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Genetic history and adaptation of Eurasian wild boars inform livestock breeding.

Historical expansions of wild boars (Sus scrofa) across Eurasia have shaped phenotypic variation, genetic diversity, and local adaptation of their populations. The study by Wang et al.1 investigates the demographic history and genetic adaptation of Eurasian wild boars based on 96 whole-genome sequences, informing a critical role of Central Asian populations in their expansions and identifying key genes and variants associated with their local adaptation. Also, the adaptive variants are potentially useful for domestic pig breeding in future.

Animals↗

Senior volunteerism policies at the local level: adaptation and leadership in the 21st century.

This study explores several key senior volunteerism policy issues that need to be addressed from a local perspective in order to meet the challenges of the twenty-first century. Using inputs from a national survey of Voluntary Action Centers, prominent volunteer agencies in the United States, this study examines the impact of the national economy on senior volunteerism, the status of funding, the relationship between local senior volunteerism and employment, the role of risk management, and the affect of an aging society of senior volunteerism.

Aged↗

Local initiatives and adaptation to climate change.

Climate change is expected to lead to an increase in the number and strength of natural hazards produced by climatic events. This paper presents some examples of the experiences of community-based organisations (CBOs) and non-governmental organisations (NGOs) of variations in climate, and looks at how they have incorporated their findings into the design and implementation of local adaptation strategies. Local organisations integrate climate change and climatic hazards into the design and development of their projects as a means of adapting to their new climatic situation. Projects designed to boost the resilience of local livelihoods are good examples of local adaptation strategies. To upscale these adaptation initiatives, there is a need to improve information exchange between CBOs, NGOs and academia. Moreover, there is a need to bridge the gap between scientific and local knowledge in order to create projects capable of withstanding stronger natural hazards.

Community Networks↗

Changes in VOR adaptation after local injection of beta-noradrenergic agents in the flocculus of rabbits.

Noradrenaline (NA) has been implicated as a neuromodulator in plasticity, presumably facilitating adaptive processes. Since the flocculus receives noradrenergic afferents, and ablation of the flocculus interferes with the normal adaptive changes in the VOR gain, experiments were performed to find out whether bilateral injection of monoaminergic substances into the flocculus of rabbits could modify the adaptive changes of the VOR. The visual world surrounding the rabbit was oscillated in opposite direction to the platform on which the rabbit was mounted, which resulted in an adaptive increase in the VOR gain; this adaptation was measured either in light or in darkness. Floccular injection of the beta-agonist isoproterenol did not greatly affect the adaptation of the VOR measured in light. In darkness, however, the increase in gain after injection of isoproterenol was larger than during normal adaptation. The beta-antagonist sotalol reduced the adaptation of the VOR gain significantly in light as well as in darkness. In a control condition without pressure for adaptation (only intermittent testing of the VOR gain over a period of 2.5 h), the gain of the VOR was not significantly affected by similar injections of beta-adrenergic agents. We conclude that the noradrenergic system facilitates the adaptation of the VOR gain to retinal slip in rabbits without affecting the VOR gain directly. At least part of this influence is exerted through beta-receptors located in the cerebellar flocculus.

Adaptation, Physiological↗

Is the Prunella (Lamiaceae) hybrid zone structured by an environmental gradient? Evidence from a reciprocaltransplant experiment.

Hybrid zones may be structured by environmentally independent selection against intrinsically unfit hybrids (tension zone models), or by environmentally dependent fitness differences among parental species and hybrids (ecological selection-gradient models). A 30-m slope in a mountain grassland harbors a hybrid zone of the clonal perennials, Prunella grandiflora and P. vulgaris (Lamiaceae), with P. grandiflora in the upper, P. vulgaris in the lower, and both parental species and P. grandiflora × P. vulgaris Hybrids in a narrow middle part. We found gradients for soil depth and water content, and vegetation height and biomass along the slope. A reciprocal transplant experiment yielded crossing reaction norms for vegetative reproduction. Parental species were locally adapted to their home sites, while the three taxa did not differ in vegetative reproduction in the Hybrid transplant site. Local adaptation for vegetative reproduction of P. grandiflora was mediated through higher survival and that of P. vulgaris through higher ramet number, indicating adaptation of their clonal growth strategies (phalanx vs. guerrilla) to the different habitats. Hybrid performance was intermediate between that of the parental species in all three sites, although Hybrids flowered more often than the parental species in the Hybrid site. Our results support ecological selection-gradient rather than tension zone models.

Journal Article↗

Food-plant effects on larval performance do not translate into differences in fitness between populations of Panolis flammea (Lepidoptera: Noctuidae).

