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Combining evolutionary games with adaptive networks, an entangled model between strategy evolution and structure adaptation is researched in this paper. We consider a large population of cooperators C and defectors D placed in the networks, playing the repeated prisoner׳s dilemma (PD) games. Because of the conflicts between social welfare and personal rationality, both strategy and structure are allowed to change. In this paper, the dynamics of strategy originates form the partner imitation based on social learning and the dynamics of structure is driven by the active linking and neighbourhood reaction. Notably, the neighbourhood reaction is investigated considering the changes of interfaces between cooperators and defectors, where some neighbours may get away from the interface once the focal agent changes to different strategy. A rich landscape is demonstrated by changing various embedding parameters, which sheds light upon that reacting promptly to the shifted neighbour will promote the prevalence of cooperation. Our model encapsulates the dynamics of strategy, reaction and structure into the evolutionary games, which manifests some intriguing principles in the competition between two groups in natural populations, artificial systems and even human societies. [ABSTRACT FROM AUTHOR]

Effective stakeholder involvement is crucial for the management of protected areas, especially when new challenges like adaptation to climate change need to be addressed. Under these circumstances, science-based stakeholder involvement is required. However, there is often a gap between the information produced by science and the need for information from stakeholders. Along with the design and implementation of adaptive management strategies and policies, efforts must be taken to adjust messages about conservation and adaptation issues, to make them easier to understand, relevant and acceptable for stakeholders. In this paper, the experience of closing the gap between scientific information and the user needs of stakeholders in the Biebrza Valley is documented. The requirements of efficient stakeholder dialogue and the raising of awareness are then indicated. We conclude that many attempts to raise awareness of environmental conservation require improvements. Messages often need to be adjusted for different stakeholders and their various perception levels to efficiently anticipate the potential impacts of the changing climate on ecosystem management. We also revealed that the autonomous adaptation measures implemented by stakeholders to mitigate impacts of climatic change often contradict adaptive management planned and implemented by environmental authorities. We conclude that there is a demand for boundary spanners that can build a bridge between complex scientific outputs and stakeholder needs. [ABSTRACT FROM AUTHOR]

Abstract: The Namib is a relatively well-studied hyperarid desert. Much of the research effort was coordinated through the institutional framework of the Gobabeb Research and Training Centre, which was established in the middle of this desert fifty years ago. The initial discoveries focused on the Namib''s remarkably high biodiversity and adaptations to desert conditions, analysed against the foundations of research into this desert''s particular climate, geomorphology and geology. The antiquity of this desert, its extreme hyperaridity, and strong climatic gradients provided unusual windows into ecosystem drivers in arid lands, past and present. The Gobabeb Centre itself evolved to translate much of its knowledge into application and is today geared to increase this trend even further, driven by the urgent need for knowledge-based environmental management, such as ecological restoration of mining areas. The current volume collates nine papers which review a cross-section of Namib research, with special focus on projects conducted through Gobabeb. These papers concern different facets of geomorphology where Namib research has led global understanding, reviewed in three papers, and one climatological review of the moisture regime. A review of reptile research illustrates the relationship between biodiversity processes and environmental factors, which is further sharpened in a comparison of dune lizard ecology between continents. The review of botanical research in the Central Namib fittingly binds much of the accumulated knowledge of desert plants into a detailed vegetation map. A review of research on the highly variable ephemeral river systems of the Namib illustrates how academic knowledge accumulated at Gobabeb connects to applied research, which is also the topic of the final paper concerning the knowledge gaps and research needs to provide the information required for ecological restoration. [Copyright &y& Elsevier]

Abstract: Southern Spain’s semi-arid habitats are a Mediterranean ecosystem modelled mainly by historic factors which make them unique in comparison with North African deserts. Southern Spanish vertebrates have adapted to the recent emergence of semi-arid habitats in varying degrees of success. This paper reviews the current status of these terrestrial vertebrates (amphibians, reptiles, birds and mammals), their origins and their main features in relation to this biogeographic area. The vertebrate fauna of the semi-arid southeast of the Iberian peninsula differs widely from the one in the semi-arid Maghreb mainly because the former is composed by generalist vertebrates and much less so by species adapted to arid conditions. Moreover, a large fraction of the vertebrates in the semi-arid Iberia does not exploit the semi-arid areas but depends on riparian and human-managed habitats. The species diversity is rather low since only a small fraction of Palaearctic, European or Mediterranean species can adapt to the ecological limitations imposed by aridity and dwell in these semi-arid habitats. Such adaptations comprehend features like trophic plasticity, low morphological specialization, high dispersal ability, shortened life cycles and behavioural mechanisms to exploit the limited resources available. This paper identifies major conservation issues and proposes specific courses of action. [Copyright &y& Elsevier]

