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  • 1.
    Hill, Jason
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Uppsala University, Sweden.
    Rastas, Pasi
    Hornett, Emily A.
    Neethiraj, Ramprasad
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Clark, Nathan
    Morehouse, Nathan
    de la Paz Celorio-Mancera, Maria
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Carnicer Cols, Jofre
    Dircksen, Heinrich
    Stockholm University, Faculty of Science, Department of Zoology, Functional Morphology.
    Meslin, Camille
    Keehnen, Naomi
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Pruisscher, Peter
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Sikkink, Kristin
    Vives, Maria
    Vogel, Heiko
    Wiklund, Christer
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Woronik, Alyssa
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. New York University, USA.
    Boggs, Carol L.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution2019In: Science Advances, E-ISSN 2375-2548, Vol. 5, no 6, article id eaau3648Article in journal (Refereed)
    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.

  • 2.
    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.

  • 3.
    Kurland, Sara
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Celorio Mancera, Maria de la Paz
    Stockholm University, Faculty of Science, Department of Zoology.
    Kutschera, Verena E.
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Hill, Jason
    Stockholm University, Faculty of Science, Department of Zoology.
    Andersson, Anastasia
    Stockholm University, Faculty of Science, Department of Zoology.
    Rubin, Carl-Johan
    Andersson, Leif
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species2019In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 9, p. 11448-11463Article in journal (Refereed)
    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.

  • 4. 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.

  • 5.
    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.

  • 6. 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.

  • 7.
    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.

  • 8.
    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)
1 - 8 of 8
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