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  • 1051.
    Sanchez, Sophie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Dupret, Vincent
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Ryll, Bettina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Trinajstic, Kate
    Curtin University, Western Australia.
    Wretman, Lovisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Zylberberg, Louise
    Université Pierre et Marie Curie, UPMC, Paris, France.
    Tafforeau, Paul
    European Synchrotron Radiation Facility, Grenoble, France.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Fossil bone histology revealed in 3D thanks to the synchrotron light: palaeobiological implications2011Conference paper (Refereed)
  • 1052.
    Sanchez, Sophie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Dupret, Vincent
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Ryll, Bettina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Trinajstic, Kate
    Curti University, Western Australia.
    Wretman, Lovisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Zylberberg, Louise
    Université Pierre et Marie Curie, UPMC, Paris, France.
    Tafforeau, Paul
    European Synchrotron Radiation Facility, Grenoble, France.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Synchrotron virtual palaeohistology: a new tool for studying the evolution of bone microstructures in 3D2011Conference paper (Refereed)
  • 1053.
    Sanchez, Sophie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Schoch, Rainer
    Environmental and metabolic plasticity revealed by bonehistology as a successful evolutionary strategy in a long-lived homeostatic triassic temnospondyl2013Conference paper (Other academic)
  • 1054.
    Sanchez, Sophie
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. European Synchrotron Radiat Facil, 71 Ave Martyrs,CS 40220, F-38043 Grenoble, France..
    Tafforeau, Paul
    European Synchrotron Radiat Facil, 71 Ave Martyrs,CS 40220, F-38043 Grenoble, France..
    Clack, Jennifer A.
    Univ Cambridge, Univ Museum Zool, Dept Zool, Downing St, Cambridge CB2 3EJ, England..
    Ahlberg, Per E.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Life history of the stem tetrapod Acanthostega revealed by synchrotron microtomography2016In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 537, no 7620, p. 408-+Article in journal (Refereed)
    Abstract [en]

    The transition from fish to tetrapod was arguably the most radical series of adaptive shifts in vertebrate evolutionary history. Data are accumulating rapidly for most aspects of these events(1-5), but the life histories of the earliest tetrapods remain completely unknown, leaving a major gap in our understanding of these organisms as living animals. Symptomatic of this problem is the unspoken assumption that the largest known Devonian tetrapod fossils represent adult individuals. Here we present the first, to our knowledge, life history data for a Devonian tetrapod, from the Acanthostega mass-death deposit of Stensio Bjerg, East Greenland(6,7). Using propagation phase-contrast synchrotron microtomography (PPC-SR mu CT)(8) to visualize the histology of humeri (upper arm bones) and infer their growth histories, we show that even the largest individuals from this deposit are juveniles. A long early juvenile stage with unossified limb bones, during which individuals grew to almost final size, was followed by a slow-growing late juvenile stage with ossified limbs that lasted for at least six years in some individuals. The late onset of limb ossification suggests that the juveniles were exclusively aquatic, and the predominance of juveniles in the sample suggests segregated distributions of juveniles and adults at least at certain times. The absolute size at which limb ossification began differs greatly between individuals, suggesting the possibility of sexual dimorphism, adaptive strategies or competition-related size variation.

  • 1055.
    Sanyal, Anushree
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Picardie Jules Verne, FRE CNRS 3498, Unite Ecol & Dynam Syst Anthropises EDYSAN, 1 Rue Louvels, FR-80037 Amiens, France..
    Decocq, Guillaume
    Univ Picardie Jules Verne, FRE CNRS 3498, Unite Ecol & Dynam Syst Anthropises EDYSAN, 1 Rue Louvels, FR-80037 Amiens, France..
    Adaptive evolution of seed oil content in angiosperms: accounting for the global patterns of seed oils2016In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 16, article id 187Article in journal (Refereed)
    Abstract [en]

    Background: Studies of the biogeographic distribution of seed oil content in plants are fundamental to understanding the mechanisms of adaptive evolution in plants as seed oil is the primary energy source needed for germination and establishment of plants. However, seed oil content as an adaptive trait in plants is poorly understood. Here, we examine the adaptive nature of seed oil content in 168 angiosperm families occurring in different biomes across the world. We also explore the role of multiple seed traits like seed oil content and composition in plant adaptation in a phylogenetic and nonphylogenetic context. Result: It was observed that the seed oil content in tropical plants (28.4 %) was significantly higher than the temperate plants (24.6 %). A significant relationship between oil content and latitude was observed in three families Papaveraceae, Sapindaceae and Sapotaceae indicating that selective forces correlated with latitude influence seed oil content. Evaluation of the response of seed oil content and composition to latitude and the correlation between seed oil content and composition showed that multiple seed traits, seed oil content and composition contribute towards plant adaptation. Investigation of the presence or absence of phylogenetic signals across 168 angiosperm families in 62 clades revealed that members of seven clades evolved to have high or low seed oil content independently as they did not share a common evolutionary path. Conclusion: The study provides us an insight into the biogeographical distribution and the adaptive role of seed oil content in plants. The study indicates that multiple seed traits like seed oil content and the fatty acid composition of the seed oils determine the fitness of the plants and validate the adaptive hypothesis that seed oil quantity and quality are crucial to plant adaptation.

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  • 1056.
    Satler, Jordan D.
    et al.
    Iowa State Univ, Dept Ecol Evolut & Organismal Biol, Ames, IA 50011 USA.
    Herre, Edward Allen
    Smithsonian Trop Res Inst, Unit 9100,POB 0498,Diplomat PO, Washington, DC 34002 USA.
    Jandér, K. Charlotte
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Eaton, Deren A. R.
    Columbia Univ, Dept Ecol Evolut & Environm Biol, New York, NY 10027 USA.
    Machado, Carlos A.
    Univ Maryland, Dept Biol, College Pk, MD 20742 USA.
    Heath, Tracy A.
    Iowa State Univ, Dept Ecol Evolut & Organismal Biol, Ames, IA 50011 USA.
    Nason, John D.
    Iowa State Univ, Dept Ecol Evolut & Organismal Biol, Ames, IA 50011 USA.
    Inferring processes of coevolutionary diversification in a community of Panamanian strangler figs and associated pollinating wasps2019In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 73, no 11, p. 2295-2311Article in journal (Refereed)
    Abstract [en]

    The fig and pollinator wasp obligate mutualism is diverse (∼750 described species), ecologically important, and ancient (∼80 Ma). Once thought to be an example of strict one‐to‐one cospeciation, current thinking suggests genera of pollinator wasps codiversify with corresponding sections of figs, but the degree to which cospeciation or other processes contribute to the association at finer scales is unclear. Here, we use genome‐wide sequence data from a community of Panamanian strangler figs and associated wasp pollinators to estimate the relative contributions of four evolutionary processes generating cophylogenetic patterns in this mutualism: cospeciation, host switching, pollinator speciation, and pollinator extinction. Using a model‐based approach adapted from the study of gene family evolution, our results demonstrate the importance of host switching of pollinator wasps at this fine phylogenetic and regional scale. Although we estimate a modest amount of cospeciation, simulations reveal the number of putative cospeciation events to be consistent with what would be expected by chance. Additionally, model selection tests identify host switching as a critical parameter for explaining cophylogenetic patterns in this system. Our study demonstrates a promising approach through which the history of evolutionary association between interacting lineages can be rigorously modeled and tested in a probabilistic phylogenetic framework.

  • 1057.
    Savolainen, Outi
    et al.
    Univ Oulu, Dept Genet & Physiol, Oulu 90014, Finland.;Univ Oulu, Bioctr Oulu, Oulu 90014, Finland..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    GENOMICS Geography matters for Arabidopsis2016In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 537, no 7620, p. 314-315Article in journal (Other academic)
    Abstract [en]

    A free database describes genome sequences, gene expression and molecular modifications to DNA for more than 1,000 Arabidopsis thaliana plants, providing valuable information on the complex history and current variation of this species.

  • 1058.
    Sayadi, Ahmed
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Immonen, Elina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Tellgren-Roth, Christian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    The Evolution of Dark Matter in the Mitogenome of Seed Beetles2017In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, no 10, p. 2697-2706Article in journal (Refereed)
    Abstract [en]

    Animal mitogenomes are generally thought of as being economic and optimized for rapid replication and transcription. We use long-read sequencing technology to assemble the remarkable mitogenomes of four species of seed beetles. These are the largest circular mitogenomes ever assembled in insects, ranging from 24,496 to 26,613 bp in total length, and are exceptional in that some 40% consists of non-coding DNA. The size expansion is due to two very long intergenic spacers (LIGSs), rich in tandem repeats. The two LIGSs are present in all species but vary greatly in length (114-10,408 bp), show very low sequence similarity, divergent tandem repeat motifs, a very high AT content and concerted length evolution. The LIGSs have been retained for at least some 45 my but must have undergone repeated reductions and expansions, despite strong purifying selection on protein coding mtDNA genes. The LIGSs are located in two intergenic sites where a few recent studies of insects have also reported shorter LIGSs (>200 bp). These sites may represent spaces that tolerate neutral repeat array expansions or, alternatively, the LIGSs may function to allow a more economic translational machinery. Mitochondrial respiration in adult seed beetles is based almost exclusively on fatty acids, which reduces the need for building complex I of the oxidative phosphorylation pathway (NADH dehydrogenase). One possibility is thus that the LIGSs may allow depressed transcription of NAD genes. RNA sequencing showed that LIGSs are partly transcribed and transcriptional profiling suggested that all seven mtDNA NAD genes indeed show low levels of transcription and co-regulation of transcription across sexes and tissues.

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  • 1059.
    Sayadi, Ahmed
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Martínez Barrio, Álvaro
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Immonen, Elina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Dainat, Jacques
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Berger, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Tellgren-Roth, Christian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Nystedt, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Uppsala Univ, Dept Ecol & Genet, Anim Ecol, Uppsala, Sweden.
    The genomic footprint of sexual conflict2019In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 3, no 12, p. 1725-1730Article in journal (Refereed)
    Abstract [en]

    Genes with sex-biased expression show a number of unique properties and this has been seen as evidence for conflicting selection pressures in males and females, forming a genetic 'tug-of-war' between the sexes. However, we lack studies of taxa where an understanding of conflicting phenotypic selection in the sexes has been linked with studies of genomic signatures of sexual conflict. Here, we provide such a link. We used an insect where sexual conflict is unusually well understood, the seed beetle Callosobruchus maculatus, to test for molecular genetic signals of sexual conflict across genes with varying degrees of sex-bias in expression. We sequenced, assembled and annotated its genome and performed population resequencing of three divergent populations. Sex-biased genes showed increased levels of genetic diversity and bore a remarkably clear footprint of relaxed purifying selection. Yet, segregating genetic variation was also affected by balancing selection in weakly female-biased genes, while male-biased genes showed signs of overall purifying selection. Female-biased genes contributed disproportionally to shared polymorphism across populations, while male-biased genes, male seminal fluid protein genes and sex-linked genes did not. Genes showing genomic signatures consistent with sexual conflict generally matched life-history phenotypes known to experience sexually antagonistic selection in this species. Our results highlight metabolic and reproductive processes, confirming the key role of general life-history traits in sexual conflict.

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  • 1060.
    Schlebusch, Carina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa..
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa..
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Coutinho, Alexandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Edlund, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Munters, Arielle R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Vicente, Mário
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Steyn, Maryna
    Human Variation and Identification Research Unit, School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, South Africa..
    Soodyall, Himla
    Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa..
    Lombard, Marlize
    Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa.; Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Marais Street, Stellenbosch, 7600, South Africa. .
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa..
    Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago2017In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 358, no 6363, p. 652-655Article in journal (Refereed)
    Abstract [en]

    Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. The remains of three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, and those of four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record.

  • 1061. Schultz, Stewart T.
    et al.
    Scofield, Douglas
    Mutation Accumulation in Real Branches: Fitness Assays for Genomic Deleterious Mutation Rate and Effect in Large-Statured Plants2009In: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 174, no 2, p. 163-175Article in journal (Refereed)
    Abstract [en]

    The genomic deleterious mutation rate and mean effect are central to the biology and evolution of all species. Large‐statured plants, such as trees, are predicted to have high mutation rates due to mitotic mutation and the absence of a sheltered germ line, but their size and generation time has hindered genetic study. We develop and test approaches for estimating deleterious mutation rates and effects from viability comparisons within the canopy of large‐statured plants. Our methods, inspired by E. J. Klekowski, are a modification of the classic Bateman‐Mukai mutation‐accumulation experiment. Within a canopy, cell lineages accumulate mitotic mutations independently. Gametes or zygotes produced at more distal points by these cell lineages contain more mitotic mutations than those at basal locations, and within‐flower selfs contain more homozygous mutations than between‐flower selfs. The resulting viability differences allow demonstration of lethal mutation with experiments similar in size to assays of genetic load and allow estimates of the rate and effect of new mutations with moderate precision and bias similar to that of classic mutation‐accumulation experiments in small‐statured organisms. These methods open up new possibilities with the potential to provide valuable new insights into the evolutionary genetics of plants.

