| 1. |
- Onuț-Brännström, Ioana, 1978-
(författare)
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The puzzle of lichen symbiosis : Pieces from Thamnolia
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Symbiosis brought important evolutionary novelties to life on Earth. Lichens, the symbiotic entities formed by fungi, photosynthetic organisms and bacteria, represent an example of a successful adaptation in surviving hostile environments. Yet many aspects of the lichen symbiosis remain unexplored. This thesis aims at bringing insights into lichen biology and the importance of symbiosis in adaptation. I am using as model system a successful colonizer of tundra and alpine environments, the worm lichens Thamnolia, which seem to only reproduce vegetatively through symbiotic propagules. When the genetic architecture of the mating locus of the symbiotic fungal partner was analyzed with genomic and transcriptomic data, a sexual self-incompatible life style was revealed. However, a screen of the mating types ratios across natural populations detected only one of the mating types, suggesting that Thamnolia has no potential for sexual reproduction because of lack of mating partners. Genetic data based on molecular markers revealed the existence of three morphologically cryptic Thamnolia lineages. One lineage had a clear recombination structure and was found in the tundra region of Siberia, shorelines of Scandinavia, and Aleutian Islands. The other lineage was allopatric with the previous, and was highly clonal; only two haplotypes were found across the alpine region of central and southeastern Europe. However, the third lineage was sympatric with the other two, had a worldwide distribution, and although highly clonal, showed a recombinant population structure. Our data could not reveal whether the signs of recombination resulted from rare recombination events due to the extreme low frequency of the other mating type or ancestral variation before the loss of sexual reproduction. However, investigation of Thamnolia’s green algal population showed that in different localities, different algal genotypes were associated with the same fungal genotype. Furthermore, data suggest that Thamnolia carried several algal genotypes within its thalli and shared them with other distantly related but ecologically similar fungal species.
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| 2. |
- Ament-Velásquez, Sandra Lorena, M.Sc. 1988-
(författare)
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Drivers of evolutionary change in Podospora anserina
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Genomic diversity is shaped by a myriad of forces acting in different directions. Some genes work in concert with the interests of the organism, often shaped by natural selection, while others follow their own interests. The latter genes are considered “selfish”, behaving either neutrally to the host, or causing it harm. In this thesis, I focused on genes that have substantial fitness effects on the fungus Podospora anserina and relatives, but whose effects are very contrasting. In Papers I and II, I explored the evolution of a particular type of selfish genetic elements that cause meiotic drive. Meiotic drivers manipulate the outcome of meiosis to achieve overrepresentation in the progeny, thus increasing their likelihood of invading and propagating in a population. In P. anserina there are multiple meiotic drivers but their genetic basis was previously unknown. In Paper I, we demonstrated that drive is caused by members of the Spok gene family. We discovered two new Spok genes, Spok3 and Spok4, which locate in different chromosomes in different strains. In Paper II, we showed that Spok3 and Spok4 are found on a gigantic (up to 247 Kb long) variant of Enterprise, a Crypton-like transposable element. Enterprise likely mobilize through the action of a putative tyrosine-recombinase that we call Kirc. When carrying the Spoks, this element has double selfish properties: transposition and meiotic drive. In addition, we found that homologs of the Spoks (Paper I) and of Kirc (Paper II) are widespread in fungi but their phylogenies are discordant with that of the species, suggesting that they have undergone horizontal gene transfer. In Papers III and IV, I turned the focus into genes that have an adaptive function. In fungi, the het genes control conspecific self/non-self recognition. Such genes are expected to evolve under frequency-dependent balancing selection. In Paper III, we found evidence of balancing selection acting on some het genes across the P. anserina species complex. Unexpectedly, we also discovered that het genes of the HNWD gene family are duplicated in a transposon-like manner, broadening our understanding of their potential fitness effects. Finally, in Paper IV we show how het genes with pleiotropic effects on sexual recognition lead to the evolution of strong reproductive isolation, and hence speciation. Overall, the results of my thesis highlight the functional intersection between mobile selfish genetic elements and other genes, either selfish or adaptive, and their effects on genome architecture and population structure.
