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  • 1.
    Audusseau, Hélène
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen. Paris-Est Créteil University, France.
    Celorio-Mancera, Maria de la Paz
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Janz, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Nylin, Sören
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Why stay in a bad relationship? The effect of local host phenology on a generalist butterfly feeding on a low-ranked host2016Ingår i: BMC Evolutionary Biology, E-ISSN 1471-2148, Vol. 16, artikel-id 144Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: In plant-feeding insects, the evolutionary retention of polyphagy remains puzzling. A better understanding of the relationship between these organisms and changes in the metabolome of their host plants is likely to suggest functional links between them, and may provide insights into how polyphagy is maintained. Results: We investigated the phenological change of Cynoglossum officinale, and how a generalist butterfly species, Vanessa cardui, responded to this change. We used untargeted metabolite profiling to map plant seasonal changes in both primary and secondary metabolites. We compared these data to differences in larval performance on vegetative plants early and late in the season. We also performed two oviposition preference experiments to test females' ability to choose between plant developmental stages (vegetative and reproductive) early and late in the season. We found clear seasonal changes in plant primary and secondary metabolites that correlated with larval performance. The seasonal change in plant metabolome reflected changes in both nutrition and toxicity and resulted in zero survival in the late period. However, large differences among families in larval ability to feed on C. officinale suggest that there is genetic variation for performance on this host. Moreover, females accepted all plants for oviposition, and were not able to discriminate between plant developmental stages, in spite of the observed overall differences in metabolite profile potentially associated with differences in suitability as larval food. Conclusions: In V. cardui, migratory behavior, and thus larval feeding times, are not synchronized with plant phenology at the reproductive site. This lack of synchronization, coupled with the observed lack of discriminatory oviposition, obviously has potential fitness costs. However, this opportunistic behavior may as well function as a source of potential host plant evolution, promoting for example the acceptance of new plants.

  • 2.
    Celorio-Mancera, Maria de la Paz
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Ahn, Seung-Joon
    Vogel, Heiko
    Heckel, David G.
    Transcriptional responses underlying the hormetic and detrimental effects of the plant secondary metabolite gossypol on the generalist herbivore Helicoverpa armigera2011Ingår i: BMC Genomics, E-ISSN 1471-2164, Vol. 12, s. 575-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Hormesis is a biphasic biological response characterized by the stimulatory effect at relatively low amounts of chemical compounds which are otherwise detrimental at higher concentrations. A hormetic response in larval growth rates has been observed in cotton-feeding insects in response to increasing concentrations of gossypol, a toxic metabolite found in the pigment glands of some plants in the family Malvaceae. We investigated the developmental effect of gossypol in the cotton bollworm, Helicoverpa armigera, an important heliothine pest species, by exposing larvae to different doses of this metabolite in their diet. In addition, we sought to determine the underlying transcriptional responses to different gossypol doses. Results: Larval weight gain, pupal weight and larval development time were measured in feeding experiments and a hormetic response was seen for the first two characters. On the basis of net larval weight gain responses to gossypol, three concentrations (0%, 0.016% and 0.16%) were selected for transcript profiling in the gut and the rest of the body in a two-color double reference design microarray experiment. Hormesis could be observed at the transcript level, since at the low gossypol dose, genes involved in energy acquisition such as beta-fructofuranosidases were up-regulated in the gut, and genes involved in cell adhesion were down-regulated in the body. Genes with products predicted to be integral to the membrane or associated with the proteasome core complex were significantly affected by the detrimental dose treatment in the body. Oxidoreductase activity-related genes were observed to be significantly altered in both tissues at the highest gossypol dose. Conclusions: This study represents the first transcriptional profiling approach investigating the effects of different concentrations of gossypol in a lepidopteran species. H. armigera's transcriptional response to gossypol feeding is tissue-and dose-dependent and involves diverse detoxifying mechanisms not only to alleviate direct effects of gossypol but also indirect damage such as pH disturbance and oxygen radical formation. Genes discovered through this transcriptional approach may be additional candidates for understanding gossypol detoxification and coping with gossypol-induced stress. In a generalist herbivore that has evolved transcriptionally-regulated responses to a variety of different plant compounds, hormesis may be due to a lower induction threshold of growth-promoting, stress-coping responses and a higher induction threshold of detoxification pathways that are costly and cause collateral damage to the cell.

