Life history evolution in seasonal environments: phenological and environmental determinants of thermal adaptation in Wyeomyia smithii

Environmental variation poses a major evolutionary challenge to organisms. This is particularly true for seasonal environments where environmental factors fluctuate radically but predictably on an annual basis. Dormant life history stages often evolve to mitigate exposure to harsh seasonal environments (e.g., winter). In addition, norms of reaction, or the relationship between phenotype and environment, often evolve as a response to local environmental heterogeneity. My thesis explores how the seasonal timing of dormancy affects selection on reaction norms of active, non-dormant life history stages in temperate insects. Changing the dates of initiation and termination of winter dormancy changes the thermal habitat experienced during active growth and reproduction. Thus, geographic variation in the timing of dormancy complicates geographic patterns of thermal selection on active life history stages. Using available inter- and intraspecific life history data in conjunction with long-term weather data, I show that geographic clines in dormancy timing cause populations along the cline to experience similar exposure to cold temperatures during active growth. As a result, strong latitudinal trends in the timing of dormancy predict weaker latitudinal trends in thermal adaptation of active stages. I further illustrate this concept by examining geographic variation in the timing of winter dormancy, thermal sensitivity of development, and tolerance to thermal stress in the pitcher plant mosquito, Wyeomyia smithii. The results from W. smithii suggest that selection applied specifically by the thermal environment of the growing season best explains geographic variation in the thermal sensitivity of development time. In contrast, geographic variation in the thermal environment of the entire year best explains geographic trends in thermal stress tolerance of active life history stages. These results suggest two major conclusions. First, thermal sensitivity and thermal tolerance can exhibit local adaptation in populations that also demonstrate local adaptation in diapause timing. Thus the evolution of one type of adaptation does not preclude the other. Second, dormancy timing unquestionably influences direct selection on active life history stages, but correlated selection on overwinter survival may strongly influence temperature tolerance of active life history stages

Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis

<p>Abstract</p> <p>Background</p> <p>Flesh flies in the genus <it>Sarcophaga </it>are important models for investigating endocrinology, diapause, cold hardiness, reproduction, and immunity. Despite the prominence of <it>Sarcophaga </it>flesh flies as models for insect physiology and biochemistry, and in forensic studies, little genomic or transcriptomic data are available for members of this genus. We used massively parallel pyrosequencing on the Roche 454-FLX platform to produce a substantial EST dataset for the flesh fly <it>Sarcophaga crassipalpis</it>. To maximize sequence diversity, we pooled RNA extracted from whole bodies of all life stages and normalized the cDNA pool after reverse transcription.</p> <p>Results</p> <p>We obtained 207,110 ESTs with an average read length of 241 bp. These reads assembled into 20,995 contigs and 31,056 singletons. Using BLAST searches of the NR and NT databases we were able to identify 11,757 unique gene elements (E<0.0001) representing approximately 9,000 independent transcripts. Comparison of the distribution of <it>S. crassipalpis </it>unigenes among GO Biological Process functional groups with that of the <it>Drosophila melanogaster </it>transcriptome suggests that our ESTs are broadly representative of the flesh fly transcriptome. Insertion and deletion errors in 454 sequencing present a serious hurdle to comparative transcriptome analysis. Aided by a new approach to correcting for these errors, we performed a comparative analysis of genetic divergence across GO categories among <it>S. crassipalpis</it>, <it>D. melanogaster</it>, and <it>Anopheles gambiae</it>. The results suggest that non-synonymous substitutions occur at similar rates across categories, although genes related to response to stimuli may evolve slightly faster. In addition, we identified over 500 potential microsatellite loci and more than 12,000 SNPs among our ESTs.</p> <p>Conclusion</p> <p>Our data provides the first large-scale EST-project for flesh flies, a much-needed resource for exploring this model species. In addition, we identified a large number of potential microsatellite and SNP markers that could be used in population and systematic studies of <it>S. crassipalpis </it>and other flesh flies.</p

