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  • Caputo, Andrea, 1988- (författare)
  • Genomic and morphological diversity of marine planktonic diatom-diazotroph associations : a continuum of integration and diversification through geological time
  • 2019
  • Doktorsavhandling (övrigt vetenskapligt)abstract
    • Symbioses between eukaryotes and nitrogen (N2)-fixing cyanobacteria (or diazotrophs) are quite common in the plankton community. A few genera of diatoms (Bacillariophyceae) such as Rhizosolenia, Hemiaulus and Chaetoceros are well known to form symbioses with the heterocystous diazotrophic cyanobacteria Richelia intracellularis and Calothrix rhizosoleniae. The latter are also called diatom-diazotroph associations, or DDAs. Up to now, the prokaryotic partners have been morphologically and genetically characterized, and the phylogenetic reconstruction of the well conserved nifH gene (encodes for the nitrogenase enzyme) placed the symbionts in 3 clusters based on their host-specificity, i.e. het-1 (Rhizosolenia-R. intracellularis), het-2 (Hemiaulus-R. intracellularis), and het-3 (Chaetoceros-C- rhizosoleniae). Conversely, the diatom-hosts, major representative of the phytoplankton community and crucial contributors to the carbon (C) biogeochemical cycle, have been understudied.The first aim of this thesis was to genetically and morphologically characterize the diatom-hosts, and to reconstruct the evolutionary background of the partnerships and the symbiont integration in the host. The molecular-clock analysis reconstruction showed the ancient appearance of the DDAs, and the traits characterizing the ancestors. In addition, diatom-hosts bearing internal symbionts (with more eroded draft genomes) appeared earlier than diatom-hosts with external symbionts. Finally a blast survey highlighted a broader distribution of the DDAs than expected.The second aim of this thesis was to compare genetic and physiological characteristics of the DDAs symbionts with the other eukaryote-diazotroph symbiosis, i.e. prymnesiophyte-UCYN-A (or Candidatus Atelocyanobacterium thalassa). The genome comparison highlighted more genes for transporters in het-3 (external symbiont) and in the UCYN-A based symbiosis, suggesting that symbiont location might be relevant also for metabolic exchanges and interactions with the host and/or environment. Moreover, a summary of methodological biases that brought to an underestimation of the DDAs is reported.The third aim of this thesis was to determine the distribution of the DDAs in the South Pacific Ocean using a quantitative polymerase chain reaction (qPCR) approach and to outline the environmental drivers of such distribution. Among the het-groups, het-1 was the most abundant/detected and co-occurred with the other 2 symbiotic strains, all responding similarly to the influence of abiotic factors, such as temperature and salinity (positive and negative correlation, respectively). Globally, Trichodesmium dominated the qPCR detections, followed by UCYN-B. UCYN-A phylotypes (A-1, A-2) were detected without their proposed hosts, for which new oligonucleotides were designed. The latter suggested a facultative symbiosis. Finally, microscopy observations of the het-groups highlighted a discrepancy with the qPCR counts (i.e. the former were several order of magnitudes lower), leading to the idea of developing a new approach to quantify the DDAs.  The fourth aim of this thesis was to develop highly specific in situ hybridization assays (CARD-FISH) to determine the presence of alternative life-stages and/or free-living partners. The new assays were applied to samples collected in the South China Sea and compared with abundance estimates from qPCR assays for the 3 symbiotic strains. Free-living cells were indeed detected along the transect, mainly at deeper depths. Free-living symbionts had two morphotypes: trichomes and single-cells. The latter were interpreted as temporary life-stages. Consistent co-occurrence of the 3 het-groups was also found in the SCS and application of a SEM model predicted positive interactions between the het groups. We interpreted the positive interaction as absence of intra-specific competition, and consistent with the previous study, temperature and salinity were predicted as major drivers of the DDAs distribution.
  • Koch, Kamilla, et al. (författare)
  • Morphological differences in the ovary of Libellulidae (Odonata)
  • 2009
  • Ingår i: International Journal of Odonatology. - Oxford : Taylor & Francis. - 1388-7890. ; 12:1, s. 147-156
  • Tidskriftsartikel (refereegranskat)abstract
    • All female Odonata have been assumed to produce oocytes continuously during their mature life span. However, a recent study of ovariole orientation and development led to the suggestion that Libellulidae are divided into two groups of species, one with continuous, the other with stepwise oocyte production. To find more evidence of this division, we compared the size variation and growth within the vitellarium of the ovary, studying oocytes, and follicle cells. We found that morphological characters discriminate between the two ovary types in eight of the 10 investigated species. In both types we found an increase in all measurements from the anterior to the posterior end of the vitellarium. The increase in oocyte width and follicle cell length was significantly higher in species with a continuous oocyte production. We also noted that follicle cells may have more than one nucleus and that their number can vary during vitellogenesis. Our study confirmed the hypotheses that two different ovary types exist in Libellulidae. The two species not fitting into this grouping could be an artefact of small samp le size due to intraspecific phenotypic plasticity, or else there might be more than two ovary groups, or even a continuum. We could not offer an explanation as to how the process of stepwise oocyte production differs from continuous based production on morphological characters.
