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  • 1. Andersson, Markus
    et al.
    Van Nieuwerburgh, Lies
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Snoeijs, Pauli
    Pigment transfer from phytoplankton to zooplankton with emphasis on astaxanthin production in the Baltic Sea food web2003In: Marine Ecology Progress Series, Vol. 254, p. 312-224Article in journal (Refereed)
  • 2.
    Borge, Thomas
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Haavie, Jon
    Saether, Stein Are
    Bures, Stanislav
    Saetre, Glenn-Peter
    Paternally determined species recognition in female flycathcer hybridsManuscript (Other academic)
  • 3.
    Borge, Thomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Lindroos, Katarina
    Nadvornik, Petr
    Syvänen, Ann-Christine
    Saetre, Glenn-Peter
    Rate of introgression in island versus clinal hybrid zones of Ficedula flycatchers are consistent with regional differences in hybrid fertilityManuscript (Other academic)
  • 4.
    Borge, Thomas
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Webster, Matthew Thomas
    Andersson, Gunilla
    Saetre, Glenn-Peter
    Recurrent selective sweeps on the Z chromosome characterize the evolutionary history of two closely related flycatcher species (Ficedula hypoleuca and F. albicollis)Manuscript (Other academic)
  • 5.
    Canbäck, Björn
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    In silico Studies of Early Eukaryotic Evolution2002Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    A question of great interest in evolutionary biology is how and why the eukaryotic cell evolved. Several hypotheses have been proposed, ranging from an early emergence of a primitive eukaryotic cell, to various fusion models like the hydrogen hypothesis. Within this context, relevant bacterial gene families and genomes are examined in this thesis.

    The mitochondrion, the energy producing organelle in the eukaryotic cell, is generally believed to be of α-proteobacterial descent. To learn more about mitochondrial evolution, and therefore eukaryotic evolution, the genomes of the α-proteobacteria Bartonella henselae and Bartonella quintana were sequenced. Software was developed and used in the annotation of these genomes.

    Several gene products of nuclear-encoded genes are exported to the mitochondrion. Many of these genes are thought to originate from the emerging organelle. An analysis of the more than 400 genes encoding proteins targeted to the yeast mitochondrion indicates that one set of genes originated from the bacterial symbiont, while the eukaryotic host contributed another. Thus, the mitochondrial proteome has a dual origin.

    The hydrogen hypothesis postulates that the glycolytic genes belong to the group of genes that were transferred from symbiont to host. These genes are thoroughly analysed from a phylogenetic perspective. Contrary to the predictions of the hydrogen hypothesis, the results provide no support for a close relationship between nuclear genes encoding glycolytic enzymes and their α-proteobacterial homologs.

    In general, it is thought that intensive gene transfers may limit our ability to reconstruct gene and species evolution, especially among microbes. A phylogenetic analysis of a large cohort of genes from the AT-rich genome of the γ-proteobacterium Buchnera aphidicola (Sg) resulted in a high fraction of atypical tree topologies, previously interpreted as horizontal gene transfers. By applying methods that accommodate for asymmetric nucleotide substitutions, it is shown that many well-supported gene topologies are drastically altered, so that they now agree with the rRNA topology. The conclusion is that atypical topologies may not necessarily be evidence for horizontal gene transfers.

  • 6.
    Castensson, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    High-resolution Studies of mRNA Expression in Brain: A Search for Genes Differently Expressed in Schizophrenia2003Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Gene expression differences between patients and controls can be used to find susceptibility genes and drug targets for a disease. High-resolution strategies are required because the differences between the investigated groups may be small and numerous factors may affect the mRNA quantity. This thesis is based on the use of real-time RT-PCR combined with a new statistical approach, developed to detect small differences between patients and controls and differences due to patient subgroups.

    Comparisons between human brain biopsy and autopsy samples showed that post-mortem tissue can be used to make conclusions on the relative mRNA levels in the living brain.

