Efficiency of bio-indicators for low-level radiation under field conditions

Relatively little is known about biological consequences of natural variation in background radiation, and variation in exposure due to nuclear accidents, or even the long term consequences to human health stemming from the over-use of nuclear medicine and imaging technologies (i.e. CAT scans). This realization emphasizes the need for assessment and quantification of biological effects of radiation on living organisms. Here we report the results of an environmental analysis based on extensive censuses of abundance of nine animal taxa (spiders, dragonflies, grasshoppers, bumblebees, butterflies, amphibians, reptiles, birds, mammals) around Chernobyl in Ukraine and Belarus during 2006–2009. Background levels of radiation explained 1.5–26.5% of the variance in abundance of these nine taxa, birds and mammals having the strongest effects, accounting for a difference of a factor 18 among taxa. These effects were retained in analyses that accounted for potentially confounding effects. Effect size estimated as the amount of variance in abundance explained by background level of radiation was highly consistent among years, with weaker effects in years with low density. Effect sizes were greater in taxa with longer natal dispersal distances and in taxa with higher population density. These results are consistent with the hypotheses that costs of dispersal (i.e. survival) were accentuated under conditions of radioactive contamination, or that high density allowed detection of radiation effects. This suggests that standard breeding bird censuses can be used as an informative bio-indicator for the effects of radiation on abundance of animals.     

Widespread evidence for incipient ecological speciation: a meta‐analysis of isolation‐by‐ecology

Ecologically mediated selection has increasingly become recognised as an important driver of speciation. The correlation between neutral genetic differentiation and environmental or phenotypic divergence among populations, to which we collectively refer to as isolation‐by‐ecology (IBE), is an indicator of ecological speciation. In a meta‐analysis framework, we determined the strength and commonality of IBE in nature. On the basis of 106 studies, we calculated a mean effect size of IBE with and without controlling for spatial autocorrelation among populations. Effect sizes were 0.34 (95% CI 0.24–0.42) and 0.26 (95% CI 0.13–0.37), respectively, indicating that an average of 5% of the neutral genetic differentiation among populations was explained purely by ecological contrast. Importantly, spatial autocorrelation reduced IBE correlations for environmental variables, but not for phenotypes. Through simulation, we showed how the influence of isolation‐by‐distance and spatial autocorrelation of ecological variables can result in false positives or underestimated correlations if not accounted for in the IBE model. Collectively, this meta‐analysis showed that ecologically induced genetic divergence is pervasive across time‐scales and taxa, and largely independent of the choice of molecular marker. We discuss the importance of these results in the context of adaptation and ecological speciation and suggest future research avenues.     

MUTATION AND EXTINCTION: THE ROLE OF VARIABLE MUTATIONAL EFFECTS,SYNERGISTIC EPISTASIS,BENEFICIAL MUTATIONS,AND DEGREE OF OUTCROSSING

Recent theoretical studies have illustrated the potential role of spontaneous deleterious mutation as a cause of extinction in small populations. However, these studies have not addressed several genetic issues, which can in principle have a substantial influence on the risk of extinction. These include the presence of synergistic epistasis, which can reduce the rate of mutation accumulation by progressively magnifying the selective effects of mutations, and the occurrence of beneficial mutations, which can offset the effects of previous deleterious mutations. In stochastic simulations of small populations (effective sizes on the order of 100 or less), we show that both synergistic epistasis and the rate of beneficial mutation must be unrealistically high to substantially reduce the risk of extinction due to random fixation of deleterious mutations. However, in analytical calculations based on diffusion theory, we show that in large, outcrossing populations (effective sizes greater than a few hundred), very low levels of beneficial mutation are sufficient to prevent mutational decay. Further simulation results indicate that in populations small enough to be highly vulnerable to mutational decay, variance in deleterious mutational effects reduces the risk of extinction, assuming that the mean deleterious mutational effect is on the order of a few percent or less. We also examine the magnitude of outcrossing that is necessary to liberate a predominantly selfing population from the threat of long-term mutational deterioration. The critical amount of outcrossing appears to be greater than is common in near-obligately selfing plant species, supporting the contention that such species are generally doomed to extinction via random drift of new mutations. Our results support the hypothesis that a long-term effective population size in the neighborhood of a few hundred individuals defines an approximate threshold, below which outcrossing populations are vulnerable to extinction via fixation of deleterious mutations, and above which immunity is acquired.     

