| 1. |
- Halvarsson, Peter
(författare)
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Host-Parasite Interactions in Natural Populations
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Parasitism is one of the most common ways of living and it has arised in many taxa. Parasites feed and live inside or on their hosts resulting in both long and short term consequences for the host. This thesis is exploring the phenotypic and genotypic effects of animals living with parasitic infections. I have been studying three different parasite groups and their associated host species: the great snipe, a lekking freshwater wader bird that migrates between Africa and Northern Europe; the tree sparrow, a stationary passerine found close to human settlements and lastly the water vole, a large rodent living in riparian habitats.Avian malaria is one of the most commonly studied parasites affecting birds. Atoxoplasma, an intestinal protozoan parasite is less studied but is thought to be endemic in free-ranging birds. Given the freshwater habitat great snipes inhabit, a prevalence of 30% avian malaria infections is not high and that the prevalence fluctuated among years. Sequencing of the avian malaria cytochrome b gene revealed that parasites are similar to avian malaria parasites found in African birds suggesting that they were infected on the wintering grounds in Africa. Tree sparrows had few malaria infected individuals, a result that is consistent with other studies of stationary birds at high latitudes. Atoxoplasma infections were common in tree sparrows and capture-recapture analyses show decreased survival in infected compared to uninfected birds and signs of lower mating success among infected.Genetic analyses comparing the transcriptome between mated and unmated great snipe males revealed that the genotype is important for mating success and health status for some of the expressed genes. That variations in some of these genes are involved in maintaining a good health status and mating success supports handicap models for sexual selection in this lek mating system.The major histocompatibility complex (MHC) is a part of the immune system and it contains genes involved in immune response. In water voles, a number of new MHC alleles were identified. Based on their in silico phenotype they were grouped into supertypes to facilitate studies on how helminth infections affect the MHC diversity in the water voles. Some of these MHC supertypes provided resistance to one helminth species, but the same supertype caused the opposite effect for other helminth parasites. Overall, parasites are a driving force for maintaining genetic diversity and parasite infections lowers survival rate, which would lead to a lower lifetime breeding success.
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| 2. |
- Kozma, Radoslav, 1987-
(författare)
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Inferring demographic history and speciation of grouse using whole genome sequences
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- From an ecological perspective, knowledge of demographic history is highly valuable because population size fluctuations can be matched to known climatic events, thereby revealing great insight into a species’ reaction to past climate change. This in turn enables us to predict how they might respond to future climate scenarios. Prominently, with the advent of high-throughput sequencing it is now becoming possible to assemble genomes of non-model organisms thereby providing unprecedented resolution to the study of demographic history and speciation. This thesis utilises four species of grouse (Aves, subfamily Tetraoninae) in order to explore the demographic history and speciation within this lineage; the willow grouse, red grouse, rock ptarmigan and the black grouse. I, and my co-authors, begin by reviewing the plethora of methods used to estimate contemporary effective population size (Ne) and demographic history that are available to animal conservation practitioners. We find that their underlying assumptions and necessary input data can bias in their application, and thus we provide a summary of their applicability.I then use the whole genomes of the black grouse, willow grouse and rock ptarmigan to infer their population dynamics within the last million years. I find three dominant periods that shape their demographic history: early Pleistocene cooling (3-0.9 Mya), the mid-Brunhes event (430 kya) and the last glacial period (110-10 kya). I also find strong signals of local population history – recolonization and subdivision events – affecting their demography. In the subsequent study, I explore the grouse dynamics within the last glacial period in more detail by including more distant samples and using ecological modelling to track habitat distribution changes. I further uncover strong signals of local population history, with multiple fringe populations undergoing severe bottlenecks. I also determine that future climate change is expected to drastically constrict the distribution of the studied grouse.Lastly, I use whole genome sequencing to uncover 6 highly differentiated regions, containing 7 genes, hinting at their role in adaptation and speciation in three grouse taxa. I also locate a region of low differentiation, containing the Agouti pigmentation gene, indicating its role in the grouse plumage coloration.
