Additive genetic effects in interacting species jointly determine the outcome of caterpillar herbivory.

Plant-insect interactions are common and important in basic and applied biology. Trait and genetic variation can affect the outcome and evolution of these interactions, but the relative contributions of plant and insect genetic variation and how these interact remain unclear and are rarely subject to assessment in the same experimental context. Here, we address this knowledge gap using a recent host-range expansion onto alfalfa by the Melissa blue butterfly. Common garden rearing experiments and genomic data show that caterpillar performance depends on plant and insect genetic variation, with insect genetics contributing to performance earlier in development and plant genetics later. Our models of performance based on caterpillar genetics retained predictive power when applied to a second common garden. Much of the plant genetic effect could be explained by heritable variation in plant phytochemicals, especially saponins, peptides, and phosphatidyl cholines, providing a possible mechanistic understanding of variation in the species interaction. We find evidence of polygenic, mostly additive effects within and between species, with consistent effects of plant genotype on growth and development across multiple butterfly species. Our results inform theories of plant-insect coevolution and the evolution of diet breadth in herbivorous insects and other host-specific parasites.

Insects and recent climate change.

Insects have diversified through more than 450 million y of Earth's changeable climate, yet rapidly shifting patterns of temperature and precipitation now pose novel challenges as they combine with decades of other anthropogenic stressors including the conversion and degradation of land. Here, we consider how insects are responding to recent climate change while summarizing the literature on long-term monitoring of insect populations in the context of climatic fluctuations. Results to date suggest that climate change impacts on insects have the potential to be considerable, even when compared with changes in land use. The importance of climate is illustrated with a case study from the butterflies of Northern California, where we find that population declines have been severe in high-elevation areas removed from the most immediate effects of habitat loss. These results shed light on the complexity of montane-adapted insects responding to changing abiotic conditions. We also consider methodological issues that would improve syntheses of results across long-term insect datasets and highlight directions for future empirical work.

Codependency between plant and arbuscular mycorrhizal fungal communities: what is the evidence?

That arbuscular mycorrhizal (AM) fungi covary with plant communities is clear, and many papers report nonrandom associations between symbiotic partners. However, these studies do not test the causal relationship, or 'codependency', whereby the composition of one guild affects the composition of the other. Here we outline underlying requirements for codependency, compare important drivers for both plant and AM fungal communities, and assess how host preference - a pre-requisite for codependency - changes across spatiotemporal scales and taxonomic resolution for both plants and AM fungi. We find few examples in the literature designed to test for codependency and those that do have been conducted within plots or mesocosms. Also, while plants and AM fungi respond similarly to coarse environmental filters, most variation remains unexplained, with host identity explaining less than 30% of the variation in AM fungal communities. These results combined question the likelihood of predictable co-occurrence, and therefore evolution of codependency, between plant and AM fungal taxa across locations. We argue that codependency is most likely to occur in homogeneous environments where specific plant - AM fungal pairings have functional consequences for the symbiosis. We end by outlining critical aspects to consider moving forward.

Bacterial communities of the Salvia lyrata rhizosphere explained by spatial structure and sampling grain.

Advancements in molecular technology have reduced the constraints that the grain of observation, or the spatial resolution and volume of the sampling unit, has on the characterization of plant-associated microbiomes. With discrete ecological sampling and massive parallel sequencing, we can more precisely portray microbiome community assembly and microbial recruitment to host tissue over space and time. Here, we differentiate rarefied community richness and relative abundance in bacterial microbiomes of Salvia lyrata dependent on three spatial depths, which are discrete physical distances from the soil surface within the rhizosphere microhabitat as a proxy for the root system zones. To assess the impact of sampling grain on rarefied community richness and relative abundance, we evaluated the variation of these metrics between samples pooled prior to DNA extraction and samples pooled after sequencing. A distance-based redundancy analysis with the quantitative Jaccard distance revealed that rhizosphere microbiomes vary in richness between rhizosphere soil depths. At all orders of diversity, rarefied microbial richness was consistently lowest at the deepest samples taken (approximately 4 cm from soil surface) in comparison with other rhizosphere soil depths. We additionally show that finer grain sampling (i.e., three samples of equal volume pooled after sequencing) recovers greater microbial richness when using 16S rRNA gene sequencing to describe microbial communities found within the rhizosphere system. In summary, to further elucidate the extent host-specific microbiomes assemble within the rhizosphere, the grain at which bacterial communities are sampled should reflect and encompass fine-scale heterogeneity of the system.

