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  • 1001. Shoda-Kagaya, E.
    et al.
    Saito, S.
    Okada, M.
    Nozaki, A.
    Nunokawa, K.
    Tsuda, Yoshiaki
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Genetic structure of the oak wilt vector beetle Platypus quercivorus: inferences toward the process of damaged area expansion2010In: BMC Ecology, ISSN 1472-6785, E-ISSN 1472-6785, Vol. 10, no 21Article in journal (Refereed)
  • 1002.
    Siepielski, Adam M.
    et al.
    Univ Arkansas, Dept Biol Sci, Fayetteville, AR 72701 USA..
    Morrissey, Michael B.
    Univ St Andrews, Sch Biol, St Andrews, Fife, Scotland..
    Buoro, Mathieu
    Univ Calif Berkeley, Dept Environm Sci Policy & Management, Berkeley, CA 94720 USA.;Univ Pau & Pays Adour, Inst Natl Rech Agron, St Pee Sur Nivelle, France..
    Carlson, Stephanie M.
    Univ Calif Berkeley, Dept Environm Sci Policy & Management, Berkeley, CA 94720 USA..
    Caruso, Christina M.
    Univ Guelph, Dept Integrat Biol, Guelph, ON, Canada..
    Clegg, Sonya M.
    Univ Oxford, Edward Grey Inst, Dept Zool, Oxford, England..
    Coulson, Tim
    Univ Cambridge, Dept Zool, Cambridge, England..
    DiBattista, Joseph
    Curtin Univ, Dept Environm & Agr, Perth, WA, Australia..
    Gotanda, Kiyoko M.
    Univ Cambridge, Dept Zool, Cambridge, England.;McGill Univ, Redpath Museum, Montreal, PQ, Canada.;McGill Univ, Dept Biol, Montreal, PQ, Canada..
    Francis, Clinton D.
    Calif Polytech State Univ San Luis Obispo, Dept Biol Sci, San Luis Obispo, CA 93407 USA..
    Hereford, Joe
    Univ Calif Davis, Dept Evolut & Ecol, Davis, CA 95616 USA..
    Kingsolver, Joel G.
    Univ N Carolina, Dept Biol, Chapel Hill, NC USA..
    Augustine, Kate E.
    Univ N Carolina, Dept Biol, Chapel Hill, NC USA..
    Kruuk, Loeske E. B.
    Australian Natl Univ, Res Sch Biol, Canberra, ACT, Australia..
    Martin, Ryan A.
    Case Western Reserve Univ, Dept Biol, Cleveland, OH 44106 USA..
    Sheldon, Ben C.
    Univ Oxford, Edward Grey Inst, Dept Zool, Oxford, England..
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Svensson, Erik I.
    Lund Univ, Dept Biol, Lund, Sweden..
    Wade, Michael J.
    Indiana Univ, Dept Biol, Bloomington, IN USA..
    MacColl, Andrew D. C.
    Univ Nottingham, Sch Life Sci, Nottingham, England..
    Response to Comment on "Precipitation drives global variation in natural selection"2018In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 359, no 6374, article id eaan5760Article in journal (Other academic)
    Abstract [en]

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

  • 1003.
    Siljestam, Mattias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Östman, Örjan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    The combined effects of temporal autocorrelation and the costs of plasticity on the evolution of plasticity2017In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 30, no 7, p. 1361-1371Article in journal (Refereed)
    Abstract [en]

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

  • 1004.
    Silva, C. N. S.
    et al.
    Univ Helsinki, Dept Biosci, Metapopulat Res Ctr, Helsinki, Finland;James Cook Univ, Coll Marine & Environm Sci, Ctr Sustainable Trop Fisheries & Aquaculture, Townsville, Qld, Australia.
    McFarlane, S. Eryn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Hagen, I. J.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Ronnegard, L.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden;Dalarna Univ, Sch Technol & Business Studies, Falun, Sweden.
    Billing, A. M.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Kvalnes, T.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Kemppainen, P.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Ronning, B.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Ringsby, T. H.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Saether, B-E
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Jensen, H.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Husby, A.
    Univ Helsinki, Dept Biosci, Metapopulat Res Ctr, Helsinki, Finland;Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Insights into the genetic architecture of morphological traits in two passerine bird species2017In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 119, no 3, p. 197-205Article in journal (Refereed)
    Abstract [en]

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

  • 1005.
    Silva, Willian T. A. F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Non-genetic processes in development and heredity2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

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

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

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

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

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

    Place, publisher, year, edition, pages
    John Wiley & Sons, 2019
    Keywords
    DNA damage, sexual selection, sperm competition, trade‐offs
    National Category
    Evolutionary Biology Zoology Genetics
    Identifiers
    urn:nbn:se:uu:diva-359415 (URN)10.1111/jeb.13435 (DOI)000472662300002 ()30817032 (PubMedID)
    Funder
    EU, European Research Council, HapSelA-336633Knut and Alice Wallenberg Foundation
    Available from: 2018-09-01 Created: 2018-09-01 Last updated: 2019-08-13Bibliographically approved
    4. Social environment of fathers affects gene expression patterns in early offspring
    Open this publication in new window or tab >>Social environment of fathers affects gene expression patterns in early offspring
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Developmental Biology Genetics Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-359417 (URN)
    Available from: 2018-09-01 Created: 2018-09-01 Last updated: 2018-09-05
  • 1006.
    Silva, Willian T. A. F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Jolly, Cécile
    Alavioon, Ghazal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Kiehl, Berrit
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Immler, Simone
    Social environment of fathers affects gene expression patterns in early offspringManuscript (preprint) (Other academic)
  • 1007.
    Silva, Willian T. A. F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Otto, Sarah P.
    Immler, Simone
    Evolution of small RNA production under fluctuating environmental conditionsManuscript (preprint) (Other academic)
  • 1008.
    Silva, Willian T. A. F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Sáez-Espinosa, Paula
    Department of Biotechnology, University of Alicante, Alicante, Spain.
    Torrijo-Boix, Stéphanie
    Department of Biotechnology, University of Alicante, Alicante, Spain.
    Romero, Alejandro
    Department of Biotechnology, University of Alicante, Alicante, Spain.
    Devaux, Caroline
    School of Biological Sciences, University of East Anglia, Norwich, UK.
    Durieux, Mathilde
    School of Biological Sciences, University of East Anglia, Norwich, UK.
    Gómez-Torres, María José
    Department of Biotechnology, University of Alicante, Alicante, Spain;Cátedra Human Fertility, University of Alicante, Alicante, Spain.
    Immler, Simone
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. School of Biological Sciences, University of East Anglia, Norwich, UK.
    The effects of male social environment on sperm phenotype and genome integrity2019In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 32, no 6, p. 535-544Article in journal (Refereed)
    Abstract [en]

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

  • 1009.
    Singer, David
    et al.
    Univ Neuchatel, Inst Biol, Lab Soil Biodivers, Neuchatel, Switzerland;Univ Sao Paulo, Inst Biosci, Dept Zool, Sao Paulo, Brazil.
    Mitchell, Edward A. D.
    Univ Neuchatel, Inst Biol, Lab Soil Biodivers, Neuchatel, Switzerland;Jardin Bot Neuchatel, Neuchatel, Switzerland.
    Payne, Richard J.
    Univ York, Environm, York, N Yorkshire, England.
    Blandenier, Quentin
    Univ Neuchatel, Inst Biol, Lab Soil Biodivers, Neuchatel, Switzerland;CSIC, Real Jardin Bot, Madrid, Spain.
    Duckert, Clement
    Univ Neuchatel, Inst Biol, Lab Soil Biodivers, Neuchatel, Switzerland.
    Fernandez, Leonardo D.
    Univ Neuchatel, Inst Biol, Lab Soil Biodivers, Neuchatel, Switzerland;Univ Bernardo OHiggins, Ctr Invest Recursos Nat & Sustentabilidad CIRENYS, Santiago, Chile.
    Fournier, Bertrand
    Concordia Univ, Dept Biol, Community & Quantitat Ecol Lab, Montreal, PQ, Canada.
    Hernandez, Cristian E.
    Barrio Univ Concepcion, Univ Concepcion, Dept Zool, Fac Ciencias Nat & Oceanog, Concepcion, Chile.
    Granath, Gustaf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Bragazza, Luca
    WSL Swiss Fed Inst Forest Snow & Landscape Res, Lausanne, Switzerland;Ecole Polytech Fed Lausanne, Sch Architecture Civil & Environm Engn ENAC, Lab Ecol Syst ECOS, Lausanne, Switzerland;Univ Ferrara, Dept Life Sci & Biotechnol, Ferrara, Italy.
    Koronatova, Natalia G.
    Russian Acad Sci, Siberian Branch, Inst Soil Sci & Agrochem, Lab Biogeocenol, Novosibirsk, Russia.
    Goia, Irina
    Babes Bolyai Univ, Fac Biol & Geol, Dept Taxon & Ecol, Cluj Napoca, Romania.
    Harris, Lorna I.
    McMaster Univ, Sch Geog & Earth Sci, Hamilton, ON, Canada.
    Kajukalo, Katarzyna
    Adam Mickiewicz Univ, Fac Geog & Geol Sci, Lab Wetland Ecol & Monitoring, Poznan, Poland;Adam Mickiewicz Univ, Dept Biogeog & Paleoecol, Poznan, Poland.
    Kosakyan, Anush
    Czech Acad Sci, Biol Ctr, Inst Parasitol, Ceske Budejovice, Czech Republic.
    Lamentowicz, Mariusz
    Adam Mickiewicz Univ, Fac Geog & Geol Sci, Lab Wetland Ecol & Monitoring, Poznan, Poland;Adam Mickiewicz Univ, Dept Biogeog & Paleoecol, Poznan, Poland.
    Kosykh, Natalia P.
    Russian Acad Sci, Siberian Branch, Inst Soil Sci & Agrochem, Lab Biogeocenol, Novosibirsk, Russia.
    Vellak, Kai
    Univ Tartu, Nat Hist Museum, Inst Ecol & Earth Sci, Tartu, Estonia.
    Lara, Enrique
    Univ Neuchatel, Inst Biol, Lab Soil Biodivers, Neuchatel, Switzerland;CSIC, Real Jardin Bot, Madrid, Spain.
    Dispersal limitations and historical factors determine the biogeography of specialized terrestrial protists2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 12, p. 3089-3100Article in journal (Refereed)
    Abstract [en]

