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750 results for “heterogeneous data”
Data from: Adaptation to local climate in a multi-trait space: evidence from silver fir (Abies alba Mill.) populations across a heterogeneous environment
Heterogeneous environments, such as mountainous landscapes, create spatially varying selection pressure that potentially affects several traits simultaneously across different life stages, yet little is known about the general patterns and drivers of adaptation in such complex settings. We studied silver fir (Abies alba Mill.) populations across Switzerland and characterized their mountainous landscape using downscaled historical climate data. We sampled 387 trees from 19 populations and genotyped them at 374 single-nucleotide polymorphisms (SNPs) to estimate their demographic distances. Seedling morphology, growth and phenology traits were recorded in a common garden, and a proxy for water use efficiency was estimated for adult trees. We tested whether populations have more strongly diverged at quantitative traits than expected based on genetic drift alone in a multi-trait framework, and identified potential environmental drivers of selection. We found two main responses to selection: (i) populations from warmer and more thermally stable locations have evolved towards a taller stature, and (ii) the growth timing of populations evolved towards two extreme strategies, "start early and grow slowly" or "start late and grow fast", driven by precipitation seasonality. Populations following the "start early and grow slowly" strategy had higher water use efficiency and came from inner Alpine valleys characterized by pronounced summer droughts. Our results suggest that contrasting adaptive life-history strategies exist in silver fir across different life stages (seedling to adult), and that some of the characterized populations may provide suitable seed sources for tree growth under future climatic conditions.
Data from: Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification
The binary-state speciation and extinction (BiSSE) model has been used in many instances to identify state-dependent diversification and reconstruct ancestral states. However, recent studies have shown that the standard procedure of comparing the fit of the BiSSE model to constant-rate birth–death models often inappropriately favours the BiSSE model when diversification rates vary in a state-independent fashion. The newly developed HiSSE model enables researchers to identify state-dependent diversification rates while accounting for state-independent diversification at the same time. The HiSSE model also allows researchers to test state-dependent models against appropriate state-independent null models that have the same number of parameters as the state-dependent models being tested. We reanalyse two data sets that originally used BiSSE to reconstruct ancestral states within squamate reptiles and reached surprising conclusions regarding the evolution of toepads within Gekkota and viviparity across Squamata. We used this new method to demonstrate that there are many shifts in diversification rates across squamates. We then fit various HiSSE submodels and null models to the state and phylogenetic data and reconstructed states under these models. We found that there is no single, consistent signal for state-dependent diversification associated with toepads in gekkotans or viviparity across all squamates. Our reconstructions show limited support for the recently proposed hypotheses that toepads evolved multiple times independently in Gekkota and that transitions from viviparity to oviparity are common in Squamata. Our results highlight the importance of considering an adequate pool of models and null models when estimating diversification rate parameters and reconstructing ancestral states.
Data from: Recent range expansion and agricultural landscape heterogeneity have only minimal effect on the spatial genetic structure of the plant pathogenic fungus Mycosphaerella fijiensis
Understanding how geographical and environmental features affect genetic variation at both the population and individual levels is crucial in biology, especially in the case of pathogens. However, distinguishing between these factors and the effects of historical range expansion on spatial genetic structure remains challenging. In the present study, we investigated the case of Mycosphaerella fijiensis-a plant pathogenic fungus that has recently colonized an agricultural landscape characterized by the presence of potential barriers to gene flow, including several commercial plantations in which disease control practises such as the use of fungicides are applied frequently, and low host density areas. We first genotyped 300 isolates sampled at a global scale on untreated plants in 2 dimensions over a 50x80 Km area. Using two different clustering algorithms, no genetic structure was detected in the studied area, suggesting expansion of large populations and/or no influ ence of potential barriers. Second, we investigated the potential effect of disease control practises on M. fijiensis diversity by comparing populations sampled in commercial vs. food-crop plantations. At this local scale, we detected significantly higher allelic richness inside commercial plantations compared to the surrounding food-crop plantation populations. Analysis of molecular variance (AMOVA) indicated that 99% of the total genetic variance occurred within populations. We discuss the suggestion that high population size and/or high migration rate between populations might be responsible for the absence of any effect of disease control practises on genetic diversity and differentiation.
