Deciphering life history transcriptomes in different environments

Phenotypic Plasticity Drives the Successful Expansion of the Invasive Plant Pedicularis kansuensis in Bayanbulak, China

To better understand the phenotypic plasticity of the highly invasive native weed, Pedicularis kansuensis, we investigated and compared phenotypes (morphology, biomass, and nutrient composition) at different levels of invasion (low: 0 < cover ≤ 30%; medium: 30% < cover ≤ 70%; and high: cover > 70%). With the increase in invasion level, the plasticity of inflorescence length, single-leaf thickness, and specific leaf area increased, while the plasticity of single-leaf area and crown width decreased. During the invasion process, we observed significant density-dependent effects, including changed morphological characteristics, increased total aboveground biomass, and decreased plant height, inflorescence length, root length, crown width, single-leaf area, structure biomass of structures (root, stem, inflorescence), and individual biomass (p < 0.05). During the reproductive period of P. kansuensis, the resource allocation (C, N, and P content, total biomass, biomass allocation) to inflorescence was significantly higher than to root and stem, while the elemental ratios (C:N, C:P, N:P) of inflorescences were significantly lower than those of roots and stems (p < 0.05). When the invasion level increased, the ratio of inflorescence C:N and biomass allocation to roots increased significantly; conversely, inflorescence N and biomass allocation to inflorescences and stems decreased significantly (p < 0.05). This led to a decrease in resource allocation to aboveground parts and more resources allocated to the roots, significantly increasing the root-to-shoot ratio (p < 0.05). Based on the phenotypic differences among different invasion levels, we suggest that P. kansuensis adapted to a competitive environment by regulating morphology, biomass, and nutrient allocation, thereby enhancing the potential of invasion and spread.

Where Is Natural History in Ecological, Evolutionary, and Behavioral Science?

Natural history is the careful observation of nature, wherever nature is. Ultimately, it is what ecological, evolutionary, and behavioral science are supposed to explain. It is difficult to use natural history alone to test hypotheses in these fields because of the complex paths between process and pattern. Few patterns are predicted by one and only one hypothesis, so experiments are almost always necessary. However, the robustness of experimental results depends on how well experimental conditions reflect the integration of natural history. Natural history also plays a vital role in how well we can apply Krogh's principle to our work. Krogh's principle is that scientists begin with an important hypothesis and find a system (organism, habitat, species interaction) with which to test it. However, natural history is essential for knowing whether the question applies to the system or whether we are forcing the question on the system. There is value in beginning one's research not by identifying an interesting question and searching for the right system but by identifying an interesting system in which to ask the right question. This approach carries the danger of parochialism, which can be avoided only by having a command of theory as well as natural history. A command of both areas allows nature to tell us which question to ask instead of demanding that nature answer the question we find most interesting.

Evolutionary genomics of host plant adaptation: insights from Drosophila

Variation in gene expression in response to the use of alternate host plants can reveal genetic and physiological mechanisms explaining why insect-host relationships vary from host specialism to generalism. Interpreting transcriptome variation relies on well-annotated genomes, making drosophilids valuable model systems, particularly those species with tractable ecological associations. Patterns of whole genome expression and alternate gene splicing in response to growth on different hosts have revealed expression of gene networks of known detoxification genes as well as novel functionally enriched genes of diverse metabolic and structural functions. Integrating trancriptomic responses with fitness differences and levels of phenotypic plasticity in response to alternate hosts will help to reveal the general nature of genotype-phenotype relationships.

Gene Expression and Diet Breadth in Plant-Feeding Insects: Summarizing Trends

Transcriptomic studies lend insights into the role of transcriptional plasticity in adaptation and specialization. Recently, there has been growing interest in understanding the relationship between variation in herbivorous insect gene expression and the evolution of diet breadth. We review the studies that have emerged on insect gene expression and host plant use, and outline the questions and approaches in the field. Many candidate genes underlying herbivory and specialization have been identified, and a few key studies demonstrate increased transcriptional plasticity associated with generalist compared with specialist species. Addressing the roles that transcriptional variation plays in insect diet breadth will have important implications for our understanding of the evolution of specialization and the genetic and environmental factors that govern insect-plant interactions.