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

  • 1010.
    Sirkiä, Päivi M
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    McFarlane, S. Eryn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Jones, William
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Wheatcroft, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ålund, Murielle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Rybinski, Jakub
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Climate-driven build-up of temporal isolation within a recently formed avian hybrid zone.2018In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 72, no 2, p. 363-374Article in journal (Refereed)
    Abstract [en]

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

  • 1011.
    Sjödin, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Skoglund, Pontus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Assessing the Maximum Contribution from Ancient Populations2014In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 31, no 5, p. 1248-1260Article in journal (Refereed)
    Abstract [en]

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

  • 1012.
    Sjöstrand, Agnès E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Origins and Adaptation in Humans: A Case Study of Taste and Lifestyle2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

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

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

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

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

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

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

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

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

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

    Keywords
    Local adaptation, Haplotype, Positive selection, Human height
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-228475 (URN)10.1186/1471-2156-15-61 (DOI)000336863400001 ()
    Available from: 2014-07-15 Created: 2014-07-15 Last updated: 2017-12-05Bibliographically approved
    3. Patterns of local adaptation in Africans
    Open this publication in new window or tab >>Patterns of local adaptation in Africans
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    (English)Manuscript (preprint) (Other academic)
    Keywords
    Adaptation, lifestyle, selection scans
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-263084 (URN)
    Available from: 2015-09-25 Created: 2015-09-25 Last updated: 2015-11-10
    4. Taste and lifestyle: insights from SNP-chip data.
    Open this publication in new window or tab >>Taste and lifestyle: insights from SNP-chip data.
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Keywords
    Taste, GWAS, lifestyle, adaptation
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-263083 (URN)
    Available from: 2015-09-25 Created: 2015-09-25 Last updated: 2015-11-10
  • 1013. Skarpe, C.
    et al.
    Bergström, R.
    Makhabu, S.
    Rooke, T.
    Hytteborn, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Danell, K.
    Plant-Herbivore Interactions2014In: Elephants and Savanna Woodland Ecosystems: A Study from Chobe National Park, Botswana / [ed] C. Skarpe, J. T. du Toit and S. R. Moe, Wiley-Blackwell, 2014, p. 189-206Chapter in book (Refereed)
    Abstract [en]

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

  • 1014.
    Skoglund, Pontus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Reconstructing the Human Past using Ancient and Modern Genomes2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

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

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

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

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

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

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

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

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

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

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

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

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

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

    National Category
    Biological Sciences
    Research subject
    Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-206756 (URN)10.1093/molbev/msu192 (DOI)000343401100022 ()
    Available from: 2013-09-04 Created: 2013-09-04 Last updated: 2017-12-06Bibliographically approved
  • 1015.
    Skoglund, Pontus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Archaic human ancestry in East Asia2011In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 108, no 45, p. 18301-18306Article in journal (Refereed)
    Abstract [en]

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

  • 1016.
    Skoglund, Pontus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Malmstrom, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Omrak, Ayca
    Raghavan, Maanasa
    Valdiosera, Cristina
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Hall, Per
    Tambets, Kristiina
    Parik, Jueri
    Sjogren, Karl-Goran
    Apel, Jan
    Willerslev, Eske
    Stora, Jan
    Gotherstrom, Anders
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers2014In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 344, no 6185, p. 747-750Article in journal (Refereed)
    Abstract [en]

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

  • 1017.
    Skulason, Skuli
    et al.
    Holar Univ, Dept Aquaculture & Fish Biol, IS-551 Sauoarkrokur, Iceland;Iceland Museum Nat Hist, Brynjolfsgata 5, IS-107 Reykjavik, Iceland.
    Parsons, Kevin J.
    Univ Glasgow, Inst Biodivers Anim Hlth & Comparat Med, Glasgow G12 8QQ, Lanark, Scotland.
    Svanbäck, Richard
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Rasanen, Katja
    EAWAG, Swiss Fed Inst Aquat Sci & Technol, Dept Aquat Ecol, Ueberlandstr 133, CH-8600 Dubendorf, Switzerland;Swiss Fed Inst Technol, Inst Integrat Biol, Ueberlandstr 133, CH-8600 Dubendorf, Switzerland.
    Ferguson, Moira M.
    Univ Guelph, Dept Integrat Biol, Guelph, ON N1G 2W1, Canada.
    Adams, Colin E.
    Univ Glasgow, Scottish Ctr Ecol & Nat Environm, IBAHCM, Glasgow G12 8QQ, Lanark, Scotland.
    Amundsen, Per-Arne
    Univ Tromso, Freshwater Ecol Grp, Dept Arctic & Marine Biol, Fac Biosci Fisheries & Econ, N-9037 Tromso, Norway.
    Bartels, Pia
    Umea Univ, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden.
    Bean, Colin W.
    Scottish Nat Heritage, Caspian House,Clydebank Business Pk, Clydebank G81 2NR, Scotland.
    Boughman, Janette W.
    Michigan State Univ, Dept Integrat Biol, E Lansing, MI 48824 USA.
    Englund, Goeran
    Umea Univ, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden.
    Gudbrandsson, Johannes
    Univ Iceland, Inst Life & Environm Sci, IS-101 Reykjavik, Iceland.
    Hooker, Oliver E.
    PR Stat LTD, 53 Morrison St, Glasgow G5 8LB, Lanark, Scotland.
    Hudson, Alan G.
    Umea Univ, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden.
    Kahilainen, Kimmo K.
    Inland Norway Univ Appl Sci, Dept Forestry & Wildlife Management, Campus Evenstad,Anne Evenstadvei 80, NO-2480 Koppang, Norway.
    Knudsen, Rune
    Univ Tromso, Freshwater Ecol Grp, Dept Arctic & Marine Biol, Fac Biosci Fisheries & Econ, N-9037 Tromso, Norway.
    Kristjansson, Bjarni K.
    Holar Univ, Dept Aquaculture & Fish Biol, IS-551 Sauoarkrokur, Iceland.
    Leblanc, Camille A-L.
    Holar Univ, Dept Aquaculture & Fish Biol, IS-551 Sauoarkrokur, Iceland.
    Jonsson, Zophonias
    Univ Iceland, Inst Life & Environm Sci, IS-101 Reykjavik, Iceland.
    Ohlund, Gunnar
    Umea Univ, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden.
    Smith, Carl
    Univ St Andrews, Sch Biol, St Andrews KY16 9AJ, Fife, Scotland.
    Snorrason, Sigurdur S.
    Univ Iceland, Inst Life & Environm Sci, IS-101 Reykjavik, Iceland.
    A way forward with eco evo devo: an extended theory of resource polymorphism with postglacial fishes as model systems2019In: Biological Reviews, ISSN 1464-7931, E-ISSN 1469-185X, Vol. 94, no 5, p. 1786-1808Article in journal (Refereed)
    Abstract [en]

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

  • 1018.
    Sletvold, Nina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Trunschke, Judith
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Smit, Mart
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Verbeek, Jeffrey
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Strong pollinator-mediated selection for increased flower brightness and contrast in a deceptive orchid2016In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 70, no 3, p. 716-724Article in journal (Refereed)
    Abstract [en]

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

  • 1019.
    Sletvold, Nina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala Univ, EBC, Dept Ecol & Genet, Plant Ecol & Evolut, SE-75236 Uppsala, Sweden..
    Nonlinear costs of reproduction in a long-lived plant2015In: Journal of Ecology, ISSN 0022-0477, E-ISSN 1365-2745, Vol. 103, no 5, p. 1205-1213Article in journal (Refereed)
    Abstract [en]

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

  • 1020.
    Sletvold, Nina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    There is More to Pollinator-Mediated Selection than Pollen Limitation2014In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 68, no 7, p. 1907-1918Article in journal (Refereed)
    Abstract [en]

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

  • 1021.
    Smeds, Linnea
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Kawakami, Takeshi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Burri, Reto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bolivar, Paulina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Husby, Arild
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Uebbing, Severin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 5448-Article in journal (Refereed)
    Abstract [en]

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

  • 1022.
    Smeds, Linnea
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Kojola, Ilpo
    Nat Resources Inst Finland Luke, Rovaniemi, Finland.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    The evolutionary history of grey wolf Y chromosomes2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 9, p. 2173-2191Article in journal (Refereed)
    Abstract [en]

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

  • 1023.
    Smeds, Linnea
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Direct estimate of the rate of germline mutation in a bird2016In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 26, no 9, p. 1211-1218Article in journal (Refereed)
    Abstract [en]

    The fidelity of DNA replication together with repair mechanisms ensure that the genetic material is properly copied from one generation to another. However, on extremely rare occasions when damages to DNA or replication errors are not repaired, germline mutations can be transmitted to the next generation. Because of the rarity of these events, studying the rate at which new mutations arise across organisms has been a great challenge, especially in multicellular nonmodel organisms with large genomes. We sequenced the genomes of 11 birds from a three-generation pedigree of the collared flycatcher (Ficedula albicollis) and used highly stringent bioinformatic criteria for mutation detection and used several procedures to validate mutations, including following the stable inheritance of new mutations to subsequent generations. We identified 55 de novo mutations with a 10-fold enrichment of mutations at CpG sites and with only a modest male mutation bias. The estimated rate of mutation per site per generation was 4.6 x 10(-9), which corresponds to 2.3 x 10(-9) mutations per site per year. Compared to mammals, this is similar to mouse but about half of that reported for humans, which may be due to the higher frequency of male mutations in humans. We confirm that mutation rate scales positively with genome size and that there is a strong negative relationship between mutation rate and effective population size, in line with the drift-barrier hypothesis. Our study illustrates that it should be feasible to obtain direct estimates of the rate of mutation in essentially any organism from which family material can be obtained.

