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Advances in studying the role of genetic divergence and recombination in adaptation in non-model species
Stockholm University, Faculty of Science, Department of Zoology.ORCID iD: 0000-0001-7313-3734
2019 (English)Doctoral 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.

Place, publisher, year, edition, pages
Stockholm: Department of Zoology, Stockholm University , 2019.
Keywords [en]
Recombination, Genetic divergence, Lepidoptera, Genetic variation, Genetic diversity, Holocentric chromosomes, cis-regulatory variation, Allele-specific expression
National Category
Evolutionary Biology Zoology
Research subject
Population Genetics
Identifiers
URN: urn:nbn:se:su:diva-163416ISBN: 978-91-7797-574-8 (print)ISBN: 978-91-7797-575-5 (electronic)OAI: oai:DiVA.org:su-163416DiVA, id: diva2:1274535
Public defence
2019-02-22, Vivi Täckholmsalen (Q-salen), NPQ-huset, Svante Arrhenius väg 20, Stockholm, 13:30 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.

Available from: 2019-01-30 Created: 2019-01-01 Last updated: 2019-01-24Bibliographically approved
List of papers
1. Investigating the genomic basis of discrete phenotypes using a Pool-Seq-only approach: New insights into the genetics underlying colour variation in diverse taxa
Open this publication in new window or tab >>Investigating the genomic basis of discrete phenotypes using a Pool-Seq-only approach: New insights into the genetics underlying colour variation in diverse taxa
2017 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 19, p. 4990-5002Article in journal (Refereed) Published
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.

Keywords
adaptive variation, colour patterns, genome, nonmodel organisms, Pool-Seq
National Category
Biological Sciences
Research subject
Population Genetics
Identifiers
urn:nbn:se:su:diva-148850 (URN)10.1111/mec.14205 (DOI)000413375500011 ()28614599 (PubMedID)
Available from: 2017-11-23 Created: 2017-11-23 Last updated: 2019-01-01Bibliographically approved
2. Holocentric chromosomes facilitate recombination and genetic variation in Lepidoptera
Open this publication in new window or tab >>Holocentric chromosomes facilitate recombination and genetic variation in Lepidoptera
(English)Manuscript (preprint) (Other academic)
National Category
Evolutionary Biology Zoology Genetics
Research subject
Population Genetics
Identifiers
urn:nbn:se:su:diva-163413 (URN)
Available from: 2019-01-01 Created: 2019-01-01 Last updated: 2019-01-02Bibliographically approved
3. A dark melanic morph of Pieris napi shares its origins with other dark morphs of Lepidoptera
Open this publication in new window or tab >>A dark melanic morph of Pieris napi shares its origins with other dark morphs of Lepidoptera
Show others...
(English)Manuscript (preprint) (Other academic)
National Category
Ecology Evolutionary Biology Genetics
Research subject
Population Genetics
Identifiers
urn:nbn:se:su:diva-163414 (URN)
Available from: 2019-01-01 Created: 2019-01-01 Last updated: 2019-01-02Bibliographically approved
4. Investigating cis-regulatory variation within and between populations reveals significant enrichment of genes in central metabolism
Open this publication in new window or tab >>Investigating cis-regulatory variation within and between populations reveals significant enrichment of genes in central metabolism
(English)Manuscript (preprint) (Other academic)
National Category
Evolutionary Biology Ecology
Research subject
Population Genetics
Identifiers
urn:nbn:se:su:diva-163415 (URN)
Available from: 2019-01-01 Created: 2019-01-01 Last updated: 2019-01-02Bibliographically approved

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