  • 1062.
    Schuster, Astrid
    et al.
    Ludwig Maximilians Univ Munchen, Dept Earth & Environm Sci Palaeontol & Geobiol, Richard Wagner Str 10, D-80333 Munich, Germany..
    Lopez, Jose V.
    Nova Southeastern Univ, Halmos Coll Nat Sci & Oceanog, Dania, FL 33004 USA..
    Becking, Leontine E.
    Wageningen Univ & Res Ctr, Marine Anim Ecol, POB, NL-3700 AH Wageningen, Netherlands.;Naturalis Biodivers Ctr, Marine Zool Dept, POB 95172300RA, Leiden, Netherlands..
    Kelly, Michelle
    Natl Inst Water & Atmospher Res, Natl Ctr Aquat Biodivers & Biosecur, POB 109-695, Auckland, New Zealand..
    Pomponi, Shirley A.
    Florida Atlantic Univ, Harbor Branch Oceanog Inst, 5600 S 1 North, Ft Pierce, FL 34946 USA..
    Woerheide, Gert
    Ludwig Maximilians Univ Munchen, Dept Earth & Environm Sci Palaeontol & Geobiol, Richard Wagner Str 10, D-80333 Munich, Germany.;SNSB, Bavarian State Collect Palaeontol & Geol, Richard Wagner Str 10, D-80333 Munich, Germany.;Ludwig Maximilians Univ Munchen, GeoBio CenterLMU, Richard Wagner Str 10, D-80333 Munich, Germany..
    Erpenbeck, Dirk
    Ludwig Maximilians Univ Munchen, Dept Earth & Environm Sci Palaeontol & Geobiol, Richard Wagner Str 10, D-80333 Munich, Germany.;Ludwig Maximilians Univ Munchen, GeoBio CenterLMU, Richard Wagner Str 10, D-80333 Munich, Germany..
    Cárdenas, Paco
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Evolution of group I introns in Porifera: new evidence for intron mobility and implications for DNA barcoding2017In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 17, article id 82Article in journal (Refereed)
    Abstract [en]

    Background: Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarians, placozoans and one annelid species. Within demosponges, group I and group II introns are present in six families. Based on different insertion sites within the cox1 gene and secondary structures, four types of group I and two types of group II introns are known, which can harbor up to three encoding homing endonuclease genes (HEG) of the LAGLIDADG family (group I) and/or reverse transcriptase (group II). However, only little is known about sponge intron mobility, transmission, and origin due to the lack of a comprehensive dataset. We analyzed the largest dataset on sponge mitochondrial group I introns to date: 95 specimens, from 11 different sponge genera which provided novel insights into the evolution of group I introns. Results: For the first time group I introns were detected in four genera of the sponge family Scleritodermidae (Scleritoderma, Microscleroderma, Aciculites, Setidium). We demonstrated that group I introns in sponges aggregate in the most conserved regions of cox1. We showed that co-occurrence of two introns in cox1 is unique among metazoans, but not uncommon in sponges. However, this combination always associates an active intron with a degenerating one. Earlier hypotheses of HGT were confirmed and for the first time VGT and secondary losses of introns conclusively demonstrated. Conclusion: This study validates the subclass Spirophorina (Tetractinellida) as an intron hotspot in sponges. Our analyses confirm that most sponge group I introns probably originated from fungi. DNA barcoding is discussed and the application of alternative primers suggested.

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  • 1063.
    Schweizer, Manuel
    et al.
    Nat Hist Museum Bern, Bern, Switzerland.
    Warmuth, Vera
    Ludwig Maximilians Univ Munchen, Dept Biol 2, Evolutionary Biol, Martinsried, Germany.
    Kakhki, Niloofar Alaei
    Ferdowsi Univ Mashhad, Dept Biol, Fac Sci, Mashhad, Iran.
    Aliabadian, Mansour
    Ferdowsi Univ Mashhad, Dept Biol, Fac Sci, haMashd, Iran.
    Foerschler, Marc
    Black Forest Natl Pk, Dept Ecosyst Monitoring Res & Conservat, Freudenstadt, Germany.
    Shirihai, Hadoram
    Zürich, Switzerland.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Burri, Reto
    Friedrich Schiller Univ Jena, Inst Ecol & Evolut, Dept Populat Ecol, Jena, Germany.
    Parallel plumage colour evolution and introgressive hybridization in wheatears2019In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 32, no 1, p. 100-110Article in journal (Refereed)
    Abstract [en]

    Genetic and phenotypic mosaics, in which various phenotypes and different genomic regions show discordant patterns of species or population divergence, offer unique opportunities to study the role of ancestral and introgressed genetic variation in phenotypic evolution. Here, we investigated the evolution of discordant phenotypic and genetic divergence in a monophyletic clade of four songbird taxa-pied wheatear (O. pleschanka), Cyprus wheatear (Oenanthe cypriaca), and western and eastern subspecies of black-eared wheatear (O. h. hispanica and O. h. melanoleuca). Phenotypically, black back and neck sides distinguish pied and Cyprus wheatears from the white-backed/necked black-eared wheatears. Meanwhile, mitochondrial variation only distinguishes western black-eared wheatear. In the absence of nuclear genetic data, and given frequent hybridization among eastern black-eared and pied wheatear, it remains unclear whether introgression is responsible for discordance between mitochondrial divergence patterns and phenotypic similarities, or whether plumage coloration evolved in parallel. Multispecies coalescent analyses of about 20,000 SNPs obtained from RAD data mapped to a draft genome assembly resolve the species tree, provide evidence for the parallel evolution of colour phenotypes and establish western and eastern black-eared wheatears as independent taxa that should be recognized as full species. The presence of the entire admixture spectrum in the Iranian hybrid zone and the detection of footprints of introgression from pied into eastern black-eared wheatear beyond the hybrid zone despite strong geographic structure of ancestry proportions furthermore suggest a potential role for introgression in parallel plumage colour evolution. Our results support the importance of standing heterospecific and/or ancestral variation in phenotypic evolution.

  • 1064.
    Schweizer, Manuel
    et al.
    Nat Hist Museum Burgergemeinde Bern, Bernastr 15, CH-3005 Bern, Switzerland.
    Warmuth, Vera M.
    Ludwig Maximilians Univ Munchen, Dept Biol 2, Evolutionary Biol, Biozentrum Martinsried, D-82152 Martinsried, Germany.
    Kakhki, Niloofar Alaei
    Ferdowsi Univ Mashhad, Fac Sci, Dept Biol, Mashhad, Razavi Khorasan, Iran;Ferdowsi Univ Mashhad, RDZI, Inst Appl Zool, Mashhad, Razavi Khorasan, Iran.
    Aliabadian, Mansour
    Ferdowsi Univ Mashhad, Fac Sci, Dept Biol, Mashhad, Razavi Khorasan, Iran;Ferdowsi Univ Mashhad, RDZI, Inst Appl Zool, Mashhad, Razavi Khorasan, Iran.
    Foerschler, Marc
    Dept Ecosyst Monitoring Res & Conservat, Black Forest Natl Pk, D-72250 Freudenstadt, Germany.
    Shirihai, Hadoram
    Ausserdorfstr 6, CH-8052 Zurich, Switzerland.
    Ewels, Phil
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, SE-10691 Stockholm, Sweden.
    Gruselius, Joel
    Karolinska Inst, Dept Biosci & Nutr, Sci Life Lab, Stockholm, Sweden.
    Olsen, Remi-Andre
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, SE-10691 Stockholm, Sweden.
    Schielzeth, Holger
    Friedrich Schiller Univ Jena, Inst Ecol & Evolut, Dept Populat Ecol, D Dornburger Str 159, D-07743 Jena, Germany.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Burri, Reto
    Friedrich Schiller Univ Jena, Inst Ecol & Evolut, Dept Populat Ecol, D Dornburger Str 159, D-07743 Jena, Germany.
    Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats2019In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 139, article id 106568Article in journal (Refereed)
    Abstract [en]

    In wheatears and related species ('open-habitat chats'), molecular phylogenetics has led to a comprehensively revised understanding of species relationships and species diversity. Phylogenetic analyses have suggested that, in many cases, phenotypic similarities do not reflect species' relationships, revealing traditionally defined genera as non-monophyletic. This led to the suggestion of pervasive parallel evolution of open-habitat chats' plumage coloration and ecological phenotypes. However, to date, the molecular evidence for the phylogenetic relationships among open-habitat chats is mainly limited to mitochondrial DNA. Here, we assessed whether the mitochondrial relationships are supported by genome-wide data. To this end, we reconstructed the species tree among 14 open-habitat chat taxa using multi-species coalescent analyses based on similar to 1'300 SNPs. Our results confirm previous ones based chiefly on mitochondrial DNA; notably the paraphyly of the Oenanthe lugens complex and the clustering of individual species formerly placed in the genera Cercomela and Myrmecocichla within Oenanthe. Since several variable morphological and ecological characteristics occur in multiple places across the open-habitat chat phylogeny, our study consolidates the evidence for pervasive parallel evolution in the plumage coloration and ecology of open-habitat chats.

  • 1065.
    Schäfer, Martin A.
    et al.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland.
    Berger, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland.
    Rohner, Patrick T.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland.
    Kjaersgaard, Anders
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland.
    Bauerfeind, Stephanie S.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland.
    Guillaume, Frederic
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland.
    Fox, Charles W.
    Univ Kentucky, Dept Entomol, Lexington, KY 40506 USA.
    Blanckenhorn, Wolf U.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland.
    Geographic clines in wing morphology relate to colonization history in New World but not Old World populations of yellow dung flies2018In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 72, no 8, p. 1629-1644Article in journal (Refereed)
    Abstract [en]

    Geographic dines offer insights about putative targets and agents of natural selection as well as tempo and mode of adaptation. However, demographic processes can lead to dines that are indistinguishable from adaptive divergence. Using the widespread yellow dung fly Scathophaga stercoraria (Diptera: Scathophagidae), we examine quantitative genetic differentiation (Q(ST)) of wing shape across North America, Europe, and Japan, and compare this differentiation with that of ten microsatellites (F-ST). Morphometric analyses of 28 populations reared at three temperatures revealed significant thermal plasticity, sexual dimorphism, and geographic differentiation in wing shape. In North America morphological differentiation followed the decline in microsatellite variability along the presumed route of recent colonization from the southeast to the northwest. Across Europe, where S. stercoraria presumably existed for much longer time and where no molecular pattern of isolation by distance was evident, clinal variation was less pronounced despite significant morphological differentiation (Q(ST) >F-ST). Shape vector comparisons further indicate that thermal plasticity (hot-to-cold) does not mirror patterns of latitudinal divergence (south-to-north), as might have been expected under a scenario with temperature as the major agent of selection. Our findings illustrate the importance of detailed phylogeographic information when interpreting geographic dines of dispersal traits in an adaptive evolutionary framework.

  • 1066.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A definitive demonstration of fitness effects due to somatic mutation in a plant2014In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 112, no 4, p. 361-362Article in journal (Other academic)
  • 1067. Scofield, Douglas
    et al.
    Lynch, Michael
    Evolutionary Diversification of the Sm Family of RNA-Associated Proteins2008In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 25, no 11, p. 2255-2267Article in journal (Refereed)
    Abstract [en]

    The Sm family of proteins is closely associated with RNA metabolismthroughout all life. These proteins form homomorphic and heteromorphic rings consisting of six or seven subunits with a characteristic central pore, the presence of which is critical for binding U-rich regions of single-stranded RNA. Eubacteria and Archaea typically carry one or two forms ofSm proteins and assemble one homomorphic ring per Sm protein. Eukaryotes typically carry 16 or more Sm proteins that assemble to form heteromorphic rings which lie at the center of a number of critical RNA-associated small nuclear ribonucleoproteins (snRNPs). High Sm protein diversity and heteromorphic Sm rings are features stretching back to the origin of eukaryotes; very deep phylogenetic divisions among existing Smproteins indicate simultaneous evolution across essentially all existing eukaryotic life. Two basic forms of heteromorphic Sm rings are found in eukaryotes. Fixed Sm rings are highly stable and static and are assembled around an RNA cofactor. Flexible Sm rings also stabilize and chaperone RNA but assemble in the absence of an RNA substrate and, more significantly, associate with and dissociate from RNA substrates more freely than fixed rings. This suggests that the conformation of flexible Smrings might be modified in some specific manner to facilitate association and dissociation with RNA. Diversification of eukaryotic Sm proteins may have been initiated by gene transfers and/or genome clashes that accompanied the origin of the eukaryotic cell itself, with further diversification driven by a greater need for steric specificity within increasingly complex snRNPs.