  • 1024.
    Smolla, Marco
    et al.
    Univ Penn, Dept Biol, Philadelphia, PA 19104 USA;Univ Manchester, Fac Sci & Engn, Sch Earth & Environm Sci, Manchester, Lancs, England.
    Rosher, Charlotte
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Univ Manchester, Fac Sci & Engn, Sch Earth & Environm Sci, Manchester, Lancs, England;Uppsala Univ, Dept Ecol & Genet, Uppsala, Sweden.
    Gilman, R. Tucker
    Univ Manchester, Fac Sci & Engn, Sch Earth & Environm Sci, Manchester, Lancs, England.
    Shultz, Susanne
    Univ Manchester, Fac Sci & Engn, Sch Earth & Environm Sci, Manchester, Lancs, England.
    Reproductive skew affects social information use2019In: Royal Society Open Science, E-ISSN 2054-5703, Vol. 6, no 7, article id 182084Article in journal (Refereed)
    Abstract [en]

    Individuals vary in their propensity to use social learning, the engine of cultural evolution, to acquire information about their environment. The causes of those differences, however, remain largely unclear. Using an agent-based model, we tested the hypothesis that as a result of reproductive skew differences in energetic requirements for reproduction affect the value of social information. We found that social learning is associated with lower variance in yield and is more likely to evolve in risk-averse low-skew populations than in high-skew populations. Reproductive skew may also result in sex differences in social information use, as empirical data suggest that females are often more risk-averse than males. To explore how risk may affect sex differences in learning strategies, we simulated learning in sexually reproducing populations where one sex experiences more reproductive skew than the other. When both sexes compete for the same resources, they tend to adopt extreme strategies: the sex with greater reproductive skew approaches pure individual learning and the other approaches pure social learning. These results provide insight into the conditions that promote individual and species level variation in social learning and so may affect cultural evolution.

  • 1025.
    Sniegula, Szymon
    et al.
    Polish Acad Sci, Inst Nat Conservat, Dept Ecosyst Conservat, Al Mickiewicza 33, PL-31120 Krakow, Poland.
    Golab, Maria J.
    Polish Acad Sci, Inst Nat Conservat, Dept Ecosyst Conservat, Al Mickiewicza 33, PL-31120 Krakow, Poland.
    Drobniak, Szymon M.
    Jagiellonian Univ, Inst Environm Sci, Populat Ecol Grp, Krakow, Poland.
    Johansson, Frank
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    The genetic variance but not the genetic covariance of life-history traits changes towards the north in a time-constrained insect2018In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 31, no 6, p. 853-865Article in journal (Refereed)
    Abstract [en]

    Seasonal time constraints are usually stronger at higher than lower latitudes and can exert strong selection on life-history traits and the correlations among these traits. To predict the response of life-history traits to environmental change along a latitudinal gradient, information must be obtained about genetic variance in traits and also genetic correlation between traits, that is the genetic variance-covariance matrix, G. Here, we estimated G for key life-history traits in an obligate univoltine damselfly that faces seasonal time constraints. We exposed populations to simulated native temperatures and photoperiods and common garden environmental conditions in a laboratory set-up. Despite differences in genetic variance in these traits between populations (lower variance at northern latitudes), there was no evidence for latitude-specific covariance of the life-history traits. At simulated native conditions, all populations showed strong genetic and phenotypic correlations between traits that shaped growth and development. The variance-covariance matrix changed considerably when populations were exposed to common garden conditions compared with the simulated natural conditions, showing the importance of environmentally induced changes in multivariate genetic structure. Our results highlight the importance of estimating variance-covariance matrixes in environments that mimic selection pressures and not only trait variances or mean trait values in common garden conditions for understanding the trait evolution across populations and environments.

  • 1026.
    Sniegula, Szymon
    et al.
    Polish Acad Sci, Inst Nat Conservat, Dept Ecosyst Conservat, Al Mickiewicza 33, PL-31120 Krakow, Poland..
    Golab, Maria J.
    Polish Acad Sci, Inst Nat Conservat, Dept Ecosyst Conservat, Al Mickiewicza 33, PL-31120 Krakow, Poland..
    Johansson, Frank
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Cannibalism and activity rate in larval damselflies increase along a latitudinal gradient as a consequence of time constraints2017In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 17, article id 167Article in journal (Refereed)
    Abstract [en]

    Background: Predation is ubiquitous in nature. One form of predation is cannibalism, which is affected by many factors such as size structure and resource density. However, cannibalism may also be influenced by abiotic factors such as seasonal time constraints. Since time constraints are greater at high latitudes, cannibalism could be stronger at such latitudes, but we know next to nothing about latitudinal variation in cannibalism. In this study, we examined cannibalism and activity in larvae of the damselfly Lestes sponsa along a latitudinal gradient across Europe. We did this by raising larvae from the egg stage at different temperatures and photoperiods corresponding to different latitudes. Results: We found that the more seasonally time-constrained populations in northern latitudes and individuals subjected to greater seasonal time constraints exhibited a higher level of cannibalism. We also found that activity was higher at north latitude conditions, and thus correlated with cannibalism, suggesting that this behaviour mediates higher levels of cannibalism in time-constrained animals. Conclusions: Our results go counter to the classical latitude-predation pattern which predicts higher predation at lower latitudes, since we found that predation was stronger at higher latitudes. The differences in cannibalism might have implications for population dynamics along the latitudinal gradients, but further experiments are needed to explore this.

  • 1027. Sniegula, Szymon
    et al.
    Prus, Monika A.
    Golab, Maria J.
    Outomuro, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Do males with higher mating success invest more in armaments?: An across-populations study in damselflies2017In: Ecological Entomology, ISSN 0307-6946, E-ISSN 1365-2311, Vol. 42, no 4, p. 526-530Article in journal (Refereed)
    Abstract [en]

    1. Males with higher mating success would be expected to invest more in traits that facilitate mating, leading to steeper allometry of those traits with respect to body size. Across-population studies following latitudinal variation in male mating success are an excellent study system to address this question.

    2. Males of the damselfly Lestes sponsa were used to investigate whether the allometric patterns of the length and width of the anal appendages, used for grasping the female prior tomating, corresponded to male mating success. Across a large latitudinal gradient, it was hypothesised that there is a larger investment in the grasping apparatus, i.e. a steeper allometric slope, following higher mating success.

    3. Behavioural observations in field enclosures showed the highest mating success at high latitude, while there were no significant differences in mating success between the central and low latitudes. Positive allometry was found for the length of the anal appendages in high-latitude males, while central-and low-latitude males showed no significant regressions of the traits on body size.

    4. These results partially support the hypothesis, as high-latitude, more successful males invested more in the length ( but not the width) of the grasping apparatus than did central-and low-latitude males. Therefore, higher mating success might be facilitated by larger investment in armaments. Intraspecific studies on allometric patterns of traits that participate in mating success might offer new insights into the role of those traits in the reproductive behaviour of a species.

  • 1028.
    Sokolovskis, Kristaps
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Lund University, MEEL, Bensch group.
    Genetics of bird migration: Study on East Siberian willow warblers (Phylloscopus trochilus)2017Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Seasonal long-distance bird migration between wintering and breeding grounds is oneof the most remarkable phenomena in the history of life on earth. Migration strategies androutes vary greatly. Some birds migrate in social groups whilst others migrate alone at night,some cross few hundreds of km whilst others cover thousands of km. Avian migration has beenstudied extensively nevertheless numerous important questions remain unanswered. This studyaims to contribute to the understanding of the genetic basis of the innate migratory program ofa common songbird.From results of classical crossbreeding and orientation experiments with captiveblackcaps (Sylvia atricapilla) we can be sure that songbird migration directions as well asdurations are traits that are being inherited genetically and most likely have a multi-locusgenetic architecture. The chosen model species for my project is the willow warbler(Phylloscopus trochilus), one of the most common leaf warblers in the Palearctic. The willowwarbler has a continuous breeding distribution from the coast of the Atlantic to the coast ofPacific. They overwinter in sub-Saharan Africa. Three subspecies have been recognized: P. t.trochilus (breeding in central/western Europe and migrating SSW to western Africa), P. t.acredula (breeding in northern and eastern Europe, migrating SSE to east and south Africa)and P. t. yakutensis (breeding east of Ural Mountains, presumably migrating to SouthernAfrica). Morphological differences across the willow warbler subspecies are subtle and it has

    been previously shown that genome wide FST is close to zero. The low level of neutral back-ground divergence offers a good system for studying the genetics of passerine migration. This

    report contributes with novel data on phenotypes and genotypes of the subspecies yakutensisstudied at Chaun river delta, at the very eastern range limit of the species. As a proxy for thewintering location of yakutensis I used C and N stable isotope signatures from winter grownfeathers and inferred wintering range to be in Southern Africa. I genotyped 36 yakutensis fromChaun on four nuclear markers, of which three are located on the only divergent regions thatdiffers between the migratory phenotypes in Europe + CLOCK gene (a candidate for timing ofmigration). Analyzes revealed that yakutensis, despite strong differences in migration direction,distance, timing and wintering ground location cannot be separated from acredula genetically.

