Gene discovery in the horned beetle Onthophagus taurus

<p>Abstract</p> <p>Background</p> <p>Horned beetles, in particular in the genus <it>Onthophagus</it>, are important models for studies on sexual selection, biological radiations, the origin of novel traits, developmental plasticity, biocontrol, conservation, and forensic biology. Despite their growing prominence as models for studying both basic and applied questions in biology, little genomic or transcriptomic data are available for this genus. We used massively parallel pyrosequencing (Roche 454-FLX platform) to produce a comprehensive EST dataset for the horned beetle <it>Onthophagus taurus</it>. To maximize sequence diversity, we pooled RNA extracted from a normalized library encompassing diverse developmental stages and both sexes.</p> <p>Results</p> <p>We used 454 pyrosequencing to sequence ESTs from all post-embryonic stages of <it>O. taurus. </it>Approximately 1.36 million reads assembled into 50,080 non-redundant sequences encompassing a total of 26.5 Mbp. The non-redundant sequences match over half of the genes in <it>Tribolium castaneum</it>, the most closely related species with a sequenced genome. Analyses of Gene Ontology annotations and biochemical pathways indicate that the <it>O. taurus </it>sequences reflect a wide and representative sampling of biological functions and biochemical processes. An analysis of sequence polymorphisms revealed that SNP frequency was negatively related to overall expression level and the number of tissue types in which a given gene is expressed. The most variable genes were enriched for a limited number of GO annotations whereas the least variable genes were enriched for a wide range of GO terms directly related to fitness.</p> <p>Conclusions</p> <p>This study provides the first large-scale EST database for horned beetles, a much-needed resource for advancing the study of these organisms. Furthermore, we identified instances of gene duplications and alternative splicing, useful for future study of gene regulation, and a large number of SNP markers that could be used in population-genetic studies of <it>O. taurus </it>and possibly other horned beetles.</p

Tolerance of Novel Toxins through Generalized Mechanisms: Simulating Gradual Host Shifts of ButterfliesKristin

Organisms encounter a wide range of toxic compounds in their environments, from chemicals that serve anticonsumption or anticompetition functions to pollutants and pesticides. Although we understand many detoxification mechanisms that allow organisms to consume toxins typical of their diet, we know little about why organisms vary in their ability to tolerate entirely novel toxins. We tested whether variation in generalized stress responses, such as antioxidant pathways, may underlie variation in reactions to novel toxins and, if so, their associated costs. We used an artificial diet to present cabbage white butterfly caterpillars (Pieris rapae) with plant material containing toxins not experienced in their evolutionary history. Families that maintained high performance (e.g., high survival, fast development time, large body size) on diets containing one novel toxic plant also performed well when exposed to two other novel toxic plants, consistent with a generalized response. Variation in constitutive (but not induced) expression of genes involved in oxidative stress responses was positively related to performance on the novel diets. While we did not detect reproductive trade-offs of this generalized response, there was a tendency to have less melanin investment in the wings, consistent with the role of melanin in oxidative stress responses. Taken together, our results support the hypothesis that variation in generalized stress responses, such as genes involved in oxidative stress responses, may explain the variation in tolerance to entirely novel toxins and may facilitate colonization of novel hosts and environments

Cost-effective Roadside Revegetation Methods to Support Insect Pollinators

(c) 1036212Roadsides contain promising habitat for insect pollinators, yet roadside restorations can be expensive and are rarely evaluated for effectiveness. Where do we establish pollinator-friendly revegetation to maximize benefits? How effective are current revegetation practices at providing habitat for pollinators? We address these questions with two studies. Chapter 2 examines the impact of roadside-adjacent habitat that has been identified as pollinator-friendly for bumble bees. We use pollinator habitat maps to examine associations between the amount of nearby pollinator-friendly habitat and bumble bees (abundance and richness). We also regroup land covers to more specifically align with bumble bee habitat needs and compare the ability of both land cover categorizations to predict bumble bee metrics. This study can help refine predictors in mapping efforts to prioritize locations for pollinator habitat enhancements. Chapters 3 and 4 combine detailed insect and floral surveys of sites with known revegetation history to test efficacy of current revegetation methods for providing habitat for insect pollinators. We show which plants establish after seeding and how communities change as they age. We find that native flowering plants are more likely to establish in roadsides when they are planted, but native and non-native seeded sites converge in the plant community through time. Bumble bee and butterfly abundance and diversity is tied to flowering plant abundance and diversity, regardless of their status as native plants. This work identifies where pollinator-friendly restorations should be implemented and how current seeding practices could be modified to improve benefits to pollinators while reducing costs

