Many traditional mobile telemetry systems require permanently mounting a rod through the cabin of a vehicle to serve as the mast for a directional antenna. In this article we present an alternative to this configuration by providing a platform that can be placed atop the vehicle in which the antenna mast can be mounted and controlled from the cabin of the vehicle. Thereby making this design a viable option for researchers who share vehicles with others that may not approve of permanent vehicle modifications such as placing a hole in the roof of the vehicle as required by traditional mobile configurations. We tested the precision and accuracy of detachable mobile and adjustable telemetry system (DMATS) in an urban park with varying terrain, tree stands, overhead wires, and other structures that can contribute to signal deflection. We placed three radiocollars 50 m apart and 1.2 m above the ground then established three testing stations ~280 m from the location of the radiocollars. The DMATS platform required 12 h for completion and cost $1059 USD. Four technicians were randomly assigned radio collars to triangulate using DMATS and a handheld telemetry system. We used a one-way analysis of variance (ANOVA) with a Scheffe post hoc test to compare error ellipses between azimuths taken using DMATS and the hand held system. Average error ellipses for all testers was 1.96 ± 1.22 ha. No significant differences were found between error ellipses of testers (P = 0.292). Our design, the DMATS, does not require any vehicle modification; thereby, making this a viable option for researchers sharing vehicles with others that may not approve of permanent vehicle alterations.

In this article we present an alternative to this configuration by providing a platform that can be placed atop the vehicle in which the antenna mast can be mounted and controlled from the cabin of the vehicle.

Environmental factors frequently act nonindependently to determine growth and development of insects. Because age and size at maturity strongly influence population dynamics, interaction effects among environmental variables complicate the task of predicting dynamics of insect populations under novel conditions. We reared larvae of the African malaria mosquito Anopheles gambiae sensu stricto (s.s.) under three factors relevant to changes in climate and land use: food level, water depth, and temperature. Each factor was held at two levels in a fully crossed design, for eight experimental treatments. Larval survival, larval development time, and adult size (wing length) were measured to indicate the importance of interaction effects upon population-level processes. For age and size at emergence, but not survival, significant interaction effects were detected for all three factors, in addition to sex. Some of these interaction effects can be understood as consequences of how the different factors influence energy usage in the context of a nonindependent relationship between age and size. Experimentally assessing interaction effects for all potential future sets of conditions is intractable. However, considering how different factors affect energy usage within the context of an insect's evolved developmental program can provide insight into the causes of complex environmental effects on populations.

Interactions among environmental factors that affect development time and body size were assessed for the African malaria mosquito Anopheles gambiae sensu stricto. A 2 × 2 × 2 factorial larval rearing experiment revealed interactions among food level, water depth, and temperature. An L-shaped relationship between development time and body size across resource levels provides an explanation of food-by-depth interactions, while temperature effects are more complex.

Reports indicate that leaf onset (leaf flush) of deciduous trees in cool-temperate ecosystems is occurring earlier in the spring in response to global warming. In this study, we created two types of phenology models, one driven only by warmth (spring warming [SW] model) and another driven by both warmth and winter chilling (parallel chill [PC] model), to predict such phenomena in the Japanese Islands at high spatial resolution (500 m). We calibrated these models using leaf onset dates derived from satellite data (Terra/MODIS) and in situ temperature data derived from a dense network of ground stations Automated Meteorological Data Acquisition System. We ran the model using future climate predictions created by the Japanese Meteorological Agency's MRI-AGCM3.1S model. In comparison to the first decade of the 2000s, our results predict that the date of leaf onset in the 2030s will advance by an average of 12 days under the SW model and 7 days under the PC model throughout the study area. The date of onset in the 2090s will advance by 26 days under the SW model and by 15 days under the PC model. The greatest impact will occur on Hokkaido (the northernmost island) and in the central mountains.

In the end of 21st century, the date of leaf onset of forest trees in Japan will advance 15–26 days. The greatest impact is likely to occur in Hokkaido and the central mountains.

Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability.

Comparing environmental DNA of the most abundant microbial groups in the open ocean, we discovered key ecosystem-specific stress-response adaptations. For example, in the Red Sea, we found adaptations to its high-salinity levels and high solar irradiation. We found that the Red Sea's SAR11 (alphaproteobacteria) population carries more genes for obtaining energy and nutrients from osmolytes, produced by other organisms to survive high salt; and the Red Sea's Prochlorococcus (cyanobacteria) population carries extra genes for repairing UV-damaged DNA.

Life-history traits such as fecundity and offspring size are shaped by investment trade-offs faced by mothers and mediated by environmental conditions. We use a 21-year time series for three populations of wild sockeye salmon (Oncorhynchus nerka) to test predictions for such trade-offs and responses to conditions faced by females during migration, and offspring during incubation. In years when their 1100 km upstream migration was challenged by high water discharges, females that reached spawning streams had invested less in gonads by producing smaller but not fewer eggs. These smaller eggs produced lighter juveniles, and this effect was further amplified in years when the incubation water was warm. This latter result suggests that there should be selection for larger eggs to compensate in populations that consistently experience warm incubation temperatures. A comparison among 16 populations, with matching migration and rearing environments but different incubation environments (i.e., separate spawning streams), confirmed this prediction; smaller females produced larger eggs for their size in warmer creeks. Taken together, these results reveal how maternal phenotype and environmental conditions can shape patterns of reproductive investment and consequently juvenile fitness-related traits within and among populations.

Maternal influences on juvenile life history traits are driven by trade-offs faced by mothers and shaped by environmental conditions. We found strong effects of both maternal phenotype and environmental conditions on egg size and subsequent juvenile fitness-related traits in wild populations of sockeye salmon.

Dispersal and mating features strongly influence the evolutionary dynamics and the spatial genetic structure (SGS) of marine populations. For the first time in a marine invertebrate, we examined individual reproductive success, by conducting larval paternity assignments after a natural spawning event, combined with a small-scale SGS analysis within a population of the gorgonian Paramuricea clavata. Thirty four percent of the larvae were sired by male colonies surrounding the brooding female colonies, revealing that the bulk of the mating was accomplished by males from outside the studied area. Male success increased with male height and decreased with increasing male to female distance. The parentage analyses, with a strong level of self-recruitment (25%), unveiled the occurrence of a complex family structure at a small spatial scale, consistent with the limited larval dispersal of this species. However, no evidence of small scale SGS was revealed despite this family structure. Furthermore, temporal genetic structure was not observed, which appears to be related to the rather large effective population size. The low level of inbreeding found suggests a pattern of random mating in this species, which disagrees with expectations that limited larval dispersal should lead to biparental inbreeding. Surface brooding and investment in sexual reproduction in P. clavata contribute to multiple paternity (on average 6.4 fathers were assigned per brood), which enhance genetic diversity of the brood. Several factors may have contributed to the lack of biparental inbreeding in our study such as (i) the lack of sperm limitation at a small scale, (ii) multiple paternity, and (iii) the large effective population size. Thus, our results indicate that limited larval dispersal and complex family structure do not necessarily lead to biparental inbreeding and SGS. In the framework of conservation purposes, our results suggested that colony size, proximity among colonies and the population size should be taken into consideration for restoration projects.

In this study, for the first time in a marine invertebrate, we assessed relative individual reproductive success, by conducting larval paternity assignments after a natural spawning event, combined with an analysis of spatial genetic structure (SGS) at short distance, within a population of the red gorgonian Paramuricea clavata. Thirty four percent of the larvae were sired by male colonies surrounding the brooding female colonies. Male success increased with male height and decreased with increasing male to female distance. Our results indicate that limited larval dispersal and complex family structure do not necessarily lead to biparental inbreeding and SGS.

The rDNA internal transcribed spacer (ITS) region has been accepted as a DNA barcoding marker for fungi and is widely used in phylogenetic studies; however, intragenomic ITS variability has been observed in a broad range of taxa, including prokaryotes, plants, animals, and fungi, and this variability has the potential to inflate species richness estimates in molecular investigations of environmental samples. In this study 454 amplicon pyrosequencing of the ITS1 region was applied to 99 phylogenetically diverse axenic single-spore cultures of fungi (Dikarya: Ascomycota and Basidiomycota) to investigate levels of intragenomic variation. Three species (one Basidiomycota and two Ascomycota), in addition to a positive control species known to contain ITS paralogs, displayed levels of molecular variation indicative of intragenomic variation; taxon inflation due to presumed intragenomic variation was ≈9%. Intragenomic variability in the ITS region appears to be widespread but relatively rare in fungi (≈3–5% of species investigated in this study), suggesting this problem may have minor impacts on species richness estimates relative to PCR and/or pyrosequencing errors. Our results indicate that 454 amplicon pyrosequencing represents a powerful tool for investigating levels of ITS intragenomic variability across taxa, which may be valuable for better understanding the fundamental mechanisms underlying concerted evolution of repetitive DNA regions.

454 amplicon pyrosequencing was used to survey intragenomic divergence in the internal transcribed spacer (ITS) rDNA region of fungi, a region of DNA that is widely used in phylogenetics and serves as a “DNA barcode.” A large number of studies are utilizing next-generation sequencing of the ITS region to estimate species richness in environmental samples, and intragenomic variation could significantly affect the conclusions of these studies. We discovered significant variation in a small number of fungal species (3–5%), suggesting that intragenomic variability is rare but widespread in kingdom Fungi and should have a minor impact on species richness estimates of fungi in environmental studies relative to PCR and/or pyrosequencing error.

Host ecological traits may limit exposure to infectious disease, thereby generating the wide variation in disease incidence observed between host populations or species. The exclusion of disease by ecological traits may then allow selection to act against physiological defenses when they are costly to maintain in the absence of disease. This study investigates ecological resistance in the Silene-Microbotryum pathosystem. An estimated 80% of perennial Silene species host the anther-smut disease while no annuals harbor the disease in nature. Artificial inoculations of annual and perennial Silene plants, obtained from both natural and horticultural populations, demonstrate that the absence of disease in annuals is not explained by elevated physiological resistance. The annual habit is thus a powerful form of ecological defense against anther smut. Moreover, the higher susceptibility of annual species to anther smut relative to perennials supports the hypothesis of a loss of costly physiological resistance under ecological protection. The observation in annuals that physiological susceptibility is correlated with lower rates of flowering (i.e., lower fitness) suggests that variation in physiological resistance is costly in the absence of disease, even in a naїve Silene species. The absence of disease in natural populations of annuals combined with their high physiological susceptibility attest to the strength of host ecology in shaping the distribution of disease and to the dynamic nature of disease resistance.

Anther-smut disease is absent from annual plant species in nature. The current study demonstrates that this distribution is not due to intrinsic physiological resistance in annuals, which appear more susceptible than natural perennial hosts. Moreover, the study shows that such naive annual species may vary in susceptibility, which incurs costs for the less susceptible genotypes that are similar to observation in natural perennial hosts. This image shows experimentally-produced anther-smut disease on the naive, annual species, Silene colorata.

The central assumption of evolutionary theory is that natural selection drives the adaptation of populations to local environmental conditions, resulting in the evolution of adaptive phenotypes. The three-spined stickleback (Gasterosteus aculeatus) displays remarkable phenotypic variation, offering an unusually tractable model for understanding the ecological mechanisms underpinning adaptive evolutionary change. Using populations on North Uist, Scotland we investigated the role of predation pressure and calcium limitation on the adaptive evolution of stickleback morphology and behavior. Dissolved calcium was a significant predictor of plate and spine morph, while predator abundance was not. Stickleback latency to emerge from a refuge varied with morph, with populations with highly reduced plates and spines and high predation risk less bold. Our findings support strong directional selection in three-spined stickleback evolution, driven by multiple selective agents.

