Landscape‐scale variation in an anthropogenic factor shapes immune gene variation within a wild population

Understanding the spatial scale at which selection acts upon adaptive genetic variation in natural populations is fundamental to our understanding of evolutionary ecology, and has important ramifications for conservation. The environmental factors to which individuals of a population are exposed can vary at fine spatial scales, potentially generating localized patterns of adaptation. Here, we compared patterns of neutral and major histocompatibility complex (MHC) variation within an island population of Berthelot's pipit (Anthus berthelotii) to assess whether landscape‐level differences in pathogen‐mediated selection generate fine‐scale spatial structuring in these immune genes. Specifically, we tested for spatial associations between the distribution of avian malaria, and the factors previously shown to influence that distribution, and MHC variation within resident individuals. Although we found no overall genetic structure across the population for either neutral or MHC loci, we did find localized associations between environmental factors and MHC variation. One MHC class I allele (ANBE48) was directly associated with malaria infection risk, while the presence of the ANBE48 and ANBE38 alleles within individuals correlated (positively and negatively, respectively) with distance to the nearest poultry farm, an anthropogenic factor previously shown to be an important determinant of disease distribution in the study population. Our findings highlight the importance of considering small spatial scales when studying the patterns and processes involved in evolution at adaptive loci.     

Adaptation in temporally variable environments: stickleback armor in periodically breaching bar‐built estuaries

The evolutionary consequences of temporal variation in selection remain hotly debated. We explored these consequences by studying threespine stickleback in a set of bar‐built estuaries along the central California coast. In most years, heavy rains induce water flow strong enough to break through isolating sand bars, connecting streams to the ocean. New sand bars typically re‐form within a few weeks or months, thereby re‐isolating populations within the estuaries. These breaching events cause severe and often extremely rapid changes in abiotic and biotic conditions, including shifts in predator abundance. We investigated whether this strong temporal environmental variation can maintain within‐population variation while eroding adaptive divergence among populations that would be caused by spatial variation in selection. We used neutral genetic markers to explore population structure and then analysed how stickleback armor traits, the associated genes Eda and Pitx1 and elemental composition (%P) varies within and among populations. Despite strong gene flow, we detected evidence for divergence in stickleback defensive traits and Eda genotypes associated with predation regime. However, this among‐population variation was lower than that observed among other stickleback populations exposed to divergent predator regimes. In addition, within‐population variation was very high as compared to populations from environmentally stable locations. Elemental composition was strongly associated with armor traits, Eda genotype and the presence of predators, thus suggesting that spatiotemporal variation in armor traits generates corresponding variation in elemental phenotypes. We conclude that gene flow, and especially temporal environmental variation, can maintain high levels of within‐population variation while reducing, but not eliminating, among‐population variation driven by spatial environmental variation.     

The ecology of an adaptive radiation of three‐spined stickleback from North Uist,Scotland

There has been a large focus on the genetics of traits involved in adaptation, but knowledge of the environmental variables leading to adaptive changes is surprisingly poor. Combined use of environmental data with morphological and genomic data should allow us to understand the extent to which patterns of phenotypic and genetic diversity within a species can be explained by the structure of the environment. Here, we analyse the variation of populations of three‐spined stickleback from 27 freshwater lakes on North Uist, Scotland, that vary greatly in their environment, to understand how environmental and genetic constraints contribute to phenotypic divergence. We collected 35 individuals per population and 30 abiotic and biotic environmental parameters to characterize variation across lakes and analyse phenotype–environment associations. Additionally, we used RAD sequencing to estimate the genetic relationships among a subset of these populations. We found a large amount of phenotypic variation among populations, most prominently in armour and spine traits. Despite large variation in the abiotic environment, namely in ion composition, depth and dissolved organic Carbon, more phenotypic variation was explained by the biotic variables (presence of predators and density of predator and competitors), than by associated abiotic variables. Genetic structure among populations was partly geographic, with closer populations being more similar. Altogether, our results suggest that differences in body shape among stickleback populations are the result of both canalized genetic and plastic responses to environmental factors, which shape fish morphology in a predictable direction regardless of their genetic starting point.     

