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Sökning: WFRF:(Backström Niclas) > Doktorsavhandling

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1.
  • Backström, Niclas, 1969- (författare)
  • Gene Mapping in Ficedula Flycatchers
  • 2009
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • In order to get full understanding of how evolution proceeds in natural settings it is necessary to reveal the genetic basis of the phenotypic traits that play a role for individual fitness in different environments. There are a few possible approaches, most of which stem from traditional mapping efforts in domestic animals and other model species. Here we set the stage for gene mapping in natural populations of birds by producing a large number of anchor markers of broad utility for avian genetical research and use these markers to generate a genetic map of the collared flycatcher (Ficedula albicollis). The map reveals a very high degree of synteny and gene order conservation between bird species separated by as much as 100 million years. This is encouraging for later stages of mapping procedures in natural populations since this means that there is a possibility to use the information from already characterized avian genomes to track candidate genes for detailed analysis in non-model species. One interesting aspect of the low degree of rearrangements occurring in the avian genomes is that this could play a role in the low rate of hybridization barriers formed in birds compared to for instance mammals. An analysis of Z-linked gene markers reveals relatively long-range linkage disequilibrium (LD) in collared flycatchers compared to other outbred species but still, LD seems to decay within < 50 kb indicating that > 20.000 markers would be needed to cover the genome in an association scan. A detailed scan of 74 Z-linked genes evenly distributed along the chromosome in both the collared flycatcher and the pied flycatcher (Ficedula hypoleuca) indicates that there are regions that evolve under directional selection, regions that might harbor loci of importance for adaptive divergence and/or hybrid inviability.
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2.
  • Höök, Lars, 1980- (författare)
  • The Evolution of Sex Chromosomes and Dosage Compensation in Structurally Dynamic Butterfly Genomes
  • 2023
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Dimorphic sex chromosomes have evolved independently throughout evolution from initially homologous autosomes. Recombination suppression between the sex chromosomes causes one sex chromosome to degenerate, which will influence evolution of sex-linked genes. This thesis investigated the evolution of genes and regulatory mechanisms on the sex chromosomes in Leptidea butterflies. Butterflies are female heterogametic, and females carry a dimorphic Z/W pair, while males have two homologous Z chromosomes. Dosage compensation is expected to evolve to equalize gene expression differences which are caused by this imbalance. Our analyses showed that Z-linked gene expression was reduced in males to parity with females, and reduced compared to autosomal levels. This is likely an adaptation to homogenize expression patterns between the sexes. However, the Z chromosome was enriched with male-biased genes, and sex-biased genes were not downregulated, suggesting that specific tuning occur for subsets of genes. An exploration of the Leptidea genomes revealed an unprecedented amount of chromosomal rearrangements, and detection of chromosomal heterozygotes suggests that the process is ongoing. Transposable elements were enriched in fused chromosome regions and are likely promoting rearrangements. The observed restructuring has formed several neo-sex chromosomes, which makes Leptidea useful for studies of evolutionary dynamics of  sex chromosomes. Z-linked genes showed a faster-Z effect, which was strongest for female-biased genes. In addition, the neo-Z chromosomes revealed a temporal dynamic, with younger Z chromosomes diverging faster. This could potentially be caused by an increased adaptive potential compared to the ancestral Z chromosome. Dualistic dosage compensation was found on the neo-Z chromosomes, with some chromosome regions being downregulated in males, and some regions being upregulated in females, in both cases resulting in inter-sexual expression balance. One Leptidea neo-W chromosome is largely intact, and analyses of allele specific expression provided strong evidence for W gametolog expression. Furthermore, male Z-linked expression was reduced for genes that lacked W gametologs, indicating that gene regulation has evolved rapidly to achieve dosage balance. This work has led to several interesting discoveries about gene regulation, chromosome rearrangements and sequence divergence of sex chromosomes, and in general revealed a more complex picture of how these specific chromosomes evolve.
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3.
