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  • 1. Ahola, Virpi
    et al.
    Lehtonen, Rainer
    Somervuo, Panu
    Salmela, Leena
    Koskinen, Patrik
    Rastas, Pasi
    Valimaki, Niko
    Paulin, Lars
    Kvist, Jouni
    Wahlberg, Niklas
    Tanskanen, Jaakko
    Hornett, Emily A.
    Ferguson, Laura C.
    Luo, Shiqi
    Cao, Zijuan
    de Jong, Maaike A.
    Duplouy, Anne
    Smolander, Olli-Pekka
    Vogel, Heiko
    McCoy, Rajiv C.
    Qian, Kui
    Chong, Wong Swee
    Zhang, Qin
    Ahmad, Freed
    Haukka, Jani K.
    Joshi, Aruj
    Salojarvi, Jarkko
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Grosse-Wilde, Ewald
    Hughes, Daniel
    Katainen, Riku
    Pitkanen, Esa
    Ylinen, Johannes
    Waterhouse, Robert M.
    Turunen, Mikko
    Vaharautio, Anna
    Ojanen, Sami P.
    Schulman, Alan H.
    Taipale, Minna
    Lawson, Daniel
    Ukkonen, Esko
    Makinen, Veli
    Goldsmith, Marian R.
    Holm, Liisa
    Auvinen, Petri
    Frilander, Mikko J.
    Hanski, Ilkka
    The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 4737-Article in journal (Refereed)
    Abstract [en]

    Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n = 31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n = 31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.

  • 2.
    Celorio-Mancera, Maria de la Paz
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Huss, Mikael
    Stockholm University, Science for Life Laboratory (SciLifeLab).
    Vezzi, Francesco
    Stockholm University, Science for Life Laboratory (SciLifeLab).
    Neethiraj, Ramprasad
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Reimegård, Johan
    Stockholm University, Science for Life Laboratory (SciLifeLab).
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Janz, Niklas
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly2016In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 16, article id 59Article in journal (Refereed)
    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.

  • 3.
    Celorio-Mancera, Maria de la Paz
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Vogel, Heiko
    Söderlind, Lina
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Janz, Niklas
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Mechanisms of macroevolution: polyphagous plasticity in butterfly larvae revealed by RNA-Seq2013In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 22, no 19, p. 4884-4895Article in journal (Refereed)
    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.

  • 4. Dhaygude, Kishor
    et al.
    Trontti, Kalevi
    Paviala, Jenni
    Morandin, Claire
    Wheat, Christopher
    Stockholm University, Faculty of Science, Department of Zoology.
    Sundström, Liselotte
    Helanterä, Heikki
    Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta2017In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 5, article id e3998Article in journal (Refereed)
    Abstract [en]

    Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon.

  • 5. Edger, Patrick P.
    et al.
    Heidel-Fischer, Hanna M.
    Bekaert, Michael
    Rota, Jadranka
    Gloeckner, Gernot
    Platts, Adrian E.
    Heckel, David G.
    Der, Joshua P.
    Wafula, Eric K.
    Tang, Michelle
    Hofberger, Johannes A.
    Smithson, Ann
    Hall, Jocelyn C.
    Blanchette, Matthieu
    Bureau, Thomas E.
    Wright, Stephen I.
    dePamphilis, Claude W.
    Schranz, M. Eric
    Barker, Michael S.
    Conant, Gavin C.
    Wahlberg, Niklas
    Vogel, Heiko
    Pires, J. Chris
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    The butterfly plant arms-race escalated by gene and genome duplications2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 27, p. 8362-8366Article in journal (Refereed)
    Abstract [en]

    Coevolutionary interactions are thought to have spurred the evolution of key innovations and driven the diversification of much of life on Earth. However, the genetic and evolutionary basis of the innovations that facilitate such interactions remains poorly understood. We examined the coevolutionary interactions between plants (Brassicales) and butterflies (Pieridae), and uncovered evidence for an escalating evolutionary arms-race. Although gradual changes in trait complexity appear to have been facilitated by allelic turnover, key innovations are associated with gene and genome duplications. Furthermore, we show that the origins of both chemical defenses and of molecular counter adaptations were associated with shifts in diversification rates during the arms-race. These findings provide an important connection between the origins of biodiversity, coevolution, and the role of gene and genome duplications as a substrate for novel traits.

  • 6.
    Keehnen, Naomi L. P.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Hill, Jason
    Stockholm University, Faculty of Science, Department of Zoology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Microevolutionary selection dynamics acting on immune genes of the green-veined white butterfly, Pieris napi2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 13, p. 2807-2822Article in journal (Refereed)
    Abstract [en]

    Insects rely on their innate immune system to successfully mediate complex interactions with their microbiota, as well as the microbes present in the environment. Previous work has shown that components of the canonical immune gene repertoire evolve rapidly and have evolutionary characteristics originating from interactions with fast-evolving microorganisms. Although these interactions are likely to vary among populations, there is a poor understanding of the microevolutionary dynamics of immune genes, especially in non-Dipteran insects. Here, we use the full set of canonical insect immune genes to investigate microevolutionary dynamics acting on these genes between and among populations by comparing three allopatric populations of the green-veined white butterfly, Pieris napi (Linne; Lepidoptera, Pieridae). Immune genes showed increased genetic diversity compared to genes from the rest of the genome and various functional categories exhibited different types of signatures of selection, at different evolutionary scales, presenting a complex pattern of selection dynamics. Signatures of balancing selection were identified in 10 genes, and 17 genes appear to be under positive selection. Genes involved with the cellular arm of the immune response as well as the Toll pathway appear to be enriched among our outlier loci, regardless of functional category. This suggests that the targets of selection might focus upon an entire pathway, rather than functional subsets across pathways. Our microevolutionary results are similar to previously observed macroevolutionary patterns from diverse taxa, suggesting that either the immune system is robust to dramatic differences in life history and microbial communities, or that diverse microbes exert similar selection pressures.