  • 1068. Scofield, Douglas
    et al.
    Schultz, Stewart
    Mitosis, stature and evolution of plant mating systems: low-Phi and high-Phi plants2006In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 273, no 1584, p. 275-282Article in journal (Refereed)
    Abstract [en]

    There is a long-recognized association in plants between small stature and selfing, and large stature and outcrossing. Inbreeding depression is central to several hypotheses for this association, but differences in the evolutionary dynamics of inbreeding depression associated with differences in stature are rarely considered. Here, we propose and test the Phi model of plant mating system evolution, which assumes that the per-generation mutation rate of a plant is a function of the number of mitoses (Phi) that occur from zygote to gamete, and predicts fundamental differences between low-Phi (small-statured) and high-Phi (large-statured) plants in the outcomes of the joint evolution of outcrossing rate and inbreeding depression. Using a large dataset of published population genetic studies of angiosperms and conifers, we compute fitted values of inbreeding depression and deleterious mutation rates for small- and large-statured plants. Consistent with our Phi model, we find that populations of small-statured plants exhibit a range of mating systems, significantly lower mutation rates, and intermediate inbreeding depression, while large-statured plants exhibit very high mutation rates and the maximum inbreeding depression of unity. These results indicate that (i) inbred progeny typically observed in large-statured plant populations are completely lost prior to maturity in nearly all populations; (ii) evolutionary shifts from outcrossing to selfing are generally not possible in large-statured species, rather, large-statured species are more likely to evolve mating systems that avoid selfing such as self-incompatibility and dioecy; (iii) destabilization of the mating system-high selfing rate with high-inbreeding depression-might be a common occurrence in large-statured species; and (iv) large-statured species in fragmented populations might be at higher risk of extinction than previously thought. Our results help to unify and simplify a large and diverse field of research, and serve to emphasize the importance that developmental and genetic constraints play in the evolution of plant mating systems.

  • 1069. Seeger, C.
    et al.
    Dyrhage, K.
    Mahajan, M.
    Andersson, S.G.E.
    The subcellular proteome suggests that the replication machinery is located distinct from other information processing systems in the Gemmata-related bacterium Tuwongella immobilis.2019Manuscript (preprint) (Other (popular science, discussion, etc.))
  • 1070.
    Segelbacher, Gernot
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Strand, Tanja M.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Quintela, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Axelsson, Tomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
    Jansman, Hugh A.H.
    Koelewijn, Hans-Peter
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Analyses of historical and current populations of black grouse in Central Europe reveal strong effects of genetic drift and loss of genetic diversity2014In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 15, no 5, p. 1183-1195Article in journal (Refereed)
    Abstract [en]

    Black grouse (Tetrao tetrix) in Central Europe have undergone a severe contraction of their range in recent decades with only a few small isolated remaining populations. Here we compare genetic diversity of two contemporary isolated populations (Sallandse Heuvelrug, Netherlands and Lüneburger Heide, Germany) with historical samples from the same region collected within the last one hundred years. We use markers with both putatively neutral and functional variation to test whether the present small and highly fragmented populations hold lower genetic diversity compared to the former larger population. For this we applied three different types of genetic markers: nine microsatellites and 21 single nucleotide polymorphisms (SNPs), both sets which have been found to be neutral, and two functional major histocompatibility complex (MHC) genes for which there is evidence they are under selection. The contemporary small isolated populations displayed lower neutral genetic diversity compared to the corresponding historical samples. Furthermore, samples from Denmark showed that this now extinct population displayed lower genetic variation in the period immediately prior to the local extinction. Population structure was more pronounced among contemporary populations compared to historical populations for microsatellites and SNPs. This effect was not as distinct for MHC which is consistent with the possibility that MHC has been subjected to balancing selection in the past, a process which maintains genetic variation and may minimize population structure for such markers. Genetic differentiation among the present populations highlights the strong effects of population decline on the genetic structure of natural populations, which can be ultimately attributed to habitat loss following anthropogenic land use changes.

  • 1071.
    Segelbacher, Gernot
    et al.
    Dept Wildlife Ecology and Management, University Freiburg.
    Strand, Tanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Quintela, Maria
    Dept of Animal Biology, Plant Biology and Ecology, Faculty of Science, University of A Coruña.
    Axelsson, Tomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine.
    Jansman, Hugh
    Alterra Wageningen UR.
    Koelewijn, Peter
    Nunhems BV.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Historic and current populations of black grouse in central Europe – evidence for rapid loss of genetic diversity2011Article in journal (Other academic)
    Abstract [en]

    Black grouse (Tetrao tetrix) in central Europe have undergone a severe contraction of their range with only a few small isolated remaining populations. We here compare genetic diversity of two contemporary populations (Sallandse Heuvelrug, Netherlands and Lüneburger Heide, Germany) with historic samples from the same range collected decades ago. We use both neutral and MHC markers to test whether present small and highly fragmented populations hold lower genetic diversity compared to the former larger population. For this we applied three different types of genetic markers: nine microsatellites and 21 SNPs (Single Nucleotide Polymorphisms) which both have been found to be neutral, and two functional MHC (Major Histocompatibility Complex) genes that are presumably under selection. The contemporary small isolated populations displayed lower neutral genetic diversity compared to the historic samples. A similar trend was found for genotypes at MHC class II loci. Furthermore, population structure was more pronounced among contemporary populations compared to historic populations for microsatellites and SNPs. This effect was not as distinct for MHC which suggests that MHC has been subjected to balancing selection in the past, a process upholding genetic variation and minimizing population structure for such markers. As predicted from theory, drift is the most potent evolutionary processes affecting genetic variation at small population sizes. Genetic differentiation among present populations highlights the strong affects of population decline and habitat loss due to anthropogenic land use changes on genetic structure of natural populations. 

  • 1072.
    Shafer, Aaron B. A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Miller, Joshua M.
    Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT USA..
    Kardos, Marty
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Cross-Species Application of SNP Chips is Not Suitable for Identifying Runs of Homozygosity2016In: Journal of Heredity, ISSN 0022-1503, E-ISSN 1465-7333, Vol. 107, no 2, p. 193-195Article in journal (Refereed)
    Abstract [en]

    Cross-species application of single-nucleotide polymorphism (SNP) chips is a valid, relatively cost-effective alternative to the high-throughput sequencing methods generally required to obtain a genome-wide sampling of polymorphisms. Kharzinova et al. (2015) examined the applicability of SNP chips developed in domestic bovids (cattle and sheep) to a semi-wild cervid (reindeer). The ancestors of bovids and cervids diverged between 20 and 30 million years ago (Hassanin and Douzery 2003; Bibi et al. 2013). Empirical work has shown that for a SNP chip developed in a bovid and applied to a cervid species, approximately 50% genotype success with 1% of the loci being polymorphic is expected (Miller et al. 2012). The genotyping of Kharzinova et al. (2015) follows this pattern; however, these data are not appropriate for identifying runs of homozygosity (ROH) and can be problematic for estimating linkage disequilibrium (LD) and we caution readers in this regard.

  • 1073.
    Shafer, Aaron B. A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Trent Univ, Forens Sci & Environm & Life Sci, 2014 East Bank Dr, Peterborough, ON K9J 7B8, Canada..
    Peart, Claire R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Tusso, Sergio
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Maayan, Inbar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Brelsford, Alan
    Univ Lausanne, Dept Ecol & Evolut, CH-1015 Lausanne, Switzerland..
    Wheat, Christopher W.
    Stockholm Univ, Dept Zool, S-10691 Stockholm, Sweden..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, Fac Biol, Grosshaderner Str 2, D-82152 Planegg Martinsried, Germany..
    Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference2017In: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 8, no 8, p. 907-917Article in journal (Refereed)
    Abstract [en]

    1. Restriction site-associated DNA sequencing (RAD-seq) provides high-resolution population genomic data at low cost, and has become an important component in ecological and evolutionary studies. As with all high-throughput technologies, analytic strategies require critical validation to ensure precise and unbiased interpretation. 2. To test the impact of bioinformatic data processing on downstream population genetic inferences, we analysed mammalian RAD-seq data (>100 individuals) with 312 combinations of methodology (de novo vs. mapping to references of increasing divergence) and filtering criteria (missing data, HWE, F-IS, coverage, mapping and genotype quality). In an effort to identify commonalities and biases in all pipelines, we computed summary statistics (nr. loci, nr. SNP, pi, Het(obs), F-IS, F-ST, N-e and m) and compared the results to independent null expectations (isolation-by-distance correlation, expected transition-to-transversion ratio T-s/T-v and Mendelian mismatch rates of known parent-offspring trios). 3. We observed large differences between reference-based and de novo approaches, the former generally calling more SNPs and reducing F-IS and T-s/T-v. Data completion levels showed little impact on most summary statistics, and FST estimates were robust across all pipelines. The site frequency spectrum was highly sensitive to the chosen approach as reflected in large variance of parameter estimates across demographic scenarios (single-population bottlenecks and isolation-with-migration model). Null expectations were best met by reference-based approaches, although contingent on the specific criteria. 4. We recommend that RAD-seq studies employ reference-based approaches to a closely related genome, and due to the high stochasticity associated with the pipeline advocate the use of multiple pipelines to ensure robust population genetic and demographic inferences.

  • 1074.
    Shafer, Aaron B. A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Alves, Paulo C.
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, P-4485661 Oporto, Portugal.;Fac Ciencias, P-4485661 Oporto, Portugal..
    Bergström, Linnea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Colling, Guy
    Musee Natl Hist Nat Luxembourg, Populat Biol, L-2160 Luxembourg, Luxembourg..
    Dalen, Love
    Swedish Museum Nat Hist, Bioinformat & Genet, S-10405 Stockholm, Sweden..
    De Meester, Luc
    KU Leuven Univ Leuven, Aquat Ecol Evolut & Conservat, B-3000 Leuven, Belgium..
    Ekblom, Robert
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Fior, Simone
    Swiss Fed Inst Technol, Integrat Biol, CH-8092 Zurich, Switzerland..
    Hajibabaei, Mehrdad
    Univ Guelph, Integrat Biol, Guelph, ON N1G 2W1, Canada..
    Hoezel, A. Rus
    Univ Durham, Biol & Biomed Sci, Durham DH1 3LE, England..
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Jensen, Evelyn L.
    Univ British Columbia Okanagan, Biol, Kelowna, BC V1V 1V7, Canada..
    Kruetzen, Michael
    Univ Zurich, Anthropol Inst & Museum, CH-8057 Zurich, Switzerland..
    Norman, Anita J.
    Swedish Univ Agr Sci, Wildlife Fish & Environm Studies, S-90183 Umea, Sweden..
    Osterling, E. Martin
    Karlstad Univ, Biol, S-65188 Karlstad, Sweden..
    Ouborg, N. Joop
    Radboud Univ Nijmegen, Expt Plant Ecol, NL-6500 GL Nijmegen, Netherlands..
    Piccolo, John
    Primmer, Craig R.
    Univ Turku, Biol, Turku 20014, Finland..
    Reed, Floyd A.
    Univ Hawaii Manoa, Biol, Honolulu, HI 96822 USA..
    Roumet, Marie
    Swiss Fed Inst Technol, Integrat Biol, CH-8092 Zurich, Switzerland..
    Salmona, Jordi
    Inst Gulbenkian Ciencias, Populat & Conservat Genet Grp, P-2780156 Oeiras, Portugal..
    Schwartz, Michael K.
    USDA, Forest Serv, Rocky Mt Res Stn, Missoula, MT 59801 USA..
    Segelbacher, Gernot
    Univ Freiburg, Wildlife Ecol & Management, D-79106 Freiburg, Germany..
    Thaulow, Jens
    Norwegian Inst Water Res, Freshwater Biol, N-0349 Oslo, Norway..
    Valtonen, Mia
    Univ Eastern Finland, Biol, Joensuu 80101, Finland..
    Vergeer, Philippine
    Wageningen Univ, Nat Conservat & Plant Ecol, NL-6708 PB Wageningen, Netherlands..
    Weissensteiner, Matthias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wheat, Christopher W.
    Stockholm Univ, Zool, S-10691 Stockholm, Sweden..
    Vila, Carlese
    Estn Biol Donana, Conservat & Evolutionary Genet Grp, Seville 41092, Spain..
    Zielinski, Piotr
    Jagiellonian Univ, Inst Environm Sci, PL-30387 Krakow, Poland..
    Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application Reply2016In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 31, no 2, p. 83-84Article in journal (Refereed)
  • 1075.
    Sharwood, Robert
    et al.
    Australian Natl Univ, Res Sch Biol, Canberra, ACT 2601, Australia.; Australian Natl Univ, ARC Ctr Excellence Translat Photosynthesis, Canberra, ACT 2601, Australia..
    Ghannoum, Oula
    Australian Natl Univ, ARC Ctr Excellence Translat Photosynthesis, Canberra, ACT 2601, Australia.; Univ Western Sydney, Hawkesbury Inst Environm, Richmond, NSW 2753, Australia..
    Kapralov, Maxim
    Liverpool John Moores Univ, Sch Nat Sci & Psychol, Liverpool L3 3AF, Merseyside, England..
    Gunn, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Australian Natl Univ, Res Sch Biol, Canberra, ACT 2601, Australia..
    Whitney, Spencer
    Australian Natl Univ, Res Sch Biol, Canberra, ACT 2601, Australia.; Australian Natl Univ, ARC Ctr Excellence Translat Photosynthesis, Canberra, ACT 2601, Australia..
    Temperature responses of Rubisco from Paniceae grasses provide opportunities for improving C3 photosynthesis2016In: Nature Plants, ISSN 2055-0278, Vol. 2, no 12, article id 16186Article in journal (Refereed)
    Abstract [en]