Population Size Affects Adaptation in Complex Ways: Simulations on Empirical Adaptive Landscapes

Do large populations always outcompete smaller ones? Does increasing the mutation rate have a similar effect to increasing the population size, with respect to the adaptation of a population? How important are substitutions in determining the adaptation rate? In this study, we ask how population size and mutation rate interact to affect adaptation on empirical adaptive landscapes. Using such landscapes, we do not need to make many ad hoc assumption about landscape topography, such as about epistatic interactions among mutations or about the distribution of fitness effects. Moreover, we have a better understanding of all the mutations that occur in a population and their effects on the average fitness of the population than we can know in experimental studies. Our results show that the evolutionary dynamics of a population cannot be fully explained by the population mutation rate \(N\mu\); even at constant \(N\mu\), there can be dramatic differences in the adaptation of populations of different sizes. Moreover, the substitution rate of mutations is not always equivalent to the adaptation rate, because we observed populations adapting to high adaptive peaks without fixing any mutations. Finally, in contrast to some theoretical predictions, even on the most rugged landscapes we study, small population size is never an advantage over larger population size. These result show that complex interactions among multiple factors can affect the evolutionary dynamics of populations, and simple models should be taken with caution.     

New markers for new species: microsatellite loci and the East African cichlids

The radiation of the East African cichlid fishes has engaged biologists for over a century. Because so much taxonomic diversity has evolved recently, they are an ideal natural system in which to study the process of speciation. Hypervariable microsatellite loci have been used to verify multiple paternity and maternity in cichlid broods, to quantify the fitness of cooperative breeders and reproductive parasites, to estimate effective population sizes in captive populations, and to illuminate the spatial and temporal scale of gene flow among natural populations. The patterns that have emerged from these studies often reflect important biological differences among taxa. The cichlid species of East Africa represent a large amount of taxonomic and adaptive diversity all neatly packaged into a single lineage and confined to a modest geographical area. Data from microsatellite loci are now providing us with the means to understand one of the world's most intriguing and instructive comparative evolutionary systems.     

Insular shifts and trade-offs in life-history traits in pond frogs in the Zhoushan Archipelago, China

Island and mainland populations of animal species often differ strikingly in life-history traits such as clutch size, egg size, total reproductive effort and body size. However, despite widespread recognition of insular shifts in these life-history traits in birds, mammals and reptiles, there have been no reports of such life-history shifts in amphibians. Furthermore, most studies have focused on one specific life-history trait without explicit consideration of coordinated evolution among these intimately linked life-history traits, and thus the relationships among these traits are poorly studied. Here we provide the first evidence of insular shifts and trade-offs in a coordinated suite of life-history traits for an amphibian species, the pond frog Rana nigromaculata . Life-history data were collected from eight islands in the Zhoushan Archipelago and neighboring mainland China. We found consistent, significant shifts in all life-history traits between mainland and island populations. Island populations had smaller clutch sizes, larger egg sizes, larger female body size and invested less in total reproductive effort than mainland populations. Significant negative relationships were found between egg size and clutch size and between egg size and total reproductive effort among frog populations after controlling for the effects of body size. Therefore, decreased reproductive effort and clutch size, larger egg size and body size in pond frogs on islands were selected through trade-offs as an overall life-history strategy. Our findings contribute to the formation of a broad, repeatable ecological generality for insular shifts in life-history traits across a range of terrestrial vertebrate taxa.     

Adjustment of sperm allocation under high risk of sperm competition across taxa: a meta-analysis

Sperm competition theory predicts that under high risk of sperm competition, males will increase the number of sperm that they allocate to a female. This prediction has been supported by some experimental studies but not by others. Here, I conducted a meta-analysis to determine whether the increase in sperm allocation under high risk of sperm competition is a generalized response across taxa. I collected data from 39 studies and 37 species. Across taxa, males under a high risk of sperm competition respond by increasing their sperm allocation (mean effect size=0.32). Number of offspring did not explain a significant portion of the variation in effect sizes. A traditional meta-analysis (i.e. without phylogenetic information) described the variation among effect sizes better than a meta-analysis that incorporates the phylogenetic relationships among species, suggesting that the increase in sperm allocation under high risk of sperm competition is similarly prevalent across taxa.     