  • 1029. Soliani, Carolina
    et al.
    Tsuda, Yoshiaki
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Bagnoli, Francesca
    Gallo, Leonardo A.
    Vendramin, Giovanni G.
    Marchelli, Paula
    Halfway encounters: Meeting points of colonization routes among the southern beeches Nothofagus pumilio and N. antarctica2015In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 85, p. 197-207Article in journal (Refereed)
    Abstract [en]

    The Patagonian region is characterized by a complex biogeographic history, with evidence of deep phylogeographic breaks shared among species. Of particular interest to conservation is the nature of colonization and settlement patterns after the last glacial period, including the detection of secondary contact between different lineages and/or hybridization among related species around phylogeographic breaks. Here we studied population demography and past hybridization of two widespread tree species endemic to South America, Nothofagus pumilio and N. antarctica. Using 8 nuclear microsatellites we genotyped 41 populations of both species. Genetic variation and structure across the geographic region were evaluated within and among species and the past demographic history of hybridization between the two species was inferred using Approximate Bayesian Computation (ABC). Northern and southern lineages were identified in each species, and Bayesian clustering revealed their convergence at mid latitudes (42 degrees S). Spatial genetic structure (SGS) also indicated the existence of a genetic discontinuity at these latitudes, which is in agreement with previous data from maternal DNA markers. Several populations around 42-44 degrees S presented high levels of genetic diversity with a decrease toward southern populations. Even though the species are clearly differentiated (G'(ST) = 0.335), admixed gene pools were observed in both species. Two independent runs of ABC suggested that inter species admixture-like patterns occurred within the timescale of the Last Glacial Maximum (around 20,000 BP). We also provide evidences of recent and bi-directional hybridization/introgression between the two Nothofagus species and describe features of the populations demography in the past. The settlement of a secondary contact zone in Nothofagus species around 42-44 degrees S coincides with the phylogeographic breaks and hotspots of genetic diversity found in other plant and animal species in Patagonia, highlighting its importance as reservoir of diversity. The characterization of the population history of native species can contribute substantially to long-term conservation and management policies.

  • 1030.
    Song, Gang
    et al.
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing, Peoples R China.
    Zhang, Ruiying
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing, Peoples R China; Chinese Acad Sci, Inst Genet & Dev Biol, Ctr Dev Biol, Beijing, Peoples R China.
    Alström, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing, Peoples R China; Swedish Univ Agr Sci, Swedish Species Informat Ctr, Uppsala, Sweden.
    Irestedt, Martin
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden.
    Cai, Tianlong
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing, Peoples R China; Univ Chinese Acad Sci, Coll Life Sci, Beijing, Peoples R China; Univ Copenhagen, Nat Hist Museum Denmark, Ctr Macroecol Evolut & Climate, Copenhagen, Denmark.
    Qu, Yanhua
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing, Peoples R China.
    Ericson, Per G. P.
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden.
    Fjeldså, Jon
    Univ Copenhagen, Nat Hist Museum Denmark, Ctr Macroecol Evolut & Climate, Copenhagen, Denmark.
    Lei, Fumin
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing, Peoples R China; Univ Chinese Acad Sci, Coll Life Sci, Beijing, Peoples R China.
    Complete taxon sampling of the avian genus Pica (magpies) reveals ancient relictual populations and synchronous Late-Pleistocene demographic expansion across the Northern Hemisphere2018In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 49, no 2, article id UNSP e01612Article in journal (Refereed)
    Abstract [en]

    Previous studies have suggested that bird populations in east Asia were less affected by Pleistocene climatic fluctuations than those in Europe and North America. However, this is mainly based on comparisons among species. It would be more relevant to analyse geographical populations of widespread species or species complexes. We analyzed two mitochondrial genes and two nuclear introns for all taxa of Pica to investigate 1) which Earth history factors have shaped the lineage divergence, and 2) whether different geographical populations were differently affected by the Pleistocene climatic changes. Our mitochondrial tree recovered three widespread lineages, 1) in east Asia, 2) across north Eurasia, and 3) in North America, respectively, with three isolated lineages in northwest Africa, Arabia and the Qinghai‐Tibet Plateau, respectively. Divergences among lineages took place 1.4–3.1 million yr ago. The northwest African population was sister to the others, which formed two main clades. In one of these, Arabia was sister to Qinghai‐Tibet, and these formed the sister clade to the east Asia clade. The other main clade comprised the North American and north Eurasian clades. There was no or very slight structure within these six geographical clades, including a lack of differentiation between the two North American species black‐billed magpie P. hudsonia and yellow‐billed magpie P. nutalli. Demographic expansion was recorded in the three most widespread lineages after 0.06 Ma. Asymmetric gene flow was recorded in the north Eurasian clade from southwestern Europe eastward, whereas the east Asian clade was rooted in south central China. Our results indicate that the fragmentation of the six clades of Pica was related to climatic cooling and aridification during periods of the Pliocene–Pleistocene. Populations on both sides of the Eurasian continent were similarly influenced by the Pleistocene climate changes and expanded concomitantly with the expansion of steppes. Based on results we also propose a revised taxonomy recognising seven species of Pica.

  • 1031.
    Sorenson, Michael D
    et al.
    University of Michigan, Museum of Zoology and Department of Biology.
    Ast, Jennifer C
    University of Michigan, Museum of Zoology and Department of Biology.
    Dimcheff, Derek E
    University of Michigan, Museum of Zoology and Department of Biology.
    Yuri, Tamaki
    University of Michigan, Museum of Zoology and Department of Biology.
    Mindell, David P
    University of Michigan, Museum of Zoology and Department of Biology.
    Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates1999In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 12, p. 105-114Article in journal (Refereed)
  • 1032.
    Sork, Victoria L.
    et al.
    Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA 90095 USA.;Univ Calif Los Angeles, Inst Environm & Sustainabil, Los Angeles, CA 90095 USA..
    Smouse, Peter E.
    Rutgers State Univ, Dept Ecol Evolut & Nat Resources, New Brunswick, NJ 08901 USA..
    Grivet, Delphine
    CIFOR Natl Inst Agr & Food Res & Technol, Ctr Forest Res, Dept Forest Ecol & Genet, Madrid, Spain..
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA 90095 USA..
    Impact of asymmetric male and female gamete dispersal on allelic diversity and spatial genetic structure in valley oak (Quercus lobata Nee)2015In: Evolutionary Ecology, ISSN 0269-7653, E-ISSN 1573-8477, Vol. 29, no 6, p. 927-945Article in journal (Refereed)
    Abstract [en]

    The distribution and abundance of genetic diversity in plant populations is initiated by sexually asymmetric propagule dispersal through pollen and seeds. Because these processes occur serially, it is not transparent how each contributes to subsequent patterns of genetic diversity. Using combined seedling/seed coat assay for naturally distributed seedlings of Quercus lobata N,e, we extracted male and female gametic genotypes, and then assessed (wind-vectored) paternal and (gravity- and animal-vectored) maternal contributions to spatially distributed allelic diversity. We evaluated 200 naturally recruited seedlings from 4 open patches away from any adult canopies (denoted 'open'), and 174 seedlings from 14 patches immediately beneath adult canopies (denoted 'canopy'). The open patches included 19 % long distant dispersal events of > 1 km while the canopy patches contained seedlings from one tree overhead. For each patch type, we partitioned average allelic diversity for six microsatellite loci for the whole study site (gamma) into separate within-patch (alpha) and among-patch (beta) components, translated into among-patch divergence (delta). We found that alpha-diversity resulting from seed dispersal was much less than that from pollen dispersal in both patch types, while total gamma-diversity across the site was similar. Divergence (delta) among canopy patches was significantly greater than delta among open patches. We then evaluated spatial genetic autocorrelation (kinship) patterns for both open and canopy strata, separately for male and female gametes. Female gametes showed sharply declining kinship with increasing distance for canopy patches and modestly for open patches. In sharp contrast, male gametes from both patches showed only subtle decline of kinship, but seedlings still showed significant structure across patch types. On balance, sexual asymmetry in propagule dispersal shapes both the abundance and distribution of allelic diversity, with pollen dispersal promoting overall diversity but reducing spatial structure, but seed-dispersal reduces overall diversity and markedly increases spatial genetic structure.

  • 1033.
    Sotero-Caio, Cibele G.
    et al.
    Texas Tech Univ, Dept Biol Sci, Lubbock, TX 79409 USA..
    Platt, Roy N., II
    Texas Tech Univ, Dept Biol Sci, Lubbock, TX 79409 USA..
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ray, David A.
    Texas Tech Univ, Dept Biol Sci, Lubbock, TX 79409 USA..
    Evolution and Diversity of Transposable Elements in Vertebrate Genomes2017In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, no 1, p. 161-177Article in journal (Refereed)
    Abstract [en]

    Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4-60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genomeevolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes.

  • 1034.
    Spagopoulou, Foteini
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Condition-dependence in life history evolution2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Ageing is the progressive physiological deterioration that appears with increasing age and eventually leads to a decline in survival and reproduction. This physiological process is omnipresent across the tree of life, but the expected trajectory can widely vary between and within species. Classic theories predict that the evolution of senescence is strongly influenced by the level of extrinsic mortality. Furthermore, variation in early-life developmental environments can shape individual condition and thus lead to alternative life-history strategies. The interplay between early-life environment and individual condition might therefore predict the trajectory of ageing and is of importance when studying life history evolution. In this thesis, I focus on condition dependent life-history strategies and how this can translate in differential ageing patterns. Moreover, I specifically investigate the influence of early-life environment on key life history traits (i.e. survival and reproduction) and how this might eventually carry-over to future generations via nongenetic inheritance. First, I used an experimental approach involving lab populations of the nematode Caenorhabditis remanei to show that males, but not females, pay the cost for the evolution of increased lifespan (Paper I). Second, I used an empirical dataset based on 25 years of observations, to investigate the long-term effects of early-life environment on reproduction and survival (Paper II). Reproductive success of low-condition females in natural populations of collared flycatchers (Ficedula albicollis) peaks later in life, when high-condition females are already in steep reproductive decline and suffer from high mortality rates. Third, I used the neriid fly Telostylinus angusticollis in an experimental environment, to test whether condition-dependent investment in secondary sexual traits affects the life-history strategies of males (Paper III). High-condition males developed and aged faster than low-condition males, but interaction with rival males did not affect male reproductive ageing. Finally, continuing the T. angusticollis experiment, I also found that parental diet interacts with parental sex and offspring sex, ultimately affecting offspring life-histories. Parental effects can thus play an important role in shaping between-individual variation in reproductive and actuarial senescence (Paper IV). Overall, in this thesis I have explored the interaction between environment, condition and ageing in both experimental and natural settings.