    Enhancing the catalytic properties of the CO2-fixing enzyme Rubisco is a target for improving agricultural crop productivity. Here, we reveal extensive diversity in the kinetic response between 10 and 37 °C by Rubisco from C3 and C4 species within the grass tribe Paniceae. The CO2 fixation rate (kccat) for Rubisco from the C4 grasses with nicotinamide adenine dinucleotide (NAD) phosphate malic enzyme (NADP-ME) and phosphoenolpyruvate carboxykinase (PCK) photosynthetic pathways was twofold greater than the kccat of Rubisco from NAD-ME species across all temperatures. The declining response of CO2/O2 specificity with increasing temperature was less pronounced for PCK and NADP-ME Rubisco, which would be advantageous in warmer climates relative to the NAD-ME grasses. Modelled variation in the temperature kinetics of Paniceae C3 Rubisco and PCK Rubisco differentially stimulated C3 photosynthesis relative to tobacco above and below 25 °C under current and elevated CO2. Amino acid substitutions in the large subunit that could account for the catalytic variation among Paniceae Rubisco are identified; however, incompatibilities with Paniceae Rubisco biogenesis in tobacco hindered their mutagenic testing by chloroplast transformation. Circumventing these bioengineering limitations is critical to tailoring the properties of crop Rubisco to suit future climates.

  • 1076.
    Shefferson, Richard P.
    et al.
    Univ Tokyo, Org Programs Environm Sci, Meguro Ku, Tokyo, Japan.
    Kull, Tiiu
    Estonian Univ Life Sci, Tartu, Estonia.
    Hutchings, Michael J.
    Univ Sussex, Sch Life Sci, Brighton BN1 9QG, E Sussex, England.
    Selosse, Marc-Andre
    Sorbonne Univ, CNRS, Museum Natl Hist Nat, Inst Systemat Evolut Biodivers ISYEB,EPHE, 57 Rue Cuvier,CP39, F-75005 Paris, France;Univ Gdansk, Dept Plant Taxon & Nat Conservat, Gdansk, Poland.
    Jacquemyn, Hans
    Katholieke Univ Leuven, Dept Biol, Leuven, Belgium.
    Kellett, Kimberly M.
    Univ Georgia, Odum Sch Ecol, Athens, GA 30602 USA.
    Menges, Eric S.
    Archbold Biol Stn, Venus, FL USA.
    Primack, Richard B.
    Boston Univ, Dept Biol, 5 Cummington St, Boston, MA 02215 USA.
    Tuomi, Juha
    Univ Turku, Dept Biol, Turku, Finland.
    Alahuhta, Kirsi
    Univ Oulu, Dept Ecol & Genet, Oulu, Finland.
    Hurskainen, Sonja
    Univ Oulu, Dept Ecol & Genet, Oulu, Finland.
    Alexander, Helen M.
    Univ Kansas, Dept Ecol & Evolutionary Biol, Lawrence, KS 66045 USA.
    Anderson, Derek S.
    Dept Nat Resources, St Paul, MN USA.
    Brys, Rein
    Res Inst Nat & Forest, Brussels, Belgium.
    Brzosko, Emilia
    Univ Bialystok, Inst Biol, Bialystok, Poland.
    Dostalik, Slavomir
    Gregg, Katharine
    West Virginia Wesleyan Coll, Dept Biol, Buckhannon, WV USA.
    Ipser, Zdenek
    Univ South Bohemia, Fac Sci, Dept Biol Ecosyst, Ceske Budejovice, Czech Republic.
    Jakalaniemi, Anne
    Univ Oulu, Dept Ecol & Genet, Oulu, Finland.
    Jersakova, Jana
    Univ South Bohemia, Fac Sci, Dept Biol Ecosyst, Ceske Budejovice, Czech Republic.
    Kettle, W. Dean
    Univ Kansas, Kansas Biol Survey, Lawrence, KS USA.
    McCormick, Melissa K.
    Smithsonian Environm Res Ctr, POB 28, Edgewater, MD 21037 USA.
    Mendoza, Ana
    Univ Nacl Autonoma Mexico, Inst Ecol, Ciudad Univ, Mexico City, DF, Mexico.
    Miller, Michael T.
    LGL Ltd, Sidney, BC, Canada.
    Moen, Asbjorn
    NTNU Univ Museum, Dept Nat Hist, Trondheim, Norway.
    Oien, Dag-Inge
    NTNU Univ Museum, Dept Nat Hist, Trondheim, Norway.
    Puttsepp, Ulle
    Estonian Univ Life Sci, Tartu, Estonia.
    Roy, Melanie
    Univ Paul Sabatier, CNRS, Lab Evolut & Divers Biol, Toulouse, France.
    Sather, Nancy
    Dept Nat Resources, St Paul, MN USA.
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Stipkova, Zuzana
    Czech Acad Sci, Global Change Res Inst, Brno, Czech Republic.
    Tali, Kadri
    Estonian Univ Life Sci, Tartu, Estonia.
    Warren, Robert J., II
    SUNY Buffalo State, Dept Biol, Buffalo, NY USA.
    Whigham, Dennis F.
    Smithsonian Environm Res Ctr, POB 28, Edgewater, MD 21037 USA.
    Drivers of vegetative dormancy across herbaceous perennial plant species2018In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 21, no 5, p. 724-733Article in journal (Refereed)
    Abstract [en]

    Vegetative dormancy, that is the temporary absence of aboveground growth for 1year, is paradoxical, because plants cannot photosynthesise or flower during dormant periods. We test ecological and evolutionary hypotheses for its widespread persistence. We show that dormancy has evolved numerous times. Most species displaying dormancy exhibit life-history costs of sprouting, and of dormancy. Short-lived and mycoheterotrophic species have higher proportions of dormant plants than long-lived species and species with other nutritional modes. Foliage loss is associated with higher future dormancy levels, suggesting that carbon limitation promotes dormancy. Maximum dormancy duration is shorter under higher precipitation and at higher latitudes, the latter suggesting an important role for competition or herbivory. Study length affects estimates of some demographic parameters. Our results identify life historical and environmental drivers of dormancy. We also highlight the evolutionary importance of the little understood costs of sprouting and growth, latitudinal stress gradients and mixed nutritional modes.

  • 1077.
    Sheikh, Sanea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Microsatellites in the Flycatcher Genome2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
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  • 1078.
    Shipilina, Daria
    et al.
    Lomonosov Moscow State Univ, Dept Vertebrate Zool, Moscow, Russia..
    Serbyn, Maksym
    Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA..
    Ivanitskii, Vladimir
    Lomonosov Moscow State Univ, Dept Vertebrate Zool, Moscow, Russia..
    Marova, Irina
    Lomonosov Moscow State Univ, Dept Vertebrate Zool, Moscow, Russia..
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Patterns of genetic, phenotypic, and acoustic variation across a chiffchaff (Phylloscopus collybita abietinus/tristis) hybrid zone2017In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 7, no 7, p. 2169-2180Article in journal (Refereed)
    Abstract [en]

    Characterizing patterns of evolution of genetic and phenotypic divergence between incipient species is essential to understand how evolution of reproductive isolation proceeds. Hybrid zones are excellent for studying such processes, as they provide opportunities to assess trait variation in individuals with mixed genetic background and to quantify gene flow across different genomic regions. Here, we combine plumage, song, mtDNA and whole-genome sequence data and analyze variation across a sympatric zone between the European and the Siberian chiffchaff (Phylloscopus collybita abietinus/tristis) to study how gene exchange between the lineages affects trait variation. Our results show that chiffchaff within the sympatric region show more extensive trait variation than allopatric birds, with a large proportion of individuals exhibiting intermediate phenotypic characters. The genomic differentiation between the subspecies is lower in sympatry than in allopatry and sympatric birds have a mix of genetic ancestry indicating extensive ongoing and past gene flow. Patterns of phenotypic and genetic variation also vary between regions within the hybrid zone, potentially reflecting differences in population densities, age of secondary contact, or differences in mate recognition or mate preference. The genomic data support the presence of two distinct genetic clades corresponding to allopatric abietinus and tristis and that genetic admixture is the force underlying trait variation in the sympatric region-the previously described subspecies ("fulvescens") from the region is therefore not likely a distinct taxon. In addition, we conclude that subspecies identification based on appearance is uncertain as an individual with an apparently distinct phenotype can have a considerable proportion of the genome composed of mixed alleles, or even a major part of the genome introgressed from the other subspecies. Our results provide insights into the dynamics of admixture across subspecies boundaries and have implications for understanding speciation processes and for the identification of specific chiffchaff individuals based on phenotypic characters.

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  • 1079. Shoda-Kagaya, E.
    et al.
    Saito, S.
    Okada, M.
    Nozaki, A.
    Nunokawa, K.
    Tsuda, Yoshiaki
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Genetic structure of the oak wilt vector beetle Platypus quercivorus: inferences toward the process of damaged area expansion2010In: BMC Ecology, ISSN 1472-6785, E-ISSN 1472-6785, Vol. 10, no 21Article in journal (Refereed)
  • 1080.
    Siepielski, Adam M.
    et al.
    Univ Arkansas, Dept Biol Sci, Fayetteville, AR 72701 USA..
    Morrissey, Michael B.
    Univ St Andrews, Sch Biol, St Andrews, Fife, Scotland..
    Buoro, Mathieu
    Univ Calif Berkeley, Dept Environm Sci Policy & Management, Berkeley, CA 94720 USA.;Univ Pau & Pays Adour, Inst Natl Rech Agron, St Pee Sur Nivelle, France..
    Carlson, Stephanie M.
    Univ Calif Berkeley, Dept Environm Sci Policy & Management, Berkeley, CA 94720 USA..
    Caruso, Christina M.
    Univ Guelph, Dept Integrat Biol, Guelph, ON, Canada..
    Clegg, Sonya M.
    Univ Oxford, Edward Grey Inst, Dept Zool, Oxford, England..
    Coulson, Tim
    Univ Cambridge, Dept Zool, Cambridge, England..
    DiBattista, Joseph
    Curtin Univ, Dept Environm & Agr, Perth, WA, Australia..
    Gotanda, Kiyoko M.
    Univ Cambridge, Dept Zool, Cambridge, England.;McGill Univ, Redpath Museum, Montreal, PQ, Canada.;McGill Univ, Dept Biol, Montreal, PQ, Canada..
    Francis, Clinton D.
    Calif Polytech State Univ San Luis Obispo, Dept Biol Sci, San Luis Obispo, CA 93407 USA..
    Hereford, Joe
    Univ Calif Davis, Dept Evolut & Ecol, Davis, CA 95616 USA..
    Kingsolver, Joel G.
    Univ N Carolina, Dept Biol, Chapel Hill, NC USA..
    Augustine, Kate E.
    Univ N Carolina, Dept Biol, Chapel Hill, NC USA..
    Kruuk, Loeske E. B.
    Australian Natl Univ, Res Sch Biol, Canberra, ACT, Australia..
    Martin, Ryan A.
    Case Western Reserve Univ, Dept Biol, Cleveland, OH 44106 USA..
    Sheldon, Ben C.
    Univ Oxford, Edward Grey Inst, Dept Zool, Oxford, England..
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Svensson, Erik I.
    Lund Univ, Dept Biol, Lund, Sweden..
    Wade, Michael J.
    Indiana Univ, Dept Biol, Bloomington, IN USA..
    MacColl, Andrew D. C.
    Univ Nottingham, Sch Life Sci, Nottingham, England..
    Response to Comment on "Precipitation drives global variation in natural selection"2018In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 359, no 6374, article id eaan5760Article in journal (Other academic)
    Abstract [en]

    The comment by Myers-Smith and Myers focuses on three main points: (i) the lack of a mechanistic explanation for climate-selection relationships, (ii) the appropriateness of the climate data used in our analysis, and (iii) our focus on estimating climate-selection relationships across (rather than within) taxonomic groups. We address these critiques in our response.