Data from: Successful by chance? the power of mixed models and neutral simulations for the detection of individual fixed heterogeneity in fitness components
Heterogeneity in fitness components consists of fixed heterogeneity due to latent differences fixed throughout life (e.g. genetic variation), and dynamic heterogeneity generated by stochastic variation. Their relative magnitude is crucial for evolutionary processes, as only the former may allow for adaptation. However, the importance of fixed heterogeneity in small populations has recently been questioned. Using neutral simulations (NS), several studies failed to detect fixed heterogeneity, thus challenging previous results from mixed models (MM). To understand the causes of this discrepancy, we estimate the statistical power and false positive rate of both methods, and apply them to empirical data from a wild rodent population. While MM show high false positive rates if confounding factors are not accounted for, they have high statistical power to detect real fixed heterogeneity. In contrast, NS are also subject to high false positive rates, but have always low power. Indeed, MM analyses of the rodent population data show significant fixed heterogeneity in reproductive success, whereas NS analyses do not. We suggest that fixed heterogeneity may be more common than is suggested by NS, and that NS are useful only if more powerful methods are not applicable and if they are complemented by a power analysis.
Data from: Hidden survival heterogeneity of three common eider populations in response to climate fluctuations
(1) Understanding how individuals and populations respond to fluctuations in climatic conditions is critical to explain and anticipate changes in ecological systems. Most such studies focus on climate impacts on single populations without considering inter- and intra-population heterogeneity. However, comparing geographically dispersed populations limits the risk of faulty generalizations and helps to improve ecological and demographic models. (2) We aimed to determine whether differences in migration tactics among and within populations would induce inter- or intra-population heterogeneity in survival in relation to winter climate fluctuations. Our study species was the Common eider (Somateria mollissima), a marine duck with a circumpolar distribution, which is strongly affected by climatic conditions during several phases of its annual cycle. (3) Capture-mark-recapture (CMR) data were collected in two arctic (northern Canada and Svalbard) and one subarctic (northern Norway) population over a period of 18, 15 and 29 years, respectively. These three populations have different migration tactics and experience different winter climatic conditions. Using multi-event and mixture modelling, we assessed the association between adult female eider survival and winter conditions as measured by the North Atlantic Oscillation index. (4) We found that winter weather conditions affected survival of female eiders from each of these three populations. However, different mechanisms seemed to be involved. Survival of the two migrating arctic populations was impacted directly by changes in the NAO, whereas the subarctic resident population was affected by the NAO with time lags of two to three years. Moreover, we found evidence for intra-population heterogeneity in the survival response to the winter NAO in the Canadian eider population, where individuals migrate to distinct wintering areas. (5) Our results illustrate how individuals and populations of the same species can vary in their responses to climate variation. We suspect that the found variation in survival response of birds to winter conditions is partly explained by differences in migration tactic. Detecting and accounting for inter- and intra-population heterogeneity will improve our predictions concerning the response of wildlife to global changes.
