than the 5% given by the ILD test and increased with the number of sites and the degree to which the tree was asymmetric. Finally, the comparison of the two data sets, simulated under contrasting tree structures (symmetric vs. asymmetric) but under the same evolutionary conditions, led us to reject the hypothesis of congruence, albeit weakly, particularly when the number of informative sites was low and among-site substitution rate heterogeneous. We conclude that the ILD test has only limited power to detect incongruence caused by differences in the evolutionary conditions or in the tree topology, except when numerous characters are present and the substitution rate is homogeneous from site to site.     

Thermodynamic extremal principles in evolution

Summary An evolutionary ecosystem may be described in terms of a quasi autocatalytic model, i.e. in terms of a sequence of different autocatalytic systems. Such a sequence can exhibit considerable evolutionary change (for example, adjustment of various rate constants) even if the dissipation function remains essentially the same. Under these conditions the dissipation is always a monotonically increasing function of the concentration of catalyst (biomass) and certain rate constants (the catalytic capacity). Biomass and catalytic capacity are complementary in the sense that the quasi autocatalytic system always assumes a steady state by varying these quantities in the opposite direction (all other conditions remaining constant). This means that evolutionary systems cannot exhibit orthogenetic increases in both rate of operation and biomass, at least within any given evolutionary epoch. This has implications for the importance of spatial heterogeneity in stabilizing the behavior of evolutionary systems.     

On the reconstruction of an evolutionary order

The problem of reconstructing an evolutionary order from various taxonomic criteria may be thought of as specifying a computer program or evolution function e that takes as input the taxonomic orders based on the criteria and produces a single composite evolutionary order as output. We specify four conditions that any such e should satisfy. Taken separately the conditions seem reasonable but taken together they are inconsistent.     

Evolutionary genetics of plant adaptation

Plants provide unique opportunities to study the mechanistic basis and evolutionary processes of adaptation to diverse environmental conditions. Complementary laboratory and field experiments are important for testing hypotheses reflecting long-term ecological and evolutionary history. For example, these approaches can infer whether local adaptation results from genetic tradeoffs (antagonistic pleiotropy), where native alleles are best adapted to local conditions, or if local adaptation is caused by conditional neutrality at many loci, where alleles show fitness differences in one environment, but not in a contrasting environment. Ecological genetics in natural populations of perennial or outcrossing plants can also differ substantially from model systems. In this review of the evolutionary genetics of plant adaptation, we emphasize the importance of field studies for understanding the evolutionary dynamics of model and nonmodel systems, highlight a key life history trait (flowering time) and discuss emerging conservation issues.     

Change and aging senescence as an adaptation

Understanding why we age is a long-lived open problem in evolutionary biology. Aging is prejudicial to the individual, and evolutionary forces should prevent it, but many species show signs of senescence as individuals age. Here, I will propose a model for aging based on assumptions that are compatible with evolutionary theory: i) competition is between individuals; ii) there is some degree of locality, so quite often competition will be between parents and their progeny; iii) optimal conditions are not stationary, and mutation helps each species to keep competitive. When conditions change, a senescent species can drive immortal competitors to extinction. This counter-intuitive result arises from the pruning caused by the death of elder individuals. When there is change and mutation, each generation is slightly better adapted to the new conditions, but some older individuals survive by chance. Senescence can eliminate those from the genetic pool. Even though individual selection forces can sometimes win over group selection ones, it is not exactly the individual that is selected but its lineage. While senescence damages the individuals and has an evolutionary cost, it has a benefit of its own. It allows each lineage to adapt faster to changing conditions. We age because the world changes.     