    List of papers
    1. Evolution of male age-specific reproduction under differential risks and causes of death: males pay the cost of high female fitness
    Open this publication in new window or tab >>Evolution of male age-specific reproduction under differential risks and causes of death: males pay the cost of high female fitness
    2016 (English)In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 29, no 4, p. 848-856Article in journal (Refereed) Published
    Abstract [en]

    Classic theories of ageing evolution predict that increased extrinsic mortality due to an environmental hazard selects for increased early reproduction, rapid ageing and short intrinsic lifespan. Conversely, emerging theory maintains that when ageing increases susceptibility to an environmental hazard, increased mortality due to this hazard can select against ageing in physiological condition and prolong intrinsic lifespan. However, evolution of slow ageing under high-condition-dependent mortality is expected to result from reallocation of resources to different traits and such reallocation may be hampered by sex-specific trade-offs. Because same life-history trait values often have different fitness consequences in males and females, sexually antagonistic selection can preserve genetic variance for lifespan and ageing. We previously showed that increased condition-dependent mortality caused by heat shock leads to evolution of long-life, decelerated late-life mortality in both sexes and increased female fecundity in the nematode, Caenorhabditis remanei. Here, we used these cryopreserved lines to show that males evolving under heat shock suffered from reduced early-life and net reproduction, while mortality rate had no effect. Our results suggest that heat-shock resistance and associated long-life trade-off with male, but not female, reproduction and therefore sexually antagonistic selection contributes to maintenance of genetic variation for lifespan and fitness in this population.

    Keywords
    heat shock, intralocus sexual conflict, life-history trade-off, senescence, sex-specific pleiotropy
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-295550 (URN)10.1111/jeb.12833 (DOI)000373929000015 ()26801472 (PubMedID)
    Available from: 2016-06-08 Created: 2016-06-08 Last updated: 2018-04-09Bibliographically approved
    2. “Silver-spoon” natal conditions increase early-life fitness but accelerate reproductive ageing in a wild bird
    Open this publication in new window or tab >>“Silver-spoon” natal conditions increase early-life fitness but accelerate reproductive ageing in a wild bird
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Early-life conditions can have long-lasting effects and organisms that experience a poor start in life are often expected to age at a faster rate. Alternatively, individuals raised in high-quality environments can overinvest in early-reproduction resulting in rapid ageing. Here we use long-term experimental manipulation of early-life conditions in a natural population of collared flycatchers (Ficedula albicollis), to show that females raised in a low-competition environment have higher early-life reproduction but lower late-life reproduction than females raised in high-competition environment. We experimentally created either artificially increased (high-competition) or reduced (low-competition) broods. Reproductive success of high-competition females peaked in late-life, when low-competition females were already in steep reproductive decline and suffered from higher mortality rate. Our results demonstrate that “silver spoon” effects can increase female early-life performance at the cost of faster reproductive ageing and increased late-life mortality. These findings support the evolutionary theory of ageing and show that early-life environmental conditions shape reproductive and demographic ageing in nature.

    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Animal Ecology
    Identifiers
    urn:nbn:se:uu:diva-347831 (URN)
    Available from: 2018-04-08 Created: 2018-04-08 Last updated: 2018-04-09
    3. Ontogenetic timing as a condition-dependent life history trait: High-condition males develop quickly, peak early, and age fast
    Open this publication in new window or tab >>Ontogenetic timing as a condition-dependent life history trait: High-condition males develop quickly, peak early, and age fast
    Show others...
    2017 (English)In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 71, no 3, p. 671-685Article in journal (Refereed) Published
    Abstract [en]

    Within-population variation in ageing remains poorly understood. In males, condition-dependent investment in secondary sexual traits may incur costs that limit ability to invest in somatic maintenance. Moreover, males often express morphological and behavioral secondary sexual traits simultaneously, but the relative effects on ageing of investment in these traits remain unclear. We investigated the condition dependence of male life history in the neriid fly Telostylinus angusticollis. Using a fully factorial design, we manipulated male early-life condition by varying nutrient content of the larval diet and, subsequently, manipulated opportunity for adult males to interact with rival males. We found that high-condition males developed more quickly and reached their reproductive peak earlier in life, but also experienced faster reproductive ageing and died sooner than low-condition males. By contrast, interactions with rival males reduced male lifespan but did not affect male reproductive ageing. High-condition in early life is therefore associated with rapid ageing in T. angusticollis males, even in the absence of damaging male-male interactions. Our results show that abundant resources during the juvenile phase are used to expedite growth and development and enhance early-life reproductive performance at the expense of late-life performance and survival, demonstrating a clear link between male condition and ageing.

    Place, publisher, year, edition, pages
    WILEY, 2017
    Keywords
    Condition dependence, costs of secondary sexual traits, life history, reproductive ageing, senescence, sexual selection
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-320842 (URN)10.1111/evo.13172 (DOI)000396039000012 ()28067402 (PubMedID)
    Funder
    Australian Research CouncilEU, European Research CouncilSwedish Research Council
    Available from: 2017-04-26 Created: 2017-04-26 Last updated: 2018-04-09Bibliographically approved
    4. Early-life parental diet effects on ageing depend on the sex of parents and their offspring
    Open this publication in new window or tab >>Early-life parental diet effects on ageing depend on the sex of parents and their offspring
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Animal Ecology
    Identifiers
    urn:nbn:se:uu:diva-347832 (URN)
    Available from: 2018-04-09 Created: 2018-04-09 Last updated: 2018-04-09
  • 1035.
    Spagopoulou, Foteini
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Hooper, Amy
    Evolution and Ecology Research Centre, University of New South Wales.
    Wylde, Zacharia
    Evolution and Ecology Research Centre, University of New South Wales.
    Bonduriansky, Russel
    Evolution and Ecology Research Centre, University of New South Wales.
    Maklakov, Alexei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Early-life parental diet effects on ageing depend on the sex of parents and their offspringManuscript (preprint) (Other academic)
  • 1036.
    Spagopoulou, Foteini
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Teplitsky, Celine
    Centre D'Ecologie Fonctionelle & Evolutive.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Maklakov, Alexei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    “Silver-spoon” natal conditions increase early-life fitness but accelerate reproductive ageing in a wild birdManuscript (preprint) (Other academic)
    Abstract [en]

    Early-life conditions can have long-lasting effects and organisms that experience a poor start in life are often expected to age at a faster rate. Alternatively, individuals raised in high-quality environments can overinvest in early-reproduction resulting in rapid ageing. Here we use long-term experimental manipulation of early-life conditions in a natural population of collared flycatchers (Ficedula albicollis), to show that females raised in a low-competition environment have higher early-life reproduction but lower late-life reproduction than females raised in high-competition environment. We experimentally created either artificially increased (high-competition) or reduced (low-competition) broods. Reproductive success of high-competition females peaked in late-life, when low-competition females were already in steep reproductive decline and suffered from higher mortality rate. Our results demonstrate that “silver spoon” effects can increase female early-life performance at the cost of faster reproductive ageing and increased late-life mortality. These findings support the evolutionary theory of ageing and show that early-life environmental conditions shape reproductive and demographic ageing in nature.

  • 1037.
    Spagopoulou, Foteini
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Blom, Mozes P. K.
    Naturhistoriska Riksmuseet, Department of Bioinformatic and Genetics, Stockholm, Sweden.
    Digest: Life history evolution in Darwin's dream ponds2018In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 72, no 5, p. 1186-1188Article in journal (Refereed)
    Abstract [en]

    Can variation in sex‐specific parental investment lead to sexual dimorphism in immune response? Keller et al. (2018) measured immune cell parameters, expression of candidate genes and composition of buccal microbiota in mouthbrooding cichlid species from Lake Tanganyika that show either maternal or biparental care. They found that maternal mouthbrooding species have increased sexual dimorphism in immune parameters, while biparental mouthbrooders exhibit an upregulated adaptive immune response, suggesting resource allocation shifts between parental investment and the immune system.

  • 1038.
    Spang, Anja
    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.
    Caceres, Eva F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life.2017In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 357, no 6351, article id eaaf3883Article, review/survey (Refereed)
    Abstract [en]

    About 40 years ago, Archaea were recognized as a major prokaryotic domain of life besides Bacteria. Recently, cultivation-independent sequencing methods have produced a wealth of genomic data for previously unidentified archaeal lineages, several of which appear to represent newly revealed branches in the tree of life. Analyses of some recently obtained genomes have uncovered previously unknown metabolic traits and provided insights into the evolution of archaea and their relationship to eukaryotes. On the basis of our current understanding, much archaeal diversity still defies genomic exploration. Efforts to obtain and study genomes and enrichment cultures of uncultivated microbial lineages will likely further expand our knowledge about archaeal phylogenetic and metabolic diversity and their cell biology and ecological function.

