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  • 1.
    de la Paz Celorio-Mancera, Maria
    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
    Vezzi, Francesco
    Neethiraj, Ramprasad
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Reimegård, Johan
    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.

  • 2.
    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.

  • 3.
    Neethiraj, Ramprasad
    Stockholm University, Faculty of Science, Department of Zoology.
    Advances in studying the role of genetic divergence and recombination in adaptation in non-model species2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Understanding the role of genetic divergence and recombination in adaptation is crucial to understanding the evolutionary potential of species since they can directly affect the levels of genetic variation present within populations or species. Genetic variation in the functional parts of the genome such as exons or regulatory regions is the raw material for evolution, because natural selection can only operate on phenotypic variation already present in the population. When natural selection acts on a phenotype, it usually results in reduction in the levels of genetic variation at the causal loci, and the surrounding linked loci, due to recombination dynamics (i.e. linkage); the degree to which natural selection influences the genetic differentiation in the linked regions depends on the local recombination rates.

    Studies investigating the role of genetic divergence and recombination are common in model species such as Drosophila melanogaster. Only recently have genomic tools allowed us to start investigating their role in shaping genetic variation in non-model species. This thesis adds to the growing research in that domain. In this thesis, I have asked a diverse set of questions to understand the role of genetic divergence and recombination in adaptation in non-model species, with a focus on Lepidoptera.

    First, how do we identify causal genetic variation causing adaptive phenotypes? This question is fundamental to evolutionary biology and addressing it requires a well-assembled genome, the generation of which is a cost, labor, and time intensive task. In paper I, I present a tool, MESPA, that stitches together exonic sequences in fragmented assemblies to produce high-quality gene models. These high-quality gene models can be used by researchers in the downstream analyses, providing genomic insights for a fraction of cost of a high quality genome. 

    Second, what does the pattern of recombination rate look like in chromosomes that lack centromeres (i.e.holocentric chromosomes)? In paper II, I compare the recombination landscape and the patterns of nucleotide diversity in three Lepidotera with holocentric chromosomes, Pieris napi, Bombyx mandarina, and Bombyx mori, with a monocentric species. Our results show that on average these three Lepidoptera have high rates of recombination across the vast majority of their genome. Our results also suggest that given similar effective population sizes, these species are likely to harbor more genetic diversity compared to monocentric species, which has important evolutionary consequences for these species.

    Third, what is the potential for parallelism at the genetic level in convergent melanic phenotypes? In paper III, I investigated the genetic basis of the female-limited melanic phenotype in the green-veined white (Pieris napi) butterfly, and found a 20kb region, approximately 50kb from the gene cortex, associated with this trait. This gene has been implicated in melanic phenotypes in other Lepidoptera that diverged from Pieris approximately 100my, indicating very high predictability for this trait.

    Finally, what is the role of cis-regulatory variation in local adaptation? In paper IV, I analyzed the relationship between allele specific expression (ASE) and genetic divergence (FST) in the F1 hybrids of Pieris napi napi and Pieris napi adalwinda. I show that intersecting results from ASE with FST is a powerful approach to identify genes involved in local adaptation.

  • 4.
    Neethiraj, Ramprasad
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    de la Paz Celorio-Mancera, Maria
    Stockholm University, Faculty of Science, Department of Zoology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher
    Stockholm University, Faculty of Science, Department of Zoology.
    Investigating cis-regulatory variation within and between populations reveals significant enrichment of genes in central metabolismManuscript (preprint) (Other academic)
  • 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.
    Neethiraj, Ramprasad
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher
    Stockholm University, Faculty of Science, Department of Zoology.
    Holocentric chromosomes facilitate recombination and genetic variation in LepidopteraManuscript (preprint) (Other academic)
  • 7.
    Neethiraj, Ramprasad
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Pruisscher, Peter
    Stockholm University, Faculty of Science, Department of Zoology.
    Pruisscher Keehnen, Naomi
    Stockholm University, Faculty of Science, Department of Zoology.
    Woronik, Alyssa
    Gotthard, Karl
    Stockholm University, Faculty of Science, Department of Zoology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher
    Stockholm University, Faculty of Science, Department of Zoology.
    A dark melanic morph of Pieris napi shares its origins with other dark morphs of LepidopteraManuscript (preprint) (Other academic)
  • 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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