  • 7.
    Keehnen, Naomi L. P.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Rolff, Jens
    Theopold, Ulrich
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Insect Antimicrobial Defences: A Brief History, Recent Findings, Biases, and a Way Forward in Evolutionary Studies2017In: Advances in Insect Physiology, ISSN 0065-2806, E-ISSN 2213-6800, Vol. 52, p. 1-33Article in journal (Refereed)
    Abstract [en]

    We propose that an evolutionary and phenotype-driven approach, harnessing current technological developments, has much to offer for our understanding of insect immunity. After briefly reviewing the history of the discovery of canonical immune system, the current understanding of its components is reviewed and then we argue that the current paradigm of research may be biassed due to (a) its limited taxonomic perspective, (b) the evolutionary time scale being studied, and (c) a focus primarily if not exclusively, upon the canonical, humoural gene set. For the rest of the review, we then discuss the importance of a phenotype down approach as an understudied perspective, exemplified by the need for understanding the basis of cellular responses and wounding as a source of selection on immunity in the wild. We propose that research on those topics almost certainly will provide new insights into the evolution of the insect immune system.

  • 8.
    Lehmann, Philipp
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Pruisscher, Peter
    Stockholm University, Faculty of Science, Department of Zoology.
    Kostal, Vladimir
    Moos, Martin
    Simek, Petr
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Agren, Rasmus
    Varemo, Leif
    Wiklund, Christer
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Gotthard, Karl
    Stockholm University, Faculty of Science, Department of Zoology.
    Metabolome dynamics of diapause in the butterfly Pieris napi: distinguishing maintenance, termination and post-diapause phases2018In: Journal of Experimental Biology, ISSN 0022-0949, E-ISSN 1477-9145, Vol. 221, no 2, article id UNSP jeb169508Article in journal (Refereed)
    Abstract [en]

    Diapause is a deep resting stage facilitating temporal avoidance of unfavourable environmental conditions, and is used by many insects to adapt their life cycle to seasonal variation. Although considerable work has been invested in trying to understand each of the major diapause stages (induction, maintenance and termination), we know very little about the transitions between stages, especially diapause termination. Understanding diapause termination is crucial for modelling and predicting spring emergence and winter physiology of insects, including many pest insects. In order to gain these insights, we investigated metabolome dynamics across diapause development in pupae of the butterfly Pieris napi, which exhibits adaptive latitudinal variation in the length of endogenous diapause that is uniquely well characterized. By employing a time-series experiment, we show that the whole-body metabolome is highly dynamic throughout diapause and differs between pupae kept at a diapause-terminating (low) temperature and those kept at a diapause-maintaining (high) temperature. We showmajor physiological transitions through diapause, separate temperature-dependent from temperature-independent processes and identify significant patterns of metabolite accumulation and degradation. Together, the data show that although the general diapause phenotype (suppressed metabolism, increased cold tolerance) is established in a temperature-independent fashion, diapause termination is temperature dependent and requires a cold signal. This revealed several metabolites that are only accumulated under diapause-terminating conditions and degraded in a temperature-unrelated fashion during diapause termination. In conclusion, our findings indicate that some metabolites, in addition to functioning as cryoprotectants, for example, are candidates for having regulatory roles as metabolic clocks or time-keepers during diapause.

  • 9.
    Lehmann, Philipp
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Pruisscher, Peter
    Stockholm University, Faculty of Science, Department of Zoology.
    Posledovich, Diana
    Stockholm University, Faculty of Science, Department of Zoology.
    Carlsson, Mikael
    Stockholm University, Faculty of Science, Department of Zoology.
    Käkelä, Reijo
    Tang, Patrik
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Wiklund, Christer
    Stockholm University, Faculty of Science, Department of Zoology.
    Gotthard, Karl
    Stockholm University, Faculty of Science, Department of Zoology.
    Energy and lipid metabolism during direct and diapause development in a pierid butterfly2016In: Journal of Experimental Biology, ISSN 0022-0949, E-ISSN 1477-9145, Vol. 219, no 19, p. 3049-3060Article in journal (Refereed)
    Abstract [en]

    Diapause is a fundamental component of the life-cycle in the majority of insects living in environments characterized by strong seasonality. The present study addresses poorly understood associations and trade-offs between endogenous diapause duration, thermal sensitivity of development, energetic cost of development and cold tolerance. Diapause intensity, metabolic rate trajectories and lipid profiles of directly developing and diapausing animals were studied using pupae and adults of Pieris napi butterflies from a population for which endogenous diapause is well studied. Endogenous diapause was terminated after 3 months and termination required chilling. Metabolic and postdiapause development rates increased with diapause duration, while the metabolic cost of postdiapause development decreased, indicating that once diapause is terminated development proceeds at a low rate even at low temperature. Diapausing pupae had larger lipid stores than the directly developing pupae and lipids constituted the primary energy source during diapause. However, during diapause lipid stores did not decrease. Thus, despite lipid catabolism meeting the low energy costs of the diapausing pupae, primary lipid store utilization did not occur until the onset of growth and metamorphosis in spring. In line with this finding, diapausing pupae contained low amounts of mitochondria-derived cardiolipins, which suggests a low capacity for fatty acid β-oxidation. While ontogenic development had a large effect on lipid and fatty acid profiles, only small changes in these were seen during diapause. The data therefore indicate that the diapause lipidomic phenotype is built early, when pupae are still at high temperature, and retained until diapause post-diapause development.