  • 1039.
    Spang, Anja
    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 J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Archaeal evolution: The methanogenic roots of Archaea2017In: Nature Microbiology, E-ISSN 2058-5276, Vol. 2, article id 17109Article in journal (Other academic)
  • 1040.
    Spang, Anja
    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.
    Saw, Jimmy H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Jorgensen, Steffen L.
    Zaremba-Niedzwiedzka, Katarzyna
    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.
    Lind, Anders 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.
    van Eijk, Roel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Schleper, Christa
    Guy, Lionel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Complex archaea that bridge the gap between prokaryotes and eukaryotes2015In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 521, no 7551, p. 173-179Article in journal (Refereed)
    Abstract [en]

    The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.

  • 1041.
    Spang, Anja
    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.
    Stairs, Courtney W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Dombrowski, Nina
    NIOZ, Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, Ab Den Burg, Netherlands;Univ Utrecht, Ab Den Burg, Netherlands;Univ Texas Austin, Inst Marine Sci, Dept Marine Sci, Port Aransas, TX USA.
    Eme, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lombard, Jonathan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Caceres, Eva F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Greening, Chris
    Monash Univ, Sch Biol Sci, Clayton, Vic, Australia.
    Baker, BrettJ
    Univ Texas Austin, Inst Marine Sci, Dept Marine Sci, Port Aransas, TX USA.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism2019In: Nature Microbiology, E-ISSN 2058-5276, Vol. 4, no 7, p. 1138-1148Article in journal (Refereed)
    Abstract [en]

    The origin of eukaryotes represents an unresolved puzzle in evolutionary biology. Current research suggests that eukaryotes evolved from a merger between a host of archaeal descent and an alphaproteobacterial endosymbiont. The discovery of the Asgard archaea, a proposed archaeal superphylum that includes Lokiarchaeota, Thorarchaeota, Odinarchaeota and Heimdallarchaeota suggested to comprise the closest archaeal relatives of eukaryotes, has helped to elucidate the identity of the putative archaeal host. Whereas Lokiarchaeota are assumed to employ a hydrogen-dependent metabolism, little is known about the metabolic potential of other members of the Asgard superphylum. We infer the central metabolic pathways of Asgard archaea using comparative genomics and phylogenetics to be able to refine current models for the origin of eukaryotes. Our analyses indicate that Thorarchaeota and Lokiarchaeota encode proteins necessary for carbon fixation via the Wood-Ljungdahl pathway and for obtaining reducing equivalents from organic substrates. By contrast, Heimdallarchaeum LC2 and LC3 genomes encode enzymes potentially enabling the oxidation of organic substrates using nitrate or oxygen as electron acceptors. The gene repertoire of Heimdallarchaeum AB125 and Odinarchaeum indicates that these organisms can ferment organic substrates and conserve energy by coupling ferredoxin reoxidation to respiratory proton reduction. Altogether, our genome analyses suggest that Asgard representatives are primarily organoheterotrophs with variable capacity for hydrogen consumption and production. On this basis, we propose the 'reverse flow model', an updated symbiogenetic model for the origin of eukaryotes that involves electron or hydrogen flow from an organoheterotrophic archaeal host to a bacterial symbiont.

  • 1042.
    Stam, Remco
    et al.
    Tech Univ Munich, Sch Life Sci Weihenstephan, Chair Phytopathol, Munich, Germany.
    Münsterkötter, Martin
    Univ Sopron, Res Ctr Forestry & Wood Ind, Funct Genom & Bioinformat, Sopron, Hungary;Helmholtz Ctr Munich, Inst Bioinformat & Syst Biol, Neuherberg, Germany.
    Pophaly, Saurabh Dilip
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Tech Univ Munich, Sch Life Sci Weihenstephan, Sect Populat Genet, Munich, Germany;Ludwig Maximilians Univ Munchen, Fac Biol 2, Div Evolutionary Biol, Munich, Germany.
    Fokkens, Like
    Univ Amsterdam, Swammerdam Inst Life Sci, Mol Plant Pathol, Amsterdam, Netherlands.
    Sghyer, Hind
    Tech Univ Munich, Sch Life Sci Weihenstephan, Chair Phytopathol, Munich, Germany.
    Güldener, Ulrich
    Tech Univ Munich, Sch Life Sci Weihenstephan, Dept Bioinformat, Munich, Germany.
    Hückelhoven, Ralph
    Tech Univ Munich, Sch Life Sci Weihenstephan, Chair Phytopathol, Munich, Germany.
    Hess, Michael
    Tech Univ Munich, Sch Life Sci Weihenstephan, Chair Phytopathol, Munich, Germany.
    A New Reference Genome Shows the One-Speed Genome Structure of the Barley Pathogen Ramularia collo-cygni2018In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 10, no 12, p. 3243-3249Article in journal (Refereed)
    Abstract [en]

    Ramularia leaf spot has recently emerged as a major threat to barley production world-wide, causing 25% yield loss in many barley growing regions. Here, we provide a new reference genome of the causal agent, the Dothideomycete Ramularia collo-cygni. The assembly of 32 Mb consists of 78 scaffolds. We used RNA-seq to identify 11,622 genes of which 1,303 and 282 are coding for predicted secreted proteins and putative effectors respectively. The pathogen separated from its nearest sequenced relative, Zymoseptoria tritici similar to 27Ma. We calculated the divergence of the two species on protein level and see remarkably high synonymous and nonsynonymous divergence. Unlike in many other plant pathogens, the comparisons of transposable elements and gene distributions, show a very homogeneous genome for R. collo-cygni. We see no evidence for higher selective pressure on putative effectors or other secreted proteins and repetitive sequences are spread evenly across the scaffolds. These findings could be associated to the predominantly endophytic life-style of the pathogen. We hypothesize that R. collo-cygni only recently became pathogenic and that therefore its genome does not yet show the typical pathogen characteristics. Because of its high scaffold length and improved CDS annotations, our new reference sequence provides a valuable resource for the community for future comparative genomics and population genetics studies.

  • 1043.
    Steige, Kim A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Reimegård, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Koenig, Daniel
    Max Planck Inst Dev Biol, Dept Mol Biol, Tubingen, Germany..
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Slotte, Tanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Stockholm Univ, Sci Life Lab, Dept Ecol Environm & Plant Sci, S-10691 Stockholm, Sweden..
    Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella2015In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 32, no 10, p. 2501-2514Article in journal (Refereed)
    Abstract [en]

    The selfing syndrome constitutes a suite of floral and reproductive trait changes that have evolved repeatedly across many evolutionary lineages in response to the shift to selfing. Convergent evolution of the selfing syndrome suggests that these changes are adaptive, yet our understanding of the detailed molecular genetic basis of the selfing syndrome remains limited. Here, we investigate the role of cis-regulatory changes during the recent evolution of the selfing syndrome in Capsella rubella, which split from the outcrosser Capsella grandiflora less than 200 ka. We assess allele-specific expression (ASE) in leaves and flower buds at a total of 18,452 genes in three interspecific F1 C. grandiflora x C. rubella hybrids. Using a hierarchical Bayesian approach that accounts for technical variation using genomic reads, we find evidence for extensive cis-regulatory changes. On average, 44% of the assayed genes show evidence of ASE; however, only 6% show strong allelic expression biases. Flower buds, but not leaves, show an enrichment of cis-regulatory changes in genomic regions responsible for floral and reproductive trait divergence between C. rubella and C. grandiflora. We further detected an excess of heterozygous transposable element (TE) insertions near genes with ASE, and TE insertions targeted by uniquely mapping 24-nt small RNAs were associated with reduced expression of nearby genes. Our results suggest that cis-regulatory changes have been important during the recent adaptive floral evolution in Capsella and that differences in TE dynamics between selfing and outcrossing species could be important for rapid regulatory divergence in association with mating system shifts.

  • 1044.
    Stocks, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Neutral and Adaptive Processes Shaping Genetic Variation in Spruce Species2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Population genetic analyses can provide information about both neutral and selective evolutionary processes shaping genetic variation. In this thesis, extensive population genetic methods were used to make inferences about genetic drift and selection in spruce species. In paper I we studied four species from the Qinghai-Tibetan Plateau (QTP): Picea likiangensis, P. purpurea, P. wilsonii and P. schrenkiana. Big differences in estimates of genetic diversity and Ne were observed in the more restricted species, P. schrenkiana, and the other more widely distributed species. Furthermore, P. purpurea appears to be a hybrid between P. likiangensis and P. wilsonii. In paper II we used Approximate Bayesian Computation (ABC) to find that the data support a drastic reduction of Ne in Taiwan spruce around 300-500 kya, in line with evidence from the pollen records. The split from P. wilsonii was dated to between 4-8 mya, around the time that Taiwan was formed. These analyses relied on a small sample size, and so in Paper III we investigated the impact of small datasets on the power to distinguish between models in ABC. We found that when genetic diversity is low there is little power to distinguish between simple coalescent models and this can determine the number of samples and loci required.

    In paper IV we studied the relative importance of genetic drift and selection in four spruce species with differing Ne: P. abies, P. glauca, P. jezoensis and P. breweriana. P. breweriana, which has a low Ne, exhibits a low fraction of adaptive substitutions, while P. abies has high Ne and a high fraction of adaptive substitutions. The other two spruce, however, do not support this suggesting other factors a more important. In paper V we find that several SNPs correlate with both a key adaptive trait (budset) and latitude. The expression of one in particular (PoFTL2) correlates with budset and was previously indentified in P. abies. These studies have helped characterise the importance of different population genetic processes in shaping genetic variation in spruce species and has laid some solid groundwork for future studies of spruce.