Genetic consequences of habitat fragmentation in plant populations: susceptible signals in plant traits and methodological approaches

Conservation of genetic diversity, one of the three main forms of biodiversity, is a fundamental concern in conservation biology as it provides the raw material for evolutionary change and thus the potential to adapt to changing environments. By means of meta‐analyses, we tested the generality of the hypotheses that habitat fragmentation affects genetic diversity of plant populations and that certain life history and ecological traits of plants can determine differential susceptibility to genetic erosion in fragmented habitats. Additionally, we assessed whether certain methodological approaches used by authors influence the ability to detect fragmentation effects on plant genetic diversity. We found overall large and negative effects of fragmentation on genetic diversity and outcrossing rates but no effects on inbreeding coefficients. Significant increases in inbreeding coefficient in fragmented habitats were only observed in studies analyzing progenies. The mating system and the rarity status of plants explained the highest proportion of variation in the effect sizes among species. The age of the fragment was also decisive in explaining variability among effect sizes: the larger the number of generations elapsed in fragmentation conditions, the larger the negative magnitude of effect sizes on heterozygosity. Our results also suggest that fragmentation is shifting mating patterns towards increased selfing. We conclude that current conservation efforts in fragmented habitats should be focused on common or recently rare species and mainly outcrossing species and outline important issues that need to be addressed in future research on this area.     

Seed banks cause elevated generation times and effective population sizes of Arabidopsis thaliana in northern Europe

It is commonly found that effective population sizes of natural populations are much smaller than census sizes of plants and animals. However, theoretical studies have shown that factors rarely investigated empirically, like seed banks in plants and diapause in animals, may have profound influence on effective sizes. Here we investigate whether the presence of seed banks can explain the relatively high genetic variability observed in northern European Arabidopsis thaliana populations with small census sizes. We have genotyped three above- and below- ground cohorts in 27 Norwegian populations using single nucleotide polymorphism markers. Although the populations varied extensively in levels of variability within and between cohorts, standard genetic population measures were comparable to those obtained in previous studies on above-ground cohorts using microsatellite markers. Estimated effective population sizes are larger for total populations (containing both seed bank and above-ground cohorts for 1 year) compared to each of the cohorts considered separately. Using a conservative approach, we find that the effective sizes are larger than census sizes of local populations, and that the effective generation time is higher than 1 year (3–4 years, on average), making A. thaliana a perennial semelparous plant at many northern European localities.     

Mutation accumulation in populations of varying size: the distribution of mutational effects for fitness correlates in Caenorhabditis elegans

The consequences of mutation for population-genetic and evolutionary processes depend on the rate and, especially, the frequency distribution of mutational effects on fitness. We sought to approximate the form of the distribution of mutational effects by conducting divergence experiments in which lines of a DNA repair-deficient strain of Caenorhabditis elegans, msh-2, were maintained at a range of population sizes. Assays of these lines conducted in parallel with the ancestral control suggest that the mutational variance is dominated by contributions from highly detrimental mutations. This was evidenced by the ability of all but the smallest population-size treatments to maintain relatively high levels of mean fitness even under the 100-fold increase in mutational pressure caused by knocking out the msh-2 gene. However, we show that the mean fitness decline experienced by larger populations is actually greater than expected on the basis of our estimates of mutational parameters, which could be consistent with the existence of a common class of mutations with small individual effects. Further, comparison of the total mutation rate estimated from direct sequencing of DNA to that detected from phenotypic analyses implies the existence of a large class of evolutionarily relevant mutations with no measurable effect on laboratory fitness.     