  • 10.
    Lehmann, Philipp
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Van der Bijl, Wouter
    Stockholm University, Faculty of Science, Department of Zoology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Gotthard, Karl
    Stockholm University, Faculty of Science, Department of Zoology.
    Timing of diapause termination in relation to variation in winter climate2017In: Physiological entomology (Print), ISSN 0307-6962, E-ISSN 1365-3032, Vol. 42, no 3, p. 232-238Article in journal (Refereed)
    Abstract [en]

    In temperate insects, winters are typically endured by entering diapause, which comprises a deep resting stage. Correct timing of diapause termination is vital for synchronization of emergence with conspecifics and for mobilizing resources when conditions for growth and reproduction become favourable. Although critical to survival, the intrinsic and extrinsic drivers of diapause termination timing are poorly understood. In the present study, we investigate diapause development under a range of durations (10-24weeks) spent at different temperatures (-2 to 10 degrees C) in the pupal diapausing butterfly Pieris napi Linnaeus (Lepidoptera: Pieridae). We determine: (i) the maximum cold temperature for diapause development; (ii) if pupae in diapause count cold days or cold sums; and (iii) whether diapause termination is distinct or gradual. The results indicate large and idiosyncratic effects of high and low nonlethal temperatures on diapause development in P. napi. Although all temperatures tested lead to diapause termination, a thermal optimum between 2 and 4 degrees C is observed. Lower temperatures lead to decreased eclosion propensity, whereas higher temperatures slow down development and increase emergence desynchronization. These data suggest that, rather than a simple cold-summing process with a distinct diapause termination point, there are trade-offs between time and temperature at the low and high end of the thermal range, resulting in a nonlinear thermal landscape showing a ridge of increasing eclosion propensity at moderate temperatures. The present study suggests that the effects of temperature on diapause development should be included in projections on post-winter phenology models of insects, including pest species.

  • 11. Morandin, C.
    et al.
    Dhaygude, K.
    Paviala, J.
    Trontti, K.
    Wheat, Christopher
    Stockholm University, Faculty of Science, Department of Zoology.
    Helanterä, H.
    Caste-biases in gene expression are specific to developmental stage in the ant Formica exsecta2015In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 28, no 9, p. 1705-1718Article in journal (Refereed)
    Abstract [en]

    Understanding how a single genome creates and maintains distinct phenotypes is a central goal in evolutionary biology. Social insects are a striking example of co-opted genetic backgrounds giving rise to dramatically different phenotypes, such as queen and worker castes. A conserved set of molecular pathways, previously envisioned as a set of 'toolkit' genes, has been hypothesized to underlie queen and worker phenotypes in independently evolved social insect lineages. Here, we investigated the toolkit from a developmental point of view, using RNA-Seq to compare caste-biased gene expression patterns across three life stages (pupae, emerging adult and old adult) and two female castes (queens and workers) in the ant Formica exsecta. We found that the number of genes with caste-biased expression increases dramatically from pupal to old adult stages. This result suggests that phenotypic differences between queens and workers at the pupal stage may derive from a relatively low number of caste-biased genes, compared to higher number of genes required to maintain caste differences at the adult stage. Gene expression patterns were more similar among castes within developmental stages than within castes despite the extensive phenotypic differences between queens and workers. Caste-biased expression was highly variable among life stages at the level of single genes, but more consistent when gene functions (gene ontology terms) were investigated. Finally, we found that a large part of putative toolkit genes were caste-biased at least in some life stages in F. exsecta, and the caste-biases, but not their direction, were more often shared between F. exsecta and other ant species than between F. exsecta and bees. Our results indicate that gene expression should be examined across several developmental stages to fully reveal the genetic basis of polyphenisms.

  • 12. Nallu, Sumitha
    et al.
    Hill, Jason A.
    Stockholm University, Faculty of Science, Department of Zoology.
    Don, Kristine
    Sahagun, Carlos
    Zhang, Wei
    Meslin, Camille
    Snell-Rood, Emilie
    Clark, Nathan L.
    Morehouse, Nathan I.
    Bergelson, Joy
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Kronforst, Marcus R.
    The molecular genetic basis of herbivory between butterflies and their host plants2018In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 2, no 9, p. 1418-1427Article in journal (Refereed)
    Abstract [en]

    Interactions between herbivorous insects and their host plants are a central component of terrestrial food webs and a critical topic in agriculture, where a substantial fraction of potential crop yield is lost annually to pests. Important insights into plant-insect interactions have come from research on specific plant defences and insect detoxification mechanisms. Yet, much remains unknown about the molecular mechanisms that mediate plant-insect interactions. Here we use multiple genome-wide approaches to map the molecular basis of herbivory from both plant and insect perspectives, focusing on butterflies and their larval host plants. Parallel genome-wide association studies in the cabbage white butterfly, Pieris rapae, and its host plant, Arabidopsis thaliana, pinpointed a small number of butterfly and plant genes that influenced herbivory. These genes, along with much of the genome, were regulated in a dynamic way over the time course of the feeding interaction. Comparative analyses, including diverse butterfly/plant systems, showed a variety of genome-wide responses to herbivory, as well as a core set of highly conserved genes in butterflies as well as their host plants. These results greatly expand our understanding of the genomic causes and evolutionary consequences of ecological interactions across two of nature's most diverse taxa, butterflies and flowering plants.