A population׳s survival depends on its ability to adapt to constraints impinging upon it. As such, adaptation is at the heart of an increasing number of theoretical models. In this paper, we propose a bottom-up evolutionary model to explore the relationship between individual evolutionary dynamics and population-level survival. To do so, we extend a well-established model of gene network evolution by introducing a cost for reproduction. As a result population sizes fluctuate and populations can even go extinct. We find that if a population survives a small and critical number of generations, it will reach a quasi-stationary state which ensures long-term survival. In a constant environment, individual adaptation occurs in response to changes in a populations genetic composition. We show that genetic compatibility increases over generations as a by-product of selection for robustness, thus preventing extinction. We also demonstrate that the number of reproductive opportunities per individual, initial population size, and mutation rates all influence population survival. Finally, mixing different populations reveals that individual properties of gene networks co-evolve with the genetic composition of the population in order to maximize an individuals reproductive success. [ABSTRACT FROM AUTHOR]

Evolutionary games typically come with the interplays between evolution of individual strategy and adaptation to network structure. How these dynamics in the co-evolution promote (or obstruct) the cooperation is regarded as an important topic in social, economic, and biological fields. Combining spatial selection with partner choice, the focus of this paper is to identify which neighbour should be selected as a role to imitate during the process of co-evolution. Age, an internal attribute and kind of local piece of information regarding the survivability of the agent, is a significant consideration for the selection strategy. The analysis and simulations presented, demonstrate that older partner selection for strategy imitation could foster the evolution of cooperation. The younger partner selection, however, may decrease the level of cooperation. Our model highlights the importance of agent׳s age on the promotion of cooperation in evolutionary games, both efficiently and effectively. [ABSTRACT FROM AUTHOR]

Mediterranean trout populations display a diversity of phenotypes, representing a valuable model for the study of adaptation and a puzzling dilemma for taxonomists and biogeographers, which is further entangled by the widespread introgression of allochthonous genes. In this paper we analysed DNA polymorphism at multiple loci (sequence variation of the mitochondrial control region and eight nuclear fragments and length variation at eleven nuclear microsatellite loci) in representative samples of the autochthonous taxonomic diversity described in Italian trout populations ( Salmo marmoratus , S. carpio , S. cenerinus , S. cettii and S. fibreni ) and in samples from hatchery-originated strains of Atlantic S. trutta . We employed model-based clustering and Approximate Bayesian Computation in order to: (i) describe the phylogeographic structure of Italian autochthonous trout populations; (ii) evaluate a set of evolutionary/biogeographic models. The inclusion of hatchery-originated strains allowed to account for man-mediated allochthonous introgression in Italian populations. Our results (i) showed that the analysed sample consists of two main autochthonous evolutionary lineages, including the marble trout populations on one side (‘marble’ lineage) and the three peninsular populations of S. cettii , S. cenerinus and S. fibreni on the other side (‘peninsular’ lineage); (ii) indicated that S. carpio originated from a ‘peninsular’ population, with a possible, limited contribution from the ‘marble’ lineage; (iii) pointed out that the ‘marble’ lineage started diverging before the separation of the ‘peninsular’ lineage from Atlantic S. trutta ; (iv) suggested that a model of divergence involving gene flow from the ‘peninsular’ population into the ancestral gene pool of ‘marble’ trout is most consistent with the genetic data; (v) provided evidence that the autochthonous trout gene pools in the Tyrrhenian and Adriatic basins of the Italian peninsula started diverging very recently (most likely after the last glacial maximum). [ABSTRACT FROM AUTHOR]

