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  • 1101.
    Tedersoo, Leho
    et al.
    Univ Tartu, Nat Hist Museum, 14a Ravila, EE-50411 Tartu, Estonia;Univ Tartu, Inst Ecol & Earth Sci, 14a Ravila, EE-50411 Tartu, Estonia;Estonian Young Acad Sci, 6 Kohtu, Tallinn, Estonia.
    Sanchez-Ramirez, Santiago
    Univ Toronto, Dept Ecol & Evolutionary Biol, 25 Willcocks St, Toronto, ON M5S 3B2, Canada.
    Koljalg, Urmas
    Univ Tartu, Inst Ecol & Earth Sci, 14a Ravila, EE-50411 Tartu, Estonia.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Estonian Young Acad Sci, 6 Kohtu, Tallinn, Estonia.
    Doring, Markus
    Global Biodivers Informat Facil, Copenhagen, Denmark.
    Schigel, Dmitry
    Global Biodivers Informat Facil, Copenhagen, Denmark;Univ Helsinki, Dept Biosci, Helsinki, Finland.
    May, Tom
    Royal Bot Gardens Victoria, Birdwood Ave, Melbourne, Vic 3004, Australia.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Abarenkov, Kessy
    Univ Tartu, Nat Hist Museum, 14a Ravila, EE-50411 Tartu, Estonia.
    High-level classification of the Fungi and a tool for evolutionary ecological analyses2018In: Fungal diversity, ISSN 1560-2745, E-ISSN 1878-9129, Vol. 90, no 1, p. 135-159Article in journal (Refereed)
    Abstract [en]

    High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum-and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomophthoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set.

  • 1102. Tegelström, Håkan
    et al.
    Wyöni, Per-Ivan
    Gelter, Hans
    Jaarola, Maarit
    Concordant divergence in proteins and mitochondrial DNA between two vole species in the genus Clethrionomys1988In: Biochemical Genetics, ISSN 0006-2928, E-ISSN 1573-4927, Vol. 26, no 3-4, p. 223-237Article in journal (Refereed)
  • 1103.
    Thompson, John N.
    et al.
    Univ Calif Santa Cruz, Dept Ecol & Evolutionary Biol, Santa Cruz, CA 95064 USA..
    Schwind, Christopher
    Univ Calif Santa Cruz, Dept Ecol & Evolutionary Biol, Santa Cruz, CA 95064 USA..
    Friberg, Magne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Diversification of Trait Combinations in Coevolving Plant and Insect Lineages2017In: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 190, no 2, p. 171-184Article in journal (Refereed)
    Abstract [en]

    Closely related species often have similar traits and sometimes interact with the same species. A crucial problem in evolutionary ecology is therefore to understand how coevolving species diverge when they interact with a set of closely related species from another lineage rather than with a single species. We evaluated geographic differences in the floral morphology of all woodland star plant species (Lithophragma, Saxifragaceae) that are pollinated by Greya (Prodoxidae) moths. Flowers of each woodland star species differed depending on whether plants interact locally with one, two, or no pollinating moth species. Plants of one species grown in six different environments showed few differences in floral traits, suggesting that the geographic differences are not due significantly to trait plasticity. Greya moth populations also showed significant geographic divergence in morphology, depending on the local host and on whether the moth species co-occurred locally. Divergence in the plants and the moths involved shifts in combinations of partially correlated traits, rather than any one trait. The results indicate that the geographic mosaic of coevolution can be amplified as coevolving lineages diversify into separate species and come together in different combinations in different ecosystems.

  • 1104. Thompson, John N.
    et al.
    Schwind, Christopher
    Guimaraes, Paulo R
    Friberg, Magne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Diversification through multi-trait evolution in a coevolving interaction2013In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 110, no 28, p. 11487-11492Article in journal (Refereed)
    Abstract [en]

    Mutualisms between species are interactions in which reciprocal exploitation results in outcomes that are mutually beneficial. This reciprocal exploitation is evident in the more than a thousand plant species that are pollinated exclusively by insects specialized to lay their eggs in the flowers they pollinate. By pollinating each flower in which she lays eggs, an insect guarantees that her larval offspring have developing seeds on which to feed, whereas the plant gains a specialized pollinator at the cost of some seeds. These mutualisms are often reciprocally obligate, potentially driving not only ongoing coadaptation but also diversification. The lack of known intermediate stages in most of these mutualisms, however, makes it difficult to understand whether these interactions could have begun to diversify even before they became reciprocally obligate. Experimental studies of the incompletely obligate interactions between woodland star (Lithophragma; Saxifragaceae) plants and their pollinating floral parasites in the moth genus Greya (Prodoxidae) show that, as these lineages have diversified, the moths and plants have evolved in ways that maintain effective oviposition and pollination. Experimental assessment of pollination in divergent species and quantitative evaluation of time-lapse photographic sequences of pollination viewed on surgically manipulated flowers show that various combinations of traits are possible for maintaining the mutualism. The results suggest that at least some forms of mutualism can persist and even diversify when the interaction is not reciprocally obligate.

  • 1105.
    Thulin, Mats
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Moore, Abigail J.
    Brown Univ, Dept Ecol & Evolutionary Biol, 80 Waterman St,Box G-W, Providence, RI 02912 USA..
    El-Seedi, Hesham
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy. Univ Malaya, Dept Chem, Kuala Lumpur 50603, Malaysia..
    Larsson, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Christin, Pascal-Antoine
    Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England..
    Edwards, Erika J.
    Brown Univ, Dept Ecol & Evolutionary Biol, 80 Waterman St,Box G-W, Providence, RI 02912 USA..
    Phylogeny and generic delimitation in Molluginaceae, new pigment data in Caryophyllales, and the new family Corbichoniaceae2016In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 65, no 4, p. 775-793Article in journal (Refereed)
    Abstract [en]

    The circumscription of Molluginaceae has changed radically in recent years, with Corbichonia being moved to Lophiocarpaceae, Limeum to Limeaceae, Macarthuria to Macarthuriaceae and all species of Hypertelis, except the type, to Kewa in Kewaceae. In a broad analysis of core Caryophyllales using plastid trnK-matK and rbcL, sequences, the position of Molluginaceae in a strict sense as sister to the Portulacineae Glade is corroborated, as are the positions of Corbichonia, Limeum and Kewa outside the family. The phylogeny of Molluginaceae is reconstructed based on trnK-matK and nuclear ITS sequences of about half of the currently recognized species in the family and with representatives from all recognized genera. Mollugo is found to be polyphyletic and a new taxonomy for the family with 11 genera is proposed. Mollugo in its new restricted sense is a mainly American genus of about 15 species, including M. ulei comb. nov., previously placed in the monotypic Glischrothamnus. The Australian and Asian genus Trigastrotheca is resurrected for T. molluginea, T. pentaphylla comb. nov. and T. stricta comb. nov. The name Paramollugo nom. nov. is proposed for the Mollugo nudicaulis group and the combinations P. angustifolia comb. nov., P. cuneifolia comb. nov., P. decandra comb. nov., P. deltoidea comb. nov., P. navassensis comb. nov. and P. nudicaulis comb. nov. are made. Hypertelis is expanded to include, besides the type H. spergulacea, also H. cerviana comb. nov., H. fragilis comb. nov., H. umbellata comb. nov. and H. walteri comb. nov. In Pharnaceum, the new combination P. namaquense comb. nov. is made, Hypertelis longifolia is treated as a synonym of P. lineare and Mollugo tenella as a synonym of P. subtile. Corbichonia is proposed to be treated as a family of its own, Corbichoniaceae fam. nov. Several names are lectotypified, including the Linnaean Mollugo pentaphylla and M stricta. An anthocyanin is reported for the first time from Simmondsiaceae. The detection of anthocyanins in members of Kewaceae and Molluginaceae agree with previous reports and corroborate the view that these families represent reversals from betalains to anthocyanins. The report of an anthocyanin in Limeaceae, previously regarded as unpigmented, apparently represents a newly detected reversal from betalains to anthocyanins in this family.

  • 1106.
    Thunga, Venkata Raghava Pavankumar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Nucleotide diversity and Linkage disequilibrium in Norway spruce (Picea abies)2014Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Pattern of Linkage Disequilibrium (LD) is a major factor largely determining the power of association mapping studies. Along with nucleotide diversities and DNA polymorphism, knowledge of patterns of LD along the genome needs to be to known to effectively design association mapping studies. In this study, patterns of nucleotide diversity, population structure, LD was estimated in Norway spruce (Picea abies). The data used for this were 23 nuclear loci sequenced in around 90 individuals originating from natural populations of Norway spruce throughout the current distribution range in Sweden and Finland. The observed levels of nucleotide diversity are variable among loci varying between 0.002 and 0.008 if measured by average pairwise nucleotide diversity. Despite the samples stretching large part of Finland and Sweden there were no evidence for strong population structure. As in earlier studies LD decays fast with distance and the average pattern of the squared correlation of allele frequencies drops to less than 0.2 within 100bp. In order to put the data in perspective previously generated data sets were re-analyzed and compared to the inferred results. 

  • 1107.
    Toljagic, Olja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Enigmatic basal archosauromorph from the Late Triassic of Poland2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Choristodera, a lineage of basal archosauromorphs (Reptilia: Diapsida), first appeared in Early/Middle Jurassic (possibly Late Triassic; approximately 201 million years ago) and extended all the way into early Miocene (approximately 23 million years ago). Choristoderans are the only group of more basal archosauromorphs that survived after the Jurassic period, along with Archosauriformes (a more derived group of Archosauromorphs). The time of origin of the lineage is still speculative and preceded with long ghost lineages, a timespan when the animals were known to be alive, but are not represented in the fossil record. Unresolved phylogenetic position and inter-relationships, along with limited information about such an important group of early semi-aquatic reptiles, set choristodera in the focus of tetrapod evolution. In order to add information to gaps in the fossil records during the long temporal range of the group, new discoveries and descriptions of early choristoderan taxa are needed. Here, a description of long bones of a choristodere-like animal from the Late Triassic of Poland is presented adding information to the basal archosauromorpha and possibly shifting back the time of choristodera origin. Furthermore, bone histology analysis was conducted for the first time for choristodera, adding new information to the group. The other description of postcranial material of a possible early choristodere from Storrs et al. (1996) sets the origin of the group to Latest Triassic (Rhaetian, approximately 201 Mya). Description of newly discovered fossil material along with the histology sections of such an important group of tetrapods that are choristoders is of great significance, not only for the Triassic tetrapod communities, but for tetrapod evolution, development, ecology and life history in general.

  • 1108.
    Topper, Timothy P
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Holmer, Lars E
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Skovsted, Christian B
    Department of Palaeozoology, Swedish Museum of Natural History, Stockholm, Sweden.
    Brock, Glenn A
    Department of Biological Sciences, Macquarie University, Sydney, Australia.
    Balthasar, Uwe
    School of Geographical and Earth Sciences, Gregory Building, Lilybank Gardens, University of Glasgow, UK.
    Larsson, Cecilia M
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Pettersson Stolk, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Harper, David A T
    The oldest brachiopods from the lower Cambrian of South Australia2013In: Acta Palaeontologica Polonica, ISSN 0567-7920, E-ISSN 1732-2421, Vol. 58, no 1, p. 93-109Article in journal (Refereed)
    Abstract [en]

    The morphology and organophosphatic shell structure of the paterinate brachiopod Askepasma is documented using new and previously collected specimens from the lower Cambrian of South Australia. Lack of adequately preserved material has seen the majority of paterinate specimens previously reported from South Australia referred to the genus Askepasma and treated under open nomenclature. Large collections of paterinates from the lower Cambrian Wilkawillina, Ajax, and Wirrapowie limestones in the Arrowie Basin, South Australia have prompted redescription of the type species Askepasma toddense and the erection of a new species, Askepasma saproconcha sp. nov. Askepasma saproconcha sp. nov. currently represents the oldest known brachiopod from the lower Cambrian successions in South Australia with a FAD in pre-trilobitic (Terreneuvian, Cambrian Stage 2, lower Atdabanian) strata in the basal part of the Wilkawillina and Wirrapowie limestones. Askepasma toddense predominantly occurs in Abadiella huoi Zone equivalent strata (Unnamed Cambrian Series 2, Stage 3, middle upper Atdabanian) in the upper part of the lower Wilkawillina, Wirrapowie, and Ajax limestones. The shell microstructure of Askepasma suggests a proximal stem group position within the Brachiopoda and similarities with tommotiid taxa provides further evidence that the ancestry of crown group brachiopods is firmly entrenched within the Tommotiida.

  • 1109.
    Toräng, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Pollinators, Enemies, Drought, and the Evolution of Reproductive Traits in Primula farinosa2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, I combined comparative and experimental approaches to examine selection on reproductive traits and population differentiation in the insect-pollinated, self-incompatible, perennial herb Primula farinosa. More specifically, I (1) determined whether the effects of floral display and interactions with pollinators and seed predators, and plant reproductive success were frequency-dependent and affected by surrounding vegetation context, (2) examined the consequences of intermittent drought years on population dynamics using numerical simulations based on demographic data collected over seven years, (3) analyzed among-population differentiation in flowering phenology and reproductive allocation, and its relationship to soil-depth at the site of origin.

    A field experiment suggested that conspicuous plants facilitate inconspicuous plants in terms of pollinator attraction, and that the facilitation effect is contingent on the height of the surrounding vegetation. Further experiments revealed that both mutualistic and antagonistic interactions can result in frequency-dependent selection on floral display. Among inconspicuous plants, both fruit initiation, and damage from seed predators increased with the proportion of the conspicuous morph. The relative strength of these effects, and therefore their net outcome on the relationship between morph ratio and seed production varied among years.

    I combined information on vital rates and their relation to environmental conditions in simulations to predict future population viability in changing environments. Simulated stochastic population growth rate decreased with increasing frequency of drought years.

    Reproductive allocation varied significantly among populations both in the field and in a common-garden experiment, but was correlated with soil depth at the site of origin only in the field. The results suggest that among-population variation in reproductive effort in the field mainly reflects plastic responses to environmental conditions, and that this plasticity may be adaptive. The common-garden experiment suggested that the study populations have diverged genetically in flowering time.