Costs of Plasticity in Host Use in Butterflies

Phenotypic plasticity, the ability of a genotype to express different phenotypes in different environments, allows organisms to cope with variation in resources and invade novel environments. Biologists have long been fascinated with the costs and tradeoffs that generate and maintain variation in plasticity, such as possible increases in brain size and delays in reproduction associated with the evolution of learning. However, the costs of plasticity vary: many studies have failed to find costs of plasticity, the degree of costs often vary with the system or environments considered, and many costs of plasticity are variable even within the lifetime of an individual. This research adopts a developmental perspective to predict the degree and incidence of costs of plasticity, using host learning in butterflies as a case study. Learning, a mechanism of plasticity that develops through a trial-and-error sampling process, should result in developmental costs and allocation of energy towards development (at the expense of reproduction). Furthermore, costs of learning should be less pronounced in environments for which organisms have innate biases and for learned traits underlain by short-term memory, relative to long-term memory (which requires more developmental re-structuring). This research found support for all three predictions across three levels of costs: behavioral costs, tissue costs, and fecundity trade-offs. Butterflies exhibited genetic variation in their ability to learn to recognize different colored hosts. Genotypes with higher proxies for long-term memory emerged with relatively larger neural investment and smaller reproductive investment. In contrast to these costs of long-term learning, proxies of short-term learning were only correlated with increased exploration of a range of possible resources (types of non-hosts) early in the host-learning process. Family-level costs of plasticity emerged from the ability to learn to locate a red host, for which butterflies do not have an innate bias. Costs of learning were also induced by learning itself: following exposure to novel (red) host environments, individual butterflies, regardless of genetic background, increased exploratory behavior, increased neural investment, and re-allocated energy away from reproduction towards other functions (e.g., flight). Considering developmental mechanisms helps to predict how costs will influence the evolution of learning and plasticity

cranial capacity in mammals Anthropogenic environments exert variable selection on &quot;Data Supplement&quot; References Subject collections Anthropogenic environments exert variable selection on cranial capacity in mammals

It is thought that behaviourally flexible species will be able to cope with novel and rapidly changing environments associated with human activity. However, it is unclear whether such environments are selecting for increases in behavioural plasticity, and whether some species show more pronounced evolutionary changes in plasticity. To test whether anthropogenic environments are selecting for increased behavioural plasticity within species, we measured variation in relative cranial capacity over time and space in 10 species of mammals. We predicted that urban populations would show greater cranial capacity than rural populations and that cranial capacity would increase over time in urban populations. Based on relevant theory, we also predicted that species capable of rapid population growth would show more pronounced evolutionary responses. We found that urban populations of two small mammal species had significantly greater cranial capacity than rural populations. In addition, species with higher fecundity showed more pronounced differentiation between urban and rural populations. Contrary to expectations, we found no increases in cranial capacity over time in urban populations-indeed, two species tended to have a decrease in cranial capacity over time in urban populations. Furthermore, rural populations of all insectivorous species measured showed significant increases in relative cranial capacity over time. Our results provide partial support for the hypothesis that urban environments select for increased behavioural plasticity, although this selection may be most pronounced early during the urban colonization process. Furthermore, these data also suggest that behavioural plasticity may be simultaneously favoured in rural environments, which are also changing because of human activity

Life History Data

Data set with life history data for all individuals included in the main study. The data set includes adult and larval treatment and measured values for choosiness, fecundity, egg area in mm squared (measure of egg size), forewing length in mm (as a proxy for body size), and thorax protein in mg protein per g thorax. Thorax protein values in this file are the two replicate values from the ThoraxProtein file averaged together for each individual. All individuals in the study were female

Spermatophore counts of low and high larval nutrition females

Data set showing spermatophore counts for a subset of 10 adult females from each of the two larval treatments- low and high nutrition. These data are a different subset of individuals from the other two files

Data from: Adult nutritional stress decreases oviposition choosiness and fecundity in female butterflies

Despite the benefits of careful decision-making, not all animals are choosy. One explanation is that choosiness can cost time and energy and thus depend on nutrition. However, it is not clear how allocation to choosiness versus other components of life history shifts in the face of nutritional stress. We tested two hypotheses about the effects of nutritional stress on choosiness and other life history traits: 1) poor nutrition leads to compensatory shifts in life history strategy towards greater investment per offspring in terms of choosy oviposition behavior and egg resources, and 2) poor nutrition negatively affects a range of life history traits. Cabbage white butterfly (Pieris rapae) females were reared under low or high nutrition conditions during the larval and adult stage in a fully factorial design. Choosiness was quantified as avoidance of conspecific models during oviposition. Adult life history traits included egg number, egg size, and thorax protein. Females that experienced nutritional stress as adults were less choosy and less fecund, in support of the second hypothesis. Yet females that were stressed as larvae invested more in thorax muscle, consistent with the first hypothesis. Overall, adult nutritional stress decreased investment in multiple reproductive traits, including a behavioral trait, but larval stress increased investment in flight, potentially to disperse away from nutritionally poor environments

Thorax Protein Data (non-averaged between duplicates)

Data set with thorax protein data, showing larval and adult treatment, batch, and the duplicate mg protein/g thorax values for all individuals included in the main study, plus ten "reference" females from each larval treatment