Natural radioactivity can explain clinal variation in the expression of melanin-based traits

A recent study shows that the expression of pheomelanin-based coloration in barn owls follows a continuous gradient across Europe as a result of local adaptation. The selective pressures that promote local adaptation remain, however, unknown. Here we hypothesize and test that natural radioactivity levels follow a similar spatial gradient to that of pheomelanin-based color in Europe and thus represents a potential selective pressure. The rationale is that the production of pheomelanin consumes glutathione (GSH), a key intracellular antioxidant, and that GSH is particularly susceptible to ionizing radiation, which depletes antioxidants. As predicted, the intensity of pheomelanin-based coloration in 18 populations of barn owls was negatively associated with terrestrial γ-dose rates across Europe. Therefore, we propose that natural selection acts against barn owls that present the molecular basis to produce large amounts of pheomelanin in those populations that are exposed to high levels of natural radioactivity, as in these populations individuals would require higher antioxidant resources to combat oxidative stress. This is the first time that natural radioactivity levels are related to the expression of a phenotypic trait.     

A quantitative review of MHC‐based mating preference: the role of diversity and dissimilarity

Sexual selection hypotheses stipulate that the major histocompatibility complex genes (MHC) constitute a key molecular underpinning for mate choice in vertebrates. The last four decades saw growing empirical literature on the role of MHC diversity and dissimilarity in mate choice for a wide range of vertebrate animals, but with mixed support for its significance in natural populations. Using formal phylogenetic meta‐analysis and meta‐regression techniques, we quantitatively review the existing literature on MHC‐dependent mating preferences in nonhuman vertebrates with a focus on the role of MHC diversity and dissimilarity. Overall, we found small, statistically nonsignificant, average effect sizes for both diversity‐ and dissimilarity‐based mate choice (r = 0.113 and 0.064, respectively). Importantly, however, meta‐regression models revealed statistically significant support regarding female choice for diversity, and choice for dissimilarity (regardless of choosy sex) only when dissimilarity is characterized across multiple loci. Little difference was found among vertebrate taxa; however, the lack of statistical power meant statistically significant effects were limited to some taxa. We found little sign of publication bias; thus, our results are likely to be robust. In light of our quantitative assessment, methodological improvements and fruitful future avenues of research are highlighted.     

Age, area and avian diversification

Using coarse resolution data on the spatial distribution of the entire New World avifauna, we test for phylogenclic patterns in the mean and total geographic range sizes of taxa. The analyses reveal that (i) the species-range size distribution is only approximately normalized, and remains significantly left-skewed, under logarithmic transformation. Most variance in range sizes is explained at the level of species within genera; (ii) there is no effect of the age of taxa on mean clade range size, although older taxa are more likely to have larger total range sizes; (iii) there is some evidence that taxa comprising more species have larger total range sizes; (iv) there is little or no evidence for a relationship between rate of cladogenesis and range size. The results suggest that geographic range size is a labile trait, at least for New World birds, and that the influence of evolutionary history is only weakly detectable in the range size variation of extant taxa, at least at the scale of analysis used here. In addition to these conclusions, two general and important procedural issues emerge.     

Fifty years of chasing lizards: new insights advance optimal escape theory

Systematic reviews and meta‐analyses often examine data from diverse taxa to identify general patterns of effect sizes. Meta‐analyses that focus on identifying generalisations in a single taxon are also valuable because species in a taxon are more likely to share similar unique constraints. We conducted a comprehensive phylogenetic meta‐analysis of flight initiation distance in lizards. Flight initiation distance (FID) is a common metric used to quantify risk‐taking and has previously been shown to reflect adaptive decision‐making. The past decade has seen an explosion of studies focused on quantifying FID in lizards, and, because lizards occur in a wide range of habitats, are ecologically diverse, and are typically smaller and differ physiologically from the better studied mammals and birds, they are worthy of detailed examination. We found that variables that reflect the costs or benefits of flight (being engaged in social interactions, having food available) as well as certain predator effects (predator size and approach speed) had large effects on FID in the directions predicted by optimal escape theory. Variables that were associated with morphology (with the exception of crypsis) and physiology had relatively small effects, whereas habitat selection factors typically had moderate to large effect sizes. Lizards, like other taxa, are very sensitive to the costs of flight.     