    List of papers
    1. Facilitation in an insect pollinated herb with a floral display dimorphism
    Open this publication in new window or tab >>Facilitation in an insect pollinated herb with a floral display dimorphism
    2006 (English)In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 87, no 8, p. 2113-2117Article in journal (Refereed) Published
    Abstract [en]

    Population context should influence pollination success and selection on. oral display in animal-pollinated plants because attraction of pollinators depends not only on the characteristics of individual plants, but also on the attractiveness of co-occurring conspecifics. The insect-pollinated herb Primula farinosa is polymorphic for inflorescence height. Natural populations may include both long-scaped plants, which present their flowers well above the soil surface, and short-scaped plants, with their flowers positioned close to the ground. We experimentally tested whether seed production in short-scaped P. farinosa varied with local morph frequency and surrounding vegetation height. In tall vegetation, short-scaped plants in polymorphic populations produced more fruit and tended to produce more seeds than short-scaped plants did in monomorphic populations. In low vegetation, population composition did not significantly affect fruit and seed output of short-scaped plants. The results suggest that long-scaped plants facilitate short-scaped plants in terms of pollinator attraction and that the facilitation effect is contingent on the height of the surrounding vegetation. The documented facilitation should contribute to the maintenance of the scape length polymorphism in ungrazed areas where litter accumulates and vegetation grows tall.

    Keywords
    alternative reproductive strategies, facilitation, floral display, plant height, pollination, positive interactions, predation, Primula farinosa
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96192 (URN)000239833400028 ()16937650 (PubMedID)
    Available from: 2007-09-21 Created: 2007-09-21 Last updated: 2017-12-14Bibliographically approved
    2. Mutualists and antagonists mediate frequency-dependent selection on floral display
    Open this publication in new window or tab >>Mutualists and antagonists mediate frequency-dependent selection on floral display
    2008 (English)In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 89, no 6, p. 1564-1572Article in journal (Refereed) Published
    Abstract [en]

    Theory predicts that, with conflicting selection pressures mediated by mutualists and antagonists, alternative reproductive strategies can be maintained by negative frequency-dependent selection if it results in rare-morph advantage. We combined field experiments and surveys of natural populations to determine whether selection on. oral display is frequency dependent in the self-incompatible herb Primula farinosa, which is polymorphic for inflorescence height and occurs in a short-scaped and a long-scaped morph. Among short-scaped plants, both pollination success, quantified as initiation of fruits and seeds, and seed predation were positively correlated with the relative frequency of the long-scaped morph. The relative strength of these effects and the direction of the resulting frequency-dependent selection on scape morph varied among years and populations. The results suggest that both mutualists and antagonists may mediate frequency-dependent selection and that frequency dependence may vary from positive to negative with rare-morph advantage, depending on the relative strength of these interactions.

    Keywords
    alternative reproductive strategies, facilitation, floral display, frequency-dependent selection, genetic diversity, pollination, positive interactions, predation, Primula farinosa, Sweden
    National Category
    Ecology
    Research subject
    Ecological Botany
    Identifiers
    urn:nbn:se:uu:diva-96193 (URN)10.1890/07-1283.1 (DOI)000256540300010 ()
    Available from: 2007-09-21 Created: 2007-09-21 Last updated: 2017-12-14Bibliographically approved
    3. Linking climate data and demography to predict future population viability of a perennial herb
    Open this publication in new window or tab >>Linking climate data and demography to predict future population viability of a perennial herb
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-96194 (URN)
    Available from: 2007-09-21 Created: 2007-09-21 Last updated: 2010-01-13Bibliographically approved
    4. Site quality and among-population differentiation in flowering phenology and reproductive allocation in the perennial herb Primula farinosa
    Open this publication in new window or tab >>Site quality and among-population differentiation in flowering phenology and reproductive allocation in the perennial herb Primula farinosa
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-96195 (URN)
    Available from: 2007-09-21 Created: 2007-09-21 Last updated: 2010-01-13Bibliographically approved
  • 1110.
    Toräng, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Skovde, Sch Biosci, SE-54128 Skovde, Sweden..
    Vikström, Linus
    Uppsala Univ, Dept Plant Ecol & Evolut, Evolutionary Biol Ctr, Norbyvagen 18D, SE-75236 Uppsala, Sweden..
    Wunder, Jörg
    Max Planck Inst Plant Breeding Res, Dept Plant Dev Biol, Carl von Linne Weg 10, D-50829 Cologne, Germany..
    Wötzel, Stefan
    Max Planck Inst Plant Breeding Res, Dept Plant Dev Biol, Carl von Linne Weg 10, D-50829 Cologne, Germany..
    Coupland, George
    Max Planck Inst Plant Breeding Res, Dept Plant Dev Biol, Carl von Linne Weg 10, D-50829 Cologne, Germany..
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Evolution of the selfing syndrome: Anther orientation and herkogamy together determine reproductive assurance in a self-compatible plant2017In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 71, no 9, p. 2206-2218Article in journal (Refereed)
    Abstract [en]

    Capacity for autonomous self-fertilization provides reproductive assurance, has evolved repeatedly in the plant kingdom, and typically involves several changes in flower morphology and development (the selfing syndrome). Yet, the relative importance of different traits and trait combinations for efficient selfing and reproductive success in pollinator-poor environments is poorly known. In a series of experiments, we tested the importance of anther-stigma distance and the less studied trait anther orientation for efficiency of selfing in the perennial herb Arabis alpina. Variation in flower morphology among eight self-compatible European populations was correlated with efficiency of self-pollination and with pollen limitation in a common-garden experiment. To examine whether anther-stigma distance and anther orientation are subject to directional and/or correlational selection, and whether this is because these traits affect pollination success, we planted a segregating F2 population at two native field sites. Selection strongly favored a combination of introrse anthers and reduced anther-stigma distance at a site where pollinator activity was low, and supplemental hand-pollination demonstrated that this was largely because of their effect on securing self-pollination. The results suggest that concurrent shifts in more than one trait can be crucial for the evolution of efficient self-pollination and reproductive assurance in pollinator-poor habitats.

  • 1111.
    Trunschke, Judith
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Sletvold, Nina
    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.
    Interaction intensity and pollinator-mediated selection2017In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 214, no 3, p. 1381-1389Article in journal (Refereed)
    Abstract [en]

    In animal-pollinated plants, the opportunity for selection and the strength of pollinatormediated selection are expected to increase with the degree of pollen limitation. However, whether differences in pollen limitation can explain variation in pollinator-mediated and net selection among animal-pollinated species is poorly understood. In the present study, we quantified pollen limitation, variance in relative fitness and pollinator- mediated selection on five traits important for pollinator attraction (flowering start, plant height, flower number, flower size) and pollination efficiency (spur length) in natural populations of 12 orchid species. Pollinator-mediated selection was quantified by subtracting estimates of selection gradients for plants receiving supplemental hand-pollination from estimates obtained for open-pollinated control plants. Mean pollen limitation ranged from zero to 0.96. Opportunity for selection, pollinatormediated selection and net selection were all positively related to pollen limitation, whereas nonpollinator-mediated selection was not. Opportunity for selection varied five-fold, strength of pollinator-mediated selection varied three-fold and net selection varied 1.5-fold among species. Supplemental hand-pollination reduced both opportunity for selection and selection on floral traits. The results show that the intensity of biotic interactions is an important determinant of the selection regime, and indicate that the potential for pollinator-mediated selection and divergence in floral traits is particularly high in species that are strongly pollen-limited.

  • 1112.
    Tsuboi, Masahito
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Thinking in water: Brain size evolution in Cichlidae and Syngnathidae2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Brain size varies greatly among vertebrates. It has been proposed that the diversity of brain size is produced and maintained through a balance of adaptations to different types and levels of cognitive ability and constraints for adaptive evolution. Phylogenetic comparative studies have made major contributions to our understanding of brain size evolution. However, previous studies have nearly exclusively focused on mammalian and avian taxa and almost no attempts have been made to investigate brain size evolution in ectothermic vertebrates.

    In my thesis, I studied brain size evolution in two groups of fish with extreme diversity in ecology, morphology and life history, Cichlidae and Syngnathidae. Using phylogenetic comparative methods, I investigated four key questions in vertebrate brain size evolution; cognitive adaptation, sexual selection, phenotypic integration and energetic constraints.

    I have demonstrated i) that phenotypic integration can link functionally unrelated traits, and this may constrain independent evolution of each part involved or promote concerted evolution of an integrated whole, ii) that brain-body static allometry constrains the direction of brain size evolution, even though the static-allometry showed ability to evolve, allowing evolution of relative brain size under allometric constraints, iii) that the energetic constraints of development and maintenance of brain tissue is an important factor in forming the diversity in brain size in cichlids and syngnathids, both at macroevolutionary and microevolutionary time scales, and iv) that adaptation for feeding and female mating competition may have played key roles in the adaptive evolution of brain size in pipefishes and seahorses. To conclude, my thesis shows the strong benefit of using fish as a model system to study brain size evolution with a phylogenetic comparative framework.

    List of papers
    1. Phenotypic integration of brain size and head morphology in Lake Tanganyika Cichlids
    Open this publication in new window or tab >>Phenotypic integration of brain size and head morphology in Lake Tanganyika Cichlids
    2014 (English)In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 14, p. 39-Article in journal (Refereed) Published
    Abstract [en]

    Background: Phenotypic integration among different anatomical parts of the head is a common phenomenon across vertebrates. Interestingly, despite centuries of research into the factors that contribute to the existing variation in brain size among vertebrates, little is known about the role of phenotypic integration in brain size diversification. Here we used geometric morphometrics on the morphologically diverse Tanganyikan cichlids to investigate phenotypic integration across key morphological aspects of the head. Then, while taking the effect of shared ancestry into account, we tested if head shape was associated with brain size while controlling for the potentially confounding effect of feeding strategy. Results: The shapes of the anterior and posterior parts of the head were strongly correlated, indicating that the head represents an integrated morphological unit in Lake Tanganyika cichlids. After controlling for phylogenetic non-independence, we also found evolutionary associations between head shape, brain size and feeding ecology. Conclusions: Geometric morphometrics and phylogenetic comparative analyses revealed that the anterior and posterior parts of the head are integrated, and that head morphology is associated with brain size and feeding ecology in Tanganyikan cichlid fishes. In light of previous results on mammals, our results suggest that the influence of phenotypic integration on brain diversification is a general process.

    Keywords
    Phenotypic integration, Geometric morphometrics, Phylogenetic comparative analysis, Lake Tanganyika cichlid, Brain evolution, Constraints
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-225106 (URN)10.1186/1471-2148-14-39 (DOI)000334458900001 ()
    Available from: 2014-05-27 Created: 2014-05-27 Last updated: 2017-12-05Bibliographically approved
    2. Evolution of brain-body allometry in Lake Tanganyika cichlids
    Open this publication in new window or tab >>Evolution of brain-body allometry in Lake Tanganyika cichlids
    Show others...
    2016 (English)In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 70, no 7, p. 1559-1568Article in journal (Refereed) Published
    Abstract [en]

    Brain size is strongly associated with body size at all taxonomic levels. This relationship has been hypothesized to be an important constraint on adaptive brain size evolution. The essential assumption of this idea is that allometry has a limited ability to evolve, and that evolution of relative brain size is therefore constrained to occur along the direction of static (i.e. within species) allometry. However, recent studies have reported mixed support for this view. Here, we examine if static allometry has affected the rate of relative brain size evolution in Lake Tanganyika cichlids. The evolution of brain-body allometry showed a recent rapid divergence whereas brain size evolution represented a more gradual phenotypic divergence across the history of diversification. Accordingly, we found no support for that static allometry affected the rate of absolute or relative brain size evolution in this group. Instead, we detected low, but existing evolvability of static allometry. Moreover, static allometry evolved faster in species with relatively small and large brains than in species with medium brain size. We propose that a combination of allometric constraints and partial evolvability of static allometry have allowed for independent evolution of brain size in Lake Tanganyika cichlids. Overall, our results demonstrate a complex, yet important, role of brain-body allometry in brain size evolution. 

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-262069 (URN)10.1111/evo.12965 (DOI)000380023200011 ()27241216 (PubMedID)
    External cooperation:
    Funder
    Helge Ax:son Johnsons stiftelse Swedish Research Council, 621-2012-3624
    Note

    Title in Thesis list of papers: Brain size evolution under allometric constraints in Lake Tanganyika cichlids

    Available from: 2015-09-08 Created: 2015-09-08 Last updated: 2018-06-26Bibliographically approved
    3. Comparative support for the expensive tissue hypothesis: Big brains are correlated with smaller gut and greater parental investment in Lake Tanganyika cichlids
    Open this publication in new window or tab >>Comparative support for the expensive tissue hypothesis: Big brains are correlated with smaller gut and greater parental investment in Lake Tanganyika cichlids
    Show others...
    2015 (English)In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 69, no 1, p. 190-200Article in journal (Refereed) Published
    Abstract [en]

    The brain is one of the most energetically expensive organs in the vertebrate body. Consequently, the energetic requirements of encephalization are suggested to impose considerable constraints on brain size evolution. Three main hypotheses concerning how energetic constraints might affect brain evolution predict covariation between brain investment and (1) investment into other costly tissues, (2) overall metabolic rate, and (3) reproductive investment. To date, these hypotheses have mainly been tested in homeothermic animals and the existing data are inconclusive. However, there are good reasons to believe that energetic limitations might play a role in large-scale patterns of brain size evolution also in ectothermic vertebrates. Here, we test these hypotheses in a group of ectothermic vertebrates, the Lake Tanganyika cichlid fishes. After controlling for the effect of shared ancestry and confounding ecological variables, we find a negative association between brain size and gut size. Furthermore, we find that the evolution of a larger brain is accompanied by increased reproductive investment into egg size and parental care. Our results indicate that the energetic costs of encephalization may be an important general factor involved in the evolution of brain size also in ectothermic vertebrates.

