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  • 1.
    Bloch, Natasha, I
    et al.
    UCL, Dept Genet Evolut & Environm, London, England.
    Corral-Lopez, Alberto
    Stockholm Univ, Dept Zool Ethol, Stockholm, Sweden.
    Buechel, Severine D.
    Stockholm Univ, Dept Zool Ethol, Stockholm, Sweden.
    Kotrschal, Alexander
    Stockholm Univ, Dept Zool Ethol, Stockholm, Sweden.
    Kolm, Niclas
    Stockholm Univ, Dept Zool Ethol, Stockholm, Sweden.
    Mank, Judith E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. UCL, Dept Genet Evolut & Environm, London, England.
    Early neurogenomic response associated with variation in guppy female mate preference2018Inngår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 2, nr 11, s. 1772-1781Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Understanding the evolution of mate choice requires dissecting the mechanisms of female preference, particularly how these differ among social contexts and preference phenotypes. Here, we studied the female neurogenomic response after only 10 min of mate exposure in both a sensory component (optic tectum) and a decision-making component (telencephalon) of the brain. By comparing the transcriptional response between females with and without preferences for colourful males, we identified unique neurogenomic elements associated with the female preference phenotype that are not present in females without preference. A network analysis revealed different properties for this response at the sensory-processing and the decision-making levels, and we show that this response is highly centralized in the telencephalon. Furthermore, we identified an additional set of genes that vary in expression across social contexts, beyond mate evaluation. We show that transcription factors among these loci are predicted to regulate the transcriptional response of the genes we found to be associated with female preference.

  • 2.
    Chapron, Guillaume
    et al.
    Swedish University of Agricultural Sciences, Department of Ecology, Grimsö Wildlife Research Station, Riddarhyttan, Sweden.
    Epstein, Yaffa
    Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Juridiska fakulteten, Juridiska institutionen.
    Trouwborst, Arie
    Tilburg University, Department of European and International Law, Tilburg, The Netherlands.
    Vicente López-Bao, José
    Oviedo University, Research Unit of Biodiversity (UO/CSIC/PA), Mieres, Spain.
    Bolster Legal Boundaries to Stay within Planetary Boundaries2017Inngår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 1, nr 3, artikkel-id UNSP 0086Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The mounting threats posed to the global environment by harmful human activities cannot be averted without effective legislation controlling those activities. However, the environmental laws designed for this purpose are themselves under global attack. Because it is binding and enforceable, legislation is a unique and essential instrument in the overall effort to keep humanity’s impacts on the planet from transgressing critical thresholds. For instance, biodiversity laws do so by designating and protecting natural areas and controlling the exploitation of wildlife populations. Yet, due to short-term economic and other interests, such laws face constant pressures aimed at weakening their regulating impact on human activities. 

    This new study reveals and illustrates the staggering number and diversity of tactics used to weaken biodiversity legislation across the globe. This ‘taxonomy of tactics’ encompasses dozens of categories, ranging from the creative re-definition of terms to the ‘fast-tracking’ of environmentally harmful projects, and from limiting concerned citizens’ access to court, to the silent or even express refusal of appointed authorities to enforce biodiversity laws.

    Whereas the predicament of the planet’s wild fauna and flora would have been even worse without the legal protection they have received so far, the onslaught against biodiversity laws has prevented these from fully performing their assigned function. The global acceleration of wildlife population declines bears witness to this. To stem the tide, strategic approaches are needed to anticipate and counter attacks on biodiversity legislation; to make the most of existing laws, including in court if need be; and to develop new or improved laws where necessary.