Low evolutionary potential for egg‐to‐adult viability in Drosophila melanogaster at high temperatures

To cope with the increasing and less‐predictable temperature forecasts under climate change, many terrestrial ectotherms will have to migrate or rely on adaptation through plastic or evolutionary means. Studies suggest that some ectotherms have a limited potential to change their upper thermal limits via evolutionary shifts, but research has mostly focused on adult life stages under laboratory conditions. Here we use replicate populations of Drosophila melanogaster and a nested half‐sib/full‐sib quantitative genetic design to estimate heritabilities and genetic variance components for egg‐to‐adult viability under both laboratory and seminatural field conditions, encompassing cold, benign, and hot temperatures in two separate populations. The results demonstrated temperature‐specific heritabilities and additive genetic variances for egg‐to‐adult viability. Heritabilities and genetic variances were higher under cold and benign compared to hot temperatures when tested under controlled laboratory conditions. Tendencies toward lower evolutionary potential at higher temperatures were also observed under seminatural conditions although the results were less clear in the field setting. Overall the results suggest that ectotherms that already experience temperatures close to their upper thermal tolerance limits have a restricted capacity to adapt to higher temperatures by evolutionary means.     

Selective extinction and rapid loss of evolutionary history in the bird fauna

The extinction of species results in a permanent loss of evolutionary history. Recent theoretical studies show that this loss may be proportionally much smaller than the loss of species, but under some conditions can exceed it. Such conditions occur when the phylogenetic tree that describes the evolutionary relationships among species is highly imbalanced due to differences between lineages in past speciation and/or extinction rates. I used the taxonomy by C. G. Sibley and B. L. Monroe Jr to estimate the global loss of bird evolutionary history from historical and predicted extinctions, and to quantify the ensuing changes in balance of the bird phylogenetic tree. In the global bird fauna, evolutionary history is being lost at a high rate, similar to the rate of species extinction. The bird phylogenetic tree is highly imbalanced, and the imbalance is increased significantly by anthropogenic extinction. Historically, the elevated loss of bird evolutionary history has been fuelled mostly by phylogenetic non-randomness in the extinction of species, but the direct effect of tree imbalance is substantial and could dominate in the future.     

Evolutionary stability on graphs

Evolutionary stability is a fundamental concept in evolutionary game theory. A strategy is called an evolutionarily stable strategy (ESS), if its monomorphic population rejects the invasion of any other mutant strategy. Recent studies have revealed that population structure can considerably affect evolutionary dynamics. Here we derive the conditions of evolutionary stability for games on graphs. We obtain analytical conditions for regular graphs of degree k>2. Those theoretical predictions are compared with computer simulations for random regular graphs and for lattices. We study three different update rules: birth-death (BD), death-birth (DB), and imitation (IM) updating. Evolutionary stability on sparse graphs does not imply evolutionary stability in a well-mixed population, nor vice versa. We provide a geometrical interpretation of the ESS condition on graphs.     

Rapid evolutionary adaptation to elevated salt concentrations in pathogenic freshwater bacteria Serratia marcescens

Rapid evolutionary adaptions to new and previously detrimental environmental conditions can increase the risk of invasion by novel pathogens. We tested this hypothesis with a 133‐day‐long evolutionary experiment studying the evolution of the pathogenic Serratia marcescens bacterium at salinity niche boundary and in fluctuating conditions. We found that S. marcescens evolved at harsh (80 g/L) and extreme (100 g/L) salt conditions had clearly improved salt tolerance than those evolved in the other three treatments (ancestral conditions, nonsaline conditions, and fluctuating salt conditions). Evolutionary theories suggest that fastest evolutionary changes could be observed in intermediate selection pressures. Therefore, we originally hypothesized that extreme conditions, such as our 100 g/L salinity treatment, could lead to slower adaptation due to low population sizes. However, no evolutionary differences were observed between populations evolved in harsh and extreme conditions. This suggests that in the study presented here, low population sizes did not prevent evolution in the long run. On the whole, the adaptive potential observed here could be important for the transition of pathogenic S. marcescens bacteria from human‐impacted freshwater environments, such as wastewater treatment plants, to marine habitats, where they are known to infect and kill corals (e.g., through white pox disease).     

Opinion: Is gene mapping in wild populations useful for understanding and predicting adaptation to global change?