    List of papers
    1. Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci
    Open this publication in new window or tab >>Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci
    Show others...
    2010 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 27, no 5, p. 1001-1014Article in journal (Refereed) Published
    Abstract [en]

    Nucleotide variation at 12 to 16 nuclear loci was studied in three spruce species from the Qinghai-Tibetan Plateau (QTP), Picea likiangensis, P. wilsonii and P. purpurea, and one species from the Tian Shan mountain range, P. schrenkiana. Silent nucleotide diversity was limited in P. schrenkiana and high in the three species from the QTP, with values higher than in boreal spruce species, despite their much more restricted distributions compared to that of the boreal species. In contrast to European boreal species that have experienced severe bottlenecks in the past, coalescent-based analysis suggests that DNA polymorphism in the species from the QTP and adjacent areas is compatible with the standard neutral model (P. likiangensis, P. wilsonii, P. schrenkiana) or with population growth (P. purpurea). In order to test if P. purpurea is a diploid hybrid of P. likiangensis and P. wilsonii, we used a combination of approaches, including model based inference of population structure, Isolation-with-Migration models and recent theoretical results on the effect of introgression on the geographic distribution of diversity. In contrast to the three other species, each of which was predominantly assigned to a single cluster in the Structure analysis, P. purpurea individuals were scattered over the three main clusters and not, as we had expected, confined to the P. likiangensis and P. wilsonii clusters. Furthermore the contribution of P. schrenkiana was by far the largest one. In agreement with this, the divergence between P. purpurea and P. schrenkiana was lower than the divergence of either P. likiangensis or P. wilsonii from P. schrenkiana. These results, together with previous ones showing that P. purpurea and P. wilsonii share the same haplotypes at both chloroplast and mitochondrial markers, suggest that P. purpurea has a complex origin, possibly involving additional species.

    Keywords
    Picea, Qinghai Tibetan Plateau, effective population size, divergence time, introgression, speciation
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-121399 (URN)10.1093/molbev/msp301 (DOI)000276994800004 ()20031927 (PubMedID)
    Available from: 2010-03-23 Created: 2010-03-23 Last updated: 2017-12-12Bibliographically approved
    2. Origin and demographic history of the endemic Taiwan spruce (Picea morrisonicola)
    Open this publication in new window or tab >>Origin and demographic history of the endemic Taiwan spruce (Picea morrisonicola)
    2013 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 3, no 10, p. 3320-3333Article in journal (Refereed) Published
    Abstract [en]

    Taiwan spruce (Picea morrisonicola) is a vulnerable conifer species endemic to the island of Taiwan. A warming climate and competition from subtropical tree species has limited the range of Taiwan spruce to the higher altitudes of the island. Using seeds sampled from an area in the central mountain range of Taiwan, 15 nuclear loci were sequenced in order to measure genetic variation and to assess the long-term genetic stability of the species. Genetic diversity is low and comparable to other spruce species with limited ranges such as Picea breweriana, Picea chihuahuana, and Picea schrenkiana. Importantly, analysis using approximate Bayesian computation (ABC) provides evidence for a drastic decline in the effective population size approximately 0.3–0.5 million years ago (mya). We used simulations to show that this is unlikely to be a false-positive result due to the limited sample used here. To investigate the phylogenetic origin of Taiwan spruce, additional sequencing was performed in the Chinese spruce Picea wilsonii and combined with previously published data for three other mainland China species, Picea purpurea, Picea likiangensis, and P. schrenkiana. Analysis of population structure revealed that P. morrisonicola clusters most closely with P. wilsonii, and coalescent analyses using the program MIMAR dated the split to 4–8 mya, coincidental to the formation of Taiwan. Considering the population decrease that occurred after the split, however, led to a much more recent origin.

    National Category
    Natural Sciences Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Functional Genomics
    Identifiers
    urn:nbn:se:uu:diva-198100 (URN)10.1002/ece3.698 (DOI)000324932600011 ()
    Note

    De två (2) första författarna delar förstaförfattarskapet.

    Available from: 2013-04-09 Created: 2013-04-09 Last updated: 2017-12-06Bibliographically approved
    3. Amount of information needed for model choice in Approximate Bayesian Computation
    Open this publication in new window or tab >>Amount of information needed for model choice in Approximate Bayesian Computation
    2014 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 6, p. e99581-Article in journal (Other academic) Published
    Abstract [en]

    Approximate Bayesian Computation (ABC) has become a popular technique in evolutionary genetics for elucidating population structure and history due to its flexibility. The statistical inference framework has benefited from significant progress in recent years. In population genetics, however, its outcome depends heavily on the amount of information in the dataset, whether that be the level of genetic variation or the number of samples and loci. Here we look at the power to reject a simple constant population size coalescent model in favor of a bottleneck model in datasets of varying quality. Not only is this power dependent on the number of samples and loci, but it also depends strongly on the level of nucleotide diversity in the observed dataset. Whilst overall model choice in an ABC setting is fairly powerful and quite conservative with regard to false positives, detecting weaker bottlenecks is problematic in smaller or less genetically diverse datasets and limits the inferences possible in non-model organism where the amount of information regarding the two models is often limited. Our results show it is important to consider these limitations when performing an ABC analysis and that studies should perform simulations based on the size and nature of the dataset in order to fully assess the power of the study.

    Keywords
    approximate bayesian computation, population genetics, bottlenecks, summary statistics
    National Category
    Evolutionary Biology Probability Theory and Statistics
    Identifiers
    urn:nbn:se:uu:diva-207706 (URN)10.1371/journal.pone.0099581 (DOI)000338633900009 ()24959900 (PubMedID)
    Available from: 2013-09-18 Created: 2013-09-18 Last updated: 2017-12-06Bibliographically approved
    4. Molecular adaptation in spruce species
    Open this publication in new window or tab >>Molecular adaptation in spruce species
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-207710 (URN)
    Available from: 2013-09-18 Created: 2013-09-18 Last updated: 2014-01-23
    5. Clinal variation in allele frequency and gene expression at photoperiodic and circadian genes in Siberian spruce: an example of parallel evolution?
    Open this publication in new window or tab >>Clinal variation in allele frequency and gene expression at photoperiodic and circadian genes in Siberian spruce: an example of parallel evolution?
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology Genetics
    Research subject
    Biology with specialization in Evolutionary Functional Genomics; Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-177529 (URN)
    Available from: 2012-07-13 Created: 2012-07-13 Last updated: 2014-01-23
  • 1045.
    Stocks, Michael
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Chen, Jun
    Institut fur Populationsgenetik, Wien.
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Bousquet, Jean
    Universite Laval, Quebec.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Molecular adaptation in spruce speciesManuscript (preprint) (Other academic)
  • 1046.
    Stocks, Michael
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Siol, Mathieu
    Institut National de la Recherche Agronomique (INRA), UMR Agroecologie, Dijon.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    De Mita, Stéphane
    Institut National de la Recherche Agronomique (INRA), UMR Interactions Arbres-Microorganismes, Nancy.
    Amount of information needed for model choice in Approximate Bayesian Computation2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 6, p. e99581-Article in journal (Other academic)
    Abstract [en]

    Approximate Bayesian Computation (ABC) has become a popular technique in evolutionary genetics for elucidating population structure and history due to its flexibility. The statistical inference framework has benefited from significant progress in recent years. In population genetics, however, its outcome depends heavily on the amount of information in the dataset, whether that be the level of genetic variation or the number of samples and loci. Here we look at the power to reject a simple constant population size coalescent model in favor of a bottleneck model in datasets of varying quality. Not only is this power dependent on the number of samples and loci, but it also depends strongly on the level of nucleotide diversity in the observed dataset. Whilst overall model choice in an ABC setting is fairly powerful and quite conservative with regard to false positives, detecting weaker bottlenecks is problematic in smaller or less genetically diverse datasets and limits the inferences possible in non-model organism where the amount of information regarding the two models is often limited. Our results show it is important to consider these limitations when performing an ABC analysis and that studies should perform simulations based on the size and nature of the dataset in order to fully assess the power of the study.

  • 1047.
    Strand, Tanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    European Black Grouse: MHC Genetic Diversity and Population Structure2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Black grouse Tetrao tetrix is a bird species composed of large, continuous as well as severely reduced and fragmented populations, making it an optimal species to investigate how genetic diversity is affected by habitat fragmentation. I have focused on genetic diversity in the Major Histocompatibility Complex (MHC) to measure the ability of the black grouse to respond to environmental changes.

    I partly characterized MHC class II in black grouse and found striking similarities with chicken MHC class II. I demonstrated that black grouse possess a similar compact MHC as chicken with few MHC class II B (BLB) and Y (YLB) loci. I did not find evidence of balancing selection in YLB so I concentrated further studies on BLB.

    I developed a PCR-based screening method for amplifying and separating expressed BLB alleles in European black grouse populations. Small fragmented populations had lost neutral genetic diversity (based on microsatellites and SNPs) compared to samples from the historical distribution and contemporary large populations. There was also a trend, albeit less pronounced, for reduced MHC diversity in these populations. Neutral markers in small isolated populations were affected by increased levels of genetic drift and were therefore genetically differentiated compared to other populations. MHC markers on the other hand, were not subjected to genetic drift to the same extent probably due a long historic process of balancing selection.

    Inferences of heterozygosity and evolutionary patterns as well as detailed correlations to reproductive success and diseases cannot be performed until MHC can be amplified in a locus-specific manner. Therefore, I developed a single locus sequence-based typing method for independently amplifying MHC class II B loci (BLB1 and BLB2). I found that BLB1 and BLB2 were duplicated in a common ancestor to chickens and black grouse and that these loci are subjected to homogenizing concerted evolution due to inter-genetic exchange between loci after species divergence.  I could also verify that both BLB1 and BLB2 were transcribed in black grouse and under balancing selection.

    This collection of work has significance for future conservation of black grouse as well as research and management of zoonotic diseases.