    Keywords
    Brain evolution, constraints, encephalization, phylogenetic comparative methods, the expensive tissue hypothesis, trade-offs
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-243668 (URN)10.1111/evo.12556 (DOI)000347462800015 ()25346264 (PubMedID)
    Available from: 2015-02-20 Created: 2015-02-11 Last updated: 2017-12-04Bibliographically approved
    4. Within species support for the expensive tissue hypothesis: a negative association between brain size and visceral fat storage in females of Pacific seaweed pipefish
    Open this publication in new window or tab >>Within species support for the expensive tissue hypothesis: a negative association between brain size and visceral fat storage in females of Pacific seaweed pipefish
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The brain is one of the most energetically expensive organs in the vertebrate body. Consequently, the high cost of brain development and maintenance is predicted to constrain adaptive brain size evolution (the expensive tissue hypothesis, ETH). Here, we test the ETH in a teleost fish with predominant female mating competition (reversed sex-roles) and male pregnancy, the pacific seaweed pipefish Syngnathus schlegeli. The relative size of the brain and other energetically expensive organs (kidney, liver, heart, gut, visceral fat, ovary/testis) was compared among three groups: pregnant males, non-pregnant males and egg producing females. Brood size in pregnant males was unrelated to brain size or the size of any other organ, whereas positive relationships were found between ovary size, kidney size and liver size in females. Moreover, we found that the size a suite of energetically expensive organs (brain, heart, gut, kidney, liver) as well as the amount of visceral fat did not differ between pregnant and non-pregnant males. However, we found marked differences in relative size of the expensive organs between sexes. Females had larger liver and kidney than males, whereas males stored more visceral fat than females. Furthermore, in females we found a negative correlation between brain size and the amount of visceral fat, whereas in males a positive trend between brain size and both liver and heart size was found. These results suggest that, while the majority of variation in the size of various expensive organs in this species likely reflects that individuals in good condition can afford to allocate resources to several organs, the cost of the expensive brain was visible in the visceral fat content of females, possibly due to the high costs associated with female egg production. 

    Keywords
    The expensive tissue hypothesis, Brain size evolution, pipefish
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-262071 (URN)
    Available from: 2015-09-08 Created: 2015-09-08 Last updated: 2018-06-26
    5. Prey motility, egg size and female mating competition: brain size evolution in pipefishes and seahorses
    Open this publication in new window or tab >>Prey motility, egg size and female mating competition: brain size evolution in pipefishes and seahorses
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Brain size varies greatly at all taxonomic levels. Feeding ecology, life history and sexual selection have been proposed as key components in generating the existing contemporary diversity in brain size across vertebrates. Analyses of brain size evolution have, however, been limited to lineages where males predominantly compete for mating and females choose mates. Here, we present the first original data set of brain sizes in pipefishes and seahorses (Syngnathidae). In this group, intense female mating competition occurs in many species (i.e. reversed sex-roles), and mating patterns include monogamy, polygynandry and polyandry. After controlling for the effect of shared ancestry and overall body size, relatively larger brains were positively correlated with relatively longer snout length, which is related to the propensity for feeding on motile and evasive prey items in Syngnathidae, and larger egg size. Furthermore, we found that females, on average, had 4.3% heavier brains than males and that polyandrous species tended to demonstrate female-favored brain size dimorphism. Our results suggest that adaptations for feeding on motile prey items, energetic constraints associated with production of large-brained juveniles and sexual selection in females are important factors in brain size evolution of pipefishes and seahorses.

    Keywords
    Brain size evolution, Phylogenetic comparative methods, Syngnathidae
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-262073 (URN)
    Available from: 2015-09-08 Created: 2015-09-08 Last updated: 2018-06-26
  • 1113.
    Tsuboi, Masahito
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Gonzalez-Voyer, Alejandro
    Kolm, Niclas
    Functional coupling constrains craniofacial diversification in Lake Tanganyika cichlids2015In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 11, no 5, article id 20141053Article in journal (Refereed)
    Abstract [en]

    Functional coupling, where a singlemorphological trait performs multiple functions, is a universal feature of organismal design. Theory suggests that functional coupling may constrain the rate of phenotypic evolution, yet empirical tests of this hypothesis are rare. In fish, the evolutionary transition from guarding the eggs on a sandy/rocky substrate (i.e. substrate guarding) to mouthbrooding introduces a novel function to the craniofacial system and offers an ideal opportunity to test the functional coupling hypothesis. Using a combination of geometric morphometrics and a recently developed phylogenetic comparative method, we found that head morphology evolution was 43% faster in substrate guarding species than in mouthbrooding species. Furthermore, for species in which females were solely responsible for mouthbrooding the males had a higher rate of head morphology evolution than in those with biparental mouthbrooding. Our results support the hypothesis that adaptations resulting in functional coupling constrain phenotypic evolution.

  • 1114.
    Tsuboi, Masahito
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Kotrschal, Alexander
    Stockholm Univ, Dept Zool Ethol, Svante Arrhenius Vag 18B, SE-10691 Stockholm, Sweden.
    Hayward, Alexander
    Stockholm Univ, Dept Zool Ethol, Svante Arrhenius Vag 18B, SE-10691 Stockholm, Sweden.
    Buechel, Séverine
    Stockholm Univ, Dept Zool Ethol, Svante Arrhenius Vag 18B, SE-10691 Stockholm, Sweden.
    Zidar, Josefina
    Linkoping Univ, IFM Biol, Campus Valla, SE-58183 Linkoping, Sweden.
    Løvlie, Hanne
    Linkoping Univ, IFM Biol, Campus Valla, SE-58183 Linkoping, Sweden.
    Kolm, Niclas
    Stockholm Univ, Dept Zool Ethol, Svante Arrhenius Vag 18B, SE-10691 Stockholm, Sweden.
    Evolution of brain-body allometry in Lake Tanganyika cichlids2016In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 70, no 7, p. 1559-1568Article in journal (Refereed)
    Abstract [en]

    Brain size is strongly associated with body size at all taxonomic levels. This relationship has been hypothesized to be an important constraint on adaptive brain size evolution. The essential assumption of this idea is that allometry has a limited ability to evolve, and that evolution of relative brain size is therefore constrained to occur along the direction of static (i.e. within species) allometry. However, recent studies have reported mixed support for this view. Here, we examine if static allometry has affected the rate of relative brain size evolution in Lake Tanganyika cichlids. The evolution of brain-body allometry showed a recent rapid divergence whereas brain size evolution represented a more gradual phenotypic divergence across the history of diversification. Accordingly, we found no support for that static allometry affected the rate of absolute or relative brain size evolution in this group. Instead, we detected low, but existing evolvability of static allometry. Moreover, static allometry evolved faster in species with relatively small and large brains than in species with medium brain size. We propose that a combination of allometric constraints and partial evolvability of static allometry have allowed for independent evolution of brain size in Lake Tanganyika cichlids. Overall, our results demonstrate a complex, yet important, role of brain-body allometry in brain size evolution. 

  • 1115.
    Tsuboi, Masahito
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lim, A. C. O.
    Univ Malaya, Inst Biol Sci, Fac Sci, Kuala Lumpur, Malaysia.; Save Our Seahorses Malaysia, Petaling Jaya, Selangor, Malaysia..
    Ooi, B. L.
    Univ Malaya, Inst Biol Sci, Fac Sci, Kuala Lumpur, Malaysia.; Save Our Seahorses Malaysia, Petaling Jaya, Selangor, Malaysia..
    Yip, M. Y.
    Univ Malaya, Inst Biol Sci, Fac Sci, Kuala Lumpur, Malaysia.; Save Our Seahorses Malaysia, Petaling Jaya, Selangor, Malaysia..
    Chong, V. C.
    Univ Malaya, Inst Biol Sci, Fac Sci, Kuala Lumpur, Malaysia.; Univ Malaya, Inst Ocean & Earth Sci, Kuala Lumpur, Malaysia..
    Ahnesjö, Ingrid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Kolm, N.
    Stockholm Univ, Dept Zool Ethol, Stockholm, Sweden..
    Brain size evolution in pipefishes and seahorses: the role of feeding ecology, life history and sexual selection2017In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 30, no 1, p. 150-160Article in journal (Refereed)
    Abstract [en]

    Brain size varies greatly at all taxonomic levels. Feeding ecology, life history and sexual selection have been proposed as key components in generating contemporary diversity in brain size across vertebrates. Analyses of brain size evolution have, however, been limited to lineages where males predominantly compete for mating and females choose mates. Here, we present the first original data set of brain sizes in pipefishes and seahorses (Syngnathidae) a group in which intense female mating competition occurs in many species. After controlling for the effect of shared ancestry and overall body size, brain size was positively correlated with relative snout length. Moreover, we found that females, on average, had 4.3% heavier brains than males and that polyandrous species demonstrated more pronounced (11.7%) female-biased brain size dimorphism. Our results suggest that adaptations for feeding on mobile prey items and sexual selection in females are important factors in brain size evolution of pipefishes and seahorses. Most importantly, our study supports the idea that sexual selection plays a major role in brain size evolution, regardless of on which sex sexual selection acts stronger.

  • 1116.
    Tsuboi, Masahito
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lim, Adam Chee Ooi
    Ooi, Boon Leong
    Mei, Yee Yip
    Chong, Ving Ching
    Ahnesjö, Ingrid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Kolm, Niclas
    Prey motility, egg size and female mating competition: brain size evolution in pipefishes and seahorsesManuscript (preprint) (Other academic)
    Abstract [en]

    Brain size varies greatly at all taxonomic levels. Feeding ecology, life history and sexual selection have been proposed as key components in generating the existing contemporary diversity in brain size across vertebrates. Analyses of brain size evolution have, however, been limited to lineages where males predominantly compete for mating and females choose mates. Here, we present the first original data set of brain sizes in pipefishes and seahorses (Syngnathidae). In this group, intense female mating competition occurs in many species (i.e. reversed sex-roles), and mating patterns include monogamy, polygynandry and polyandry. After controlling for the effect of shared ancestry and overall body size, relatively larger brains were positively correlated with relatively longer snout length, which is related to the propensity for feeding on motile and evasive prey items in Syngnathidae, and larger egg size. Furthermore, we found that females, on average, had 4.3% heavier brains than males and that polyandrous species tended to demonstrate female-favored brain size dimorphism. Our results suggest that adaptations for feeding on motile prey items, energetic constraints associated with production of large-brained juveniles and sexual selection in females are important factors in brain size evolution of pipefishes and seahorses.

  • 1117.
    Tsuboi, Masahito
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Shoji, Jun
    Sogabe, Atsushi
    Ahnesjö, Ingrid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Kolm, Niclas
    Within species support for the expensive tissue hypothesis: a negative association between brain size and visceral fat storage in females of Pacific seaweed pipefishManuscript (preprint) (Other academic)
    Abstract [en]

    The brain is one of the most energetically expensive organs in the vertebrate body. Consequently, the high cost of brain development and maintenance is predicted to constrain adaptive brain size evolution (the expensive tissue hypothesis, ETH). Here, we test the ETH in a teleost fish with predominant female mating competition (reversed sex-roles) and male pregnancy, the pacific seaweed pipefish Syngnathus schlegeli. The relative size of the brain and other energetically expensive organs (kidney, liver, heart, gut, visceral fat, ovary/testis) was compared among three groups: pregnant males, non-pregnant males and egg producing females. Brood size in pregnant males was unrelated to brain size or the size of any other organ, whereas positive relationships were found between ovary size, kidney size and liver size in females. Moreover, we found that the size a suite of energetically expensive organs (brain, heart, gut, kidney, liver) as well as the amount of visceral fat did not differ between pregnant and non-pregnant males. However, we found marked differences in relative size of the expensive organs between sexes. Females had larger liver and kidney than males, whereas males stored more visceral fat than females. Furthermore, in females we found a negative correlation between brain size and the amount of visceral fat, whereas in males a positive trend between brain size and both liver and heart size was found. These results suggest that, while the majority of variation in the size of various expensive organs in this species likely reflects that individuals in good condition can afford to allocate resources to several organs, the cost of the expensive brain was visible in the visceral fat content of females, possibly due to the high costs associated with female egg production. 

  • 1118.
    Tsuda, Yoshiaki
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. CNR, Inst Biosci & Bioresources, Via Madonna del Piano 10, I-50019 Florence, Italy..
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Stocks, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Sonstebo, Jorn Henrik
    Norwegian Inst Bioecon Res, Post Box 115, N-1431 As, Norway..
    Parducci, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Semerikov, Vladimir
    Russian Acad Sci, Inst Plant & Anim Ecol, Urals Div, 8 Marta Str,202, Ekaterinburg 620144, Russia..
    Sperisen, Christoph
    Swiss Fed Res Inst Forest, Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland..
    Politov, Dmitry
    Russian Acad Sci, Vavilov Inst Gen Genet, Gubkin Str 3, Moscow 119991, Russia..
    Ronkainen, Tiina
    Univ Helsinki, Dept Environm Sci, Environm Change Res Unit, POB 65, FI-00014 Helsinki, Finland..
    Valiranta, Minna
    Univ Helsinki, Dept Environm Sci, Environm Change Res Unit, POB 65, FI-00014 Helsinki, Finland..
    Vendramin, Giovanni Giuseppe
    CNR, Inst Biosci & Bioresources, Via Madonna del Piano 10, I-50019 Florence, Italy..
    Tollefsrud, Mari Mette
    Norwegian Inst Bioecon Res, Post Box 115, N-1431 As, Norway..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies): cryptic refugia as stepping stones to the west?2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 12, p. 2773-2789Article in journal (Refereed)
    Abstract [en]

    Boreal species were repeatedly exposed to ice ages and went through cycles of contraction and expansion while sister species alternated periods of contact and isolation. The resulting genetic structure is consequently complex, and demographic inferences are intrinsically challenging. The range of Norway spruce (Picea abies) and Siberian spruce (Picea obovata) covers most of northern Eurasia; yet their geographical limits and histories remain poorly understood. To delineate the hybrid zone between the two species and reconstruct their joint demographic history, we analysed variation at nuclear SSR and mitochondrial DNA in 102 and 88 populations, respectively. The dynamics of the hybrid zone was analysed with approximate Bayesian computation (ABC) followed by posterior predictive STRUCTURE plot reconstruction and the presence of barriers across the range tested with estimated effective migration surfaces. To estimate the divergence time between the two species, nuclear sequences from two well-separated populations of each species were analysed with ABC. Two main barriers divide the range of the two species: one corresponds to the hybrid zone between them, and the other separates the southern and northern domains of Norway spruce. The hybrid zone is centred on the Urals, but the genetic impact of Siberian spruce extends further west. The joint distribution of mitochondrial and nuclear variation indicates an introgression of mitochondrial DNA from Norway spruce into Siberian spruce. Overall, our data reveal a demographic history where the two species interacted frequently and where migrants originating from the Urals and the West Siberian Plain recolonized northern Russia and Scandinavia using scattered refugial populations of Norway spruce as stepping stones towards the west.