  • 3.
    Celorio-Mancera, Maria de la Paz
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Courtiade, Juliette
    Muck, Alexander
    Heckel, David G.
    Musser, Richard O.
    Vogel, Heiko
    Sialome of a Generalist Lepidopteran Herbivore: Identification of Transcripts and Proteins from Helicoverpa armigera Labial Salivary Glands2011Ingår i: PLOS ONE, E-ISSN 1932-6203, Vol. 6, nr 10, s. e26676-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Although the importance of insect saliva in insect-host plant interactions has been acknowledged, there is very limited information on the nature and complexity of the salivary proteome in lepidopteran herbivores. We inspected the labial salivary transcriptome and proteome of Helicoverpa armigera, an important polyphagous pest species. To identify the majority of the salivary proteins we have randomly sequenced 19,389 expressed sequence tags (ESTs) from a normalized cDNA library of salivary glands. In parallel, a non-cytosolic enriched protein fraction was obtained from labial salivary glands and subjected to two-dimensional gel electrophoresis (2-DE) and de novo peptide sequencing. This procedure allowed comparison of peptides and EST sequences and enabled us to identify 65 protein spots from the secreted labial saliva 2DE proteome. The mass spectrometry analysis revealed ecdysone, glucose oxidase, fructosidase, carboxyl/cholinesterase and an uncharacterized protein previously detected in H. armigera midgut proteome. Consistently, their corresponding transcripts are among the most abundant in our cDNA library. We did find redundancy of sequence identification of saliva-secreted proteins suggesting multiple isoforms. As expected, we found several enzymes responsible for digestion and plant offense. In addition, we identified non-digestive proteins such as an arginine kinase and abundant proteins of unknown function. This identification of secreted salivary gland proteins allows a more comprehensive understanding of insect feeding and poses new challenges for the elucidation of protein function.

  • 4.
    Celorio-Mancera, Maria de la Paz
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Rastas, Pasi
    Steward, Rachel A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Nylin, Sören
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Wheat, Christopher W.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Chromosome Level Assembly of the Comma Butterfly (Polygonia c-album)2021Ingår i: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 13, nr 5, artikel-id evab054Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The comma butterfly (Polygonia c-album, Nymphalidae, Lepidoptera) is a model insect species, most notably in the study of phenotypic plasticity and plant-insect coevolutionary interactions. In order to facilitate the integration of genomic tools with a diverse body of ecological and evolutionary research, we assembled the genome of a Swedish comma using 10X sequencing, scaffolding with matepair data, genome polishing, and assignment to linkage groups using a high-density linkage map. The resulting genome is 373 Mb in size, with a scaffold N50 of 11.7 Mb and contig N50 of 11,2Mb. The genome contained 90.1% of single-copy Lepidopteran orthologs in a BUSCO analysis of 5,286 genes. A total of 21,004 gene-models were annotated on the genome using RNA-Seq data from larval and adult tissue in combination with proteins from the Arthropoda database, resulting in a high-quality annotation for which functional annotations were generated. We further documented the quality of the chromosomal assembly via synteny assessment with Melitaea cinxia. The resulting annotated, chromosome-level genome will provide an important resource for investigating coevolutionary dynamics and comparative analyses in Lepidoptera.