  • 13.
    Neethiraj, Ramprasad
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Pennsylvania State University, USA.
    Hornett, Emily A.
    Hill, Jason A.
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Investigating the genomic basis of discrete phenotypes using a Pool-Seq-only approach: New insights into the genetics underlying colour variation in diverse taxa2017In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 19, p. 4990-5002Article in journal (Refereed)
    Abstract [en]

    While large-scale genomic approaches are increasingly revealing the genetic basis of polymorphic phenotypes such as colour morphs, such approaches are almost exclusively conducted in species with high-quality genomes and annotations. Here, we use Pool-Seq data for both genome assembly and SNP frequency estimation, followed by scanning for F-ST outliers to identify divergent genomic regions. Using paired-end, short-read sequencing data from two groups of individuals expressing divergent phenotypes, we generate a de novo rough-draft genome, identify SNPs and calculate genomewide F-ST differences between phenotypic groups. As genomes generated by Pool-Seq data are highly fragmented, we also present an approach for super-scaffolding contigs using existing protein-coding data sets. Using this approach, we reanalysed genomic data from two recent studies of birds and butterflies investigating colour pattern variation and replicated their core findings, demonstrating the accuracy and power of a Pool-Seq-only approach. Additionally, we discovered new regions of high divergence and new annotations that together suggest novel parallels between birds and butterflies in the origins of their colour pattern variation.

  • 14. Nowell, Reuben W.
    et al.
    Elsworth, Ben
    Oostra, Vicencio
    Zwaan, Bas J.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Saastamoinen, Marjo
    Saccheri, Ilik J.
    Van't Hof, Arjen E.
    Wasik, Bethany R.
    Connahs, Heidi
    Aslam, Muhammad L.
    Kumar, Sujai
    Challis, Richard J.
    Monteiro, Antonia
    Brakefield, Paul M.
    Blaxter, Mark
    A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana2017In: GigaScience, ISSN 2047-217X, E-ISSN 2047-217X, Vol. 6, no 7Article in journal (Refereed)
    Abstract [en]

    The mycalesine butterfly Bicyclus anynana, the Squinting bush brown, is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illumina data was filtered to 124 Gb and assembled to a final size of 475 Mb (similar to x260 assembly coverage). Contigs were scaffolded using mate-pair, transcriptome, and PacBio data into 10 800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements and encodes a total of 22 642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html).

  • 15.
    Nylin, Sören
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Agosta, Salvatore
    Bensch, Staffan
    Boeger, Walter A.
    P. Braga, Mariana
    Stockholm University, Faculty of Science, Department of Zoology.
    Brooks, Daniel R.
    Forister, Matthew L.
    Hambäck, Peter A.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Hoberg, Eric P.
    Nyman, Tommi
    Schäpers, Alexander
    Stockholm University, Faculty of Science, Department of Zoology.
    Stigall, Alycia L.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Österling, Martin
    Janz, Niklas
    Stockholm University, Faculty of Science, Department of Zoology.
    Embracing Colonizations: A New Paradigm for Species Association Dynamics2018In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 33, no 1, p. 4-14Article, review/survey (Refereed)
    Abstract [en]

    Parasitehost and insectplant research have divergent traditions despite the fact that most phytophagous insects live parasitically on their host plants. In parasitology it is a traditional assumption that parasites are typically highly specialized; cospeciation between parasites and hosts is a frequently expressed default expectation. Insectplant theory has been more concerned with host shifts than with cospeciation, and more with hierarchies among hosts than with extreme specialization. We suggest that the divergent assumptions in the respective fields have hidden a fundamental similarity with an important role for potential as well as actual hosts, and hence for host colonizations via ecological fitting. A common research program is proposed which better prepares us for the challenges from introduced species and global change.

  • 16. Oostra, Vicencio
    et al.
    Saastamoinen, Marjo
    Zwaan, Bas J.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Strong phenotypic plasticity limits potential for evolutionary responses to climate change2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 1005Article in journal (Refereed)
    Abstract [en]

    Phenotypic plasticity, the expression of multiple phenotypes from one genome, is a wide-spread adaptation to short-term environmental fluctuations, but whether it facilitates evolutionary adaptation to climate change remains contentious. Here, we investigate seasonal plasticity and adaptive potential in an Afrotropical butterfly expressing distinct phenotypes in dry and wet seasons. We assess the transcriptional architecture of plasticity in a full-factorial analysis of heritable and environmental effects across 72 individuals, and reveal pervasive gene expression differences between the seasonal phenotypes. Strikingly, intra-population genetic variation for plasticity is largely absent, consistent with specialisation to a particular environmental cue reliably predicting seasonal transitions. Under climate change, deteriorating accuracy of predictive cues will likely aggravate maladaptive phenotype-environment mismatches and increase selective pressures on reaction norms. However, the observed paucity of genetic variation for plasticity limits evolutionary responses, potentially weakening prospects for population persistence. Thus, seasonally plastic species may be especially vulnerable to climate change.