  • 1119.
    Tsuda, Yoshiaki
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. CNR, Div Florence, Inst Biosci & Bioresources, Via Madonna del Piano 10, I-50019 Florence, Italy..
    Semerikov, Vladimir
    Russian Acad Sci, Ural Branch, Inst Plant & Anim Ecol, Ekaterinburg 620144, Russia..
    Sebastiani, Federico
    CNR, Div Florence, Inst Biosci & Bioresources, Via Madonna del Piano 10, I-50019 Florence, Italy..
    Vendramin, Giovanni Giuseppe
    CNR, Div Florence, Inst Biosci & Bioresources, Via Madonna del Piano 10, I-50019 Florence, Italy..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala Univ, Sci Life Lab, Evolutionary Biol Ctr, Dept Ecol & Genet, Norbyvagen 18D, S-75236 Uppsala, Sweden..
    Multispecies genetic structure and hybridization in the Betula genus across Eurasia2017In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 2, p. 589-605Article in journal (Refereed)
    Abstract [en]

    Boreal and cool temperate forests are the major land cover of northern Eurasia, and information about continental-scale genetic structure and past demographic history of forest species is important from an evolutionary perspective and has conservation implications. However, although many population genetic studies of forest tree species have been conducted in Europe or Eastern Asia, continental-scale genetic structure and past demographic history remain poorly known. Here, we focus on the birch genus Betula, which is commonly distributed in boreal and cool temperate forests, and examine 129 populations of two tetraploid and four diploid species collected from Iceland to Japan. All individuals were genotyped at seven to 18 nuclear simple sequence repeats (nSSRs). Pairwise <mml:msubsup>FST</mml:msubsup> among the six species ranged from 0.285 to 0.903, and genetic differentiation among them was clear. structure analysis suggested that Betula pubescens is an allotetraploid and one of the parental species was Betula pendula. In both species pairs of B.pendula and B.plathyphylla, and B.pubescens and B.ermanii, genetic diversity was highest in central Siberia. A hybrid zone was detected around Lake Baikal for eastern and western species pairs regardless of ploidy level. Approximate Bayesian computation suggested that the divergence of B.pendula and B.platyphylla occurred around the beginning of the last ice age (36300years BP, 95% CI: 15330-92700) and hybridization between them was inferred to have occurred after the last glacial maximum (1614years BP, 95% CI: 561-4710), with B.pendula providing a higher contribution to hybrids.

  • 1120.
    Tsutsumi, Chie
    et al.
    Natl Museum Nat & Sci, Dept Bot, Amakubo 4-1-1, Tsukuba, Ibaraki 3050005, Japan..
    Chen, Cheng-Wei
    Taiwan Forestry Res Inst, Bot Garden Div, Taipei 100, Taiwan..
    Larsson, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hirayama, Yumiko
    Natl Museum Nat & Sci, Dept Bot, Amakubo 4-1-1, Tsukuba, Ibaraki 3050005, Japan..
    Kato, Masahiro
    Natl Museum Nat & Sci, Dept Bot, Amakubo 4-1-1, Tsukuba, Ibaraki 3050005, Japan..
    Phylogeny and classification of Davalliaceae on the basis of chloroplast and nuclear markers2016In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 65, no 6, p. 1236-1248Article in journal (Refereed)
    Abstract [en]

    Davalliaceae have been classified on the basis of morphological data or morphological and molecular data. The family has been divided into various genera, the circumscription of which may differ between authors. Previous phylogenetic analyses used limited numbers of genes and taxa. We studied the molecular phylogeny of the family by using two nuclear markers (LEAFY intron 1, gapCp intron) and a long chloroplast marker (atpB-rbcL-accD) in 55 specimens of 41 species. The results indicated that Davalliaceae are divided into seven clades, six of which coincide with the genera and sections sensu Kato & Tsutsumi. The relationships among the clades were inconsistent with respect to the markers analyzed, and a species tree derived from all datasets did not resolve the relationships. In addition, the clades were not well characterized to be classified at the genus level. Therefore, we propose to classify Davalliaceae in the single genus Davallia with seven sections, i.e., sect. Araiostegiella, sect. Davallia (comprising only D. canariensis), sect. Davallodes (including Araiostegia p.p. and Paradavallodes), sect. Humata (including Pachypleuria and Parasorus), sect. Scyphularia (s.l. = sect. Davallia sensu Kato & Tsutsumi excluding the type), sect. Trogostolon (s.l. = sect. Trogostolon sensu Kato & Tsutsumi), and sect. Cordisquama (s.l. = Wibelia sensu Kato & Tsutsumi). A key to the sections and a table of characters for the sections are provided.

  • 1121.
    Tusso Gomez, Sergio Ivan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Division of Evolutionary Biology, Faculty of Biology, LMU Munich.
    Adaptive divergence in fission yeast: From experimental evolution to evolutionary genomics2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    How adaptation and population differentiation occur is fundamental to understand the origin of biodiversity. Work in speciation alongside the increased ease of generating genomic data have allowed the exploration of genomic changes relevant to adaptation. However, it remains challenging to infer the underlying mechanisms from genomic patterns of divergence governed by both genomic properties and external selective pressures. The chronological order of genomic changes, evolutionary history and selective forces can rarely be inferred from natural populations.

    Currently, I see two promising ways to tackle the problem of the genomic underpinnings of divergence: (1) evolution experiments simulating adaptation and population divergence and measuring genomic changes as they occur through time; (2) empirical studies of closely related populations in which the extent of divergence varies, allowing us to infer the chronology of the genomic changes. In my Ph.D. research I applied these two approaches, using the fungus Schizosaccharomyces pombe. First, I experimentally tested the potential for ecological divergence with gene flow, and investigated genomic and phenotypic changes associated with this process. Next, I studied genomic data obtained from natural populations sampled worldwide.  In both cases, the genetic inference relied on different sequencing technologies including the Illumina, Pacific Biosciences and Oxford Nanopore platforms.

    The experiment explored the effect of gene flow on phenotype and fitness, and uncovered potential molecular mechanisms underlying adaptive divergence. In paper I we demonstrate the emergence of specialisation under low gene flow, but generalist strategies when gene flow was high. Evolved phenotypes were largely influenced by standing genetic variation subject to opposite antagonistic pleiotropy complemented by new mutations enriched in a subset of genes. In paper II, we show that the experimental selective regime also had an effect on mating strategies, result of temporal ecological heterogeneity and selection for mating efficiency. We found that the evolution of mating strategies was explained by a trade-off between mating efficiency and asexual growth rate dependent on environmental stability. Papers III and IV consider the role of gene flow in natural populations. In paper III, we provide evidence that gene flow also played a predominant role in adaptive divergence in nature. All strains resulted from recent hybridization between two ancestral groups manifested in large phenotypic variation and reproductive isolation.This demographic history of hybridization was confirmed in paper IV focusing on patterns of mitochondrial diversity, adding evidence for the geographic distribution of the ancestral populations and potential for horizontal gene transfer from a distant yeast clade. 

    List of papers
    1. Parallelism in adaptive divergence and the modulating effect of gene flow
    Open this publication in new window or tab >>Parallelism in adaptive divergence and the modulating effect of gene flow
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Keywords
    adaptive divergence, gene flow, experimental evolution
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-392416 (URN)
    Available from: 2019-09-03 Created: 2019-09-03 Last updated: 2019-09-03
    2. Repeated evolution of self-compatibility for reproductive assurance
    Open this publication in new window or tab >>Repeated evolution of self-compatibility for reproductive assurance
    Show others...
    2018 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 1639Article in journal (Refereed) Published
    Abstract [en]

    Sexual reproduction in eukaryotes requires the fusion of two compatible gametes of opposite sexes or mating types. To meet the challenge of finding a mating partner with compatible gametes, evolutionary mechanisms such as hermaphroditism and self-fertilization have repeatedly evolved. Here, by combining the insights from comparative genomics, computer simulations and experimental evolution in fission yeast, we shed light on the conditions promoting separate mating types or self-compatibility by mating-type switching. Analogous to multiple independent transitions between switchers and non-switchers in natural populations mediated by structural genomic changes, novel switching genotypes readily evolved under selection in the experimental populations. Detailed fitness measurements accompanied by computer simulations show the benefits and costs of switching during sexual and asexual reproduction, governing the occurrence of both strategies in nature. Our findings illuminate the trade-off between the benefits of reproductive assurance and its fitness costs under benign conditions facilitating the evolution of self-compatibility.

    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-354954 (URN)10.1038/s41467-018-04054-6 (DOI)000430674000028 ()29691402 (PubMedID)
    Funder
    Swedish Research CouncilEU, European Research Council, HapSelA-336633Carl Tryggers foundation
    Note

    These authors jointly supervised this work: Jochen B.W. Wolf, Simone Immler.

    Available from: 2018-06-25 Created: 2018-06-25 Last updated: 2019-09-03Bibliographically approved
    3. Ancestral admixture is the main determinant of global biodiversity in fission yeast
    Open this publication in new window or tab >>Ancestral admixture is the main determinant of global biodiversity in fission yeast
    Show others...
    2019 (English)In: Molecular Biology and EvolutionArticle in journal (Refereed) Published
    Abstract [en]

    Abstract. Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodive

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-390729 (URN)10.1093/molbev/msz126 (DOI)
    Available from: 2019-08-14 Created: 2019-08-14 Last updated: 2019-09-03
    4. Intraspecific diversity of fission yeast mitochondrial genomes
    Open this publication in new window or tab >>Intraspecific diversity of fission yeast mitochondrial genomes
    Show others...
    2019 (English)In: Genome Biology and EvolutionArticle in journal (Refereed) Published
    Abstract [en]

    Abstract. The fission yeast Schizosaccharomyces pombe is an important model organism, but its natural diversity and evolutionary history remain under-studied.

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-390730 (URN)10.1093/gbe/evz165 (DOI)
    Available from: 2019-08-14 Created: 2019-08-14 Last updated: 2019-09-03
  • 1122.
    Tusso, Sergio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Morcinek, Kerstin
    Vogler, Catherine
    Schupp, Peter J.
    Caballes, Ciemon F.
    Vargas, Sergio
    Wörheide, Gert
    Genetic structure of the crown-of-thorns seastar in the Pacific Ocean, with focus on Guam2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4Article in journal (Refereed)
    Abstract [en]

    Population outbreaks of the corallivorous crown-of-thorns seastar (COTS), Acanthaster ‘planci’ L., are among the most important biological disturbances of tropical coral reefs. Over the past 50 years, several devastating outbreaks have been documented around Guam, an island in the western Pacific Ocean. Previous analyses have shown that in the Pacific Ocean, COTS larval dispersal may be geographically restricted to certain regions. Here, we assess the genetic structure of Pacific COTS populations and compared samples from around Guam with a number of distant localities in the Pacific Ocean, and focused on determining the degree of genetic structure among populations previously considered to be isolated. Using microsatellites, we document substantial genetic structure between 14 localities from different geographical regions in the Pacific Ocean. Populations from the 14 locations sampled were found to be structured in three significantly differentiated groups: (1) all locations immediately around Guam, as well as Kingman Reef and Swains Island; (2) Japan, Philippines, GBR and Vanuatu; and (3) Johnston Atoll, which was significantly different from all other localities. The lack of genetic differentiation between Guam and extremely distant populations from Kingman Reef and Swains Island suggests potential long-distance dispersal of COTS in the Pacific.

  • 1123.
    Tusso, Sergio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nieuwenhuis, Bart P. S.
    Sedlazeck, Fritz J.
    Davey, John W.
    Jeffares, Daniel C.
    Wolf, Jochen B. W.
    Ancestral admixture is the main determinant of global biodiversity in fission yeast2019In: Molecular Biology and EvolutionArticle in journal (Refereed)
    Abstract [en]

    Abstract. Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodive

  • 1124.
    Tusso, Sergio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nieuwenhuis, Bart P.S.
    Weissensteiner, Bernadette
    Immler, Simone
    Wolf, Jochen B.W.
    Parallelism in adaptive divergence and the modulating effect of gene flowManuscript (preprint) (Other academic)
  • 1125.
    Uebbing, Severin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    On the Evolution of the Avian Transcriptome2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Change in gene expression is a powerful tool for evolution, because seemingly small expression changes can contribute important steps towards adaptation without necessarily affecting the whole organism. There is still much to learn about how gene expression evolves on genome- and population-wide levels, especially in non-model organisms. This thesis addresses some important questions in gene expression evolution via the quantitative measurement of RNA and protein levels in birds.

    First, I confirmed the state of incomplete dosage compensation in birds by sequencing the transcriptome of collared flycatchers (Ficedula albicollis). I showed that pleiotropy governs the evolution of expression male-bias from the Z chromosome. Sex-linked genes in females were more highly expressed than half the male expression level, indicative of a partial up-regulation. A comparison with data from ostrich (Struthio camelus), a bird with non-degenerated sex chromosomes, showed that sex-linked expression male-bias evolved following sex chromosome degradation.

    Second, using a combination of RNA sequencing and proteome mass spectrometry in chicken (Gallus gallus), I asked whether complete dosage compensation was achieved through regulation at translation. I showed that this was not the case and that incomplete dosage compensation extends to the protein level in birds. In addition, sex-linked genes showed more often an increased amount of regulation at translational level than autosomal genes.

    Third, I investigated gene expression divergence between collared and pied flycatchers (Ficedula hypoleuca) using RNA sequencing in multiple tissues and individuals. Tissues differed in the degree of expression variance and in the number of divergent genes, which I identified using expression QST. Variance within species was negatively correlated with expression breadth and protein interactivity, indicating that evolutionary constraints act predominantly within interbreeding populations. Among genes unique to one of the species, I identified one gene, DPP7, falling into a large genomic deletion fixed in pied flycatchers.

    Fourth, I investigated allele-specific expression (ASE) in the two flycatcher populations. ASE was identified from genetic variants within transcripts using RNA sequencing reads. We developed a Bayesian negative binomial approach that gained statistical power by estimating expression variance from combined SNPs within a transcript and overdispersion from the whole dataset.

