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  • 1151.
    Warsi, Omar M.
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. SUNY Stony Brook, Dept Ecol & Evolut, Stony Brook, NY 11794 USA.
    Dykhuizen, Daniel E.
    SUNY Stony Brook, Dept Ecol & Evolut, Stony Brook, NY 11794 USA..
    Evolutionary implications of Liebig's law of the minimum: Selection under low concentrations of two nonsubstitutable nutrients2017In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 7, no 14, p. 5296-5309Article in journal (Refereed)
    Abstract [en]

    Interactions between different axes of an organism's niche determine the evolutionary trajectory of a population. An extreme case of these interactions is predicted from ecological theory in Liebig's law of the minimum. This law states that in environments where multiple nutrients are in relatively low concentrations, only one nutrient will affect the growth of the organism. This implies that the evolutionary response of the population would be dictated by the most growth-limiting nutrient. Alternatively, it is possible that an initial adaptation to the most limiting nutrient results in other nutrients present in low concentration affecting the evolutionary dynamics of the population. To test these hypotheses, we conducted twelve evolution experiments in chemostats using Escherichia coli populations: four under nitrogen limitation, four under magnesium limitation, and four in which both nitrogen and magnesium are in low concentrations. In the last environment, only magnesium seems to limit growth (Low Nitrogen Magnesium Limited environment, LNML). We observe a decrease in nitrogen concentration in the LNML environment over the course of our evolution experiment indicating that nitrogen might become limiting in these environments. Genetic reconstruction results show that clones adapted to magnesium limitation have genes involved in nitrogen starvation, that is, glnG (nitrogen starvation transcriptional regulator) and amtB (transport protein) to be upregulated only in the LNML environment as compared to magnesium-limiting environments. Together, our results highlights that in low-nutrient environments, adaptation to the growth-limiting nutrient results in other nutrients at low concentrations to play a role in the evolutionary dynamics of the population.

  • 1152.
    Warsi, Omar M.
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Lundin, Erik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Lustig, Ulrika
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Näsvall, Joakim
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Andersson, Dan I
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Selection for novel metabolic capabilities in Salmonella enterica2019In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 73, no 5, p. 990-1000Article in journal (Refereed)
    Abstract [en]

    Bacteria are known to display extensive metabolic diversity and many studies have shown that they can use an extensive repertoire of small molecules as carbon‐ and energy sources. However, it is less clear to what extent a bacterium can expand its existing metabolic capabilities by acquiring mutations that, for example, rewire its metabolic pathways. To investigate this capability and potential for evolution of novel phenotypes, we sampled large populations of mutagenized Salmonella enterica to select very rare mutants that can grow on minimal media containing 124 low molecular weight compounds as sole carbon sources. We found mutants growing on 18 of these novel carbon sources, and identified the causal mutations that allowed growth for four of them. Mutations that relieve physiological constraints or increase expression of existing pathways were found to be important contributors to the novel phenotypes. For the remaining 14 novel phenotypes, whole genome sequencing of independent mutants and genetic analysis suggested that these novel metabolic phenotypes result from a combination of multiple mutations. This work, by virtue of identifying the genetic and mechanistic basis for new metabolic capabilities, sheds light on the properties of adaptive landscapes underlying the evolution of novel phenotypes.

  • 1153. Watson, P J
    et al.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Stallmann, R R
    Sexual conflict and the energetic costs of mating and mate choice in water striders1998In: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 151, no 1, p. 46-58Article in journal (Refereed)
  • 1154.
    Weber, Claudia C.
    et al.
    Temple Univ, Dept Biol, Ctr Computat Genet & Genom, Philadelphia, PA 19122 USA;European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Hinxton, England.
    Whelan, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Physicochemical Amino Acid Properties Better Describe Substitution Rates in Large Populations2019In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 36, no 4, p. 679-690Article in journal (Refereed)
    Abstract [en]

    Substitutions between chemically distant amino acids are known to occur less frequently than those between more similar amino acids. This knowledge, however, is not reflected in most codon substitution models, which treat all nonsynonymous changes as if they were equivalent in terms of impact on the protein. A variety of methods for integrating chemical distances into models have been proposed, with a common approach being to divide substitutions into radical or conservative categories. Nevertheless, it remains unclear whether the resulting models describe sequence evolution better than their simpler counterparts. We propose a parametric codon model that distinguishes between radical and conservative substitutions, allowing us to assess if radical substitutions are preferentially removed by selection. Applying our new model to a range of phylogenomic data, we find differentiating between radical and conservative substitutions provides significantly better fit for large populations, but see no equivalent improvement for smaller populations. Comparing codon and amino acid models using these same data shows that alignments from large populations tend to select phylogenetic models containing information about amino acid exchangeabilities, whereas the structure of the genetic code is more important for smaller populations. Our results suggest selection against radical substitutions is, on average, more pronounced in large populations than smaller ones. The reduced observable effect of selection in smaller populations may be due to stronger genetic drift making it more challenging to detect preferences. Our results imply an important connection between the life history of a phylogenetic group and the model that best describes its evolution.

  • 1155. Weeks, Andrew R.
    et al.
    Sgro, Carla M.
    Young, Andrew G.
    Frankham, Richard
    Mitchell, Nicki J.
    Miller, Kim A.
    Byrne, Margaret
    Coates, David J.
    Eldridge, Mark D. B.
    Sunnucks, Paul
    Breed, Martin F.
    Australian Centre for Evolutionary Biology and Biodiversity, and School of Earth and Environmental Science, University of Adelaide.
    James, Elizabeth A.
    Hoffmann, Ary A.
    Assessing the benefits and risks of translocations in changing environments: a genetic perspective2011In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 4, no 6, p. 709-725Article in journal (Refereed)
    Abstract [en]

    Translocations are being increasingly proposed as a way of conserving biodiversity, particularly in the management of threatened and keystone species, with the aims of maintaining biodiversity and ecosystem function under the combined pressures of habitat fragmentation and climate change. Evolutionary genetic considerations should be an important part of translocation strategies, but there is often confusion about concepts and goals. Here, we provide a classification of translocations based on specific genetic goals for both threatened species and ecological restoration, separating targets based on ‘genetic rescue’ of current population fitness from those focused on maintaining adaptive potential. We then provide a framework for assessing the genetic benefits and risks associated with translocations and provide guidelines for managers focused on conserving biodiversity and evolutionary processes. Case studies are developed to illustrate the framework.

  • 1156.
    Wei, Chentao
    et al.
    Beijing Normal Univ, Coll Life Sci, Key Lab Biodivers & Ecol Engn, Minist Educ, Beijing 100875, Peoples R China.
    Dong, Lu
    Beijing Normal Univ, Coll Life Sci, Key Lab Biodivers & Ecol Engn, Minist Educ, Beijing 100875, Peoples R China.
    Li, Shou-Hsien
    Natl Taiwan Normal Univ, Dept Life Sci, Taipei 11677, Taiwan.
    Alström, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Swedish Univ Agr Sci, Swedish Species Informat Ctr, Box 7007, SE-75007 Uppsala, Sweden;Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, 1 Beichen West Rd, Beijing 100101, Peoples R China.
    Liu, Yang
    Sun Yat Sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangzhou 510275, Guangdong, Peoples R China;Sun Yat Sen Univ, Sch Life Sci, Dept Ecol, Guangzhou 510275, Guangdong, Peoples R China.
    Xia, Canwei
    Beijing Normal Univ, Coll Life Sci, Key Lab Biodivers & Ecol Engn, Minist Educ, Beijing 100875, Peoples R China.
    Yao, Cheng-Te
    Endem Species Res Inst, Medium Altitude Expt Stn, Chichi 15, Nantou 552, Taiwan.
    Zhang, Yanyun
    Beijing Normal Univ, Coll Life Sci, Key Lab Biodivers & Ecol Engn, Minist Educ, Beijing 100875, Peoples R China.
    From the Himalayas to a continental Island: Integrative species delimitation in the Brownish-flanked Bush Warbler Horornis fortipes complex2019In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 131, p. 219-227Article in journal (Refereed)
    Abstract [en]

    As species serve as basic units of study in many fields of biology, assessments of species limits are fundamental for such studies. Here, we used a multilocus dataset and different coalescent-based methods to analyze species delimitation and phylogenetic relationships in the Brownish-flanked Bush Warbler Horornis fortipes complex, which is widespread in the Sino-Himalayan region. We also examined the vocal and morphometric divergence within this complex. Our genetic results suggested that Horornis fortipes is composed of at least three independently evolving lineages, which diverged 1.1-1.8 million years ago. However, these lineages have hardly diverged in song or morphometrics and only very slightly in plumage. Our result indicate that there are three incipient species in Horonis fortipes complex diverged in central Himalayas and Hengduan Mountains, but not between the continent and Taiwan island.

  • 1157.
    Weissensteiner, Matthias H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Evolutionary genomics in Corvids: – From single nucleotides to structural variants2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Heritable genetic variation is the raw material of evolution and can occur in many different forms, from altering single nucleotides to rearranging stretches of millions at once. DNA mutations that result in phenotypic differences are the basis upon which natural selection can act, leading to a shift of the frequency of those mutations.

    In this thesis I aim to comprehensively characterize and quantify genetic variation in a natural system, the songbird genus Corvus.

    First, we expand on previous work from a hybrid zone of different populations of Eurasian crows. All black carrion crows and black-and-grey hooded crows meet in a narrow hybrid zone in central Europe, and also in central and Southeast Asia. Comparing population genetic data acquired from these three hybrid zones yielded no single genetic region as a candidate responsible for phenotypic divergence, yet a parallelism in sets of genes and gene networks was evident.

    Second, we capitalize on varying evolutionary timescales to investigate the driver of the heterogeneous genetic differentiation landscape observed in multiple avian species. Genetic diversity, and thus differentiation, seems to be correlated both between populations within single species and between species which diverged 50 million years ago. This pattern is best explained by conserved broad-scale recombination rate variation, which is in turn likely associated with chromosomal features such as centromeres and telomeres.

    Third, we introduce a de-novo assembly of the hooded crow based on long-read sequencing and optical mapping. The use of this technology allowed a glimpse into previously hidden regions of the genome, and uncovered large-scale tandem repeat arrays consisting of a 14-kbp satellite repeat or its 1.2-kpb subunit. Furthermore, these tandem repeat arrays are associated with regions of reduced recombination rate.

    Lastly, we extend the population genetic analysis to structural genomic variation, such as insertions and deletions. A large-scale population re-sequencing data set based on short-read and long-read technologies, spread across the entire genus is the foundation of a fine-scale genome-wide map of structural variation. A differentiation outlier approach between all-black carrion and black-and-grey hooded crows identified a 2.25-kilobase LTR retrotransposon inserted 20-kb upstream of the NDP gene. The element, which is fixed in the hooded crow population, is associated with decreased expression of NDP and may be responsible for differences in plumage color.

    List of papers
    1. Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex
    Open this publication in new window or tab >>Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex
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    2016 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 13195Article in journal (Refereed) Published
    Abstract [en]

    Uncovering the genetic basis of species diversification is a central goal in evolutionary biology. Yet, the link between the accumulation of genomic changes during population divergence and the evolutionary forces promoting reproductive isolation is poorly understood. Here, we analysed 124 genomes of crow populations with various degrees of genome-wide differentiation, with parallelism of a sexually selected plumage phenotype, and ongoing hybridization. Overall, heterogeneity in genetic differentiation along the genome was best explained by linked selection exposed on a shared genome architecture. Superimposed on this common background, we identified genomic regions with signatures of selection specific to independent phenotypic contact zones. Candidate pigmentation genes with evidence for divergent selection were only partly shared, suggesting context-dependent selection on a multigenic trait architecture and parallelism by pathway rather than by repeated single-gene effects. This study provides insight into how various forms of selection shape genome-wide patterns of genomic differentiation as populations diverge.

    National Category
    Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-308915 (URN)10.1038/ncomms13195 (DOI)000386500600001 ()27796282 (PubMedID)
    Funder
    Knut and Alice Wallenberg FoundationSwedish Research Council, 621-2010-5553EU, European Research Council, ERCStG-336536
    Available from: 2016-12-01 Created: 2016-12-01 Last updated: 2019-01-07Bibliographically approved
    2. Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa
    Open this publication in new window or tab >>Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa
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    2017 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 16, p. 4284-4295Article in journal (Refereed) Published
    Abstract [en]

    Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (N-e) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage-specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in N-e. Utilizing population-level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in N-e would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population-scaled recombination rate (rho), nucleotide diversity (pi) and measures of genetic differentiation between populations (F-ST, PBS, d(xy)) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.

    Place, publisher, year, edition, pages
    WILEY, 2017
    Keywords
    background selection, genetic diversity, genetic draft, genetic hitchhiking, linked selection, recombination rate, speciation genetics
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-333716 (URN)10.1111/mec.14195 (DOI)000407255100013 ()28570015 (PubMedID)
    Funder
    Swedish Research Council, 621-2010-5553, 2014-6325, 2013-08721EU, European Research Council, ERCStG-336536Knut and Alice Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC)
    Available from: 2017-11-16 Created: 2017-11-16 Last updated: 2019-01-07Bibliographically approved
    3. Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
    Open this publication in new window or tab >>Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
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    2017 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 27, no 5, p. 697-708Article in journal (Refereed) Published
    Abstract [en]

    Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [ OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (rho) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently.