Abstract: Energy storage is a common adaptation of fish living in seasonal environments. For some species, the energy accumulated during the growing season, and stored primarily as lipids, is crucial to preventing starvation mortality over winter. Thus, in order to understand the adaptive responses of fish life history to climate, it is important to determine how energy should be allocated to storage and how it trades off with the other body components that contribute to fitness. In this paper, we extend previous life history theory to include an explicit representation of how the seasonal allocation of energy to storage acts as a constraint on fish growth. We show that a strategy that privileges allocation to structural mass in the first part of the growing season and switches to storage allocation later on, as observed empirically in several fish species, is the strategy that maximizes growth efficiency and hence is expected to be favored by natural selection. Stochastic simulations within this theoretical framework demonstrate that the relative performance of this switching strategy is robust to a wide range of fluctuations in growing season length, and to moderate short-term (i.e., daily) fluctuations in energy intake and/or expenditure within the growing season. We then integrate this switching strategy with a biphasic growth modeling framework to predict typical growth rates of walleye Sander vitreus, a cool water species, and lake trout Salvelinus namaycush, a cold water specialist, across a climatic gradient in North America. As predicted, growth rates increased linearly with the duration of the growing season. Regression line intercepts were negative, indicating that growth can only occur when growing season length exceeds a threshold necessary to produce storage for winter survival. The model also reveals important differences between species, showing that observed growth rates of lake trout are systematically higher than those of walleye in relatively colder lakes. This systematic difference is consistent with both (i) the expected superior capacity of lake trout to withstand harsh winter conditions, and (ii) some degree of counter gradient adaptation of lake trout growth capacity to the climatic gradient covered by our data. [Copyright &y& Elsevier]

Abstract: Protein–Protein interaction (PPI) is one of the most important data in understanding the cellular processes. Many interesting methods have been proposed in order to predict PPIs. However, the methods which are based on the sequence of proteins as a prior knowledge are more universal. In this paper, a sequence-based, fast, and adaptive PPI prediction method is introduced to assign two proteins to an interaction class (yes, no). First, in order to improve the presentation of the sequences, twelve physicochemical properties of amino acid have been used by different representation methods to transform the sequence of protein pairs into different feature vectors. Then, for speeding up the learning process and reducing the effect of noise PPI data, principal component analysis (PCA) is carried out as a proper feature extraction algorithm. Finally, a new and adaptive Learning Vector Quantization (LVQ) predictor is designed to deal with different models of datasets that are classified into balanced and imbalanced datasets. The accuracy of 93.88%, 90.03%, and 89.72% has been found on S. cerevisiae, H. pylori, and independent datasets, respectively. The results of various experiments indicate the efficiency and validity of the method. [Copyright &y& Elsevier]

Abstract: In this paper, with the methods of adaptive dynamics and critical function analysis, we investigate the evolutionary branching phenomenon of predator species. We assume that both the prey and predators are density-dependent and the predator’s attack ability can adaptively evolve, but this has a cost in terms of its death rate. First, we identify the general properties of trade-off relationships that allow for a continuously stable strategy and evolutionary branching in the predator strategy. It is found that if the trade-off curve is weakly concave near the singular strategy, then the singular strategy may be an evolutionary branching point. Second, we find that after the branching has occurred in the predator strategy, if the trade-off curve is convex–concave–convex, the predator species will eventually evolve into two different types, which can stably coexist on the much longer evolutionary timescale and no further branching is possible. [Copyright &y& Elsevier]

Abstract: This paper explores the evolution of land use and natural resource management strategies over the past twenty to fifty years in a remote Sahelian region. The empirical example is Karagou village in SE Niger. Building on an in-depth survey from 1992 and a targeted, follow-up analysis of contemporary land use strategies in 2011, the change process is scrutinized. The analysis uses the conceptual lenses of land systems science, human–environmental timelines, and the notion of multiple exposures. Enabling and constraining conditions for local livelihoods in terms of the resource base (landscape, water, and population) are described. Results characterize how land use strategies have developed and how local people opportunistically use different landscape elements such as dune landscapes, valley bottoms (bas-fonds) and oases (cuvettes). Major concerns are rainfall variability, saturation of cropland, and perceived dwindling groundwater resources. It is concluded that the land use and livelihood strategies have remained remarkably stable in the face of the changing socio-ecological fringe conditions, but that this situation may hamper a sustainable transformation. [Copyright &y& Elsevier]

Abstract: The rich theory of infectious disease modelling using the Susceptible–Infectious–Recovered () framework is mainly based on the assumption of a well-mixed population, under which evolutionary behaviours (typically derived using adaptive dynamics) are shown to depend critically on the qualitative features of a virulence-transmission trade-off. Spatial extensions of this work, using simulation studies, show multiple evolutionary outcomes, which strongly depend on trade-off shape and, additionally, the length scale of the infectious process. In this paper, we aim to shed analytical insight into the mechanisms underlying these spatial evolutionary outcomes. In particular, why there is a qualitative difference observed in the evolutionary predicted virulence rates between linear and decelerating trade-offs between transmission and virulence and how recovery can weaken the effect of space. We use both pair approximations and cellular automata to model the spatial populations and the analysis exploits small neighbourhood variations in the spatial settings. The evolutionary outcomes are derived using adaptive dynamics. [Copyright &y& Elsevier]