    Power analysis based on human brain mRNA expression from 14 genes adjusted with two reference genes, revealed that a sample size of 50 patients and 50 controls was required to detect a 2-fold difference with a power and a confidence of 95%. A similar study in rats revealed that approximately the same sample size was required for rat brain mRNA expression studies.

    The mRNA levels of several genes were studied in 55 schizophrenia and 55 control prefrontal brain autopsies, using a novel and more powerful statistical analysis. The serotonin receptor 2C gene (HTR2C) showed a significant 1.5-fold decrease in the patients as compared to controls, and the monoamine oxidase B gene (MAOB) a 1.2-fold increase.

    The mechanism behind the decrease of HTR2C mRNA levels was investigated by studying the correlation of drug treatment and HTR2C promoter polymorphisms to the HTR2C expression levels. The observed decrease was present in untreated patients, suggesting that the HTR2C mRNA decrease is correlated with the disease and not the treatment. There was no association between promoter polymorphisms and HTR2C expression levels. Thus, the molecular mechanism for the decreased expression remains unclear. Nevertheless, the results support a role for monoaminergic synapses in schizophrenia.

    List of papers
    1. High-resolution quantification of specific mRNA levels in human brain autopsies and biopsies
    Open this publication in new window or tab >>High-resolution quantification of specific mRNA levels in human brain autopsies and biopsies
    2000 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 10, no 8, p. 1219-29Article in journal (Refereed) Published
    Abstract [en]

    Quantification of mRNA levels in human cortical brain biopsies and autopsies was performed using a fluorogenic 5' nuclease assay. The reproducibility of the assay using replica plates was 97%-99%. Relative quantities of mRNA from 16 different genes were evaluated using a statistical approach based on ANCOVA analysis. Comparison of the relative mRNA levels between two groups of samples with different time postmortem revealed unchanged relative expression levels for most genes. Only CYP26A1 mRNA levels showed a significant decrease with prolonged time postmortem (p = 0.00004). Also, there was a general decrease in measured mRNA levels for all genes in autopsies compared to biopsies; however, on comparing mRNA levels after adjusting with reference genes, no significant differences were found between mRNA levels in autopsies and biopsies. This observation indicates that studies of postmortem material can be performed to reveal the relative in vivo mRNA levels of genes. Power calculations were done to determine the number of individuals necessary to detect differences in mRNA levels of 1.5-fold to tenfold using the strategy described here. This analysis showed that samples from at least 50 individuals per group, patients and controls, are required for high-resolution ( approximately twofold changes) differential expression screenings in the human brain. Experiments done on ten individuals per group will result in a resolution of approximately fivefold changes in expression levels. In general, the sensitivity and resolution of any differential expression study will depend on the sample size used and the between-individual variability of the genes analyzed.

    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-90900 (URN)10.1101/gr.10.8.1219 (DOI)10958640 (PubMedID)
    Available from: 2003-10-14 Created: 2003-10-14 Last updated: 2017-12-14Bibliographically approved
    2. Analysis of gene expression in the rat hippocampus using Real Time PCR reveals high inter-individual variation in mRNA expression levels
    Open this publication in new window or tab >>Analysis of gene expression in the rat hippocampus using Real Time PCR reveals high inter-individual variation in mRNA expression levels
    Show others...
    2002 (English)In: Journal of Neuroscience Research, ISSN 0360-4012, E-ISSN 1097-4547, Vol. 67, no 2, p. 225-34Article in journal (Refereed) Published
    Abstract [en]

    In mammals, gene transcription is a step subjected to tight regulation mechanisms. In fact, changes in mRNA levels in the central nervous system (CNS) can account for numerous phenotypic differences in brain function. We performed a high-resolution analysis of mRNA expression levels for 37 genes selected from a normal rat hippocampus cDNA library. mRNA amounts were quantified using a Real Time PCR SYBR Green assay. We found that, in general, individuals from an inbred rat population (n = 20) have shown 2-3 times differences in the basal level of expression of the genes analyzed. Up to several fold differences among individuals were observed for certain genes. These inter-individual differences were obtained after correction for the different amounts of mRNA in each sample. Power calculations were performed to determine the number of individuals required to detect reliable differences in expression levels between a control and an experimental group. These data indicated that, depending on the variability of the candidate gene selected, it was necessary to analyze from five to 135 individuals in each group to detect differences of 50% in the levels of mRNA expression between two groups investigated. The comparison of mRNA abundance from different genes revealed a wide range of expression levels for the 37 genes, showing a 26,000-fold difference between the highest and lowest expressed gene.