Mate choice and gene expression signatures associated with nutritional adaptation in the medfly (Ceratitis capitata)

Evolutionary responses to nutrition are key to understanding host shifts and the resulting potential for reproductive isolation. Experimental evolution has previously been used to describe the responses of the medfly (Ceratitis capitata) to larval diets with different nutritional properties. Within 30 generations this led to divergence in larval development time, egg to adult survival and adaptation in adult body size. Here we used mRNA-seq to identify differences in gene expression patterns in these same populations, using males from the 60^th generation of nutritional selection. We validated differential expression by using qRT-PCR and found that genes linked to metabolism, oxidative phosphorylation and proteolysis were significantly over-represented among the differentially expressed genes. The results provide the first genome-wide survey of the putative mechanisms underpinning evolved responses to nutritional adaptation. In addition, we tested the hypothesis that nutritional adaptation can alter mating patterns. We found evidence for assortative mating by diet at generation 60, but not 90. Hence, the pattern was variable across generations and there was no evidence overall for any isolating mating divergence between the lines. Overall, the results provide insight into the mechanisms underpinning dietary adaptation and extend our knowledge of which traits represent core responses to nutritional selection.

Pupal emergence pattern in cactophilic Drosophila and the effect of host plants

Drosophila buzzatii and D. koepferae are sibling cactophilic species. The former breeds primarily on prickly pears (genus Opuntia) whereas the latter breeds on columnar cacti of the genera Cereus and Trichocereus, although with certain degree of niche overlapping. We examined the interspecific differences in diurnal temporal patterns of adult emergence from puparia and evaluated whether this behavior is affected by rearing in the different cactus hosts available in nature. We detected important host-dependent genetic variation for this trait differentially affecting the emergence schedule of these species. Diurnal pattern of emergence time was directly correlated with developmental time and negatively correlated with adult wing size, suggesting that early emergences are at least indirectly correlated with increased fitness. We discussed our results in terms of their putative effects on fitness and the genetic-metabolic pathways that would be presumably affected by host's nutritional-chemical differences.

Gene expression hallmarks of cellular ageing

Ageing leads to dramatic changes in the physiology of many different tissues resulting in a spectrum of pathology. Nonetheless, many lines of evidence suggest that ageing is driven by highly conserved cell intrinsic processes, and a set of unifying hallmarks of ageing has been defined. Here, we survey reports of age-linked changes in basal gene expression across eukaryotes from yeast to human and identify six gene expression hallmarks of cellular ageing: downregulation of genes encoding mitochondrial proteins; downregulation of the protein synthesis machinery; dysregulation of immune system genes; reduced growth factor signalling; constitutive responses to stress and DNA damage; dysregulation of gene expression and mRNA processing. These encompass widely reported features of ageing such as increased senescence and inflammation, reduced electron transport chain activity and reduced ribosome synthesis, but also reveal a surprising lack of gene expression responses to known age-linked cellular stresses. We discuss how the existence of conserved transcriptomic hallmarks relates to genome-wide epigenetic differences underlying ageing clocks, and how the changing transcriptome results in proteomic alterations where data is available and to variations in cell physiology characteristic of ageing. Identification of gene expression events that occur during ageing across distant organisms should be informative as to conserved underlying mechanisms of ageing, and provide additional biomarkers to assess the effects of diet and other environmental factors on the rate of ageing.

Gut Transcriptome Analysis Shows Different Food Utilization Efficiency by the Grasshopper Oedaleous asiaticus (Orthoptera: Acrididae)

Oedaleus asiaticus B. Bienko is a persistent pest occurring in north Asian grasslands. We found that O. asiaticus feeding on Stipa krylovii Roshev. had higher approximate digestibility (AD), efficiency of conversion of ingested food (ECI), and efficiency of conversion of digested food (ECD), compared with cohorts feeding on Leymus chinensis (Trin.) Tzvel, Artemisia frigida Willd., or Cleistogenes squarrosa (Trin.) Keng. Although this indicated high food utilization efficiency for S. krylovii, the physiological processes and molecular mechanisms underlying these biological observations are not well understood. Transcriptome analysis was used to examine how gene expression levels in O. asiaticus gut are altered by feeding on the four plant species. Nymphs (fifth-instar female) that fed on S. krylovii had the largest variation in gene expression profiles, with a total of 88 genes significantly upregulated compared with those feeding on the other three plants, mainly including nutrition digestive genes of protein, carbohydrate, and lipid digestion. GO and KEGG enrichment also showed that feeding S. krylovii could upregulate the nutrition digestion-related molecular function, biological process, and pathways. These changes in transcripts levels indicate that the physiological processes of activating nutrition digestive enzymes and metabolism pathways can well explain the high food utilization of S. krylovii by O. asiaticus.