In the UK, Panolis flammea (Denis & Schiffermüller) is a pest of monocultures of non-native lodgepole pine Pinus contorta Douglas, but not of the indigenous host Scots pine P. sylvestrisL. This difference in population dynamics may be due to the adaptation of P. flammea populations to the phenology, chemical composition and natural enemy complement of lodgepole pine. To ascertain if there was local adaptation of P. flammea populations to lodgepole pine, this study tested for improved performance of both larvae and adults on the host plant species from which they were sourced, compared with their performance on the alternative host plant species. No difference was found in the relative mean performance of populations sourced from Scots pine or lodgepole pine plantations, when fed on Scots or lodgepole pine foliage. Larvae grew faster on Scots pine but this difference did not translate into differences in pupal weight, female body weight or fecundity. Indeed, those insects that had fed on lodgepole pine had a longer lifespan than those that had fed on Scots pine, which, if translated into greater probability of mating or higher fecundity, could contribute to the observed outbreak dynamics in the field. The prediction that the observed outbreak dynamics of P. flammea can be explained by the existence of populations locally adapted to lodgepole pine was not supported. These results cast doubt on the use of larval growth parameters as surrogates of fitness in Lepidoptera.

Adaptation, Physiological↗

Structured coalescent processes on different time scales.

It is demonstrated that the structured coalescent model can readily be extended to include phenomena such as partial selfing and background selection through the use of an approximation based on separation of time scales. A model that includes these phenomena, as well as geographic subdivision and linkage to a polymorphism maintained either by local adaptation or by balancing selection, is derived, and the expected coalescence time for a pair of genes is calculated. It is found that background selection reduces coalescence times within subpopulations and allelic classes, leading to a high degree of apparent differentiation. Extremely high levels of subpopulation differentiation are also expected for regions of the genome surrounding loci important in local adaptation. These regions will be wider the stronger the local selection, and the higher the selfing rate.

Alleles↗

Geographical patterns of adaptation within a species' range: interactions between drift and gene flow.

We use individual-based stochastic simulations and analytical deterministic predictions to investigate the interaction between drift, natural selection and gene flow on the patterns of local adaptation across a fragmented species' range under clinally varying selection. Migration between populations follows a stepping-stone pattern and density decreases from the centre to the periphery of the range. Increased migration worsens gene swamping in small marginal populations but mitigates the effect of drift by replenishing genetic variance and helping purge deleterious mutations. Contrary to the deterministic prediction that increased connectivity within the range always inhibits local adaptation, simulations show that low intermediate migration rates improve fitness in marginal populations and attenuate fitness heterogeneity across the range. Such migration rates are optimal in that they maximize the total mean fitness at the scale of the range. Optimal migration rates increase with shallower environmental gradients, smaller marginal populations and higher mutation rates affecting fitness.

Adaptation, Biological↗

VO2peak and the gas-exchange anaerobic threshold during incremental arm cranking in able-bodied and paraplegic men.

Resting energy expenditure, peak oxygen uptake (VO2peak) and the gas-exchange anaerobic threshold (Than) were measured during incremental arm cranking (15 W x min(-1)) in six able-bodied (AB) and six paraplegic (P) subjects. Only male subjects with traumatic spinal cord injuries in the area of the 10-12th thoracic segment were included in the P group. All AB and P subjects were physically active. Mean (SE) values for age and body mass were 28 (2) years and 78.9 (3.9) kg for the AB group and 32 (4) years and 70.8 (7.9) kg for the P group (P>0.05). Resting energy expenditure values were not found to be significantly different between AB [5.8 (0.2) kJ x min(-1)] and P [5.1 (0.3) kJ min(-1)] subjects. Mean VO2peak values were 29.3 (2.4) ml x kg(-1) min(-1) and 29.6 (2.2) ml x kg(-1) x min(-1) for the AB and P groups, respectively (P>0.05). Absolute oxygen uptake values measured at two gas-exchange anaerobic threshold (Than) were not significantly different between the two groups. However, the Than occurred at a significantly higher percentage of VO2peak in the P [58.9 (1.7)%] group than in the AB [50.0 (2.8)%] group (P<0.05). Moreover, respiratory exchange ratio (R) values obtained at the Than and at 15, 45, 60, 75 and 90 W of incremental exercise were significantly lower in the P group than in the AB group. Heart rates were significantly elevated at every submaximal work stage (15-120 W) in the P group compared to the AB group (P<0.05). These findings suggest that chronic daily wheelchair activity produces local adaptations in the functional upper-body musculature, which reduce glycogenolysis and increase the rate of lipid utilization (lower R) during arm exercise. These local adaptations may be in part responsible for the significantly higher Than observed for arm exercise in P subjects, even though VO2peak values were essentially the same for both groups.