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| 3. |
- Künstner, Axel
(författare)
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Birds as a Model for Comparative Genomic Studies
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Comparative genomics provides a tool to investigate large biological datasets, i.e. genomic datasets. In my thesis I focused on inferring patterns of selection in coding and non-coding regions of avian genomes. Until recently, large comparative studies on selection were mainly restricted to model species with sequenced genomes. This limitation has been overcome with advances in sequencing technologies and it is now possible to gather large genomic data sets for non-model species. Next-generation sequencing data was used to study patterns of nucleotide substitutions and from this we inferred how selection has acted in the genomes of 10 non-model bird species. In general, we found evidence for a negative correlation between neutral substitution rate and chromosome size in birds. In a follow up study, we investigated two closely related bird species, to study expression levels in different tissues and pattern of selection. We found that between 2% and 18% of all genes were differentially expressed between the two species. We showed that non-coding regions adjacent to genes are under evolutionary constraint in birds, which suggests that noncoding DNA plays an important functional role in the genome. Regions downstream to genes (3’) showed particularly high level of constraint. The level of constraint in these regions was not correlated to the length of untranslated regions, which suggests that other causes play also a role in sequence conservation. We compared the rate of nonsynonymous substitutions to the rate of synonymous substitutions in order to infer levels of selection in protein-coding sequences. Synonymous substitutions are often assumed to evolve neutrally. We studied synonymous substitutions by estimating constraint on 4-fold degenerate sites of avian genes and found significant evolutionary constraint on this category of sites (between 24% and 43%). These results call for a reappraisal of synonymous substitution rates being used as neutral standards in molecular evolutionary analysis (e.g. the dN/dS ratio to infer positive selection). Finally, the problem of sequencing errors in next-generation sequencing data was investigated. We developed a program that removes erroneous bases from the reads. We showed that low coverage sequencing projects and large genome sequencing projects will especially gain from trimming erroneous reads.
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| 4. |
- Svedberg, Jesper, 1981-
(författare)
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Catching the Spore killers : Genomic conflict and genome evolution in Neurospora
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- A genome is shaped by many different forces. Recombination can for instance both create and maintain genetic diversity, but the need to locally reduce recombination rates will also leave specific signatures. Genetic elements can act selfishly and spreading at the expense of the rest of the genome can leave marks of their activity, as can mechanisms that suppresses them, in a phenomenon known as genomic conflict. In this thesis, I have studied the forces driving genome evolution, using modern genome sequencing techniques and with a special focus on a class of selfish genetic elements known as Spore killers found in the fungus Neurospora. First, we show novel findings on large-scale suppression of recombination by non-structural means in the N. tetrasperma genomes. In contrary, in the genomic region harbouring the spore killer elements Sk-2 and Sk-3 of N. intermedia, a dense set of inversions that are interspersed with transposable elements have accumulated. The inversions are unique for each killer type, showing that they have a long separated evolutionary history and likely have established themselves independently. For the Sk-2 haplotype, where we have polymorphism data, we see signs of relaxed selection, which is consistent with the hypothesis that recombination suppression reduces the efficacy of selection in this region. These results show the strong effects the divergent selective forces of genomic conflicts can have on chromosome architecture. Furthermore, we investigate the hypothesis that spore killing can drive reproductive isolation, by comparing the fertility of crosses between N. metzenbergii and either killer or non-killer N. intermedia strains. We show that crosses with spore killer strains have lower fertility, which cannot be explained by the killing itself, but is potentially caused by an incompatibility gene captured in the non-recombining region. Finally, we identified the genetic element responsible for causing spore killing in the Sk-1 spore killer strains found in N. sitophila. Unlike the Sk-2 and Sk-3 elements, Sk-1 is not connected to a large, non-recombining region, but is caused by a single locus, and we also find indications that this locus was introgressed from N. hispaniola.
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| 5. |
- Hiltunen, Markus
(författare)
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Full circle : Rise and fate of genetic variation in Marasmius oreades fairy rings
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Genetic variation is a prerequisite for evolution. The degree of variability within a species is governed by forces including mutation, recombination and selection. In the kingdom of fungi, where periodic sexual reproduction may be interleaved with extended vegetative phases, generators of variability are not restricted to act only during sexual cycles. Such generators may be in the form of mutations to the genome, affecting single base pairs up to large-scale rearrangements, movement of transposable elements, or non-meiotic shuffling of genetic variants by mitotic recombination or parasexuality. Particularly in mushroom-forming fungi, where mycelia may become large and old, the evolutionary potential of variation acquired over vegetative growth is expected to be large. In this thesis, I have studied the rise and fate of variation gained during vegetative growth in the mushroom-forming fungus Marasmius oreades: a non-model species known for growing in ‘fairy rings’. By taking advantage of state-of-the-art genome sequencing technology and developing new bioinformatics methods, the genome sequence of M. oreades was successfully reconstructed. This resource was combined with genome re-sequencing to identify different types of mutations in M. oreades fairy rings, and to investigate the transmission of such mutations into the next generation through sexual spores. The results presented in this thesis reveal that the M. oreades genome is extremely stable at all levels during vegetative growth in its natural environment. Furthermore, the few mutations that arise do not seem to be transferred to the sexual spores. A significant amount of transposon movement was however revealed in monokaryotic strains when separated from dikaryons and grown in the laboratory. The combination of these results suggests that fungi possess an unknown system to suppress the accumulation of mutations during growth in nature, and that the apparent lack of a segregated germline in fungi potentially has to be reconsidered. Thus, contrary to expectations, the vegetative life stage in long-lived mushroom-forming fungi does not contribute much genetic variation, making these organisms more similar to animals and plants than previously considered. Further studies are needed to reveal how fungi control mutation accumulation, and elucidate if transposon activity is high also in naturally derived monokaryons in the form of meiotic progeny. The findings in this thesis add to what is known about how genetic variation is introduced into natural populations, how fungi deal with mutations, and highlight the complexity of genetic systems in mushroom-forming fungi.