  • 17.
    Pečnerová, Patrícia
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Palkopoulou, Eleftheria
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden; Harvard Medical School, Massachusetts.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Skoglund, Pontus
    Vartanyan, Sergey
    Tikhonov, Alexei
    Nikolskiy, Pavel
    van der Plicht, Johannes
    Díez-del-Molino, David
    Dalén, Love
    Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size2017In: Evolution Letters, ISSN 2056-3744, Vol. 1, no 6, p. 292-303Article in journal (Refereed)
    Abstract [en]

    The onset of the Holocene was associated with a global temperature increase, which led to a rise in sea levels and isolation of the last surviving population of woolly mammoths on Wrangel Island. Understanding what happened with the population's genetic diversity at the time of the isolation and during the ensuing 6000 years can help clarify the effects of bottlenecks and subsequent limited population sizes in species approaching extinction. Previous genetic studies have highlighted questions about how the Holocene Wrangel population was established and how the isolation event affected genetic diversity. Here, we generated high-quality mitogenomes from 21 radiocarbon-dated woolly mammoths to compare the ancestral large and genetically diverse Late Pleistocene Siberian population and the small Holocene Wrangel population. Our results indicate that mitogenome diversity was reduced to one single haplotype at the time of the isolation, and thus that the Holocene Wrangel Island population was established by a single maternal lineage. Moreover, we show that the ensuing small effective population size coincided with fixation of a nonsynonymous mutation, and a comparative analysis of mutation rates suggests that the evolutionary rate was accelerated in the Holocene population. These results suggest that isolation on Wrangel Island led to an increase in the frequency of deleterious genetic variation, and thus are consistent with the hypothesis that strong genetic drift in small populations leads to purifying selection being less effective in removing deleterious mutations.

  • 18.
    Pruisscher, Peter
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Larsdotter-Mellström, Helena
    Stockholm University, Faculty of Science, Department of Zoology. The University of Western Australia, Australia.
    Stefanescu, Constantí
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Gotthard, Karl
    Stockholm University, Faculty of Science, Department of Zoology.
    Sex-linked inheritance of diapause induction in the butterfly Pieris napi2017In: Physiological entomology (Print), ISSN 0307-6962, E-ISSN 1365-3032, Vol. 42, no 3, p. 257-265Article in journal (Refereed)
    Abstract [en]

    Many temperate insects survive harsh environmental conditions, such as winter, by entering a state of developmental arrest. This diapause state is predominantly induced by photoperiod. The photoperiod varies with latitude and has led to local adaptation in the photoperiodic induction of diapause in many insects. To understand the rapid evolution of the photoperiodic threshold, it is important to investigate and understand the underlying genetic mechanisms. In the present study, the genetic basis of photoperiodic diapause induction is investigated in the green-veined white butterfly Pieris napi (Lepidoptera, Pieridae) by assaying diapause induction in a range of conditions for a Swedish and Spanish population. Furthermore, the inheritance of diapause induction is assessed in reciprocal F1 hybrids and backcrosses between the two populations. The southern population shows a clear photoperiodic threshold determining diapause or direct development, whereas the northern populations show a high incidence of diapause, regardless of photoperiod. The hybrid crosses reveal that the inheritance of diapause induction is strongly sex-linked, and that diapause incidence in the genetic crosses is highly dependent on photoperiod. This emphasizes the importance of assaying a range of conditions in diapause inheritance studies. The results indicate a strongly heritable diapause induction with a major component on the Z-chromosome, as well as a minor effect of the autosomal background.

  • 19. Saastamoinen, Marjo
    et al.
    Bocedi, Greta
    Cote, Julien
    Legrand, Delphine
    Guillaume, Frederic
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Fronhofer, Emanuel A.
    Garcia, Cristina
    Henry, Roslyn
    Husby, Arild
    Baguette, Michel
    Bonte, Dries
    Coulon, Aurelie
    Kokko, Hanna
    Matthysen, Erik
    Niitepold, Kristjan
    Nonaka, Etsuko
    Stevens, Virginie M.
    Travis, Justin M. J.
    Donohue, Kathleen
    Bullock, James M.
    del Mar Delgado, Maria
    Genetics of dispersal2018In: Biological Reviews, ISSN 1464-7931, E-ISSN 1469-185X, Vol. 93, no 1, p. 574-599Article, review/survey (Refereed)
    Abstract [en]

    Dispersal is a process of central importance for the ecological and evolutionary dynamics of populations and communities, because of its diverse consequences for gene flow and demography. It is subject to evolutionary change, which begs the question, what is the genetic basis of this potentially complex trait? To address this question, we (i) review the empirical literature on the genetic basis of dispersal, (ii) explore how theoretical investigations of the evolution of dispersal have represented the genetics of dispersal, and (iii) discuss how the genetic basis of dispersal influences theoretical predictions of the evolution of dispersal and potential consequences. Dispersal has a detectable genetic basis in many organisms, from bacteria to plants and animals. Generally, there is evidence for significant genetic variation for dispersal or dispersal-related phenotypes or evidence for the micro-evolution of dispersal in natural populations. Dispersal is typically the outcome of several interacting traits, and this complexity is reflected in its genetic architecture: while some genes of moderate to large effect can influence certain aspects of dispersal, dispersal traits are typically polygenic. Correlations among dispersal traits as well as between dispersal traits and other traits under selection are common, and the genetic basis of dispersal can be highly environment-dependent. By contrast, models have historically considered a highly simplified genetic architecture of dispersal. It is only recently that models have started to consider multiple loci influencing dispersal, as well as non-additive effects such as dominance and epistasis, showing that the genetic basis of dispersal can influence evolutionary rates and outcomes, especially under non-equilibrium conditions. For example, the number of loci controlling dispersal can influence projected rates of dispersal evolution during range shifts and corresponding demographic impacts. Incorporating more realism in the genetic architecture of dispersal is thus necessary to enable models to move beyond the purely theoretical towards making more useful predictions of evolutionary and ecological dynamics under current and future environmental conditions. To inform these advances, empirical studies need to answer outstanding questions concerning whether specific genes underlie dispersal variation, the genetic architecture of context-dependent dispersal phenotypes and behaviours, and correlations among dispersal and other traits.