We investigated the ecological mechanisms that underpin adaptive evolutionary change in the three-spined stickleback. On the Hebridean Island of North Uist, where sticklebacks have undergone a striking morphological radiation, we investigated alternative hypotheses; calcium availability and predation as the major selective agents. We detected a significant effect of dissolved calcium on morphology but no effect of predation, contradicting the generally held view that predation is the primary agent of plate and spine morph selection.

Anthropogenic deforestation in tropical countries is responsible for a significant part of global carbon dioxide emissions in the atmosphere. To plan efficient climate change mitigation programs (such as REDD+, Reducing Emissions from Deforestation and forest Degradation), reliable forecasts of deforestation and carbon dioxide emissions are necessary. Although population density has been recognized as a key factor in tropical deforestation, current methods of prediction do not allow the population explosion that is occurring in many tropical developing countries to be taken into account. Here, we propose an innovative approach using novel computational and statistical tools, including R/GRASS scripts and the new phcfM R package, to model the intensity and location of deforestation including the effect of population density. We used the model to forecast anthropogenic deforestation and carbon dioxide emissions in five large study areas in the humid and spiny-dry forests of Madagascar. Using our approach, we were able to demonstrate that the current rapid population growth in Madagascar (+3.39% per year) will significantly increase the intensity of deforestation by 2030 (up to +1.17% per year in densely populated areas). We estimated the carbon dioxide emissions associated with the loss of aboveground biomass to be of 2.24 and 0.26 tons per hectare and per year in the humid and spiny-dry forest, respectively. Our models showed better predictive ability than previous deforestation models (the figure of merit ranged from 10 to 23). We recommend this approach to reduce the uncertainty associated with deforestation forecasts. We also underline the risk of an increase in the speed of deforestation in the short term in tropical developing countries undergoing rapid population expansion.

Using new methods and statistical tools (including R/GRASS scripts and the new phcfM R package), we demonstrate that the fast population growth in Madagascar (+3.39% per year) can be expected to significantly increase the intensity of deforestation by 2030 (up to +1.17% per year in densely populated areas) and estimate the corresponding CO₂ emissions to be of 2.28 and 0.26 ton.ha⁻¹.year⁻¹ in the humid and spiny-dry forest, respectively. We underline the risk of an increase in the speed of deforestation at the global scale due to rapid population expansion in tropical developing countries where people rely heavily on forests for their livelihoods.

In terms of evolutionary biology, a population admixture of more than two distinct lineages may lead to strengthened genetic variation through hybridization. However, a population admixture arising from artificial secondary contact poses significant problems in conservation biology. In urban Tokyo, a population admixture has emerged from two lineages of Japanese common toad: native Bufo japonicus formosus and nonnative B. japonicus japonicus, of which the latter was introduced in the early 20th century. To evaluate the degree of genetic disturbance in the admixed population of these two subspecies, we analyzed genotypes of toads distributed within and outside Tokyo by assessing mtDNA and seven microsatellite loci. We found that the introduced B. japonicus japonicus genotype dominates six local populations in the Tokyo admixture zone and was clearly derived from past introgressive hybridization between the two subspecies. These observations were supported by morphological assessments. Furthermore, the average larval survival rate in Tokyo was significantly higher than that outside Tokyo, suggesting that the temporary contribution of introduced toads occurred through introgression. The fitness of toads in urban Tokyo may thus be increasing with the assistance of nonnative individuals.

In urban Tokyo, a population admixture has emerged from two lineages of Japanese common toad: native Bufo japonicus formosus and non-native B. japonicus japonicus, of which the latter was introduced in the early 20th century. Our genetic clustering analyses of the admixed populations revealed that genotype displacement from native B. japonicus formosus to introduced B. japonicus japonicus had occurred. And assessment of larval viability indicated that the fitness of the Japanese common toad B. japonicus in urban Tokyo may be increasing with the assistance of non-native individuals.

Intraspecific genetic variation can affect decomposition, nutrient cycling, and interactions between plants and their associated belowground communities. However, the effects of genetic variation on ecosystems can also be indirect, meaning that genes in a focal plant may affect ecosystems by altering the phenotype of interacting (i.e., neighboring) individuals. We manipulated genotype identity, species identity, and the possibility of belowground interactions between neighboring Solidago plants. We hypothesized that, because our plants were nitrogen (N) limited, the most important interactions between focal and neighbor plants would occur belowground. More specifically, we hypothesized that the genotypic identity of a plant's neighbor would have a larger effect on belowground biomass than on aboveground biomass, but only when neighboring plants were allowed to interact belowground. We detected species- and genotype-level variation for aboveground biomass and ramet production. We also found that belowground biomass and ramet production depended on the interaction of neighbor genotype identity and the presence or absence of belowground interactions. Additionally, we found that interspecific indirect genetic effects (IIGEs; changes in focal plant traits due to the genotype identity of a heterospecific neighbor) had a greater effect size on belowground biomass than did focal genotype; however, this effect only held in pots that allowed belowground interactions. These results expand the types of natural processes that can be attributed to genotypes by showing that, under certain conditions, a plant's phenotype can be strongly determined by the expression of genes in its neighbor. By showing that IIGEs are dependent upon plants being able to interact belowground, our results also provide a first step for thinking about how genotype-based, belowground interactions influence the evolutionary outcomes of plant-neighbor interactions.

Intraspecific genetic variation can affect a range of properties associated with a focal plant, but the effects of genetic variation in a focal plant's neighbors has received less attention. We found that genotypic variation in neighboring plants indirectly affected the traits of focal plants, with implications for plant evolution and productivity. The effects of neighbors were strongest when plants were allowed to interact belowground, and when the response variable was belowground biomass.

Performance assessment, impact detection, and the assessment of regulatory compliance are common scientific problems for the management of protected areas. Some habitats in protected areas, however, are rare and/or variable and are not often selected for study by ecologists because they preclude comparison with controls and high community variability makes meaningful change detection difficult. Shallow coastal saline lagoons are habitats that experience comparatively high levels of stress due to high physical variability. Lagoons are rare, declining habitats found in coastal regions throughout Europe (and elsewhere) where they are identified as one of the habitats most in need of protected area management. The infauna in the sediments of 25 lagoons were sampled. Temporal and spatial variation in three of these [protected] lagoons was investigated further over 5 years. In a multivariate analysis of community structure similarities were found between some lagoons, but in other cases communities were unique or specific to only two sites. The protected lagoons with these unique/specific communities showed significant temporal and spatial variation, yet none of the changes observed were attributed to human impacts and were interpreted as inherent variability. Multivariate control charts can operate without experimental controls and were used to assess community changes within the context of ‘normal’ lagoon variability. The aim of control chart analysis is to characterize background variability in a parameter and identify when a new observation deviates more than expected. In only 1 year was variability more than expected and corresponded with the coldest December in over 100 years. Multivariate control charts are likely to have wide application in the management of protected areas and other natural systems where variability and/or rarity preclude conventional analytical and experimental approaches but where assessments of condition, impact or regulatory compliance are nonetheless required.

The aim of the study was to explore how traditional and multivariate control chart (MCC) approaches to the assessment of management success would apply to rare, variable habitats in protected areas. In this paper we show how the relatively novel MCC tool can be applied by environmental managers who are beset by significant variation in protected communities, have little scope for comparison elsewhere, but nevertheless are compelled by logic and legislation to make assessments. The issues highlighted are common problems in terrestrial and marine conservation as well as environmental management as a whole.

As the evolutionary interests of males and females are frequently divergent, a trait value that is optimal for the fitness of one sex is often not optimal for the other. A shared genome also means that the same genes may underlie the same trait in both sexes. This can give rise to a form of sexual antagonism, known as intralocus sexual conflict (IASC). Here, a tug-of-war over allelic expression can occur, preventing the sexes from reaching optimal trait values, thereby causing sex-specific reductions in fitness. For some traits, it appears that IASC can be resolved via sex-specific regulation of genes that subsequently permits sexual dimorphism; however, it seems that whole-genome resolution may be impossible, due to the genetic architecture of certain traits, and possibly due to the changing dynamics of selection. In this review, we explore the evolutionary mechanisms of, and barriers to, IASC resolution. We also address the broader consequences of this evolutionary feud, the possible interactions between intra- and interlocus sexual conflict (IRSC: a form of sexual antagonism involving different loci in each sex), and draw attention to issues that arise from using proxies as measurements of conflict. In particular, it is clear that the sex-specific fitness consequences of sexual dimorphism require characterization before making assumptions concerning how this relates to IASC. Although empirical data have shown consistent evidence of the fitness effects of IASC, it is essential that we identify the alleles mediating these effects in order to show IASC in its true sense, which is a “conflict over shared genes.”

Intralocus sexual conflict (IASC) is a form of sexual antagonism that arises when the same genes control the same phenotype in both sexes, but optimal trait values differ for males and females. We consider the maintenance, resolution, and consequences of this evolutionary feud, suggest areas for future research, and draw attention to issues relating to current empirical work.

Extensive ongoing degradation of coral reef habitats worldwide has lead to declines in abundance of coral reef fishes and local extinction of some species. Those most vulnerable are ecological specialists and endemic species. Determining connectivity between locations is vital to understanding recovery and long-term persistence of these species following local extinction. This study explored population connectivity in the ecologically-specialized endemic three-striped butterflyfish (Chaetodon tricinctus) using mt and msatDNA (nuclear microsatellites) to distinguish evolutionary versus contemporary gene flow, estimate self-replenishment and measure genetic diversity among locations at the remote Australian offshore coral reefs of Middleton Reef (MR), Elizabeth Reef (ER), Lord Howe Island (LHI), and Norfolk Island (NI). Mt and msatDNA suggested genetic differentiation of the most peripheral location (NI) from the remaining three locations (MR, ER, LHI). Despite high levels of mtDNA gene flow, there is limited msatDNA gene flow with evidence of high levels of self-replenishment (≥76%) at all four locations. Taken together, this suggests prolonged population recovery times following population declines. The peripheral population (NI) is most vulnerable to local extinction due to its relative isolation, extreme levels of self-replenishment (95%), and low contemporary abundance.

Ongoing degradation of coral reefs has caused declines in the coral reef fish associated with them. Here we show that the endemic coral reef fish, Chaetodon tricinctus, is abundant and has high mtDNA and msatDNA gene flow within its central region. However, the peripheral location receives little mtDNA and msatDNA gene flow and is most at risk should local extinction occur.

Fire is thought to profoundly change the ecology of the sagebrush steppe. The Idaho National Laboratory provides an ideal setting to compare the effects of fire and physical disturbance on plant diversity in high-native-cover sagebrush steppe. Seventy-eight 1-hectare transects were established along paved, green-striped, gravel, and two-track roads, in overgrazed rangeland, and within sagebrush steppe involving different fire histories. Transects were sampled for the diversity and abundance of all vascular plants. Alpha, beta, and phylogenetic beta diversity were analyzed as a response to fire and physical disturbance. Postfire vegetation readily rebounds to prefire levels of alpha plant diversity. Physical disturbance, in contrast, strongly shapes patterns of alpha, beta, and especially phylogenetic beta diversity much more profoundly than fire disturbance. If fire is a concern in the sagebrush steppe then the degree of physical-disturbance should be more so. This finding is probably not specific to the study area but applicable to the northern and eastern portions of the sagebrush biome, which is characterized by a pulse of spring moisture and cold mean minimum winter temperatures. The distinction of sagebrush steppe from Great Basin sagebrush should be revised especially with regard to reseeding efforts and the control of annual grasses.