  • 5.
    Celorio-Mancera, Maria de la Paz
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Sundmalm, Sara M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Vogel, Heiko
    Rutishauser, Dorothea
    Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Ytterberg, A. Jimmy
    Zubarev, Roman A.
    Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Janz, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Chemosensory proteins, major salivary factors in caterpillar mandibular glands2012Ingår i: Insect Biochemistry and Molecular Biology, ISSN 0965-1748, E-ISSN 1879-0240, Vol. 42, nr 10, s. 796-805Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Research in the field of insect-host plant interactions has indicated that constituents of insect saliva play an important role in digestion and affect host chemical defense responses. However, most efforts have focused on studying the composition and function of regurgitant or saliva produced in the labial glands. Acknowledging the need for understanding the role of the mandibular glands in herbivory, we sought to make a qualitative and semi-quantitative comparison of soluble luminal fractions between mandibular and labial glands of Vanessa gonerilla butterfly larvae. Amylase and lysozyme were inspected as possible major enzymatic activities in the mandibular glands aiding in pre-digestion and antimicrobial defense. Although detected, neither of these enzymatic activities was prominent in the luminal protein preparation of a particular type of gland. Proteins isolated from the glands were identified by mass spectrometry and by searching an EST-library database generated for four other nymphalid butterfly species, in addition to the public NCBI database. The identified proteins were also quantified from thedata using “Quanty”, an in-house program. The proteomic analysis detected chemosensory proteins as the most abundant luminal proteins in the mandibular glands. In comparison to these proteins, the relative amounts of amylase and lysozyme were much lower in both gland types. Therefore, we speculate that the primary role of the mandibular glands in Lepidopteran larvae is chemoreception which may include the detection of microorganisms on plant surfaces, host plant recognition and communication with conspecifics.

  • 6.
    Celorio-Mancera, Maria de la Paz
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Wheat, Christopher W.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    Vogel, Heiko
    Söderlind, Lina
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Janz, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Nylin, Sören
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Mechanisms of macroevolution: polyphagous plasticity in butterfly larvae revealed by RNA-Seq2013Ingår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 22, nr 19, s. 4884-4895Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Transcriptome studies of insect herbivory are still rare, yet studies in model systems have uncovered patterns of transcript regulation that appear to provide insights into how insect herbivores attain polyphagy, such as a general increase in expression breadth and regulation of ribosomal, digestion- and detoxification-related genes. We investigated the potential generality of these emerging patterns, in the Swedish comma, Polygonia c-album, which is a polyphagous, widely-distributed butterfly. Urtica dioica and Ribes uva-crispa are hosts of P. c-album, but Ribes represents a recent evolutionary shift onto a very divergent host. Utilizing the assembled transcriptome for read mapping, we assessed gene expression finding that caterpillar life-history (i.e. 2nd vs. 4th-instar regulation) had a limited influence on gene expression plasticity. In contrast, differential expression in response to host-plant identified genes encoding serine-type endopeptidases, membrane-associated proteins and transporters. Differential regulation of genes involved in nucleic acid binding was also observed suggesting that polyphagy involves large scale transcriptional changes. Additionally, transcripts coding for structural constituents of the cuticle were differentially expressed in caterpillars in response to their diet indicating that the insect cuticle may be a target for plant defence. Our results state that emerging patterns of transcript regulation from model species appear relevant in species when placed in an evolutionary context.

  • 7.
    Celorio-Mancera, Maria de la Paz
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Ytterberg, A. Jimmy
    Rutishauser, Dorothea
    Janz, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Zubarev, Roman A.
    Effect of host plant and immune challenge on the levels of chemosensory and odorant-binding proteins in caterpillar salivary glands2015Ingår i: Insect Biochemistry and Molecular Biology, ISSN 0965-1748, E-ISSN 1879-0240, Vol. 61, s. 34-45Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    More than half of the proteome from mandibular glands in caterpillars is represented by chemosensory proteins. Based on sequence similarity, these proteins are putative transporters of ligands to gustatory receptors in sensory organs of insects. We sought to determine whether these proteins are inducible by comparing, both qualitatively and quantitatively, the salivary (mandibular and labial) proteomes from caterpillars (Vanessa cardui) reared on different plants and artificial diet containing either bacteria or bacterial cell-walls. We included a treatment where the caterpillars were switched from feeding on artificial diet to plant material at some point in their development. Additionally, we evaluated the degree of overlap between the proteomes in the hemolymph-filled coelom and salivary glands of caterpillars reared on plant material. We found that the quality and quantity of the identified proteins differed clearly between hemolymph-filled coelome, labial and mandibular glands. Our results indicated that even after molting and two-day feeding on a new diet, protein production is affected by the previous food source used by the caterpillar. Candidate proteins involved in chemosensory perception by insects were detected: three chemosensory (CSPs) and two odorant-binding proteins (OBPs). Using the relative amounts of these proteins across tissues and treatments as criteria for their classification, we detected hemolymph- and mandibular gland-specific CSPs and observed that their levels were affected by caterpillar diet. Moreover, we could compare the protein and transcript levels across tissues and treatment for at least one CSP and one OBP. Therefore, we have identified specific isoforms for testing the role of CSPs and OBPs in plant and pathogen recognition. We detected catalase, immune-related protein and serine proteases and their inhibitors in high relative levels in the mandibular glands in comparison to the labial glands. These findings suggest that the mandibular glands of caterpillars may play an important role protecting the caterpillar from oxidative stress, pathogens and aiding in digestion. Contamination with hemolymph proteins during dissection of salivary glands from caterpillars may occur but it is not substantial since the proteomes from hemolymph, mandibular and labial glands were easily discriminated from each other by principal component analysis of proteomic data.