  • 20.
    Schäpers, Alexander
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Petrén, Hampus
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Wiklund, Christer
    Stockholm University, Faculty of Science, Department of Zoology.
    Friberg, Magne
    Female fecundity variation affects reproducibility of experiments on host plant preference and acceptance in a phytophagous insect2017In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1849, article id 20162643Article in journal (Refereed)
    Abstract [en]

    Reproducibility is a scientific cornerstone. Many recent studies, however, describe a reproducibility crisis and call for assessments of reproducibility across scientific domains. Here, we explore the reproducibility of a classic ecological experiment—that of assessing female host plant preference and acceptance in phytophagous insects, a group in which host specialization is a key driver of diversification. We exposed multiple cohorts of Pieris napi butterflies from the same population to traditional host acceptance and preference tests on three Brassicaceae host species. Whereas the host plant rank order was highly reproducible, the propensity to oviposit on low-ranked hosts varied significantly even among cohorts exposed to similar conditions. Much variation could be attributed to among-cohort variation in female fecundity, a trait strongly correlated both to female size and to the size of the nuptial gift a female receives during mating. Small males provide small spermatophores, and in our experiment small females that mated with small males had a disproportionally low propensity to oviposit on low-ranked hosts. Hence, our results provide empirical support to the theoretical prediction that female host utilization is strongly affected by non-genetic, environmental variation, and that such variation can affect the reproducibility of ecological experiments even under seemingly identical conditions.

  • 21. Shafer, Aaron B. A.
    et al.
    Peart, Claire R.
    Tusso, Sergio
    Maayan, Inbar
    Brelsford, Alan
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Wolf, Jochen B. W.
    Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference2017In: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 8, no 8, p. 907-917Article in journal (Refereed)
    Abstract [en]

    1. Restriction site-associated DNA sequencing (RAD-seq) provides high-resolution population genomic data at low cost, and has become an important component in ecological and evolutionary studies. As with all high-throughput technologies, analytic strategies require critical validation to ensure precise and unbiased interpretation. 2. To test the impact of bioinformatic data processing on downstream population genetic inferences, we analysed mammalian RAD-seq data (>100 individuals) with 312 combinations of methodology (de novo vs. mapping to references of increasing divergence) and filtering criteria (missing data, HWE, F-IS, coverage, mapping and genotype quality). In an effort to identify commonalities and biases in all pipelines, we computed summary statistics (nr. loci, nr. SNP, pi, Het(obs), F-IS, F-ST, N-e and m) and compared the results to independent null expectations (isolation-by-distance correlation, expected transition-to-transversion ratio T-s/T-v and Mendelian mismatch rates of known parent-offspring trios). 3. We observed large differences between reference-based and de novo approaches, the former generally calling more SNPs and reducing F-IS and T-s/T-v. Data completion levels showed little impact on most summary statistics, and FST estimates were robust across all pipelines. The site frequency spectrum was highly sensitive to the chosen approach as reflected in large variance of parameter estimates across demographic scenarios (single-population bottlenecks and isolation-with-migration model). Null expectations were best met by reference-based approaches, although contingent on the specific criteria. 4. We recommend that RAD-seq studies employ reference-based approaches to a closely related genome, and due to the high stochasticity associated with the pipeline advocate the use of multiple pipelines to ensure robust population genetic and demographic inferences.

  • 22. Shafer, Aaron B. A.
    et al.
    Wolf, Jochen B. W.
    Alves, Paulo C.
    Bergstrom, Linnea
    Bruford, Michael W.
    Brannstrom, Ioana
    Colling, Guy
    Dalen, Love
    De Meester, Luc
    Ekblom, Robert
    Fawcett, Katie D.
    Fior, Simone
    Hajibabaei, Mehrdad
    Hill, Jason A.
    Stockholm University, Faculty of Science, Department of Zoology.
    Hoezel, A. Rus
    Hoglund, Jacob
    Jensen, Evelyn L.
    Krause, Johannes
    Kristensen, Torsten N.
    Kruetzen, Michael
    McKay, John K.
    Norman, Anita J.
    Ogden, Rob
    Osterling, E. Martin
    Ouborg, N. Joop
    Piccolo, John
    Popovic, Danijela
    Primmer, Craig R.
    Reed, Floyd A.
    Roumet, Marie
    Salmona, Jordi
    Schenekar, Tamara
    Schwartz, Michael K.
    Segelbacher, Gernot
    Senn, Helen
    Thaulow, Jens
    Valtonen, Mia
    Veale, Andrew
    Vergeer, Philippine
    Vijay, Nagarjun
    Vila, Caries
    Weissensteiner, Matthias
    Wennerström, Lovisa
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Zielinski, Piotr
    Genomics and the challenging translation into conservation practice2015In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 30, no 2, p. 78-87Article in journal (Refereed)
    Abstract [en]

    The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners.