    National Category
    Genetics Physiology
    Identifiers
    urn:nbn:se:uu:diva-90901 (URN)10.1002/jnr.10105 (DOI)
    Available from: 2003-10-14 Created: 2003-10-14 Last updated: 2018-01-13Bibliographically approved
    3. Decrease of serotonin receptor 2C in schizophrenia brains identified by high-resolution mRNA expression analysis
    Open this publication in new window or tab >>Decrease of serotonin receptor 2C in schizophrenia brains identified by high-resolution mRNA expression analysis
    2003 (English)In: Biological Psychiatry, ISSN 0006-3223, E-ISSN 1873-2402, Vol. 54, no 11, p. 1212-1221Article in journal (Refereed) Published
    Abstract [en]

    BACKGROUND: RNA expression profiling can provide hints for the selection of candidate susceptibility genes, for formulation of hypotheses about the development of a disease, and/or for selection of candidate gene targets for novel drug development. We measured messenger RNA expression levels of 16 candidate genes in brain samples from 55 schizophrenia patients and 55 controls. This is the largest sample so far used to identify genes differentially expressed in schizophrenia brains. METHODS: We used a sensitive real-time polymerase chain reaction methodology and a novel statistical approach, including the development of a linear model of analysis of covariance type. RESULTS: We found two genes differentially expressed: monoamine oxidase B was significantly increased in schizophrenia brain (p =.001), whereas one of the serotonin receptor genes, serotonin receptor 2C, was significantly decreased (p =.001). Other genes, previously proposed to be differentially expressed in schizophrenia brain, were invariant in our analysis. CONCLUSIONS:The differential expression of serotonin receptor 2C is particularly relevant for the development of new atypical antipsychotic drugs. The strategy presented here is useful to evaluate hypothesizes for the development of the disease proposed by other investigators.

    National Category
    Physiology Genetics
    Identifiers
    urn:nbn:se:uu:diva-90902 (URN)10.1016/S0006-3223(03)00526-2 (DOI)
    Available from: 2003-10-14 Created: 2003-10-14 Last updated: 2018-01-13Bibliographically approved
    4. Statistical methodology in case-control 5'-nuclease assays: statistical design, modelling and inference for identification of differentially expressed genes
    Open this publication in new window or tab >>Statistical methodology in case-control 5'-nuclease assays: statistical design, modelling and inference for identification of differentially expressed genes
    (English)Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-90903 (URN)
    Available from: 2003-10-14 Created: 2003-10-14 Last updated: 2010-02-11Bibliographically approved
    5. Serotonin receptor 2C (HTR2C) and schizophrenia: effect of medication and genetic variants on expression levels
    Open this publication in new window or tab >>Serotonin receptor 2C (HTR2C) and schizophrenia: effect of medication and genetic variants on expression levels
    Show others...
    (English)Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-90904 (URN)
    Available from: 2003-10-14 Created: 2003-10-14 Last updated: 2010-02-11Bibliographically approved
  • 7.
    Castensson, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Emilsson, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Preece, Paul
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    High-resolution quantification of specific mRNA levels in human brain autopsies and biopsies2000In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 10, no 8, p. 1219-29Article in journal (Refereed)
    Abstract [en]