In the highly seasonal semi-arid North American sagebrush steppe, physical disturbance changes not just the alpha diversity of the community, but also the beta and phylogenetic beta diversity. Fire disturbance by itself does not have such an effect. Physical disturbance much more than fire fundamentally changes the plant biodiversity that is available to regenerate a plant community postdisturbance in much of the sagebrush steppe.

Communities of post-dispersal granivores can shape the density and dispersion of exotic plants and invasive weeds, yet plant ecologists have a limited perception of the relative trophic linkages between a seed species and members of its granivore community. Dandelion seeds marked with Rabbit IgG were disseminated into replicated plots in the recipient habitat (South Dakota) and the native range (Czech Republic). Arthropods were collected in pitfall traps, and their guts were searched for the protein marker using enzyme-linked immunosorbent assay (ELISA). Seed dishes were placed in each plot, and dandelion seed removal rates were measured. The entire experiment was repeated five times over the dandelion flowering period. Gut analysis revealed that approximately 22% of specimens tested positive for the seed marker. A more diverse granivore community had trophic linkages to seeds than has been previously realized under field conditions. This community included taxa such as isopods, millipedes, weevils, rove beetles, and caterpillars, in addition to the traditionally recognized ants, crickets, and carabid beetles. Rarefaction and Chao analysis estimated approximately 16 and 27 species in the granivore communities of the Czech Republic and South Dakota, respectively. Synthesis: Generalist granivore communities are diverse and polyphagous, and are clearly important as a form of biotic resistance to invasive and weedy plants. These granivore communities can be managed to limit population growth of these pests.

Pairing gut content analysis of arthropods with protein-marking of seeds revealed a much more diverse community of post-dispersal granivores than has previously been predicted for a single seed species. Linkage strength of particular granivores did not always correlate well with seed removal rates, potentially due to the fact that relative densities of these taxa were not well measured by pitfall traps. The method of seed marking thus has merit as a tool used in conjunction with other methods (e.g., seed removal, laboratory feeding trials, etc.) to help resolve which species are potentially important granivores of plants.

In species with indeterminate growth, age-related size variation of reproductive competitors within each sex is often high. This selects for divergence in reproductive tactics of same-sex competitors, particularly in males. Where alternative tactics are fixed for life, the causality of tactic choice is often unclear. In the African cichlid Lamprologus callipterus, large nest males collect and present empty snail shells to females that use these shells for egg deposition and brood care. Small dwarf males attempt to fertilize eggs by entering shells in which females are spawning. The bourgeois nest males exceed parasitic dwarf males in size by nearly two orders of magnitude, which is likely to result from greatly diverging growth patterns. Here, we ask whether growth patterns are heritable in this species, or whether and to which extent they are determined by environmental factors. Standardized breeding experiments using unrelated offspring and maternal half-sibs revealed highly divergent growth patterns of male young sired by nest or dwarf males, whereas the growth of female offspring of both male types did not differ. As expected, food had a significant modifying effect on growth, but neither the quantity of breeding substrate in the environment nor ambient temperature affected growth. None of the environmental factors tested influenced the choice of male life histories. We conclude that in L. callipterus growth rates of bourgeois and parasitic males are paternally inherited, and that male and female growth is phenotypically plastic to only a small degree.

Standardized breeding experiments using unrelated offspring and maternal half-sibs revealed highly divergent growth patterns of male young sired by bourgeois or parasitic males, whereas the growth of female offspring of both male types did not differ. Food had a significant modifying effect on growth, but neither the quantity of breeding substrate nor ambient temperature affected growth, and none of the environmental factors tested influenced the choice of male life histories. We conclude that in Lamprologus callipterus growth rates of bourgeois and parasitic males are paternally inherited, and that male and female growth is phenotypically plastic to only a small degree.

Parallel phenotypic evolution occurs when independent populations evolve similar traits in response to similar selective regimes. However, populations inhabiting similar environments also frequently show some phenotypic differences that result from non-parallel evolution. In this study, we quantified the relative importance of parallel evolution to similar foraging regimes and non-parallel lake-specific effects on morphological variation in European whitefish (Coregonus lavaretus). We found evidence for both lake-specific morphological characteristics and parallel morphological divergence between whitefish specializing in feeding on profundal and littoral resources in three separate lakes. Foraging specialists expressed similar phenotypes in different lakes in both overall body shape and selected measured morphological traits. The morphology of the two whitefish specialists resembled that predicted from other fish species, supporting the conclusion of an adaptive significance of the observed morphological characteristics. Our results indicate that divergent natural selection resulting from foraging specialization is driving and/or maintaining the observed parallel morphological divergence. Whitefish in this study may represent an early stage of divergence towards the evolution of specialized morphs.

This study demonstrates parallel morphological divergence between sympatric foraging specialists within populations of whitefish in three different lakes. Together with previous knowledge about these systems, this suggests that these populations may be in an early stage of divergence of specialized morphs.

We evaluated the mtDNA divergence and relationships within Geomys pinetis to assess the status of formerly recognized Geomys taxa. Additionally, we integrated new hypothesis-based tests in ecological niche models (ENM) to provide greater insight into causes for divergence and potential barriers to gene flow in Southeastern United States (Alabama, Florida, and Georgia). Our DNA sequence dataset confirmed and strongly supported two distinct lineages within G. pinetis occurring east and west of the ARD. Divergence date estimates showed that eastern and western lineages diverged about 1.37 Ma (1.9 Ma–830 ka). Predicted distributions from ENMs were consistent with molecular data and defined each population east and west of the ARD with little overlap. Niche identity and background similarity tests were statistically significant suggesting that ENMs from eastern and western lineages are not identical or more similar than expected based on random localities drawn from the environmental background. ENMs also support the hypothesis that the ARD represents a ribbon of unsuitable climate between more suitable areas where these populations are distributed. The estimated age of divergence between eastern and western lineages of G. pinetis suggests that the divergence was driven by climatic conditions during Pleistocene glacial–interglacial cycles. The ARD at the contact zone of eastern and western lineages of G. pinetis forms a significant barrier promoting microgeographic isolation that helps maintain ecological and genetic divergence.

We evaluated the mtDNA divergence and relationships within Geomys pinetis to assess the status of formerly recognized Geomys taxa. Additionally, we integrated new hypothesis-based tests in ecological niche models (ENM) to provide greater insight into causes for divergence and potential barriers to gene flow. Populations of G. pinetis are separated by a ribbon of unsuitable habitat at the contact zone of eastern and western lineages that forms a significant barrier promoting microgeographic isolation that helps maintain ecological and genetic divergence.

The study of the morphological defects unique to interspecific hybrids can reveal which developmental pathways have diverged between species. Drosophila melanogaster and D. santomea diverged more than 10 million years ago, and when crossed produce sterile adult females. Adult hybrid males are absent from all interspecific crosses. We aimed to determine the fate of these hybrid males. To do so, we tracked the development of hybrid females and males using classic genetic markers and techniques. We found that hybrid males die predominantly as embryos with severe segment-specification defects while a large proportion of hybrid females embryos hatch and survive to adulthood. In particular, we show that most male embryos show a characteristic abdominal ablation phenotype, not observed in either parental species. This suggests that sex-specific embryonic developmental defects eliminate hybrid males in this interspecific cross. The study of the developmental abnormalities that occur in hybrids can lead to the understanding of cryptic molecular divergence between species sharing a conserved body plan.

Drosophila melanogaster and D. santomea diverged more than 10 million years ago, and when crossed produce sterile adult females. Adult hybrid males are absent from all interspecific crosses. We found that hybrid males die predominantly as embryos with severe segment-specification defects while a large proportion of hybrid females embryos hatch and survive to adulthood.

Global climate change has the potential to seriously and adversely affect marine ecosystem functioning. Numerous experimental and modeling studies have demonstrated how predicted ocean acidification and increased ultraviolet radiation (UVR) can affect marine microbes. However, researchers have largely ignored interactions between ocean acidification, increased UVR and anthropogenic pollutants in marine environments. Such interactions can alter chemical speciation and the bioavailability of several organic and inorganic pollutants with potentially deleterious effects, such as modifying microbial-mediated detoxification processes. Microbes mediate major biogeochemical cycles, providing fundamental ecosystems services such as environmental detoxification and recovery. It is, therefore, important that we understand how predicted changes to oceanic pH, UVR, and temperature will affect microbial pollutant detoxification processes in marine ecosystems. The intrinsic characteristics of microbes, such as their short generation time, small size, and functional role in biogeochemical cycles combined with recent advances in molecular techniques (e.g., metagenomics and metatranscriptomics) make microbes excellent models to evaluate the consequences of various climate change scenarios on detoxification processes in marine ecosystems. In this review, we highlight the importance of microbial microcosm experiments, coupled with high-resolution molecular biology techniques, to provide a critical experimental framework to start understanding how climate change, anthropogenic pollution, and microbiological interactions may affect marine ecosystems in the future.

Global climate change has the potential to seriously and adversely affect marine ecosystem functioning. In this review, we highlight the importance of microbial microcosm experiments, coupled with high-resolution molecular biology techniques, to provide a critical experimental framework to start understanding how climate change, anthropogenic pollution and microbiological interactions may affect marine ecosystems in the future.

Genetic variation at the major histocompatibility complex (MHC) is vitally important for wildlife populations to respond to pathogen threats. As natural populations can fluctuate greatly in size, a key issue concerns how population cycles and bottlenecks that could reduce genetic diversity will influence MHC genes. Using 454 sequencing, we characterized genetic diversity at the DRB Class II locus in montane voles (Microtus montanus), a North American rodent that regularly undergoes high-amplitude fluctuations in population size. We tested for evidence of historic balancing selection, recombination, and gene duplication to identify mechanisms maintaining allelic diversity. Counter to our expectations, we found strong evidence of purifying selection acting on the DRB locus in montane voles. We speculate that the interplay between population fluctuations and gene duplication might be responsible for the weak evidence of historic balancing selection and strong evidence of purifying selection detected. To further explore this idea, we conducted a phylogenetically controlled comparative analysis across 16 rodent species with varying demographic histories and MHC duplication events (based on the maximum number of alleles detected per individual). On the basis of phylogenetic generalized linear model-averaging, we found evidence that the estimated number of duplicated loci was positively related to allelic diversity and, surprisingly, to the strength of purifying selection at the DRB locus. Our analyses also revealed that species that had undergone population bottlenecks had lower allelic richness than stable species. This study highlights the need to consider demographic history and genetic structure alongside patterns of natural selection to understand resulting patterns of genetic variation at the MHC.

An unresolved challenge for evolutionary biology and wildlife conservation is to better understand how species that routinely experience high degrees of genetic drift can maintain immunogenetic diversity over evolutionary timescales. In this study we characterized variation at the Major Histocompatibility Complex (MHC) in the cyclic montane vole (Microtus montanus), and investigated the influence of population dynamics (i.e., stable, cyclic, or bottlenecked populations) and gene duplication on patterns of allelic diversity and signals of selection across 16 rodent species.