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| 6. |
- Peona, Valentina, 1990-
(författare)
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The exploration and evolution of the avian genomic dark matter
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The development and improvement of genome sequencing technologies in the last decade revolutionised the entire field of biology with genome assemblies of virtually any organism. Despite this tremendous progress, complex genomic regions are systematically missing from genome assemblies and form the so-called "genomic dark matter". The presence of genomic dark matter entails that such regions cannot be fully studied and the effects and/or functions thereof (if any) on the organisms remain hidden. Therefore, it is key to be able to explore those dark genomic corners to fully understand the evolution and physiology of organisms without biasing the interpretations. In this thesis, I contribute to the understanding of the use of new sequencing technologies to assemble complex genomic regions and to investigate the evolution of such regions throughout the avian phylogeny. First, I assessed the best combination of technologies and assembly methods to maximise the resolution of genomic dark matter using genomic data from the paradise crow. This included testing for the presence of repetitive elements, GC-rich regions, G-quadruplex motifs, non-recombining sex chromosomes, and microchromosomes. Then, the high-quality assemblies for the paradise crow and other birds allowed the discovery that the avian W chromosome features more than half of potentially active transposable elements (TEs), especially endogenous retroviruses, of the genome. This characteristic makes the W chromosome potentially "toxic" for females. The female-biased accumulation of active TEs could also play a role in the origin of genetic incompatibilities and be an explanatory variable for Haldane’s rule in birds. Next, I investigated the genetic variability of birds-of-paradise chromosomes originating from structural rearrangements with a special focus on the W chromosome. The analysis revealed more genetic variability than previously reported suggesting that all sources of genetic variability should be considered to understand the evolution of sex-limited chromosomes. Finally, I explored the evolution of another main component of avian genomic dark matter, satellite DNA, throughout the phylogeny of birds-of-paradise and closely related crow species. I found that the avian satellitome evolves in different modes in the two groups and a more comprehensive species sampling is necessary to establish which evolutionary mode is the most prevalent in birds. Altogether, the results of this thesis provide a case study for how to investigate the most complex genomic regions, highlight their possible evolutionary roles, and therefore showcase the necessity for the field to shed light into the dark corners of genomes. Mind the gap!
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| 7. |
- Pereira, Raquel
(författare)
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In Murky waters : Swedish demosponges and their genealogies
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Swedish Sponge fauna last updated happened over 80’s years ago. This fact explains, partially, the country’s low sponge. In this thesis, I update our knowledge of the swedish demosponge fauna (Paper I and II) and, give an insight to the relationship within one of the most common sponge groups in the country belonging to order Suberitida (Paper III and IV), as well as to investigate possible dispersal barriers for freshwater sponges (Paper I). I relied on my own sampling, museum specimens and the marine inventory by STI. In total, we found nine new reports for Sweden (one freshwater and eight in sea water) and one new species to science (sea water). In the freshwater survey using Spongilla lacustris (Paper I) we tested if catchment areas represented dispersal barriers, but with the marker used we could not observe a clear population structure. For the marine environment the collected material contained what appear to be several species Suberites (Paper II). This genus, and many taxa within the order, is known for a paucity of morphological characters and long taxonomic history. This while being known for not representing a natural group. Thus, in order to know what species of Suberites present in Sweden we had to answer: What is the circumscription for the genus? What are its relationships with other suberitids? What are the oldest available names for the genus and the species within?In Paper III, we use phylogenetics to infer the relationships within Suberitida. The trees showed two separate clades for Suberites - A and B. Clade B was together with the genus Aaptos, a Homaxinella species and Stylocordyla - family Stylocordylidae and, given that result we argued for expansion of Stylocordylidae. In Paper IV, we did an extensive literature review of the senior names for clade A and B. Plus, we presented species delimitation and their names for 30 species found in the Northern Temperate Atlantic realm. We argue for the resurrection of Syringella as the name for clade B. While, in clade A (under the name of Suberites), we make the case for S. ficus proper name to be S. subereus and, we solved the homonymy with the name S. virgultosus by naming the species found by Bowerbank - Suberites sp. ”misterbeanii”.
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