Effects of population size and isolation on heterosis, mean fitness, and inbreeding depression in a perennial plant

? In small isolated populations, genetic drift is expected to increase chance fixation of partly recessive, mildly deleterious mutations, reducing mean fitness and inbreeding depression within populations and increasing heterosis in outcrosses between populations. ? We estimated relative effective sizes and migration among populations and compared mean fitness, heterosis, and inbreeding depression for eight large and eight small populations of a perennial plant on the basis of fitness of progeny produced by hand pollinations within and between populations. ? Migration was limited, and, consistent with expectations for drift, mean fitness was 68% lower in small populations; heterosis was significantly greater for small (mean?=?70%, SE?=?14) than for large populations (mean?=?7%, SE?=?27); and inbreeding depression was lower, although not significantly so, in small (mean?=?-0.29%, SE?=?28) than in large (mean?=?0.28%, SE?=?23) populations. ? Genetic drift promotes fixation of deleterious mutations in small populations, which could threaten their persistence. Limited migration will exacerbate drift, but data on migration and effective population sizes in natural populations are scarce. Theory incorporating realistic variation in population size and patterns of migration could better predict genetic threats to small population persistence.     

Evolution to alternative levels of stable diversity leaves areas of niche space unexplored

One of the oldest and most persistent questions in ecology and evolution is whether natural communities tend to evolve toward saturation and maximal diversity. Robert MacArthur’s classical theory of niche packing and the theory of adaptive radiations both imply that populations will diversify and fully partition any available niche space. However, the saturation of natural populations is still very much an open area of debate and investigation. Additionally, recent evolutionary theory suggests the existence of alternative evolutionary stable states (ESSs), which implies that some stable communities may not be fully saturated. Using models with classical Lotka-Volterra ecological dynamics and three formulations of evolutionary dynamics (a model using adaptive dynamics, an individual-based model, and a partial differential equation model), we show that following an adaptive radiation, communities can often get stuck in low diversity states when limited by mutations of small phenotypic effect. These low diversity metastable states can also be maintained by limited resources and finite population sizes. When small mutations and finite populations are considered together, it is clear that despite the presence of higher-diversity stable states, natural populations are likely not fully saturating their environment and leaving potential niche space unfilled. Additionally, within-species variation can further reduce community diversity from levels predicted by models that assume species-level homogeneity.     

Has the inbreeding load for a condition‐dependent sexual signalling trait been purged in insular lizard populations?

Sexually selected traits are often condition‐dependent and are expected to be affected by genome‐wide distributed deleterious mutations and inbreeding. However, sexual selection is a powerful selective force that can counteract inbreeding through purging of deleterious mutations. Inbreeding and purging of the inbreeding load for sexually selected traits has rarely been studied across natural populations with different degrees of inbreeding. Here we investigate inbreeding effects (measured as marker‐based heterozygosity) on condition‐dependent sexually selected signalling trait and other morphological traits across islet‐ and mainland populations (n = 15) of an endemic lizard species (Podarcis gaigeae). Our data suggest inbreeding depression on a condition‐dependent sexually selected signalling character among mainland subpopulations with low or intermediate levels of inbreeding, but no sign of inbreeding depression among small and isolated islet populations despite their higher overall inbreeding levels. In contrast, there was no such pattern among ten other morphological traits which are primarily naturally selected and presumably not involved in sexual signalling. These results are in line with purging of recessive deleterious alleles, or purging in combination with stochastic fixation of alleles by genetic drift, for a sexual signalling character in the islet environment, which is characterized by low population sizes and strong sexual selection. Higher clutch sizes in islet populations also raise interesting questions regarding the possibility of antagonistic pleiotropy. Purging and other non‐exclusive explanations of our results are discussed.     

No evidence of radiation effect on mutation rates at hypervariable minisatellite loci in the germ cells of atomic bomb survivors

Human minisatellites consist of tandem arrays of short repeat sequences, and some are highly polymorphic in numbers of repeats among individuals. Since these loci mutate much more frequently than coding sequences, they make attractive markers for screening populations for genetic effects of mutagenic agents. Here we report the results of our analysis of mutations at eight hypervariable minisatellite loci in the offspring (61 from exposed families in 60 of which only one parent was exposed, and 58 from unexposed parents) of atomic bomb survivors with mean doses of >1 Sv. We found 44 mutations in paternal alleles and eight mutations in maternal alleles with no indication that the high doses of acutely applied radiation had caused significant genetic effects. Our finding contrasts with those of some other studies in which much lower radiation doses, applied chronically, caused significantly increased mutation rates. Possible reasons for this discrepancy are discussed.