Many plant species combine sexual and clonal reproduction. Clonal propagation has ecological costs mainly related to inbreeding depression and pollen discounting; at the same time, species able to reproduce clonally have ecological and evolutionary advantages being able to persist when conditions are not favorable for sexual reproduction. The presence of clonality has profound consequences on the genetic structure of populations, especially when it represents the predominant reproductive strategy in a population. Theoretical studies suggest that high rate of clonal propagation should increase the effective number of alleles and heterozygosity in a population, while an opposite effect is expected on genetic differentiation among populations and on genotypic diversity. In this study, we ask how clonal propagation affects the genetic diversity of rare insular species, which are often characterized by low levels of genetic diversity, hence at risk of extinction. We used eight polymorphic microsatellite markers to study the genetic structure of the critically endangered insular endemic Ruta microcarpa. We found that clonality appears to positively affect the genetic diversity of R. microcarpa by increasing allelic diversity, polymorphism, and heterozygosity. Moreover, clonal propagation seems to be a more successful reproductive strategy in small, isolated population subjected to environmental stress. Our results suggest that clonal propagation may benefit rare species. However, the advantage of clonal growth may be only short-lived for prolonged clonal growth could ultimately lead to monoclonal populations. Some degree of sexual reproduction may be needed in a predominantly clonal species to ensure long-term viability.

We investigated the effects of clonal propagation on the genetic structure of rare, insular species using the Canarian endemic Ruta microcarpa as a model. We found that, even though clonality has genetic costs related to inbreeding depression, clonal reproduction seems to positively affect genetic diversity of species and may help in their short-term survival. Moreover, the extent of clonality seems to be related to population size, degree of isolation and presence of environmental stress characterising different populations.

Greater sage-grouse Centrocercus urophasianus (Bonaparte) currently occupy approximately half of their historical distribution across western North America. Sage-grouse are a candidate for endangered species listing due to habitat and population fragmentation coupled with inadequate regulation to control development in critical areas. Conservation planning would benefit from accurate maps delineating required habitats and movement corridors. However, developing a species distribution model that incorporates the diversity of habitats used by sage-grouse across their widespread distribution has statistical and logistical challenges. We first identified the ecological minimums limiting sage-grouse, mapped similarity to the multivariate set of minimums, and delineated connectivity across a 920,000 km² region. We partitioned a Mahalanobis D² model of habitat use into k separate additive components each representing independent combinations of species–habitat relationships to identify the ecological minimums required by sage-grouse. We constructed the model from abiotic, land cover, and anthropogenic variables measured at leks (breeding) and surrounding areas within 5 km. We evaluated model partitions using a random subset of leks and historic locations and selected D² (k = 10) for mapping a habitat similarity index (HSI). Finally, we delineated connectivity by converting the mapped HSI to a resistance surface. Sage-grouse required sagebrush-dominated landscapes containing minimal levels of human land use. Sage-grouse used relatively arid regions characterized by shallow slopes, even terrain, and low amounts of forest, grassland, and agriculture in the surrounding landscape. Most populations were interconnected although several outlying populations were isolated because of distance or lack of habitat corridors for exchange. Land management agencies currently are revising land-use plans and designating critical habitat to conserve sage-grouse and avoid endangered species listing. Our results identifying attributes important for delineating habitats or modeling connectivity will facilitate conservation and management of landscapes important for supporting current and future sage-grouse populations.

Habitat loss is a significant concern to conserving greater sage-grouse, a candidate for endangered species listing in the United States. We mapped current habitat availability based on presence of ecological minimum requirements to guide conservation actions within population boundaries and in connecting corridors. Our emphasis on minimum requirements rather than on models describing average or optimum conditions provides a conceptual and statistical foundation for modeling habitats in future unknown distributions predicted under climate change.

The phenotype-linked fertility hypothesis proposes that male fertility is advertised via phenotypic signals, explaining female preference for highly sexually ornamented males. An alternative view is that highly attractive males constrain their ejaculate allocation per mating so as to participate in a greater number of matings. Males are also expected to bias their ejaculate allocation to the most fecund females. We test these hypotheses in the African stalk-eyed fly, Diasemopsis meigenii. We ask how male ejaculate allocation strategy is influenced by male eyespan and female size. Despite large eyespan males having larger internal reproductive organs, we found no association between male eyespan and spermatophore size or sperm number, lending no support to the phenotype-linked fertility hypothesis. However, males mated for longer and transferred more sperm to large females. As female size was positively correlated with fecundity, this suggests that males gain a selective advantage by investing more in large females. Given these findings, we consider how female mate preference for large male eyespan can be adaptive despite the lack of obvious direct benefits.

Male attractiveness in stalk-eyed flies (large eyespan) is not associated with greater ejaculate transfer (spermatophore size or sperm number), despite attractive males having bigger testes and accessory glands. This does not support the hypothesis that females gain fertility benefits from mating with attractive males. Such males appear to restrict ejaculate allocation per mating so as to participate in a greater number of mating events.

Mountains host greater avian diversity than lowlands at the same latitude due to their greater diversity of habitats stratified along an elevation gradient. Here we test whether this greater ecological heterogeneity promotes sympatric speciation. We selected accentors (Prunellidae), an avian family associated with mountains of the Palearctic, as a model system. Accentors differ in their habitat/elevation preferences and south-central Siberia and Himalayan regions each host 6 of the 13 species in the family. We used sequences of the mtDNA ND2 gene and the intron 9 of the Z chromosome specific ACO1 gene to reconstruct a complete species-level phylogeny of Prunellidae. The tree based on joint analysis of both loci was used to reconstruct the family's biogeographic history and to date the diversification events. We also analyzed the relationship between the node age and sympatry, to determine the geographic mode of speciation in Prunellidae. Our data suggest a Miocene origin of Prunellidae in the Himalayan region. The major division between alpine species (subgenus Laiscopus) and species associated with shrubs (subgenus Prunella) and initial diversification events within the latter happened within the Himalayan region in the Miocene and Pliocene. Accentors colonized other parts of the Palearctic during the Pliocene-Pleistocene transition. This spread across the Palearctic resulted in rapid diversification of accentors. With only a single exception dating to 0.91 Ma, lineages younger than 1.5 Ma are allopatric. In contrast, sympatry values for older nodes are >0. There was no relationship between node age and range symmetry. Allopatric speciation (not to include peripatric) is the predominant geographic mode of speciation in Prunellidae despite the favorable conditions for ecological diversification in the mountains and range overlaps among species.

In this study, we test whether greater diversity of habitats stratified along an elevation gradient in the mountains promotes sympatric speciation in birds. Using sequences of one mtDNA gene and one sex specific intron, we reconstructed a complete species-level phylogeny of Prunellidae, which we used to reconstruct the family's biogeographic history. Our data suggest that allopatric speciation (not to include peripatric) is the predominant geographic mode of speciation in Prunellidae despite the favorable conditions for ecological diversification in the mountains and range overlaps among species.

Parasite communities of fishes are known to respond directly to the abiotic environment of the host, for example, to water quality and water temperature. Biotic factors are also important as they affect the exposure profile through heterogeneities in parasite distribution in the environment. Parasites in a particular environment may pose a strong selection on fish. For example, ecological differences in selection by parasites have been hypothesized to facilitate evolutionary differentiation of freshwater fish morphs specializing on different food types. However, as parasites may also respond directly to abiotic environment the parasite risk does not depend only on biotic features of the host environment. It is possible that different morphs experience specific selection gradients by parasites but it is not clear how consistent the selection is when abiotic factors change. We examined parasite pressure in sympatric morphs of threespine stickleback (Gasterosteus aculeatus) across a temperature gradient in two large Icelandic lakes, Myvatn and Thingvallavatn. Habitat-specific temperature gradients in these lakes are opposite. Myvatn lava rock morph lives in a warm environment, while the mud morph lives in the cold. In Thingvallavatn, the lava rock morph lives in a cold environment and the mud morph in a warm habitat. We found more parasites in fish living in higher temperature in both lakes, independent of the fish morph, and this pattern was similar for the two dominating parasite taxa, trematodes and cestodes. However, at the same time, we also found higher parasite abundance in a third morph living in deep cold–water habitat in Thingvallavatn compared to the cold-water lava morph, indicating strong effect of habitat-specific biotic factors. Our results suggest complex interactions between water temperature and biotic factors in determining the parasite community structure, a pattern that may have implications for differentiation of stickleback morphs.

Ecological differences in selection by parasites have recently been hypothesized to facilitate evolutionary differentiation of freshwater fish morphs. However, as parasites may also respond directly to abiotic environment, such as water temperature, it is not clear how consistent these selection gradients are when abiotic factors change. We examined parasite pressure in sympatric morphs of threespine stickleback in two Icelandic lakes with opposing habitat-specific water temperature gradients. We found higher infestation in fish living in higher temperature irrespective of the fish morph, but also a strong effect of host ecology in a morph living in deep cold water habitat. These results suggest complex interactions between water temperature and biotic factors in determining the parasite community structure, a pattern that may have implications for differentiation of stickleback morphs.

Population level response to hypoxia has become an issue of global significance because of increased frequency and intensity of hypoxic events worldwide, and the potential for global warming to exacerbate hypoxic stress. In this study, we sequenced two nuclear intronic regions and a single mitochondrial region across seven populations of the African cyprinid, Barbus neumayeri from two river drainages in Uganda: the Rwembaita Swamp-Njuguta River System and the Dura River. We then examined two indices of population structure, G_ST and Jost's D, to detect links between oxygen availability and genetic variation and to determine if population genetic structure was associated with (i) dissolved oxygen regime (hypoxia or normoxia), (ii) geographical distance, or (iii) a combination of dissolved oxygen regime and geographical distance. Our results indicate that over a large scale (between drainages), geographical distance significantly affects the genetic structure of populations. However, within a single drainage, dissolved oxygen regime plays a key role in determining the genetic structure of populations. Within the Rwembaita-Njuguta system, gene flow was high between locations of similar oxygen regimes, but low between areas characterized by divergent oxygen regimes. Interestingly, G_ST analyses appear to yield less realistic measures of population structure than Jost's D, suggesting that caution must be taken when interpreting and comparing the results from different studies. These results support the idea that aquatic dissolved oxygen can act as a selective force limiting gene flow among populations of aquatic species and therefore should be considered when implementing conservation plans and assessing environmental impact of human activities.

Barbus neumayeri population structure across oxygen regimes.

In heterogeneous environments, landscape features directly affect the structure of genetic variation among populations by functioning as barriers to gene flow. Resource-associated population genetic structure, in which populations that use different resources (e.g., host plants) are genetically distinct, is a well-studied example of how environmental heterogeneity structures populations. However, the pattern that emerges in a given landscape should depend on its particular combination of resources. If resources constitute barriers to gene flow, population differentiation should be lowest in homogeneous landscapes, and highest where resources exist in equal proportions. In this study, we tested whether host community diversity affects population genetic structure in a beetle (Bolitotherus cornutus) that exploits three sympatric host fungi. We collected B. cornutus from plots containing the three host fungi in different proportions and quantified population genetic structure in each plot using a panel of microsatellite loci. We found no relationship between host community diversity and population differentiation in this species; however, we also found no evidence of resource-associated differentiation, suggesting that host fungi are not substantial barriers to gene flow. Moreover, we detected no genetic differentiation among B. cornutus populations separated by several kilometers, even though a previous study demonstrated moderate genetic structure on the scale of a few hundred meters. Although we found no effect of community diversity on population genetic structure in this study, the role of host communities in the structuring of genetic variation in heterogeneous landscapes should be further explored in a species that exhibits resource-associated population genetic structure.