Biogeography of parasitism in freshwater fish: spatial patterns in hot spots of infection

Contrary to species occurrence, little is known about the determinants of spatial patterns of intraspecific variation in abundance, particularly for parasitic organisms. In this study, we provide a multi‐faceted overview of spatial patterns in parasite abundance and examine several potential underlying processes. We first tested for a latitudinal gradient in local abundance of the regionally most common parasite species and whether these species achieve higher abundances at the same localities (shared hot spots of infection). Secondly, we tested whether intraspecific similarity in local abundance between sites follows a spatial distance decay pattern or is better explained by variation in extrinsic biotic and abiotic factors between localities related to local parasite transmission success. We examined the infection landscape of a model fish host system (common and upland bullies, genus Gobiomorphus: Eleotridae) across its entire distributional range. We applied general linear models to test the effect of latitude on each species local abundance independently, including the abundance of each co‐infecting species as another predictor. We computed multiple regressions on distance matrices among localities based on abundance of each of the four most common trematode species, as well as for geographic distance, biotic and abiotic distinctness of the localities. Our results showed that the most widely distributed parasites of bullies also achieve the highest mean local abundances, following the abundance – occupancy relationship. Variation in local abundance of any focal parasite species was independent of latitude, the abundance of co‐occurring species and spatial distance or disparity in biotic attributes between localities. For only one parasite species, similarity of abundance between sites covaried with the extent of abiotic differences between sites. The lack of association between hot spots of infection for co‐occurring species reinforces the geographic mosaic scenario in which hosts and parasites coevolve by suggesting non‐deterministic, species‐specific variation in parasite abundance across space.     

Bacterial predator–prey dynamics in microscale patchy landscapes

Soil is a microenvironment with a fragmented (patchy) spatial structure in which many bacterial species interact. Here, we explore the interaction between the predatory bacterium Bdellovibrio bacteriovorus and its prey Escherichia coli in microfabricated landscapes. We ask how fragmentation influences the prey dynamics at the microscale and compare two landscape geometries: a patchy landscape and a continuous landscape. By following the dynamics of prey populations with high spatial and temporal resolution for many generations, we found that the variation in predation rates was twice as large in the patchy landscape and the dynamics was correlated over shorter length scales. We also found that while the prey population in the continuous landscape was almost entirely driven to extinction, a significant part of the prey population in the fragmented landscape persisted over time. We observed significant surface-associated growth, especially in the fragmented landscape and we surmise that this sub-population is more resistant to predation. Our results thus show that microscale fragmentation can significantly influence bacterial interactions.     

Microhabitat selection in the common lizard: implications of biotic interactions,age, sex,local processes,and model transferability among populations

Modeling species' habitat requirements are crucial to assess impacts of global change, for conservation efforts and to test mechanisms driving species presence. While the influence of abiotic factors has been widely examined, the importance of biotic factors and biotic interactions, and the potential implications of local processes are not well understood. Testing their importance requires additional knowledge and analyses at local habitat scale. Here, we recorded the locations of species presence at the microhabitat scale and measured abiotic and biotic parameters in three different common lizard (Zootoca vivipara) populations using a standardized sampling protocol. Thereafter, space use models and cross‐evaluations among populations were run to infer local processes and estimate the importance of biotic parameters, biotic interactions, sex, and age. Biotic parameters explained more variation than abiotic parameters, and intraspecific interactions significantly predicted the spatial distribution. Significant differences among populations in the relationship between abiotic parameters and lizard distribution, and the greater model transferability within populations than between populations are in line with effects predicted by local adaptation and/or phenotypic plasticity. These results underline the importance of including biotic parameters and biotic interactions in space use models at the population level. There were significant differences in space use between sexes, and between adults and yearlings, the latter showing no association with the measured parameters. Consequently, predictive habitat models at the population level taking into account different sexes and age classes are required to understand a specie's ecological requirements and to allow for precise conservation strategies. Our study therefore stresses that future predictive habitat models at the population level and their transferability should take these parameters into account.     