Changing environmental conditions will inevitably alter selection pressures. Over the long term, populations have to adapt to these altered conditions by evolutionary change to avoid extinction. Quantifying the ‘evolutionary potential’ of populations to predict whether they will be able to adapt fast enough to forecasted changes is crucial to fully assess the threat for biodiversity posed by climate change. Technological advances in sequencing and high‐throughput genotyping have now made genomic studies possible in a wide range of species. Such studies, in theory, allow an unprecedented understanding of the genomics of ecologically relevant traits and thereby a detailed assessment of the population's evolutionary potential. Aimed at a wider audience than only evolutionary geneticists, this paper gives an overview of how gene‐mapping studies have contributed to our understanding and prediction of evolutionary adaptations to climate change, identifies potential reasons why their contribution to understanding adaptation to climate change may remain limited, and highlights approaches to study and predict climate change adaptation that may be more promising, at least in the medium term.     

When do mixotrophs specialize? Adaptive dynamics theory applied to a dynamic energy budget model

In evolutionary history, several events have occurred at which mixotrophs specialized into pure autotrophs and heterotrophs. We studied the conditions under which such events take place, using the Dynamic Energy Budget (DEB) theory for physiological rules of the organisms' metabolism and Adaptive Dynamics (AD) theory for evolutionary behavior of parameter values. We modeled a population of mixotrophs that can take up dissolved inorganic nutrients by autotrophic assimilation and detritus by heterotrophic assimilation. The organisms have a certain affinity for both pathways; mutations that occur in the affinities enable the population to evolve. One of the possible evolutionary outcomes is a branching point which provides an opportunity for the mixotrophic population to split up and specialize into separate autotrophs and heterotrophs. Evolutionary branching is not a common feature of the studied system, but is found to occur only under specific conditions. These conditions depend on intrinsic properties such as the cost function, the level of the costs and the boundaries of the trait space: only at intermediate cost levels and when an explicit advantage exists to pure strategies over mixed ones may evolutionary branching occur. Usually, such an advantage (and hence evolutionary branching) can be induced by interference between the two affinities, but this result changes due to the constraints on the affinities. Now, only some of the more complicated cost functions give rise to a branching point. In contrast to the intrinsic properties, extrinsic properties such as the total nutrient content or light intensity were found to have no effect on the evolutionary outcomes at all.     

Understanding the establishment success of non-indigenous fishes: lessons from population genetics

During the last 10 years, an increasing number of studies have explored evolutionary aspects of biological invasions. It is becoming increasingly clear that evolutionary processes play an important role during the establishment of non-native species. Genetic drift during the colonization process followed by strong selection imposed through a change in biotic conditions and co-evolutionary disequilibrium set the conditions for rapid evolutionary change in introduced populations. Different hypotheses, which have been proposed to explain how evolutionary and genetic processes, can facilitate invasiveness are explored and their relevance for fish invasions is discussed. Empirical evidence increasingly suggests that admixture after multiple introductions, hybridization between native and non-native species and enemy release can all catalyse the evolution of invasiveness. A number of studies also suggest that genetic bottlenecks might represent less of genetic paradox than previously thought. Much of the theoretical developments and empirical evidence concerning the importance of evolution during biological invasions has been provided from studies on invasive plants. Despite their prominence, fish invasions have received little attention from evolutionary biologists. Recent advances in population genetic analysis such as non-equilibrium methods and genomic techniques such as microarray technology provide suitable tools to address such issues.     

Strong evolutionary equilibrium and the war of attrition

In developing the concept of an evolutionarily stable strategy, Maynard Smith proposed formal conditions for stability. These conditions have since been shown to be neither necessary nor sufficient for evolutionary stability in finite populations. This paper provides a strong stability condition which is sensitive to the population size. It is then demonstrated that in the war of attrition with uncertain rewards there is a unique “strong evolutionary equilibrium” strategy. As the population becomes large this is shown to approach the solution strategy proposed by Bishop, Cannings and Maynard Smith.The analysis is then extended to wars of attrition between different populations. It is concluded that for such contests there is a whole family of potential strong evolutionary equilibria.     

Latitudinal gradients in species diversity and Rapoport's rule revisited: a review of recent work and what can parasites teach us about the causes of the gradients?