Data from: Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages
Molecular phylogenetic studies of homologous sequences of nucleotides often assume that the underlying evolutionary process was globally stationary, reversible and homogeneous (SRH), and that a model of evolution with one or more site-specific and time-reversible rate matrices (e.g., the GTR rate matrix) is enough to accurately model the evolution of data over the whole tree. However, an increasing body of data suggests that evolution under these conditions is an exception, rather than the norm. To address this issue, several non-SRH models of molecular evolution have been proposed, but they either ignore heterogeneity in the substitution process across sites (HAS) or assume it can be modelled accurately using the Γ distribution. As an alternative to these models of evolution, we introduce a family of mixture models that approximate HAS without the assumption of an underlying predefined statistical distribution. This family of mixture models is combined with non-SRH models of evolution that account for heterogeneity in the substitution process across lineages (HAL). We also present two algorithms for searching model space and identifying an optimal model of evolution that is less likely to over- or under-parameterize the data. The performance of the two new algorithms was evaluated using alignments of nucleotides with 10,000 sites simulated under complex non-SRH conditions on a 25-tipped tree. The algorithms were found to be very successful, identifying the correct HAL model with a 75% success rate (the average success rate for assigning rate matrices to the tree's 48 edges was 99.25%) and, for the correct HAL model, identifying the correct HAS model with a 98% success rate. Finally, parameter estimates obtained under the correct HAL-HAS model were found to be accurate and precise. The merits of our new algorithms were illustrated with an analysis of 42,337 second codon sites extracted from a concatenation of 106 alignments of orthologous genes encoded by the nuclear genomes of Saccharomyces cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, S. castellii, S. kluyveri, S. bayanus, and Candida albicans. Our results show that second codon sites in the ancestral genome of these species contained 49.1% invariable sites, 39.6% variable sites belonging to one rate category (V1), and 11.3% variable sites belonging to a second rate category (V2). The ancestral nucleotide content was found to differ markedly across these 3 sets of sites, and the evolutionary processes operating at the variable sites were found to be non-SRH and best modelled by a combination of 8 edge-specific rate matrices (4 for V1 and 4 for V2). The number of substitutions per site at the variable sites also differed markedly, with sites belonging to V1 evolving slower than those belonging to V2 along the lineages separating the 7 species of Saccharomyces. Finally, sites belonging to V1 appeared to have ceased evolving along the lineages separating S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus, implying that they might have become so selectively constrained that they could be considered invariable sites in these species.
Data from: Natural habitat loss and exotic plants reduce the functional diversity of flower visitors in a heterogeneous subtropical landscape
1. Functional diversity (FD) of pollinators can increase plant reproductive output and the stability of plant-pollinator communities. Yet, in times of worldwide pollinator declines, effects of global change on pollinator FD remain poorly understood. Loss of natural habitat and exotic plant invasions are two major drivers of global change that particularly threaten pollinator diversity. 2. In a subtropical South African landscape, we investigated changes in the FD of flower visitor assemblages on native and exotic plants along gradients of natural habitat loss and relative abundance of exotic plants. We used a dataset of 1434 flower visitor individuals sampled on 131 focal plants and calculated the FD in three flower visitor traits that are strongly related to plant-flower visitor interactions and pollination processes: proboscis length, proboscis diameter and body length. 3. Multivariate FD of flower visitors decreased with both increasing natural habitat loss and relative exotic abundance. Importantly, changes in FD went beyond those in flower visitor richness. Furthermore, flower visitor richness was not related to either natural habitat loss or relative exotic abundance. Loss in multivariate FD seemed to be mediated by complementary reductions of FD in proboscis length with natural habitat loss and of FD in body length with both global change drivers. Correspondingly, we recorded lower abundances of long-tongued flower visitors with natural habitat loss and reduced variance in body size with both drivers. In contrast, FD in proboscis diameter was unaffected by either driver. All effects of the two global change drivers were non-interactive. 4. Our results show that both natural habitat loss and exotic plants negatively affect flower visitor FD, which may imperil pollination of specialised plant species in degraded habitats. In contrast, flower visitor richness may not cover all facets of flower visitor FD that are relevant to pollination processes, and here future studies are needed. Distinct responses of visitor traits to the two drivers suggest limited options to infer relations of one trait to another. Finally, additive effects of natural habitat loss and exotic plant invasions highlight the need to consider multiple drivers of global change when investigating ecosystem processes at a community scale.