Nest substrate, more than ant activity, drives fungal pathogen community dissimilarity in seed-dispersing ant nests.

Myrmecochory is a widespread mutualism in which plants benefit from seed dispersal services by ants. Ants might also be providing seeds with an additional byproduct benefit via reduced plant pathogen loads in the ant nest environment through their antimicrobial glandular secretions. We investigate this byproduct benefit by identifying fungal communities in ant nests and surrounding environments and quantifying fungal community change (1) through time, (2) between different nest substrates, and (3) as a function of average ant activity levels within nests (based on observed ant activity at nest entrances throughout the summer). We split fungal communities by functional guild to determine seed-dispersing ant-induced changes in the overall fungal community, the animal pathogen fungal community, the plant pathogen fungal community, and the myrmecochore pathogen fungal community. Nest substrate (soil or log) explained much of the variation in fungal community dissimilarity, while substrate occupation (ant nest or control sample) and time had no influence on fungal community composition. Average ant activity had no effect on the community turnover in fungal communities except for the myrmecochore pathogenic fungal community. In this community, higher ant activity throughout the summer resulted in more fluctuation in the pathogenic community in the ant nest. Our results are not consistent with a byproduct benefit framework in myrmecochory, but suggest that nest substrate drives dissimilarity in fungal communities. The influence of nest substrate on fungal communities has important implications for seeds taken into ant nests, as well as ant nest location choice by queens and during nest relocation.

Extreme heterogeneity of population response to climatic variation and the limits of prediction.

Certain general facets of biotic response to climate change, such as shifts in phenology and geographic distribution, are well characterized; however, it is not clear whether the observed similarity of responses across taxa will extend to variation in other population-level processes. We examined population response to climatic variation using long-term incidence data (collected over 42 years) encompassing 149 butterfly species and considerable habitat diversity (10 sites along an elevational gradient from sea level to over 2,700 m in California). Population responses were characterized by extreme heterogeneity that was not attributable to differences in species composition among sites. These results indicate that habitat heterogeneity might be a buffer against climate change and highlight important questions about mechanisms maintaining interpopulation differences in responses to weather. Despite overall heterogeneity of response, population dynamics were accurately predicted by our model for many species at each site. However, the overall correlation between observed and predicted incidence in a cross validation analysis was moderate (Pearson's r = 0.23, SE 0.01), and 97% of observed data fell within the predicted 95% credible intervals. Prediction was most successful for more abundant species as well as for sites with lower annual turnover. Population-level heterogeneity in response to climate variation and the limits of our predictive power highlight the challenges for a future of increasing climatic variability.

Vertical differentiation in tropical forest butterflies: a novel mechanism generating insect diversity?

Many tropical fruit-feeding nymphalid butterflies are associated with either the forest canopy or the understorey; however, the exceptions offer insights into the origins of tropical diversity. As it occurs in both habitats of tropical forests in Ecuador and Peru, Archaeoprepona demophon is one such exception. We compared patterns of occurrence of A. demophon in the canopy and understorey and population genomic variation for evidence of ecological and genetic differentiation between habitats. We found that butterfly occurrences in the canopy were largely uncorrelated with occurrences in the understorey at both localities, indicating independent demographic patterns in the two habitats. We also documented modest, significant genome-level differentiation at both localities. Genetic differentiation between habitat types (separated by approx. 20 m in elevation) was comparable to levels of differentiation between sampling locations (approx. 1500 km). We conclude that canopy and understorey populations of A. demophon represent incipient independent evolutionary units. These findings support the hypothesis that divergence between canopy and understorey-associated populations might be a mechanism generating insect diversity in the tropics.

The predictability of genomic changes underlying a recent host shift in Melissa blue butterflies.

Despite accumulating evidence that evolution can be predictable, studies quantifying the predictability of evolution remain rare. Here, we measured the predictability of genome-wide evolutionary changes associated with a recent host shift in the Melissa blue butterfly (Lycaeides melissa). We asked whether and to what extent genome-wide patterns of evolutionary change in nature could be predicted (i) by comparisons among instances of repeated evolution and (ii) from SNP × performance associations in a laboratory experiment. We delineated the genetic loci (SNPs) most strongly associated with host use in two L. melissa lineages that colonized alfalfa. Whereas most SNPs were strongly associated with host use in none or one of these lineages, we detected a an approximately twofold excess of SNPs associated with host use in both lineages. Similarly, we found that host-associated SNPs in nature could also be partially predicted from SNP × performance (survival and weight) associations in a laboratory rearing experiment. But the extent of overlap, and thus degree of predictability, was somewhat reduced. Although we were able to predict (to a modest extent) the SNPs most strongly associated with host use in nature (in terms of parallelism and from the experiment), we had little to no ability to predict the direction of evolutionary change during the colonization of alfalfa. Our results show that different aspects of evolution associated with recent adaptation can be more or less predictable and highlight how stochastic and deterministic processes interact to drive patterns of genome-wide evolutionary change.