    Quantification of mRNA levels in human cortical brain biopsies and autopsies was performed using a fluorogenic 5' nuclease assay. The reproducibility of the assay using replica plates was 97%-99%. Relative quantities of mRNA from 16 different genes were evaluated using a statistical approach based on ANCOVA analysis. Comparison of the relative mRNA levels between two groups of samples with different time postmortem revealed unchanged relative expression levels for most genes. Only CYP26A1 mRNA levels showed a significant decrease with prolonged time postmortem (p = 0.00004). Also, there was a general decrease in measured mRNA levels for all genes in autopsies compared to biopsies; however, on comparing mRNA levels after adjusting with reference genes, no significant differences were found between mRNA levels in autopsies and biopsies. This observation indicates that studies of postmortem material can be performed to reveal the relative in vivo mRNA levels of genes. Power calculations were done to determine the number of individuals necessary to detect differences in mRNA levels of 1.5-fold to tenfold using the strategy described here. This analysis showed that samples from at least 50 individuals per group, patients and controls, are required for high-resolution ( approximately twofold changes) differential expression screenings in the human brain. Experiments done on ten individuals per group will result in a resolution of approximately fivefold changes in expression levels. In general, the sensitivity and resolution of any differential expression study will depend on the sample size used and the between-individual variability of the genes analyzed.

  • 8.
    Castensson, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Emilsson, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Sundberg, Rolf
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Decrease of serotonin receptor 2C in schizophrenia brains identified by high-resolution mRNA expression analysis2003In: Biological Psychiatry, ISSN 0006-3223, E-ISSN 1873-2402, Vol. 54, no 11, p. 1212-1221Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: RNA expression profiling can provide hints for the selection of candidate susceptibility genes, for formulation of hypotheses about the development of a disease, and/or for selection of candidate gene targets for novel drug development. We measured messenger RNA expression levels of 16 candidate genes in brain samples from 55 schizophrenia patients and 55 controls. This is the largest sample so far used to identify genes differentially expressed in schizophrenia brains. METHODS: We used a sensitive real-time polymerase chain reaction methodology and a novel statistical approach, including the development of a linear model of analysis of covariance type. RESULTS: We found two genes differentially expressed: monoamine oxidase B was significantly increased in schizophrenia brain (p =.001), whereas one of the serotonin receptor genes, serotonin receptor 2C, was significantly decreased (p =.001). Other genes, previously proposed to be differentially expressed in schizophrenia brain, were invariant in our analysis. CONCLUSIONS:The differential expression of serotonin receptor 2C is particularly relevant for the development of new atypical antipsychotic drugs. The strategy presented here is useful to evaluate hypothesizes for the development of the disease proposed by other investigators.

  • 9.
    Castensson, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Åberg, Karolina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    McCarthy, Shane
    Andersson, Björn
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Serotonin receptor 2C (HTR2C) and schizophrenia: effect of medication and genetic variants on expression levelsManuscript (Other academic)
  • 10.
    Ekblom, Robert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
    Sæther, Stein Are
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Grahn, Mats
    Fiske, Peder
    Kålås, John Atle
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
    Major histocompatibility complex variation and mate choice in a lekking bird, the great snipe (Gallinago media)2004In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 13, no 12, p. 3821-3828Article in journal (Refereed)
    Abstract [en]

    Genes of the major histocompatibility complex (MHC) play a major part in the activation of the vertebrate immune system. In addition, they also appear to function as cues for mate choice. In mammals especially, several kinds of MHC-dependent mate choice have been hypothesized and observed. These include choice of mates that share no or few alleles with the choosing individual, choice of mates with alleles that differ as much as possible from the choosing individual, choice of heterozygous mates, choice of certain genotypes and choice of rare alleles. We investigated these different aspects of mate choice in relation to MHC in a lekking bird species, the great snipe (Gallinago media). We found no evidence for MHC disassortative mating, no preference for males with many MHC alleles and no preference for rare alleles. However, we did find that some allelic lineages were more often found in males with mating success than in males without mating success. Females do not seem to use themselves as references for the MHC-dependent mate choice, rather they seem to prefer males with certain allele types. We speculate that these alleles may be linked to resistance to common parasites.