Abstract: Genetic control of enzyme activity drives metabolic adaptations to environmental changes, and therefore the feedback interaction between gene expression and metabolism is essential to cell fitness. In this paper we develop a new formalism to detect the equilibrium regimes of an unbranched metabolic network under transcriptional feedback from one metabolite. Our results indicate that one-to-all transcriptional feedback can induce a wide range of metabolic phenotypes, including mono-, multistability and oscillatory behavior. The analysis is based on the use of switch-like models for transcriptional control and the exploitation of the time scale separation between metabolic and genetic dynamics. For any combination of activation and repression feedback loops, we derive conditions for the emergence of a specific phenotype in terms of genetic parameters such as enzyme expression rates and regulatory thresholds. We find that metabolic oscillations can emerge under uniform thresholds and, in the case of operon-controlled networks, the analysis reveals how nutrient-induced bistability and oscillations can emerge as a consequence of the transcriptional feedback. [Copyright &y& Elsevier]

Abstract: In this paper, we study the predator–prey coevolutionary dynamics when a prey''s defense and a predator''s offense change in an adaptive manner, either by genetic evolution or phenotypic plasticity, or by behavioral choice. Results are: (1) The coevolutionary dynamics are more likely to be stable if the predator adapts faster than the prey. (2) The prey population size can be nearly constant but the predator population can show very large amplitude fluctuations. (3) Both populations may oscillate in antiphase. All of these are not observed when the handling time is short and the prey''s density dependence is weak. (4) The population dynamics and the trait dynamics show resonance: the amplitude of the population fluctuation is the largest when the speed of adaptation is intermediate. These results may explain experimental studies with microorganisms. [Copyright &y& Elsevier]

Abstract: Different physical features of an organism are often measured concurrently, because their correlations can be used as predictors of longevity, future health, or adaptability to an ecological niche. Since, in general, we do not know a priori if the temporal variations in the measured quantities are causally related, it may be useful to have a method that could help us to identify possible correlations and to obtain parameters that may vary from population to population. In this paper we develop a procedure that may detect underlying relationships. We do this by generalizing the recently introduced concept of phenomenological universalities to the complex field. In this generalization, allometric growth is described by a complex function, whose real and imaginary parts represent two phenotypic traits of the same organism. As particular solutions of the resulting problem, we obtain generalizations of the Gompertz and the von Bertalanffy–West growth equations. We then apply the procedure to two biological systems in order to show how to determine the existence of mutual interference between trait variations. [Copyright &y& Elsevier]

Abstract: Interpretations of the postcranial anatomy of East African early and middle Miocene large-bodied hominoids (e.g., Proconsul, Afropithecus, Turkanapithecus, Nacholapithecus) have suggested that these diverse primates utilized positional behaviors dominated by arboreal quadrupedalism. Preliminary descriptions of the Equatorius africanus partial skeleton (KNM-TH 28860) and other forelimb specimens, however, have argued that this animal relied more on terrestrial locomotion compared to its contemporaries, possibly similar to extant large papionin monkeys. In this paper, we reevaluate this interpretation by examining intrinsic hand proportions based on the lengths of the third proximal phalanx and fifth metacarpal in Equatorius in reference to a large sample of extant catarrhine primate taxa. We focused on the lengths of these hand bones because the ratio between phalanx and metacarpal lengths has been previously documented to discriminate terrestrial from arboreal mammalian taxa, including primates. The Equatorius hand displays semi-terrestrial hand proportions with a relatively shorter proximal phalanx compared to most arboreal monkeys. Its proximal phalanx, however, is relatively longer than those of habitually terrestrial monkeys (e.g., Theropithecus, Papio). Accordingly, although Equatorius retains some arboreal quadrupedal characteristics, these results corroborate the previous inference that it engaged in more terrestrial locomotion than earlier Miocene apes such as Proconsul. We suggest that the postcranial skeleton of Equatorius evinces the earliest signs of semi-terrestriality in the hominoid fossil record. It is likely that the terrestrial specialization utilized by living hominoids, e.g., knuckle-walking, evolved separately. [Copyright &y& Elsevier]