Data from: The scale-of-choice effect and how estimates of assortative mating in the wild can be biased due to heterogeneous samples
The mode in which sexual organisms choose mates is a key evolutionary process, as it can have a profound impact on fitness and speciation. One way to study mate choice in the wild is by measuring trait correlation between mates. Positive assortative mating is inferred when individuals of a mating pair display traits that are more similar than those expected under random mating while negative assortative mating is the opposite. A recent review of 1134 trait correlations found that positive estimates of assortative mating were more frequent and larger in magnitude than negative estimates. Here we describe the scale-of-choice effect (SCE), which occurs when mate choice exists at a smaller scale than that of the investigator's sampling, while simultaneously the trait is heterogeneously distributed at the true scale-of-choice. We demonstrate the SCE by Monte Carlo simulations and estimate it in two organisms showing positive (Littorina saxatilis) and negative (L. fabalis) assortative mating. Our results show that both positive and negative estimates are biased by the SCE by different magnitudes, typically towards positive values. Therefore, the low frequency of negative assortative mating observed in the literature may be due to the SCE's impact on correlation estimates, which demands new experimental evaluation.
Data from: Modelling unbiased dispersal kernels over continuous space by accounting for spatial heterogeneity in marking and observation efforts
1. Although a key demographic trait determining the spatial dynamics of wild populations, dispersal is notoriously difficult to estimate in the field. Indeed, dispersal distances obtained from the monitoring of marked individuals typically lead to biased estimations of dispersal kernels as a consequence of i) restricted spatial scale of the study areas compared to species potential dispersal and ii) heterogeneity in marking and observation efforts and therfore in detection probability across space. 2. Here we propose a novel method to circumvent these issues that does not require data on observation effort per se, to correct for the variability in detection of marked individuals across space. Observed dispersal events were weighted by the distribution of departure points and an eroded spatial window approach was applied so as to deal with border effect. We conducted a set of simulations which indicated that our method was successful in correcting the effect of spatially heterogeneous detectability and produce unbiased dispersal kernels. 3. We applied this method to a real dataset on Montagu's harrier (>5000 chicks tagged), providing ca. 6000 resightings collected in entire France by a network of 1200 volunteers within a citizen-science program. The median dispersal distance observed was 32 km (range: 0.1-627 km). Once corrected for spatial heterogeneity in marking and observation efforts and border effect, the modelled dispersal kernel indicated a median dispersal distance of 78-123 km depending on the spatial scale considered (constrained within French borders or not, respectively). 4. Synthesis and applications: The current rise of citizen-science programs is likely to stretch our estimate of the ecologically-relevant spatial scale at which dispersal takes place for many taxa. Our method is particularly suited for such large scale data that typically suffer from high spatial heterogeneity in marking and observation efforts and offers the possibility to derive unbiased dispersal kernels, a key component for modelling population dynamics and species distribution in a context of environmental change. Currently, our method assumes homogeneity in both habitat and dispersal behaviour across individuals. We discuss however how to relax these hypotheses to further investigate the effect of e.g. local conspecific density or habitat quality on dispersal propensity.
Data from: The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: threespine sticklebacks in divergent environments
Heterogeneous genomic divergence between populations may reflect selection, but should also be seen in conjunction with gene flow and drift, particularly population bottlenecks. Marine and freshwater threespine stickleback (Gasterosteus aculeatus) populations often exhibit different lateral armor plate morphs. Moreover, strikingly parallel genomic footprints across different marine-freshwater population pairs are interpreted as parallel evolution and gene reuse. Nevertheless, in some geographic regions like the North Sea and Baltic Sea different patterns are observed. Freshwater populations in coastal regions are often dominated by marine morphs, suggesting that gene flow overwhelms selection, and genomic parallelism may also be less pronounced. We used RAD sequencing for analyzing 28,888 SNPs in two marine and seven freshwater populations in Denmark, Europe. Freshwater populations represented a variety of environments: river populations accessible to gene flow from marine sticklebacks and large and small isolated lakes with and without fish predators. Sticklebacks in an accessible river environment showed minimal morphological and genome-wide divergence from marine populations, supporting the hypothesis of gene flow overriding selection. Allele frequency spectra suggested bottlenecks in all freshwater populations, and particularly two small lake populations. However, genomic footprints ascribed to selection could nevertheless be identified. No genomic regions were consistent freshwater-marine outliers, and parallelism was much lower than in other comparable studies. Two genomic regions previously described to be under divergent selection in freshwater and marine populations were outliers between different freshwater populations. We ascribe these patterns to stronger environmental heterogeneity among freshwater populations in our study as compared to most other studies, although the demographic history involving bottlenecks should also be considered in the interpretation of results.