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| 3. |
- Meurling, Sara, 1977-
(författare)
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The response in native wildlife to an invading pathogen: Swedish amphibians and Batrachochytrium dendrobatidis
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Emerging infectious diseases are causing mortality and declines in wildlife populations globally. My thesis aims to get as clear a picture as possible of the effect the invasive chytrid fungus Batrachochytrium dendrobatidis has on the Swedish amphibian community.In Paper I I performed a large-scale survey testing for the presence of Bd in three regions in Sweden (Southern, Central and Northern). I sampled 1917 amphibians from 101 localities and found that Bd was widespread in southern and central Sweden, occurring in all nine investigated species and in 45.5 % of the sampled sites with an overall prevalence of 13.8%. I found a positive correlation between the temperature at spawning for each species and species prevalence. Species that require higher temperatures for egg-laying are distributed in the southern parts of the country, which led to a higher prevalence in the southern region.In Paper II, I investigated which local environmental factors in breeding habitats, landscape structure and amphibian community affect the occurrence and prevalence of Bd among breeding sites in southern Sweden. Bd prevalence in the four species with the highest prevalence (Bombina bombina, Bufotes variabilis, Epidalea calamita and Rana arvalis) was higher in ponds surrounded by less mature forest, few wetlands, and higher pH.In Papers III and IV, I looked at species and population differences in responses to Bd infection. I performed an infection experiment described in Paper III, where I exposed individuals from two common Swedish species (moor frog R. arvalis and common toad Bufo bufo) originating from two regions (north and south) with two different strains of Bd (from Sweden and the UK). I found that infection led to lower survival and growth in both species, more so in B. bufo than in R. arvalis. Small size proved to be a strong determinant of survival. As individuals from the northern population were significantly smaller than the southern ones, this may have led to the northern populations being more affected by Bd infection. In Paper IV, I studied variation in MHC Class IIB loci in B. bufo along a latitudinal gradient across Sweden. Variation in MCH genes decreased from south to north. Also, differences in survival from the experiment in Paper III could be explained by MHC haplotypes. I found that survival in the southern region was dependent on both Bd-strain and MHC haplotype.
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| 4. |
- Rödin Mörch, Patrik, 1985-
(författare)
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Population divergence at different spatial scales in a wide-spread amphibian
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- To study the distribution of genetic and phenotypic variation in different environments and at different spatial scales is important in order to understand the process of local adaptation and how populations will respond to future climate change. In my thesis I study populations of moor frogs (Rana arvalis) at different spatial scales, first along a 1700 km latitudinal gradient (Paper I, II, IV) and, second, in a system of inter-connected wetlands (III, IV). In Paper I, I present evidence for a major latitudinal break-point in larval life-history traits which is linked to a post glacial contact zone between two lineages that colonized Scandinavia after the last ice age. Using QST-FST comparisons I found divergent selection acting on life-history traits, where a major source of differentiation comes from the two colonization routes. In Paper II I focus on genomic variation, demographic history and selection along the gradient. Using demographic modeling I confirm the proposed demographic history and show historical signatures of gene flow between regions and over the contact zone. In terms of genetic variation showing extreme differentiation as well as associations with growing season length I identify numerous variants under putative divergent selection, some of which have functions relating to immunity and development. I further show that differentiation outlier variation is higher in the north, as compared to neutral variation and variation associated with growing season length, which both decrease with latitude. These patterns are shaped by gene flow over the contact zone and the increased strength of drift at higher latitudes. I reduce the spatial scale in Paper III and characterize larval environments, landscape and geographical distance, to partition their influence on genetic variation. I show that environment explained more of the genetic variation than landscape and geographic distance, indicating that adaptive divergence can persist under high gene flow. Using the environmental variables, I identify genetic variants under putative divergent selection with functions associated with development and immunity. Using data from both scales, QST-FST comparisons and gene-phenotype associations I show in Paper IV that selection on both larval traits aligns across scales, whereas selection on plasticity only aligns in size at metamorphosis. This further connects to the influence of temperature and seasonal time constraints in colder environments. Finally, I find several genetic variants associated with the traits and plasticity at both spatial scales with functions relating to immunity and metamorphosis.
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