  • 8.
    Celorio-Mancera, Maria P.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Labavitch, John M.
    Salivary Gland Secretions of Phytophagous Arthropods2016Ingår i: Extracellular Composite Matrices in Arthropods / [ed] Ephraim Cohen, Bernard Moussian, Springer, 2016, s. 601-623Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    Thousands of arthropod species use plants as their main food source. Plants in turn are not completely passive towards arthropod herbivory. Arthropod saliva constitutes an important point of contact which initiates phytophagy and mediates chemical communication. Here we present a summary of those communications studying the constituents of arthropod saliva and their effect on plants. Particular attention has been dedicated to those reports identifying salivary gland genes and proteins in their entirety (transcriptomes and proteomes). The anatomy of salivary glands is highly variable and much of its complexity remains unstudied in various groups of phytophagous arthropods. Some important factors dictating the function of saliva in herbivory are the feeding strategy used by the arthropod, the developmental stage of the animal and the ecological niche in question. The function of many salivary components, such as the chemosensory proteins identified in arthropods, is still largely unknown. We consider the use of heterologous expression of these genes, chemoinformatic, molecular modeling and immunohistochemical studies to be of substantial importance for the elucidation of the functions of these genes as well as the functions of many other unknown proteins in arthropod systems. Additionally, the role of hemolymph proteins such as apolipophorins and storage proteins in saliva is unclear and therefore attention must be devoted to the understanding of protein movement in the arthropod body.

  • 9.
    de la Paz Celorio-Mancera, Maria
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    Wheat, Christopher W.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    Huss, Mikael
    Vezzi, Francesco
    Neethiraj, Ramprasad
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    Reimegård, Johan
    Nylin, Sören
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Janz, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly2016Ingår i: BMC Evolutionary Biology, E-ISSN 1471-2148, Vol. 16, artikel-id 59Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Although most insect species are specialized on one or few groups of plants, there are phytophagous insects that seem to use virtually any kind of plant as food. Understanding the nature of this ability to feed on a wide repertoire of plants is crucial for the control of pest species and for the elucidation of the macroevolutionary mechanisms of speciation and diversification of insect herbivores. Here we studied Vanessa cardui, the species with the widest diet breadth among butterflies and a potential insect pest, by comparing tissue-specific transcriptomes from caterpillars that were reared on different host plants. We tested whether the similarities of gene-expression response reflect the evolutionary history of adaptation to these plants in the Vanessa and related genera, against the null hypothesis of transcriptional profiles reflecting plant phylogenetic relatedness. Result: Using both unsupervised and supervised methods of data analysis, we found that the tissue-specific patterns of caterpillar gene expression are better explained by the evolutionary history of adaptation of the insects to the plants than by plant phylogeny. Conclusion: Our findings suggest that V. cardui may use two sets of expressed genes to achieve polyphagy, one associated with the ancestral capability to consume Rosids and Asterids, and another allowing the caterpillar to incorporate a wide range of novel host-plants.