A hierarchical Bayesian model to incorporate uncertainty into methods for diversity partitioning.

Recently there have been major theoretical advances in the quantification and partitioning of diversity within and among communities, regions, and ecosystems. However, applying those advances to real data remains a challenge. Ecologists often end up describing their samples rather than estimating the diversity components of an underlying study system, and existing approaches do not easily provide statistical frameworks for testing ecological questions. Here we offer one avenue to do all of the above using a hierarchical Bayesian approach. We estimate posterior distributions of the underlying "true" relative abundances of each species within each unit sampled. These posterior estimates of relative abundance can then be used with existing formulae to estimate and partition diversity. The result is a posterior distribution of diversity metrics describing our knowledge (or beliefs) about the study system. This approach intuitively leads to statistical inferences addressing biologically motivated hypotheses via Bayesian model comparison. Using simulations, we demonstrate that our approach does as well or better at approximating the "true" diversity of a community relative to naïve or ad-hoc bias-corrected estimates. Moreover, model comparison correctly distinguishes between alternative hypotheses about the distribution of diversity within and among samples. Finally, we use an empirical ecological dataset to illustrate how the approach can be used to address questions about the makeup and diversities of assemblages at local and regional scales.

Pairwise beta diversity resolves an underappreciated source of confusion in calculating species turnover.

Beta diversity is an important metric in ecology quantifying differentiation or disparity in composition among communities, ecosystems, or phenotypes. To compare systems with different sizes (N, number of units within a system), beta diversity is often converted to related indices such as turnover or local/regional differentiation. Here we use simulations to demonstrate that these naive measures of dissimilarity depend on sample size and design. We show that when N is the number of sampled units (e.g., quadrats) rather than the "true" number of communities in the system (if such exists), these differentiation measures are biased estimators. We propose using average pairwise dissimilarity as an intuitive solution. That is, instead of attempting to estimate an N-community measure, we advocate estimating the expected dissimilarity between any random pair of communities (or sampling units)-especially when the "true" N is unknown or undefined. Fortunately, measures of pairwise dissimilarity or overlap have been used in ecology for decades, and their properties are well known. Using the same simulations, we show that average pairwise metrics give consistent and unbiased estimates regardless of the number of survey units sampled. We advocate pairwise dissimilarity as a general standardization to ensure commensurability of different study systems.

A tale of two communities: Neotropical butterfly assemblages show higher beta diversity in the canopy compared to the understory.

Tropical fruit-feeding nymphalid butterflies generally restrict adult foraging exclusively to either the canopy or understory strata. We compared canopy and understory butterfly communities using data from four long-term studies in Central and South America. At all study sites we found little similarity in species composition between canopy and understory, with most species showing a strong affinity for one of the two habitats. There was a consistent phylogenetic signal for canopy and understory association, suggesting a substantial evolutionary history with these habitats. In addition to compositional differences, we found different patterns of beta diversity between canopy and understory communities. Across all study sites, the canopy had greater temporal and spatial beta diversity compared to the understory. Although these two communities are composed of the same feeding guild and separated only by a relatively small vertical space, each has its own stratum-specific species composition and community dynamics.

Understanding a migratory species in a changing world: climatic effects and demographic declines in the western monarch revealed by four decades of intensive monitoring.

Migratory animals pose unique challenges for conservation biologists, and we have much to learn about how migratory species respond to drivers of global change. Research has cast doubt on the stability of the eastern monarch butterfly (Danaus plexippus) population in North America, but the western monarchs have not been as intensively examined. Using a Bayesian hierarchical model, sightings of western monarchs over approximately 40 years were investigated using summer flight records from ten sites along an elevational transect in Northern California. Multiple weather variables were examined, including local and regional temperature and precipitation. Population trends from the ten focal sites and a subset of western overwintering sites were compared to summer and overwintering data from the eastern migration. Records showed western overwintering grounds and western breeding grounds had negative trends over time, with declines concentrated early in the breeding season, which were potentially more severe than in the eastern population. Temporal variation in the western monarch also appears to be largely independent of (uncorrelated with) the dynamics in the east. For our focal sites, warmer temperatures had positive effects during winter and spring, and precipitation had a positive effect during spring. These climatic associations add to our understanding of biotic-abiotic interactions in a migratory butterfly, but shifting climatic conditions do not explain the overall, long-term, negative population trajectory observed in our data.