  • 11.
    Ekblom, Robert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population Biology.
    Sæther, Stein Are
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Hasselquist, Dennis
    Hannersjö, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
    Fiske, Peder
    Kålås, John Atle
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
    Female choice and male humoral immune response in the lekking great snipe (Gallinago media)2005In: Behavioral Ecology, ISSN 1045-2249, E-ISSN 1465-7279, Vol. 16, no 2, p. 346-351Article in journal (Refereed)
    Abstract [en]

    Parasites and diseases constitute major evolutionary forces in many natural populations, and thus having an efficient immune defense to resist infections is crucial for many organisms. Properties of the immune response may also influence mate choice decisions in many animals. Theory predicts several advantages for females when choosing males with superior immune systems. These benefits can be both direct (e.g. increased paternal care and reduced disease transmission) and indirect (good genes). We have investigated female choice with respect to antibody response to two novel antigens in males of a lekking bird, the great snipe (Gallinago media). Because of the lek mating system, female choice probably mainly incurs indirect (genetic) rather than direct benefits. Males responded to vaccination with diphtheria and tetanus toxoids by producing specific antibodies to both antigens. Triggering the immune system had no negative impact on display activities or survival. Males that were chosen by females as mates had on average higher antibody response to the tetanus antigen than their neighbors. We did not, however, find any covariance between the strength of the antibody response and male mating success.

  • 12.
    Gustafsson, C.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    The effect of timing and amount of leaf removal on survival, growth and reproduction in the perennial herb Sanicula europaeaArticle in journal (Refereed)
  • 13.
    Gustafsson, C.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Ehrlén, J.
    Effects of intraspecific and interspecific density on the demography of a perennial herb, Sanicula europaea2003In: Oikos, Vol. 100, p. 317-324.Article in journal (Refereed)
  • 14.
    Gustafsson, C.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Ehrlén, J.
    Flowering and cost of reproduction in the perennial herb Sanicula europaea.Manuscript (Other academic)
  • 15.
    Gustafsson, C.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Ehrlén, J.
    Population dynamics and grazing in the perennial herb Sanicula europaeaManuscript (Other academic)
  • 16.
    Gustafsson, C.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Ehrlén, J.
    Seed availability and recruitment of the perennial herb Sanicula europaea2002In: Ecoscience, Vol. 9, p. 526-532.Article in journal (Refereed)
  • 17.
    Gustafsson, C.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Ehrlén, J.
    Eriksson, O.
    Recruitment in Dentaria bulbifera; the roles of dispersal, habitat quality and mollusc herbivory2002In: Journal of Vegetation Science, Vol. 13, p. 719-724.Article in journal (Refereed)
  • 18.
    Gustafsson, Christel
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Plant Population Dynamics and Biotic Interactions in two Forest Herbs2003Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In Sweden today, deciduous woodlands are often restricted to small isolated remnants of what it once was. Managing practices have changed concerning both cattle grazing and logging. Thus, dispersal, habitat requirements and their importance for forest species distributions become a relevant issue. Most of the species found in the deciduous flora are perennial herbs. I have examined population dynamics in the forest perennial Sanicula europaea, and its relation to environmental factors such as grazing, competition and spatial and temporal variation in such factors. Moreover I examined species distributions in relation to dispersal and habitat suitability in S. europaea and Dentaria bulbifera. To understand mechanisms behind the observed patterns I performed a number of experiments.

    The results clearly demonstrated that the distribution and abundance of S. europaea was not dispersal limited, whereas the opposite held true for D. bulbifera. Moreover, mollusc exclusion increased recruitment thus influencing population dynamics in D. bulbifera. Leaf losses had negative effects on S. europaea individuals. These negative effects depended both on the extent, frequency and timing of the leaf losses and early losses were more severe than late. Population level effects of grazing were not negative as negative direct effects were counterblanced by positive indirect effects. The positive effects of grazing were mainly in terms of an increased recruitment.

    In S. europaea, high variation in a life cycle transition was always coupled to low elasticity, and traits that varied much due to the examined environmental factors had little importance to population growth rate. A population level perspective is required to assess total effects of environmental factors. In perennial organisms such evaluations need to calculate integrated measures of the effects over the entire life cycle. Field studies spanning several years and demographic models are important to achieve these objectives.