Divergence of the diapause transcriptome in apple maggot flies: winter regulation and post-winter transcriptional repression

Citation: Meyers, P. J., Powell, T. H. Q., Walden, K. K. O., Schieferecke, A. J., Feder, J. L., Hahn, D. A., . . . Ragland, G. J. (2016). Divergence of the diapause transcriptome in apple maggot flies: winter regulation and post-winter transcriptional repression. Journal of Experimental Biology, 219(17), 2613-2622. doi:10.1242/jeb.140566The duration of dormancy regulates seasonal timing in many organisms and may be modulated by day length and temperature. Though photoperiodic modulation has been well studied, temperature modulation of dormancy has received less attention. Here, we leverage genetic variation in diapause in the apple maggot fly, Rhagoletis pomonella, to test whether gene expression during winter or following spring warming regulates diapause duration. We used RNAseq to compare transcript abundance during and after simulated winter between an apple-infesting population and a hawthorn-infesting population where the apple population ends pupal diapause earlier than the hawthorn-infesting population. Marked differences in transcription between the two populations during winter suggests that the 'early' apple population is developmentally advanced compared with the 'late' hawthorn population prior to spring warming, with transcripts participating in growth and developmental processes relatively up-regulated in apple pupae during the winter cold period. Thus, regulatory differences during winter ultimately drive phenological differences that manifest themselves in the following summer. Expression and polymorphism analysis identify candidate genes in the Wnt and insulin signaling pathways that contribute to population differences in seasonality. Both populations remained in diapause and displayed a pattern of up-and then down-regulation (or vice versa) of growth-related transcripts following warming, consistent with transcriptional repression. The ability to repress growth stimulated by permissive temperatures is likely critical to avoid mismatched phenology and excessive metabolic demand. Compared with diapause studies in other insects, our results suggest some overlap in candidate genes/pathways, though the timing and direction of changes in transcription are likely species specific

Patterns of Genomic Differentiation between Ecologically Differentiated M and S Forms of Anopheles gambiae in West and Central Africa

Anopheles gambiae M and S are thought to be undergoing ecological speciation by adapting to different larval habitats. Toward an improved understanding of the genetic determinants and evolutionary processes shaping their divergence, we used a 400,000 single-nucleotide polymorphism (SNP) genotyping array to characterize patterns of genomic differentiation between four geographically paired M and S population samples from West and Central Africa. In keeping with recent studies based on more limited genomic or geographic sampling, divergence was not confined to a few isolated “speciation islands.” Divergence was both widespread across the genome and heterogeneous. Moreover, we find consistent patterns of genomic divergence across sampling sites and mutually exclusive clustering of M and S populations using genetic distances based on all 400,000 SNPs, implying that M and S are evolving collectively across the study area. Nevertheless, the clustering of local M and S populations using genetic distances based on SNPs from genomic regions of low differentiation is consistent with recent gene flow and introgression. To account for these data and reconcile apparent paradoxes in reported patterns of M–S genomic divergence and hybridization, we propose that extrinsic ecologically based postmating barriers vary in strength as environmental conditions fluctuate or change

Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella

Background The full power of modern genetics has been applied to the study of speciation in only a small handful of genetic model species - all of which speciated allopatrically. Here we report the first large expressed sequence tag (EST) study of a candidate for ecological sympatric speciation, the apple maggot Rhagoletis pomonella, using massively parallel pyrosequencing on the Roche 454-FLX platform. To maximize transcript diversity we created and sequenced separate libraries from larvae, pupae, adult heads, and headless adult bodies. Results We obtained 239,531 sequences which assembled into 24,373 contigs. A total of 6810 unique protein coding genes were identified among the contigs and long singletons, corresponding to 48% of all known Drosophila melanogaster protein-coding genes. Their distribution across GO classes suggests that we have obtained a representative sample of the transcriptome. Among these sequences are many candidates for potential R. pomonella speciation genes (or barrier genes ) such as those controlling chemosensory and life-history timing processes. Furthermore, we identified important marker loci including more than 40,000 single nucleotide polymorphisms (SNPs) and over 100 microsatellites. An initial search for SNPs at which the apple and hawthorn host races differ suggested at least 75 loci warranting further work. We also determined that developmental expression differences remained even after normalization; transcripts expected to show different expression levels between larvae and pupae in D. melanogaster also did so in R. pomonella. Preliminary comparative analysis of transcript presences and absences revealed evidence of gene loss in Drosophila and gain in the higher dipteran clade Schizophora. Conclusions These data provide a much needed resource for exploring mechanisms of divergence in this important model for sympatric ecological speciation. Our description of ESTs from a substantial portion of the R. pomonella transcriptome will facilitate future functional studies of candidate genes for olfaction and diapause-related life history timing, and will enable large scale expression studies. Similarly, the identification of new SNP and microsatellite markers will facilitate future population and quantitative genetic studies of divergence between the apple and hawthorn-infesting host races

Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

Theory predicts that speciation-with-gene-flow is more likely when the consequences of selection for population divergence transitions from mainly direct effects of selection acting on individual genes to a collective property of all selected genes in the genome. Thus, understanding the direct impacts of ecologically based selection, as well as the indirect effects due to correlations among loci, is critical to understanding speciation. Here, we measure the genome-wide impacts of host-associated selection between hawthorn and apple host races of Rhagoletis pomonella (Diptera: Tephritidae), a model for contemporary speciation-with-gene-flow. Allele frequency shifts of 32 455 SNPs induced in a selection experiment based on host phenology were genome wide and highly concordant with genetic divergence between co-occurring apple and hawthorn flies in nature. This striking genome-wide similarity between experimental and natural populations of R. pomonella underscores the importance of ecological selection at early stages of divergence and calls for further integration of studies of eco-evolutionary dynamics and genome divergence

Genome-wide variation and transcriptional changes in diverse developmental processes underlie the rapid evolution of seasonal adaptation

Many organisms enter a dormant state in their life cycle to deal with predictable changes in environments over the course of a year. The timing of dormancy is therefore a key seasonal adaptation, and it evolves rapidly with changing environments. We tested the hypothesis that differences in the timing of seasonal activity are driven by differences in the rate of development during diapause in Rhagoletis pomonella, a fly specialized to feed on fruits of seasonally limited host plants. Transcriptomes from the central nervous system across a time series during diapause show consistent and progressive changes in transcripts participating in diverse developmental processes, despite a lack of gross morphological change. Moreover, population genomic analyses suggested that many genes of small effect enriched in developmental functional categories underlie variation in dormancy timing and overlap with gene sets associated with development rate in Drosophila melanogaster. Our transcriptional data also suggested that a recent evolutionary shift from a seasonally late to a seasonally early host plant drove more rapid development during diapause in the early fly population. Moreover, genetic variants that diverged during the evolutionary shift were also enriched in putative cis regulatory regions of genes differentially expressed during diapause development. Overall, our data suggest polygenic variation in the rate of developmental progression during diapause contributes to the evolution of seasonality in R. pomonella. We further discuss patterns that suggest hourglass-like developmental divergence early and late in diapause development and an important role for hub genes in the evolution of transcriptional divergence

Understanding Evolutionary Impacts of Seasonality: An Introduction to the Symposium