Data from: Mitochondrial DNA (COI) analyses reveal that amphipod diversity is associated with environmental heterogeneity in deep-sea habitats
The relationship between species diversity and environmental parameters is poorly understood for the mobile macrofauna of deep-sea habitats due to under-sampling and subsequent lack of accurate taxonomic information. To redress this, cytochrome oxidase c subunit I (COI) DNA sequences were used to estimate species diversity and to compare phoxocephalid amphipod assemblages among 20 stations encompassing a range of environmental conditions. Two regions, east (Chatham Rise) and west (Challenger Plateau) of New Zealand were sampled to depths of 200 – 1200 m with an epibenthic sled. Using a comparison among identified morphospecies, we found a clear gap in sequence divergences between 6 and 13% and used a 6% threshold to designate molecular operational taxonomic units (MOTUs), as a surrogate to putative species. DNA sequences (n=297) revealed high total diversity (n=49 MOTUs), as well as high beta diversity (28 MOTUs found at single location only). Novel phoxocephalid MOTUs were found at most stations, especially on Challenger Plateau and the flanks of Chatham Rise. Analyses of inter-station assemblages revealed a major split between regions, indicating minimal overlap in taxon distributions. A cluster of highly similar stations was identified, broadly distributed over the crest of Chatham Rise, in association with elevated food availability, probably resulting from higher surface productivity and relatively shallow depth. Accordingly, multivariate analysis revealed a strong correlation between phoxocephalid assemblages and food supply. This study highlights the value of molecular approaches, in particular COI sequences, for quantifying and comparing diversity in under-sampled and/or under-studied taxa.
Data from: Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus); a dietary-specialist species distributed across heterogeneous environments
The Australian koala is an iconic marsupial with specific dietary requirements distributed across heterogeneous environments, over a large geographic range. The distribution and genetic structure of koala populations has been heavily influenced by human actions, specifically habitat modification, hunting and translocation of koalas. There is currently limited information on population diversity and gene-flow at a species-wide scale, or with consideration to the potential impacts of local adaptation. Using species-wide sampling across heterogeneous environments, and high-density genome-wide markers (SNPs and PAVs), we show that most koala populations display levels of diversity comparable to other outbred species, except for those populations impacted by population reductions. Genetic clustering analysis and phylogenetic reconstruction reveals a lack of support for taxonomic classification of three koala sub-species, with only a single evolutionary significant unit supported. Furthermore, ~70% of genetic variance is accounted for at the individual level. The Sydney Basin region is highlighted as a unique reservoir of genetic diversity, having higher diversity levels (ie. Blue Mountains region; AvHecorr=0.20, PL%=68.6). Broad-scale population differentiation is primarily driven by an Isolation by Distance genetic structure model (49% of genetic variance), with clinal local adaptation corresponding to habitat bioregions. Signatures of selection were detected between bioregions, with no single region returning evidence of strong selection. The results of this study show that although the koala is widely considered to be a dietary-specialist species, this apparent specialisation has not limited the koala's ability to maintain gene-flow and adapt across divergent environments as long as the required food source is available.