    List of papers
    1. Transcriptome Sequencing Reveals the Character of Incomplete Dosage Compensation across Multiple Tissues in Flycatchers
    Open this publication in new window or tab >>Transcriptome Sequencing Reveals the Character of Incomplete Dosage Compensation across Multiple Tissues in Flycatchers
    2013 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 5, no 8, p. 1555-1566Article in journal (Refereed) Published
    Abstract [en]

    Sex chromosome divergence, which follows the cessation of recombination and degeneration of the sex-limited chromosome, can cause a reduction in expression level for sex-linked genes in the heterozygous sex, unless some mechanisms of dosage compensation develops to counter the reduction in gene dose. Because large-scale perturbations in expression levels arising from changes in gene dose might have strong deleterious effects, the evolutionary response should be strong. However, in birds and in at least some other female heterogametic organisms, wholesale sex chromosome dosage compensation does not seem to occur. Using RNA-seq of multiple tissues and individuals, we investigated male and female expression levels of Z-linked and autosomal genes in the collared flycatcher, a bird for which a draft genome sequence recently has been reported. We found that male expression of Z-linked genes was on average 50% higher than female expression, although there was considerable variation in the male-to-female ratio among genes. The ratio for individual genes was well correlated among tissues and there was also a correlation in the extent of compensation between flycatcher and chicken orthologs. The relative excess of male expression was positively correlated with expression breadth, expression level, and number of interacting proteins (protein connectivity), and negatively correlated with variance in expression. These observations lead to a model of compensation occurring on a gene-by-gene basis, supported by an absence of clustering of genes on the Z chromosome with respect to the extent of compensation. Equal mean expression level of autosomal and Z-linked genes in males, and 50% higher expression of autosomal than Z-linked genes in females, is compatible with that partial compensation is achieved by hypertranscription from females' single Z chromosome. A comparison with male-to-female expression ratios in orthologous Z-linked genes of ostriches, where Z-W recombination still occurs, suggests that male-biased expression of Z-linked genes is a derived trait after avian sex chromosome divergence.

    Keywords
    sex chromosomes, dosage compensation, sex-biased gene expression, expression variance, collared flycatcher
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-209498 (URN)10.1093/gbe/evt114 (DOI)000324595000009 ()
    Available from: 2013-10-21 Created: 2013-10-21 Last updated: 2018-02-22Bibliographically approved
    2. Quantitative Mass Spectrometry Reveals Partial Translational Regulation for Dosage Compensation in Chicken
    Open this publication in new window or tab >>Quantitative Mass Spectrometry Reveals Partial Translational Regulation for Dosage Compensation in Chicken
    Show others...
    2015 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 32, no 10, p. 2716-2725Article in journal (Refereed) Published
    Abstract [en]

    There is increasing evidence that dosage compensation is not a ubiquitous feature following sex chromosome evolution, especially not in organisms where females are the heterogametic sex, like in birds. Even when it occurs, compensation can be incomplete and limited to dosage-sensitive genes. However, previous work has mainly studied transcriptional regulation of sex-linked genes, which may not reflect expression at the protein level. Here, we used liquid chromatography–tandem mass spectrometry to detect and quantify expressed levels of more than 2,400 proteins in ten different tissues of male and female chicken embryos. For comparison, transcriptome sequencing was performed in the same individuals, five of each sex. The proteomic analysis revealed that dosage compensation was incomplete, with a mean male-to-female (M:F) expression ratio of Z-linked genes of 1.32 across tissues, similar to that at the RNA level (1.29). The mean Z chromosome-to-autosome expression ratio was close to 1 in males and lower than 1 in females, consistent with partly reduced Z chromosome expression in females. Although our results exclude a general mechanism for chromosome-wide dosage compensation at translation, 30% of all proteins encoded from Z-linked genes showed a significant change in the M:F ratio compared with the corresponding ratio at the RNA level. This resulted in a pattern where some genes showed balanced expression between sexes and some close to 2-fold higher expression in males. This suggests that proteomic analyses will be necessary to reveal a more complete picture of gene regulation and sex chromosome evolution.

    Keywords
    sex chromosome evolution, dosage compensation, chicken, proteomics, mass spectrometry
    National Category
    Evolutionary Biology Genetics
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-258796 (URN)10.1093/molbev/msv147 (DOI)000361987100019 ()26108680 (PubMedID)
    Funder
    Swedish Research Council, 2010-5650, 2013-8271, 2011-4423EU, European Research Council, AdG 249976Knut and Alice Wallenberg Foundation
    Available from: 2015-07-20 Created: 2015-07-20 Last updated: 2018-02-22Bibliographically approved
    3. Divergence in gene expression within and between two closely related flycatcher species
    Open this publication in new window or tab >>Divergence in gene expression within and between two closely related flycatcher species
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Compared to DNA sequence evolution, relatively little is known about the character of gene expression evolution as species diverge. For example, it is unclear if gene expression generally evolves in a clock-like manner (by stabilizing selection or from neutral evolution) or if there are frequent episodes of directional selection. To gain insights into the evolutionary divergence of gene expression patterns, we sequenced and compared the transcriptomes of multiple tissues from population samples of collared (Ficedula albicollis) and pied flycatchers (F. hypoleuca), a species pair which diverged less than one million years ago. Tissues resolved into separate clusters in non-metric multidimensional scaling ordination analysis and samples from the two species generally clustered by tissue rather than by species. Tissues differed in the degrees of expression variance within species and divergence between species. Variance was positively correlated with expression breadth and negatively correlated with protein interactivity, suggesting that pleiotropic constraints reduce gene expression variance within species. Variance was correlated with between-species divergence, consistent with a pattern expected from stabilizing selection and neutral evolution. Using an expression QST approach, we identified genes differentially expressed between species. We also identified 10 genes uniquely expressed in one of the species. For one such gene (DPP7, uniquely expressed in collared flycatcher), the absence of expression in pied flycatchers could be associated with a fixed ≈ 20 kb deletion including 11 out of 13 exons in this species. This study conducted in a young vertebrate speciation model system expands our knowledge of how gene expression evolves in natural populations.

    Keywords
    Gene regulation, speciation, transcriptomics, collared flycatcher, pied flycatcher, Ficedula
    National Category
    Evolutionary Biology Genetics
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-258798 (URN)
    Available from: 2015-08-04 Created: 2015-07-20 Last updated: 2015-10-01
    4. Allele-specific gene expression inferred by a Bayesian negative binomial approach indicates abundant cis-regulatory variation in natural flycatcher populations
    Open this publication in new window or tab >>Allele-specific gene expression inferred by a Bayesian negative binomial approach indicates abundant cis-regulatory variation in natural flycatcher populations
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Polymorphisms in cis-regulatory sequences can make the two alleles of a gene be expressed at different levels, providing a starting point for the evolution of divergence in gene expression. However, little is known about the genome-wide abundance of regulatory variation in natural populations. We performed RNA-seq of multiple tissues from population samples of two closely related flycatcher species and developed a Bayesian algorithm that maximises data usage by borrowing overdispersion estimates over the whole dataset and combines several SNPs per transcript to detect allele-specific expression (ASE). Of 2,576 transcripts analysed in collared flycatcher, ASE was detected in 185 (7.2%). A similar frequency was seen in the pied flycatcher but these frequencies are likely to be underestimates for several reasons. The proportion of ASE transcripts varied among tissues, being lowest in testis and highest in muscle. Often, ASE was seen in several tissues for particular gene-individual combinations. This is one of only very few large-scale studies investigating the incidence of ASE in the wild. The results suggest that genetic variation in regulatory sequences commonly affect gene expression in natural populations and that it provides a seedbed for phenotypic evolution via divergence in gene expression.

    Keywords
    regulatory sequences, gene expression evolution, ASE, RNA-seq
    National Category
    Evolutionary Biology Genetics
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-258797 (URN)
    Available from: 2015-08-05 Created: 2015-07-20 Last updated: 2015-10-01
  • 1126.
    Uebbing, Severin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Backström, Niclas
    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.
    Burri, Reto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ludovic, Dutoit
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Mugal, Carina F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nater, Alexander
    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.
    Divergence in gene expression within and between two closely related flycatcher speciesManuscript (preprint) (Other academic)
    Abstract [en]

    Compared to DNA sequence evolution, relatively little is known about the character of gene expression evolution as species diverge. For example, it is unclear if gene expression generally evolves in a clock-like manner (by stabilizing selection or from neutral evolution) or if there are frequent episodes of directional selection. To gain insights into the evolutionary divergence of gene expression patterns, we sequenced and compared the transcriptomes of multiple tissues from population samples of collared (Ficedula albicollis) and pied flycatchers (F. hypoleuca), a species pair which diverged less than one million years ago. Tissues resolved into separate clusters in non-metric multidimensional scaling ordination analysis and samples from the two species generally clustered by tissue rather than by species. Tissues differed in the degrees of expression variance within species and divergence between species. Variance was positively correlated with expression breadth and negatively correlated with protein interactivity, suggesting that pleiotropic constraints reduce gene expression variance within species. Variance was correlated with between-species divergence, consistent with a pattern expected from stabilizing selection and neutral evolution. Using an expression QST approach, we identified genes differentially expressed between species. We also identified 10 genes uniquely expressed in one of the species. For one such gene (DPP7, uniquely expressed in collared flycatcher), the absence of expression in pied flycatchers could be associated with a fixed ≈ 20 kb deletion including 11 out of 13 exons in this species. This study conducted in a young vertebrate speciation model system expands our knowledge of how gene expression evolves in natural populations.

  • 1127.
    Uebbing, Severin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Konzer, Anne
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Xu, Luohao
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Brunström, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Bergquist, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Quantitative Mass Spectrometry Reveals Partial Translational Regulation for Dosage Compensation in Chicken2015In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 32, no 10, p. 2716-2725Article in journal (Refereed)
    Abstract [en]

    There is increasing evidence that dosage compensation is not a ubiquitous feature following sex chromosome evolution, especially not in organisms where females are the heterogametic sex, like in birds. Even when it occurs, compensation can be incomplete and limited to dosage-sensitive genes. However, previous work has mainly studied transcriptional regulation of sex-linked genes, which may not reflect expression at the protein level. Here, we used liquid chromatography–tandem mass spectrometry to detect and quantify expressed levels of more than 2,400 proteins in ten different tissues of male and female chicken embryos. For comparison, transcriptome sequencing was performed in the same individuals, five of each sex. The proteomic analysis revealed that dosage compensation was incomplete, with a mean male-to-female (M:F) expression ratio of Z-linked genes of 1.32 across tissues, similar to that at the RNA level (1.29). The mean Z chromosome-to-autosome expression ratio was close to 1 in males and lower than 1 in females, consistent with partly reduced Z chromosome expression in females. Although our results exclude a general mechanism for chromosome-wide dosage compensation at translation, 30% of all proteins encoded from Z-linked genes showed a significant change in the M:F ratio compared with the corresponding ratio at the RNA level. This resulted in a pattern where some genes showed balanced expression between sexes and some close to 2-fold higher expression in males. This suggests that proteomic analyses will be necessary to reveal a more complete picture of gene regulation and sex chromosome evolution.

  • 1128.
    Uebbing, Severin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Künstner, Axel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Mäkinen, Hannu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Backström, Niclas
    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.
    Burri, Reto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Dutoit, Ludovic
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Mugal, Carina F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nater, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Aken, Bronwen
    Flicek, Paul
    Martin, Fergal J
    Searle, Stephen M J
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Divergence in gene expression within and between two closely related flycatcher species2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 9, p. 2015-2028Article in journal (Refereed)
    Abstract [en]

    Relatively little is known about the character of gene expression evolution as species diverge. It is for instance unclear if gene expression generally evolves in a clock-like manner (by stabilizing selection or neutral evolution) or if there are frequent episodes of directional selection. To gain insights into the evolutionary divergence of gene expression, we sequenced and compared the transcriptomes of multiple organs from population samples of collared (Ficedula albicollis) and pied flycatchers (F. hypoleuca), two species which diverged less than one million years ago. Ordination analysis separated samples by organ rather than by species. Organs differed in their degrees of expression variance within species and expression divergence between species. Variance was negatively correlated with expression breadth and protein interactivity, suggesting that pleiotropic constraints reduce gene expression variance within species. Variance was correlated with between-species divergence, consistent with a pattern expected from stabilizing selection and neutral evolution. Using an expression PST approach, we identified genes differentially expressed between species and found 16 genes uniquely expressed in one of the species. For one of these, DPP7, uniquely expressed in collared flycatcher, the absence of expression in pied flycatcher could be associated with a ≈ 20 kb deletion including 11 out of 13 exons. This study of a young vertebrate speciation model system expands our knowledge of how gene expression evolves as natural populations become reproductively isolated.

  • 1129.
    Undin, Malin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Spatial variation in the pollinator community in a nursey pollination system with tremendous floral display variation2017Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Interactions between species are strong drivers of both diversification and maintenance of biodiversity. According to the geographic mosaic theory of coevolution, an interaction between the same species pair can have different outcomes when occurring in different environments. Several recent studies indicate that a key factor affecting the coevolutionary outcome is the local species community composition. For example, the interaction between Woodland Star plants (Lithophragma spp., Saxifragaceae) and the highly specialized nursery pollinator Greya politella (Prodoxidae) can be affected by the local presence of other Greya species. In some populations of the species L. parviflorum, high abundance of co-pollinators also affects the interaction, because the plants in these populations are no longer depending on the nursey pollinator for reproduction. In the remaining Greya-pollinated Lithophragma species, however, the plant-moth interaction has traditionally been considered a close to obligate mutualism. Therefore, it is interesting that recent data report tremendous among- and within-species variation in several floral traits important for Greya moth attraction. This contrasts with predictions from coevolutionary theory, which suggest that selection should act stabilizing on traits important for tight mutualisms in stable environments. Here, I investigate whether spatial variation in the presence of co-pollinators could help explain this variation, focusing on the species L. bolanderi. To do this, I utilize that G. politella oviposition leave readily detectable traces in the Lithophragma capsules. This unique feature provides the possibility to score the contribution of G. politella oviposition to pollination post-flowering. In total, I collected developing capsules from nine L. bolanderi populations distributed across its Sierra Nevadan range to investigate the importance of G. politella versus co-pollinators for seed set. In addition, using two of these populations, I first conducted laboratory pollination efficacy experiments to determine the Greya moth contribution to pollination during nectaring. Second, I conducted repeated flower visitor observations to assess among-population variation in visitation rate by Greya moths and more generalized pollinators. Together, my results show (i) that the importance of G. politella pollination varies dramatically among L. bolanderi populations, (ii) that nectaring Greya moths are probably only weakly contributing to pollination, and (iii) that the contribution to pollination by generalist co-pollinators, such as solitary bees, is spatially variable and may outweigh the pollination by G. politella in some populations. This suggests that the large among-population variation in the floral display traits of L. bolanderi could be generated in a selection mosaic of populations relying to different extents on pollination by G. politella and more generalized co-pollinators. 