    Place, publisher, year, edition, pages
    COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2017
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-323040 (URN)10.1101/gr.215095.116 (DOI)000400392400005 ()28360231 (PubMedID)
    Funder
    Knut and Alice Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC)Swedish Research Council, 621-2010-5553EU, European Research Council, ERCStG-336536
    Available from: 2017-06-01 Created: 2017-06-01 Last updated: 2019-01-07Bibliographically approved
    4. Fine-scale analysis of Structural Genomic Variation in Natural Populations
    Open this publication in new window or tab >>Fine-scale analysis of Structural Genomic Variation in Natural Populations
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    (English)Manuscript (preprint) (Other (popular science, discussion, etc.))
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-369880 (URN)
    Available from: 2019-01-07 Created: 2019-01-07 Last updated: 2019-01-07
  • 1158.
    Weissensteiner, Matthias H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Division of Evolutionary Biology Faculty of Biology Ludwig-Maximilians-Universität München Grosshaderner Strasse 2 82152 Planegg-Martinsried GERMANY.
    Bunikis, Ignas
    Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden.
    Knief, Ulrich
    2Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany.
    Peona, Valentina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Pophaly, Saurabh D.
    2Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Sedlazeck, Fritz J.
    5Human Genome Sequencing Center at Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
    Warmuth, Vera
    2Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany.
    Wolf, Jochen B.W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. 2Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany.
    Fine-scale analysis of Structural Genomic Variation in Natural PopulationsManuscript (preprint) (Other (popular science, discussion, etc.))
  • 1159.
    Westerberg, Ivar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    CpG islands, but not their methylation level, are key in the regulation of meiotic recombination in chicken (Gallus gallus)2019Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Meiotic recombination plays a fundamental role in many sexually reproducing species. Recombination shuffles the genetic material during the first meiotic cell division resulting in new combinations of alleles within each chromosome. In many organisms, the rate of recombination is not uniform across the genome but consists of so called hotspots where the recombination rate is remarkably higher than the genome average. In mammals, the regulation and location of recombination hotspots is regulated by a gene called PRDM9. Many nonmammalian animals, like birds, lack this gene and the precise mechanism for recombination rate regulation is still unknown. Previous findings in passerine birds have observed an association between recombination rate and a genomic feature known as CpG islands (CGIs). CGIs are often located in promoter regions of genes and depending on their methylation status constitute accessible chromatin regions. It has therefore been suggested that the proteins involved in the regulation of recombination have better access to less condense chromatin regions. In this study, I tested if the association between recombination rate and CGIs found in passerine birds is also true in chicken. I also tested if methylation levels of CGIs play a role in recombination rate regulation in chicken. To this end, I used previously published data for CGI locations and a methylation map in chicken, and unpublished data of recombination rate estimates. I found that the association between recombination rate and CGIs observed in passerine birds extends to chicken, suggesting that this is an ancestral trait in birds. I did not, however, find a negative association between methylation levels and recombination rate as hypothesised based on a relationship between methylation level and chromatin accessibility. This suggests that DNA methylation level at CGIs is not a strong determinant of recombination in chicken, although there may be some workflow artefacts or unknown factors remaining in my analysis obscuring the relationship between these two variables.

  • 1160.
    Whelan, Simon
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Allen, James E.
    Blackburne, Benjamin P.
    Talavera, David
    ModelOMatic: Fast and Automated Model Selection between RY, Nucleotide, Amino Acid, and Codon Substitution Models2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 1, p. 42-55Article in journal (Refereed)
    Abstract [en]

    Molecular phylogenetics is a powerful tool for inferring both the process and pattern of evolution from genomic sequence data. Statistical approaches, such as maximum likelihood and Bayesian inference, are now established as the preferred methods of inference. The choice of models that a researcher uses for inference is of critical importance, and there are established methods for model selection conditioned on a particular type of data, such as nucleotides, amino acids, or codons. A major limitation of existing model selection approaches is that they can only compare models acting upon a single type of data. Here, we extend model selection to allow comparisons between models describing different types of data by introducing the idea of adapter functions, which project aggregated models onto the originally observed sequence data. These projections are implemented in the program ModelOMatic and used to perform model selection on 3722 families from the PANDIT database, 68 genes from an arthropod phylogenomic data set, and 248 genes from a vertebrate phylogenomic data set. For the PANDIT and arthropod data, we find that amino acid models are selected for the overwhelming majority of alignments; with progressively smaller numbers of alignments selecting codon and nucleotide models, and no families selecting RY-based models. In contrast, nearly all alignments from the vertebrate data set select codon-based models. The sequence divergence, the number of sequences, and the degree of selection acting upon the protein sequences may contribute to explaining this variation in model selection. Our ModelOMatic program is fast, with most families from PANDIT taking fewer than 150 s to complete, and should therefore be easily incorporated into existing phylogenetic pipelines. ModelOMatic is available at https://code.google.com/p/modelomatic/.

  • 1161.
    Whittle, Carrie A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Sun, Yu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Dynamics of transcriptome evolution in the model eukaryote Neurospora2014In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 27, no 6, p. 1125-1135Article in journal (Refereed)
    Abstract [en]

    Mounting evidence indicates that changes in the transcriptome contribute significantly to the phenotypic differentiation of closely related species. Nonetheless, further genome-wide studies, spanning a broad range of organisms, are needed to decipher the factors driving transcriptome evolution. The model Neurospora (Ascomycota) comprises a simple system for empirically studying the evolutionary dynamics of the transcriptome. Here, we studied the evolution of gene expression in Neurospora crassa and Neurospora tetrasperma and show that patterns of transcriptome evolution are connected to genome evolution, tissue type and sexual identity (mating types, mat A and mat a) in these eukaryotes. Based on the comparisons of inter- and intraspecies expression divergence, our data reveal that rapid expression divergence is more apt to occur in sexual/female (SF) than vegetative/male (VM) tissues. In addition, interspecies gene expression and protein sequence divergence were strongly correlated for SF, but not VM, tissue. A correlation between transcriptome and protein evolution parallels findings from certain animals, but not yeast, and add support for the theory that expression evolution differs fundamentally among multicellular and unicellular eukaryotes. Finally, we found that sexual identity in these hermaphroditic Neurospora species is connected to interspecies expression divergence in a tissue-dependent manner: rapid divergence occurred for mat A- and mat a-biased genes from SF and VM tissues, respectively. Based on these findings, it is hypothesized that rapid interspecies transcriptome evolution is shifting the mating types of Neurospora towards distinct female and male phenotypes, that is, sexual dimorphism.

  • 1162.
    Whittle, Carrie A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Sun, Yu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Evolution of Synonymous Codon Usage in Neurospora tetrasperma and Neurospora discreta2011In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 3, p. 332-343Article in journal (Refereed)
    Abstract [en]

    Neurospora comprises a primary model system for the study of fungal genetics and biology. In spite of this, little is known about genome evolution in Neurospora. For example, the evolution of synonymous codon usage is largely unknown in this genus. In the present investigation, we conducted a comprehensive analysis of synonymous codon usage and its relationship to gene expression and gene length (GL) in Neurospora tetrasperma and Neurospora discreta. For our analysis, we examined codon usage among 2,079 genes per organism and assessed gene expression using large-scale expressed sequenced tag (EST) data sets (279,323 and 453,559 ESTs for N. tetrasperma and N. discreta, respectively). Data on relative synonymous codon usage revealed 24 codons (and two putative codons) that are more frequently used in genes with high than with low expression and thus were defined as optimal codons. Although codon-usage bias was highly correlated with gene expression, it was independent of selectively neutral base composition (introns); thus demonstrating that translational selection drives synonymous codon usage in these genomes. We also report that GL (coding sequences [CDS]) was inversely associated with optimal codon usage at each gene expression level, with highly expressed short genes having the greatest frequency of optimal codons. Optimal codon frequency was moderately higher in N. tetrasperma than in N. discreta, which might be due to variation in selective pressures and/or mating systems.

  • 1163.
    Williams, Laura
    et al.
    Univ Kaiserslautern, Plant Ecol & Systemat, Inst Biol, Kaiserslautern, Germany..
    Colesie, Claudia
    Univ Kaiserslautern, Plant Ecol & Systemat, Inst Biol, Kaiserslautern, Germany..
    Ullmann, Anna
    Univ Kaiserslautern, Plant Ecol & Systemat, Inst Biol, Kaiserslautern, Germany..
    Westberg, Martin
    Uppsala University, Music and Museums, Museum of Evolution.
    Wedin, Mats
    Swedish Museum Nat Hist, Dept Bot, Stockholm, Sweden..
    Büdel, Burkhard
    Univ Kaiserslautern, Plant Ecol & Systemat, Inst Biol, Kaiserslautern, Germany..
    Lichen acclimation to changing environments: Photobiont switching vs. climate-specific uniqueness in Psora decipiens2017In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 7, no 8, p. 2560-2574Article in journal (Refereed)
    Abstract [en]

    Unraveling the complex relationship between lichen fungal and algal partners has been crucial in understanding lichen dispersal capacity, evolutionary processes, and responses in the face of environmental change. However, lichen symbiosis remains enigmatic, including the ability of a single fungal partner to associate with various algal partners. Psora decipiens is a characteristic lichen of biological soil crusts (BSCs), across semi-arid, temperate, and alpine biomes, which are particularly susceptible to habitat loss and climate change. The high levels of morphological variation found across the range of Psora decipiens may contribute to its ability to withstand environmental change. To investigate Psora decipiens acclimation potential, individuals were transplanted between four climatically distinct sites across a European latitudinal gradient for 2years. The effect of treatment was investigated through a morphological examination using light and SEM microscopy; 26S rDNA and rbcL gene analysis assessed site-specific relationships and lichen acclimation through photobiont switching. Initial analysis revealed that many samples had lost their algal layers. Although new growth was often determined, the algae were frequently found to have died without evidence of a new photobiont being incorporated into the thallus. Mycobiont analysis investigated diversity and determined that new growth was a part of the transplant, thus, revealing that four distinct fungal clades, closely linked to site, exist. Additionally, P.decipiens was found to associate with the green algal genus Myrmecia, with only two genetically distinct clades between the four sites. Our investigation has suggested that P.decipiens cannot acclimate to the substantial climatic variability across its environmental range. Additionally, the different geographical areas are home to genetically distinct and unique populations. The variation found within the genotypic and morpho-physiological traits of P.decipiens appears to have a climatic determinant, but this is not always reflected by the algal partner. Although photobiont switching occurs on an evolutionary scale, there is little evidence to suggest an active environmentally induced response. These results suggest that this species, and therefore, other lichen species, and BSC ecosystems themselves may be significantly vulnerable to climate change and habitat loss.

  • 1164.
    Williams, Tom A.
    et al.
    Univ Bristol, Sch Earth Sci, Bristol BS8 1TQ, Avon, England.;Newcastle Univ, Inst Cell & Mol Biosci, Newcastle Upon Tyne NE2 4HH, Tyne & Wear, England..
    Szollosi, Gergely J.
    MTA ELTE Lendulet Evolutionary Genom Res Grp, H-1117 Budapest, Hungary..
    Spang, Anja
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Foster, Peter G.
    Nat Hist Museum, Dept Life Sci, London SW7 5BD, England..
    Heaps, Sarah E.
    Newcastle Univ, Inst Cell & Mol Biosci, Newcastle Upon Tyne NE2 4HH, Tyne & Wear, England.;Newcastle Univ, Sch Math & Stat, Newcastle Upon Tyne NE1 7RU, Tyne & Wear, England..
    Boussau, Bastien
    Univ Lyon 1, CNRS, Lab Biometrie & Biol Evolut, UMR5558, F-69622 Villeurbanne, France..
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Embley, T. Martin
    Newcastle Univ, Inst Cell & Mol Biosci, Newcastle Upon Tyne NE2 4HH, Tyne & Wear, England..
    Integrative modeling of gene and genome evolution roots the archaeal tree of life2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 23, p. E4602-E4611Article in journal (Refereed)
    Abstract [en]

    A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO2 to acetate via the Wood-Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.

  • 1165. Wingler, Astrid
    et al.
    Stångberg, Emma Josefine
    Saxena, Triambak
    Mistry, Rupal
    Interactions between temperature and sugars in the regulation of leaf senescence in the perennial herb Arabis alpina L.2012In: Journal of integrative plant biology, ISSN 1744-7909, Vol. 54, no 8, p. 595-605Article in journal (Refereed)
    Abstract [en]

    Annual plants usually flower and set seed once before senescence results in the death of the whole plant (monocarpic senescence). Leaf senescence also occurs in polycarpic perennials; even in "evergreen" species individual leaves senesce. In the annual model Arabidopsis thaliana sugars accumulate in the senescent leaves and senescence is accelerated by high sugar availability. Similar to A. thaliana, sugar contents increased with leaf age in the perennial Arabis alpina grown under warm conditions (22 °C day/18 night). At 5 °C, sugar contents in non-senescent leaves were higher than at a warm temperature, but dependent on the accession, either sugars did not accumulate or their contents decreased in old leaves. In A. alpina plants grown in their natural habitat in the Alps, sugar contents declined with leaf age. Growth at a cold temperature slightly delayed senescence in A. alpina. In both warm and cold conditions, an external glucose supply accelerated senescence, but natural variation was found in this response. In conclusion, sugar accumulation under warm conditions could accelerate leaf senescence in A. alpina plants, but genotype-specific responses and interactions with growth temperature are likely to influence senescence under natural conditions.

  • 1166. Winternitz, J. C.
    et al.
    Promerova, M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Polakova, R.
    Vinker, M.
    Schnitzer, J.
    Munclinger, P.
    Babik, W.
    Radwan, J.
    Bryja, J.
    Albrecht, T.
    Effects of heterozygosity and MHC diversity on patterns of extra-pair paternity in the socially monogamous scarlet rosefinch2015In: Behavioral Ecology and Sociobiology, ISSN 0340-5443, E-ISSN 1432-0762, Vol. 69, no 3, p. 459-469Article in journal (Refereed)
    Abstract [en]

    Extra-pair copulation without apparent direct benefits is an evolutionary puzzle that requires indirect fitness benefits to females to explain its ubiquity in socially monogamous mating systems. Using wild scarlet rosefinches (Carpodacus erythrinus), we tested if genetic benefits in the form of global (microsatellite) heterozygote advantage, adaptive genes (major histocompatibility complex), or complementary genes (using both markers) were responsible for female extra-pair mate choice, while considering that the benefits of mate choice may be conditional on female genotype. We found no evidence for assortative or relatedness-based mating (complementary genes), but higher MHC diversity, microsatellite heterozygosity, and condition were significantly related to male extra-pair paternity (EPP) success. In contrast, female probability of having extra-pair offspring decreased with increasing heterozygosity. Interestingly, extra-pair and within-pair males had higher heterozygosity than their female mates and extra-pair males had higher MHC supertype diversity. The only genetic difference between extra-pair and within-pair offspring was lower variance in MHC allelic diversity within extra-pair offspring, providing limited support for indirect genetic fitness benefits for the markers tested. Offspring had both higher neutral heterozygosity and number of MHC supertypes than adults, as well as significant identity disequilibrium, potentially suggesting that mates are chosen to increase offspring diversity in the period of the present study. Overall, our results point to an EPP heterozygote advantage for males, especially when involving less heterozygous females, and suggest that heterozygosity effects on reproduction may differ between the sexes.