  • 1081.
    Siljestam, Mattias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Östman, Örjan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    The combined effects of temporal autocorrelation and the costs of plasticity on the evolution of plasticity2017In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 30, no 7, p. 1361-1371Article in journal (Refereed)
    Abstract [en]

    Adaptive phenotypic plasticity is an important source of intraspecific variation, and for many plastic traits, the costs or factors limiting plasticity seem cryptic. However, there are several different factors that may constrain the evolution of plasticity, but few models have considered costs and limiting factors simultaneously. Here we use a simulation model to investigate how the optimal level of plasticity in a population depends on a fixed maintenance fitness cost for plasticity or an incremental fitness cost for producing a plastic response in combination with environmental unpredictability (environmental fluctuation speed) limiting plasticity. Our model identifies two mechanisms that act, almost separately, to constrain the evolution of plasticity: (i) the fitness cost of plasticity scaled by the nonplastic environmental tolerance, and (ii) the environmental fluctuation speed scaled by the rate of phenotypic change. That is, the evolution of plasticity is constrained by the high cost of plasticity in combination with high tolerance for environmental variation, or fast environmental changes in combination with slow plastic response. Qualitatively similar results are found when maintenance and incremental fitness costs of plasticity are incorporated, although a larger degree of plasticity is selected for with an incremental cost. Our model highlights that it is important to consider direct fitness costs and phenotypic limitations in relation to nonplastic environmental tolerance and environmental fluctuations, respectively, to understand what constrains the evolution of phenotypic plasticity.

  • 1082.
    Silva, C. N. S.
    et al.
    Univ Helsinki, Dept Biosci, Metapopulat Res Ctr, Helsinki, Finland;James Cook Univ, Coll Marine & Environm Sci, Ctr Sustainable Trop Fisheries & Aquaculture, Townsville, Qld, Australia.
    McFarlane, S. Eryn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Hagen, I. J.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Ronnegard, L.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden;Dalarna Univ, Sch Technol & Business Studies, Falun, Sweden.
    Billing, A. M.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Kvalnes, T.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Kemppainen, P.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Ronning, B.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Ringsby, T. H.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Saether, B-E
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Jensen, H.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Husby, A.
    Univ Helsinki, Dept Biosci, Metapopulat Res Ctr, Helsinki, Finland;Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Insights into the genetic architecture of morphological traits in two passerine bird species2017In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 119, no 3, p. 197-205Article in journal (Refereed)
    Abstract [en]

    Knowledge about the underlying genetic architecture of phenotypic traits is needed to understand and predict evolutionary dynamics. The number of causal loci, magnitude of the effects and location in the genome are, however, still largely unknown. Here, we use genome-wide single-nucleotide polymorphism (SNP) data from two large-scale data sets on house sparrows and collared flycatchers to examine the genetic architecture of different morphological traits (tarsus length, wing length, body mass, bill depth, bill length, total and visible badge size and white wing patches). Genomic heritabilities were estimated using relatedness calculated from SNPs. The proportion of variance captured by the SNPs (SNP-based heritability) was lower in house sparrows compared with collared flycatchers, as expected given marker density (6348 SNPs in house sparrows versus 38 689 SNPs in collared flycatchers). Indeed, after downsampling to similar SNP density and sample size, this estimate was no longer markedly different between species. Chromosome-partitioning analyses demonstrated that the proportion of variance explained by each chromosome was significantly positively related to the chromosome size for some traits and, generally, that larger chromosomes tended to explain proportionally more variation than smaller chromosomes. Finally, we found two genome-wide significant associations with very small-effect sizes. One SNP on chromosome 20 was associated with bill length in house sparrows and explained 1.2% of phenotypic variation (V-P), and one SNP on chromosome 4 was associated with tarsus length in collared flycatchers (3% of V-P). Although we cannot exclude the possibility of undetected large-effect loci, our results indicate a polygenic basis for morphological traits.

  • 1083.
    Silva, Willian T. A. F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Non-genetic processes in development and heredity2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    There is a swiftly increasing amount of empirical evidence that non-genetic factors, such as DNA methylation and small RNAs, play an important role not only in development but also in heredity and, therefore, evolutionary dynamics. One of the most interesting aspects of non-genetic processes is their responsiveness to environmental conditions, which has been shown to affect not only the phenotype and fitness of the individuals directly exposed to the stimulus, but also their offspring even when the stimulus is no longer present, indicating that the transmission of non-genetic factors across generations might work analogously to immunization against recurring conditions. In this thesis, I explored the effects and consequences of non-genetic processes in development and heredity, from both theoretical and experimental perspectives. In Article I, I created a mathematical model of DNA methylation dynamics during the maternal-to-zygotic transition, leading to the zygotic genome activation. I found that there is a developmental constraint on the transition between different cell lineages, with an increasing flexibility of active methylation and decreasing flexibility of maintenance (de-)methylation. In Article II, we explored the dynamics of small RNA production throughout development, including their amplification, transgenerational transmission and responsiveness to environmental conditions. Responsiveness of small RNA production resulted in greater benefits when soma and germline are both responsive, especially in highly correlated environmental conditions. In Article III, I carried out experiments on zebrafish to explore the effects of the male social environment on sperm production in terms of sperm morphology and DNA quality. Males exposed to different social treatments produced sperm with different morphologies and DNA integrity levels. In Article IV, we used the same experimental design to look at the effects of the male social environment on offspring development in terms of differential gene expression patterns. Males exposed to different social treatments sired offspring that showed different expression patterns of genes involved in post-transcriptional processes of gene expression regulation.  Our findings shed light on the importance of non-genetic processes in development and heredity and contributes to the current knowledge about which and how non-genetic mechanisms can potentially affect evolutionary dynamics.

    List of papers
    1. Methylation dynamics during the maternal-to-zygotic genome transition in dioecious species
    Open this publication in new window or tab >>Methylation dynamics during the maternal-to-zygotic genome transition in dioecious species
    2018 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 13, no 7, article id e0200028Article in journal (Refereed) Published
    Abstract [en]

    The starting point of a new generation in sexually reproducing species is fertilization. In many species, fertilization is followed by cell divisions controlled primarily by maternal transcripts, with little to no zygotic transcription. The activation of the zygotic genome (ZGA) is part of a process called maternal-to-zygotic transition (MZT), during which transcripts from the zygotic genome take control of development, setting the conditions for cellular specialization. While we know that epigenetic processes (e.g. methylation) are involved in the MZT, their roles and interplay in the transition are largely unknown. I developed a model and used simulations to elucidate the interaction between possible epigenetic processes, namely methylation processes, involved in the MZT. The model focuses on the dynamics of global methylation levels and how these interact with factors such as a parental repressor and the nucleocytoplasmic ratio to trigger the ZGA, followed by development from fertilization to adulthood. In addition, I included transgenerational effects transmitted to the zygote from both parents through their gametes to show that these may set the stage for plastic developmental processes. I demonstrate that the rates of maintenance methylation and demethylation, which are important for the achievement of the final methylation levels of an individual, exhibit a certain level of flexibility in terms of parameter values. I find that high final methylation levels require more restricted combinations of parameter values. The model is discussed in the context of the current empirical knowledge and provide suggestions for directions of future empirical and theoretical studies.

    National Category
    Genetics
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-356599 (URN)10.1371/journal.pone.0200028 (DOI)000438170300026 ()29990374 (PubMedID)
    Available from: 2018-08-02 Created: 2018-08-02 Last updated: 2018-09-25Bibliographically approved
    2. Evolution of small RNA production under fluctuating environmental conditions
    Open this publication in new window or tab >>Evolution of small RNA production under fluctuating environmental conditions
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology Genetics Developmental Biology Ecology
    Identifiers
    urn:nbn:se:uu:diva-359418 (URN)
    Available from: 2018-09-01 Created: 2018-09-01 Last updated: 2018-09-05
    3. The effects of male social environment on sperm phenotype and genome integrity
    Open this publication in new window or tab >>The effects of male social environment on sperm phenotype and genome integrity
    Show others...
    2019 (English)In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 32, no 6, p. 535-544Article in journal (Refereed) Published
    Abstract [en]

    Sperm function and quality are primary determinants of male reproductive performance and hence fitness. The presence of rival males has been shown to affect ejaculate and sperm traits in a wide range of taxa. However, male physiological conditions may not only affect sperm phenotypic traits but also their genetic and epigenetic signatures, affecting the fitness of the resulting offspring. We investigated the effects of male-male competition on sperm quality using TUNEL assays and geometric morphometrics in the zebrafish, Danio rerio. We found that the sperm produced by males exposed to high male-male competition had smaller heads but larger midpiece and flagellum than sperm produced by males under low competition. Head and flagella also appeared less sensitive to the osmotic stress induced by activation with water. In addition, more sperm showed signals of DNA damage in ejaculates of males under high competition. These findings suggest that the presence of a rival male may have positive effects on sperm phenotypic traits but negative effects on sperm DNA integrity. Overall, males facing the presence of rival males may produce faster swimming and more competitive sperm but this may come at a cost for the next generation.

    Place, publisher, year, edition, pages
    John Wiley & Sons, 2019
    Keywords
    DNA damage, sexual selection, sperm competition, trade‐offs
    National Category
    Evolutionary Biology Zoology Genetics
    Identifiers
    urn:nbn:se:uu:diva-359415 (URN)10.1111/jeb.13435 (DOI)000472662300002 ()30817032 (PubMedID)
    Funder
    EU, European Research Council, HapSelA-336633Knut and Alice Wallenberg Foundation
    Available from: 2018-09-01 Created: 2018-09-01 Last updated: 2019-08-13Bibliographically approved
    4. Social environment of fathers affects gene expression patterns in early offspring
    Open this publication in new window or tab >>Social environment of fathers affects gene expression patterns in early offspring
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Developmental Biology Genetics Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-359417 (URN)
    Available from: 2018-09-01 Created: 2018-09-01 Last updated: 2018-09-05
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  • 1084.
    Silva, Willian T. A. F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Jolly, Cécile
    Alavioon, Ghazal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Kiehl, Berrit
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Immler, Simone
    Social environment of fathers affects gene expression patterns in early offspringManuscript (preprint) (Other academic)
  • 1085.
    Silva, Willian T. A. F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Otto, Sarah P.
    Immler, Simone
    Evolution of small RNA production under fluctuating environmental conditionsManuscript (preprint) (Other academic)
  • 1086.
    Silva, Willian T. A. F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Sáez-Espinosa, Paula
    Department of Biotechnology, University of Alicante, Alicante, Spain.
    Torrijo-Boix, Stéphanie
    Department of Biotechnology, University of Alicante, Alicante, Spain.
    Romero, Alejandro
    Department of Biotechnology, University of Alicante, Alicante, Spain.
    Devaux, Caroline
    School of Biological Sciences, University of East Anglia, Norwich, UK.
    Durieux, Mathilde
    School of Biological Sciences, University of East Anglia, Norwich, UK.
    Gómez-Torres, María José
    Department of Biotechnology, University of Alicante, Alicante, Spain;Cátedra Human Fertility, University of Alicante, Alicante, Spain.
    Immler, Simone
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. School of Biological Sciences, University of East Anglia, Norwich, UK.
    The effects of male social environment on sperm phenotype and genome integrity2019In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 32, no 6, p. 535-544Article in journal (Refereed)
    Abstract [en]

    Sperm function and quality are primary determinants of male reproductive performance and hence fitness. The presence of rival males has been shown to affect ejaculate and sperm traits in a wide range of taxa. However, male physiological conditions may not only affect sperm phenotypic traits but also their genetic and epigenetic signatures, affecting the fitness of the resulting offspring. We investigated the effects of male-male competition on sperm quality using TUNEL assays and geometric morphometrics in the zebrafish, Danio rerio. We found that the sperm produced by males exposed to high male-male competition had smaller heads but larger midpiece and flagellum than sperm produced by males under low competition. Head and flagella also appeared less sensitive to the osmotic stress induced by activation with water. In addition, more sperm showed signals of DNA damage in ejaculates of males under high competition. These findings suggest that the presence of a rival male may have positive effects on sperm phenotypic traits but negative effects on sperm DNA integrity. Overall, males facing the presence of rival males may produce faster swimming and more competitive sperm but this may come at a cost for the next generation.