Data from: Functional decoupling between flowers and leaves in the Ameroglossum pernambucense complex can facilitate local adaptation across a pollinator and climatic heterogeneous landscape
Decoupling between floral and leaf traits is expected in plants with specialized pollination systems to assure a precise flower–pollinator fit, irrespective of leaf variation associated with environmental heterogeneity (functional modularity). Nonetheless, developmental interactions among floral traits also decouple flowers from leaves regardless of selection pressures (developmental modularity). We tested functional modularity in the hummingbird-pollinated flowers of the Ameroglossum pernambucense complex while controlling for developmental modularity. Using two functional traits responsible for flower–pollinator fit [floral tube length (TL) and anther–nectary distance (AN)], one floral trait not linked to pollination [sepal length (SL), control for developmental modularity] and one leaf trait [leaf length (LL)], we found evidence of flower functional modularity. Covariation between TL and AN was ca. two-fold higher than the covariation of either of these traits with sepal and leaf lengths, and variations in TL and AN, important for a precise flower–pollinator fit, were smaller than SL and LL variations. Furthermore, we show that previously reported among-population variation of flowers associated with local pollinator phenotypes was independent from SL and LL variations. These results suggest that TL and AN are functionally linked to fit pollinators and sufficiently decoupled from developmentally related floral traits (SL) and vegetative traits (LL). These results support previous evidences of population differentiation due to local adaptation in the A. pernambucense complex and shed light on the role of flower–leaf decoupling for local adaptation in species distributed across biotic and abiotic heterogeneous landscapes.
Data from: Beyond dispersal versus philopatry? Alternative behavioural tactics of juvenile roe deer in a heterogeneous landscape
Although inter-individual heterogeneity in many aspects of dispersal behaviour is widely reported, this key life-history trait is predominantly modelled as a dichotomous state of philopatry vs. dispersal. The increasing body of evidence for dispersal syndromes (i.e. a suite of correlated morphological, behavioural, and life-history traits associated with dispersal) implies substantial but, to date, undocumented individual heterogeneity in behavioural tactics during dispersal. Using a large sample (N = 154) of GPS monitored juvenile roe deer (<i>Capreolus capreolus</i>), we evaluated among-individual behavioural heterogeneity in dispersal tactics, and the individual and environmental drivers of these alternative tactics. We developed a sequential three-stage decision tree based on space use stability, exploration events and the directionality of movement. We identified six discrete alternative behavioural tactics during the dispersal period which were characterised by different timing, amplitude and duration in movement: slightly less than half of the deer were sedentary, either "strictly philopatric" or "explorers", which subsequently settled on their natal range; around 40% dispersed ("classic dispersal"), of which, one in six subsequently aborted, moving back to their natal range ("aborted dispersal"); finally, around 15% expressed either a "progressive dispersal" tactic, gradually moving away from their natal area to settle elsewhere, or a "multi-range" tactic. The propensity to express an alternative dispersal tactic was strongly influenced by an individual's local environment. In particular, when landscape heterogeneity, resource quality, and human-related disturbance in the natal range were low, individuals were (i) more likely to adopt the alternative tactics of either progressive dispersal or multi-ranging, but (ii) also more likely to abort their dispersal attempt. Our work indicates that natal dispersal is likely not a single uniform behaviour, but that individuals may adopt a variety of alternative movement tactics which are likely governed by different selection pressures, with potentially important impacts for population dynamics and functioning.
Data from: Microhabitat heterogeneity and a non-native avian frugivore drive the population dynamics of an island endemic shrub, Cyrtandra dentata
Understanding of the role of environmental change in the decline of endangered species is critical to designing scale-appropriate restoration plans. For locally endemic rare plants on the brink of extinction, frugivory can drastically reduce local recruitment by dispersing seeds away from geographically isolated populations. Dispersal of seeds away from isolated populations can ultimately lead to population decline. For localized endemic plants, fine-scale changes in microhabitat can further limit population persistence. Evaluating the individual and combined impact of frugivores and microhabitat heterogeneity on the short-term (i.e. transient) and long-term (i.e. asymptotic) dynamics of plants will provide insight into the drivers of species rarity. In this study, we used four years of demographic data to develop matrix projection models for a long-lived shrub, Cyrtandra dentata (H. St. John & Storey) (Gesneriaceae), which is endemic to the island of O'ahu in Hawai'i. Furthermore, we evaluated the individual and combined influence of a non-native frugivorous bird, Leiothrix lutea, and microhabitat heterogeneity on the short-term and long-term C. dentata population dynamics. Frugivory by L. lutea decreased the short-term and long-term population growth rates. However, under the current level of frugivory at the field site the C. dentata population was projected to persist over time. Conversely, the removal of optimum microhabitat for seedling establishment (i.e. rocky gulch walls and boulders in the gulch bottom) reduced the short-term and long-term population growth rates from growing to declining. Survival of mature C. dentata plants had the greatest influence on long-term population dynamics, followed by the growth of seedlings and immature plants. The importance of mature plant survival was even greater when we simulated the combined effect of frugivory and the loss of optimal microhabitat, relative to population dynamics based on field conditions. In the short-term (10 years), however, earlier life stages had the greatest influence on population growth rate. Synthesis and applications. This study emphasizes how important it is to decouple rare plant management strategies in the short versus long-term in order to prioritize restoration actions, particularly when faced with multiple stressors not all of which can be feasibly managed. From an applied conservation perspective, our findings also illustrate that the life stage that, if improved by management, would have the greatest influence on population dynamics is dependent on the timeframe of interest and initial conditions of the population.