  • 1167. Witsenburg, F.
    et al.
    Clement, L.
    Lopez-Baucells, A.
    Palmeirim, J.
    Pavlinic, I.
    Scaravelli, D.
    Sevcik, M.
    Dutoit, Ludovic
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Salamin, N.
    Goudet, J.
    Christe, P.
    How a haemosporidian parasite of bats gets around: the genetic structure of a parasite, vector and host compared2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 4, p. 926-940Article in journal (Refereed)
    Abstract [en]

    Parasite population structure is often thought to be largely shaped by that of its host. In the case of a parasite with a complex life cycle, two host species, each with their own patterns of demography and migration, spread the parasite. However, the population structure of the parasite is predicted to resemble only that of the most vagile host species. In this study, we tested this prediction in the context of a vector-transmitted parasite. We sampled the haemosporidian parasite Polychromophilus melanipherus across its European range, together with its bat fly vector Nycteribia schmidlii and its host, the bent-winged bat Miniopterus schreibersii. Based on microsatellite analyses, the wingless vector, and not the bat host, was identified as the least structured population and should therefore be considered the most vagile host. Genetic distance matrices were compared for all three species based on a mitochondrial DNA fragment. Both host and vector populations followed an isolation-by-distance pattern across the Mediterranean, but not the parasite. Mantel tests found no correlation between the parasite and either the host or vector populations. We therefore found no support for our hypothesis; the parasite population structure matched neither vector nor host. Instead, we propose a model where the parasite's gene flow is represented by the added effects of host and vector dispersal patterns.

  • 1168.
    Wojczulanis-Jakubas, Katarzyna
    et al.
    Univ Gdansk, Dept Vertebrate Ecol & Zool, Fac Biol, Wita Stwosza 59, PL-80308 Gdansk, Poland..
    Drobniak, Szymon M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland.
    Jakubas, Dariusz
    Univ Gdansk, Dept Vertebrate Ecol & Zool, Fac Biol, Wita Stwosza 59, PL-80308 Gdansk, Poland..
    Kulpinska-Chamera, Monika
    Univ Gdansk, Dept Vertebrate Ecol & Zool, Fac Biol, Wita Stwosza 59, PL-80308 Gdansk, Poland..
    Chastel, Olivier
    CNRS, CEBC, UMR 7372, F-79360 Villiers En Bois, France.;Univ Rochelle, F-79360 Villiers En Bois, France..
    Assortative mating patterns of multiple phenotypic traits in a long-lived seabird2018In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 160, no 2, p. 464-469Article in journal (Refereed)
    Abstract [en]

    Choosing the right mate is crucial for successful breeding, particularly in monogamous species with long and extensive bi-parental care, and when the breeding pair is presumed to last many seasons. We investigated the degree of assortative mating in the Little Auk Alle alle, a long-lived seabird with long-term pair bonds and bi-parental care for fixed (morphological) and labile (physiological, behavioural) traits. Using randomization tests, we suggest assortative mating with respect to wing length, extent of the white area on the upper eyelid and hormonal stress response (the difference between stress-induced and baseline corticosterone levels). We discuss how the assortative mating patterns that we found in the Little Auk may be adaptive.

  • 1169.
    Wolf, Jochen B. W.
    et al.
    Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemannstr. 2, 24306 Plön, Germany.
    Bayer, Till
    Haubold, Bernhard
    Schilhabel, Markus
    Rosenstiel, Philip
    Tautz, Diethard
    Nucleotide divergence versus gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no Suppl. 1, p. 162-175Article in journal (Refereed)
    Abstract [en]

    Recent advances in sequencing technology promise to provide new strategies for studying population differentiation and speciation phenomena in their earliest phases. We focus here on the black carrion crow (Corvus [corone] corone), which forms a zone of hybridization and overlap with the grey coated hooded crow (Corvus [corone] cornix). However, although these semispecies are taxonomically distinct, previous analyses based on several types of genetic markers did not reveal significant molecular differentiation between them. We here corroborate this result with sequence data obtained from a set of 25 nuclear intronic loci. Thus, the system represents a case of a very early phase of species divergence that requires new molecular approaches for its description. We have therefore generated RNAseq expression profiles using barcoded massively parallel pyrosequencing of brain mRNA from six individuals of the carrion crow and five individuals from a hybrid zone with the hooded crow. We obtained 856 675 reads from two runs, with average read length of 270 nt and coverage of 8.44. Reads were assembled de novo into 19 552 contigs, 70% of which could be assigned to annotated genes in chicken and zebra finch. This resulted in a total of 7637 orthologous genes and a core set of 1301 genes that could be compared across all individuals. We find a clear clustering of expression profiles for the pure carrion crow animals and disperse profiles for the animals from the hybrid zone. These results suggest that gene expression differences may indeed be a sensitive indicator of initial species divergence.

  • 1170.
    Wright, Alison E.
    et al.
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield, S Yorkshire, England.
    Fumagalli, Matteo
    Imperial Coll London, Dept Life Sci, Silwood Pk Campus, London, England.
    Cooney, Christopher R.
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield, S Yorkshire, England.
    Bloch, Natasha, I
    UCL, Dept Genet Evolut & Environm, London, England.
    Vieira, Filipe G.
    Univ Copenhagen, Ctr GeoGenet, Nat Hist Museum Denmark, Copenhagen, Denmark.
    Buechel, Severine D.
    Stockholm Univ, Dept Zool, Stockholm, Sweden.
    Kolm, Niclas
    Stockholm Univ, Dept Zool, Stockholm, Sweden.
    Mank, Judith E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. UCL, Dept Genet Evolut & Environm, London, England.
    Male-biased gene expression resolves sexual conflict through the evolution of sex-specific genetic architecture2018In: EVOLUTION LETTERS, ISSN 2056-3744, Vol. 2, no 2, p. 52-61Article in journal (Refereed)
    Abstract [en]

    Many genes are subject to contradictory selection pressures in males and females, and balancing selection resulting from sexual conflict has the potential to substantially increase standing genetic diversity in populations and thereby act as an important force in adaptation. However, the underlying causes of sexual conflict, and the potential for resolution, remains hotly debated. Using transcriptome-resequencing data from male and female guppies, we use a novel approach, combining patterns of genetic diversity and intersexual divergence in allele frequency, to distinguish the different scenarios that give rise to sexual conflict, and how this conflict may be resolved through regulatory evolution. We show that reproductive fitness is the main source of sexual conflict, and this is resolved via the evolution of male-biased expression. Furthermore, resolution of sexual conflict produces significant differences in genetic architecture between males and females, which in turn lead to specific alleles influencing sex-specific viability. Together, our findings suggest an important role for sexual conflict in shaping broad patterns of genome diversity, and show that regulatory evolution is a rapid and efficient route to the resolution of conflict.

  • 1171.
    Wright, Alison E.
    et al.
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield, S Yorkshire, England.
    Rogers, Thea F.
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield, S Yorkshire, England.
    Fumagalli, Matteo
    Imperial Coll London, Dept Life Sci, London, England.
    Cooney, Christopher R.
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield, S Yorkshire, England.
    Mank, Judith E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. UCL, Dept Genet Evolut & Environm, London, England; Univ British Columbia, Dept Zool, Vancouver, BC, Canada.
    Phenotypic sexual dimorphism is associated with genomic signatures of resolved sexual conflict2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 11, p. 2860-2871Article in journal (Refereed)
    Abstract [en]

    Intralocus sexual conflict, where an allele benefits one sex at the expense of the other, has an important role in shaping genetic diversity of populations through balancing selection. However, the potential for mating systems to exert balancing selection through sexual conflict on the genome remains unclear. Furthermore, the nature and potential for resolution of sexual conflict across the genome has been hotly debated. To address this, we analysed de novo transcriptomes from six avian species, chosen to reflect the full range of sexual dimorphism and mating systems. Our analyses combine expression and population genomic statistics across reproductive and somatic tissue, with measures of sperm competition and promiscuity. Our results reveal that balancing selection is weakest in the gonad, consistent with the resolution of sexual conflict and evolutionary theory that phenotypic sex differences are associated with lower levels of ongoing conflict. We also demonstrate a clear link between variation in sexual conflict and levels of genetic variation across phylogenetic space in a comparative framework. Our observations suggest that this conflict is short-lived, and is resolved via the decoupling of male and female gene expression patterns, with important implications for the role of sexual selection in adaptive potential and role of dimorphism in facilitating sex-specific fitness optima.

  • 1172.
    Xiong, Ye
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Molecular Ecology and Evolution Lab , Lund University.
    Early dietary effects of arachidonic acid on gene expression linked to  immune response and metabolism in rural and urban Great Tit (Parus Major) nestlings2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This study was conducted to test the silver spoon hypothesis that earlylife nutritional conditions impact development, performance and fitness of the birdsgreat tit (Parus major) nestlings. We investigated whether fatty acid affects immunityand metabolism during the altricial period by examining the expressions of geneTLR4 (immunity related) and COX 2 (metabolism related) against a dietarymanipulation on great tit nestlings in urban vs. rural environments. The resultssuggested that arachidonic acid had no significant effect on TLR4 expression, but atendency to induce immune response, regardless of urban or rural conditions. Thestrength of immune response was however negatively correlated with laying date. Theurban great tit nestlings had a higher COX 2 gene expression than rural ones, andarachidonic acid suppressed COX 2.Thus no strong support to the hypothesis was found for the studied great titpopulations. It showed, however, i) there is a tendency of increasing immune responsewith extra fatty acid in the diet, and ii) arachidonic acid suppress metabolism. Fattyacid involved in a multiple physiological processes and this complex need to beelaborated in future studies.

  • 1173.
    Xu, Bo
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Evolutionary and Pharmacological Studies of NPY and QRFP Receptors2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    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.

    List of papers
    1. Cloning and pharmacological characterization of the neuropeptide Y receptor Y5 in the sea lamprey, Petromyzon marinus
    Open this publication in new window or tab >>Cloning and pharmacological characterization of the neuropeptide Y receptor Y5 in the sea lamprey, Petromyzon marinus
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    2013 (English)In: Peptides, ISSN 0196-9781, E-ISSN 1873-5169, Vol. 39, p. 64-70Article in journal (Refereed) Published
    Abstract [en]

    The neuropeptide Y system is known to have expanded in early vertebrate evolution. Three neuropeptide Y receptors have been proposed to have existed before the two basal vertebrate tetraploidizations, namely a VI-like, a Y2-like, and a Y5-like receptor, with their genes in the same chromosomal region. Previously we have described a VI-subfamily and a Y2-subfamily receptor in the river lamprey, Lampetra fluviatilis. Here we report the identification of a Y5 receptor in the genome of the sea lamprey, Petromyzon marinus. In phylogenetic analyses, the Y5 receptor clusters together with gnathostome Y5 receptors with high bootstrap value and shares the long intracellular loop 3. This lamprey receptor has an even longer loop 3 than the gnathostome Y5 receptors described so far, with the expansion of amino acid repeats. Functional expression in a human cell line, co-transfected with a modified human G-protein, resulted in inositol phosphate turnover in response to the three lamprey NPY-family peptides NPY, PYY and PMY at nanomolar concentrations. Our results confirm that the Y1-Y2-Y5 receptor gene triplet arose before the cyclostome-gnathostome divergence. However, it is not clear from the NPY receptors whether cyclostomes diverged from the gnathostome lineage after the first or the second tetraploidization. Duplicates resulting from the tetraploidizations exist for both Y1 and Y2 in gnathostomes, but only a single copy of Y5 has survived in all vertebrates characterized to date, making the physiological roles of Y5 interesting to explore.

    Keywords
    Lamprey, Neuropeptide Y, Peptide YY, Y5 receptor
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-198074 (URN)10.1016/j.peptides.2012.11.007 (DOI)000315839300011 ()
    Available from: 2013-04-09 Created: 2013-04-08 Last updated: 2019-01-03Bibliographically approved
    2. Neuropeptide Y family receptors Y1 and Y2 from sea lamprey, Petromyzon marinus: cloning and pharmacological characterization
    Open this publication in new window or tab >>Neuropeptide Y family receptors Y1 and Y2 from sea lamprey, Petromyzon marinus: cloning and pharmacological characterization
    2015 (English)In: General and Comparative Endocrinology, ISSN 0016-6480, E-ISSN 1095-6840, Vol. 222, p. 106-115Article in journal (Other academic) Published
    Abstract [en]

    The vertebrate gene family for neuropeptide Y (NPY) receptors expanded by duplication of the chromosome carrying the ancestral Y1–Y2–Y5 gene triplet. After loss of some duplicates, the ancestral jawed vertebrate had seven receptor subtypes forming the Y1 (including Y1, Y4, Y6, Y8), Y2 (including Y2, Y7) and Y5 (only Y5) subfamilies. Lampreys are considered to have experienced the same chromosome duplications as gnathostomes and should also be expected to have multiple receptor genes. However, previously only a Y4-like and a Y5 receptor have been cloned and characterized. Here we report the cloning and characterization of two additional receptors from the sea lamprey Petromyzon marinus. Sequence phylogeny alone could not with certainty assign their identity, but based on synteny comparisons of P. marinus and the Arctic lamprey, Lethenteron camtschaticum, with jawed vertebrates, the two receptors most likely are Y1 and Y2. Both receptors were expressed in human HEK293 cells and inositol phosphate assays were performed to determine the response to the three native lamprey peptides NPY, PYY and PMY. The three peptides have similar potencies in the nanomolar range for Y1. No obvious response to the three peptides was detected for Y2. Synteny analysis supports identification of the previously cloned receptor as Y4. No additional NPY receptor genes could be identified in the presently available lamprey genome assemblies. Thus, four NPY-family receptors have been identified in lampreys, orthologs of the same subtypes as in humans (Y1, Y2, Y4 and Y5), whereas many other vertebrate lineages have retained additional ancestral subtypes.