Biogeography of parasite abundance: latitudinal gradient and distance decay of similarity in the abundance of fleas and mites,parasitic on small mammals in the Palearctic,at three spatial scales

We tested whether biogeographic patterns characteristic for biological communities can also apply to populations and investigated geographic patterns of variation in abundance of ectoparasites (fleas and mites) collected from bodies of their small mammalian hosts (rodents and shrews) in the Palearctic at continental, regional and local scales. We asked whether (i) there is a relationship between latitude and abundance and (ii) similarity in abundance follows a distance decay pattern or it is better explained by variation in extrinsic biotic and abiotic factors. We analysed the effect of latitude on mean intraspecific abundance using general linear models including proportional abundance of its principal host as an additional predictor variable. Then, we examined the relative effect of geographic distance, biotic and abiotic dissimilarities among regions, subregions or localities on the intraspecific dissimilarity in abundance among regions, subregions or localities using Generalized Dissimilarity Modelling. We found no relationship between latitude and intraspecific flea or mite abundance. In both taxa, environmental dissimilarity explained the largest part of the deviance of spatial variation in abundance, whereas the effect of the dissimilarity in the principal host abundance was of secondary importance and the effect of geographic distance was minor. These patterns were generally consistent across the three spatial scales, although environmental variation and dissimilarity in principal host abundance were equally important at the local scale in fleas but not in mites. We conclude that biogeographic patterns related to latitude and geographic distance do not apply to spatial variation of ectoparasite abundance. Instead, the geographic distribution of abundance in arthropod ectoparasites depends on their responses, mainly to the off-host environment and to a lesser extent the abundance of their principal hosts.     

Developmental thermal plasticity among Drosophila melanogaster populations

Many biotic and abiotic variables influence the dispersal and distribution of organisms. Temperature has a major role in determining these patterns because it changes daily, seasonally and spatially, and these fluctuations have a significant impact on an organism's behaviour and fitness. Most ecologically relevant phenotypes that are adaptive are also complex and thus they are influenced by many underlying loci that interact with the environment. In this study, we quantified the degree of thermal phenotypic plasticity within and among populations by measuring chill‐coma recovery times of lines reared from egg to adult at two different environmental temperatures. We used sixty genotypes from six natural populations of Drosophila melanogaster sampled along a latitudinal gradient in South America. We found significant variation in thermal plasticity both within and among populations. All populations exhibit a cold acclimation response, with flies reared at lower temperatures having increased resistance to cold. We tested a series of environmental parameters against the variation in population mean thermal plasticity and discovered the mean thermal plasticity was significantly correlated with altitude of origin of the population. Pairing our data with previous experiments on viability fitness assays in the same populations in fixed and variable environments suggests an adaptive role of this thermal plasticity in variable laboratory environments. Altogether, these data demonstrate abundant variation in adaptive thermal plasticity within and among populations.     

Species' borders and dispersal barriers

Range limits of species are determined by combined effects of physical, historical, ecological, and evolutionary forces. We consider a subset of these factors by using spatial models of competition, hybridization, and local adaptation to examine the effects of partial dispersal barriers on the locations of borders between similar species. Prompted by results from population genetic models and biogeographic observations, we investigate the conditions under which species' borders are attracted to regions of reduced dispersal. For borders maintained by competition or hybridization, we find that dispersal barriers can attract borders whose positions would otherwise be either neutrally stable or moving across space. Borders affected strongly by local adaptation and gene flow, however, are repelled from dispersal barriers. These models illustrate how particular biotic and abiotic factors may combine to limit species' ranges, and they help to elucidate mechanisms by which range limits of many species may coincide.     

Drivers of genetic differentiation in a generalist insect‐pollinated herb across spatial scales

The isolation‐by‐distance model (IBD) predicts that genetic differentiation among populations increases with geographic distance. Yet, empirical studies show that a variety of ecological, topographic and historical factors may override the effect of geographic distance on genetic variation. This may particularly apply to species with narrow but highly heterogeneous distribution ranges, such as those occurring along elevational gradients. Using nine SSR markers, we study the genetic differentiation of the montane pollination‐generalist herb, Erysimum mediohispanicum. Because the effects of any given factor may depend on the geographic scale considered, we investigate the contribution of different environmental and historical factors at three different spatial scales. We evaluate five competing models that put forward the role of geographic distance, local environmental factors [biotic interactions (IBEb) and climatic variables (IBEa)], landscape resistance (IBR) and phylogeographic patterns (IBP), respectively. We find significant IBD regardless of the spatial scale and the genetic distance estimator considered. However, IBEa and IBP also play a prominent role in shaping genetic differentiation patterns at the larger spatial scales, and IBR is significant at the fine spatial scale. Overall, our results highlight the importance of combining different estimators, statistical approaches and spatial scales to disentangle the relative importance of the various ecological factors contributing to the shaping of genetic divergence patterns in natural populations.     