Data from: Spatially heterogeneous perturbations homogenize the regulation of insect herbivores
Anthropogenic influences on resources and consumers can affect food web regulation, with impacts on trophic structure and ecosystem processes. Identifying how these impacts unfold is challenging because alterations to one or both resources and consumers can similarly transform community structure, especially for intermediate consumers. To date, empirical testing of perturbations on trophic regulation has been limited by the difficulty in separating the direct effect of perturbations on species composition and diversity from those unfolding indirectly via altered feeding pathways. Moreover, disentangling the independent and interactive impacts of covarying stressors that characterize human-altered systems has been an ongoing analytical challenge. We used a large-scale metacommunity experiment in grasslands to test how resource inputs, stand perturbation, and spatial factors affect regulation of insect herbivores in tritrophic grassland food webs. Using path-model comparisons, we observed significant simplification of food web regulation on insect herbivores, shifting from mixed predator-resource regulation in unaltered mainland areas to strictly resource-based regulation with landscape perturbation and fragmentation. Most changes were attributed to homogenization of plant community caused by landscape fragmentation and the deterministic influence of eutrophication that reduced among-patch beta diversity. This led to a simplified food web dominated by fewer but more abundant herbivore taxa. Our work implies that anthropogenic perturbation relating to resources and spatial isolation can transform the regulation of food web diversity, structure, and function.
Data from: Heterogeneous genomic differentiation in marine threespine sticklebacks: adaptation along an environmental gradient
Evolutionary divergence among populations occupying ecologically distinct environments can occur even in the face of on-going gene flow. However, the genetic underpinnings, as well as the scale and magnitude at which this differentiation occurs in marine habitats are not well understood. We investigated the patterns and degree of genomic heterogeneity in threespine sticklebacks (Gasterosteus aculeatus) by assessing genetic variability in 20 nongenic and 20 genic (associated with genes important for freshwater adaptation) microsatellite loci in samples collected from 38 locations spanning the entire Baltic Sea coast to the North Sea boundary. Population divergence (FST ≈ 0.026) and structuring (five genetic clusters) was significantly more pronounced in the genic as compared to nongenic markers (FST ≈ 0.008; no genetic clusters). Patterns of divergence in the genic markers—45% of which were identified as outliers—correlated with local differences in salinity. Yet, a strong positive correlation between divergence in genic and nongenic markers, and their association with environmental factors suggests that adaptive divergence is reducing gene flow across the genome. Apart from providing a clear demonstration of heterogeneous genomic patterns of differentiation in a marine species, the results are indicative of adaptive population structuring across the relatively young Baltic Sea in spite of ample opportunities for gene flow.