A review is given of recent work on latitudinal gradients in species diversity and their explanations, including Rapoport's rule. Energy input, measured by temperature or potential evapotranspiration. correlates best with the gradients. However, such a correlation does not "explain" them. It merely suggests explanations, which may be either different ceilings to diversity set by different energy levels under equilibrium conditions, recent historical events, or a gradient in effective evolutionary time (determined by speed of evolution directly driven by temperature, and by relative constancy of conditions over evolutionary time) under non-equilibrium conditions. Marine parasites are used to show that equilibrium conditions are the exception rather than the rule among animals, It is concluded that latitudinal gradients in species diversity result from a gradient in effective evolutionary time modulated by several other factors. Dispersal abilities of many marine invertebrates are likely to be greater at low than at high latitudes, suggesting an opposite Rapppoport effect.
This is an invited Minireview on the occasion of the 50th anniversary of the Nordic Ecological Society Oikos.     

Effects of exotic species on evolutionary diversification

Exotic species invasions create almost ideal conditions for promoting evolutionary diversification: establishment of allopatric populations in new environmental conditions; altered ecological opportunities for native species; and new opportunities for hybridization between previously allopatric taxa. Here, we review recent studies of the evolutionary consequences of species invasions, revealing abundant and widespread examples of exotic species promoting evolutionary diversification via increased genetic differentiation among populations of both exotic and native species and the creation of new hybrid lineages. Our review indicates that, although the well-documented reductions to biodiversity caused by exotic species might outweigh the increases resulting from diversification, a complete understanding of the net effects of exotic species on biodiversity in the long term will require consideration of both.     

Non-adaptive complexity and biochemical function

Intricate biochemical structures are usually thought to be useful, because natural selection preserves them from degradation by a constant hail of destructive mutations. Biochemists therefore often deliberately disrupt them to understand how complexity improves protein function or fitness. However, evolutionary theory suggests that even useless complexity that never improved fitness can become completely essential if a simple set of evolutionary conditions is fulfilled. We review evidence that stable protein complexes, protein–chaperone interactions, and complexes consisting of several paralogs all fulfill these conditions. This makes reverse genetics or destructive mutagenesis unsuitable for assigning functions to these kinds of complexity. Instead, we advocate that incorporating evolutionary approaches into biochemistry overcomes this difficulty and allows us to distinguish useless from useful biochemical complexity.     

Biological invasion as a natural experiment of the evolutionary processes: introduction of the special feature

Although biological invasion has a devastating impact on biodiversity, it also provides a valuable opportunity for natural experiments on evolutionary responses. Alien populations are often subject to strong natural selection when they are exposed to new abiotic and biotic conditions. Native populations can also undergo strong selection when interacting with introduced enemies and competitors. This special feature aims to highlight how evolutionary studies take advantage of biological invasion and, at the same time, emphasizes how studying evolutionary processes deepens our understanding of biological invasions. We hope this special feature stimulates more invasion studies taking evolutionary processes into account. Those studies should provide fundamental information essential for formulating effective measures in conserving native biodiversity, as well as valuable empirical tests for evolutionary theories.     

Eco-evolutionary feedbacks,adaptive dynamics and evolutionary rescue theory

Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause ‘evolutionary suicide’. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called ‘evolutionary trapping’. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps.     

Evolutionary rescue in vertebrates: evidence,applications and uncertainty

The current rapid rate of human-driven environmental change presents wild populations with novel conditions and stresses. Theory and experimental evidence for evolutionary rescue present a promising case for species facing environmental change persisting via adaptation. Here, we assess the potential for evolutionary rescue in wild vertebrates. Available information on evolutionary rescue was rare and restricted to abundant and highly fecund species that faced severe intentional anthropogenic selective pressures. However, examples from adaptive tracking in common species and genetic rescues in species of conservation concern provide convincing evidence in favour of the mechanisms of evolutionary rescue. We conclude that low population size, long generation times and limited genetic variability will result in evolutionary rescue occurring rarely for endangered species without intervention. Owing to the risks presented by current environmental change and the possibility of evolutionary rescue in nature, we suggest means to study evolutionary rescue by mapping genotype → phenotype → demography → fitness relationships, and priorities for applying evolutionary rescue to wild populations.