  • 1130.
    Uribe, Juan E.
    et al.
    CSIC, MNCN, Dept Biodivers & Evolutionary Biol, Jose Gutierrez Abascal 2, Madrid 28006, Spain;Smithonian Inst, Natl Museum Nat Hist, Dept Invertebrate Zool, 10th St & Constitut Ave NW, Washington, DC 20560 USA;Univ Magdalena, Grp Evoluc Sistemat & Ecol Mol, Carrera 32,Numero 22, Santa Marta, Magdalena, Colombia.
    Irisarri, Iker
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. CSIC, MNCN, Dept Biodivers & Evolutionary Biol, Jose Gutierrez Abascal 2, Madrid 28006, Spain.
    Templado, Jose
    CSIC, MNCN, Dept Biodivers & Evolutionary Biol, Jose Gutierrez Abascal 2, Madrid 28006, Spain.
    Zardoya, Rafael
    CSIC, MNCN, Dept Biodivers & Evolutionary Biol, Jose Gutierrez Abascal 2, Madrid 28006, Spain.
    New patellogastropod mitogenomes help counteracting long-branch attraction in the deep phylogeny of gastropod mollusks2019In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 133, p. 12-23Article in journal (Refereed)
    Abstract [en]

    Long-branch attraction (LBA) is a well-known artifact in phylogenetic reconstruction. Sparse taxon sampling and extreme heterogeneity of evolutionary rates among lineages generate propitious situations for LBA, even defying probabilistic methods of phylogenetic inference. A clear example illustrating LBA challenges is the difficulty of reconstructing the deep gastropod phylogeny, particularly using mitochondrial (mt) genomes. Previous studies consistently obtained unorthodox phylogenetic relationships due to the LBA between the mitogenomes of patellogastropods (true limpets, represented only by Lottia digitalis), heterobranchs, and outgroup taxa. Here, we use the reconstruction of the gastropod mitogenomic phylogeny as a case exercise to test the effect of key methodological approaches proposed to counteract LBA, including the selection of slow-evolving representatives, the use of different outgroups, the application of site-heterogeneous evolutionary models, and the removal of fast-evolving sites. In this regard, we sequenced three new patellogastropod mt genomes, which displayed shorter branches than the one of Lottia as well as gene organizations more similar to that of the hypothetical gastropod ancestor. Phylogenetic analyses incorporating the mt genomes of Patella ferruginea, Patella vulgata, and Cellana radiata allowed eliminating the artificial clustering of Patellogastropoda and Heterobranchia that had prevailed in previous studies. Furthermore, the use of site-heterogeneous models with certain combinations of lineages within the outgroup allowed eliminating also the LBA between Heterobranchia and the outgroup, and recovering Apogastropoda (i.e., Caenogastropoda + Heterobranchia). Hence, for the first time, we were able to obtain a mitogenomic phylogeny of gastropods that is congruent with both morphological and nuclear datasets.

  • 1131.
    van der Valk, Tom
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Durazo, Frida Lona
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Toronto, Dept Anthropol, Mississauga, ON, Canada..
    Dalen, Love
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden..
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Whole mitochondrial genome capture from faecal samples and museum-preserved specimens2017In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, no 6, p. e111-e121Article in journal (Refereed)
    Abstract [en]

    Population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. The use of noninvasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 noninvasively collected faecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee. We show that the applied method is suitable for a wide range of sample types that differ in endogenous DNA content, increasing the proportion of target reads to over 300-fold. By systematically evaluating biases introduced during target enrichment of pooled museum samples, we show that capture is less efficient for fragments shorter or longer than the baits, that the proportion of human contaminating reads increases postcapture although capture efficiency is lower for human compared to gorilla fragments with a gorilla-generated bait, and that the rate of jumping PCR is considerable, but can be controlled for with a double-barcoding approach. We succeed in capturing complete mitochondrial genomes from faecal samples, but observe reduced capture efficiency as sequence divergence increases between the bait and target species. As previously shown for museum specimens, we demonstrate here that mitochondrial genome capture from field-collected faecal samples is a robust and reliable approach for population-wide studies of nonmodel organisms.

  • 1132.
    van der Valk, Tom
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Díez-Del-Molino, David
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden.
    Marques-Bonet, Tomas
    UPF CSIC, PRBB, Inst Evolutionary Biol, Barcelona, Spain; Catalan Inst Res & Adv Studies ICREA, Barcelona, Spain; BIST, CRG, CNAG CRG, Barcelona, Spain; Univ Autonoma Barcelona, Inst Catala Paleontol Miguel Crusafont, Edif ICTA ICP, Barcelona, Spain.
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Dalén, Love
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden.
    Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas2019In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 29, no 1, p. 165-170.e6, article id S0960-9822(18)31554-9Article in journal (Refereed)
    Abstract [en]

    Many endangered species have experienced severe population declines within the last centuries [1, 2]. However, despite concerns about negative fitness effects resulting from increased genetic drift and inbreeding, there is a lack of empirical data on genomic changes in conjunction with such declines [3-7]. Here, we use whole genomes recovered from century-old historical museum specimens to quantify the genomic consequences of small population size in the critically endangered Grauer's and endangered mountain gorillas. We find a reduction of genetic diversity and increase in inbreeding and genetic load in the Grauer's gorilla, which experienced severe population declines in recent decades. In contrast, the small but relatively stable mountain gorilla population has experienced little genomic change during the last century. These results suggest that species histories as well as the rate of demographic change may influence how population declines affect genome diversity.

  • 1133.
    van Hamelsveld, Sophie
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Studies on possible global suppressor mutations in the hisA gene of Salmonella enterica2018Report (Other academic)
    Abstract [en]

    Global suppressor mutations have recently been recognised as an important factor in enzyme evolution. These are mutations that compensate for deleterious mutations by stabilising the protein’s structure. Their implication in the development of resistance to antibiotics, including the ever-prevalent β-lactamase enzymes responsible for widespread resistance towards drugs such as ampicillin, has made global suppressors the focus of recent research. Model enzyme systems are often used to study how genes evolve in a laboratory system. In this project, the hisA gene of Salmonella enterica was studied; specifically, a set of previously-isolated mutations thought to represent global suppressors. Using an optimised method of λ Red Recombineering and techniques to measure the relative growth rate of bacteria, these experiments aimed to study possible compensatory mutations and understand how they affected fitness. In doing so we have found further mutations which appear to compensate for harmful mutations by reducing their fitness cost.

  • 1134. VanBuren, Collin S.
    et al.
    Campione, Nicolas E.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Evans, David C.
    Head size, weaponry, and cervical adaptation: Testing craniocervical evolutionary hypotheses in Ceratopsia2015In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 69, no 7, p. 1728-1744Article, review/survey (Refereed)
    Abstract [en]

    The anterior cervical vertebrae form the skeletal connection between the cranial and postcranial skeletons in higher tetrapods. As a result, the morphology of the atlas-axis complex is likely to be shaped by selection pressures acting on either the head or neck. The neoceratopsian (Reptilia:Dinosauria) syncervical represents one of the most highly modified atlas-axis regions in vertebrates, being formed by the complete coalescence of the three most anterior cervical vertebrae. In ceratopsids, the syncervical has been hypothesized to be an adaptation to support a massive skull, or to act as a buttress during intraspecific head-to-head combat. Here, we test these functional/adaptive hypotheses within a phylogenetic framework and critically examine the previously proposed methods for quantifying relative head size in the fossil record for the first time. Results indicate that neither the evolution of cranial weaponry nor large head size correlates with the origin of cervical fusion in ceratopsians, and we, therefore, reject both adaptive hypotheses for the origin of the syncervical. Anterior cervical fusion has evolved independently in a number of amniote clades, and further research on extant groups with this peculiar anatomy is needed to understand the evolutionary basis for cervical fusion in Neoceratopsia.

  • 1135.
    Varg, Javier Edo.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Host, its microbiota and their interactions2018Report (Other academic)
    Abstract [en]

    The development of sequencing technologies has advanced the field of host-associated microbiology by showing the huge diversity and functionality of the omnipresent microbes of all multicellular life. With these advances, new interesting questions have been raised with regards to microbial community composition, pollutants that can interact with the host microbial community, the factors that can affect the host microbial community and the processes that determine the enormous variety of the microbiota among hosts of the same species or genotype. However, conceptual disagreement regarding the ecology, genetics and evolutionary concepts regulating microbial diversity are frequently occurring in this field. Concepts such as symbiont, holobiont, and hologenome are generating discordances in the scientific community regarding microbial host associations and microbial communities. Then it is important to take into account the definitions and clarify the bases of these concepts: the holobiont refers to the host and their symbiotic microbes. Therefore, the hologenome are the genes of host plus the genes of their symbionts. However, the symbiont definition is wide open and when we use it at the holobiont level it can be misinterpreted as all microbes in a host. To separate symbionts from non-symbionts, it is necessary to search at the functional level for the emergence or enhancement of traits at the holobiont level. For that reason, not all of the microbiota are symbionts and, therefore the holobiont should only include the host and all the microbial symbionts that inhabit it. Consequently, host-associated microbes are part of the amalgam in the complex organisation of an organism and can also be explained by ecological associations. Understanding these complex interactions between host and its microbiota can, for instance, give us insight into how this community can influence the host’s regulatation of pollutants as stress factors. More important, to understand synergistic effects of pollutants such as microplastics and metals on the host and their microorganisms, constitute one of the new frontiers in toxicology. Finally, it is important to take into account how stress factors such as competition, environmental changes, pollution, and diet can influence the fitness, genome dynamics and diversification between organisms. 

  • 1136.
    Varshney, Gaurav K.
    et al.
    NHGRI, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    Zhang, Suiyuan
    NHGRI, Computat & Stat Genom Branch, NIH, Bethesda, MD 20892 USA..
    Pei, Wuhong
    NHGRI, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    Adomako-Ankomah, Ashrifia
    NHGRI, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    Fohtung, Jacob
    NHGRI, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    Schaffer, Katherine
    NHGRI, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    Carrington, Blake
    NHGRI, Zebrafish Core, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    Maskeri, Anoo
    NHGRI, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    Slevin, Claire
    NHGRI, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    Wolfsberg, Tyra
    NHGRI, Computat & Stat Genom Branch, NIH, Bethesda, MD 20892 USA..
    Ledin, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Sood, Raman
    NHGRI, Zebrafish Core, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    Burgess, Shawn M.
    NHGRI, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    CRISPRz: a database of zebrafish validated sgRNAs2016In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 44, no D1, p. D822-D826Article in journal (Refereed)
    Abstract [en]

    CRISPRz (http://research.nhgri.nih.gov/CRISPRz/) is a database of CRISPR/Cas9 target sequences that have been experimentally validated in zebrafish. Programmable RNA-guided CRISPR/Cas9 has recently emerged as a simple and efficient genome editing method in various cell types and organisms, including zebrafish. Because the technique is so easy and efficient in zebrafish, the most valuable asset is no longer a mutated fish (which has distribution challenges), but rather a CRISPR/Cas9 target sequence to the gene confirmed to have high mutagenic efficiency. With a highly active CRISPR target, a mutant fish can be quickly replicated in any genetic background anywhere in the world. However, sgRNA's vary widely in their activity and models for predicting target activity are imperfect. Thus, it is very useful to collect in one place validated CRISPR target sequences with their relative mutagenic activities. A researcher could then select a target of interest in the database with an expected activity. Here, we report the development of CRISPRz, a database of validated zebrafish CRISPR target sites collected from published sources, as well as from our own in-house large-scale mutagenesis project. CRISPRz can be searched using multiple inputs such as ZFIN IDs, accession number, UniGene ID, or gene symbols from zebrafish, human and mouse.

  • 1137.
    Vasconcelos, Paula
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Multidimensional Adaptive Dynamics and evolutionary diversification2017Report (Other academic)
  • 1138.
    Vaskaninova, Valeria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Charles Univ Prague, Fac Sci, Inst Geol & Palaeontol, Prague, Czech Republic..
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Unique diversity of acanthothoracid placoderms (basal jawed vertebrates) in the Early Devonian of the Prague Basin, Czech Republic: A new look at Radotina and Holopetalichthys2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 4, article id e0174794Article in journal (Refereed)
    Abstract [en]

    The taxonomy of Early Devonian placoderm material from the Lochkovian and Pragian of the Prague basin, previously attributed to the genera Radotina and Holopetalichthys, is revised. The Pragian species Radotina tesselata Gross 1958 shares detailed similarities with the holotype of the Lochkovian Radotina kosorensis Gross 1950, which is also the holotype of the genus; the assignation of both species to Radotina is supported. However, the Lochkovian material previously attributed to Radotina kosorensis also contains two unrecognised taxa, distinguishable from Radotina at the generic level: these are here named Tlamaspis and Sudaspis. The disputed genus Holopetalichthys, synonymised with Radotina by some previous authors, is shown to be valid. Furthermore, whereas Radotina, Tlamaspis and Sudaspis can all be assigned to the group Acanthothoracii, on the basis of several features including possession of a projecting prenasal region of the endocranium, Holopetalichthys lacks such a region and is probably not an acanthothoracid. Skull roof patterns and other aspects of morphology vary greatly between these taxa. Radotina has a substantially tesselated skull roof, whereas the skull roofs of Tlamaspis and Holopetalichthys appear to lack tesserae altogether. Tlamaspis has an extremely elongated facial region and appears to lack a premedian plate. Sudaspis has a long prenasal region, but unlike Tlamaspis the postnasal face is not elongated. Past descriptions of the braincase of ' Radotina' and the skull roofs of ' Radotina' and ' Holopetalichthys' incorporate data from more than one taxon, giving rise to spurious characterisations including an apparently extreme degree of skull roof variability. These descriptions should all be disregarded.