    List of papers
    1. The MHC class II of the Black grouse (Tetrao tetrix) consists of low numbers of B and Y genes with variable diversity and expression
    Open this publication in new window or tab >>The MHC class II of the Black grouse (Tetrao tetrix) consists of low numbers of B and Y genes with variable diversity and expression
    Show others...
    2007 (English)In: Immunogenetics, ISSN 0093-7711, E-ISSN 1432-1211, Vol. 59, no 9, p. 725-734Article in journal (Refereed) Published
    Abstract [en]

    We found that the Black grouse (Tetrao tetrix) possess low numbers of Mhc class II B (BLB) and Y (YLB) genes with variable diversity and expression. We have therefore shown, for the first time, that another bird species (in this case, a wild lek-breeding galliform) shares several features of the simple Mhc of the domestic chicken (Gallus gallus). The Black grouse BLB genes showed the same level of polymorphism that has been reported in chicken, and we also found indications of balancing selection in the peptide-binding regions. The YLB genes were less variable than the BLB genes, also in accordance with earlier studies in chicken, although their functional significance still remains obscure. We hypothesize that the YLB genes could have been under purifying selection, just as the mammal Mhc-E gene cluster.

    Keywords
    Mhc class II, YLB, Rfp-Y, BLB, Avian Mhc, Purifying selection
    National Category
    Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-14669 (URN)10.1007/s00251-007-0234-6 (DOI)000249503200004 ()17653538 (PubMedID)
    Available from: 2008-01-31 Created: 2008-01-31 Last updated: 2017-12-11Bibliographically approved
    2. Genotyping of black grouse MHC class II B using Reference Strand-Mediated Conformational Analysis (RSCA)
    Open this publication in new window or tab >>Genotyping of black grouse MHC class II B using Reference Strand-Mediated Conformational Analysis (RSCA)
    2011 (English)In: BMC Research Notes, ISSN 1756-0500, E-ISSN 1756-0500, Vol. 4, no 183Article in journal (Refereed) Published
    Abstract [en]

    Background

    The Major Histocompatibility Complex (MHC) is a cluster of genes involved in the vertebrate immune system and includes loci with an extraordinary number of alleles. Due to the complex evolution of MHC genes, alleles from different loci within the same MHC class can be very similar and therefore difficult to assign to separate loci. Consequently, single locus amplification of MHC genes is hard to carry out in species with recently duplicated genes in the same MHC class, and multiple MHC loci have to be genotyped simultaneously. Since amplified alleles have the same length, accurate genotyping is difficult. Reference Strand-Mediated Conformational Analysis (RSCA), which is increasingly used in studies of natural populations with multiple MHC genes, is a genotyping method capable to provide high resolution and accuracy in such cases.

    Findings

    We adapted the RSCA method to genotype multiple MHC class II B (BLB) genes in black grouse (Tetrao tetrix), a non-model galliform bird species, using a 96-Capillary Array Electrophoresis, the MegaBACE™ 1000 DNA Analysing System (GE Healthcare). In this study we used fluorescently labelled reference strands from both black grouse and hazel grouse and observed good agreement between RSCA and cloning/sequencing since 71 alleles were observed by cloning/sequencing and 76 alleles by RSCA among the 24 individuals included in the comparison. At the individual level however, there was a trend towards more alleles scored with RSCA (1-6 per individual) than cloning/sequencing (1-4 per individual). In 63% of the pair-wise comparison, the identical allele was scored in RSCA as in cloning/sequencing. Nine out of 24 individuals had the same number of alleles in RSCA as in cloning/sequencing. Our RSCA protocol allows a faster RSCA genotyping than presented in many other RSCA studies.

    Conclusions

    In this study, we have developed the RSCA typing method further to work on a 96-Capillary Array Electrophoresis (MegaBACE™ 1000). Our RSCA protocol can be applied to fast and reliable screening of MHC class II B diversity of black grouse populations. This will facilitate future large-scale population studies of black grouse and other galliformes species with multiple inseparable MHC loci.

    National Category
    Genetics
    Research subject
    Population Biology
    Identifiers
    urn:nbn:se:uu:diva-159185 (URN)10.1186/1756-0500-4-183 (DOI)
    Available from: 2011-10-13 Created: 2011-09-23 Last updated: 2017-12-08Bibliographically approved
    3. Can balancing selection on MHC loci counteract genetic drift in small fragmented populations of black grouse?
    Open this publication in new window or tab >>Can balancing selection on MHC loci counteract genetic drift in small fragmented populations of black grouse?
    Show others...
    2012 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 2, no 2, p. 341-353Article in journal (Refereed) Published
    Abstract [en]

    The ability of natural populations to adapt to new environmental conditions is crucial for their survival and partly determined by the standing genetic variation in each population. Populations with higher genetic diversity are more likely to contain individuals that are better adapted to new circumstances than populations with lower genetic diversity. Here we use both neutral and MHC markers to test whether small and highly fragmented populations hold lower genetic diversity than large ones. We use black grouse as it is distributed across Europe and found in populations with varying degrees of isolation and size. We sampled eleven different populations; five continuous, three isolated and three small and isolated. We tested patterns of genetic variation in these populations using three different types of genetic markers: nine microsatellites and 21 SNPs (Single Nucleotide Polymorphisms) which both were found to be neutral, and two functional MHC (Major Histocompatibility Complex) genes that are presumably under selection. The small isolated populations displayed significantly lower neutral genetic diversity compared to continuous populations. A similar trend, but not as pronounced, was found for genotypes at MHC class II loci. Populations were less divergent at MHC genes compared to neutral markers. Measures of genetic diversity and population genetic structure were positively correlated among microsatellites and SNPs, but none of them were correlated to MHC when comparing all populations. Our results suggest that balancing selection at MHC loci does not counteract the power of genetic drift when populations get small and fragmented. 

    Keywords
    Fragmentation; genetic drift; MHC; population isolation; SNP
    National Category
    Ecology Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-160034 (URN)10.1002/ece3.86 (DOI)000312442500006 ()22423328 (PubMedID)
    Funder
    Swedish Research Council
    Available from: 2011-10-13 Created: 2011-10-13 Last updated: 2017-12-08Bibliographically approved
    4. Historic and current populations of black grouse in central Europe – evidence for rapid loss of genetic diversity
    Open this publication in new window or tab >>Historic and current populations of black grouse in central Europe – evidence for rapid loss of genetic diversity
    Show others...
    2011 (English)Article in journal (Other academic) Submitted
    Abstract [en]

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

    National Category
    Ecology Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-160037 (URN)
    Available from: 2011-10-13 Created: 2011-10-13 Last updated: 2015-06-24Bibliographically approved
    5. Evolutionary history of black grouse BLB1 and BLB2 revealed through single locus sequence-based typing
    Open this publication in new window or tab >>Evolutionary history of black grouse BLB1 and BLB2 revealed through single locus sequence-based typing
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-160040 (URN)
    Available from: 2011-10-13 Created: 2011-10-13 Last updated: 2011-11-10
  • 1048.
    Strand, Tanja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Segelbacher, Gernot
    Dept Wildlife Ecology and Management, University Freiburg.
    Quintela, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Dept of Animal Biology, Plant Biology and Ecology, Faculty of Science, University of A Coruña.
    Xiao, Lyngyun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Axelsson, Tomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Can balancing selection on MHC loci counteract genetic drift in small fragmented populations of black grouse?2012In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 2, no 2, p. 341-353Article in journal (Refereed)
    Abstract [en]

    The ability of natural populations to adapt to new environmental conditions is crucial for their survival and partly determined by the standing genetic variation in each population. Populations with higher genetic diversity are more likely to contain individuals that are better adapted to new circumstances than populations with lower genetic diversity. Here we use both neutral and MHC markers to test whether small and highly fragmented populations hold lower genetic diversity than large ones. We use black grouse as it is distributed across Europe and found in populations with varying degrees of isolation and size. We sampled eleven different populations; five continuous, three isolated and three small and isolated. We tested patterns of genetic variation in these populations using three different types of genetic markers: nine microsatellites and 21 SNPs (Single Nucleotide Polymorphisms) which both were found to be neutral, and two functional MHC (Major Histocompatibility Complex) genes that are presumably under selection. The small isolated populations displayed significantly lower neutral genetic diversity compared to continuous populations. A similar trend, but not as pronounced, was found for genotypes at MHC class II loci. Populations were less divergent at MHC genes compared to neutral markers. Measures of genetic diversity and population genetic structure were positively correlated among microsatellites and SNPs, but none of them were correlated to MHC when comparing all populations. Our results suggest that balancing selection at MHC loci does not counteract the power of genetic drift when populations get small and fragmented. 

  • 1049.
    Strand, Tanja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Wang, Biao
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Meyer-Lucht, Yvonne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Evolutionary history of black grouse BLB1 and BLB2 revealed through single locus sequence-based typingManuscript (preprint) (Other academic)
  • 1050.
    Strand, Tanja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Westerdahl, Helena
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Alatalo, Rauno V.
    Siitari, Heli
    The MHC class II of the Black grouse (Tetrao tetrix) consists of low numbers of B and Y genes with variable diversity and expression2007In: Immunogenetics, ISSN 0093-7711, E-ISSN 1432-1211, Vol. 59, no 9, p. 725-734Article in journal (Refereed)
    Abstract [en]

    We found that the Black grouse (Tetrao tetrix) possess low numbers of Mhc class II B (BLB) and Y (YLB) genes with variable diversity and expression. We have therefore shown, for the first time, that another bird species (in this case, a wild lek-breeding galliform) shares several features of the simple Mhc of the domestic chicken (Gallus gallus). The Black grouse BLB genes showed the same level of polymorphism that has been reported in chicken, and we also found indications of balancing selection in the peptide-binding regions. The YLB genes were less variable than the BLB genes, also in accordance with earlier studies in chicken, although their functional significance still remains obscure. We hypothesize that the YLB genes could have been under purifying selection, just as the mammal Mhc-E gene cluster.

18192021222324 1001 - 1050 of 1248
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