Data from: Highly diverse and spatially heterogeneous mycorrhizal symbiosis in a rare epiphyte is unrelated to broad biogeographic or environmental features
Symbiotic interactions are common in nature. In dynamic or degraded environments, the ability to associate with multiple partners (i.e. broad specificity) may enable species to persist through fluctuations in the availability of any particular partner. Understanding how species interactions vary across landscapes is necessary to anticipate direct and indirect consequences of environmental degradation on species conservation. We asked whether mycorrhizal symbiosis by populations of a rare epiphytic orchid (Epidendrum firmum) is related to geographic or environmental heterogeneity. The latter would suggest that interactions are governed by environmental conditions rather than historic isolation of populations and/or mycorrhizal fungi. We used DNA-based methods to identify mycorrhizal fungi from eleven E. firmum populations in Costa Rica. We used molecular and phylogenetic analyses to compare associations. Epidendrum firmum exhibited broad specificity, associating with diverse mycorrhizal fungi, including six Tulasnellaceae molecular operational taxonomic units (MOTUs), five Sebacinales MOTUs and others. Notably, diverse mycorrhizal symbioses formed in disturbed pasture and roadside habitats. Mycorrhizal fungi exhibited significant similarity within populations (spatial and phylogenetic autocorrelation) and significant differences among populations (phylogenetic community dissimilarity). However, mycorrhizal symbioses were not significantly associated with biogeographic or environmental features. Such unexpected heterogeneity among populations may result from complex combinations of fine-scale environmental factors and macro-evolutionary patterns of change in mycorrhizal specificity. Thus, E. firmum exhibits broad specificity and the potential for opportunistic associations with diverse fungi. We suggest that these characteristics could confer symbiotic assurance when mycorrhizal fungi are stochastically available, which may be crucial in dynamic or disturbed habitats such as tropical forest canopies.
Data from: Heterogeneity of genetic architecture of body size traits in a free-living population
Knowledge of the underlying genetic architecture of quantitative traits could aid in understanding how they evolve. In wild populations, it is still largely unknown whether complex traits are polygenic or influenced by few loci with major effect, due to often small sample sizes and low resolution of marker panels. Here, we examine the genetic architecture of five adult body size traits in a free-living population of Soay sheep on St Kilda using 37 037 polymorphic SNPs. Two traits (jaw and weight) show classical signs of a polygenic trait: the proportion of variance explained by a chromosome was proportional to its length, multiple chromosomes and genomic regions explained significant amounts of phenotypic variance, but no SNPs were associated with trait variance when using GWAS. In comparison, genetic variance for leg length traits (foreleg, hindleg and metacarpal) was disproportionately explained by two SNPs on chromosomes 16 (s23172.1) and 19 (s74894.1), which each explained >10% of the additive genetic variance. After controlling for environmental differences, females heterozygous for s74894.1 produced more lambs and recruits during their lifetime than females homozygous for the common allele conferring long legs. We also demonstrate that alleles conferring shorter legs have likely entered the population through a historic admixture event with the Dunface sheep. In summary, we show that different proxies for body size can have very different genetic architecture and that dense SNP helps in understanding both the mode of selection and the evolutionary history at loci underlying quantitative traits in natural populations.
Data from: Patterns of cyto-nuclear linkage disequilibrium in Silene latifolia: genomic heterogeneity and temporal stability
Non-random association of alleles in the nucleus and cytoplasmic organelles, or cyto-nuclear linkage disequilibrium (LD), is both an important component of a number of evolutionary processes and a statistical indicator of others. The evolutionary significance of cyto-nuclear LD will depend on both its magnitude and how stable those associations are through time. Here, we use a longitudinal population genetic data set to explore the magnitude and temporal dynamics of cyto-nuclear disequilibria through time. We genotyped 135 and 170 individuals from 16 and 17 patches of the plant species Silene latifolia in Southwestern VA, sampled in 1993 and 2008, respectively. Individuals were genotyped at 14 highly polymorphic microsatellite markers and a single-nucleotide polymorphism (SNP) in the mitochondrial gene, atp1. Normalized LD (D′) between nuclear and cytoplasmic loci varied considerably depending on which nuclear locus was considered (ranging from 0.005–0.632). Four of the 14 cyto-nuclear associations showed a statistically significant shift over approximately seven generations. However, the overall magnitude of this disequilibrium was largely stable over time. The observed origin and stability of cyto-nuclear LD is most likely caused by the slow admixture between anciently diverged lineages within the species' newly invaded range, and the local spatial structure and metapopulation dynamics that are known to structure genetic variation in this system.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.