  • 23. Shafer, Aaron B. A.
    et al.
    Wolf, Jochen B. W.
    Alves, Paulo C.
    Bergström, Linnea
    Colling, Guy
    Dalén, Love
    De Meester, Luc
    Ekblom, Robert
    Fior, Simone
    Hajibabaei, Mehrdad
    Hoezel, A. Rus
    Hoglund, Jacob
    Jensen, Evelyn L.
    Krützen, Michael
    Norman, Anita J.
    Österling, E. Martin
    Ouborg, N. Joop
    Piccolo, John
    Primmer, Craig R.
    Reed, Floyd A.
    Roumet, Marie
    Salmona, Jordi
    Schwartz, Michael K.
    Segelbacher, Gernot
    Thaulow, Jens
    Valtonen, Mia
    Vergeer, Philippine
    Weissensteiner, Matthias
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Vilà, Carlese
    Zieliński, Piotr
    Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application Reply2016In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 31, no 2, p. 83-84Article in journal (Refereed)
  • 24. Wahlberg, Niklas
    et al.
    Rota, Jadranka
    Braby, Michael F.
    Pierce, Naomi E.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Revised systematics and higher classification of pierid butterflies (Lepidoptera: Pieridae) based on molecular data2014In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 43, no 6, p. 641-650Article in journal (Refereed)
    Abstract [en]

    The butterfly family Pieridae comprises approximately 1000 described species placed in 85 genera, but the higher classification has not yet been settled. We used molecular data from eight gene regions (one mitochondrial and seven nuclear protein-coding genes) comprising a total of similar to 6700bp from 96 taxa to infer a well-supported phylogenetic hypothesis for the family. Based on this hypothesis, we revise the higher classification for all pierid genera. We resurrect the tribe Teracolini stat. rev. in the subfamily Pierinae to include the genera Teracolus, Pinacopteryx, Gideona, Ixias, Eronia, Colotis and most likely Calopieris. We transfer Hebomoia to the tribe Anthocharidini and assign the previously unplaced genera Belenois and Dixeia to the subtribe Aporiina. Three lineages near the base of Pierinae (Leptosia, Elodina and Nepheronia + Pareronia) remain unplaced. For each of these, we describe and delineate new tribes: Elodinini Braby tribus nova, Leptosiaini Braby tribus nova and Nepheroniini Braby tribus nova. The proposed higher classification is based on well-supported monophyletic groups and is likely to remain stable even with the addition of more data.

  • 25. Wahlberg, Niklas
    et al.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Pena, Carlos
    Timing and Patterns in the Taxonomic Diversification of Lepidoptera (Butterflies and Moths)2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 11, p. e80875-Article in journal (Refereed)
    Abstract [en]

    The macroevolutionary history of the megadiverse insect order Lepidoptera remains little-known, yet coevolutionary dynamics with their angiospermous host plants are thought to have influenced their diversification significantly. We estimate the divergence times of all higher-level lineages of Lepidoptera, including most extant families. We find that the diversification of major lineages in Lepidoptera are approximately equal in age to the crown group of angiosperms and that there appear to have been three significant increases in diversification rates among Lepidoptera over evolutionary time: 1) at the origin of the crown group of Ditrysia about 150 million years ago (mya), 2) at the origin of the stem group of Apoditrysia about 120 mya and finally 3) a spectacular increase at the origin of the stem group of the quadrifid noctuoids about 70 mya. In addition, there appears to be a significant increase in diversification rate in multiple lineages around 90 mya, which is concordant with the radiation of angiosperms. Almost all extant families appear to have begun diversifying soon after the Cretaceous/Paleogene event 65.51 mya.

  • 26.
    Wheat, Christopher W.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Hill, Jason
    Stockholm University, Faculty of Science, Department of Zoology.
    Pgi: the ongoing saga of a candidate gene2014In: Current Opinion in Insect Science, ISSN 2214-5745, Vol. 4, p. 42-47Article in journal (Refereed)
    Abstract [en]

    Numerous studies have found amino acid variation at the phosphoglucose isomerase (PGI) gene associated with organismal performance and fitness. Here we focus upon recent advances in the study of this gene, highlighting novel species being studied, new tools being used, and emerging insights into the evolutionary dynamics acting on this gene. Our synthesis highlights questions that are coming into focus, as well as the need for attention in specific areas, such as manipulative experiments to establish mechanistic insights and a causative role of allelic variation.

  • 27.
    Wheat, Christopher W.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Wahlberg, Niklas
    Critiquing blind dating: the dangers of over-confident date estimates in comparative genomics2013In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 28, no 22, p. 636-642Article in journal (Refereed)
    Abstract [en]

    Phylogenomic advances provide more rigorous estimates for the timing of evolutionary divergences than previously available (e.g., Bayesian relaxed-clock estimates with soft fossil constraints). However, because many family-level clades and higher, as well as model species within those clades, have not been included in phylogenomic studies, the literature presents temporal estimates likely harboring substantial errors. Blindly using such dates can substantially retard scientific advancement. We suggest a way forward by conducting analyses that minimize prior assumptions and use large datasets, and demonstrate how using such a phylogenomic approach can lead to significantly more parsimonious conclusions without a good fossil record. We suggest that such an approach calls for research into the biological causes of conflict between molecular and fossil signatures.