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  • 10.
    Hill, Jason
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik. Uppsala University, Sweden.
    Rastas, Pasi
    Hornett, Emily A.
    Neethiraj, Ramprasad
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    Clark, Nathan
    Morehouse, Nathan
    de la Paz Celorio-Mancera, Maria
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    Carnicer Cols, Jofre
    Dircksen, Heinrich
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för funktionell zoomorfologi.
    Meslin, Camille
    Keehnen, Naomi
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    Pruisscher, Peter
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    Sikkink, Kristin
    Vives, Maria
    Vogel, Heiko
    Wiklund, Christer
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    Woronik, Alyssa
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik. New York University, USA.
    Boggs, Carol L.
    Nylin, Sören
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    Wheat, Christopher W.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution2019Ingår i: Science Advances, E-ISSN 2375-2548, Vol. 5, nr 6, artikel-id eaau3648Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. However, a few species possess radically inflated chromosomal counts due to extensive fission and fusion events. To address this enigma of constraint in the face of an exceptional ability to change, we investigated an unprecedented reorganization of the standard lepidopteran chromosome structure in the green-veined white butterfly (Pieris napi). We find that gene content in P. napi has been extensively rearranged in large collinear blocks, which until now have been masked by a haploid chromosome number close to the lepidopteran average. We observe that ancient chromosome ends have been maintained and collinear blocks are enriched for functionally related genes suggesting both a mechanism and a possible role for selection in determining the boundaries of these genome-wide rearrangements.

  • 11.
    Kurland, Sara
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik. Uppsala University, Sweden.
    Saha, Atal
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik. University of Agder, Kristiansand, Norway.
    P. Keehnen, Naomi L.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik. SLU, Sweden.
    Celorio-Mancera, Maria de la Paz
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    Díez-del-Molino, David
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik. Centre for Palaeogenetics, Sweden; Swedish Museum of Natural History, Sweden.
    Ryman, Nils
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    Laikre, Linda
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data2024Ingår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 33, nr 2, artikel-id e17213Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    International policy recently adopted commitments to maintain genetic diversity in wild populations to secure their adaptive potential, including metrics to monitor temporal trends in genetic diversity – so-called indicators. A national programme for assessing trends in genetic diversity was recently initiated in Sweden. Relating to this effort, we systematically assess contemporary genome-wide temporal trends (40 years) in wild populations using the newly adopted indicators and whole genome sequencing (WGS). We use pooled and individual WGS data from brown trout (Salmo trutta) in eight alpine lakes in protected areas. Observed temporal trends in diversity metrics (nucleotide diversity, Watterson's ϴ and heterozygosity) lie within proposed acceptable threshold values for six of the lakes, but with consistently low values in lakes above the tree line and declines observed in these northern-most lakes. Local effective population size is low in all lakes, highlighting the importance of continued protection of interconnected systems to allow genetic connectivity for long-term viability of these populations. Inbreeding (FROH) spans 10%–30% and is mostly represented by ancient (<1 Mb) runs of homozygosity, with observations of little change in mutational load. We also investigate adaptive dynamics over evolutionarily short time frames (a few generations); identifying putative parallel selection across all lakes within a gene pertaining to skin pigmentation as well as candidates of selection unique to specific lakes and lake systems involved in reproduction and immunity. We demonstrate the utility of WGS for systematic monitoring of natural populations, a priority concern if genetic diversity is to be protected.

  • 12.
    Kurland, Sara
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Wheat, Christopher W.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Celorio Mancera, Maria de la Paz
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Kutschera, Verena E.
    Stockholms universitet, Science for Life Laboratory (SciLifeLab). Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Hill, Jason
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Andersson, Anastasia
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Rubin, Carl-Johan
    Andersson, Leif
    Ryman, Nils
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Laikre, Linda
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species2019Ingår i: Ecology and Evolution, E-ISSN 2045-7758, Vol. 9, s. 11448-11463Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual-based single nucleotide polymorphisms [SNPs]) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F-ST) between the two introduced populations exceeds that of the naturally sympatric populations (F-ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ (pi over bar approximate to 0.002 and pi over bar approximate to 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq-only approach can be suitable for detecting and quantifying genome-wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.