Phylogenetic distance–decay patterns are not explained by local community assembly processes in freshwater lake microbial communities

While water and sediment microbial communities exhibit pronounced spatio-temporal patterns in freshwater lakes, the underlying drivers are yet poorly understood. Here, we evaluated the importance of spatial and temporal variation in abiotic environmental factors for bacterial and microeukaryotic community assembly and distance–decay relationships in water and sediment niches in Hongze Lake. By sampling across the whole lake during both Autumn and Spring sampling time points, we show that only bacterial sediment communities were governed by deterministic community assembly processes due to abiotic environmental drivers. Nevertheless, consistent distance–decay relationships were found with both bacterial and microeukaryotic communities, which were relatively stable with both sampling time points. Our results suggest that spatio-temporal variation in environmental factors was important in explaining mainly bacterial community assembly in the sediment, possibly due lesser disturbance. However, clear distance–decay patterns emerged also when the community assembly was stochastic. Together, these results suggest that abiotic environmental factors do not clearly drive the spatial structuring of lake microbial communities, highlighting the need to understand the role of other potential drivers, such as spatial heterogeneity and biotic species interactions.     

Spatial and Temporal Distribution of the <Emphasis Type="Italic">Vibrionaceae</Emphasis> in Coastal Waters of Hawaii,Australia, and France

Relatively little is known about large-scale spatial and temporal fluctuations in bacterioplankton, especially within the bacterial families. In general, however, a number of abiotic factors (namely, nutrients and temperature) appear to influence distribution. Community dynamics within the Vibrionaceae are of particular interest to biologists because this family contains a number of important pathogenic, commensal, and mutualist species. Of special interest to this study is the mutualism between sepiolid squids and Vibrio fischeri and Vibrio logei, where host squids seed surrounding waters daily with their bacterial partners. This study seeks to examine the spatial and temporal distribution of the Vibrionaceae with respect to V. fischeri and V. logei in Hawaii, southeastern Australia, and southern France sampling sites. In particular, we examine how the presence of sepiolid squid hosts influences community population structure within the Vibrionaceae. We found that abiotic (temperature) and biotic (host distribution) factors both influence population dynamics. In Hawaii, three sites within squid host habitat contained communities of Vibrionaceae with higher proportions of V. fischeri. In Australia, V. fischeri numbers at host collection sites were greater than other populations; however, there were no spatial or temporal patterns seen at other sample sites. In France, host presence did not appear to influence Vibrio communities, although sampled populations were significantly greater in the winter than summer sampling periods. Results of this study demonstrate the importance of understanding how both abiotic and biotic factors interact to influence bacterial community structure within the Vibrionaceae.     

Patterns of Fusarium community structure and abundance in relation to spatial, abiotic and biotic factors in soil

Members of the Fusarium genus are important components of many plant–soil systems worldwide and are responsible for many crop diseases. Knowledge of the relative influence of biotic and abiotic factors on this genus is therefore of broad economic and ecological importance. In order to address this issue, we examined Fusarium communities in soils nearby apparently healthy and symptomatic asparagus plants in 50 fields scattered in four agricultural regions of Québec, Canada. Fusarium community structure and abundance were assessed using genus-specific PCR-denaturing gradient gel electrophoresis and CFU counts, respectively. Multivariate statistical analyses were used to detect community patterns related to spatial, abiotic and biotic factors. Results suggested that Fusarium community structure (i.e. the presence and absence of the different Fusarium sequence variants in the samples) in soil is mainly related to biotic factors (arbuscular mycorrhizal fungi and bacterial community structure), whereas Fusarium abundance is more closely related to abiotic factors (mainly clay, organic matter, NH₄, Na and Cu). Some degree of influence of spatial patterns was also observed on both Fusarium community structure and abundance with, for instance, a large regional variation in Fusarium community structure. However, Fusarium community structure was not directly related to the disease status of nearby asparagus plants.     