    National Category
    Evolutionary Biology Endocrinology and Diabetes
    Identifiers
    urn:nbn:se:uu:diva-233437 (URN)10.1016/j.ygcen.2015.08.005 (DOI)000366438000012 ()26255155 (PubMedID)
    Funder
    Swedish Research Council
    Available from: 2014-10-06 Created: 2014-10-05 Last updated: 2019-01-03Bibliographically approved
    3. Characterization of the neuropeptide Y system in the frog Silurana tropicalis (Pipidae): three peptides and six receptor subtypes
    Open this publication in new window or tab >>Characterization of the neuropeptide Y system in the frog Silurana tropicalis (Pipidae): three peptides and six receptor subtypes
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    2012 (English)In: General and Comparative Endocrinology, ISSN 0016-6480, E-ISSN 1095-6840, Vol. 177, no 3, p. 322-331Article in journal (Refereed) Published
    Abstract [en]

    Neuropeptide Y and its related peptides PYY and PP (pancreatic polypeptide) are involved in feeding behavior, regulation of the pituitary and the gastrointestinal tract, and numerous other functions. The peptides act on a family of G-protein coupled receptors with 4-7 members in jawed vertebrates. We describe here the NPY system of the Western clawed frog Silurana (Xenopus) tropicalis. Three peptides, NPY, PYY and PP, were identified together with six receptors, namely subtypes Y1, Y2, Y4, Y5, Y7 and Y8. Thus, this frog has all but one of the ancestral seven gnathostome NPY-family receptors, in contrast to mammals which have lost 2-3 of the receptors. Expression levels of mRNA for the peptide and receptor genes were analyzed in a panel of 19 frog tissues using reverse transcriptase quantitative PCR. The peptide mRNAs had broad distribution with highest expression in skin, blood and small intestine. NPY mRNA was present in the three brain regions investigated, but PYY and PP mRNAs were not detectable in any of these. All receptor mRNAs had similar expression profiles with high expression in skin, blood, muscle and heart. Three of the receptors, Y5, Y7 and Y8, could be functionally expressed in HEK-293 cells and characterized with binding studies using the three frog peptides. PYY had the highest affinity for all three receptors (K(i) 0.042-0.34 nM). Also NPY and PP bound to the Y8 receptor with high affinity (0.14 and 0.50 nM). The low affinity of NPY for the Y5 receptor (100-fold lower than PYY) differs from mammals and chicken. This may suggest a less important role of NPY on Y5 in appetite stimulation in the frog compared with amniotes. In conclusion, our characterization of the NPY system in S. tropicalis with its six receptors demonstrates not only greater complexity than in mammals but also some interesting differences in ligand-receptor preferences.

    Keywords
    NPY, PYY, G-protein-coupled receptor, Silurana tropicalis, evolution
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-129517 (URN)10.1016/j.ygcen.2012.04.027 (DOI)000306390100005 ()22565163 (PubMedID)
    Note

    Erratum in General and Comparative Endocrinology 2015:215, doi:10.1016/j.ygcen.2014.11.014.

    Available from: 2010-08-18 Created: 2010-08-18 Last updated: 2019-01-03Bibliographically approved
    4. Interactions of zebrafish peptide YYb with the neuropeptide Y-family receptors Y4, Y7, Y8a, and Y8b
    Open this publication in new window or tab >>Interactions of zebrafish peptide YYb with the neuropeptide Y-family receptors Y4, Y7, Y8a, and Y8b
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    2013 (English)In: Frontiers in Neuroscience, ISSN 1662-4548, E-ISSN 1662-453X, Vol. 7, article id 29Article in journal (Refereed) Published
    Abstract [en]

    The neuropeptide Y (NPY) system influences numerous physiological functions including feeding behavior, endocrine regulation, and cardiovascular regulation. In jawed vertebrates it consists of 3-4 peptides and 4-7 receptors. Teleost fishes have unique duplicates of NPY and PYY as well as the Y8 receptor. In the zebrafish, the NPY system consists of the peptides NPYa, PYYa, and PYYb (NPYb appears to have been lost) and at least seven NPY receptors: Y1, Y2, Y2-2, Y4, Y7, Y8a, and Y8b. Previously PYYb binding has been reported for Y2 and Y2-2. To search for peptide-receptor preferences, we have investigated PYYb binding to four of the remaining receptors and compared with NPYa and PYYa. Taken together, the most striking observations are that PYYa displays reduced affinity for Y2 (3 nM) compared to the other peptides and receptors and that all three peptides have higher affinity for Y4 (0.028-0.034 nM) than for the other five receptors. The strongest peptide preference by any receptor selectivity is the one previously reported for PYYb by the Y2 receptor, as compared to NPY and PYYa. These affinity differences may be helpful to elucidate specific details of peptide-receptor interactions. Also, we have investigated the level of mRNA expression in different organs using qPCR. All peptides and receptors have higher expression in heart, kidney, and brain. These quantitative aspects on receptor affinities and mRNA distribution help provide a more complete picture of the NPY system.

    Keywords
    Evolution, genome duplication, NPY, elephant shark
    National Category
    Natural Sciences Neurology
    Research subject
    Neuroscience
    Identifiers
    urn:nbn:se:uu:diva-205599 (URN)10.3389/fnins.2013.00029 (DOI)000346567300029 ()23508731 (PubMedID)
    Funder
    Swedish Research Council
    Available from: 2013-08-20 Created: 2013-08-20 Last updated: 2019-01-03Bibliographically approved
    5. Characterization of peptide QRFP (26RFa) and its receptor from amphioxus, Branchiostoma floridae
    Open this publication in new window or tab >>Characterization of peptide QRFP (26RFa) and its receptor from amphioxus, Branchiostoma floridae
    Show others...
    2015 (English)In: General and Comparative Endocrinology, ISSN 0016-6480, E-ISSN 1095-6840, Vol. 210, p. 107-113Article in journal (Refereed) Published
    Abstract [en]

    A peptide ending with RFamide (Arg-Phe-amide) was discovered independently by three different laboratories in 2003 and named 26RFa or QRFP. In mammals, a longer version of the peptide, 43 amino acids, was identified and found to bind to the orphan G protein-coupled receptor GPR103. We searched the genome database of Branchiostoma floridae (Bfl) for receptor sequences related to those that bind peptides ending with RFa or RYa (including receptors for NPFF, PRLH, GnIH, and NPY). One receptor clustered in phylogenetic analyses with mammalian QRFP receptors. The gene has 3 introns in Bfl and 5 in human, but all intron positions differ, implying that the introns were inserted independently. A QRFP-like peptide consisting of 25 amino acids and ending with RFa was identified in the amphioxus genome. Eight of the ten last amino acids are identical between Bfl and human. The prepro-QRFP gene in Bfl has one intron in the propeptide whereas the human gene lacks introns. The Bfl QRFP peptide was synthesized and the receptor was functionally expressed in human cells. The response was measured as inositol phosphate (IP) turnover. The Bfl QRFP peptide was found to potently stimulate the receptor's ability to induce IP turnover with an EC50 of 0.28nM. Also the human QRFP peptides with 26 and 43 amino acids were found to stimulate the receptor (1.9 and 5.1nM, respectively). Human QRFP with 26 amino acids without the carboxyterminal amide had dramatically lower potency at 1.3μM. Thus, we have identified an amphioxus QRFP-related peptide and a corresponding receptor and shown that they interact to give a functional response.

    Keywords
    Neuropeptide, receptor, evolution
    National Category
    Neurosciences
    Research subject
    Evolutionary Genetics; Neuroscience
    Identifiers
    urn:nbn:se:uu:diva-240039 (URN)10.1016/j.ygcen.2014.10.010 (DOI)000346886400012 ()25449662 (PubMedID)
    Available from: 2015-01-05 Created: 2015-01-05 Last updated: 2019-01-03Bibliographically approved
    6. Unexpected multiplicity of QRFP receptors in early vertebrate evolution
    Open this publication in new window or tab >>Unexpected multiplicity of QRFP receptors in early vertebrate evolution
    2014 (English)In: Frontiers in Neuroscience, ISSN 1662-4548, E-ISSN 1662-453X, Vol. 8, p. 337-Article in journal (Refereed) Published
    Abstract [en]

    The neuropeptide QRFP, also called 26RFa, and its G protein-coupled receptor GPR103 have been identified in all vertebrates investigated. In mammals, this peptide-receptor pair has been found to have several effects including stimulation of appetite. Recently, we reported that a QRFP peptide is present in amphioxus, Branchiostoma floridae, and we also identified a QRFP receptor (QRFPR) that mediates a functional response to sub-nanomolar concentrations of the amphioxus peptide as well as short and long human QRFP (Xu et al., submitted). Because the ancestral vertebrate underwent two tetraploidizations, it might be expected that duplicates of the QRFP gene and its receptor gene may exist. Indeed, we report here the identification of multiple vertebrate QRFPR genes. Three QRFPR genes are present in the coelacanth Latimeria chalumnae, representing an early diverging sarcopterygian lineage. Three QRFPR genes are present in the basal actinopterygian fish, the spotted gar. Phylogenetic and chromosomal analyses show that only two of these receptor genes are orthologous between the two species, thus demonstrating a total of four distinct vertebrate genes. Three of the QRFPR genes resulted from the early vertebrate tetraploidizations and were copied along with syntenic neuropeptide Y receptor genes. The fourth QRFPR gene may be an even older and distinct lineage. Because mammals and birds have only a single QRFPR gene, this means that three genes have been lost in these lineages, and at least one of these was lost independently in mammals and birds because it is still present in a turtle. In conclusion, these results show that the QRFP system gained considerable complexity in the early stages of vertebrate evolution and still maintains much of this in some lineages, and that it has been secondarily reduced in mammals.

    Keywords
    Neuropeptide, receptor, evolution
    National Category
    Natural Sciences
    Research subject
    Neuroscience; Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-240037 (URN)10.3389/fnins.2014.00337 (DOI)000346532900001 ()25386115 (PubMedID)
    Available from: 2015-01-05 Created: 2015-01-05 Last updated: 2019-01-03Bibliographically approved
    7. Mutagenesis and Computational Modeling of Human G‑Protein-Coupled Receptor Y2 for Neuropeptide Y and Peptide YY
    Open this publication in new window or tab >>Mutagenesis and Computational Modeling of Human G‑Protein-Coupled Receptor Y2 for Neuropeptide Y and Peptide YY
    Show others...
    2013 (English)In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 52, no 45, p. 7987-7998Article in journal (Refereed) Published
    Abstract [en]

    Neuropeptide Y and peptide YY receptor type 2 (Y2) is involved in appetite regulation and several other physiological processes. We have investigated the structure of the human Y2 receptor. Computational modeling of receptor–agonist interactions was used as a guide to design a series of receptor mutants, followed by binding assays using full-length and truncated peptide agonists and the Y2-specific antagonist BIIE0246. Our model suggested a hydrogen bond network among highly conserved residues Thr2.61, Gln3.32, and His7.39, which could play roles in ligand binding and/or receptor structure. In addition, the C-terminus of the peptide could make contact with residues Tyr5.38 and Leu6.51. Mutagenesis of all these positions, followed by binding assays, provides experimental support for our computational model: most of the mutants for the residues forming the proposed hydrogen bond network displayed reduced peptide agonist affinities as well as reduced hPYY3-36 potency in a functional assay. The Ala and Leu mutants of Gln3.32 and His7.39 disrupted membrane expression of the receptor. Combined with the modeling, the experimental results support roles for these hydrogen bond network residues in peptide binding as well as receptor architecture. The reduced agonist affinity for mutants of Tyr5.38 and Leu6.51 supports their role in a binding pocket surrounding the invariant tyrosine at position 36 of the peptide ligands. The results for antagonist BIIE0246 suggest several differences in interactions compared to those of the peptides. Our results lead to a new structural model for NPY family receptors and peptide binding.

    Place, publisher, year, edition, pages
    American Chemical Society (ACS), 2013
    National Category
    Natural Sciences Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-154994 (URN)10.1021/bi400830c (DOI)000330017700012 ()
    Available from: 2011-08-04 Created: 2011-06-14 Last updated: 2019-01-03Bibliographically approved
    8. Detecting ligand interactions with G protein-coupled receptors in real-time on living cells
    Open this publication in new window or tab >>Detecting ligand interactions with G protein-coupled receptors in real-time on living cells
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    2013 (English)In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 441, no 4, p. 820-824Article in journal (Refereed) Published
    Abstract [en]

    G protein-coupled receptors (GPCRs) are a large group of receptors of great biological and clinical relevance. Despite this, the tools for a detailed analysis of ligand-GPCR interactions are limited. The aim of this paper was to demonstrate how ligand binding to GPCRs can be followed in real-time on living cells. This was conducted using two model systems, the radiolabeled porcine peptide YY (pPYY) interacting with transfected human Y2 receptor (hY2R) and the bombesin antagonist RM26 binding to the naturally expressed gastrin-releasing peptide receptor (GRPR). By following the interaction over time, the affinity and kinetic properties such as association and dissociation rate were obtained. Additionally, data were analyzed using the Interaction Map method, which can evaluate a real-time binding curve and present the number of parallel interactions contributing to the curve. It was found that pPYY binds very slowly with an estimated time to equilibrium of approximately 12 h. This may be problematic in standard end-point assays where equilibrium is required. The RM26 binding showed signs of heterogeneity, observed as two parallel interactions with unique kinetic properties. In conclusion, measuring binding in real-time using living cells opens up for a better understanding of ligand interactions with GPCRs.

    Keywords
    GPCR, Real-time, LigandTracer, Interaction Map, Kinetics, Heterogeneity
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-215943 (URN)10.1016/j.bbrc.2013.10.149 (DOI)000328434800022 ()
    Note

    De två första författarna delar första författarskapet.

    Available from: 2014-01-17 Created: 2014-01-17 Last updated: 2019-01-03Bibliographically approved
  • 1174.
    Xu, Bo
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Pharmacology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lagman, David
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Pharmacology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sundström, Görel
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Larhammar, Dan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Pharmacology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Neuropeptide Y family receptors Y1 and Y2 from sea lamprey, Petromyzon marinus: cloning and pharmacological characterization2015In: General and Comparative Endocrinology, ISSN 0016-6480, E-ISSN 1095-6840, Vol. 222, p. 106-115Article in journal (Other academic)
    Abstract [en]

    The vertebrate gene family for neuropeptide Y (NPY) receptors expanded by duplication of the chromosome carrying the ancestral Y1–Y2–Y5 gene triplet. After loss of some duplicates, the ancestral jawed vertebrate had seven receptor subtypes forming the Y1 (including Y1, Y4, Y6, Y8), Y2 (including Y2, Y7) and Y5 (only Y5) subfamilies. Lampreys are considered to have experienced the same chromosome duplications as gnathostomes and should also be expected to have multiple receptor genes. However, previously only a Y4-like and a Y5 receptor have been cloned and characterized. Here we report the cloning and characterization of two additional receptors from the sea lamprey Petromyzon marinus. Sequence phylogeny alone could not with certainty assign their identity, but based on synteny comparisons of P. marinus and the Arctic lamprey, Lethenteron camtschaticum, with jawed vertebrates, the two receptors most likely are Y1 and Y2. Both receptors were expressed in human HEK293 cells and inositol phosphate assays were performed to determine the response to the three native lamprey peptides NPY, PYY and PMY. The three peptides have similar potencies in the nanomolar range for Y1. No obvious response to the three peptides was detected for Y2. Synteny analysis supports identification of the previously cloned receptor as Y4. No additional NPY receptor genes could be identified in the presently available lamprey genome assemblies. Thus, four NPY-family receptors have been identified in lampreys, orthologs of the same subtypes as in humans (Y1, Y2, Y4 and Y5), whereas many other vertebrate lineages have retained additional ancestral subtypes.