    Download full text (pdf)
    fulltext
  • 1087.
    Singer, David
    et al.
    Univ Neuchatel, Inst Biol, Lab Soil Biodivers, Neuchatel, Switzerland;Univ Sao Paulo, Inst Biosci, Dept Zool, Sao Paulo, Brazil.
    Mitchell, Edward A. D.
    Univ Neuchatel, Inst Biol, Lab Soil Biodivers, Neuchatel, Switzerland;Jardin Bot Neuchatel, Neuchatel, Switzerland.
    Payne, Richard J.
    Univ York, Environm, York, N Yorkshire, England.
    Blandenier, Quentin
    Univ Neuchatel, Inst Biol, Lab Soil Biodivers, Neuchatel, Switzerland;CSIC, Real Jardin Bot, Madrid, Spain.
    Duckert, Clement
    Univ Neuchatel, Inst Biol, Lab Soil Biodivers, Neuchatel, Switzerland.
    Fernandez, Leonardo D.
    Univ Neuchatel, Inst Biol, Lab Soil Biodivers, Neuchatel, Switzerland;Univ Bernardo OHiggins, Ctr Invest Recursos Nat & Sustentabilidad CIRENYS, Santiago, Chile.
    Fournier, Bertrand
    Concordia Univ, Dept Biol, Community & Quantitat Ecol Lab, Montreal, PQ, Canada.
    Hernandez, Cristian E.
    Barrio Univ Concepcion, Univ Concepcion, Dept Zool, Fac Ciencias Nat & Oceanog, Concepcion, Chile.
    Granath, Gustaf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Bragazza, Luca
    WSL Swiss Fed Inst Forest Snow & Landscape Res, Lausanne, Switzerland;Ecole Polytech Fed Lausanne, Sch Architecture Civil & Environm Engn ENAC, Lab Ecol Syst ECOS, Lausanne, Switzerland;Univ Ferrara, Dept Life Sci & Biotechnol, Ferrara, Italy.
    Koronatova, Natalia G.
    Russian Acad Sci, Siberian Branch, Inst Soil Sci & Agrochem, Lab Biogeocenol, Novosibirsk, Russia.
    Goia, Irina
    Babes Bolyai Univ, Fac Biol & Geol, Dept Taxon & Ecol, Cluj Napoca, Romania.
    Harris, Lorna I.
    McMaster Univ, Sch Geog & Earth Sci, Hamilton, ON, Canada.
    Kajukalo, Katarzyna
    Adam Mickiewicz Univ, Fac Geog & Geol Sci, Lab Wetland Ecol & Monitoring, Poznan, Poland;Adam Mickiewicz Univ, Dept Biogeog & Paleoecol, Poznan, Poland.
    Kosakyan, Anush
    Czech Acad Sci, Biol Ctr, Inst Parasitol, Ceske Budejovice, Czech Republic.
    Lamentowicz, Mariusz
    Adam Mickiewicz Univ, Fac Geog & Geol Sci, Lab Wetland Ecol & Monitoring, Poznan, Poland;Adam Mickiewicz Univ, Dept Biogeog & Paleoecol, Poznan, Poland.
    Kosykh, Natalia P.
    Russian Acad Sci, Siberian Branch, Inst Soil Sci & Agrochem, Lab Biogeocenol, Novosibirsk, Russia.
    Vellak, Kai
    Univ Tartu, Nat Hist Museum, Inst Ecol & Earth Sci, Tartu, Estonia.
    Lara, Enrique
    Univ Neuchatel, Inst Biol, Lab Soil Biodivers, Neuchatel, Switzerland;CSIC, Real Jardin Bot, Madrid, Spain.
    Dispersal limitations and historical factors determine the biogeography of specialized terrestrial protists2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 12, p. 3089-3100Article in journal (Refereed)
    Abstract [en]

    Recent studies show that soil eukaryotic diversity is immense and dominated by micro-organisms. However, it is unclear to what extent the processes that shape the distribution of diversity in plants and animals also apply to micro-organisms. Major diversification events in multicellular organisms have often been attributed to long-term climatic and geological processes, but the impact of such processes on protist diversity has received much less attention as their distribution has often been believed to be largely cosmopolitan. Here, we quantified phylogeographical patterns in Hyalosphenia papilio, a large testate amoeba restricted to Holarctic Sphagnum-dominated peatlands, to test if the current distribution of its genetic diversity can be explained by historical factors or by the current distribution of suitable habitats. Phylogenetic diversity was higher in Western North America, corresponding to the inferred geographical origin of the H. papilio complex, and was lower in Eurasia despite extensive suitable habitats. These results suggest that patterns of phylogenetic diversity and distribution can be explained by the history of Holarctic Sphagnum peatland range expansions and contractions in response to Quaternary glaciations that promoted cladogenetic range evolution, rather than the contemporary distribution of suitable habitats. Species distributions were positively correlated with climatic niche breadth, suggesting that climatic tolerance is key to dispersal ability in H. papilio. This implies that, at least for large and specialized terrestrial micro-organisms, propagule dispersal is slow enough that historical processes may contribute to their diversification and phylogeographical patterns and may partly explain their very high overall diversity.

  • 1088.
    Sirkiä, Päivi M
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    McFarlane, S. Eryn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Jones, William
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Wheatcroft, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ålund, Murielle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Rybinski, Jakub
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Climate-driven build-up of temporal isolation within a recently formed avian hybrid zone.2018In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 72, no 2, p. 363-374Article in journal (Refereed)
    Abstract [en]

    Divergence in the onset of reproduction can act as an important source of reproductive isolation (i.e., allochronic isolation) between co-occurring young species, but evidence for the evolutionary processes leading to such divergence is often indirect. While advancing spring seasons strongly affect the onset of reproduction in many taxa, it remains largely unexplored whether contemporary spring advancement directly affects allochronic isolation between young species. We examined how increasing spring temperatures affected onset of reproduction and thereby hybridization between pied and collared flycatchers (Ficedula spp.) across habitat types in a young secondary contact zone. We found that both species have advanced their timing of breeding in 14 years. However, selection on pied flycatchers to breed earlier was weaker, resulting in a slower response to advancing springs compared to collared flycatchers and thereby build-up of allochronic isolation between the species. We argue that a preadaptation to a broader niche use (diet) of pied flycatchers explains the slower response to raising spring temperature, but that reduced risk to hybridize may contribute to further divergence in the onset of breeding in the future. Our results show that minor differences in the response to environmental change of co-occurring closely related species can quickly cause allochronic isolation.

  • 1089.
    Sjödin, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Skoglund, Pontus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Assessing the Maximum Contribution from Ancient Populations2014In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 31, no 5, p. 1248-1260Article in journal (Refereed)
    Abstract [en]

    Ancestral relationships between populations separated by time represent an often neglected dimension in population genetics, a field which historically has focused on analysis of spatially distributed samples from the same point in time. Models are usually straightforward when two time-separated populations are assumed to be completely isolated from all other populations. However, this is usually an unrealistically stringent assumption when there is gene flow with other populations. Here, we investigate continuity in the presence of gene flow from unknown populations. This setup allows a more nuanced treatment of questions regarding population continuity in terms of "level of contribution" from a particular ancient population to a more recent population. We propose a statistical framework which makes use of a biallelic marker sampled at two different points in time to assess population contribution, and present two different interpretations of the concept. We apply the approach to published data from a prehistoric human population in Scandinavia (Malmstrom H, Gilbert MTP, Thomas MG, Brandstrom M, StorAyen J, Molnar P, Andersen PK, Bendixen C, Holmlund G, Gotherstrom A, et al. 2009. Ancient DNA reveals lack of continuity between Neolithic hunter-gatherers and contemporary Scandinavians. Curr Biol. 19:1758-1762) and Pleistocene woolly mammoth (Barnes I, Shapiro B, Lister A, Kuznetsova T, Sher A, Guthrie D, Thomas MG. 2007. Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius. Curr Biol. 17:1072-1075; Debruyne R, Chu G, King CE, Bos K, Kuch M, Schwarz C, Szpak P, Grocke DR, Matheus P, Zazula G, et al. 2008. Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths. Curr Biol. 18:1320-1326).

  • 1090.
    Sjöstrand, Agnès E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Origins and Adaptation in Humans: A Case Study of Taste and Lifestyle2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, I use population genetics and statistical approaches to investigate early human demography, infer local adaptation in diverse sets of populations, and study the genetic basis for taste perception.

    In the first paper, I examine the genomic evidence for a severe bottleneck, which has been suggested based on paleontological and climate studies to coincide with the emergence of anatomically modern humans. Using a Bayesian approach, I evaluate the genetic evidence of a bottleneck between 190,000 and 130,000 years ago and find that the data is in favor of a model without bottleneck at this time point.

    I further develop a method to detect local adaptation based on frequencies of private haplotypes. I first show, using simulated data, that this method can detect local adaption. Applied to large-scale human genotype data, this method detects known signals of positive selection in human data such as the positive selection around the lactase gene in Europeans and East Africans. Also, this method permits to improve knowledge on potential adaptation events in humans as it finds several regions potentially selected that were not previously described. I further investigate patterns of adaptation in whole genome data based on a diverse set of African populations. The results from the regions potentially selected show that diet and pathogens are the common driving forces of adaptation in all studied populations.

    There is evidence that taste perception have evolved in concert with diet, environment, and the organismal needs in humans. For this reason, I study taste perception in populations differing on lifestyle (hunter-gatherers, farmers and nomad herders). I present taste perception phenotypes for all tastes (sweet, bitter, sour, salty and umami) and relate them to high density genotype data. I show that taste and taste-involved genes have evolved with lifestyle. By performing an association study, I also show that variation in taste perception involves more genes than only the taste receptors genes.

    In this thesis, by analyzing human genetic data with a population genetics approaches, I covered several topics of human ancient demography and adaptation and show the utility of using large-scale genetic data to better understand human history.

    List of papers
    1. Resequencing Data Provide No Evidence for a Human Bottleneck in Africa during the Penultimate Glacial Period
    Open this publication in new window or tab >>Resequencing Data Provide No Evidence for a Human Bottleneck in Africa during the Penultimate Glacial Period
    2012 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 29, no 7, p. 1851-1860Article in journal (Refereed) Published
    Abstract [en]

    Based on the accumulation of genetic, climatic, and fossil evidence, a central theory in paleoanthropology stipulates that a demographic bottleneck coincided with the origin of our species Homo Sapiens. This theory proposes that anatomically modern humans-which were only present in Africa at the time-experienced a drastic bottleneck during the penultimate glacial age (130-190 kya) when a cold and dry climate prevailed. Two scenarios have been proposed to describe the bottleneck, which involve either a fragmentation of the range occupied by humans or the survival of one small group of humans. Here, we analyze DNA sequence data from 61 nuclear loci sequenced in three African populations using Approximate Bayesian Computation and numerical simulations. In contrast to the bottleneck theory, we show that a simple model without any bottleneck during the penultimate ice age has the greatest statistical support compared with bottleneck models. Although the proposed bottleneck is ancient, occurring at least 130 kya, we can discard the possibility that it did not leave detectable footprints in the DNA sequence data except if the bottleneck involves a less than a 3-fold reduction in population size. Finally, we confirm that a simple model without a bottleneck is able to reproduce the main features of the observed patterns of genetic variation. We conclude that models of Pleistocene refugium for modern human origins now require substantial revision.

    Keywords
    human origins, African genetic diversity, penultimate glacial age, approximate Bayesian computation, African bottleneck, oxygen isotope 6
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-177576 (URN)10.1093/molbev/mss061 (DOI)000305409000015 ()
    Available from: 2012-07-16 Created: 2012-07-16 Last updated: 2017-12-07Bibliographically approved
    2. Private haplotypes can reveal local adaptation
    Open this publication in new window or tab >>Private haplotypes can reveal local adaptation
    2014 (English)In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 15, p. 61-Article in journal (Refereed) Published
    Abstract [en]

    Background: Genome-wide scans for regions that demonstrate deviating patterns of genetic variation have become common approaches for finding genes targeted by selection. Several genomic patterns have been utilized for this purpose, including deviations in haplotype homozygosity, frequency spectra and genetic differentiation between populations. Results: We describe a novel approach based on the Maximum Frequency of Private Haplotypes - MFPH - to search for signals of recent population-specific selection. The MFPH statistic is straightforward to compute for phased SNP-and sequence-data. Using both simulated and empirical data, we show that MFPH can be a powerful statistic to detect recent population-specific selection, that it performs at the same level as other commonly used summary statistics (e.g. F-ST, iHS and XP-EHH), and that MFPH in some cases capture signals of selection that are missed by other statistics. For instance, in the Maasai, MFPH reveals a strong signal of selection in a region where other investigated statistics fail to pick up a clear signal that contains the genes DOCK3, MAPKAPK3 and CISH. This region has been suggested to affect height in many populations based on phenotype-genotype association studies. It has specifically been suggested to be targeted by selection in Pygmy groups, which are on the opposite end of the human height spectrum compared to the Maasai. Conclusions: From the analysis of both simulated and publicly available empirical data, we show that MFPH represents a summary statistic that can provide further insight concerning population-specific adaptation.