Adult↗

Natural selection, infectious transfer and the existence conditions for bacterial plasmids.

Despite the near-ubiquity of plasmids in bacterial populations and the profound contribution of infectious gene transfer to the adaptation and evolution of bacteria, the mechanisms responsible for the maintenance of plasmids in bacterial populations are poorly understood. In this article, we address the question of how plasmids manage to persist over evolutionary time. Empirical studies suggest that plasmids are not infectiously transmitted at a rate high enough to be maintained as genetic parasites. In part i, we present a general mathematical proof that if this is the case, then plasmids will not be able to persist indefinitely solely by carrying genes that are beneficial or sometimes beneficial to their host bacteria. Instead, such genes should, in the long run, be incorporated into the bacterial chromosome. If the mobility of host-adaptive genes imposes a cost, that mobility will eventually be lost. In part ii, we illustrate a pair of mechanisms by which plasmids can be maintained indefinitely even when their rates of transmission are too low for them to be genetic parasites. First, plasmids may persist because they can transfer locally adapted genes to newly arriving strains bearing evolutionary innovations, and thereby preserve the local adaptations in the face of background selective sweeps. Second, plasmids may persist because of their ability to shuttle intermittently favored genes back and forth between various (noncompeting) bacterial strains, ecotypes, or even species.

Bacterial Physiological Phenomena↗

Large margin nearest neighbor classifiers.

The nearest neighbor technique is a simple and appealing approach to addressing classification problems. It relies on the assumption of locally constant class conditional probabilities. This assumption becomes invalid in high dimensions with a finite number of examples due to the curse of dimensionality. Severe bias can be introduced under these conditions when using the nearest neighbor rule. The employment of a locally adaptive metric becomes crucial in order to keep class conditional probabilities close to uniform, thereby minimizing the bias of estimates. We propose a technique that computes a locally flexible metric by means of support vector machines (SVMs). The decision function constructed by SVMs is used to determine the most discriminant direction in a neighborhood around the query. Such a direction provides a local feature weighting scheme. We formally show that our method increases the margin in the weighted space where classification takes place. Moreover, our method has the important advantage of online computational efficiency over competing locally adaptive techniques for nearest neighbor classification. We demonstrate the efficacy of our method using both real and simulated data.

Algorithms↗

Subcellular localization and adaptive up-regulation of the System A (SAT2) amino acid transporter in skeletal-muscle cells and adipocytes.

The recently cloned amino acid transporter SAT2 is ubiquitously expressed and confers Na(+)-dependent transport of short-chain neutral amino acids, characteristics of the functionally defined System A transporter. Here we report the presence of SAT2 mRNA and protein in both skeletal muscle and adipocytes, and the characterization of polyclonal antibodies directed against this transporter. SAT2 protein was present in both plasma-membrane and internal-membrane fractions derived from rat skeletal muscle and adipose tissue, L6 myotubes and 3T3-L1 adipocytes, having a localization similar to that of the glucose transporter GLUT4. Moreover, consistent with the adaptive up-regulation of System A activity following chronic amino acid deprivation, a time-dependent increase in SAT2 protein abundance was observed in amino-acid-deprived L6 myotubes and 3T3-L1 adipocytes. These studies provide the first evidence regarding the subcellular distribution and adaptive up-regulation of SAT2 protein and the characterization of molecular probes for this physiologically important transporter, the function of which is altered in several disease states.

Adipocytes↗

Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant.

Centromeric H3-like histones, which replace histone H3 in the centromeric chromatin of animals and fungi, have not been reported in plants. We identified a histone H3 variant from Arabidopsis thaliana that encodes a centromere-identifying protein designated HTR12. By immunological detection, HTR12 localized at centromeres in both mitotic and meiotic cells. HTR12 signal revealed tissue- and stage-specific differences in centromere morphology, including a distended bead-like structure in interphase root tip cells. The anti-HTR12 antibody also detected spherical organelles in meiotic cells. Although the antibody does not label centromeres in the closely related species Arabidopsis arenosa, HTR12 signal was found on all centromeres in allopolyploids of these two species. Comparison of the HTR12 genes of A. thaliana and A. arenosa revealed striking adaptive evolution in the N-terminal tail of the protein, similar to the pattern seen in its counterpart in Drosophila. This finding suggests that the same evolutionary forces shape centromeric chromatin in both animals and plants.