Cultural and climatic changes shape the evolutionary history of the Uralic languages

Quantitative phylogenetic methods have been used to study the evolutionary relationships and divergence times of biological species, and recently, these have also been applied to linguistic data to elucidate the evolutionary history of language families. In biology, the factors driving macroevolutionary processes are assumed to be either mainly biotic (the Red Queen model) or mainly abiotic (the Court Jester model) or a combination of both. The applicability of these models is assumed to depend on the temporal and spatial scale observed as biotic factors act on species divergence faster and in smaller spatial scale than the abiotic factors. Here, we used the Uralic language family to investigate whether both ‘biotic’ interactions (i.e. cultural interactions) and abiotic changes (i.e. climatic fluctuations) are also connected to language diversification. We estimated the times of divergence using Bayesian phylogenetics with a relaxed‐clock method and related our results to climatic, historical and archaeological information. Our timing results paralleled the previous linguistic studies but suggested a later divergence of Finno‐Ugric, Finnic and Saami languages. Some of the divergences co‐occurred with climatic fluctuation and some with cultural interaction and migrations of populations. Thus, we suggest that both ‘biotic’ and abiotic factors contribute either directly or indirectly to the diversification of languages and that both models can be applied when studying language evolution.     

Ecology,environment and evolutionary history influence genetic structure in five mammal species from the Italian Alps

The identification and evaluation of the ecological and environmental factors shaping patterns of natural genetic variation are fundamental goals of population and conservation genetics. Many studies focus on factors affecting single species, but it is also important to test whether some influential biotic and abiotic factors are common drivers of genetic diversity across species, or if species or species groups are each affected by different forces; a multi‐species analysis is necessary for this. Here we analysed the molecular variation from five mammal species (roe deer, red deer, chamois, mountain hare and European brown hare) at mtDNA and microsatellite loci from the eastern Italian Alps. We use phylogeographical and landscape‐level analyses to test the relative influence of large‐scale geographical history and contemporary environmental characteristics of the landscape on genetic diversity and differentiation. We found: (1) all study species except brown hare are strongly differentiated into two main groups, located west and east of a major river valley; (2) significant correlations between levels of within‐population diversity at both mtDNA and microsatellite loci, and several landscape features such as alpine grassland, water courses and anthropized areas. We conclude that heterogeneous landscape has some influence on within‐population diversity, but biogeographical history has probably had the stronger influence on current genetic patterns, despite an apparently large dispersal potential of certain species. However, our results for brown hare show that management actions such as stocking may alter these large‐scale patterns.     

HOW DOES SPATIAL DISPERSAL NETWORK AFFECT THE EVOLUTION OF PARASITE LOCAL ADAPTATION?

Studying patterns of parasite local adaptation can provide insights into the spatiotemporal dynamics of host–parasite coevolution. Many factors, both biotic and abiotic, have been identified that influence parasite local adaptation. In particular, dispersal and population structuring are considered important determinants of local adaptation. We investigated how the shape of the spatial dispersal network within experimental landscapes affected local adaptation of a bacteriophage parasite to its bacterial host. Regardless of landscape topology, dispersal always led to the evolution of phages with broader infectivity range. However, when the spatial dispersal network resulted in spatial variation in the breadth of phage infectivity range, significant levels of parasite local adaptation and local maladaptation were detected within the same landscape using the local versus foreign definition of local adaptation. By contrast, local adaptation was not detected using the home versus away or local versus global definitions of local adaptation. This suggests that spatial dispersal networks may play an important role in driving parasite local adaptation, particularly when the shape of the dispersal network generates nonuniform levels of host resistance or parasite infectivity throughout a species’ range.     

Do landscape processes predict phylogeographic patterns in the wood frog?