    List of papers
    1. Flowering and cost of reproduction in the perennial herb Sanicula europaea.
    Open this publication in new window or tab >>Flowering and cost of reproduction in the perennial herb Sanicula europaea.
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-90109 (URN)
    Available from: 2003-02-14 Created: 2003-02-14 Last updated: 2010-01-13Bibliographically approved
    2. Recruitment in Dentaria bulbifera; the roles of dispersal, habitat quality and mollusc herbivory
    Open this publication in new window or tab >>Recruitment in Dentaria bulbifera; the roles of dispersal, habitat quality and mollusc herbivory
    2002 In: Journal of Vegetation Science, Vol. 13, p. 719-724.Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-90110 (URN)
    Available from: 2003-02-14 Created: 2003-02-14Bibliographically approved
    3. Seed availability and recruitment of the perennial herb Sanicula europaea
    Open this publication in new window or tab >>Seed availability and recruitment of the perennial herb Sanicula europaea
    2002 In: Ecoscience, Vol. 9, p. 526-532.Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-90111 (URN)
    Available from: 2003-02-14 Created: 2003-02-14Bibliographically approved
    4. Effects of intraspecific and interspecific density on the demography of a perennial herb, Sanicula europaea
    Open this publication in new window or tab >>Effects of intraspecific and interspecific density on the demography of a perennial herb, Sanicula europaea
    2003 In: Oikos, Vol. 100, p. 317-324.Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-90112 (URN)
    Available from: 2003-02-14 Created: 2003-02-14Bibliographically approved
    5. The effect of timing and amount of leaf removal on survival, growth and reproduction in the perennial herb Sanicula europaea
    Open this publication in new window or tab >>The effect of timing and amount of leaf removal on survival, growth and reproduction in the perennial herb Sanicula europaea
    Article in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-90113 (URN)
    Available from: 2003-02-14 Created: 2003-02-14Bibliographically approved
    6. Population dynamics and grazing in the perennial herb Sanicula europaea
    Open this publication in new window or tab >>Population dynamics and grazing in the perennial herb Sanicula europaea
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-90114 (URN)
    Available from: 2003-02-14 Created: 2003-02-14 Last updated: 2010-01-13Bibliographically approved
  • 19.
    Haavie, J
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology.
    Borge, T
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Bures, S
    Garamszegi, L
    Lampe, HM
    Moreno, J
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Animal Ecology.
    Török, J
    Saetre, GP
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Flycatcher song in allopatry and sympatry: convergence, divergence and reinforcement2004In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 17, no 2, p. 227-237Article in journal (Refereed)
    Abstract [en]

    The theory of reinforcement predicts that natural selection against the production of unfit hybrids favours traits that increase assortative mating. Whether culturally inherited traits, such as bird song, can increase assortative mating by reinforcement is largely unknown. We compared songs of pied (Ficedula hypoleuca) and collared flycatchers (F. albicollis) from two hybrid zones of different ages with songs from allopatric populations. Previously, a character divergence in male plumage traits has been shown to reinforce premating isolation in sympatric flycatchers. In contrast, we find that the song of the pied flycatcher has converged towards that of the collared flycatcher (mixed singing). However, a corresponding divergence in the collared flycatcher shows that the species differences in song characters are maintained in sympatry. Genetic analyses suggest that mixed song is not caused by introgression from the collared flycatcher, but rather due to heterospecific copying. Circumstantial evidence suggests that mixed song may increase the rate of maladaptive hybridization. In the oldest hybrid zone where reinforcement on plumage traits is most pronounced, the frequency of mixed singing and hybridization is also lowest. Thus, we suggest that reinforcement has reduced the frequency of mixed singing in the pied flycatcher and caused a divergence in the song of the collared flycatcher. Whether a culturally inherited trait promotes or opposes speciation in sympatry may depend on its plasticity. The degree of plasticity may be genetically determined and accordingly under selection by reinforcement.