The diversity of the resource community is expected to affect landscape-level population structure in heterogeneous environments because resources often function as barriers to gene flow. We found no relationship between resource community diversity and population differentiation in a beetle metapopulation, but the resources (fungi) do not appear to be barriers to gene flow in this species. The role of resource communities in structuring genetic variation should be further explored in species known to exhibit resource-associated population structure.

When organisms perform a single task, selection leads to phenotypes that maximize performance at that task. When organisms need to perform multiple tasks, a trade-off arises because no phenotype can optimize all tasks. Recent work addressed this question, and assumed that the performance at each task decays with distance in trait space from the best phenotype at that task. Under this assumption, the best-fitness solutions (termed the Pareto front) lie on simple low-dimensional shapes in trait space: line segments, triangles and other polygons. The vertices of these polygons are specialists at a single task. Here, we generalize this finding, by considering performance functions of general form, not necessarily functions that decay monotonically with distance from their peak. We find that, except for performance functions with highly eccentric contours, simple shapes in phenotype space are still found, but with mildly curving edges instead of straight ones. In a wide range of systems, complex data on multiple quantitative traits, which might be expected to fill a high-dimensional phenotype space, is predicted instead to collapse onto low-dimensional shapes; phenotypes near the vertices of these shapes are predicted to be specialists, and can thus suggest which tasks may be at play.

We studied the effect of trade-offs between tasks on the suite of variation of phenotypes. We find that, for a wide range of performance function shapes, Pareto optimal phenotypes lie in morphospace on low-dimensional polygons with mildly curved edges, whose vertices are phenotypes specialized for a single task, known as archetypes. We also present bounds on the Pareto front for general, non-monotonic performance functions, showing that the suite of variation is restricted to a region spanning the archetypes.

The impact of climate change on herbivorous insects can have far-reaching consequences for ecosystem processes. However, experiments investigating the combined effects of multiple climate change drivers on herbivorous insects are scarce. We independently manipulated three climate change drivers (CO₂, warming, drought) in a Danish heathland ecosystem. The experiment was established in 2005 as a full factorial split-plot with 6 blocks × 2 levels of CO₂ × 2 levels of warming × 2 levels of drought = 48 plots. In 2008, we exposed 432 larvae (n = 9 per plot) of the heather beetle (Lochmaea suturalis Thomson), an important herbivore on heather, to ambient versus elevated drought, temperature, and CO₂ (plus all combinations) for 5 weeks. Larval weight and survival were highest under ambient conditions and decreased significantly with the number of climate change drivers. Weight was lowest under the drought treatment, and there was a three-way interaction between time, CO₂, and drought. Survival was lowest when drought, warming, and elevated CO₂ were combined. Effects of climate change drivers depended on other co-acting factors and were mediated by changes in plant secondary compounds, nitrogen, and water content. Overall, drought was the most important factor for this insect herbivore. Our study shows that weight and survival of insect herbivores may decline under future climate. The complexity of insect herbivore responses increases with the number of combined climate change drivers.

In a multi-factor climate change experiment, we tested effects of three independent global change drivers on insect herbivore performance. We found that most drivers adversely affected herbivore performance. The most surprising result of our study, however, was that the number of global change drivers (0, 1, 2 or 3) additively affected herbivore performance.

The pathway and frequency of species' introductions can affect the extent, impact, and management of biological invasions. Here, we examine the pathway of introduction of the aquatic plant Cabomba caroliniana (fanwort) into Canada and the northern United States using plastid DNA sequence (intergenic spacers atpF-atpH, trnH-psbA, and trnL-trnF) and DNA content analyses. We test the hypothesis that the spread of fanwort is a result of commercial trade by comparing a Canadian population (Kasshabog Lake, ON) to native populations from southern U.S., introduced populations in northern U.S., and plants from commercial retailers. Thirteen plastid haplotypes were identified throughout North America, including one dominant haplotype, which was present in all C. caroliniana populations. Several rare haplotypes were used to infer shared colonization history. In particular, the Canadian population shared two rare alleles with a population from Massachusetts, suggesting range expansion of C. caroliniana from the northern U.S. However, the possibility of a commercial introduction cannot be excluded, as common alleles were shared between the Canadian population and both commercial and southern U.S. sources. Variation in C. caroliniana genome size was bimodal and populations were classified into “high” and “low” categories. The Canadian population had DNA contents similar to several northern U.S. populations (low DNA content). This may provide additional support for range expansion from these introduced populations rather than from commercial sources or populations in the southern U.S., which had high DNA content.

Cabomba caroliniana is considered an aggressive aquatic invasive species, and there is much interest in determining the source of introduced populations. Using chloroplast DNA sequences and genome size variation, our research presents evidence to suggest that the movement of C. caroliniana into Canada is from populations in the northeastern United States, and less likely to be from commercial sources. We discuss several possible pathways of introduction for C. caroliniana across North America.

Calochortus (Liliaceae) displays high species richness, restriction of many individual taxa to narrow ranges, geographic coherence of individual clades, and parallel adaptive radiations in different regions. Here we test the first part of a hypothesis that all of these patterns may reflect gene flow at small geographic scales. We use amplified fragment length polymorphism variation to quantify the geographic scales of spatial genetic structure and apparent gene flow in Calochortus albus, a widespread member of the genus, at Henry Coe State Park in the Coast Ranges south of San Francisco Bay. Analyses of 254 mapped individuals spaced 0.001–14.4 km apart show a highly significant decline in genetic identity with ln distance, implying a root-mean-square distance of gene flow σ of 5–43 m. STRUCTURE analysis implies the existence of 2–4 clusters over the study area, with frequent reversals among clusters over short distances (<200 m) and a relatively high frequency of admixture within individuals at most sampling sites. While the intensity of spatial genetic structure in C. albus is weak, as measured by the Sp statistic, that appears to reflect low genetic identity of adjacent plants, which might reflect repeated colonizations at small spatial scales or density-dependent mortality of individual genotypes by natural enemies. Small spatial scales of gene flow and spatial genetic structure should permit, under a variety of conditions, genetic differentiation within species at such scales, setting the stage ultimately for speciation and adaptive radiation as such scales as well.

Studies of spatial genetic structure in populations of Calochortus albus in northern California confirm that gene flow in this species occurs only at mean distances less than 50 m. This accords with a hypothesis to account for extensive speciation, narrow endemism, geographic cohesion of clades, and convergent patterns of adaptive radiation in the genus based on limited seed dispersal.

Aluminum (Al) toxicity is a major factor limiting plant growth in acid soils. Elevated atmospheric CO₂ [CO₂] enhances plant growth. However, there is no report on the effect of elevated [CO₂] on growth of plant genotypes differing in Al tolerance grown in acid soils. We investigated the effect of short-term elevated [CO₂] on growth of Al-tolerant (ET8) and Al-sensitive (ES8) wheat plants and malate exudation from root apices by growing them in acid soils under ambient [CO₂] and elevated [CO₂] using open-top chambers. Exposure of ET8 plants to elevated [CO₂] enhanced root biomass only. In contrast, shoot biomass of ES8 was enhanced by elevated [CO₂]. Given that exudation of malate to detoxify apoplastic Al is a mechanism for Al tolerance in wheat plants, ET8 plants exuded greater amounts of malate from root apices than ES8 plants under both ambient and elevated [CO₂]. These results indicate that elevated [CO₂] has no effect on malate exudation in both ET8 and ES8 plants. These novel findings have important implications for our understanding how plants respond to elevated [CO₂] grown in unfavorable edaphic conditions in general and in acid soils in particular.

Wheat genotypes with contrasting tolerance to aluminium showed different growth response to elevated CO₂ when grown in acid soil. Exudation of malate from root apices of aluminum-tolerant ET8 genotype was greater than those of Al-sensitive ES8 genotype under both ambient and elevated CO₂, and the malate exudation rate expressed on individual root apex was not affected by elevated CO₂. These results have important implications for our understanding how plants respond to elevated [CO₂] grown in unfavorable edaphic conditions in general and in acid soils in particular.

A historically unprecedented mountain pine beetle (MPB) outbreak affected western Montana during the past decade. We examined radial growth rates (AD 1860–2007/8) of co-occurring mature healthy and MPB-infected ponderosa pine trees collected at two sites (Cabin Gulch and Kitchen Gulch) in western Montana and: (1) compared basal area increment (BAI) values within populations and between sites; (2) used carbon isotope analysis to calculate intrinsic water-use efficiency (iWUE) at Cabin Gulch; and (3) compared climate-growth responses using a suite of monthly climatic variables. BAI values within populations and between sites were similar until the last 20–30 years, at which point the visually healthy populations had consistently higher BAI values (22–34%) than the MPB-infected trees. These results suggest that growth rates two–three decades prior to the current outbreak diverged between our selected populations, with the slower-growing trees being more vulnerable to beetle infestation. Both samples from Cabin Gulch experienced upward trends in iWUE, with significant regime shifts toward higher iWUE beginning in 1955–59 for the visually healthy trees and 1960–64 for the MPB-infected trees. Drought tolerance also varied between the two populations with the visually healthy trees having higher growth rates than MPB-infected trees prior to infection during a multi-decadal period of drying summertime conditions. Intrinsic water-use efficiency significantly increased for both populations during the past 150 years, but there were no significant differences between the visually healthy and MPB-infected chronologies.

A historically unprecedented mountain pine beetle (MPB) outbreak affected western Montana during the past decade. We examine radial growth rates of visually healthy and MPB-infected adult ponderosa pine and compare growth rates, intrinsic water-use efficiency, and drought responses at two sites. Basal area increment (BAI) values within populations and between sites were similar until the last 20–30 years, at which point the visually healthy populations had consistently lower BAI values.

Direct and indirect effects of warming are increasingly modifying the carbon-rich vegetation and soils of the Arctic tundra, with important implications for the terrestrial carbon cycle. Understanding the biological and environmental influences on the processes that regulate foliar carbon cycling in tundra species is essential for predicting the future terrestrial carbon balance in this region. To determine the effect of climate change impacts on gas exchange in tundra, we quantified foliar photosynthesis (A_net), respiration in the dark and light (R_D and R_L, determined using the Kok method), photorespiration (PR), carbon gain efficiency (CGE, the ratio of photosynthetic CO₂ uptake to total CO₂ exchange of photosynthesis, PR, and respiration), and leaf traits of three dominant species – Betula nana, a woody shrub; Eriophorum vaginatum, a graminoid; and Rubus chamaemorus, a forb – grown under long-term warming and fertilization treatments since 1989 at Toolik Lake, Alaska. Under warming, B. nana exhibited the highest rates of A_net and strongest light inhibition of respiration, increasing CGE nearly 50% compared with leaves grown in ambient conditions, which corresponded to a 52% increase in relative abundance. Gas exchange did not shift under fertilization in B. nana despite increases in leaf N and P and near-complete dominance at the community scale, suggesting a morphological rather than physiological response. Rubus chamaemorus, exhibited minimal shifts in foliar gas exchange, and responded similarly to B. nana under treatment conditions. By contrast, E. vaginatum, did not significantly alter its gas exchange physiology under treatments and exhibited dramatic decreases in relative cover (warming: −19.7%; fertilization: −79.7%; warming with fertilization: −91.1%). Our findings suggest a foliar physiological advantage in the woody shrub B. nana that is further mediated by warming and increased soil nutrient availability, which may facilitate shrub expansion and in turn alter the terrestrial carbon cycle in future tundra environments.