Effects of temperature on transcriptome and cuticular hydrocarbon expression in ecologically differentiated populations of desert Drosophila

We assessed the effects of temperature differences on gene expression using whole-transcriptome microarrays and cuticular hydrocarbon variation in populations of cactophilic Drosophila mojavensis. Four populations from Baja California and mainland Mexico and Arizona were each reared on two different host cacti, reared to sexual maturity on laboratory media, and adults were exposed for 12 hr to 15, 25, or 35°C. Temperature differences influenced the expression of 3,294 genes, while population differences and host plants affected >2,400 each in adult flies. Enriched, functionally related groups of genes whose expression changed at high temperatures included heat response genes, as well as genes affecting chromatin structure. Gene expression differences between mainland and peninsular populations included genes involved in metabolism of secondary compounds, mitochondrial activity, and tRNA synthases. Flies reared on the ancestral host plant, pitaya agria cactus, showed upregulation of genes involved in metabolism, while flies reared on organ pipe cactus had higher expression of DNA repair and chromatin remodeling genes. Population × environment (G × E) interactions had widespread effects on the transcriptome where population × temperature interactions affected the expression of >5,000 orthologs, and there were >4,000 orthologs that showed temperature × host plant interactions. Adults exposed to 35°C had lower amounts of most cuticular hydrocarbons than those exposed to 15 or 25°C, including abundant unsaturated alkadienes. For insects adapted to different host plants and climatic regimes, our results suggest that temperature shifts associated with climate change have large and significant effects on transcriptomes of genetically differentiated natural populations.

Transcriptome modulation during host shift is driven by secondary metabolites in desert Drosophila

High-throughput transcriptome studies are breaking new ground to investigate the responses that organisms deploy in alternative environments. Nevertheless, much remains to be understood about the genetic basis of host plant adaptation. Here, we investigate genome-wide expression in the fly Drosophila buzzatii raised in different conditions. This species uses decaying tissues of cactus of the genus Opuntia as primary rearing substrate and secondarily, the necrotic tissues of the columnar cactus Trichocereus terscheckii. The latter constitutes a harmful host, rich in mescaline and other related phenylethylamine alkaloids. We assessed the transcriptomic responses of larvae reared in Opuntia sulphurea and T. terscheckii, with and without the addition of alkaloids extracted from the latter. Whole-genome expression profiles were massively modulated by the rearing environment, mainly by the presence of T. terscheckii alkaloids. Differentially expressed genes were mainly related to detoxification, oxidation-reduction and stress response; however, we also found genes involved in development and neurobiological processes. In conclusion, our study contributes new data onto the role of transcriptional plasticity in response to alternative rearing environments.

The Interplay of Temperature and Genotype on Patterns of Alternative Splicing in Drosophila melanogaster

Alternative splicing is the highly regulated process of variation in the removal of introns from premessenger-RNA transcripts. The consequences of alternative splicing on the phenotype are well documented, but the impact of the environment on alternative splicing is not yet clear. We studied variation in alternative splicing among four different temperatures, 13, 18, 23, and 29°, in two Drosophila melanogaster genotypes. We show plasticity of alternative splicing with up to 10% of the expressed genes being differentially spliced between the most extreme temperatures for a given genotype. Comparing the two genotypes at different temperatures, we found <1% of the genes being differentially spliced at 18°. At extreme temperatures, however, we detected substantial differences in alternative splicing-with almost 10% of the genes having differential splicing between the genotypes: a magnitude similar to between species differences. Genes with differential alternative splicing between genotypes frequently exhibit dominant inheritance. Remarkably, the pattern of surplus of differences in alternative splicing at extreme temperatures resembled the pattern seen for gene expression intensity. Since different sets of genes were involved for the two phenotypes, we propose that purifying selection results in the reduction of differences at benign temperatures. Relaxed purifying selection at temperature extremes, on the other hand, may cause the divergence in gene expression and alternative splicing between the two strains in rarely encountered environments.

A genomic perspective on the generation and maintenance of genetic diversity in herbivorous insects

Understanding the processes that generate and maintain genetic variation within populations is a central goal in evolutionary biology. Theory predicts that some of this variation is maintained as a consequence of adapting to variable habitats. Studies in herbivorous insects have played a key role in confirming this prediction. Here, we highlight theoretical and conceptual models for the maintenance of genetic diversity in herbivorous insects, empirical genomic studies testing these models, and pressing questions within the realm of evolutionary and functional genomic studies. To address key gaps, we propose an integrative approach combining population genomic scans for adaptation, genome-wide characterization of targets of selection through experimental manipulations, mapping the genetic architecture of traits influencing fitness, and functional studies. We also stress the importance of studying the maintenance of genetic variation across biological scales-from variation within populations to divergence among populations-to form a comprehensive view of adaptation in herbivorous insects.