  • 20.
    Olsson, Jan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Berg, Otto G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Dasgupta, Santanu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Nordström, Kurt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Eclipse period during replication of plasmid R1: Contributions from Structural events and from Copy-Number-control system2003In: Molecular Microbiology, ISSN 0950-382X, E-ISSN 1365-2958, Vol. 50, no 1, p. 291-301Article in journal (Refereed)
    Abstract [en]

    The eclipse period (the time period during which a newly replicated plasmid copy is not available for a new replication) of plasmid R1 in Escherichia coli was determined with the classic Meselson-Stahl density-shift experiment. A mini-plasmid with the wild-type R1 replicon and a mutant with a thermo-inducible runaway-replication phenotype were used in this work. The eclipses of the chromosome and of the wild-type plasmid were 0.6 and 0.2 generation times, respectively, at temperatures ranging from 30 degrees C to 42 degrees C. The mutant plasmid had a similar eclipse at temperatures up to 38 degrees C. At 42 degrees C, the plasmid copy number increased rapidly because of the absence of replication control and replication reached a rate of 350-400 plasmid replications per cell and cell generation. During uncontrolled replication, the eclipse was about 3 min compared with 10 min at controlled replication (the wild-type plasmid at 42 degrees C). Hence, the copy-number control system contributed significantly to the eclipse. The eclipse in the absence of copy-number control (3 min) presumably is caused by structural requirements: the covalently closed circular plasmid DNA has to regain the right degree of superhelicity needed for initiation of replication and it takes time to assemble the initiation factors.

  • 21. Pinto, Ernani
    et al.
    Van Nieuwerburgh, Lies
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Barros, Marcelo Paes
    Pedersén, Marianne
    Colepicolo, Pio
    Snoeijs, Pauli
    Density-dependent patters of thiamine and pigment production in the diatom Nitzschia microcephala2003In: Phytochemistry, Vol. 63, no 2, p. 155-163Article in journal (Refereed)
  • 22. Saetre, Glenn-Peter
    et al.
    Borge, Thomas
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Lindell, Johan
    Moum, Truls
    Primmer, Craig R.
    Sheldon, Ben C.
    Haavie, Jon
    Johnsen, Arild
    Ellegren, Hans
    Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers2001In: Molecular Ecology, Vol. 10, p. 737-749Article in journal (Refereed)
  • 23. Saetre, Glenn-Peter
    et al.
    Borge, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Lindroos, Katarina
    Haavie, Jon
    Sheldon, Ben C.
    Primmer, Craig R.
    Syvänen, Ann-Christine
    Sex chromosome evolution and speciation in Ficedula flycatchers2003In: Proceedings of the Royal Society of London: Biological Sciences, Vol. 270, p. 53-59Article in journal (Refereed)
  • 24. Sundberg, Rolf
    et al.
    Castensson, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Statistical methodology in case-control 5'-nuclease assays: statistical design, modelling and inference for identification of differentially expressed genesManuscript (Other academic)
  • 25.
    Sundström, Hannah
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Webster, Matthew T
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Reduced variation on the chicken Z chromosome2004In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 167, no 1, p. 377-385Article in journal (Refereed)
    Abstract [en]

    Understanding the population genetic factors that shape genome variability is pivotal to the design and interpretation of studies using large-scale polymorphism data. We analyzed patterns of polymorphism and divergence at Z-linked and autosomal loci in the domestic chicken (Gallus gallus) to study the influence of mutation, effective population size, selection, and demography on levels of genetic diversity. A total of 14 autosomal introns (8316 bp) and 13 Z-linked introns (6856 bp) were sequenced in 50 chicken chromosomes from 10 highly divergent breeds. Genetic variation was significantly lower at Z-linked than at autosomal loci, with one segregating site every 39 bp at autosomal loci (θW = 5.8 ± 0.8 × 10–3) and one every 156 bp on the Z chromosome (θW = 1.4 ± 0.4 × 10–3). This difference may in part be due to a low male effective population size arising from skewed reproductive success among males, evident both in the wild ancestor—the red jungle fowl—and in poultry breeding. However, this effect cannot entirely explain the observed three- to fourfold reduction in Z chromosome diversity. Selection, in particular selective sweeps, may therefore have had an impact on reducing variation on the Z chromosome, a hypothesis supported by the observation of heterogeneity in diversity levels among loci on the Z chromosome and the lower recombination rate on Z than on autosomes. Selection on sex-linked genes may be particularly important in organisms with female heterogamety since the heritability of sex-linked sexually antagonistic alleles advantageous to males is improved when fathers pass a Z chromosome to their sons.