  • Spagopoulou, Foteini, et al. (författare)
  • Shifts in Reproductive Investment in Response to Competitors Lower Male Reproductive Success
  • 2020
  • Ingår i: ; 196:3, s. 355-368
  • Tidskriftsartikel (refereegranskat)abstract
    • In many species, males exhibit phenotypic plasticity in sexually selected traits when exposed to social cues about the intensity of sexual competition. To date, however, few studies have tested how this plasticity affects male reproductive success. We initially tested whether male mosquitofish,Gambusia holbrooki(Poeciliidae), change their investment in traits under pre- and postcopulatory sexual selection depending on the social environment. For a full spermatogenesis cycle, focal males were exposed to visual and chemical cues of rivals that were either present (competitive treatment) or absent (control). Males from the competitive treatment had significantly slower-swimming sperm but did not differ in sperm count from control males. When two males competed for a female, competitive treatment males also made significantly fewer copulation attempts and courtship displays than control males. Further, paternity analysis of 708 offspring from 148 potential sires, testing whether these changes in reproductive traits affected male reproductive success, showed that males previously exposed to cues about the presence of rivals sired significantly fewer offspring when competing with a control male. We discuss several possible explanations for these unusual findings.
  • Rest, Joshua S, et al. (författare)
  • Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome.
  • 2003
  • Ingår i: Molecular Phylogenetics and Evolution. - 1055-7903 .- 1095-9513. ; 29:2, s. 289-97
  • Tidskriftsartikel (refereegranskat)abstract
    • We provide phylogenetic analyses for primary Reptilia lineages including, for the first time, Sphenodon punctatus (tuatara) using data from whole mitochondrial genomes. Our analyses firmly support a sister relationship between Sphenodon and Squamata, which includes lizards and snakes. Using Sphenodon as an outgroup for select squamates, we found evidence indicating a sister relationship, among our study taxa, between Serpentes (represented by Dinodon) and Varanidae. Our analyses support monophyly of Archosauria, and a sister relationship between turtles and archosaurs. This latter relationship is congruent with a growing set of morphological and molecular analyses placing turtles within crown Diapsida and recognizing them as secondarily anapsid (lacking a skull fenestration). Inclusion of Sphenodon, as the only surviving member of Sphenodontia (with fossils from the mid-Triassic), helps to fill a sampling gap within previous analyses of reptilian phylogeny. We also report a unique configuration for the mitochondrial genome of Sphenodon, including two tRNA(Lys) copies and an absence of ND5, tRNA(His), and tRNA(Thr) genes.
  • Fallahshahroudi, Amir, 1981- (författare)
  • Domestication Effects on the Stress Response in Chickens : Genetics, Physiology, and Behaviour
  • 2017
  • Doktorsavhandling (övrigt vetenskapligt)abstract
    • Animal domestication, the process where animals become adapted to living in proximity to humans, is associated with the alteration of multiple traits, including decreased fearfulness and stress response. With an estimated population of 50 billion, the domesticated chicken is the most populous avian species in the world. Hundreds of chicken breeds have been developed for meat and egg production, hobby or research purposes. Multidirectional selection and the relaxation of natural selection in captivity have created immense phenotypic diversity amongst domesticates in a relatively short evolutionary time. The extensive phenotypic diversity, existence of the wild ancestor, and feasibility of intercrossing various breeds makes the chicken a suitable model animal for deciphering genetic determinants of complex traits such as stress response. We used chicken domestication as a model to gain insights about the mechanisms that regulate stress response in an avian species. We studied behavioural and physiological stress response in the ancestral Red Junglefowl and one of its domesticated progenies, White Leghorn. An advanced intercross between the aforementioned breeds was later used to map genetic loci underlying modification of stress response. The general pattern of the stress response in chickens was comparable with that reported in mammals, however we identified distinctive differences in the stress modulatory pathways in chickens. We showed that changes in the expression levels of several stress modulatory genes in the brain, the pituitary and the adrenal glands underlie the observed modified stress response in domesticated chickens. Using quantitative trait loci (QTL) mapping, several QTL underlying stress induced corticosterone, aldosterone and baseline dehydroepiandrosterone (DHEA) levels were detected. As a next step, we combined QTL mapping with gene expression (eQTL) mapping and narrowed two QTL down to the putative causal genes, SERPINA10 and PDE1C. Both of these genes were differentially expressed in the adrenal glands of White Leghorn and the Red Junglefowl, had overlapping eQTL with hormonal QTL, and their expression levels in the adrenal glands were correlated with plasma levels of corticosterone and al-dosterone. These two genes thus serve as strong candidates for further functional investigation concerning modification of the stress response during domestication. This dissertation increase the knowledge about genetics and physiology of the stress response in an avian species and its modification during domestication. Our findings expand the basic knowledge about the stress response in chicken, which can potentially be used to improve welfare through appropriate genetic selection.