When considering the carbon reservoir of the Arctic tundra and its future fate, it is important to include estimates of leaf-level physiological responses of tundra species and how they may change under future predicted conditions. Here, we present the first ecologically meaningful estimates of respiration to consider the known inhibition of respiration caused by light from the well-studied, long-term global change experiment at Toolik Lake, Alaska. Our results suggest that different functional strategies under the individual treatments may allow for the continued encroachment and expansion of woody shrubs into the Arctic tundra as temperatures warm in this region, and this has significant implications for both biodiversity and carbon storage.

Functional plant traits are likely to adapt under the sustained pressure imposed by environmental changes through natural selection. Employing Brassica napus as a model, a multi-generational study was performed to investigate the potential trajectories of selection at elevated [CO₂] in two different temperature regimes. To reveal phenotypic divergence at the manipulated [CO₂] and temperature conditions, a full-factorial natural selection regime was established in a phytotron environment over the range of four generations. It is demonstrated that a directional response to selection at elevated [CO₂] led to higher quantities of reproductive output over the range of investigated generations independent of the applied temperature regime. The increase in seed yield caused an increase in aboveground biomass. This suggests quantitative changes in the functions of carbon sequestration of plants subjected to increased levels of CO₂ over the generational range investigated. The results of this study suggest that phenotypic divergence of plants selected under elevated atmospheric CO₂ concentration may drive the future functions of plant productivity to be different from projections that do not incorporate selection responses of plants. This study accentuates the importance of phenotypic responses across multiple generations in relation to our understanding of biogeochemical dynamics of future ecosystems. Furthermore, the positive selection response of reproductive output under increased [CO₂] may ameliorate depressions in plant reproductive fitness caused by higher temperatures in situations where both factors co-occur.

A multi-generational study investigating phenotypic trajectories of selection at elevated [CO₂] in two different temperature regimes revealed an increased overall aboveground biomass and higher reproductive output as a specific response of plants selected in high [CO₂] environments. This accentuates the importance of phenotypic divergence across multiple generations in relation to our understanding of future ecosystem functioning.

The species-area relationship (SAR) has proven to be one of the few strong generalities in ecology. The temporal analog of the SAR, the species-time relationship (STR), has received considerably less attention. Recent work primarily from the temperate zone has aimed to merge the SAR and the STR into a synthetic and unified species-time-area relationship (STAR) as originally envisioned by Preston (1960). Here we test this framework using two tropical tree communities and extend it by deriving a phylogenetic-time-area relationship (PTAR). The work finds some support for Preston's prediction that diversity-time relationships, both species and phylogenetic, are sensitive to the spatial scale of the sampling. Contrary to the Preston's predictions we find a decoupling of diversity-area and diversity-time relationships in both forests as the time period used to quantify the diversity-area relationship changes. In particular, diversity-area and diversity-time relationships are positively correlated using the initial census to quantify the diversity-area relationship, but weakly or even negatively correlated when using the most recent census. Thus, diversity-area relationships could forecast the temporal accumulation of biodiversity of the forests, but they failed to “back-cast” the temporal accumulation of biodiversity suggesting a decoupling of space and time.

This work shows that the species-time area and phylogenetic-time area relationship frameworks are generalizable to diverse tropical tree communities. It also shows strong relationships between the species-area relationship (SAR) and species-time relationship (STR) scaling exponents and the phylogenetic-area relationship (PAR) and phylogenetic-time relationship (PTR) scaling exponents and suggests that it is possible to predict the temporal accumulation of species or phylogenetic diversity (e.g., STR or PTR) from the initial SAR or PAR of the two forests studied.

Extinction always results in loss of phylogenetic diversity (PD), but phylogenetically selective extinctions have long been thought to disproportionately reduce PD. Recent simulations show that tree shapes also play an important role in determining the magnitude of PD loss, potentially offsetting the effects of clustered extinctions. While patterns of PD loss under different extinction scenarios are becoming well characterized in model phylogenies, analyses of real clades that often have unbalanced tree shapes remain scarce, particularly for marine organisms. Here, we use a fossil-calibrated phylogeny of all living scleractinian reef corals in conjunction with IUCN data on extinction vulnerabilities to quantify how loss of species in different threat categories will affect the PD of this group. Our analyses reveal that predicted PD loss in corals varies substantially among different threats, with extinctions due to bleaching and disease having the largest negative effects on PD. In general, more phylogenetically clustered extinctions lead to larger losses of PD in corals, but there are notable exceptions; extinction of rare corals from distantly-related old and unique lineages can also result in substantial PD loss. Thus our results show that loss of PD in reef corals is dependent on both tree shape and the nature of extinction threats.

Using the first fossil-calibrated phylogeny of all living scleractinian reef corals, in conjunction with IUCN data on extinction vulnerabilities, we model how loss of species due to various threats can affect the future phylogenetic diversity of corals. Results reveal considerable variation in predicted loss of phylogenetic diversity across different threat categories that would be useful for setting conservation priorities.

The molecular genetic mechanisms facilitating local adaptation in salmonids continue to be poorly characterized. Gene transcription is a highly regulated step in the expression of a phenotype and it has been shown to respond to selection and thus may be one mechanism that facilitates the development of local adaptation. Advances in molecular genetic tools and an increased understanding of the functional roles of specific genes allow us to test hypotheses concerning the role of variable environments in shaping transcription at known-function candidate loci. To address these hypotheses, wild rainbow trout were collected in their first summer and subjected to metabolic and immune challenges. We assayed gene transcription at candidate loci that play a role in the molecular genetic response to these stresses, and correlated transcription with temperature data from the streams and the abundance and diversity of bacteria as characterized by massively parallel pyrosequencing. Patterns of transcriptional regulation from resting to induced levels varied among populations for both treatments. Co-inertia analysis demonstrated significant associations between resting levels of metabolic gene transcription and thermal regime (R² = 0.19, P = 0.013) as well as in response to challenge (R² = 0.39, P = 0.001) and resting state and challenged levels of cytokine gene transcription with relative abundances of bacteria (resting: R² = 0.25, P = 0.009, challenged: R² = 0.65, P = 0.001). These results show that variable environments, even within a small geographic range (<250 km), can drive divergent selection among populations for transcription of genes related to surviving stress.

Gene transcription is a highly regulated step in the expression of a phenotype that has been implicated in the development of local adaptation. We assayed candidate gene transcription in wild juvenile rainbow trout and correlated transcription with temperature data and abundance of bacteria in the sampled streams. Co-inertia analysis demonstrated significant associations between metabolic gene transcription and thermal regime and cytokine gene transcription with relative abundances of bacteria. Our results indicate that local adaptation of Babine Lake rainbow trout is mediated by gene transcription.

Recent theory in social evolution has been mainly concerned with competition and cooperation within social groups of animals and their impact on the stability of those groups. Much less attention has been paid to conflicts arising as a result of solitary floaters (outsiders) attempting to join groups of established residents (insiders). We model such conflicts over group-membership using a demographically explicit approach in which the rates of births and deaths in a population determine the availability of group-vacancies and the number of floaters competing over these vacancies. We find that the outcome of within-group competition, reflected in the partitioning of reproduction among group members, exerts surprisingly little influence on the resolution of insider-outsider conflict. The outcome of such conflict is also largely unaffected by differences in resource holding potential between insiders and outsiders. By contrast, whether or not groups form is mainly determined by demographic factors (variation in vital rates such as fecundity and mortality) and the resulting population dynamics. In particular, at high floater densities territory defense becomes too costly, and groups form because insiders give in to the intruder pressure imposed on them by outsiders. We emphasize the importance of insider-outsider conflicts in social evolution theory and highlight avenues for future research.

We model conflicts over group membership between established residents (insiders) and solitary floaters (outsiders) in a patch structured population. Our results show that whether or not groups form is mainly determined by demographic processes: If high per-group fecundity (relative to resident mortality) leads to a high degree of habitat saturation, territory defense becomes too costly, and groups form because insiders give in to the intruder pressure imposed on them by outsiders.

Sex-biased dispersal has profound impacts on a species' biology and several factors have been attributed to its evolution, including mating system, inbreeding avoidance, and social complexity. Sex-biased dispersal and its potential link to individual social interactions were examined in the Qinghai toad-headed agamid (Phrynocephalus vlangalii). We first determined the pattern of sex-biased dispersal using population genetic methods. A total of 345 specimens from 32 sites in the Qaidam Basin were collected and genotyped for nine microsatellite DNA loci. Both individual-based assignment tests and allele frequency-based analyses were conducted. Females revealed much more genetic structure than males and all results were consistent with male-biased dispersal. First-generation migrants were also identified by genetic data. We then examined eight social interaction-related morphological traits and explored their potential link to sex-biased dispersal. Female residents had larger heads and longer tails than female migrants. The well-developed signal system among females, coupled with viviparity, might make remaining on natal sites beneficial, and hence promote female philopatry. Dominant females with larger heads were more likely to stay. Contrary to females, male migrants had larger heads and belly patches than residents, suggesting that dispersal might confer selective advantages for males. Such advantages may include opportunities for multiple mating and escaping from crowded sites. Large belly patches and several other morphological traits may assist their success in obtaining mates during dispersal. Furthermore, a relatively high relatedness (R = 0.06) among females suggested that this species might have rudimentary social structure. Case studies in “less” social species may provide important evidence for a better understanding of sex-biased dispersal.

The Qinghai toad-headed agamid demonstrates a clear male-biased dispersal pattern. Social structure and associated cost-benefit dynamics may contribute to the observed pattern.

In house mice, genetic compatibility is influenced by the t haplotype, a driving selfish genetic element with a recessive lethal allele, imposing fundamental costs on mate choice decisions. Here, we evaluate the cost of genetic incompatibility and its implication for mate choice in a wild house mice population. In laboratory reared mice, we detected no fertility (number of embryos) or fecundity (ability to conceive) costs of the t, and yet we found a high cost of genetic incompatibility: heterozygote crosses produced 40% smaller birth litter sizes because of prenatal mortality. Surprisingly, transmission of t in crosses using +/t males was influenced by female genotype, consistent with postcopulatory female choice for + sperm in +/t females. Analysis of paternity patterns in a wild population of house mice showed that +/t females were more likely than +/+ females to have offspring sired by +/+ males, and unlike +/+ females, paternity of their offspring was not influenced by +/t male frequency, further supporting mate choice for genetic compatibility. As the major histocompatibility complex (MHC) is physically linked to the t, we investigated whether females could potentially use variation at the MHC to identify male genotype at the sperm or individual level. A unique MHC haplotype is linked to the t haplotype. This MHC haplotype could allow the recognition of t and enable pre- and postcopulatory mate choice for genetic compatibility. Alternatively, the MHC itself could be the target of mate choice for genetic compatibility. We predict that mate choice for genetic compatibility will be difficult to find in many systems, as only weak fertilization biases were found despite an exceptionally high cost of genetic incompatibility.

In wild house mice, a selfish genetic element called the t haplotype showed 90% drive and caused a 40% reduction in litter size through prenatal mortality in heterozygote crosses. Heterozygous females reduced the occurrence of such genetically incompatible fertilizations by preferring wild-type males in a free-living population, and through a fertilization bias in favor of + sperm in monogamous matings with heterozygote males in the laboratory. The mechanism underlying the apparent ability to discriminate between + and t is consistent with recognition of the unique MHC haplotype that we found to be linked to the t.