Diet dependent metabolic responses in three generalist insect herbivores Spodoptera spp

Adaption to dietary changes is critical in the evolution of host plant ranges in polyphagous insects. We compared three taxa of lepidopteran herbivores from the predominantly generalist genus Spodoptera showing different degrees of polyphagy: Spodoptera littoralis, with a broad host range including both mono- and dicotyledonous plants, and two Spodoptera frugiperda strains [Corn (i.e. maize) (C) and Rice (R)] adapted primarily to different grass species. When feeding on maize we show a lower performance in the broad generalist taxon compared to the grass adapted taxa. Among these taxa, the maize adapted S. frugiperda C-strain generally performed better than the R-strain on maize leaves. On artificial pinto diet, all taxa performed well. Our RNA-Seq analysis of midgut transcriptomes from 3rd instar larvae feeding on maize showed broader transcriptional readjustments in the generalist S. littoralis compared to grass adapted S. frugiperda strains. Substantial alteration in the expression levels of midgut physiological function related transcripts, such as digestive and detoxifying enzymes, transporters, immunity, and peritrophic membrane associated transcripts, existed in all taxa. We found high background expression of UDP-glucosyl transferases, which are known to neutralize maize leaf toxins, in the maize adapted S. frugiperda C-strain, contributing to its fitness on maize compared to the R-strain. Our findings provide evidence for divergent diet specific response of digestive physiology within these Spodoptera taxa. Unexpectedly, the C- and R-strains of S. frugiperda fed on the same diet showed large differences in expression patterns between these two closely related taxa.

Preadult life history variation determines adult transcriptome expression

Preadult determinants of adult fitness and behaviour have been documented in a variety of organisms with complex life cycles, but little is known about expression patterns of genes underlying these adult traits. We explored the effects of differences in egg-to-adult development time on adult transcriptome and cuticular hydrocarbon variation in order to understand the nature of the genetic correlation between preadult development time and premating isolation between populations of Drosophila mojavensis reared in different host cactus environments. Transcriptome variation was analysed separately in flies reared on each host and revealed that hundreds of genes in adults were differentially expressed (FDR P < 0.05) due to development time differences. For flies reared on pitaya agria cactus, longer preadult development times caused increased expression of genes in adults enriched for ribosome production, protein metabolism, chromatin remodelling and regulation of alternate splicing and transcription. Baja California flies reared on organ pipe cactus showed fewer differentially expressed genes in adults due to longer preadult development time, but these were enriched for ATP synthesis and the TCA cycle. Mainland flies reared on organ pipe cactus with shorter development times showed increased transcription of genes enriched for mitochondria and energy production, protein synthesis and glucose metabolism: adults with longer development times had increased expression of genes enriched for adult life span, cuticle proteins and ion binding, although most differentially expressed genes were unannotated. Differences due to population, sex, mating status and their interactions were also assessed. Adult cuticular hydrocarbon profiles also showed shifts due to egg-to-adult development time and were influenced by population and mating status. These results help to explain why preadult life history variation determines subsequent expression of the adult transcriptome along with traits involved with reproductive isolation and revealed previously undocumented connections between genetic and environmental influences over the entire life cycle in this desert insect.

Genomics of ecological adaptation in cactophilic Drosophila

Cactophilic Drosophila species provide a valuable model to study gene–environment interactions and ecological adaptation. Drosophila buzzatii and Drosophila mojavensis are two cactophilic species that belong to the repleta group, but have very different geographical distributions and primary host plants. To investigate the genomic basis of ecological adaptation, we sequenced the genome and developmental transcriptome of D. buzzatii and compared its gene content with that of D. mojavensis and two other noncactophilic Drosophila species in the same subgenus. The newly sequenced D. buzzatii genome (161.5 Mb) comprises 826 scaffolds (>3 kb) and contains 13,657 annotated protein-coding genes. Using RNA sequencing data of five life-stages we found expression of 15,026 genes, 80% protein-coding genes, and 20% noncoding RNA genes. In total, we detected 1,294 genes putatively under positive selection. Interestingly, among genes under positive selection in the D. mojavensis lineage, there is an excess of genes involved in metabolism of heterocyclic compounds that are abundant in Stenocereus cacti and toxic to nonresident Drosophila species. We found 117 orphan genes in the shared D. buzzatii–D. mojavensis lineage. In addition, gene duplication analysis identified lineage-specific expanded families with functional annotations associated with proteolysis, zinc ion binding, chitin binding, sensory perception, ethanol tolerance, immunity, physiology, and reproduction. In summary, we identified genetic signatures of adaptation in the shared D. buzzatii–D. mojavensis lineage, and in the two separate D. buzzatii and D. mojavensis lineages. Many of the novel lineage-specific genomic features are promising candidates for explaining the adaptation of these species to their distinct ecological niches.