  • Stenberg, Per, et al. (författare)
  • Cytology of Asexual Animals
  • 2009
  • Ingår i: Lost Sex. - Dordrecht : Springer Netherlands. - 9789048127696 - 9789048127702 ; , s. 63-74
  • Bokkapitel (övrigt vetenskapligt)abstract
    • We review the cytological mechanisms underlying asexual reproduction, i.e. reproduction without fertilization, in animals. Asexuality or parthenogenesis has evolved many times and the cytological mechanisms to restore the parental chromosome number can vary between and even within species. In automictic or meiotic parthenogenesis, meiosis takes place but the chromosomal constitution of the mother is restored through one or several different mechanisms. Some of these mechanisms enforce homozygosity at all loci while some other mechanisms pass the genome of the mother intact to the offspring. In apomictic or mitotic parthenogenesis the eggs are formed through what is essentially a set of mitoses. Polyploidy, is in general incompatible with chromosomal sex determination and is a rare condition in animals. However, many asexual and hermaphroditic forms are polyploid to various degrees. Polyploidy is divided into allo- and autopolyploidy. In the former mode the chromosome sets are derived from two or more different species while in autopolyploidy the multiplication has taken place within one species. We discuss the evolutionary consequences of the different cytological mechanisms involved in asexual reproduction.
  • Sundman, Ann-Sofie, 1982- (författare)
  • Dog behaviour : Intricate picture of genetics, epigenetics, and human-dog relations
  • 2019
  • Doktorsavhandling (övrigt vetenskapligt)abstract
    • Dogs, Canis familiaris, share the lives of humans all over the world. That dogs, and the behavior of dogs, are of interest to many is therefore no surprise. In this thesis, the main aim has been to identify factors that affect dogs’ behaviours.The dog, Canis familiaris, is our first domesticated animal. Since domestication, various types of dogs have developed through adaptation to an environment shared with humans and through our selective breeding, resulting in a unique variation in morphology and behaviour. Although there is an individual variation in the behaviour of dogs, there is also a difference between breeds. Moreover, selection during the last decades has split some breeds into divergent types. Labrador and golden retrievers are divided into a common type, for show and companionship, and a field type, for hunting. By comparing the breed types, we can study the effects of recent selection. In Paper I, we investigate differences in general behavioural traits between Labrador and golden retriever and between common and field type within the two breeds by using results from the standardized behaviour test Dog Mentality Assessment. There were differences between breeds and types for all behavioural traits. However, there was also an interaction between breed and type. Thus, a common/field-type Labrador does not behave like a common/field-type golden retriever. Even though they have been selected for similar traits, the selection has affected the general behavioural traits differently in the two breeds.In paper II, we were interested in dogs’ human-directed social skills. Dogs have a high social competence when it comes to humans. Two experiments commonly used to study these skills are the problem-solving test, where dogs’ human-directed behaviours when faced with a problem are measured, and the pointing test, where dogs are tested on how well they understand human gestures. We compared the social skills of German shepherds and Labrador retrievers, and of common- and field-type Labradors. Labradors were more successful in the pointing test and German shepherds stayed closer to their owners during the problem solving. Among Labrador types, the field type had more human eye contact than the common type. Importantly, when comparing the two experiments, we found no positive correlations between the problem-solving test and the pointing test, suggesting that the two tests measure different aspects of human-directed social behaviour in dogs.A previous study has identified two suggestive genetic regions for human-directed social behaviours during the problem-solving test in beagles. In paper III, we show that these SNPs are also associated to social behaviours in Labrador and golden retrievers. Moreover, the Labrador breed types differed significantly in allele frequencies. This indicates that the two SNPs have been affected by recent selection and may have a part in the differences in sociability between common and field type.The behaviour of dogs cannot simply be explained by genetics, there is also an environmental component. In paper IV, we study which factors that affect long-term stress in dogs. Long-term cortisol can be measured by hair samples. We found a clear synchronization in hair cortisol concentrations between dogs and their owners. Neither dogs’ activity levels nor their behavioural traits affected the cortisol, however, the personality of the owners did. Therefore, we suggest that dogs mirror the stress level of their owners.The mediator between genes and the environment is epigenetics, and one epigenetic factor is DNA methylation. In paper V, we compared methylation patterns of wolves and dogs as well as dog breeds. Between both wolves and dogs and among dogs there were substantial differences in methylated DNA regions, suggesting that DNA methylation is likely to contribute to the vast variation among canines. We hypothesize that epigenetic factors have been important during domestication and in breed formation.In this thesis, I cover several aspects on how dogs’ behaviours can be affected, and paint an intricate picture on how genetics, epigenetics, and human-dog relations forms dog behaviour.