    Keywords
    Local adaptation, Haplotype, Positive selection, Human height
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-228475 (URN)10.1186/1471-2156-15-61 (DOI)000336863400001 ()
    Available from: 2014-07-15 Created: 2014-07-15 Last updated: 2017-12-05Bibliographically approved
    3. Patterns of local adaptation in Africans
    Open this publication in new window or tab >>Patterns of local adaptation in Africans
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    (English)Manuscript (preprint) (Other academic)
    Keywords
    Adaptation, lifestyle, selection scans
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-263084 (URN)
    Available from: 2015-09-25 Created: 2015-09-25 Last updated: 2015-11-10
    4. Taste and lifestyle: insights from SNP-chip data.
    Open this publication in new window or tab >>Taste and lifestyle: insights from SNP-chip data.
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Keywords
    Taste, GWAS, lifestyle, adaptation
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-263083 (URN)
    Available from: 2015-09-25 Created: 2015-09-25 Last updated: 2015-11-10
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  • 1091. Skarpe, C.
    et al.
    Bergström, R.
    Makhabu, S.
    Rooke, T.
    Hytteborn, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Danell, K.
    Plant-Herbivore Interactions2014In: Elephants and Savanna Woodland Ecosystems: A Study from Chobe National Park, Botswana / [ed] C. Skarpe, J. T. du Toit and S. R. Moe, Wiley-Blackwell, 2014, p. 189-206Chapter in book (Refereed)
    Abstract [en]

    To a casual observer, the importance of large herbivores for ecosystem structure and dynamics can seem more obvious in African savannas than in many other ecosystems because of their high abundance, diversity and species richness of ungulates. African savannas have also had a long uninterrupted history of mammalian herbivory, leading to the evolution of plant traits adapted to herbivory and to reciprocal traits in herbivores. In nutrient-poor savannas such as those on Kalahari sand in the Chobe National Park, Botswana, elephants, Loxodonta africana, are a main agent creating spatial and temporal variation in the vegetation and ecosystems. Within this framework, elephants and smaller herbivores interact with individual plants and plant populations, exploiting and modifying heterogeneity at many scales. Intermittent grazing in systems of migratory or highly mobile herbivores provides food plants with a recovery period, and could be one reason for the 'success' and abundance of many migratory herbivore species.

  • 1092.
    Skoglund, Pontus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Reconstructing the Human Past using Ancient and Modern Genomes2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The study of DNA variation is one of the most promising avenues for learning about the evolutionary and historical past of humans and other species. However, the difficulty associated with obtaining DNA directly from ancient remains have for long kept genomic studies of population history trapped in time; confined to interpreting patterns of modern-day variation without direct historical observations. In this thesis, I outline new approaches for the retrieval, analysis and interpretation of large-scale genomic data from ancient populations, including solutions to overcome problems associated with limited genome coverage, modern-day contamination, temporal differences between samples, and post-mortem DNA damage. I integrate large-scale genomic data sets from ancient remains with modern-day variation to trace the human past; from traits targeted by natural selection in the early ancestors of anatomically modern humans, to their descendants' interbreeding with archaic populations in Eurasia and the spread of agriculture in Europe and Africa. By first reconstructing the earliest population diversification events of early modern humans using a novel large-scale genomic data set from Khoe-San populations in southern Africa, I devise a new approach to search for genomic patterns of selective sweeps in ancestral populations and report evidence for skeletal development as a major target of selection during the emergence of early modern humans. Comparing publicly available genomes from archaic humans, I further find that the distribution of archaic human ancestry in Eurasia is more complex than previously thought. In the first direct genomic study of population structure in prehistoric populations, I demonstrate that individuals associated with farming- and hunter-gatherer complexes in Neolithic Scandinavia were strongly genetically differentiated, and direct comparisons with modern-day populations as well as other prehistoric individuals from Southern Europe suggest that this structure originated from Northward expansion of Neolithic farming populations. Finally, I develop a bioinformatic approach for removing modern-day contamination from large-scale ancient DNA sequencing data, and use this method to reconstruct the complete mitochondrial genome sequence of a Siberian Neandertal that is affected by substantial modern-day contamination.

    List of papers
    1. Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History
    Open this publication in new window or tab >>Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History
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    2012 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 338, no 6105, p. 374-379Article in journal (Refereed) Published
    Abstract [en]

    The history of click-speaking Khoe-San, and African populations in general, remains poorly understood. We genotyped ∼2.3 million SNPs in 220 southern Africans and found that the Khoe-San diverged from other populations ≥100,000 years ago, but structure within the Khoe-San dated back to about 35,000 years ago. Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa; instead, it indicated a history of admixture and stratification. We found evidence of adaptation targeting muscle function and immune response, potential adaptive introgression of UV-light protection, and selection predating modern human diversification involving skeletal and neurological development. These new findings illustrate the importance of African genomic diversity in understanding human evolutionary history.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-181302 (URN)10.1126/science.1227721 (DOI)000309955800039 ()
    Available from: 2012-09-21 Created: 2012-09-21 Last updated: 2017-12-07
    2. Archaic human ancestry in East Asia
    Open this publication in new window or tab >>Archaic human ancestry in East Asia
    2011 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 108, no 45, p. 18301-18306Article in journal (Refereed) Published
    Abstract [en]

    Recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of Africa. At the same time, decreasing levels of human genetic diversity have been found at increasing distance from Africa as a consequence of human expansion out of Africa. We analyzed the signal of archaic ancestry in modern human populations, and we investigated how serial founder models of human expansion affect the signal of archaic ancestry using simulations. For descendants of an archaic admixture event, we show that genetic drift coupled with ascertainment bias for common alleles can cause artificial but largely predictable differences in similarity to archaic genomes. In genotype data from non-Africans, this effect results in a biased genetic similarity to Neandertals with increasing distance from Africa. However, in addition to the previously reported gene flow between Neandertals and non-Africans as well as gene flow between an archaic human population from Siberia ("Denisovans") and Oceanians, we found a significant affinity between East Asians, particularly Southeast Asians, and the Denisovagenome-a pattern that is not expected under a model of solely Neandertal admixture in the ancestry of East Asians. These results suggest admixture between Denisovans or a Denisova-related population and the ancestors of East Asians, and that the history of anatomically modern and archaic humans might be more complex than previously proposed.

    Keywords
    human origins, ancient DNA
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-162448 (URN)10.1073/pnas.1108181108 (DOI)000296700000034 ()
    Available from: 2011-12-01 Created: 2011-11-30 Last updated: 2017-12-08Bibliographically approved
    3. Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe
    Open this publication in new window or tab >>Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe
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    2012 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 336, no 6080, p. 466-469Article in journal (Refereed) Published
    Abstract [en]

    The farming way of life originated in the Near East some 11,000 years ago and had reached most of the European continent 5000 years later. However, the impact of the agricultural revolution on demography and patterns of genomic variation in Europe remains unknown. We obtained 249 million base pairs of genomic DNA from similar to 5000-year-old remains of three hunter-gatherers and one farmer excavated in Scandinavia and find that the farmer is genetically most similar to extant southern Europeans, contrasting sharply to the hunter-gatherers, whose distinct genetic signature is most similar to that of extant northern Europeans. Our results suggest that migration from southern Europe catalyzed the spread of agriculture and that admixture in the wake of this expansion eventually shaped the genomic landscape of modern-day Europe.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-174367 (URN)10.1126/science.1216304 (DOI)000303233400045 ()
    Available from: 2012-05-24 Created: 2012-05-15 Last updated: 2017-12-07Bibliographically approved
    4. Ancient genomes mirror mode of subsistence rather than geography in prehistoric Europe
    Open this publication in new window or tab >>Ancient genomes mirror mode of subsistence rather than geography in prehistoric Europe
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    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Recent ancient DNA studies have provided new evidence for prehistoric population structure associated with the contentious transition to an agricultural lifestyle in Europe. In this study, we infer human population structure and history in Holocene Europe by generating ancient genomic sequence data from 9 Scandinavian individuals associated with the foraging Pitted Ware Culture and the agricultural Funnel Beaker Culture (TRB). We obtained up to 1.1x coverage of the genomes for the nine individuals allowing direct comparisons of the two groups. We show that the Neolithic Scandinavian individuals show remarkable population structure corresponding to their cultural association. Looking beyond Scandinavia, we integrate this data with ancient genomes from Southern Europe and find that the Tyrolean Iceman from an agricultural context is most similar to Scandinavian individuals from a farming context, whereas Mesolithic Iberian hunter-gatherers are most similar to Scandinavian hunter-gatherers, opposite to what would have been predicted from their geographical origins. This finding shows that among these individuals, lifestyle is the major determinant of genetic ancestry rather than geography. Comparisons with modern populations reveal a latitudinal relationship where Southern European populations such as Sardinians are closely related with the genetic variation of the agricultural groups, whereas hunter-gatherer individuals appear to have the closest relationship with Baltic populations such as Lithuanians and present-day Scandinavians. Our results also demonstrate that while Middle Eastern populations are not the most similar to Neolithic farmers, this observation can be explained by African-related admixture in more recent times for Middle Eastern groups, which, once accounted for, reveals that the other major component of their ancestry resembles Neolithic farmers. While present-day Scandinavian populations are intermediate between the two groups, consistent with admixture, they appear genetically slightly closer to Neolithic hunter-gatherers than Neolithic farmers. This suggests a model where initial colonization by agricultural populations was followed by later admixture with hunter-gatherer populations or gene flow from other regions.

    National Category
    Biological Sciences
    Research subject
    Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-206770 (URN)
    Available from: 2013-09-04 Created: 2013-09-04 Last updated: 2014-01-23
    5. Separating endogenous ancient DNA from modern-day contamination: application to a Siberian Neandertal
    Open this publication in new window or tab >>Separating endogenous ancient DNA from modern-day contamination: application to a Siberian Neandertal
    Show others...
    2014 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 111, no 6, p. 2229-2234Article in journal (Refereed) Published
    Abstract [en]

    One of the main impediments for obtaining DNA sequences from ancient humanskeletons is the presence of contaminating modern human DNA molecules in many fossil samples and laboratory reagents. However, DNA fragments isolated from ancient specimens show a characteristic DNA damage pattern, caused by miscoding lesions, that differs from present-day DNA sequences. Here, we develop a framework for evaluating the likelihood of a sequence originating from a model with post-mortem degradation (PMD)—summarized in a PMD score—which allows the identification of DNA fragments that are unlikely to originate from present-day sources. We apply this approach to a contaminated Neandertal specimen from the Okladnikov cave in Siberia in order to isolate its endogenous DNA from modern human contaminants, and show that the reconstructed mitochondrial genome sequence is more closely related to the variation of Western Neandertals than what was discernible from previous analyses. Our method opens up the potential for genomic analysis of contaminated fossil material.

    National Category
    Biological Sciences
    Research subject
    Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-206755 (URN)10.1073/pnas.1318934111 (DOI)000330999600045 ()
    Available from: 2013-09-04 Created: 2013-09-04 Last updated: 2017-12-06Bibliographically approved
    6. Investigating population history using temporal genetic differentiation
    Open this publication in new window or tab >>Investigating population history using temporal genetic differentiation
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    2014 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 31, no 9, p. 2516-2527Article in journal (Refereed) Published
    Abstract [en]

    The rapid advance of sequencing technology coupled with improvements in molecular methods for obtaining genetic data from ancient sources holds the promise of producing a wealth of genomic data from time-separated individuals. However, the population genetic properties of time-structured samples have not been extensively explored. Here, we consider the implications of temporal sampling for analyses of genetic differentiation, and use a temporal coalescent framework to show that complex historical events such as size reductions, population replacements, and transient genetic barriers between populations leave a footprint of genetic differentiation that can be traced through history using temporal samples. Our results emphasize explicit consideration of the temporal structure when making inferences, and indicate that genomic data from ancient individuals will greatly increase our ability to reconstruct population history.

    National Category
    Biological Sciences
    Research subject
    Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-206756 (URN)10.1093/molbev/msu192 (DOI)000343401100022 ()
    Available from: 2013-09-04 Created: 2013-09-04 Last updated: 2017-12-06Bibliographically approved
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  • 1093.
    Skoglund, Pontus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Archaic human ancestry in East Asia2011In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 108, no 45, p. 18301-18306Article in journal (Refereed)
    Abstract [en]

    Recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of Africa. At the same time, decreasing levels of human genetic diversity have been found at increasing distance from Africa as a consequence of human expansion out of Africa. We analyzed the signal of archaic ancestry in modern human populations, and we investigated how serial founder models of human expansion affect the signal of archaic ancestry using simulations. For descendants of an archaic admixture event, we show that genetic drift coupled with ascertainment bias for common alleles can cause artificial but largely predictable differences in similarity to archaic genomes. In genotype data from non-Africans, this effect results in a biased genetic similarity to Neandertals with increasing distance from Africa. However, in addition to the previously reported gene flow between Neandertals and non-Africans as well as gene flow between an archaic human population from Siberia ("Denisovans") and Oceanians, we found a significant affinity between East Asians, particularly Southeast Asians, and the Denisovagenome-a pattern that is not expected under a model of solely Neandertal admixture in the ancestry of East Asians. These results suggest admixture between Denisovans or a Denisova-related population and the ancestors of East Asians, and that the history of anatomically modern and archaic humans might be more complex than previously proposed.