Adaptation, Physiological↗

Geographical distribution of selected and putatively neutral SNPs in Southeast Asian malaria parasites.

Loci targeted by directional selection are expected to show elevated geographical population structure relative to neutral loci, and a flurry of recent papers have used this rationale to search for genome regions involved in adaptation. Studies of functional mutations that are known to be under selection are particularly useful for assessing the utility of this approach. Antimalarial drug treatment regimes vary considerably between countries in Southeast Asia selecting for local adaptation at parasite loci underlying resistance. We compared the population structure revealed by 10 nonsynonymous mutations (nonsynonymous single-nucleotide polymorphisms [nsSNPs]) in four loci that are known to be involved in antimalarial drug resistance, with patterns revealed by 10 synonymous mutations (synonymous single-nucleotide polymorphisms [sSNPs]) in housekeeping genes or genes of unknown function in 755 Plasmodium falciparum infections collected from 13 populations in six Southeast Asian countries. Allele frequencies at known nsSNPs underlying resistance varied markedly between locations (F(ST) = 0.18-0.66), with the highest frequencies on the Thailand-Burma border and the lowest frequencies in neighboring Lao PDR. In contrast, we found weak but significant geographic structure (F(ST) = 0-0.14) for 8 of 10 sSNPs. Importantly, all 10 nsSNPs showed significantly higher F(ST) (P < 8 x 10(-5)) than simulated neutral expectations based on observed F(ST) values in the putatively neutral sSNPs. This result was unaffected by the methods used to estimate allele frequencies or the number of populations used in the simulations. Given that dense single-nucleotide polymorphism (SNP) maps and rapid SNP assay methods are now available for P. falciparum, comparing genetic differentiation across the genome may provide a valuable aid to identifying parasite loci underlying local adaptation to drug treatment regimes or other selective forces. However, the high proportion of polymorphic sites that appear to be under balancing selection (or linked to selected sites) in the P. falciparum genome violates the central assumption that selected sites are rare, which complicates identification of outlier loci, and suggests that caution is needed when using this approach.

Animals↗

Dispersal strategies of phytophagous insects at a local scale: adaptive potential of aphids in an agricultural environment.

BACKGROUND: The spread of agriculture greatly modified the selective pressures exerted by plants on phytophagous insects, by providing these insects with a high-level resource, structured in time and space. The life history, behavioural and physiological traits of some insect species may have evolved in response to these changes, allowing them to crowd on crops and to become agricultural pests. Dispersal, which is one of these traits, is a key concept in evolutionary biology but has been over-simplified in most theoretical studies. We evaluated the impact of the local-scale dispersal strategy of phytophagous insects on their fitness, using an individual-based model to simulate population dynamics and dispersal between leaves and plants, by walking and flying, of the aphid Aphis gossypii, a major agricultural pest, in a melon field. We compared the optimal values for dispersal parameters in the model with the corresponding observed values in experimental trials. RESULTS: We show that the rates of walking and flying disperser production on leaves were the most important traits determining the fitness criteria, whereas dispersal distance and the clustering of flying dispersers on the target plant had no effect. We further show that the effect of dispersal parameters on aphid fitness depended strongly on plant characteristics. CONCLUSION: Parameters defining the dispersal strategies of aphids at a local scale are key components of the fitness of these insects and may thus be essential in the adaptation to agricultural environments that are structured in space and time. Moreover, the fact that the effect of dispersal parameters on aphid fitness depends strongly on plant characteristics suggests that traits defining aphid dispersal strategies may be a cornerstone of host-plant specialization.

Adaptation, Physiological↗

Salinity tolerance in Daphnia magna: characteristics of genotypes hatching from mixed sediments.

The hatching of diapausing eggs is a means of temporal dispersal that can provide populations with genotypes adapted to different environments. In a salinity-variable shallow lake, we predicted that the mixing of different age-classes of eggs in the sediment may yield genotypes with different salinity optima. The alternative would be the absence of local adaptation and the presence of a homogenous population of salt-tolerant genotypes with high phenotypic plasticity. We tested these alternatives by isolating Daphnia magna resting eggs from different sediment depths, exposing them to hatching cues at different salinity levels and measuring the performance of hatched individuals. Results revealed a homogeneous sediment with generally broad-tolerance genotypes and some genotypes with low salt tolerance, which supports the second hypothesis. However, the disturbed character of the sediment hampered historical reconstruction. The absence of local adaptation in the diapausing egg bank may be the result of various scenarios in the response of D. magna populations to severe salinity changes in the lake.

Adaptation, Physiological↗