  • Näsvall, Karin, 1974- (författare)
  • Rates and patterns of genome evolution in Lepidoptera
  • 2023
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • The evolutionary consequences of genome restructuring and chromosomal rearrangements can be significant, but the underlying mechanisms are poorly understood. This thesis explores the relationships between genome restructuring, recombination, and maintenance of genetic diversity in different butterfly species. I also investigate the genetic underpinnings of different types of adaptations in two butterfly species with distinct life-history characteristics and adaptations. In Chapter I, whole genome alignments and linkage maps were used to characterize inter- and intra-specific chromosomal rearrangements in wood white butterflies (Leptidea spp.), revealing extensive reorganization of the chromosomes predominantly driven by fusions and fissions. Several fusion-fission polymorphisms were found segregating within populations, confirming the dynamic and ongoing process of karyotype evolution. In Chapter II, I used the linkage map information to show that chromosomal rearrangements have had considerable effects on the recombination landscape and maintenance of genetic diversity. Chapter III presents a detailed annotation of the genome of a long-distance migrant, the painted lady butterfly (Vanessa cardui). The annotation was used to identify expanded gene families, providing insight into the genetic underpinnings of this unique life-history. Here, I also developed linkage maps confirming a well-preserved karyotype in this species and showed that chromosome size is a major determinant of the recombination landscape. In Chapter IV, I explored the relationship between nucleotide composition, codon usage, and substitution rates across multiple Lepidoptera species, in an attempt to disentangle the relative effects of natural selection and neutral evolutionary forces on gene sequence evolution. The final two chapters focus on understanding the genetic basis of key adaptive traits in butterflies. Specifically, in Chapter V, I investigated potential local adaption in Leptidea sinapis by studying how host plant switch is associated with oviposition rates, larval growth and development, gene expression, and microbiome composition in populations experiencing different environmental conditions. In Chapter VI, I assessed the differential activation of regulatory elements in V. cardui females in response to host plant availability, which together with the gene family analysis in Chapter III, resulted in a set of candidate genes potentially associated with a migratory lifestyle. In conclusion, I have explored the complex interplay between proximate mechanisms and evolutionary forces shaping the genome structure and levels of genetic variation. I also investigated the genetic and regulatory underpinnings of adaptive traits in different butterfly species. In addition, I provided resources including chromosome-level genome assemblies, recombination maps, and annotations that will contribute to our understanding of evolutionary processes in general. 
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4.
  • Talla, Venkat (författare)
  • Speciation genetics of recently diverged species :
  • 2018
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Species differentiation can be a consequence of evolutionary forces including natural selection and random genetic drift. Patterns of genomic differentiation vary across the tree of life. This variation seems to be dependent on, for example, differences in genomic architecture and molecular mechanisms. However, the knowledge we currently possess, both regarding the processes driving speciation and the resulting genomic signatures, is from a very small subset of the overall biodiversity that resides on the planet. Therefore, characterization of the architecture of genomic divergence from more organism groups will be important to understand the effects of molecular mechanisms and evolutionary forces driving divergence between lineages. Hence it has not been possible to come to a consensus on the relative importance of genetic drift and natural selection on divergence processes in general. In this thesis, I use genomic approaches to investigate the forces underlying species and population differentiation in the European cryptic wood white butterflies (Leptidea sinapis, L. reali and L. juvernica) and two closely related bird species, the chiffchaff (Phylloscopus collybita abietinus) and the Siberian chiffchaff (P. tristis). Both these groups contain recently diverged species, a prerequisite for investigating initial differentiation processes. However, the study systems also differ in several respects, allowing for applying distinct approaches to understand the divergence process in each system.In summary, by applying a suite of genomic approaches, my thesis work gives novel insights into the speciation history of wood whites and chiffchaff. I identify candidate genes for local adaptation in both systems and concludes that genome differentiation in wood white butterflies have been driven by a combination of random genetic drift and week directional selection in allopatry. In the chiffchaff, the general differentiation landscape seems to have been shaped by recurrent background selection (and potentially selective sweeps), likely as a consequence of regional variation in the recombination rate which has also been observed in other genome-scans in birds. Potentially, some of the highly differentiated regions contain barriers to gene-flow as these regions are still present in sympatry, where species exchange genetic material at a high rate.
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