Major disjunctions among marine communities in southeastern Australia have been well documented, although explanations for biogeographic structuring remain uncertain. Converging ocean currents, environmental gradients, and habitat discontinuities have been hypothesized as likely drivers of structuring in many species, although the extent to which species are affected appears largely dependent on specific life histories and ecologies. Understanding these relationships is critical to the management of native and invasive species, and the preservation of evolutionary processes that shape biodiversity in this region. In this study we test the direct influence of ocean currents on the genetic structure of a passive disperser across a major biogeographic barrier. Donax deltoides (Veneroida: Donacidae) is an intertidal, soft-sediment mollusc and an ideal surrogate for testing this relationship, given its lack of habitat constraints in this region, and its immense dispersal potential driven by year-long spawning and long-lived planktonic larvae. We assessed allele frequencies at 10 polymorphic microsatellite loci across 11 sample locations spanning the barrier region and identified genetic structure consistent with the major ocean currents of southeastern Australia. Analysis of mitochondrial DNA sequence data indicated no evidence of genetic structuring, but signatures of a species range expansion corresponding with historical inundations of the Bassian Isthmus. Our results indicate that ocean currents are likely to be the most influential factor affecting the genetic structure of D. deltoides and a likely physical barrier for passive dispersing marine fauna generally in southeastern Australia.

Ocean currents influence the genetic structure of an intertidal mollusc in southeastern Australia – implications for predicting the movement of passive dispersers across a marine biogeographic barrier.

Online databases of biological information offer tremendous potential for evolutionary and ecological discoveries, especially if data are combined in novel ways. However, the different names and varied spellings used for many species present major barriers to linking data. Taxonome is a software tool designed to solve this problem by quickly and reproducibly matching biological names to a given reference set. It is available both as a graphical user interface (GUI) for simple interactive use, and as a library for more advanced functionality with programs written in Python. Taxonome also includes functions to standardize distribution information to a well-defined set of regions, such as the TDWG World Geographical Scheme for Recording Plant Distributions. In combination, these tools will help biologists to rapidly synthesize disparate datasets, and to investigate large-scale patterns in species traits.

Taxonome is a software package for indexing and linking data using taxon names, and for resolving synonyms. This addresses a common problem for researchers working with data on many species.

Phosphorus (P) is an essential nutrient for growth in consumers. P-limitation and parasite infection comprise one of the most common stressor pairs consumers confront in nature. We conducted a life-table study using a Daphnia–microsporidian parasite model, feeding uninfected or infected Daphnia with either P-sufficient or P-limited algae, and assessed the impact of the two stressors on life-history traits of the host. Both infection and P-limitation negatively affected some life-history traits tested. However, under P-limitation, infected animals had higher juvenile growth rate as compared with uninfected animals. All P-limited individuals died before maturation, regardless of infection. The numbers of spore clusters of the microsporidian parasite did not differ in P-limited or P-sufficient hosts. P-limitation, but not infection, decreased body phosphorus content and ingestion rates of Daphnia tested in separate experiments. As parasite spore production did not suffer even under extreme P-limitation, our results suggest that parasite was less limited by P than the host. We discuss possible interpretations concerning the stoichiometrical demands of parasite and suggest that our results are explained by parasite-driven changes in carbon (C) allocation of the hosts. We conclude that the impact of nutrient starvation and parasite infection on consumers depends not only on the stoichiometric demands of host but also those of the parasite.

The effect of parasite on host life-history traits was studied under different host nutrient regimes using Daphnia magna-microparasite system. We demonstrated that the impact of nutrient starvation and parasite infection on consumers depends not only on the stoichiometric demands of host but also those of the parasite.

Fitness is the central concept in evolutionary theory. It measures a phenotype's ability to survive and reproduce. There are different ways to represent this measure: Malthusian fitness and Wrightian fitness. One can go back and forth between the two, but when we characterize model properties or interpret data, it can be important to distinguish between them. Here, we discuss a recent experiment to show how the interpretation changes if an alternative definition is used.

To characterize model properties or interpret data, it can be important to distinguish between different ways to define fitness. We discuss a recent experiment to show how the interpretation can change if an alternative definition is used.

In terrestrial ecosystems, plant roots are colonized by various clades of mycorrhizal and endophytic fungi. Focused on the root systems of an oak-dominated temperate forest in Japan, we used 454 pyrosequencing to explore how phylogenetically diverse fungi constitute an ecological community of multiple ecotypes. In total, 345 operational taxonomic units (OTUs) of fungi were found from 159 terminal-root samples from 12 plant species occurring in the forest. Due to the dominance of an oak species (Quercus serrata), diverse ectomycorrhizal clades such as Russula, Lactarius, Cortinarius, Tomentella, Amanita, Boletus, and Cenococcum were observed. Unexpectedly, the root-associated fungal community was dominated by root-endophytic ascomycetes in Helotiales, Chaetothyriales, and Rhytismatales. Overall, 55.3% of root samples were colonized by both the commonly observed ascomycetes and ectomycorrhizal fungi; 75.0% of the root samples of the dominant Q. serrata were so cocolonized. Overall, this study revealed that root-associated fungal communities of oak-dominated temperate forests were dominated not only by ectomycorrhizal fungi but also by diverse root endophytes and that potential ecological interactions between the two ecotypes may be important to understand the complex assembly processes of belowground fungal communities.

In terrestrial ecosystems, plant roots are colonized by various clades of mycorrhizal and endophytic fungi. Focused on the root systems of an oak-dominated temperate forest in Japan, we used 454 pyrosequencing to explore how phylogenetically diverse fungi constitute an ecological community of multiple ecotypes. This study revealed that root-associated fungal communities of oak-dominated temperate forests were dominated not only by ectomycorrhizal fungi but also by diverse root endophytes and that potential ecological interactions between the two ecotypes may be important to understand the complex assembly processes of belowground fungal communities.

Estimates of population size are critical for conservation and management, but accurate estimates are difficult to obtain for many species. Noninvasive genetic methods are increasingly used to estimate population size, particularly in elusive species such as large carnivores, which are difficult to count by most other methods. In most such studies, genotypes are treated simply as unique individual identifiers. Here, we develop a new estimator of population size based on pedigree reconstruction. The estimator accounts for individuals that were directly sampled, individuals that were not sampled but whose genotype could be inferred by pedigree reconstruction, and individuals that were not detected by either of these methods. Monte Carlo simulations show that the population estimate is unbiased and precise if sampling is of sufficient intensity and duration. Simulations also identified sampling conditions that can cause the method to overestimate or underestimate true population size; we present and discuss methods to correct these potential biases. The method detected 2–21% more individuals than were directly sampled across a broad range of simulated sampling schemes. Genotypes are more than unique identifiers, and the information about relationships in a set of genotypes can improve estimates of population size.

The size of a population is one of the most basic and critical pieces of information for conservation and management but population size is difficult to measure for many species. Methods exist to estimate population size using genotypes from noninvasive samples, but these methods treat genotypes as simple markers that identify individuals. A set of genotypes contains more information than this and simulation shows that taking advantage of the information that genotypes provide about relationships between individuals can improve estimates of population size.

Recent studies suggest that higher growth rates may be associated with reduced capacities for stress tolerance and increased accumulated damage due to reactive oxygen species. We tested the response of Manduca sexta (Sphingidae) lines selected for large or small body size and short development time to hypoxia (10 kPa) and hyperoxia (25, 33, and 40 kPa); both hypoxia and hyperoxia reduce reproduction and oxygen levels over 33 kPa have been shown to increase oxidative damage in insects. Under normoxic (21 kPa) conditions, individuals from the large-selected (big-fast) line were larger and had faster growth rates, slightly longer developmental times, and reduced survival rates compared to individuals from a line selected for small size (small-fast) or an unselected control line. Individuals from the big-fast line exhibited greater negative responses to hyperoxia with greater reductions in juvenile and adult mass, growth rate, and survival than the other two lines. Hypoxia generally negatively affected survival and growth/size, but the lines responded similarly. These results are mostly consistent with the hypothesis that simultaneous acquisition of large body sizes and short development times leads to reduced capacities for coping with stressful conditions including oxidative damage. This result is of particular importance in that natural selection tends to decrease development time and increase body size.

We tested the response of Manduca sexta (Sphingidae) lines selected for large or small body size and short development time to hypoxia (10 kPa) and hyperoxia (25, 33, and 40 kPa). Individuals from the big-fast line exhibited greater negative responses to hyperoxia with greater reductions in juvenile and adult mass, growth rate and survival than the other two lines. These results are consistent with the hypothesis that simultaneous acquisition of large body sizes and short development times leads to reduced and more variable capacities for coping with stressful conditions.

Spatially intimate symbioses, such as those between scleractinian corals and unicellular algae belonging to the genus Symbiodinium, can potentially adapt to changes in the environment by altering the taxonomic composition of their endosymbiont communities. We quantified the spatial relationship between the cumulative frequency of thermal stress anomalies (TSAs) and the taxonomic composition of Symbiodinium in the corals Montipora capitata, Porites lobata, and Porites compressa across the Hawaiian archipelago. Specifically, we investigated whether thermally tolerant clade D Symbiodinium was in greater abundance in corals from sites with high frequencies of TSAs. We recovered 2305 Symbiodinium ITS2 sequences from 242 coral colonies in lagoonal reef habitats at Pearl and Hermes Atoll, French Frigate Shoals, and Kaneohe Bay, Oahu in 2007. Sequences were grouped into 26 operational taxonomic units (OTUs) with 12 OTUs associated with Montipora and 21 with Porites. Both coral genera associated with Symbiodinium in clade C, and these co-occurred with clade D in M. capitata and clade G in P. lobata. The latter represents the first report of clade G Symbiodinium in P. lobata. In M. capitata (but not Porites spp.), there was a significant correlation between the presence of Symbiodinium in clade D and a thermal history characterized by high cumulative frequency of TSAs. The endogenous community composition of Symbiodinium and an association with clade D symbionts after long-term thermal disturbance appear strongly dependent on the taxa of the coral host.

Corals form mutualistic symbioses with photosynthetic dinoflagellates belonging to the genus Symbiodinium. In this study, we show that the history of ocean thermal stress influences the community of Symbiodinium in corals, but this influence is host specific. Our results shed light on the differential response of corals to a changing ocean environment.

Tree root distribution and activity are determinants of belowground competition. However, studying root response to environmental and management conditions remains logistically challenging. Methodologically, nondestructive in situ tree root ecology analysis has lagged. In this study, we tested a nondestructive approach to determine tree coarse root architecture and function of a perennial tree crop, Theobroma cacao L., at two edaphically contrasting sites (sandstone and phyllite–granite derived soils) in Ghana, West Africa. We detected coarse root vertical distribution using ground-penetrating radar and root activity via soil water acquisition using isotopic matching of δ¹⁸O plant and soil signatures. Coarse roots were detected to a depth of 50 cm, however, intraspecifc coarse root vertical distribution was modified by edaphic conditions. Soil δ¹⁸O isotopic signature declined with depth, providing conditions for plant–soil δ¹⁸O isotopic matching. This pattern held only under sandstone conditions where water acquisition zones were identifiably narrow in the 10–20 cm depth but broader under phyllite–granite conditions, presumably due to resource patchiness. Detected coarse root count by depth and measured fine root density were strongly correlated as were detected coarse root count and identified water acquisition zones, thus validating root detection capability of ground-penetrating radar, but exclusively on sandstone soils. This approach was able to characterize trends between intraspecific root architecture and edaphic-dependent resource availability, however, limited by site conditions. This study successfully demonstrates a new approach for in situ root studies that moves beyond invasive point sampling to nondestructive detection of root architecture and function. We discuss the transfer of such an approach to answer root ecology questions in various tree-based landscapes.