Understanding factors that influence population connectivity and the spatial distribution of genetic variation is a major goal in molecular ecology. Improvements in the availability of high-resolution geographic data have made it increasingly possible to quantify the effects of landscape features on dispersal and genetic structure. However, most studies examining such landscape effects have been conducted at very fine (e.g. landscape genetics) or broad (e.g. phylogeography) spatial scales. Thus, the extent to which processes operating at fine spatial scales are linked to patterns at larger scales remains unclear. Here, we test whether factors impacting wood frog dispersal at fine spatial scales are correlated with genetic structure at regional scales. Using recently developed methods borrowed from electrical circuit theory, we generated landscape resistance matrices among wood frog populations in eastern North America based on slope, a wetness index, land cover and absolute barriers to wood frog dispersal. We then determined whether these matrices are correlated with genetic structure based on six microsatellite markers and whether such correlations outperform a landscape-free model of isolation by resistance. We observed significant genetic structure at regional spatial scales. However, topography and landscape variables associated with the intervening habitat between sites provide little explanation for patterns of genetic structure. Instead, absolute dispersal barriers appear to be the best predictor of regional genetic structure in this species. Our results suggest that landscape variables that influence dispersal, microhabitat selection and population structure at fine spatial scales do not necessarily explain patterns of genetic structure at broader scales.     

Introduction pathway and climate trump ecology and life history as predictors of establishment success in alien frogs and toads

A major goal for ecology and evolution is to understand how abiotic and biotic factors shape patterns of biological diversity. Here, we show that variation in establishment success of nonnative frogs and toads is primarily explained by variation in introduction pathways and climatic similarity between the native range and introduction locality, with minor contributions from phylogeny, species ecology, and life history. This finding contrasts with recent evidence that particular species characteristics promote evolutionary range expansion and reduce the probability of extinction in native populations of amphibians, emphasizing how different mechanisms may shape species distributions on different temporal and spatial scales. We suggest that contemporary changes in the distribution of amphibians will be primarily determined by human-mediated extinctions and movement of species within climatic envelopes, and less by species-typical traits.     

Exploring the influence of shrubs on herbaceous communities in a Mediterranean climatic context of two spatial scales

Communities of plants determine nonrandom spatial patterns defined by the intervention of abiotic and biotic factors acting at different spatial scales. We consider the influence of shrubs as one of the most important factors (biotic) affecting these spatial patterns at microscale. The macroclimate could be considered one of the most important factors (abiotic) at regional scale. To study the role and the floristic implications of each factor on the global patterns of herbaceous communities, we have developed a stratified sampling design that integrates both micro and macroscale on a 100 Km-long transect (east–west) in western central Spain. The results suggest that macroclimate could be one of the most important factors in determining herbaceous spatial patterns. Moreover, shrubs create a microspatial environmental heterogeneity that could alter such global climate patterns, modifying the spatial affinities established among species. This implies that environmental heterogeneity related to microhabitat could play a key role in spatial patterns at broad spatial scales, and consequently in the dynamics of the distribution and establishment of herbaceous species.     

Relative importance of abiotic and land use factors in explaining variation in woody vegetation in a French rural landscape

Abstract. In a rural landscape, scale vegetation patterns of woody species are controlled by both abiotic and land use factors. The woody species composition in 126 sample plots was analysed and land use factors and some abiotic parameters were quantified using land register data. The relative importance of land use and abiotic factors was differentiated using a partial Canonical Correspondence Analysis (CCA); the influence of land use in neighbouring areas was explored by changing the scale of land use sampling. The woody species composition appears to be controlled equally by land use and abiotic factors. The fraction of floristic variation in tree species composition explained by land use variables was 33.2 % in 1980 and 30.8 % in 1992, while abiotic variables accounted for 31.2 %. Part of the 17 % of the floristic variance explained is related to the surrounding land use. Thus, when the land use of the sampled plots and the surrounding land use are considered simultaneously, up to 36.9 % of the species variation may be explained. Partial CCA enabled us to quantify the respective proportion of floristic variance which could be explained by land use (36.9 %), abiotic variables alone (20.2 %), shared variance (12.0 %) and unexplained variance (31.2 %). Our results indicated that a delayed effect of variation in land use on plant populations may exist. This delay may result either from population characteristics or from inadequate land use assessment. This study indicates the need for simultaneously examining land use and abiotic patterns in ecological studies, as many Mediterranean-type ecosystems have been shaped by these patterns.