  • 28.
    Wheat, Christopher W.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Wahlberg, Niklas
    Phylogenomic Insights into the Cambrian Explosion, the Colonization of Land and the Evolution of Flight in Arthropoda2013In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 62, no 1, p. 93-109Article in journal (Refereed)
    Abstract [en]

    The timing of the origin of arthropods in relation to the Cambrian explosion is still controversial, as are the timing of other arthropod macroevolutionary events such as the colonization of land and the evolution of flight. Here we assess the power of a phylogenomic approach to shed light on these major events in the evolutionary history of life on earth. Analyzing a large phylogenomic dataset (122 taxa, 62 genes) with a Bayesian-relaxed molecular clock, we simultaneously reconstructed the phylogenetic relationships and the absolute times of divergences among the arthropods. Simulations were used to test whether our analysis could distinguish between alternative Cambrian explosion scenarios with increasing levels of autocorrelated rate variation. Our analyses support previous phylogenomic hypotheses and simulations indicate a Precambrian origin of the arthropods. Our results provide insights into the 3 independent colonizations of land by arthropods and suggest that evolution of insect wings happened much earlier than the fossil record indicates, with flight evolving during a period of increasing oxygen levels and impressively large forests. These and other findings provide a foundation for macroevolutionary and comparative genomic study of Arthropoda.

  • 29.
    Woronik, Alyssa
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Kawahara, Akito
    Warren, Andrew
    Chichvarkhin, Anton
    Wheat, Christopher
    Stockholm University, Faculty of Science, Department of Zoology.
    A phylogenetic analysis of butterflies in the genus ColiasManuscript (preprint) (Other academic)
  • 30.
    Woronik, Alyssa
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Neethiraj, Ramprasad
    Stockholm University, Faculty of Science, Department of Zoology.
    Lehmann, Philipp
    Stockholm University, Faculty of Science, Department of Zoology.
    Maria, de la Paz Celorio Mancera
    Stockholm University, Faculty of Science, Department of Zoology.
    Stefanescu, Constanti
    Hill, Jason
    Stockholm University, Faculty of Science, Department of Zoology.
    Käkelä, Reijo
    Brattstrom, Oskar
    Wheat, Christopher
    Stockholm University, Faculty of Science, Department of Zoology.
    A transposable element insertion is associated with a female-limited, alternative life history strategyManuscript (preprint) (Other academic)
  • 31.
    Woronik, Alyssa
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Stefanescu, Constanti
    Kakela, Reijo
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Lehmann, Philipp
    Stockholm University, Faculty of Science, Department of Zoology.
    Physiological differences between female limited, alternative life history strategies: The Alba phenotype in the butterfly Colias croceus2018In: Journal of insect physiology, ISSN 0022-1910, E-ISSN 1879-1611, Vol. 107, p. 257-264Article in journal (Refereed)
    Abstract [en]

    Across a wide range of taxa, individuals within populations exhibit alternative life history strategies (ALHS) where their phenotypes dramatically differ due to divergent investments in growth, reproduction and survivorship, with the resulting trade-offs directly impacting Darwinian fitness. Though the maintenance of ALHS within populations is fairly well understood, little is known regarding the physiological mechanisms that underlie ALHS and how environmental conditions can affect the evolution and expression of these phenotypes. One such ALHS, known as Alba, exists within females of many species in the butterfly genus Colias. Previous works in New World species not only found that female morphs differ in their wing color due to a reallocation of resources away from the synthesis of wing pigments to other areas of development, but also that temperature played an important role in these trade-offs. Here we build on previous work conducted in New World species by measuring life history traits and conducting lipidomics on individuals reared at hot and cold temperatures in the Old World species Colias croceus. Results suggest that the fitness of Alba and orange morphs likely varies with rearing temperature, where Alba females have higher fitness in cold conditions and orange in warm. Additionally shared traits between Old and New World species suggest the Alba mechanism is likely conserved across the genus. Finally, in the cold treatment we observe an intermediate yellow morph that may have decreased fitness due to slower larval development. This cost may manifest as disruptive selection in the field, thereby favoring the maintenance of the two discrete morphs. Taken together these results add insights into the evolution of, and the selection on, the Alba ALHS.

  • 32.
    Woronik, Alyssa
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Stefanescu, Constanti
    Käkelä, Reijo
    Wheat, Christopher
    Stockholm University, Faculty of Science, Department of Zoology.
    Lehmann, Philipp
    Stockholm University, Faculty of Science, Department of Zoology.
    Physiological differences between female limited, alternative life history strategies: the Alba phenotype in the butterfly Colias croceusManuscript (preprint) (Other academic)
  • 33.
    Woronik, Alyssa
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Advances in finding Alba: the locus affecting life history and color polymorphism in a Colias butterfly2017In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 30, no 1, p. 26-39Article in journal (Refereed)
    Abstract [en]

    Although alternative life-history strategies exist within many populations, very little is known about their genetic basis and mechanistic insight into these traits could greatly advance the understanding of eco-evolutionary dynamics. Many species of butterfly within the genus Colias exhibit a sex-limited wing colour polymorphism, called Alba, which is correlated with an alternative life-history strategy. Here, we have taken the first steps in localizing the region carrying Alba in Colias croceus, a species with no genomic resources, by generating whole genome sequence of a single Alba mother and two sequencing pools, one for her Alba and another for her orange, offspring. These data were used in a bulk-segregant analysis wherein SNPs fulfilling the Mendelian inheritance expectations of Alba were identified. Then, using the conserved synteny in Lepidoptera, the Alba locus was assigned to chromosome 15 in Bombyx mori. We then identified candidate regions within the chromosome by investigating the distribution of Alba SNPs along the chromosome and the difference in nucleotide diversity in exons between the two pools. A region spanning similar to 5.7 Mbp at the 50 end of the chromosome was identified as likely to contain the Alba locus. These insights set the stage for more detailed genomic scans and mapping of the Alba phenotype, and demonstrate an efficient use of genomic resources in a novel species.

1 - 33 of 33
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