  • 1139.
    Vavrek, Matthew J.
    et al.
    Philip J. Currie Dinosaur Museum.
    Evans, David C.
    Royal Ontario Museum.
    Braman, Dennis R.
    Canadian Journal of Earth Sciences.
    Campione, Nicolas E.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences.
    Zazula, Grant D.
    Government of Yukon.
    A Paleogene flora from the upper Bonnet Plume Formation of northeast Yukon Territory, Canada2012In: Canadian journal of earth sciences (Print), ISSN 0008-4077, E-ISSN 1480-3313, Vol. 49, no 3, p. 547-558Article in journal (Refereed)
    Abstract [en]

    Palaeontological exploration of the Bonnet Plume Basin in northwestern Yukon Territory, Canada, has revealed a Late Paleocene to Early Eocene macrofloral assemblage from a channel fill deposit. The flora is typified by cosmopolitan taxa and dominated by deciduous angiosperms, with the notable presence of ZizyphoidesEttingshausenia, and Corylites. Floras with a similar composition are known from Late Cretaceous through Early Eocene deposits in Alaska and the Canadian Arctic Archipelago, where they have been interpreted as evidence for warm, equable temperatures. This collection represents the most diverse known Paleogene plant macrofossil assemblage from the Yukon Territory and helps to expand our knowledge of ancient high-latitude floras.

  • 1140.
    Videvall, Elin
    et al.
    Lund Univ, Mol Ecol & Evolut Lab, Dept Biol, Lund, Sweden..
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Hagenblad, Jenny
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Linkoping Univ, IFM Biol, Linkoping, Sweden..
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Hansson, Bengt
    Lund Univ, Mol Ecol & Evolut Lab, Dept Biol, Lund, Sweden..
    Strong Maternal Effects on Gene Expression in Arabidopsis lyrata Hybrids2016In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, no 4, p. 984-994Article in journal (Refereed)
    Abstract [en]

    Hybridization between populations or species can have pronounced fitness consequences. Yet little is known about how hybridization affects gene regulation. Three main models have been put forward to explain gene expression patterns in hybrids: additive, dominance, or parental effects. Here, we use high throughput RNA-sequencing to examine the extent to which hybrid gene expression follows predictions by each of the three models. We performed a reciprocal crossing experiment between two differentiated populations of the perennial herb Arabidopsis lyrata and sequenced RNA in rosette leaves of 12-week-old plants grown in greenhouse conditions. The two parental populations had highly differentiated gene expression patterns. In hybrids, a majority of genes showed intermediate expression relative to that of their parental populations (i.e., additive effects), but expression was frequently more similar to the maternal than to their paternal population (i.e., maternal effects). Allele-specific expression analyses showed that in the vast majority of cases, genes with pronounced maternal effect expressed both the maternal and the paternal allele. Maternal effects on hybrid gene expression have rarely been documented previously and our study suggests it could be more common than previously assumed. Whether the maternal effect on gene expression persists to later life-stages, and whether the variation in gene expression is manifested in other aspects of the phenotype, remain to be elucidated. Our findings are relevant for understanding the consequences of outbreeding and hybridization and open up several questions for future studies.

  • 1141.
    Vijay, Nagarjun
    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.
    Bossu, Christen M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Zool Populat Genet, SE-10691 Stockholm, Sweden..
    Poelstra, Jelmer W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Weissensteiner, Matthias H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kryukov, Alexey P.
    Russian Acad Sci, Inst Biol & Soil Sci, Far East Branch, Lab Evolutionary Zool & Genet, Vladivostok 690022, Russia..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Munich, Div Evolutionary Biol, Grosshaderner St 2, D-82152 Planegg Martinsried, Germany..
    Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 13195Article in journal (Refereed)
    Abstract [en]

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

  • 1142.
    Viklund, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Phylogenomics of Oceanic Bacteria2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The focus of this thesis has been the phylogenomics and evolution of the Alphaproteobacteria. This is a very diverse group which encompasses bacteria from intraceullar parasites, such as the Rickettsiales, to freeliving bacteria such as the most abundant bacteria on earth, the SAR11. The genome sizes of the Alphaproteobacteria range between 1 Mb and 10 Mb. This group is also connected to the origin of the mitochondria.

    Several studies have placed the SAR11 clade together with the Rickettsiales and mitochon- dria. Here I have shown that this placement is an artifact of compositional heterogeneity. When choosing genes or sites less affected by heterogeneity we find that the SAR11-clade instead groups with free-living alphaproteobacteria. Gene-content analysis showed that SAR11 was missing several genes for recombination and DNA-repair. The relationships within the SAR11- clade has also been examined and questioned. Specifically, we found no support for placing the taxon referred to as HIMB59 within the SAR11. Ocean metagenomes have been investigated to determine whether the SAR11-clade is a potential relative of the mitochondria. No such relationship was found.

    Further I have shown how important it is to take the phylogenetic relationships into account when doing statistical analyzes of genomes.

    The evolution of LD12, the freshwater representative of SAR11, was investigated. Phyloge- nies and synonymous substitution frequencies showed the presence of three distinct subclades within LD12. The recombination to mutation rate was found to be extremely low. This is re- markable in light of the very high rate in the oceanic SAR11. This is may be due to adaptation to a more specialized niche.

    Finally we have compared structure-based and sequence-based methods for orthology pre- diction. A high fraction of the orfan proteins were predicted to code for intrinsically disordered proteins.

    Many phylogenetic methods are sensitive to heterogeneity and this needs to be taken into ac- count when doing phylogenies. There have been at least three independent genome reductions in the Alphaproteobacteria. The frequency of recombination differ greatly between freshwater and oceanic SAR11. Forces affecting the size of bacterial genomes and mechanisms of evolu- tionary change depend on the environmental context.

     

    List of papers
    1. Origin and evolution of the mitochondrial aminoacyl-tRNA synthetases
    Open this publication in new window or tab >>Origin and evolution of the mitochondrial aminoacyl-tRNA synthetases
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    2007 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 24, no 3, p. 743-756Article in journal (Refereed) Published
    Abstract [en]

    Many theories favor a fusion of 2 prokaryotic genomes for the origin of the Eukaryotes, but there are disagreements on the origin, timing, and cellular structures of the cells involved. Equally controversial is the source of the nuclear genes for mitochondrial proteins, although the α-proteobacterial contribution to the mitochondrial genome is well established. Phylogenetic inferences show that the nuclearly encoded mitochondrial aminoacyl-tRNA synthetases (aaRSs) occupy a position in the tree that is not close to any of the currently sequenced α-proteobacterial genomes, despite cohesive and remarkably well-resolved α-proteobacterial clades in 12 of the 20 trees. Two or more α-proteobacterial clusters were observed in 8 cases, indicative of differential loss of paralogous genes or horizontal gene transfer. Replacement and retargeting events within the nuclear genomes of the Eukaryotes was indicated in 10 trees, 4 of which also show split α-proteobacterial groups. A majority of the mitochondrial aaRSs originate from within the bacterial domain, but none specifically from the α-Proteobacteria. For some aaRS, the endosymbiotic origin may have been erased by ongoing gene replacements on the bacterial as well as the eukaryotic side. For others that accurately resolve the α-proteobacterial divergence patterns, the lack of affiliation with mitochondria is more surprising. We hypothesize that the ancestral eukaryotic gene pool hosted primordial "bacterial-like" genes, to which a limited set of α-proteobacterial genes, mostly coding for components of the respiratory chain complexes, were added and selectively maintained.

    Keywords
    Aminoacyl-tRNA synthetase, Mitochondria, Phylogeny
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-14983 (URN)10.1093/molbev/msl202 (DOI)000244662000013 ()17182897 (PubMedID)
    Available from: 2008-02-01 Created: 2008-02-01 Last updated: 2017-12-11Bibliographically approved
    2. A Phylometagenomic Exploration of Oceanic Alphaproteobacteria Reveals Mitochondrial Relatives Unrelated to the SAR11 Clade
    Open this publication in new window or tab >>A Phylometagenomic Exploration of Oceanic Alphaproteobacteria Reveals Mitochondrial Relatives Unrelated to the SAR11 Clade
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    2011 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 9, p. e24457-Article in journal (Refereed) Published
    Abstract [en]

    Background: According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from an ancestral Alphaproteobacterium. Phylogenetic studies indicate that the mitochondrial ancestor is most closely related to the Rickettsiales. Recently, it was suggested that Candidatus Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the oceans, is a sister taxon to the mitochondrial-Rickettsiales clade. The availability of ocean metagenome data substantially increases the sampling of Alphaproteobacteria inhabiting the oxygen-containing waters of the oceans that likely resemble the originating environment of mitochondria.

    Methodology/Principal Findings: We present a phylogenetic study of the origin of mitochondria that incorporates metagenome data from the Global Ocean Sampling (GOS) expedition. We identify mitochondrially related sequences in the GOS dataset that represent a rare group of Alphaproteobacteria, designated OMAC (Oceanic Mitochondria Affiliated Clade) as the closest free-living relatives to mitochondria in the oceans. In addition, our analyses reject the hypothesis that the mitochondrial system for aerobic respiration is affiliated with that of the SAR11 clade.

    Conclusions/Significance: Our results allude to the existence of an alphaproteobacterial clade in the oxygen-rich surface waters of the oceans that represents the closest free-living relative to mitochondria identified thus far. In addition, our findings underscore the importance of expanding the taxonomic diversity in phylogenetic analyses beyond that represented by cultivated bacteria to study the origin of mitochondria.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-159787 (URN)10.1371/journal.pone.0024457 (DOI)000295039700022 ()
    Available from: 2011-10-10 Created: 2011-10-10 Last updated: 2017-12-08Bibliographically approved
    3. Independent Genome Reduction and Phylogenetic Reclassification of the Oceanic SAR11 Clade
    Open this publication in new window or tab >>Independent Genome Reduction and Phylogenetic Reclassification of the Oceanic SAR11 Clade
    2011 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 29, no 2, p. 599-615Article in journal (Refereed) Published
    Abstract [en]

    The SAR11 clade, here represented by Candidatus Pelagibacter ubique, is the most successful group of bacteria in the upper surface waters of the oceans. In contrast to previous studies that have associated the 1.3 Mb genome of Ca. Pelagibacter ubique with the less than 1.5 Mb genomes of the Rickettsiales, our phylogenetic analysis suggests that Ca. Pelagibacter ubique is most closely related to soil and aquatic Alphaproteobacteria with large genomes. This implies that the SAR11 clade and the Rickettsiales have undergone genome reduction independently. A gene flux analysis of 46 representative alphaproteobacterial genomes indicates the loss of more than 800 genes in each of Ca. Pelagibacter ubique and the Rickettsiales. Consistent with their different phylogenetic affiliations, the pattern of gene loss differs with a higher loss of genes for repair and recombination processes in Ca. Pelagibacter ubique as compared with a more extensive loss of genes for biosynthetic functions in the Rickettsiales. Some of the lost genes in Ca. Pelagibacter ubique, such as mutLS, recFN, and ruvABC, are conserved in all other alphaproteobacterial genomes including the small genomes of the Rickettsiales. The mismatch repair genes mutLS are absent from all currently sequenced SAR11 genomes and also underrepresented in the global ocean metagenome data set. We hypothesize that the unique loss of genes involved in repair and recombination processes in Ca. Pelagibacter ubique has been driven by selection and that this helps explain many of the characteristics of the SAR11 population, such as the streamlined genomes, the long branch lengths, the high recombination frequencies, and the extensive sequence divergence within the population.

    Keywords
    genome reduction, SAR11, Alphaproteobacteria, mismatch repair system, ocean surface waters, Candidatus Pelagibacter ubique, recombination, gene loss
    National Category
    Microbiology Evolutionary Biology Bioinformatics and Systems Biology
    Identifiers
    urn:nbn:se:uu:diva-165703 (URN)10.1093/molbev/msr203 (DOI)000299129000013 ()21900598 (PubMedID)
    Funder
    EU, European Research CouncilSwedish Research Council, 621-2009-4813 315-2004-6676 349-2007-831 621-2008-3259Swedish Foundation for Strategic Research Göran Gustafsson Foundation for promotion of scientific research at Uppala University and Royal Institute of TechnologyKnut and Alice Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC), p2006019
    Available from: 2012-01-09 Created: 2012-01-09 Last updated: 2017-12-08Bibliographically approved
    4. Single cell genomics reveals low recombination frequencies in freshwater bacteria of the SAR11 clade
    Open this publication in new window or tab >>Single cell genomics reveals low recombination frequencies in freshwater bacteria of the SAR11 clade
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    2013 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 14, no 11, article id R130Article in journal (Refereed) Published
    Abstract [en]

    Background: The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt-and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet. Results: We isolated ten single SAR11 cells from three freshwater lakes and sequenced and assembled their genomes. A phylogeny based on 57 proteins indicates that the cells are organized into distinct microclusters. We show that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. In contrast, members of the marine SAR11 clade have one of the highest ratios. Additional metagenome reads from six lakes confirm low recombination frequencies for the genome overall and reveal lake-specific variations in microcluster abundances. We identify hypervariable regions with gene contents broadly similar to those in the hypervariable regions of the marine isolates, containing genes putatively coding for cell surface molecules. Conclusions: We conclude that recombination rates differ dramatically in phylogenetic sister groups of the SAR11 clade adapted to freshwater and marine ecosystems. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host.