Selaginella and the Satyr: Euptychia westwoodi (Lepidoptera: Nymphalidae) Oviposition Preference and Larval Performance.

Members of the plant genus Selaginella (de Beauvois 1805) have few known insect herbivores even though they are considered by some to be 'living fossils', with extant taxa virtually indistinguishable from 300 Mya fossils. Butterflies are well-known herbivores, and the satyrs are among the most speciose of them despite having radiated ∼ 35 Mya ago. Nearly all satyrs feed on grass or sedges, but members of the Neotropical genus Euptychia Hübner 1818 feed on Selaginella; little is known about the degree to which this butterfly favors this ancient plant over those that its close relatives utilize. To advance our knowledge of Euptychia natural history, we conducted a series of experiments to examine oviposition preference and growth rates across a series of potential host plants on a Euptychia westwoodi population in Costa Rica. We found that Euptychia westwoodi Butler 1867 exhibit a strong preference to oviposit on Selaginella eurynota over the sympatric Selaginella arthritica, though they perform equally well as larvae on both plants. We did not observe oviposition on a sympatric grass that is commonly consumed by close relatives of E. westwoodi, and when larvae were offered the grass they refused to eat. These results suggest that E. westwoodi in Costa Rica exhibit a strong preference for Selaginella and may have lost the ability to feed on a locally abundant grass commonly used by other Satyrinae.

Extending the Concept of Diversity Partitioning to Characterize Phenotypic Complexity.

Most components of an organism's phenotype can be viewed as the expression of multiple traits. Many of these traits operate as complexes, where multiple subsidiary parts function and evolve together. As trait complexity increases, so does the challenge of describing complexity in intuitive, biologically meaningful ways. Traditional multivariate analyses ignore the phenomenon of individual complexity and provide relatively abstract representations of variation among individuals. We suggest adopting well-known diversity indices from community ecology to describe phenotypic complexity as the diversity of distinct subsidiary components of a trait. Using a hierarchical framework, we illustrate how total trait diversity can be partitioned into within-individual complexity (α diversity) and between-individual components (ß diversity). This approach complements traditional multivariate analyses. The key innovations are (i) addition of individual complexity within the same framework as between-individual variation and (ii) a group-wise partitioning approach that complements traditional level-wise partitioning of diversity. The complexity-as-diversity approach has potential application in many fields, including physiological ecology, ecological and community genomics, and transcriptomics. We demonstrate the utility of this complexity-as-diversity approach with examples from chemical and microbial ecology. The examples illustrate biologically significant differences in complexity and diversity that standard analyses would not reveal.

The evolution of novel host use is unlikely to be constrained by trade-offs or a lack of genetic variation.

The genetic and ecological factors that shape the evolution of animal diets remain poorly understood. For herbivorous insects, the expectation has been that trade-offs exist, such that adaptation to one host plant reduces performance on other potential hosts. We investigated the genetic architecture of alternative host use by rearing individual Lycaeides melissa butterflies from two wild populations in a crossed design on two hosts (one native and one introduced) and analysing the genetic basis of differences in performance using genomic approaches. Survival during the experiment was highest when butterfly larvae were reared on their natal host plant, consistent with local adaptation. However, cross-host correlations in performance among families (within populations) were not different from zero. We found that L. melissa populations possess genetic variation for larval performance and variation in performance had a polygenic basis. We documented very few genetic variants with trade-offs that would inherently constrain diet breadth by preventing the optimization of performance across hosts. Instead, most genetic variants that affected performance on one host had little to no effect on the other host. In total, these results suggest that genetic trade-offs are not the primary cause of dietary specialization in L. melissa butterflies.

Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants.