  • 1094.
    Skoglund, Pontus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Malmstrom, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Omrak, Ayca
    Raghavan, Maanasa
    Valdiosera, Cristina
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Hall, Per
    Tambets, Kristiina
    Parik, Jueri
    Sjogren, Karl-Goran
    Apel, Jan
    Willerslev, Eske
    Stora, Jan
    Gotherstrom, Anders
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers2014In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 344, no 6185, p. 747-750Article in journal (Refereed)
    Abstract [en]

    Prehistoric population structure associated with the transition to an agricultural lifestyle in Europe remains a contentious idea. Population-genomic data from 11 Scandinavian Stone Age human remains suggest that hunter-gatherers had lower genetic diversity than that of farmers. Despite their close geographical proximity, the genetic differentiation between the two Stone Age groups was greater than that observed among extant European populations. Additionally, the Scandinavian Neolithic farmers exhibited a greater degree of hunter-gatherer-related admixture than that of the Tyrolean Iceman, who also originated from a farming context. In contrast, Scandinavian hunter-gatherers displayed no significant evidence of introgression from farmers. Our findings suggest that Stone Age foraging groups were historically in low numbers, likely owing to oscillating living conditions or restricted carrying capacity, and that they were partially incorporated into expanding farming groups.

  • 1095.
    Skulason, Skuli
    et al.
    Holar Univ, Dept Aquaculture & Fish Biol, IS-551 Sauoarkrokur, Iceland;Iceland Museum Nat Hist, Brynjolfsgata 5, IS-107 Reykjavik, Iceland.
    Parsons, Kevin J.
    Univ Glasgow, Inst Biodivers Anim Hlth & Comparat Med, Glasgow G12 8QQ, Lanark, Scotland.
    Svanbäck, Richard
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Rasanen, Katja
    EAWAG, Swiss Fed Inst Aquat Sci & Technol, Dept Aquat Ecol, Ueberlandstr 133, CH-8600 Dubendorf, Switzerland;Swiss Fed Inst Technol, Inst Integrat Biol, Ueberlandstr 133, CH-8600 Dubendorf, Switzerland.
    Ferguson, Moira M.
    Univ Guelph, Dept Integrat Biol, Guelph, ON N1G 2W1, Canada.
    Adams, Colin E.
    Univ Glasgow, Scottish Ctr Ecol & Nat Environm, IBAHCM, Glasgow G12 8QQ, Lanark, Scotland.
    Amundsen, Per-Arne
    Univ Tromso, Freshwater Ecol Grp, Dept Arctic & Marine Biol, Fac Biosci Fisheries & Econ, N-9037 Tromso, Norway.
    Bartels, Pia
    Umea Univ, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden.
    Bean, Colin W.
    Scottish Nat Heritage, Caspian House,Clydebank Business Pk, Clydebank G81 2NR, Scotland.
    Boughman, Janette W.
    Michigan State Univ, Dept Integrat Biol, E Lansing, MI 48824 USA.
    Englund, Goeran
    Umea Univ, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden.
    Gudbrandsson, Johannes
    Univ Iceland, Inst Life & Environm Sci, IS-101 Reykjavik, Iceland.
    Hooker, Oliver E.
    PR Stat LTD, 53 Morrison St, Glasgow G5 8LB, Lanark, Scotland.
    Hudson, Alan G.
    Umea Univ, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden.
    Kahilainen, Kimmo K.
    Inland Norway Univ Appl Sci, Dept Forestry & Wildlife Management, Campus Evenstad,Anne Evenstadvei 80, NO-2480 Koppang, Norway.
    Knudsen, Rune
    Univ Tromso, Freshwater Ecol Grp, Dept Arctic & Marine Biol, Fac Biosci Fisheries & Econ, N-9037 Tromso, Norway.
    Kristjansson, Bjarni K.
    Holar Univ, Dept Aquaculture & Fish Biol, IS-551 Sauoarkrokur, Iceland.
    Leblanc, Camille A-L.
    Holar Univ, Dept Aquaculture & Fish Biol, IS-551 Sauoarkrokur, Iceland.
    Jonsson, Zophonias
    Univ Iceland, Inst Life & Environm Sci, IS-101 Reykjavik, Iceland.
    Ohlund, Gunnar
    Umea Univ, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden.
    Smith, Carl
    Univ St Andrews, Sch Biol, St Andrews KY16 9AJ, Fife, Scotland.
    Snorrason, Sigurdur S.
    Univ Iceland, Inst Life & Environm Sci, IS-101 Reykjavik, Iceland.
    A way forward with eco evo devo: an extended theory of resource polymorphism with postglacial fishes as model systems2019In: Biological Reviews, ISSN 1464-7931, E-ISSN 1469-185X, Vol. 94, no 5, p. 1786-1808Article in journal (Refereed)
    Abstract [en]

    A major goal of evolutionary science is to understand how biological diversity is generated and altered. Despite considerable advances, we still have limited insight into how phenotypic variation arises and is sorted by natural selection. Here we argue that an integrated view, which merges ecology, evolution and developmental biology (eco evo devo) on an equal footing, is needed to understand the multifaceted role of the environment in simultaneously determining the development of the phenotype and the nature of the selective environment, and how organisms in turn affect the environment through eco evo and eco devo feedbacks. To illustrate the usefulness of an integrated eco evo devo perspective, we connect it with the theory of resource polymorphism (i.e. the phenotypic and genetic diversification that occurs in response to variation in available resources). In so doing, we highlight fishes from recently glaciated freshwater systems as exceptionally well-suited model systems for testing predictions of an eco evo devo framework in studies of diversification. Studies on these fishes show that intraspecific diversity can evolve rapidly, and that this process is jointly facilitated by (i) the availability of diverse environments promoting divergent natural selection; (ii) dynamic developmental processes sensitive to environmental and genetic signals; and (iii) eco evo and eco devo feedbacks influencing the selective and developmental environments of the phenotype. We highlight empirical examples and present a conceptual model for the generation of resource polymorphism - emphasizing eco evo devo, and identify current gaps in knowledge.

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  • 1096.
    Sletvold, Nina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Trunschke, Judith
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Smit, Mart
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Verbeek, Jeffrey
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Strong pollinator-mediated selection for increased flower brightness and contrast in a deceptive orchid2016In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 70, no 3, p. 716-724Article in journal (Refereed)
    Abstract [en]

    Contrasting flower color patterns that putatively attract or direct pollinators toward a reward are common among angiosperms. In the deceptive orchid Anacamptis morio, the lower petal, which makes up most of the floral display, has a light central patch with dark markings. Within populations, there is pronounced variation in petal brightness, patch size, amount of dark markings, and contrast between patch and petal margin. We tested whether pollinators mediate selection on these color traits and on morphology (plant height, number of flowers, corolla size, spur length), and whether selection is consistent with facilitated or negative frequency-dependent pollination. Pollinators mediated strong selection for increased petal brightness (Delta beta(poll) = 0.42) and contrast (Delta beta(poll) = 0.51). Pollinators also tended to mediate stabilizing selection on brightness (Delta gamma(poll) = -0.27, n.s.) favoring the most common phenotype in the population. Selection for reduced petal brightness among hand-pollinated plants indicated a fitness cost associated with brightness. The results demonstrate that flower color traits influence pollination success and seed production in A. morio, indicating that they affect attractiveness to pollinators, efficiency of pollen transfer, or both. The documented selection is consistent with facilitated pollination and selection for color convergence toward cooccurring rewarding species.

  • 1097.
    Sletvold, Nina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala Univ, EBC, Dept Ecol & Genet, Plant Ecol & Evolut, SE-75236 Uppsala, Sweden..
    Nonlinear costs of reproduction in a long-lived plant2015In: Journal of Ecology, ISSN 0022-0477, E-ISSN 1365-2745, Vol. 103, no 5, p. 1205-1213Article in journal (Refereed)
    Abstract [en]

    A trade-off between current reproduction and future performance is a key component of life-history theory, but the shape of this trade-off for any specific fitness component remains elusive. We induced three to five levels of reproductive effort (RE) by manipulating fruit set of a long-lived orchid in two populations that differed in the length of the growing season and local climate and examined survival, size and fecundity the following year. Natural fruit set was 72% higher in the long-season population, but was not associated with a significant survival cost in any population. Survival decreased linearly with experimentally increased RE in the short-season population. In both populations, natural RE incurred growth and fecundity costs, and growth costs increased nonlinearly with diminishing costs at high RE. Fecundity costs increased linearly with RE in the long-season population, but nonlinearly with diminishing costs at high RE in the other. The results demonstrate that the shape of the cost function may be nonlinear with context-dependent intercept, slope and curvature. They are consistent with the prediction that survival costs appear only when RE exceeds natural levels, while growth and fecundity costs are evident at natural RE.Synthesis. We suggest that studies inducing multiple levels of RE are required to understand life-history trade-offs and their context dependence. This kind of information is fundamental for an understanding of the link between environmental heterogeneity, adaptive differentiation and life-history evolution.

  • 1098.
    Sletvold, Nina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    There is More to Pollinator-Mediated Selection than Pollen Limitation2014In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 68, no 7, p. 1907-1918Article in journal (Refereed)
    Abstract [en]

    Spatial variation in pollinator-mediated selection (Delta beta(poll)) is a major driver of floral diversification, but we lack a quantitative understanding of its link to pollen limitation (PL) and net selection on floral traits. For 2-5 years, we quantified Delta beta(poll) on floral traits in two populations each of two orchid species differing in PL. In both species, spatiotemporal variation in Delta beta(poll) explained much of the variation in net selection. Selection was consistently stronger and the proportion that was pollinator-mediated was higher in the severely pollen-limited deceptive species than in the rewarding species. Within species, variation in PL could not explain variation in Delta beta(poll) for any trait, indicating that factors influencing the functional relationship between trait variation and pollination success govern a major part of the observed variation in Delta beta(poll). Separating the effects of variation in mean interaction intensity and in the functional significance of traits will be necessary to understand spatiotemporal variation in selection exerted by the biotic environment.

  • 1099.
    Smeds, Linnea
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Kawakami, Takeshi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Burri, Reto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bolivar, Paulina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Husby, Arild
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Uebbing, Severin
    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.
    Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 5448-Article in journal (Refereed)
    Abstract [en]

    The molecular characteristics of the pseudoautosomal region (PAR) of sex chromosomes remain elusive. Despite significant genome-sequencing efforts, the PAR of highly differentiated avian sex chromosomes remains to be identified. Here we use linkage analysis together with whole-genome re-sequencing to uncover the 630-kb PAR of an ecological model species, the collared flycatcher. The PAR contains 22 protein-coding genes and is GC rich. The genetic length is 64cM in female meiosis, consistent with an obligate crossing-over event. Recombination is concentrated to a hotspot region, with an extreme rate of > 700 cM/Mb in a 67-kb segment. We find no signatures of sexual antagonism and propose that sexual antagonism may have limited influence on PAR sequences when sex chromosomes are nearly fully differentiated and when a recombination hotspot region is located close to the PAR boundary. Our results demonstrate that a very small PAR suffices to ensure homologous recombination and proper segregation of sex chromosomes during meiosis.

  • 1100.
    Smeds, Linnea
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Kojola, Ilpo
    Nat Resources Inst Finland Luke, Rovaniemi, Finland.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    The evolutionary history of grey wolf Y chromosomes2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 9, p. 2173-2191Article in journal (Refereed)
    Abstract [en]

    Analyses of Y chromosome haplotypes uniquely provide a paternal picture of evolutionary histories and offer a very useful contrast to studies based on maternally inherited mitochondrial DNA (mtDNA). Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf (Canis lupis) Y chromosome, probably representing most of the male-specific, nonampliconic sequence from the euchromatic part of the chromosome. We characterized this sequence and then identified approximate to 1,500 Y-linked single nucleotide polymorphisms in a sample of 145 resequenced male wolves, including 75 Finnish wolf genomes newly sequenced in this study, and in 24 dogs and eight other canids. We found 53 Y chromosome haplotypes, of which 26 were seen in grey wolves, that clustered in four major haplogroups. All four haplogroups were represented in samples of Finnish wolves, showing that haplogroup lineages were not partitioned on a continental scale. However, regional population structure was indicated because individual haplotypes were never shared between geographically distant areas, and genetically similar haplotypes were only found within the same geographical region. The deepest split between grey wolf haplogroups was estimated to have occurred 125,000 years ago, which is considerably older than recent estimates of the time of divergence of wolf populations. The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, or wolf paternal introgression, starting 29,000 years ago. We also addressed the disputed origin of a recently founded population of Scandinavian wolves and observed that founding as well as most recent immigrant haplotypes were present in the neighbouring Finnish population, but not in sequenced wolves from elsewhere in the world, or in dogs.

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