  • 1175.
    Xu, Feifei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Comparative Genomics in Diplomonads: Lifestyle Variations Revealed at Genetic Level2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    As sequencing technologies advance genome studies are becoming a basic tool for studying an organism, and with more genomes available comparative genomics is maturing into a powerful tool for biological research. This thesis demonstrates the strength of a comparative genomics approach on a group of understudied eukaryotes, the diplomonads.

    Diplomonads are a group of single cell eukaryotic flagellates living in oxygen-poor environments. Most diplomonads are intestinal parasites, like the well-studied human parasite Giardia intestinalis. There are seven different G. intestinalis assemblages (genotypes) affecting different hosts, and it’s under debate whether these are one species. A genome-wide study of three G. intestinalis genomes from different assemblages reveals little inter-assemblage sexual recombination, supporting that the different G. intestinalis assemblages are genetically isolated and thus different species.

    A genomic comparison between the fish parasite S. salmonicida and G. intestinalis reveals genetic differences reflecting differences in their parasitic lifestyles. There is a tighter transcriptional regulation and a larger metabolic reservoir in S. salmonicida, likely adaptations to the fluctuating environments it encounters during its systemic infection compared to G. intestinalis which is a strict intestinal parasite.

    The S. salmonicida genome analysis also discovers genes involved in energy metabolism. Some of these are experimentally shown to localize to mitochondrion-related organelles in S. salmonicida, indicating that they possess energy-producing organelles that should be classified as hydrogenosomes, as opposed to the mitosomes in G. intestinalis.

    A transcriptome analysis of the free-living Trepomonas is compared with genomic data from the two parasitic diplomonads. The majority of the genes associated with a free-living lifestyle, like phagocytosis and a larger metabolic capacity, are of prokaryotic origin. This suggests that the ancestor of the free-living diplomonad was likely host-associated and that the free-living lifestyle is a secondary adaptation acquired through horizontal gene transfers. 

    In conclusion, this thesis uses different comparative genomics approaches to broaden the knowledge on diplomonad diversity and to provide more insight into how the lifestyle differences are reflected on the genetic level. The bioinformatics pipelines and expertise gained in these studies will be useful in other projects in diplomonads and other organismal groups.

    List of papers
    1. Genome-Wide Analyses of Recombination Suggest That Giardia intestinalis Assemblages Represent Different Species
    Open this publication in new window or tab >>Genome-Wide Analyses of Recombination Suggest That Giardia intestinalis Assemblages Represent Different Species
    2012 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 29, no 10, p. 2895-2898Article in journal (Refereed) Published
    Abstract [en]

    Giardia intestinalis is a major cause of waterborne enteric disease in humans. The species is divided into eight assemblages suggested to represent separate Giardia species based on host specificities and the genetic divergence of marker genes. We have investigated whether genome-wide recombination occurs between assemblages using the three available G. intestinalis genomes. First, the relative nonsynonymous substitution rates of the homologs were compared for 4,009 positional homologs. The vast majority of these comparisons indicate genetic isolation without interassemblage recombinations. Only a region of 6 kbp suggests genetic exchange between assemblages A and E, followed by gene conversion events. Second, recombination-detecting software fails to identify within-gene recombination between the different assemblages for most of the homologs. Our results indicate very low frequency of recombination between the syntenic core genes, suggesting that G. intestinalis assemblages are genetically isolated lineages and thus should be viewed as separated Giardia species.

    National Category
    Natural Sciences Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-175947 (URN)10.1093/molbev/mss107 (DOI)000309927900003 ()22474166 (PubMedID)
    Available from: 2012-06-14 Created: 2012-06-14 Last updated: 2017-12-07Bibliographically approved
    2. Hydrogenosomes in the diplomonad Spironucleus salmonicida
    Open this publication in new window or tab >>Hydrogenosomes in the diplomonad Spironucleus salmonicida
    Show others...
    2013 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, p. 2493-Article in journal (Refereed) Published
    Abstract [en]

    Acquisition of the mitochondrion is a key event in the evolution of the eukaryotic cell, but diversification of the organelle has occurred during eukaryotic evolution. One example of such mitochondria-related organelles (MROs) are hydrogenosomes, which produce ATP by substrate- level phosphorylation with hydrogen as a byproduct. The diplomonad parasite Giardia intestinalis harbours mitosomes, another type of MRO. Here we identify MROs in the salmon parasite Spironucleus salmonicida with similar protein import and Fe-S cluster assembly machineries as in Giardia mitosomes. We find that hydrogen production is prevalent in the diplomonad genus Spironucleus, and that S. salmonicida MROs contain enzymes characteristic of hydrogenosomes. Evolutionary analyses of known hydrogenosomal components indicate their presence in the diplomonad ancestor, and subsequent loss in Giardia. Our results suggest that hydrogenosomes are metabolic adaptations predating the split between parabasalids and diplomonads, which is deeper than the split between animals and fungi in the eukaryotic tree.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-210741 (URN)10.1038/ncomms3493 (DOI)000325534300002 ()
    Available from: 2013-11-14 Created: 2013-11-14 Last updated: 2017-12-06Bibliographically approved
    3. The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments
    Open this publication in new window or tab >>The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments
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    2014 (English)In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 10, no 2, p. e1004053-Article in journal (Refereed) Published
    Abstract [en]

    Spironucleus salmonicida causes systemic infections in salmonid fish. It belongs to the group diplomonads, binucleated heterotrophic flagellates adapted to micro-aerobic environments. Recently we identified energy-producing hydrogenosomes in S. salmonicida. Here we present a genome analysis of the fish parasite with a focus on the comparison to the more studied diplomonad Giardia intestinalis. We annotated 8067 protein coding genes in the ∼12.9 Mbp S. salmonicida genome. Unlike G. intestinalis, promoter-like motifs were found upstream of genes which are correlated with gene expression, suggesting a more elaborate transcriptional regulation. S. salmonicida can utilise more carbohydrates as energy sources, has an extended amino acid and sulfur metabolism, and more enzymes involved in scavenging of reactive oxygen species compared to G. intestinalis. Both genomes have large families of cysteine-rich membrane proteins. A cluster analysis indicated large divergence of these families in the two diplomonads. Nevertheless, one of S. salmonicida cysteine-rich proteins was localised to the plasma membrane similar to G. intestinalis variant-surface proteins. We identified S. salmonicida homologs to cyst wall proteins and showed that one of these is functional when expressed in Giardia. This suggests that the fish parasite is transmitted as a cyst between hosts. The extended metabolic repertoire and more extensive gene regulation compared to G. intestinalis suggest that the fish parasite is more adapted to cope with environmental fluctuations. Our genome analyses indicate that S. salmonicida is a well-adapted pathogen that can colonize different sites in the host.

    National Category
    Microbiology Genetics
    Identifiers
    urn:nbn:se:uu:diva-224545 (URN)10.1371/journal.pgen.1004053 (DOI)000332021500041 ()24516394 (PubMedID)
    Available from: 2014-05-14 Created: 2014-05-14 Last updated: 2019-03-19Bibliographically approved
    4. On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp PC1
    Open this publication in new window or tab >>On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp PC1
    Show others...
    2016 (English)In: BMC Biology, ISSN 1741-7007, E-ISSN 1741-7007, Vol. 14, article id 62Article in journal (Refereed) Published
    Abstract [en]

    Background: It is generally thought that the evolutionary transition to parasitism is irreversible because it is associated with the loss of functions needed for a free-living lifestyle. Nevertheless, free-living taxa are sometimes nested within parasite clades in phylogenetic trees, which could indicate that they are secondarily free-living. Herein, we test this hypothesis by studying the genomic basis for evolutionary transitions between lifestyles in diplomonads, a group of anaerobic eukaryotes. Most described diplomonads are intestinal parasites or commensals of various animals, but there are also free-living diplomonads found in oxygen-poor environments such as marine and freshwater sediments. All these nest well within groups of parasitic diplomonads in phylogenetic trees, suggesting that they could be secondarily free-living. Results: We present a transcriptome study of Trepomonas sp. PC1, a diplomonad isolated from marine sediment. Analysis of the metabolic genes revealed a number of proteins involved in degradation of the bacterial membrane and cell wall, as well as an extended set of enzymes involved in carbohydrate degradation and nucleotide metabolism. Phylogenetic analyses showed that most of the differences in metabolic capacity between free-living Trepomonas and the parasitic diplomonads are due to recent acquisitions of bacterial genes via gene transfer. Interestingly, one of the acquired genes encodes a ribonucleotide reductase, which frees Trepomonas from the need to scavenge deoxyribonucleosides. The transcriptome included a gene encoding squalene-tetrahymanol cyclase. This enzyme synthesizes the sterol substitute tetrahymanol in the absence of oxygen, potentially allowing Trepomonas to thrive under anaerobic conditions as a free-living bacterivore, without depending on sterols from other eukaryotes. Conclusions: Our findings are consistent with the phylogenetic evidence that the last common ancestor of diplomonads was dependent on a host and that Trepomonas has adapted secondarily to a free-living lifestyle. We believe that similar studies of other groups where free-living taxa are nested within parasites could reveal more examples of secondarily free-living eukaryotes.

    Keywords
    Free-living; Parasite; Diplomonad; Dollo's law; Reversibility; Trepomonas; Horizontal gene transfer; Ribonucleotide reductase
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-251638 (URN)10.1186/s12915-016-0284-z (DOI)000381184600002 ()27480115 (PubMedID)
    Funder
    Swedish Research Council Formas, 2010-899Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish Research Council
    Note

    Correction in: BMC Biology, vol. 14, article number 77

    DOI: 10.1186/s12915-016-0302-1

    Available from: 2015-04-23 Created: 2015-04-22 Last updated: 2017-12-04Bibliographically approved
  • 1176.
    Xu, Feifei
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Jerlström-Hultqvist, Jon
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kolisko, Martin
    Dalhousie Univ, Dept Biol, Halifax, NS, Canada; Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS, Canada; Univ British Columbia, Dept Bot, Vancouver, BC, Canada.
    Simpson, Alastair G. B.
    Dalhousie Univ, Dept Biol, Halifax, NS, Canada; Canadian Inst Adv Res, Integrated Microbial Biodivers Program, Toronto, ON, Canada.
    Roger, Andrew J.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS, Canada; anadian Inst Adv Res, Integrated Microbial Biodivers Program, Toronto, ON, Canada.
    Svärd, Staffan G.
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Andersson, Jan O.
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp PC12016In: BMC Biology, ISSN 1741-7007, E-ISSN 1741-7007, Vol. 14, article id 62Article in journal (Refereed)
    Abstract [en]

    Background: It is generally thought that the evolutionary transition to parasitism is irreversible because it is associated with the loss of functions needed for a free-living lifestyle. Nevertheless, free-living taxa are sometimes nested within parasite clades in phylogenetic trees, which could indicate that they are secondarily free-living. Herein, we test this hypothesis by studying the genomic basis for evolutionary transitions between lifestyles in diplomonads, a group of anaerobic eukaryotes. Most described diplomonads are intestinal parasites or commensals of various animals, but there are also free-living diplomonads found in oxygen-poor environments such as marine and freshwater sediments. All these nest well within groups of parasitic diplomonads in phylogenetic trees, suggesting that they could be secondarily free-living. Results: We present a transcriptome study of Trepomonas sp. PC1, a diplomonad isolated from marine sediment. Analysis of the metabolic genes revealed a number of proteins involved in degradation of the bacterial membrane and cell wall, as well as an extended set of enzymes involved in carbohydrate degradation and nucleotide metabolism. Phylogenetic analyses showed that most of the differences in metabolic capacity between free-living Trepomonas and the parasitic diplomonads are due to recent acquisitions of bacterial genes via gene transfer. Interestingly, one of the acquired genes encodes a ribonucleotide reductase, which frees Trepomonas from the need to scavenge deoxyribonucleosides. The transcriptome included a gene encoding squalene-tetrahymanol cyclase. This enzyme synthesizes the sterol substitute tetrahymanol in the absence of oxygen, potentially allowing Trepomonas to thrive under anaerobic conditions as a free-living bacterivore, without depending on sterols from other eukaryotes. Conclusions: Our findings are consistent with the phylogenetic evidence that the last common ancestor of diplomonads was dependent on a host and that Trepomonas has adapted secondarily to a free-living lifestyle. We believe that similar studies of other groups where free-living taxa are nested within parasites could reveal more examples of secondarily free-living eukaryotes.

  • 1177.
    Xu, Luohao
    et al.
    Zhejiang Univ, MOE Lab Biosyst Homeostasis & Protect, Life Sci Inst, Hangzhou, Zhejiang, Peoples R China;Univ Vienna, Dept Mol Evolut & Dev, Vienna, Austria.
    Auer, Gabriel
    Univ Vienna, Dept Mol Evolut & Dev, Vienna, Austria.
    Peona, Valentina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Deng, Yuan
    BGI Shenzhen, China Natl Genebank, Shenzhen, Peoples R China;BGI Shenzhen, Shenzhen, Peoples R China.
    Feng, Shaohong
    BGI Shenzhen, China Natl Genebank, Shenzhen, Peoples R China;BGI Shenzhen, Shenzhen, Peoples R China.
    Zhang, Guojie
    BGI Shenzhen, China Natl Genebank, Shenzhen, Peoples R China;Chinese Acad Sci, State Key Lab Genet Resources & Evolut, Kunming Inst Zool, Kunming, Yunnan, Peoples R China;Univ Copenhagen, Sect Ecol & Evolut, Dept Biol, Copenhagen, Denmark.
    Blom, Mozes P. K.
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden;Leibniz Inst Evolut & Biodiversitatsforsch, Museum Naturkunde, Berlin, Germany.
    Christidis, Les
    Southern Cross Univ, Natl Marin Sci Ctr, Coffs Harbour, NSW, Australia;Univ Melbourne, Sch Biosci, Victoria, Australia.
    Prost, Stefan
    Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA;Senckenberg, LOEWE Ctr Translat Biodivers Genom, Frankfurt, Germany.
    Irestedt, Martin
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden.
    Zhou, Qi
    Zhejiang Univ, MOE Lab Biosyst Homeostasis & Protect, Life Sci Inst, Hangzhou, Zhejiang, Peoples R China;Univ Vienna, Dept Mol Evolut & Dev, Vienna, Austria.
    Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds2019In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 3, no 5, p. 834-844Article in journal (Refereed)
    Abstract [en]

    Songbirds have a species number close to that of mammals and are classic models for studying speciation and sexual selection. Sex chromosomes are hotspots of both processes, yet their evolutionary history in songbirds remains unclear. We characterized genomes of 11 songbird species, with 5 genomes of bird-of-paradise species. We conclude that songbird sex chromosomes have undergone four periods of recombination suppression before species radiation, producing a gradient of pairwise sequence divergence termed 'evolutionary strata'. The latest stratum was probably due to a songbird-specific burst of retrotransposon CR1-E1 elements at its boundary, instead of the chromosome inversion generally assumed for suppressing sex-linked recombination. The formation of evolutionary strata has reshaped the genomic architecture of both sex chromosomes. We find stepwise variations of Z-linked inversions, repeat and guanine-cytosine (GC) contents, as well as W-linked gene loss rate associated with the age of strata. A few W-linked genes have been preserved for their essential functions, indicated by higher and broader expression of lizard orthologues compared with those of other sex-linked genes. We also find a different degree of accelerated evolution of Z-linked genes versus autosomal genes among species, potentially reflecting diversified intensity of sexual selection. Our results uncover the dynamic evolutionary history of songbird sex chromosomes and provide insights into the mechanisms of recombination suppression.