    National Category
    Microbiology
    Identifiers
    urn:nbn:se:uu:diva-206203 (URN)10.1186/gb-2013-14-11-r130 (DOI)000330616200009 ()24286338 (PubMedID)
    Funder
    Swedish Research Council, 349-2007-831 621-2008-3259 621-2011-4669-4669 2009-3784 2008-1923 2012-3892EU, European Research CouncilGöran Gustafsson Foundation for promotion of scientific research at Uppala University and Royal Institute of TechnologyKnut and Alice Wallenberg Foundation, KAW-2011.0148 KAW-2012.0075Swedish National Infrastructure for Computing (SNIC), p2006019 p2009043
    Available from: 2013-09-03 Created: 2013-08-29 Last updated: 2019-09-20Bibliographically approved
    5. Comparative and Phylogenomic Evidence that the Alphaproteobacterium HIMB59 is not a Member of the Oceanic SAR11 Clade
    Open this publication in new window or tab >>Comparative and Phylogenomic Evidence that the Alphaproteobacterium HIMB59 is not a Member of the Oceanic SAR11 Clade
    2013 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 11, p. e78858-Article in journal (Refereed) Published
    Abstract [en]

    SAR11 is a globally abundant group of Alphaproteobacteria in the oceans that is taxonomically not well defined. It has been suggested SAR11 should be classified into the novel order Pelagibacterales. Features such as conservation of gene content and synteny have been taken as evidence that also the divergent member HIMB59 should be included in the order. However, this proposition is controversial since phylogenetic analyses have questioned the monophyly of this grouping. Here, we performed phylogenetic analyses and reinvestigated the genomic similarity of SAR11 and HIMB59. Our phylogenetic analysis confirmed that HIMB59 is not a sister group to the other SAR11 strains. By placing the comparison in the context of the evolution of the Alphaproteobacteria, we found that none of the measures of genomic similarity supports a clustering of HIMB59 and SAR11 to the exclusion of other Alphaproteobacteria. First, pairwise sequence similarity measures for the SAR11 and HIMB59 genomes were within the range observed for unrelated pairs of Alphaproteobacteria. Second, pairwise comparisons of gene contents revealed a higher similarity of SAR11 to several other alphaproteobacterial genomes than to HIMB59. Third, the SAR11 genomes are not more similar in gene order to the HIMB59 genome than what they are to several other alphaproteobacterial genomes. Finally, in contrast to earlier reports, we observed no sequence similarity between the hypervariable region HVR2 in the SAR11 genomes and the region located at the corresponding position in the HIMB59 genome. Based on these observations, we conclude that the alphaproteobacterium HIMB59 is not monophyletic with the SAR11 strains and that genome streamlining has evolved multiple times independently in Alphaproteobacteria adapted to the upper surface waters of the oceans.

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-208438 (URN)10.1371/journal.pone.0078858 (DOI)000326499300036 ()
    Available from: 2013-10-01 Created: 2013-10-01 Last updated: 2017-12-06Bibliographically approved
    6. On the importance of taxonomically representative groups for the inference of adaptive traits in surface oceanic bacteria
    Open this publication in new window or tab >>On the importance of taxonomically representative groups for the inference of adaptive traits in surface oceanic bacteria
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-208439 (URN)
    Available from: 2013-10-01 Created: 2013-10-01 Last updated: 2013-11-06
    7. New protein functions evolve by expansion of ancestral fold architectures and evolution of disordered proteins de novo
    Open this publication in new window or tab >>New protein functions evolve by expansion of ancestral fold architectures and evolution of disordered proteins de novo
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-208436 (URN)
    Available from: 2013-10-01 Created: 2013-10-01 Last updated: 2013-11-06
  • 1143.
    Viklund, Johan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    On the importance of taxonomically representative groups for the inference of adaptive traits in surface oceanic bacteriaManuscript (preprint) (Other academic)
  • 1144.
    Viklund, Johan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Independent Genome Reduction and Phylogenetic Reclassification of the Oceanic SAR11 Clade2011In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 29, no 2, p. 599-615Article in journal (Refereed)
    Abstract [en]

    The SAR11 clade, here represented by Candidatus Pelagibacter ubique, is the most successful group of bacteria in the upper surface waters of the oceans. In contrast to previous studies that have associated the 1.3 Mb genome of Ca. Pelagibacter ubique with the less than 1.5 Mb genomes of the Rickettsiales, our phylogenetic analysis suggests that Ca. Pelagibacter ubique is most closely related to soil and aquatic Alphaproteobacteria with large genomes. This implies that the SAR11 clade and the Rickettsiales have undergone genome reduction independently. A gene flux analysis of 46 representative alphaproteobacterial genomes indicates the loss of more than 800 genes in each of Ca. Pelagibacter ubique and the Rickettsiales. Consistent with their different phylogenetic affiliations, the pattern of gene loss differs with a higher loss of genes for repair and recombination processes in Ca. Pelagibacter ubique as compared with a more extensive loss of genes for biosynthetic functions in the Rickettsiales. Some of the lost genes in Ca. Pelagibacter ubique, such as mutLS, recFN, and ruvABC, are conserved in all other alphaproteobacterial genomes including the small genomes of the Rickettsiales. The mismatch repair genes mutLS are absent from all currently sequenced SAR11 genomes and also underrepresented in the global ocean metagenome data set. We hypothesize that the unique loss of genes involved in repair and recombination processes in Ca. Pelagibacter ubique has been driven by selection and that this helps explain many of the characteristics of the SAR11 population, such as the streamlined genomes, the long branch lengths, the high recombination frequencies, and the extensive sequence divergence within the population.

  • 1145.
    Viklund, Johan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Martijn, Joran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Comparative and Phylogenomic Evidence that the Alphaproteobacterium HIMB59 is not a Member of the Oceanic SAR11 Clade2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 11, p. e78858-Article in journal (Refereed)
    Abstract [en]

    SAR11 is a globally abundant group of Alphaproteobacteria in the oceans that is taxonomically not well defined. It has been suggested SAR11 should be classified into the novel order Pelagibacterales. Features such as conservation of gene content and synteny have been taken as evidence that also the divergent member HIMB59 should be included in the order. However, this proposition is controversial since phylogenetic analyses have questioned the monophyly of this grouping. Here, we performed phylogenetic analyses and reinvestigated the genomic similarity of SAR11 and HIMB59. Our phylogenetic analysis confirmed that HIMB59 is not a sister group to the other SAR11 strains. By placing the comparison in the context of the evolution of the Alphaproteobacteria, we found that none of the measures of genomic similarity supports a clustering of HIMB59 and SAR11 to the exclusion of other Alphaproteobacteria. First, pairwise sequence similarity measures for the SAR11 and HIMB59 genomes were within the range observed for unrelated pairs of Alphaproteobacteria. Second, pairwise comparisons of gene contents revealed a higher similarity of SAR11 to several other alphaproteobacterial genomes than to HIMB59. Third, the SAR11 genomes are not more similar in gene order to the HIMB59 genome than what they are to several other alphaproteobacterial genomes. Finally, in contrast to earlier reports, we observed no sequence similarity between the hypervariable region HVR2 in the SAR11 genomes and the region located at the corresponding position in the HIMB59 genome. Based on these observations, we conclude that the alphaproteobacterium HIMB59 is not monophyletic with the SAR11 strains and that genome streamlining has evolved multiple times independently in Alphaproteobacteria adapted to the upper surface waters of the oceans.

  • 1146.
    Voeten, Dennis F. A. E.
    et al.
    European Synchrotron Radiat Facil, 71 Ave Martyrs,CS-40220, F-38043 Grenoble, France.;Palacky Univ, Dept Zool, 17 Listopadu 50, Olomouc 77146, Czech Republic.;Palacky Univ, Lab Ornithol, 17 Listopadu 50, Olomouc 77146, Czech Republic..
    Cubo, Jorge
    Sorbonne Univ, CNRS INSU, Inst Sci Terre Paris, ISTeP UMR 7193, F-75005 Paris, France..
    de Margerie, Emmanuel
    Univ Rennes 1, Univ Caen Normandie, CNRS, Lab Ethol Anim & Humaine, 263 Ave Gen Leclerc, F-35042 Rennes, France..
    Roeper, Martin
    Burgermeister Muller Museum, Bahnhofstr 8, D-91807 Solnhofen, Germany.;Bayerische Staatssammlung Palaontol & Geol, Richard Wagner Str 10, D-80333 Munich, Germany..
    Beyrand, Vincent
    European Synchrotron Radiat Facil, 71 Ave Martyrs,CS-40220, F-38043 Grenoble, France.;Palacky Univ, Dept Zool, 17 Listopadu 50, Olomouc 77146, Czech Republic.;Palacky Univ, Lab Ornithol, 17 Listopadu 50, Olomouc 77146, Czech Republic..
    Bures, Stanislav
    Palacky Univ, Dept Zool, 17 Listopadu 50, Olomouc 77146, Czech Republic.;Palacky Univ, Lab Ornithol, 17 Listopadu 50, Olomouc 77146, Czech Republic..
    Tafforeau, Paul
    European Synchrotron Radiat Facil, 71 Ave Martyrs,CS-40220, F-38043 Grenoble, France..
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. European Synchrotron Radiat Facil, 71 Ave Martyrs,CS-40220, F-38043 Grenoble, France.
    Wing bone geometry reveals active flight in Archaeopteryx2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 923Article in journal (Refereed)
    Abstract [en]

    Archaeopteryx is an iconic fossil taxon with feathered wings from the Late Jurassic of Germany that occupies a crucial position for understanding the early evolution of avian flight. After over 150 years of study, its mosaic anatomy unifying characters of both non-flying dinosaurs and flying birds has remained challenging to interpret in a locomotory context. Here, we compare new data from three Archaeopteryx specimens obtained through phase-contrast synchrotron microtomography to a representative sample of archosaurs employing a diverse array of locomotory strategies. Our analyses reveal that the architecture of Archaeopteryx's wing bones consistently exhibits a combination of cross-sectional geometric properties uniquely shared with volant birds, particularly those occasionally utilising short-distance flapping. We therefore interpret that Archaeopteryx actively employed wing flapping to take to the air through a more anterodorsally posteroventrally oriented flight stroke than used by modern birds. This unexpected outcome implies that avian powered flight must have originated before the latest Jurassic.

  • 1147.
    Vogan, Aaron
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Svedberg, Jesper
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Grudzinska-Sterno, Magdalena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Johannesson, Hanna
    Meiotic drive is associated with reproductive isolation in NeurosporaManuscript (preprint) (Other academic)
  • 1148.
    Vogel, David
    et al.
    Univ Toulouse, CNRS, CRCA, Toulouse, France..
    Nicolis, Stamatios C.
    Uppsala Univ, Dept Math, S-75238 Uppsala, Sweden..
    Perez-Escudero, Alfonso
    Univ Toulouse, CNRS, LAPLACE, Toulouse, France.;CSIC, Cajal Inst, Madrid, Spain..
    Nanjundiah, Vidyanand
    Ctr Human Genet, Bangalore 560100, Karnataka, India..
    Sumpter, David J. T.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Dussutour, Audrey
    Univ Toulouse, CNRS, CRCA, Toulouse, France..
    Phenotypic variability in unicellular organisms: from calcium signalling to social behaviour2015In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 282, no 1819, article id 20152322Article in journal (Refereed)
    Abstract [en]

    Historically, research has focused on the mean and often neglected the variance. However, variability in nature is observable at all scales: among cells within an individual, among individuals within a population and among populations within a species. A fundamental quest in biology now is to find the mechanisms that underlie variability. Here, we investigated behavioural variability in a unique unicellular organism, Physarum polycephalum. We combined experiments and models to show that variability in cell signalling contributes to major differences in behaviour underpinning some aspects of social interactions. First, following thousands of cells under various contexts, we identified distinct behavioural phenotypes: 'slow-regular-social', 'fast-regular-social' and 'fast-irregular-asocial'. Second, coupling chemical analysis and behavioural assays we found that calcium signalling is responsible for these behavioural phenotypes. Finally, we show that differences in signalling and behaviour led to alternative social strategies. Our results have considerable implications for our understanding of the emergence of variability in living organisms.

  • 1149.
    Voje, Kjetil Lysne
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences. Univ Oslo, Dept Biosci, CEES, Oslo, Norway.
    Assessing adequacy of models of phyletic evolution in the fossil record2018In: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 9, no 12, p. 2402-2413Article in journal (Refereed)
    Abstract [en]

    Comparing relative fit of different models of evolutionary dynamics to time series of phyletic change is a common tool when interpreting the fossil record. However, a measure of relative fit is no guarantee the preferred model describes the data well. Selecting a good model is essential for robust inferences, but we are currently lacking tools to investigate if a model of phyletic evolution represents an adequate description of trait dynamics in fossil data. This study develops a general statistical framework implemented in R for assessing the adequacy of the three most commonly used models of evolution in the fossil record; stasis, directional change and random walk. The statistical framework is applied to 300 fossil time series in order to assess how often the three models represent adequate descriptions of evolutionary dynamics in the fossil record. The model that showed the best relative fit to a particular fossil time series (using AICc) passed all adequacy tests in 219 out of 300 cases (73%, directional trend = 76%, stasis = 64%, random walk = 81%). It is therefore not uncommon that the best model according to AICc does not adequately describe the trait dynamics in a fossil time series. Statistical tests of model adequacy ease evaluation of whether a particular model is a good descriptor of phyletic evolution and can assist in making meaningful inferences of model parameters (e.g., as rates of evolution) and interpretations of evolution in the fossil record.

  • 1150.
    von Euler, Tove
    et al.
    Stockholm University, Department of Ecology, Environment and Plant Sciences.
    Madec, Camille
    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.
    Ehrlén, Johan
    Stockholm University, Department of Ecology, Environment and Plant Sciences.
    A demographic assessment of local adaptation in a grassland perennial herbManuscript (preprint) (Other academic)
    Abstract [en]

    Habitat heterogeneity in abiotic and biotic factors drives the evolution of adaptive population differentiation. Assessments of local adaptation among populations of perennial plants are commonly based on estimates of one or a few fitness components in reciprocal transplant experiments. However, natural selection does not act on fitness components but on life-time fitness, and local adaptation should therefore ideally be assessed based on integrated measures of the performance during the entire life cycle. We transplanted seedlings and adult plants reciprocally among four populations of the perennial herb Primula farinosa differing in abiotic and biotic conditions on the island of Öland, SE Sweden. We recorded survival, growth, flowering and fruit production during three consecutive years (2010-2012) and used integral projection models to quantify variation in total fitness, estimated as population growth rate. Transplant site had large effects on most aspects of plant performance, and the effects of population of origin on survival, growth, flowering propensity and fruit production varied among sites for several year × cohort combinations. However, no evidence of local adaptation, expressed through single fitness components or total fitness, was found. The results suggest that populations of P. farinosa differ genetically in traits influencing fitness, but these differences do not match current selection regimes. This study provides a template for how reciprocal transplant experiments can be combined with long-term demographic studies and population models to assess local adaptation in long-lived species based on estimates of total fitness.

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