Seasonality is a critically important aspect of environmental variability, and strongly shapes all aspects of life for organisms living in highly seasonal environments. Seasonality has played a key role in generating biodiversity, and has driven the evolution of extreme physiological adaptations and behaviors such as migration and hibernation. Fluctuating selection pressures on survival and fecundity between summer and winter provide a complex selective landscape, which can be met by a combination of three outcomes of adaptive evolution: genetic polymorphism, phenotypic plasticity, and bet-hedging. Here, we have identified four important research questions with the goal of advancing our understanding of evolutionary impacts of seasonality. First, we ask how characteristics of environments and species will determine which adaptive response occurs. Relevant characteristics include costs and limits of plasticity, predictability, and reliability of cues, and grain of environmental variation relative to generation time. A second important question is how phenological shifts will amplify or ameliorate selection on physiological hardiness. Shifts in phenology can preserve the thermal niche despite shifts in climate, but may fail to completely conserve the niche or may even expose life stages to conditions that cause mortality. Considering distinct environmental sensitivities of life history stages will be key to refining models that forecast susceptibility to climate change. Third, we must identify critical physiological phenotypes that underlie seasonal adaptation and work toward understanding the genetic architectures of these responses. These architectures are key for predicting evolutionary responses. Pleiotropic genes that regulate multiple responses to changing seasons may facilitate coordination among functionally related traits, or conversely may constrain the expression of optimal phenotypes. Finally, we must advance our understanding of how changes in seasonal fluctuations are impacting ecological interaction networks. We should move beyond simple dyadic interactions, such as predator prey dynamics, and understand how these interactions scale up to affect ecological interaction networks. As global climate change alters many aspects of seasonal variability, including extreme events and changes in mean conditions, organisms must respond appropriately or go extinct. The outcome of adaptation to seasonality will determine responses to climate change

Can we predict the global magnetic topology of a pre-main sequence star from its position in the Hertzsprung-Russell diagram?

ZDI studies have shown that the magnetic fields of T Tauri stars can be significantly more complex than a simple dipole and can vary markedly between sources. We collect and summarize the magnetic field topology information obtained to date and present Hertzsprung-Russell (HR) diagrams for the stars in the sample. Intriguingly, the large scale field topology of a given pre-main sequence (PMS) star is strongly dependent upon the stellar internal structure, with the strength of the dipole component of its multipolar magnetic field decaying rapidly with the development of a radiative core. Using the observational data as a basis, we argue that the general characteristics of the global magnetic field of a PMS star can be determined from its position in the HR diagram. Moving from hotter and more luminous to cooler and less luminous stars across the PMS of the HR diagram, we present evidence for four distinct magnetic topology regimes. Stars with large radiative cores, empirically estimated to be those with a core mass in excess of ~40 per cent of the stellar mass, host highly complex and dominantly non-axisymmetric magnetic fields, while those with smaller radiative cores host axisymmetric fields with field modes of higher order than the dipole dominant (typically, but not always, the octupole). Fully convective stars stars above ~0.5 MSun appear to host dominantly axisymmetric fields with strong (kilo-Gauss) dipole components. Based on similarities between the magnetic properties of PMS stars and main sequence M-dwarfs with similar internal structures, we speculate that a bistable dynamo process operates for lower mass stars (<~0.5 MSun at an age of a few Myr) and that they will be found to host a variety of magnetic field topologies. If the magnetic topology trends across the HR diagram are confirmed they may provide a new method of constraining PMS stellar evolution models.Comment: accepted for publication in the Ap

Comparison of breast cancer survival in two populations: Ardabil, Iran and British Columbia, Canada

<p>Abstract</p> <p>Background</p> <p>Patterns in survival can provide information about the burden and severity of cancer, help uncover gaps in systemic policy and program delivery, and support the planning of enhanced cancer control systems. The aim of this paper is to describe the one-year survival rates for breast cancer in two populations using population-based cancer registries: Ardabil, Iran, and British Columbia (BC), Canada.</p> <p>Methods</p> <p>All newly diagnosed cases of female breast cancer were identified in the Ardabil cancer registry from 2003 to 2005 and the BC cancer registry for 2003. The International Classification of Disease for Oncology (ICDO) was used for coding cancer morphology and topography. Survival time was determined from cancer diagnosis to death. Age-specific one-year survival rates, relative survival rates and weighted standard errors were calculated using life-tables for each country.</p> <p>Results</p> <p>Breast cancer patients in BC had greater one-year survival rates than patients in Ardabil overall and for each age group under 60.</p> <p>Conclusion</p> <p>These findings support the need for breast cancer screening programs (including regular clinical breast examinations and mammography), public education and awareness regarding early detection of breast cancer, and education of health care providers.</p