  • 1178.
    Xu, Wenbo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Cut-and-paste transposable elements in the arbuscular mycorrhizal fungi Claroideoglomus claroideum2019Independent thesis Advanced level (degree of Master (Two Years)), 80 credits / 120 HE creditsStudent thesis
    Abstract [en]

    Arbuscular mycorrhizal (AM) fungi are important symbionts to most of the terrestrial plants. Recent genome sequencing projects revealed that many AM fungi have repetitive genetic elements in their genomes and among these repetitive genetic elements, cut-and-paste DNA transposable elements were very prevalent. For example, in Rhizophagus irregularis, up to 21% of the genome assembly content was associated with cut-and-paste DNA transposable elements. In Diversispora epigaea, up to 23% of the genome content can also be attributed to cut-and-paste DNA transposable elements. While cut-and-paste DNA transposable elements are very abundant in AM fungi, detailed studies on these repetitive elements have been lacking. In this study, we revealed the diversity of cut-and-paste DNA transposable elements in Claroideoglomus claroideum and identified many potentially autonomous transposable elements in the genome assembly of C. claroideum. The evolutionary relationship between the DNA transposons we identified and the established sequences in public databases were also investigated.

  • 1179.
    Yazdi, Homa P.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Bolivar, Paulina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Mugal, Carina F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Variation in the Z Chromosome to Autosomes Ratio of Genetic Diversity across Birds and its Relationship to the Fast-Z effectManuscript (preprint) (Other academic)
  • 1180.
    Yazdi, Homa P.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Kawakami, Takeshi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Unneberg, Per
    Schou, Mads F.
    Cloete, Schalk W. P.
    Cornwallis, Charlie K.
    Patterns of Nucleotide Diversity and Linkage Disequilibrium along the Ostrich Pseudoautosomal RegionManuscript (preprint) (Other academic)
  • 1181.
    Yazdi, Homa Papoli
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    The evolution of sex chromosomes and sex-linked sequences in birds2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Identifying the processes involved in the evolution of suppressed recombination between sex chromosomes and understanding their consequences for the evolutionary dynamics of sex-linked loci have been major topics of research during the last century. In this thesis, I used the avian ZW system, where females are the heterogametic sex, to investigate the underlying processes in sex chromosome evolution in birds. I identified the gametologous genes between the largely recombining Z and W chromosomes of ostrich and dated the timing of the cessation of recombination to prior to the split of modern birds. I then constructed a genetic map of the ostrich Z chromosome and corrected its assembly in order to obtain the ancestral organization of the Z chromosome in a basal clade of birds. By analyzing the inversion events across the avian phylogeny, I concluded that a combination of Z- and possibly W-linked inversions might have been responsible for the evolution of suppressed recombination in avian sex chromosomes. To understand the determinants of levels of genetic diversity on Z chromosome compared to autosomes, I calculated Z to autosome (Z:A) genetic diversity across 32 avian species. This revealed a broad range of Z:A genetic diversity, between 0.278 – 1.27. Lineage-specific estimates of the nonsynonymous to synonymous substitution rate ratio (dN:dS) for autosomal and Z-linked genes further revealed a Fast-Z effect in the majority of birds. The lack of a significant correlation between Z:A dN:dS and Z:A genetic diversity indicated that genetic drift might not be sufficient to explain faster evolution of Z-linked genes, suggesting that positive selection might also contribute to the observed values. Finally, I calculated genetic diversity and linkage disequilibrium (LD) along the pseudoautosomal region (PAR) of the Z chromosome using population genomics data of ostrich. In contrast to theoretical expectation, levels of diversity on the PAR were not significantly higher close to the sex-determining region (SDR) compared to autosomal values. Additionally, I observed a lower level of LD on the PAR compared to the average for the Z chromosome and no significant level of LD across the PAR boundary was detected, indicating recombination allows the boundary-proximal region of PAR to behave independently of SDR. Considered together with a higher level of recombination rate in females in the proximity of the SDR, this observation might help explain the maintenance of a long PAR in ostriches and other ratites. Altogether, the results of this thesis make a modest contribution to our understanding of sex chromosome evolution in birds.

    List of papers
    1. Old but Not (So) Degenerated-Slow Evolution of Largely Homomorphic Sex Chromosomes in Ratites
    Open this publication in new window or tab >>Old but Not (So) Degenerated-Slow Evolution of Largely Homomorphic Sex Chromosomes in Ratites
    2014 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 31, no 6, p. 1444-1453Article in journal (Refereed) Published
    Abstract [en]

    Degeneration of the nonrecombining chromosome is a common feature of sex chromosome evolution, readily evident by the presence of a pair of largely heteromorphic chromosomes, like in eutherian mammals and birds. However, in ratites (order Palaeognathae, including, e.g., ostrich), the Z and W chromosomes are similar in size and largely undifferentiated, despite avian sex chromosome evolution was initiated > 130 Ma. To better understand what may limit sex chromosome evolution, we performed ostrich transcriptome sequencing and studied genes from the nonrecombining region of the W chromosome. Fourteen gametologous gene pairs present on the W chromosome and Z chromosome were identified, with synonymous sequence divergence of 0.027-0.177. The location of these genes on the Z chromosome was consistent with a sequential increase in divergence, starting 110-157 and ending 24-30 Ma. On the basis of the occurrence of Z-linked genes hemizygous in females, we estimate that about one-third of the Z chromosome does not recombine with the W chromosome in female meiosis. Pairwise d(N)/d(S) between gametologs decreased with age, suggesting strong evolutionary constraint in old gametologs. Lineage-specific d(N)/d(S) was consistently higher in W-linked genes, in accordance with the lower efficacy of selection expected in nonrecombining chromosomes. A higher ratio of GC > AT:AT > GC substitutions in W-linked genes supports a role for GC-biased gene conversion in differentially driving base composition on the two sex chromosomes. A male-to-female (M:F) expression ratio of close to one for recombining genes and close to two for Z-linked genes lacking a W copy show that dosage compensation is essentially absent. Some gametologous genes have retained active expression of the W copy in females (giving a M:F ratio of 1 for the gametologous gene pair), whereas for others W expression has become severely reduced resulting in a M:F ratio of close to 2. These observations resemble the patterns of sex chromosome evolution seen in other avian and mammalian lineages, suggesting similar underlying evolutionary processes, although the rate of sex chromosome differentiation has been atypically low. Lack of dosage compensation may be a factor hindering sex chromosome evolution in this lineage.

    Keywords
    Z chromosome, W chromosome, evolutionary strata, gametologs, nonrecombining chromosome, biased gene conversion
    National Category
    Biochemistry and Molecular Biology Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-228463 (URN)10.1093/molbev/msu101 (DOI)000337067400013 ()
    Available from: 2014-07-16 Created: 2014-07-15 Last updated: 2019-03-25Bibliographically approved
    2. A Genetic Map of Ostrich Z Chromosome and the Role of Inversions in Avian Sex Chromosome Evolution
    Open this publication in new window or tab >>A Genetic Map of Ostrich Z Chromosome and the Role of Inversions in Avian Sex Chromosome Evolution
    2018 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 10, no 8, p. 2049-2060Article in journal (Refereed) Published
    Abstract [en]

    Recombination arrest is a necessary step for the evolution of distinct sex chromosomes. Structural changes, such as inversions, may represent the mechanistic basis for recombination suppression and comparisons of the structural organization of chromosomes as given by chromosome-level assemblies offer the possibility to infer inversions across species at some detail. In birds, deduction of the process of sex chromosome evolution has been hampered by the lack of a validated chromosome-level assembly from a representative of one of the two basal clades of modern birds, Paleognathae. We therefore developed a high-density genetic linkage map of the ostrich Z chromosome and used this to correct an existing assembly, including correction of a large chimeric superscaffold and the order and orientation of other superscaffolds. We identified the pseudoautosomal region as a 52 Mb segment (approximate to 60% of the Z chromosome) where recombination occurred in both sexes. By comparing the order and location of genes on the ostrich Z chromosome with that of six bird species from the other major Glade of birds (Neognathae), and of reptilian outgroup species, 25 Z-linked inversions were inferred in the avian lineages. We defined Z chromosome organization in an early avian ancestor and identified inversions spanning the candidate sex-determining DMRT1 gene in this ancestor, which could potentially have triggered the onset of avian sex chromosome evolution. We conclude that avian sex chromosome evolution has been characterized by a complex process of probably both Z-linked and W-linked inversions (and/or other processes). This study illustrates the need for validated chromosome-level assemblies for inference of genome evolution.

    Place, publisher, year, edition, pages
    OXFORD UNIV PRESS, 2018
    Keywords
    sex chromosomes, inversions, assembly correction, linkage analysis
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-365830 (URN)10.1093/gbe/evy163 (DOI)000444553900017 ()30099482 (PubMedID)
    Funder
    Swedish Research CouncilKnut and Alice Wallenberg Foundation
    Available from: 2018-11-26 Created: 2018-11-26 Last updated: 2019-03-25Bibliographically approved
    3. Variation in the Z Chromosome to Autosomes Ratio of Genetic Diversity across Birds and its Relationship to the Fast-Z effect
    Open this publication in new window or tab >>Variation in the Z Chromosome to Autosomes Ratio of Genetic Diversity across Birds and its Relationship to the Fast-Z effect
    (English)Manuscript (preprint) (Other academic)
    Keywords
    sex chromosomes, genetic diversity, Fast-Z evolution, genetic drift, selection
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-380263 (URN)
    Available from: 2019-03-25 Created: 2019-03-25 Last updated: 2019-04-09
    4. Patterns of Nucleotide Diversity and Linkage Disequilibrium along the Ostrich Pseudoautosomal Region
    Open this publication in new window or tab >>Patterns of Nucleotide Diversity and Linkage Disequilibrium along the Ostrich Pseudoautosomal Region
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Keywords
    sex chromosomes, pseudoautosomal region, genetic diversity, linkage disequilibrium
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-380265 (URN)
    Available from: 2019-03-25 Created: 2019-03-25 Last updated: 2019-03-25
  • 1182.
    Yazdi, Homa Papoli
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Old but Not (So) Degenerated-Slow Evolution of Largely Homomorphic Sex Chromosomes in Ratites2014In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 31, no 6, p. 1444-1453Article in journal (Refereed)
    Abstract [en]

    Degeneration of the nonrecombining chromosome is a common feature of sex chromosome evolution, readily evident by the presence of a pair of largely heteromorphic chromosomes, like in eutherian mammals and birds. However, in ratites (order Palaeognathae, including, e.g., ostrich), the Z and W chromosomes are similar in size and largely undifferentiated, despite avian sex chromosome evolution was initiated > 130 Ma. To better understand what may limit sex chromosome evolution, we performed ostrich transcriptome sequencing and studied genes from the nonrecombining region of the W chromosome. Fourteen gametologous gene pairs present on the W chromosome and Z chromosome were identified, with synonymous sequence divergence of 0.027-0.177. The location of these genes on the Z chromosome was consistent with a sequential increase in divergence, starting 110-157 and ending 24-30 Ma. On the basis of the occurrence of Z-linked genes hemizygous in females, we estimate that about one-third of the Z chromosome does not recombine with the W chromosome in female meiosis. Pairwise d(N)/d(S) between gametologs decreased with age, suggesting strong evolutionary constraint in old gametologs. Lineage-specific d(N)/d(S) was consistently higher in W-linked genes, in accordance with the lower efficacy of selection expected in nonrecombining chromosomes. A higher ratio of GC > AT:AT > GC substitutions in W-linked genes supports a role for GC-biased gene conversion in differentially driving base composition on the two sex chromosomes. A male-to-female (M:F) expression ratio of close to one for recombining genes and close to two for Z-linked genes lacking a W copy show that dosage compensation is essentially absent. Some gametologous genes have retained active expression of the W copy in females (giving a M:F ratio of 1 for the gametologous gene pair), whereas for others W expression has become severely reduced resulting in a M:F ratio of close to 2. These observations resemble the patterns of sex chromosome evolution seen in other avian and mammalian lineages, suggesting similar underlying evolutionary processes, although the rate of sex chromosome differentiation has been atypically low. Lack of dosage compensation may be a factor hindering sex chromosome evolution in this lineage.

  • 1183. Yee, B.
    et al.
    Mahajan, M.
    Seeger, C.
    Hägglund, E.
    Lind, S.
    Andersson, S.G.E.
    Natural competence in the Planctomycetes and its use in transforming the Gemmata-related species Tuwongella immobilis2019Manuscript (preprint) (Other (popular science, discussion, etc.))
  • 1184.
    Zajitschek, Felix
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Zajitschek, Susanne R. K
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Canton, Cindy
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Georgolopoulos, Grigorios
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Friberg, Urban
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Maklakov, Alexei A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Evolution under dietary restriction increases male reproductive performance without survival cost2016In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 283, no 1825, article id 20152726Article in journal (Refereed)
    Abstract [en]

    Dietary restriction (DR), a reduction in nutrient intake without malnutrition, is the most reproducible way to extend lifespan in a wide range of organisms across the tree of life, yet the evolutionary underpinnings of the DR effect on lifespan are still widely debated. The leading theory suggests that this effect is adaptive and results from reallocation of resources from reproduction to somatic maintenance, in order to survive periods of famine in nature. However, such response would cease to be adaptive when DR is chronic and animals are selected to allocate more resources to reproduction. Nevertheless, chronic DR can also increase the strength of selection resulting in the evolution of more robust genotypes. We evolved Drosophila melanogaster fruit flies on ‘DR’, ‘standard’ and ‘high’ adult diets in replicate populations with overlapping generations. After approximately 25 generations of experimental evolution, male ‘DR’ flies had higher fitness than males from ‘standard’ and ‘high’ populations. Strikingly, this increase in reproductive success did not come at a cost to survival. Our results suggest that sustained DR selects for more robust male genotypes that are overall better in converting resources into energy, which they allocate mostly to reproduction.