Tree root distribution and activity are important determinants of belowground competition, particularly across edaphic conditions. We tested a nondestructive approach to determine a tree crop (Theobroma cacao) coarse root structure using ground-penetrating radar and root activity via soil water acquisition using isotopic matching of δ¹⁸O plant and soil signatures. To further answer root ecology questions in various tree-based landscapes, this study successfully demonstrates a new technique for in situ root studies that moves beyond invasive point sampling to nondestructive detection of root structure and function.

Microsatellite markers (N = 5) were developed for analysis of genetic variation in 15 populations of the columnar cactus Stenocereus stellatus, managed under traditional agriculture practices in central Mexico. Microsatellite diversity was analyzed within and among populations, between geographic regions, and among population management types to provide detailed insight into historical gene flow rates and population dynamics associated with domestication. Our results corroborate a greater diversity in populations managed by farmers compared with wild ones (H_E = 0.64 vs. 0.55), but with regional variation between populations among regions. Although farmers propagated S. stellatus vegetatively in home gardens to diversify their stock, asexual recruitment also occurred naturally in populations where more marginal conditions have limited sexual recruitment, resulting in lower genetic diversity. Therefore, a clear-cut relationship between the occurrence of asexual recruitment and genetic diversity was not evident. Two managed populations adjacent to towns were identified as major sources of gene movement in each sampled region, with significant migration to distant as well as nearby populations. Coupled with the absence of significant bottlenecks, this suggests a mechanism for promoting genetic diversity in managed populations through long distance gene exchange. Cultivation of S. stellatus in close proximity to wild populations has led to complex patterns of genetic variation across the landscape that reflects the interaction of natural and cultural processes. As molecular markers become available for nontraditional crops and novel analysis techniques allow us to detect and evaluate patterns of genetic diversity, genetic studies provide valuable insights into managing crop genetic resources into the future against a backdrop of global change. Traditional agriculture systems play an important role in maintaining genetic diversity for plant species.

Microsatellite markers (N = 5) were developed for analysis of genetic variation in 15 populations of the columnar cactus Stenocereus stellatus used or managed under traditional agriculture practices in central Mexico. Coupled with the absence of significant bottlenecks, this suggests genetic diversity in managed populations is promoted through long-distance gene exchange. Cultivation of S. stellatus in close proximity to wild populations has led to complex patterns of genetic variation across the landscape that reflects the interaction of natural and cultural processes.

The North-Atlantic has warmed faster than all other ocean basins and climate change scenarios predict sea surface temperature isotherms to shift up to 600 km northwards by the end of the 21st century. The pole-ward shift has already begun for many temperate seaweed species that are important intertidal foundation species. We asked the question: Where will climate change have the greatest impact on three foundational, macroalgal species that occur along North-Atlantic shores: Fucus serratus, Fucus vesiculosus, and Ascophyllum nodosum? To predict distributional changes of these key species under three IPCC (Intergovernmental Panel on Climate Change) climate change scenarios (A2, A1B, and B1) over the coming two centuries, we generated Ecological Niche Models with the program MAXENT. Model predictions suggest that these three species will shift northwards as an assemblage or “unit” and that phytogeographic changes will be most pronounced in the southern Arctic and the southern temperate provinces. Our models predict that Arctic shores in Canada, Greenland, and Spitsbergen will become suitable for all three species by 2100. Shores south of 45° North will become unsuitable for at least two of the three focal species on both the Northwest- and Northeast-Atlantic coasts by 2200. If these foundational species are unable to adapt to the rising temperatures, they will lose their centers of genetic diversity and their loss will trigger an unpredictable shift in the North-Atlantic intertidal ecosystem.

Climate change scenarios predict sea surface temperature isotherms in the N-Atlantic to shift up to 600 km northwards by the end of the 21st century. Based on Ecological Niche Models, we predict the impact of climate change over the coming two centuries on the distribution of three foundational, macroalgal species that occur along N-Atlantic shores: Fucus serratus, Fucus vesiculosus and Ascophyllum nodosum. Model predictions suggest that Arctic shores will become suitable for all three species but that the species will lose suitable habitat in the southern temperate provinces which can trigger an unpredictable shift in the N-Atlantic intertidal ecosystem.

How plant populations, communities, and ecosystems respond to climate change is a critical focus in ecology today. The responses of introduced species may be especially rapid. Current models that incorporate temperature and precipitation suggest that future Bromus tectorum invasion risk is low for the Colorado Plateau. With a field warming experiment at two sites in southeastern Utah, we tested this prediction over 4 years, measuring B. tectorum phenology, biomass, and reproduction. In a complimentary greenhouse study, we assessed whether changes in field B. tectorum biomass and reproductive output influence offspring performance. We found that following a wet winter and early spring, the timing of spring growth initiation, flowering, and summer senescence all advanced in warmed plots at both field sites and the shift in phenology was progressively larger with greater warming. Earlier green-up and development was associated with increases in B. tectorum biomass and reproductive output, likely due early spring growth, when soil moisture was not limiting, and a lengthened growing season. Seeds collected from plants grown in warmed plots had higher biomass and germination rates and lower mortality than seeds from ambient plots. However, in the following two dry years, we observed no differences in phenology between warmed and ambient plots. In addition, warming had a generally negative effect on B. tectorum biomass and reproduction in dry years and this negative effect was significant in the plots that received the highest warming treatment. In contrast to models that predict negative responses of B. tectorum to warmer climate on the Colorado Plateau, the effects of warming were more nuanced, relied on background climate, and differed between the two field sites. Our results highlight the importance of considering the interacting effects of temperature, precipitation, and site-specific characteristics such as soil texture, on plant demography and have direct implications for B. tectorum invasion dynamics on the Colorado Plateau.

Climate change is one of the most critical environmental challenges of the 21st century and several lines of evidence suggest that climate change may benefit nonnative plants more than native plants. With a field warming experiment at two sites in southeastern Utah, we assessed how phenology, biomass, and reproduction of an invasive grass Bromus tectorum responded to 4 years of warming and with a follow-up greenhouse experiment, tested whether changes we saw under field experimental conditions influenced offspring performance.

Spider monkeys (Genus: Ateles) are a widespread Neotropical primate with a highly plastic socioecological strategy. However, the Central American species, Ateles geoffroyi, was recently re-listed as endangered due to the accelerated loss of forest across the subcontinent. There is inconsistent evidence that spider monkey populations could persist when actively protected, but their long-term viability in unprotected, human-dominated landscapes is not known. We analyzed noninvasive genetic samples from 185 individuals in 14 putative social groups on the Rivas Isthmus in southwestern Nicaragua. We found evidence of weak but significant genetic structure in the mitochondrial control region and in eight nuclear microsatellite loci plus negative spatial autocorrelation in Fst and kinship. The overall pattern suggests strong localized mating and at least historical female-biased dispersal, as is expected for this species. Heterozygosity was significantly lower than expected under random mating and lower than that found in other spider monkey populations, possibly reflecting a recent decline in genetic diversity and a threat from inbreeding. We conclude that despite a long history of human disturbance on this landscape, spider monkeys were until recently successful at maintaining gene flow. We consider the recent decline to be further indication of accelerated anthropogenic disturbance, but also of an opportunity to conserve native biodiversity. Spider monkeys are one of many wildlife species in Central America that is threatened by land cover change, and an apt example of how landscape-scale conservation planning could be used to ensure long-term persistence.

Population genetic patterns of the Endangered spider monkey, Ateles geoffroyi, across a human-dominated landscape, the Rivas Isthmus in southwestern Nicaragua.

Species invasions can have wide-ranging biological and socio-economic effects and are generally unwanted by legislation. Identification of the source population as well as the ecology and genetics of both the invader population and the receiving community is of crucial importance. The rapid invasion of a small coregonid fish vendace (Coregonus albula) in a major northern European subarctic watercourse has resulted in a labile ecological situation in the receiving community. The ecological impact of the invasion has been thoroughly documented, but the genetics of the invasion remains to be explored. We analyzed the genetic diversity and divergence patterns among the two possible source populations from southern Finnish Lapland and three colonists populations within the Inari-Pasvik watercourse using ten microsatellite loci in order to (i) identify the most likely source of the invasion, (ii) reveal the dispersal pattern and genetic structure of the secondary expansion, and (iii) to investigate whether the initial introduction and the secondary expansion were associated with founder effects. We revealed that repeated translocation of vendace from Lake Sinettäjärvi into a tributary lake of L. Inari in 1964–1966 is the most plausible source for the invasion. Both the initial introduction and the secondary expansion were found not to be associated with significant founder effects. The secondary expansion followed a stepping stone pattern and the source and colonist populations of this expansion have undergone rapid genetic divergence within a period of 15–35 years (ca. 8–17 generations). The rapid divergence may be contributed to lack of gene flow among the source and colonist populations due to the extensive hydroelectric damming in the watercourse. Multiple introductions and substantial genetic variation in combination with the boom-and-bust population development of the species thus likely counteracted the founder effects as well as fueled the rapid establishment and expansion of this species within the Inari-Pasvik watercourse.

Severe ecological consequences have been documented following the rapid invasion of vendace (Coregonus albula) in a major northern European subarctic ecosystem. We showed that repeated translocation of vendace in 1964–1966 most likely founded the invasion and that the secondary expansion follows a stepping stone pattern. The results also reveal rapid genetic divergence among the colonist populations. Multiple introductions and substantial genetic variation in combination with the boom-and-bust population development of the species thus likely counteracted the founder effects as well as fueled the rapid establishment and expansion of this species within the Inari-Pasvik watercourse.

Accurate knowledge of the functional response of predators to prey density is essential for understanding food web dynamics, to parameterize mechanistic models of animal responses to environmental change, and for designing appropriate conservation measures. Greater flamingos (Phoenicopterus roseus), a flagship species of Mediterranean wetlands, primarily feed on Artemias (Artemia spp.) in commercial salt pans, an industry which may collapse for economic reasons. Flamingos also feed on alternative prey such as Chironomid larvae (e.g., Chironomid spp.) and rice seeds (Oryza sativa). However, the profitability of these food items for flamingos remains unknown. We determined the functional responses of flamingos feeding on Artemias, Chironomids, or rice. Experiments were conducted on 11 captive flamingos. For each food item, we offered different ranges of food densities, up to 13 times natural abundance. Video footage allowed estimating intake rates. Contrary to theoretical predictions for filter feeders, intake rates did not increase linearly with increasing food density (type I). Intake rates rather increased asymptotically with increasing food density (type II) or followed a sigmoid shape (type III). Hence, flamingos were not able to ingest food in direct proportion to their abundance, possibly because of unique bill structure resulting in limited filtering capabilities. Overall, flamingos foraged more efficiently on Artemias. When feeding on Chironomids, birds had lower instantaneous rates of food discovery and required more time to extract food from the sediment and ingest it, than when filtering Artemias from the water column. However, feeding on rice was energetically more profitable for flamingos than feeding on Artemias or Chironomids, explaining their attraction for rice fields. Crucially, we found that food densities required for flamingos to reach asymptotic intake rates are rarely met under natural conditions. This allows us to predict an immediate negative effect of any decrease in prey density upon flamingo foraging performance.

Feeding functional responses have been measured on the Greater Flamingo (Phoenicopterus roseus) feeding on Artemia, Chironomids larvae and rice. We found that contrary to theoretical predictions for filter feeders, intake rates did not increase linearly with increasing food density. These findings allows us to predict an immediate negative effect of any decrease in prey density upon flamingo foraging performance.