  • 26.
    Sætre, Glenn-Peter
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Borge, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Lindroos, Katarina
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
    Haavie, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Sheldon, Ben C
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology.
    Primmer, Craig
    Syvänen, Ann-Christine
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
    Sex chromosome evolution and speciation in Ficedula flycatchers2003In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 270, no 1510, p. 53-59Article in journal (Other academic)
    Abstract [en]

    Speciation is the combination of evolutionary processes that leads to the reproductive isolation of different populations. We investigate the significance of sex-chromosome evolution on the development of post- and prezygotic isolation in two naturally hybridizing Ficedula flycatcher species. Applying a tag-array-based mini-sequencing assay to genotype single nucleotide polymorphisms (SNPs) and interspecific substitutions, we demonstrate rather extensive hybridization and backcrossing in sympatry. However, gene flow across the partial postzygotic barrier (introgression) is almost exclusively restricted to autosomal loci, suggesting strong selection against introgression of sex-linked genes. In addition to this partial postzygotic barrier, character displacement of male plumage characteristics has previously been shown to reinforce prezygotic isolation in these birds. We show that male plumage traits involved in reinforcing prezygotic isolation are sex linked. These results suggest a major role of sex-chromosome evolution in mediating post- and prezygotic barriers to gene flow and point to a causal link in the development of the two forms of reproductive isolation.

  • 27.
    Van Nieuwerburgh, Lies
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    McCausland, Malcolm
    Snoeijs, Pauli
    Pigments dynamics in phytoplankton and copepods can be manipulated by inorganic nutrientsManuscript (Other academic)
  • 28.
    Van Nieuwerburgh, Lies
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Wänstrand, Ingrid
    Liu, Jianguo
    Snoeijs, Pauli
    Astaxanthin levels in marine pelagic copepods grazing on two different phytoplankton dietsArticle in journal (Refereed)
  • 29.
    Van Nieuwerburgh, Lies
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Wänstrand, Ingrid
    Snoeijs, Pauli
    Astaxanthin levels in copepods depend on microalgal dietArticle in journal (Refereed)
  • 30. Veen, Thor
    et al.
    Borge, Thomas
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Griffith, Simon C.
    Saetre, Glenn-Peter
    Bures, Stanislav
    Gustafsson, Lars
    Sheldon, Ben C.
    Hybridization and adaptive mate choice in flycatchers2001In: Nature, Vol. 411, p. 45-50Article in journal (Refereed)
  • 31.
    Webster, Matthew Thomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Smith, Nick G.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Fixation biases affecting human SNPs?2004In: Trends in Genetics, ISSN 0168-9525, E-ISSN 1362-4555, Vol. 20, no 3, p. 122-126Article in journal (Refereed)
    Abstract [en]

    Under neutrality all classes of mutation have an equal probability of becoming fixed in a population. In this article, we describe our analysis of the frequency distributions of >5000 human SNPs and provide evident of biases in the process of fixation of certain classes of point mutation that are most likely to be attributable to biased gene conversion. The results indicate an increased fixation probability of mutations that result in the incorporation of a GC base pair. Furthermore, in transcribed regions this process exhibits strand asymmetry, and is biased towards preserving a G base on the coding strand. Biased gene conversion has the potential to explain both existence of isochores and the compositional asymmetry in mammalian transcribed regions.

1 - 31 of 31
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