  • 13.
    Neethiraj, Ramprasad
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    de la Paz Celorio-Mancera, Maria
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Nylin, Sören
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Wheat, Christopher
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Investigating cis-regulatory variation within and between populations reveals significant enrichment of genes in central metabolismManuskript (preprint) (Övrigt vetenskapligt)
  • 14.
    Nylin, Sören
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Söderlind, Lina
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Gamberale-Stille, Gabriella
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för etologi.
    Audusseau, Hélène
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Celorio-Mancera, Maria de la Paz
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Janz, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Sperling, Felix A. H.
    Vestiges of an ancestral host plant: preference and performance in the butterfly Polygonia faunus and its sister species P. c-album2015Ingår i: Ecological Entomology, ISSN 0307-6946, E-ISSN 1365-2311, Vol. 40, nr 3, s. 307-315Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    1. In the study of the evolution of insect-host plant interactions, important information is provided by host ranking correspondences among female preference, offspring preference, and offspring performance. Here, we contrast such patterns in two polyphagous sister species in the butterfly family Nymphalidae, the Nearctic Polygonia faunus, and the Palearctic P. c-album. 2. These two species have similar host ranges, but according to the literature P. faunus does not use the ancestral host plant clade-the urticalean rosids'. Comparisons of the species can thus test the effects of a change in insect-plant associations over a long time scale. Cage experiments confirmed that P. faunus females avoid laying eggs on Urtica dioica (the preferred host of P. c-album), instead preferring Salix, Betula, and Ribes.3. However, newly hatched larvae of both species readily accept and grow well on U. dioica, supporting the general theory that evolutionary changes in host range are initiated through shifts in female host preferences, whereas larvae are more conservative and also can retain the capacity to perform well on ancestral hosts over long time spans.4. Similar rankings of host plants among female preference, offspring preference, and offspring performance were observed in P. c-album but not in P. faunus. This is probably a result of vestiges of larval adaptations to the lost ancestral host taxon in the latter species. 5. Female and larval preferences seem to be largely free to evolve independently, and consequently larval preferences warrant more attention.

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  • 15.
    Pruisscher, Peter
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Lehmann, Philipp
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    de la Paz Celorio-Mancera, Maria
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Nylin, Sören
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Gotthard, Karl
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Wheat, Christopher
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Transcriptomic profiling of pupal diapause in the butterfly Pieris napiManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Diapause is a common means of overwintering among insects that is characterized by arrested development and increased tolerance to stress and cold. Diapause is a vital aspect of life cycle timing, and while the expression of specific candidate genes during diapause have been investigated, there is no general understanding of the dynamics of the transcriptional landscape as a whole during the extended diapause phenotype. Here we performed a time-course experiment using RNA-Seq on the head and abdomen in the butterfly Pieris napi. In both body parts, comparing diapause and directly developing siblings, differentially expressed genes are detected from the first day of pupal development and onwards, varying dramatically across these formative stages. During diapause there are strong gene expression dynamics independent of environmental conditions, revealing a pre-programmed transcriptional landscape that is active during the winter. Different biological processes appear to be active in the two body parts. Still, adults emerging from either the direct or diapause pathways do not show large transcriptomic differences, suggesting the adult phenotype is strongly canalized.