  • 1185.
    Zajitschek, Susanne
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England.;CSIC, EBD, Donana Biol Stn, C Americo Vespucio S-N, Seville 41092, Spain..
    Herbert-Read, James E.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Applied Mathematics and Statistics. Stockholm Univ, Dept Zool, S-10691 Stockholm, Sweden..
    Abbasi, Nasir M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England.
    Zajitschek, Felix
    Monash Univ, Sch Biol Sci, Bldg 18, Clayton, Vic 3800, Australia..
    Immler, Simone
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England.
    Paternal personality and social status influence offspring activity in zebrafish2017In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 17, article id 157Article in journal (Refereed)
    Abstract [en]

    Background: Evidence for the transmission of non-genetic information from father to offspring is rapidly accumulating. While the impact of chemical and physical factors such as toxins or diet on the fitness of the parents and their offspring have been studied extensively, the importance of behavioural and social circumstances has only recently been recognised. Behavioural traits such as personality characteristics can be relatively stable, and partly comprise a genetic component but we know little about the non-genetic transmission of plastic behavioural traits from parents to offspring. We investigated the relative effect of personality and of social dominance as indicators at the opposite ends of the plasticity range on offspring behaviour in the zebrafish (Danio rerio). We assessed male boldness, a behavioural trait that has previously been shown previously to possess genetic underpinnings, and experimentally manipulated male social status to assess the association between the two types of behaviour and their correlation with offspring activity. Results: We found a clear interaction between the relatively stable and putative genetic effects based on inherited differences in personality and the experimentally induced epigenetic effects from changes in the social status of the father on offspring activity. Conclusions: Our study shows that offspring behaviour is determined by a combination of paternal personality traits and on-genetic effects derived from the social status of the father.

  • 1186.
    Zajitschek, Susanne
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Hotzy, Cosima
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Zajitschek, Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Immler, Simone
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Short-term variation in sperm competition causes sperm-mediated epigenetic effects on early offspring performance in the zebrafish2014In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 281, no 1785, p. 20140422-Article in journal (Refereed)
    Abstract [en]

    The inheritance of non-genetic factors is increasingly seen to play a major role in ecology and evolution. While the causes and consequences of epigenetic effects transmitted from the mother to the offspring have received ample attention, much less is known about how variation in the condition of the father affects the offspring. Here, we manipulated the intensity of sperm competition experienced by male zebrafish Danio rerio to investigate the potential for sperm-mediated epigenetic effects over a relatively short period of time. We found that the rapid responses of males to varying intensity of sperm competition not only affected sperm traits as shown previously, but also the performance of the resulting offspring. We observed that males exposed to high intensity of sperm competition produced faster swimming and more motile sperm, and sired offspring that hatched over a narrower time frame but exhibited a lower survival rate than males exposed to low intensity of sperm competition. Our results provide striking evidence for short-term paternal effects and the possible fitness consequences of such sperm-mediated non-genetic factors not only for the resulting offspring but also for the female.

  • 1187.
    Zaremba-Niedzwiedzka, Katarzyna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Fernández Cáceres, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Saw, Jimmy Hser Wah
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bäckström, Disa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Juzokaite, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Vancaester, Emmelien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Ghent, Dept Plant Syst Biol, VIB, Technol Pk 927, B-9052 Ghent, Belgium.;Univ Ghent, Dept Plant Biotechnol & Bioinformat, Technol Pk 927, B-9052 Ghent, Belgium..
    Seitz, Kiley W.
    Univ Texas Austin, Inst Marine Sci, Dept Marine Sci, Port Aransas, TX 78373 USA..
    Anantharaman, Karthik
    Univ Calif Berkeley, Dept Earth & Planetary Sci, Berkeley, CA 94720 USA.;Univ Calif Berkeley, Dept Environm Sci Policy & Management, Berkeley, CA 94720 USA..
    Starnawski, Piotr
    Aarhus Univ, Sect Microbiol, DK-8000 Aarhus, Denmark.;Aarhus Univ, Ctr Geomicrobiol, Dept Biosci, DK-8000 Aarhus, Denmark..
    Kjeldsen, Kasper U.
    Aarhus Univ, Sect Microbiol, DK-8000 Aarhus, Denmark.;Aarhus Univ, Ctr Geomicrobiol, Dept Biosci, DK-8000 Aarhus, Denmark..
    Stott, Matthew B.
    Extremophile Res Grp, GNS Sci, Private Bag 2000, Taupo 3352, New Zealand..
    Nunoura, Takuro
    Japan Agcy Marine Earth Sci & Technol, Res & Dev Ctr Marine Biosci, Yokosuka, Kanagawa 2370061, Japan..
    Banfield, Jillian F.
    Univ Calif Berkeley, Dept Earth & Planetary Sci, Berkeley, CA 94720 USA.;Univ Calif Berkeley, Dept Environm Sci Policy & Management, Berkeley, CA 94720 USA..
    Schramm, Andreas
    Aarhus Univ, Sect Microbiol, DK-8000 Aarhus, Denmark.;Aarhus Univ, Ctr Geomicrobiol, Dept Biosci, DK-8000 Aarhus, Denmark..
    Baker, Brett J.
    Univ Texas Austin, Inst Marine Sci, Dept Marine Sci, Port Aransas, TX 78373 USA..
    Spang, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Asgard archaea illuminate the origin of eukaryotic cellular complexity2017In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 541, no 7637, p. 353-+Article in journal (Refereed)
    Abstract [en]

    The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the 'Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota. Asgard archaea affiliate with eukaryotes in phylogenomic analyses, and their genomes are enriched for proteins formerly considered specific to eukaryotes. Notably, thorarchaeal genomes encode several homologues of eukaryotic membrane-trafficking machinery components, including Sec23/24 and TRAPP domains. Furthermore, we identify thorarchaeal proteins with similar features to eukaryotic coat proteins involved in vesicle biogenesis. Our results expand the known repertoire of 'eukaryote-specific' proteins in Archaea, indicating that the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.

  • 1188. Zhang, Guojie
    et al.
    Li, Cai
    Li, Qiye
    Li, Bo
    Larkin, Denis M.
    Lee, Chul
    Storz, Jay F.
    Antunes, Agostinho
    Greenwold, Matthew J.
    Meredith, Robert W.
    Ödeen, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Cui, Jie
    Zhou, Qi
    Xu, Luohao
    Pan, Hailin
    Wang, Zongji
    Jin, Lijun
    Zhang, Pei
    Hu, Haofu
    Yang, Wei
    Hu, Jiang
    Xiao, Jin
    Yang, Zhikai
    Liu, Yang
    Xie, Qiaolin
    Yu, Hao
    Lian, Jinmin
    Wen, Ping
    Zhang, Fang
    Li, Hui
    Zeng, Yongli
    Xiong, Zijun
    Liu, Shiping
    Zhou, Long
    Huang, Zhiyong
    An, Na
    Wang, Jie
    Zheng, Qiumei
    Xiong, Yingqi
    Wang, Guangbiao
    Wang, Bo
    Wang, Jingjing
    Fan, Yu
    da Fonseca, Rute R.
    Alfaro-Nunez, Alonzo
    Schubert, Mikkel
    Orlando, Ludovic
    Mourier, Tobias
    Howard, Jason T.
    Ganapathy, Ganeshkumar
    Pfenning, Andreas
    Whitney, Osceola
    Rivas, Miriam V.
    Hara, Erina
    Smith, Julia
    Farre, Marta
    Narayan, Jitendra
    Slavov, Gancho
    Romanov, Michael N.
    Borges, Rui
    Machado, Joao Paulo
    Khan, Imran
    Springer, Mark S.
    Gatesy, John
    Hoffmann, Federico G.
    Opazo, Juan C.
    Hastad, Olle
    Sawyer, Roger H.
    Kim, Heebal
    Kim, Kyu-Won
    Kim, Hyeon Jeong
    Cho, Seoae
    Li, Ning
    Huang, Yinhua
    Bruford, Michael W.
    Zhan, Xiangjiang
    Dixon, Andrew
    Bertelsen, Mads F.
    Derryberry, Elizabeth
    Warren, Wesley
    Wilson, Richard K.
    Li, Shengbin
    Ray, David A.
    Green, Richard E.
    O'Brien, Stephen J.
    Griffin, Darren
    Johnson, Warren E.
    Haussler, David
    Ryder, Oliver A.
    Willerslev, Eske
    Graves, Gary R.
    Alstroem, Per
    Fjeldsa, Jon
    Mindell, David P.
    Edwards, Scott V.
    Braun, Edward L.
    Rahbek, Carsten
    Burt, David W.
    Houde, Peter
    Zhang, Yong
    Yang, Huanming
    Wang, Jian
    Jarvis, Erich D.
    Gilbert, M. Thomas P.
    Wang, Jun
    Comparative genomics reveals insights into avian genome evolution and adaptation2014In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 346, no 6215, p. 1311-1320Article in journal (Refereed)
    Abstract [en]

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

  • 1189. Zhang, Qu
    et al.
    Hill, Geoffrey E
    Edwards, Scott V
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A house finch (Haemorhous mexicanus) spleen transcriptome reveals intra- and interspecific patterns of gene expression, alternative splicing and genetic diversity in passerines.2014In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 15, article id 305Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: With its plumage color dimorphism and unique history in North America, including a recent population expansion and an epizootic of Mycoplasma gallisepticum (MG), the house finch (Haemorhous mexicanus) is a model species for studying sexual selection, plumage coloration and host-parasite interactions. As part of our ongoing efforts to make available genomic resources for this species, here we report a transcriptome assembly derived from genes expressed in spleen.

    RESULTS: We characterize transcriptomes from two populations with different histories of demography and disease exposure: a recently founded population in the eastern US that has been exposed to MG for over a decade and a native population from the western range that has never been exposed to MG. We utilize this resource to quantify conservation in gene expression in passerine birds over approximately 50 MY by comparing splenic expression profiles for 9,646 house finch transcripts and those from zebra finch and find that less than half of all genes expressed in spleen in either species are expressed in both species. Comparative gene annotations from several vertebrate species suggest that the house finch transcriptomes contain ~15 genes not yet found in previously sequenced vertebrate genomes. The house finch transcriptomes harbour ~85,000 SNPs, ~20,000 of which are non-synonymous. Although not yet validated by biological or technical replication, we identify a set of genes exhibiting differences between populations in gene expression (n = 182; 2% of all transcripts), allele frequencies (76 FST ouliers) and alternative splicing as well as genes with several fixed non-synonymous substitutions; this set includes genes with functions related to double-strand break repair and immune response.

    CONCLUSIONS: The two house finch spleen transcriptome profiles will add to the increasing data on genome and transcriptome sequence information from natural populations. Differences in splenic expression between house finch and zebra finch imply either significant evolutionary turnover of splenic expression patterns or different physiological states of the individuals examined. The transcriptome resource will enhance the potential to annotate an eventual house finch genome, and the set of gene-based high-quality SNPs will help clarify the genetic underpinnings of host-pathogen interactions and sexual selection.

  • 1190.
    Zhang, Zebin
    et al.
    China Agr Univ, Dept Anim Genet & Breeding, Coll Anim Sci & Technol, State Key Lab Anim Nutr,Natl Engn Lab Anim Breedi, Beijing, Peoples R China.
    Jia, Yaxiong
    Chinese Acad Agr Sci, Inst Anim Sci, Beijing, Peoples R China.
    Almeida, Pedro
    UCL, Dept Genet Evolut & Environm, London, England.
    Mank, Judith E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. UCL, Dept Genet Evolut & Environm, London, England.
    van Tuinen, Marcel
    Univ Groningen, Marine Evolut & Conservat Grp, Ctr Evolutionary & Ecol Studies, Groningen, Netherlands.
    Wang, Qiong
    China Agr Univ, Dept Anim Genet & Breeding, Coll Anim Sci & Technol, State Key Lab Anim Nutr,Natl Engn Lab Anim Breedi, Beijing, Peoples R China.
    Jiang, Zhihua
    Washington State Univ, Dept Anim Sci, Ctr Reprod Biol, Vet & Biomed Res Bldg, Pullman, WA 99164 USA.
    Chen, Yu
    Beijing Municipal Gen Stn Anim Sci, Beijing, Peoples R China.
    Zhan, Kai
    Anhui Acad Agr Sci, Inst Anim Husb & Vet Med, Hefei, Anhui, Peoples R China.
    Hou, Shuisheng
    Chinese Acad Agr Sci, Inst Anim Sci, Beijing, Peoples R China.
    Zhou, Zhengkui
    Chinese Acad Agr Sci, Inst Anim Sci, Beijing, Peoples R China.
    Li, Huifang
    Chinese Acad Agr Sci, Poultry Inst, Yangzhou, Jiangsu, Peoples R China.
    Yang, Fangxi
    Inst Pekin Duck, Beijing, Peoples R China.
    He, Yong
    Cherry Valley Farms Xianghe Co Ltd, Langfang, Peoples R China.
    Ning, Zhonghua
    China Agr Univ, Dept Anim Genet & Breeding, Coll Anim Sci & Technol, State Key Lab Anim Nutr,Natl Engn Lab Anim Breedi, Beijing, Peoples R China.
    Yang, Ning
    China Agr Univ, Dept Anim Genet & Breeding, Coll Anim Sci & Technol, State Key Lab Anim Nutr,Natl Engn Lab Anim Breedi, Beijing, Peoples R China.
    Qu, Lujiang
    China Agr Univ, Dept Anim Genet & Breeding, Coll Anim Sci & Technol, State Key Lab Anim Nutr,Natl Engn Lab Anim Breedi, Beijing, Peoples R China.
    Whole-genome resequencing reveals signatures of selection and timing of duck domestication2018In: GigaScience, ISSN 2047-217X, E-ISSN 2047-217X, Vol. 7, no 4, article id giy027Article in journal (Refereed)
    Abstract [en]

    Background: The genetic basis of animal domestication remains poorly understood, and systems with substantial phenotypic differences between wild and domestic populations are useful for elucidating the genetic basis of adaptation to new environments as well as the genetic basis of rapid phenotypic change. Here, we sequenced the whole genome of 78 individual ducks, from two wild and seven domesticated populations, with an average sequencing depth of 6.42X per individual. Results: Our population and demographic analyses indicate a complex history of domestication, with early selection for separate meat and egg lineages. Genomic comparison of wild to domesticated populations suggests that genes that affect brain and neuronal development have undergone strong positive selection during domestication. Our F-ST analysis also indicates that the duck white plumage is the result of selection at the melanogenesis-associated transcription factor locus. Conclusions: Our results advance the understanding of animal domestication and selection for complex phenotypic traits.