  • Bélteky, Johan (författare)
  • Chicken domestication : Effects of tameness on brain gene expression and DNA methylation
  • 2016
  • Doktorsavhandling (övrigt vetenskapligt)abstract
    • Domestication greatly increases phenotypic variation in a short time span, with selection for a single phenotype and a plethora of associated phenotypic changes as an outcome of the process. The domestication process influences the underlying genomic architecture of a species, and the success and speed of the process is likely influenced by it. The main aims of my thesis was to study how domestication affects the brain of chickens: specifically changes in morphology, gene expression, and DNA methylation. Differences in gene expression and DNA methylation between White Leghorn and Red Junglefowl chickens were mapped, and inheritance of these patterns were quantified, indicating a faithful transmission of breed-specific epigenetic markers. Selection on the behavioral trait fearfulness, generated high and low fearful lines of Red Junglefowl. Both the parental population and the fifth selected generation were used for the analyses in this thesis. One experiment studied morphological changes in the brain and other vital organs, and found that relative total brain size increased in high fearful birds, as a consequence of an increase in cerebral hemisphere size in high fearful birds and not in low fearful birds. Also, the relative heart, liver, spleen and testis size increased in high fearful birds, indicating correlated morphological changes with selection for fearfulness. Two additional experiments examined differential gene expression in the hypothalamus and the anterior cerebral hemisphere. The hypothalamus differed in expression of genes with reproductive and immunological functions, whilst the cerebral hemisphere differed in expression of genes related to social behaviors and neurological functions especially those upregulated in low fearful birds.  These results indicate the occurrence of tissue- and species-specific changes in gene expression as overlap with other domestication events were nearly nonexistent. A fourth experiment sought to associate the change in fear levels and gene expression differences with DNA methylation. Chromosomal regions with differential DNA methylation between high and low fearful birds were identified, and genes in these regions had annotated functions relevant to phenotypic differences between the selection lines. This thesis is the first to study the genetic alterations of domestication using the wild ancestor of an already domesticated species to repeat the domestication process selecting against fear of humans. The findings corroborate results from previous comparisons of wild and domestic animals, and further support the theory that rigorous selection for a behavioral trait can cause a cascade of genetic and epigenetic changes facilitating the domestication of a population.
  • Xu, Bo, 1980- (författare)
  • Evolutionary and Pharmacological Studies of NPY and QRFP Receptors
  • 2014
  • Doktorsavhandling (övrigt vetenskapligt)abstract
    • The neuropeptide Y (NPY) system consists of 3-4 peptides and 4-7 receptors in vertebrates. It has powerful effects on appetite regulation and is involved in many other biological processes including blood pressure regulation, bone formation and anxiety. This thesis describes studies of the evolution of the NPY system by comparison of several vertebrate species and structural studies of the human Y2 receptor, which reduces appetite, to identify amino acid residues involved in peptide-receptor interactions.The NPY system was studied in zebrafish (Danio rerio), western clawed frog (Xenopus tropicalis), and sea lamprey (Petromyzon marinus). The receptors were cloned and functionally expressed and their pharmacological profiles were determined using the native peptides in either binding studies or a signal transduction assay. Some peptide-receptor preferences were observed, indicating functional specialization.A receptor family closely related to the NPY receptors, called the QRFP receptors, was investigated. A QRFP receptor was cloned from amphioxus, Branchistoma floridae, showing that the receptor arose before the origin of the vertebrates. Evolutionary studies demonstrated that the ancestral vertebrate had as many as four QRFP receptors, only one of which remains in mammals today. This correlates with the NPY receptor family, located in the same chromosomal regions, which had seven members in the ancestral vertebrate but only 4-5 in living mammals. Some vertebrates have considerably more complex NPY and QRFP receptor systems than humans and other mammals.Two studies investigated interactions of NPY-family peptides with the human Y2 receptor. Candidate residues, selected based on structural modeling and docking, were mutated to disrupt possible interactions with peptide ligands. The modified receptors were expressed in cultured cells and investigated by measuring binding and functional responses. Several receptor residues were found to influence peptide-receptor interactions, some of which are involved in maintaining receptor structure. In a pilot study, the kinetics of peptide-receptor interaction were found to be very slow, of the order several hours.In conclusion, this thesis clarifies evolutionary relationships for the complex NPY and QRFP peptide-receptor systems and improves the structural models of the human NPY-family receptors, especially Y2. These results will hopefully facilitate drug design for targeting of NPY-family receptors.
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