  • 16.
    Rego, Alexandre
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    Stajic, Dragan
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Celorio-Mancera, Maria de la Paz
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik. Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Stelkens, Rike
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    Dynamics of adaptation and trade-off evolution to complex environments in Saccharomyces cerevisiaeManuskript (preprint) (Övrigt vetenskapligt)
  • 17. Smolander, Olli-Pekka
    et al.
    Blande, Daniel
    Ahola, Virpi
    Rastas, Pasi
    Tanskanen, Jaakko
    Kammonen, Juhana
    Oostra, Vicencio
    Pellegrini, Lorenzo
    Ikonen, Suvi
    Dallas, Tad
    DiLeo, Michelle F.
    Duplouy, Anne
    Duru, Ilhan Cem
    Halimaa, Pauliina
    Kahilainen, Aapo
    Kuwar, Suyog S.
    Kärenlampi, Sirpa O.
    Lafuente, Elvira
    Luo, Shiqi
    Makkonen, Jenny
    Nair, Abhilash
    Celorio-Mancera, Maria de la Paz
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Pennanen, Ville
    Ruokolainen, Annukka
    Sundell, Tarja
    Tervahauta, Arja
    Twort, Victoria
    van Bergen, Erik
    Österman-Udd, Janina
    Paulin, Lars
    Frilander, Mikko J.
    Auvinen, Petri
    Saastamoinen, Marjo
    Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map2022Ingår i: GigaScience, E-ISSN 2047-217X, Vol. 11, s. 1-12, artikel-id giab097Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses.

    Results: The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92–94% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models.

    Conclusions: The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.

  • 18. Vogel, Heiko
    et al.
    Musser, Richard O.
    Celorio-Mancera, Maria de la Paz
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk ekologi.
    Transcriptome responses in herbivorous insects towards host plant and toxin feeding2014Ingår i: Insect-Plant Interactions / [ed] Claudia Voelckel, Georg Jander, Wiley-Blackwell, 2014, s. 197-233Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    Food source is a major determinant of physiological performance and a strong selection force for insect herbivores. The ability to adequately respond to chemical challenges posed by their host plants is the primary determinant of larval fitness. Most herbivorous insects must consume large quantities of plant material to meet their nutritional requirements and, at the same time, cope with numerous mechanical, chemical and protein-based defences posed by their sessile hosts. Despite the importance of host plants on essential life history traits of insect herbivores, data on global responses to both individual plant-derived compounds and plant feeding is scarce. Here we discuss the existing data on herbivore responses to host plant exposure, toxin feeding or nutrient limitations, and we make an attempt at identifying changes in genome-wide expression patterns of generalist and/or specialist herbivores. While generalists face an array of different plant defences, and therefore likely need to invest in broad detoxifying strategies, specialist herbivores need to fine-tune their adaptation to specific plant defences.

  • 19.
    Woronik, Alyssa
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Neethiraj, Ramprasad
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Lehmann, Philipp
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Maria, de la Paz Celorio Mancera
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Stefanescu, Constanti
    Hill, Jason
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Käkelä, Reijo
    Brattstrom, Oskar
    Wheat, Christopher
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    A transposable element insertion is associated with a female-limited, alternative life history strategyManuskript (preprint) (Övrigt vetenskapligt)
  • 20.
    Woronik, Alyssa
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Tunström, Kalle
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Perry, Michael W.
    Neethiraj, Ramprasad
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Stefanescu, Constanti
    de la Paz Celorio-Mancera, Maria
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Brattström, Oskar
    Hill, Jason
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Lehmann, Philipp
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Käkelä, Reijo
    Wheat, Christopher W.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    A transposable element insertion is associated with an alternative life history strategy2019Ingår i: Nature Communications, E-ISSN 2041-1723, Vol. 10, artikel-id 5757Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Tradeoffs affect resource allocation during development and result in fitness consequences that drive the evolution of life history strategies. Yet despite their importance, we know little about the mechanisms underlying life history tradeoffs. Many species of Colias butterflies exhibit an alternative life history strategy (ALHS) where females divert resources from wing pigment synthesis to reproductive and somatic development. Due to this reallocation, a wing color polymorphism is associated with the ALHS: either yellow/orange or white. Here we map the locus associated with this ALHS in Colias crocea to a transposable element insertion located downstream of the Colias homolog of BarH-1, a homeobox transcription factor. Using CRISPR/Cas9 gene editing, antibody staining, and electron microscopy we find white-specific expression of BarH-1 suppresses the formation of pigment granules in wing scales and gives rise to white wing color. Lipid and transcriptome analyses reveal physiological differences associated with the ALHS. Together, these findings characterize a mechanism for a female-limited ALHS.

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