  • 1191.
    Zhang, Zhifei
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Holmer, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Wang, Haizhou
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Butler, Aodhán D.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    An early Cambrian agglutinated tubular lophophorate with brachiopod characters2014In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 4, p. 4682-Article in journal (Refereed)
    Abstract [en]

    The morphological disparity of lophotrochozoan phyla makes it difficult to predict the morphology of the last common ancestor. Only fossils of stem groups can help discover the morphological transitions that occurred along the roots of these phyla. Here, we describe a tubular fossil Yuganotheca elegans gen.et sp. nov. from the Cambrian (Stage 3) Chengjiang Lagerstätte (Yunnan, China) that exhibits an unusual combination of phoronid, brachiopod and tommotiid (Cambrian problematica) characters, notably a pair of agglutinated valves, enclosing a horseshoe-shaped lophophore, supported by a lower bipartite tubular attachment structure with a long coelomic pedicle providing anchorage. The discovery has important implications for the early evolution of lophotrochozoans, suggesting rooting of brachiopods into the sessile lophotrochozoans and the origination of their bivalved bauplan preceding the biomineralization of shell valves in crown brachiopods.

  • 1192. Zhao, Lei
    et al.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Overall, Andrew D. J.
    Waxman, David
    The characteristic trajectory of a fixing allele: a consequence of fictitious selection that arises from conditioning2013In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 195, no 2, p. 993-1006Article in journal (Refereed)
    Abstract [en]

    This work is concerned with the historical progression, to fixation, of an allele in a finite population. This progression is characterized by the average frequency trajectory of alleles that achieve fixation before a given time, T. Under a diffusion analysis, the average trajectory, conditional on fixation by time T, is shown to be equivalent to the average trajectory in an unconditioned problem involving additional selection. We call this additional selection “fictitious selection”; it plays the role of a selective force in the unconditioned problem but does not exist in reality. It is a consequence of conditioning on fixation. The fictitious selection is frequency dependent and can be very large compared with any real selection that is acting. We derive an approximation for the characteristic trajectory of a fixing allele, when subject to real additive selection, from an unconditioned problem, where the total selection is a combination of real and fictitious selection. Trying to reproduce the characteristic trajectory from the action of additive selection, in an infinite population, can lead to estimates of the strength of the selection that deviate from the real selection by >1000% or have the opposite sign. Strong evolutionary forces may be invoked in problems where conditioning has been carried out, but these forces may largely be an outcome of the conditioning and hence may not have a real existence. The work presented here clarifies these issues and provides two useful tools for future analyses: the characteristic trajectory of a fixing allele and the force that primarily drives this, namely fictitious selection. These should prove useful in a number of areas of interest including coalescence with selection, experimental evolution, time series analyses of ancient DNA, game theory in finite populations, and the historical dynamics of selected alleles in wild populations.

  • 1193.
    Zhao, Lei
    et al.
    Fudan Univ, Ctr Computat Syst Biol, 220 Handan Rd, Shanghai 200433, Peoples R China..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Fudan Univ, Ctr Computat Syst Biol, 220 Handan Rd, Shanghai 200433, Peoples R China..
    Waxman, David
    Fudan Univ, Ctr Computat Syst Biol, 220 Handan Rd, Shanghai 200433, Peoples R China..
    An informational transition in conditioned Markov chains: Applied to genetics and evolution2016In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 402, p. 158-170Article in journal (Refereed)
    Abstract [en]

    In this work we assume that we have some knowledge about the state of a population at two known times, when the dynamics is governed by a Markov chain such as a Wright-Fisher model. Such knowledge could be obtained, for example, from observations made on ancient and contemporary DNA, or during laboratory experiments involving long term evolution. A natural assumption is that the behaviour of the population, between observations, is related to (or constrained by) what was actually observed. The present work shows that this assumption has limited validity. When the time interval between observations is larger than a characteristic value, which is a property of the population under consideration, there is a range of intermediate times where the behaviour of the population has reduced or no dependence on what was observed and an equilibrium-like distribution applies. Thus, for example, if the frequency of an allele is observed at two different times, then for a large enough time interval between observations, the population has reduced or no dependence on the two observed frequencies for a range of intermediate times. Given observations of a population at two times, we provide a general theoretical analysis of the behaviour of the population at all intermediate times, and determine an expression for the characteristic time interval, beyond which the observations do not constrain the population's behaviour over a range of intermediate times. The findings of this work relate to what can be meaningfully inferred about a population at intermediate times, given knowledge of terminal states.

  • 1194.
    Zhu, Min
    et al.
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China.;Univ Chinese Acad Sci, Coll Earth Sci, Beijing 100049, Peoples R China..
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Pan, Zhaohui
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China.;Univ Chinese Acad Sci, Coll Earth Sci, Beijing 100049, Peoples R China..
    Zhu, Youan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Qiao, Tuo
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China..
    Zhao, Wenjin
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China..
    Jia, Liantao
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China..
    Lu, Jing
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China..
    A Silurian maxillate placoderm illuminates jaw evolution2016In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 354, no 6310, p. 334-336Article in journal (Refereed)
    Abstract [en]

    The discovery of Entelognathus revealed the presence of maxilla, premaxilla, and dentary, supposedly diagnostic osteichthyan bones, in a Silurian placoderm. However, the relationship between these marginal jaw bones and the gnathal plates of conventional placoderms, thought to represent the inner dental arcade, remains uncertain. Here we report a second Silurian maxillate placoderm, which bridges the gnathal and maxillate conditions. We propose that the maxilla, premaxilla, and dentary are homologous to the gnathal plates of placoderms and that all belong to the same dental arcade. The gnathal-maxillate transformation occurred concurrently in upper and lower jaws, predating the addition of infradentary bones to the lower jaw.

  • 1195.
    Zhu, Min
    et al.
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China.;Univ Chinese Acad Sci, Coll Earth Sci, Beijing 100049, Peoples R China..
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Zhao, Wen-Jin
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China.;Univ Chinese Acad Sci, Coll Earth Sci, Beijing 100049, Peoples R China..
    Jia, Lian-Tao
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China..
    A Devonian tetrapod-like fish reveals substantial parallelism in stem tetrapod evolution2017In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 1, no 10, p. 1470-1476Article in journal (Refereed)
    Abstract [en]

    The fossils assigned to the tetrapod stem group document the evolution of terrestrial vertebrates from lobe-finned fishes. During the past 18 years the phylogenetic structure of this stem group has remained remarkably stable, even when accommodating new discoveries such as the earliest known stem tetrapod Tungsenia and the elpistostegid (fish-tetrapod intermediate) Tiktaalik. Here we present a large lobe-finned fish from the Late Devonian period of China that disrupts this stability. It combines characteristics of rhizodont fishes (supposedly a basal branch in the stem group, distant from tetrapods) with derived elpistostegid-like and tetrapod-like characters. This melange of characters may reflect either detailed convergence between rhizodonts and elpistostegids plus tetrapods, under a phylogenetic scenario deduced from Bayesian inference analysis, or a previously unrecognized close relationship between these groups, as supported by maximum parsimony analysis. In either case, the overall result reveals a substantial increase in homoplasy in the tetrapod stem group. It also suggest that ecological diversity and biogeographical provinciality in the tetrapod stem group have been underestimated.

  • 1196.
    Zielinski, P.
    et al.
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland..
    Nadachowska-Brzyska, Krystyna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Dudek, K.
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland..
    Babik, W.
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland..
    Divergence history of the Carpathian and smooth newts modelled in space and time2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 16, p. 3912-3928Article in journal (Refereed)
    Abstract [en]

    Information about demographic history is essential for the understanding of the processes of divergence and speciation. Patterns of genetic variation within and between closely related species provide insights into the history of their interactions. Here, we investigated historical demography and genetic exchange between the Carpathian (Lissaritan montandoni, Lm) and smooth (L. vulgaris, Lv) newts. We combine an extensive geographical sampling and multilocus nuclear sequence data with the approximate Bayesian computation framework to test alternative scenarios of divergence and reconstruct the temporal and spatial pattern of gene flow between species. A model of recent (last glacial period) interspecific gene flow was favoured over alternative models. Thus, despite the relatively old divergence (4-6 mya) and presumably long periods of isolation, the species have retained the ability to exchange genes. Nevertheless, the low migration rates (ca. 10 per gene copy per generation) are consistent with strong reproductive isolation between the species. Models allowing demographic changes were favoured, suggesting that the effective population sizes of both species at least doubled as divergence reaching the current ca. 0.2 million in Lm and 1 million in Lv. We found asymmetry in rates of interspecific gene flow between Lm and one evolutionary lineage of Lv. We suggest that intraspecific polymorphism for hybrid incompatibilities segregating within Lv could explain this pattern and propose further tests to distinguish between alternative explanations. Our study highlights the importance of incorporating intraspecific genetic structure into the models investigating the history of divergence.

  • 1197.
    Zigaite, Zivile
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Pérez-Huerta, Alberto
    University of Alabama.
    Goujet, Daniel
    Muséum national d'histoire naturelle.
    Vertebrate Microfossils as Tools in Stratigraphy: A Study of the LowerDevonian Andrée Land Group Spitsbergen2014In: Springer Geology, p. 1167-1171Article in journal (Refereed)
    Abstract [en]

    We have studied vertebrate microremains from the Lower to Middle Devonian of the Andrée Land Group, comprising the Wood Bay and Grey Hoek formations. We have defined two new thelodont assemblages, which represent different depositional phases during the late Early to early Middle Devonian formation of the Andrée Land Group. The definition of these two new thelodont assemblages allows us to precisely establish the relative ages of the Lower–Middle Devonian strata. Rare earth element (REE) abundances were measured in a number of thelodont and chondrichthyan microfossil dental tissue biominerals, using laser ablation inductively coupled plasma mass spectrometry (LA–ICP–MS). The evaluation of fossil preservation level was performed using semiquantitative spot-geochemistry analyses on finely polished thelodont scale thin-sections using Energy Dispersive X-ray Spectroscopy (EDS), and Electron Backscattering Diffractometry (EBSD) was applied to detect recrystallization. Stable oxygen isotope measurements (δ18O) of bulk biominerals were conducted in parallel, and showed lower heavy oxygen values in the fossil tissues with stronger visible alteration, such as those from the Grey Hoek Formation. Our results suggest that certain lithostratigraphic units of the Andrée Land Group must be regarded as contemporaneous lithofacies subjected to different sedimentary environments, rather than as separate stratigraphic members.

  • 1198.
    Zigaite, Zivile
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Karatajute-Talimaa, Valentina
    Vilnius University.
    Aspidin or galeaspidin: new early vertebrate histology from the Lower Silurian of Southern Siberia2011In: Program and Abstracts: 71st Annual Meeting Society of Vertebrate Paleontology, 2011, p. Sec1: 221-Conference paper (Refereed)
  • 1199.
    Zigaite, Zivile
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Karatajute-Talimaa, Valentina
    Vilnius University.
    Goujet, Daniel
    Museum national d'histoire naturelle.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Thelodont scales from the Lower and Middle Devonian Andree Land Group, Spitsbergen2013In: GFF, ISSN 1103-5897, E-ISSN 2000-0863, Vol. 135, no 1, p. 57-73Article in journal (Refereed)
    Abstract [en]

    Scales of six thelodont taxa are described from the Devonian of Spitsbergen. Numerous samples from localities widely dispersed on Spitsbergen yield several assemblages considered to represent different depositional phases of the late Lower lower Middle Devonian of the Andrée Land Group, but also support the view that certain lithostratigraphic units of the Andrée Land Group should be regarded as contemporaneous lithofacies subjected to different sedimentary environments, rather than as separate stratigraphic members. The description of Woodfjordia collisa gen. et sp. nov., Talivalia svalbardia sp. nov., Canonia cf. C. grossi, Amaltheolepis montiwatsonia sp. nov., Amaltheolepis winsnesi and Amaltheolepis austfjordia sp. nov. also allows for a comparison with similar faunas from other regions of the Northern Hemisphere and motivates further elaboration of Early-Middle Devonian thelodont biostratigraphy.

  • 1200.
    Zigaite, Zivile
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Richter, Martha
    Natural History Museum.
    Karatajute-Talimaa, Valentina
    Vilnius University.
    Meredith Smith, Moya
    King's College London, Dental Institute.
    Tissue diversity and evolutionary trends of the dermal skeleton of Silurian thelodonts2013In: Historical Biology, ISSN 0891-2963, E-ISSN 1029-2381, Vol. 25, no 2, p. 143-154Article in journal (Refereed)
    Abstract [en]

    Previously described scale morphotypes of Silurian thelodonts, constrained by their representation as isolated dermaldenticles are reassessed to provide a more robust character basis for their inclusion in future phylogenetic studies. Asrelatively common microfossils, thelodonts are important biostratigraphical markers, but their interrelationships withgeologically younger species known by complete skeletons are still unresolved. We examined scales of 21 knownmorphotypes from north-eastern Europe, Siberia and central Asia and described their distinct tissue arrangementsconsidering (1) thickness and direction of dentine tubules, (2) presence or absence of a pulp canal, (3) number and positionof pulp canals, (4) the presence or absence of a distinct outer crown layer and (5) the extent of Sharpey’s fibres penetratingthe scale base. We correlated the traditional thelodont scale type morphologies with these distinct scale histologies, as foundin Silurian thelodonts. In addition, a new histological type for thelodont scales, the Talimaalepis type, is described torepresent a new taxon, from the Early-Mid Silurian. Our study suggests that, through time, there is a general trend ofincreasing complexity in thelodont dermal tissue structures. Three types of dentine and internal scale organisations weredistinguished in Silurian species studied, namely (1) irregular, thin tubular dentine; (2) irregular, thick tubular dentine, withtwo subtypes as a function of pulp canal development and (3) regular, tubular dentine (orthodentine).

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