Detailed information about the geographic distribution of genetic and genomic variation is necessary to better understand the organization and structure of biological diversity. In particular, spatial isolation within species and hybridization between them can blur species boundaries and create evolutionary relationships that are inconsistent with a strictly bifurcating tree model. Here, we analyse genome-wide DNA sequence and genetic ancestry variation in Lycaeides butterflies to quantify the effects of admixture and spatial isolation on how biological diversity is organized in this group. We document geographically widespread and pervasive historical admixture, with more restricted recent hybridization. This includes evidence supporting previously known and unknown instances of admixture. The genome composition of admixed individuals varies much more among than within populations, and tree- and genetic ancestry-based analyses indicate that multiple distinct admixed lineages or populations exist. We find that most genetic variants in Lycaeides are rare (minor allele frequency <0.5%). Because the spatial and taxonomic distributions of alleles reflect demographic and selective processes since mutation, rare alleles, which are presumably younger than common alleles, were spatially and taxonomically restricted compared with common variants. Thus, we show patterns of genetic variation in this group are multifaceted, and we argue that this complexity challenges simplistic notions concerning the organization of biological diversity into discrete, easily delineated and hierarchically structured entities.

A hierarchical perspective on the diversity of butterfly species' responses to weather in the Sierra Nevada Mountains.

An important and largely unaddressed issue in studies of biotic-abiotic relationships is the extent to which closely related species, or species living in similar habitats, have similar responses to weather. We addressed this by applying a hierarchical, Bayesian analytical framework to a long-term data set for butterflies which allowed us to simultaneously investigate responses of the entire fauna and individual species. A small number of variables had community-level effects. In particular, higher total annual snow depth had a positive effect on butterfly occurrences, while spring minimum temperature and El Niño-Southern Oscillation (ENSO) sea-surface variables for April-May had negative standardized coefficients. Our most important finding was that variables with large impacts at the community-level did not necessarily have a consistent response across all species. Species-level responses were much more similar to each other for snow depth compared to the other variables with strong community effects. This variation in species-level responses to weather variables raises important complications for the prediction of biotic responses to shifting climatic conditions. In addition, we found that clear associations with weather can be detected when considering ecologically delimited subsets of the community. For example, resident species and non-ruderal species had a much more unified response to weather variables compared to non-resident species and ruderal species, which suggests local adaptation to climate. These results highlight the complexity of biotic-abiotic interactions and confront that complexity with methodological advances that allow ecologists to understand communities and shifting climates while simultaneously revealing species-specific variation in response to climate.

Explosive diversification following a benthic to pelagic shift in freshwater fishes.

BACKGROUND: Interspecific divergence along a benthic to pelagic habitat axis is ubiquitous in freshwater fishes inhabiting lentic environments. In this study, we examined the influence of this habitat axis on the macroevolution of a diverse, lotic radiation using mtDNA and nDNA phylogenies for eastern North America's most species-rich freshwater fish clade, the open posterior myodome (OPM) cyprinids. We used ancestral state reconstruction to identify the earliest benthic to pelagic transition in this group and generated fossil-calibrated estimates of when this shift occurred. This transition could have represented evolution into a novel adaptive zone, and therefore, we tested for a period of accelerated lineage accumulation after this historical habitat shift. RESULTS: Ancestral state reconstructions inferred a similar and concordant region of our mtDNA and nDNA based gene trees as representing the shift from benthic to pelagic habitats in the OPM clade. Two independent tests conducted on each gene tree suggested an increased diversification rate after this inferred habitat transition. Furthermore, lineage through time analyses indicated rapid early cladogenesis in the clade arising after the benthic to pelagic shift. CONCLUSIONS: A burst of diversification followed the earliest benthic to pelagic transition during the radiation of OPM cyprinids in eastern North America. As such, the benthic/pelagic habitat axis has likely influenced the generation of biodiversity across disparate freshwater ecosystems.

Compounded effects of climate change and habitat alteration shift patterns of butterfly diversity.

Climate change and habitat destruction have been linked to global declines in vertebrate biodiversity, including mammals, amphibians, birds, and fishes. However, invertebrates make up the vast majority of global species richness, and the combined effects of climate change and land use on invertebrates remain poorly understood. Here we present 35 years of data on 159 species of butterflies from 10 sites along an elevational gradient spanning 0-2,775 m in a biodiversity hotspot, the Sierra Nevada Mountains of Northern California. Species richness has declined at half of the sites, with the most severe reductions at the lowest elevations, where habitat destruction is greatest. At higher elevations, we observed clear upward shifts in the elevational ranges of species, consistent with the influence of global warming. Taken together, these long-term data reveal the interacting negative effects of human-induced changes on both the climate and habitat available to butterfly species in California. Furthermore, the decline of ruderal, disturbance-associated species indicates that the traditional focus of conservation efforts on more specialized and less dispersive species should be broadened to include entire faunas when estimating and predicting the effects of pervasive stressors.