  • 3. Gei, Maga
    et al.
    Rozendaal, Danaë M. A.
    Poorter, Lourens
    Bongers, Frans
    Sprent, Janet I.
    Garner, Mira D.
    Aide, T. Mitchell
    Andrade, José Luis
    Balvanera, Patricia
    Becknell, Justin M.
    Brancalion, Pedro H. S.
    Cabral, George A. L.
    César, Ricardo Gomes
    Chazdon, Robin L.
    Cole, Rebecca J.
    Colletta, Gabriel Dalla
    de Jong, Ben
    Denslow, Julie S.
    Dent, Daisy H.
    DeWalt, Saara J.
    Dupuy, Juan Manuel
    Durán, Sandra M.
    do Espírito Santo, Mário Marcos
    Fernandes, G. Wilson
    Nunes, Yule Roberta Ferreira
    Finegan, Bryan
    Moser, Vanessa Granda
    Hall, Jefferson S.
    Hernández-Stefanoni, José Luis
    Junqueira, André B.
    Kennard, Deborah
    Lebrija-Trejos, Edwin
    Letcher, Susan G.
    Lohbeck, Madelon
    Marín-Spiotta, Erika
    Martínez-Ramos, Miguel
    Meave, Jorge A.
    Menge, Duncan N. L.
    Mora, Francisco
    Muñoz, Rodrigo
    Muscarella, Robert
    Ochoa-Gaona, Susana
    Orihuela-Belmonte, Edith
    Ostertag, Rebecca
    Peña-Claros, Marielos
    Pérez-García, Eduardo A.
    Piotto, Daniel
    Reich, Peter B.
    Reyes-García, Casandra
    Rodríguez-Velázquez, Jorge
    Romero-Pérez, I. Eunice
    Sanaphre-Villanueva, Lucía
    Sanchez-Azofeifa, Arturo
    Schwartz, Naomi B.
    de Almeida, Arlete Silva
    Almeida-Cortez, Jarcilene S.
    Silver, Whendee
    de Souza Moreno, Vanessa
    Sullivan, Benjamin W.
    Swenson, Nathan G.
    Uriarte, Maria
    van Breugel, Michiel
    van der Wal, Hans
    Veloso, Maria das Dores Magalhães
    Vester, Hans F. M.
    Vieira, Ima Célia Guimarães
    Zimmerman, Jess K.
    Powers, Jennifer S.
    Legume abundance along successional and rainfall gradients in Neotropical forests2018Inngår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 2, nr 7Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The nutrient demands of regrowing tropical forests are partly satisfied by nitrogen-fixing legume trees, but our understanding of the abundance of those species is biased towards wet tropical regions. Here we show how the abundance of Leguminosae is affected by both recovery from disturbance and large-scale rainfall gradients through a synthesis of forest inventory plots from a network of 42 Neotropical forest chronosequences. During the first three decades of natural forest regeneration, legume basal area is twice as high in dry compared with wet secondary forests. The tremendous ecological success of legumes in recently disturbed, water-limited forests is likely to be related to both their reduced leaflet size and ability to fix N2, which together enhance legume drought tolerance and water-use efficiency. Earth system models should incorporate these large-scale successional and climatic patterns of legume dominance to provide more accurate estimates of the maximum potential for natural nitrogen fixation across tropical forests.

  • 4.
    Irisarri, Iker
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. Univ Konstanz, Dept Biol, Lehrstuhl Zool & Evolut Biol, Univ Str 10, D-78464 Constance, Germany.
    Baurain, Denis
    Univ Liege, InBioS Eukaryot Phylogen, Dept Life Sci & PhytoSYST, B-4000 Liege, Belgium.
    Brinkmann, Henner
    Leibniz Inst DSMZ German Collect Microorgan & Cell, D-38124 Braunschweig, Germany.
    Delsuc, Frédéric
    Univ Montpellier, Inst Sci Evolut, UMR 5554, CNRS,IRD,EPHE, F-34095 Montpellier, France.
    Sire, Jean-Yves
    Sorbonne Univ, Inst Biol Paris Seine, UMR7138, F-75005 Paris, France.
    Kupfer, Alexander
    Stuttgart State Museum Nat Hist, Dept Zool, D-70191 Stuttgart, Germany.
    Petersen, Jörn
    Leibniz Inst DSMZ German Collect Microorgan & Cell, D-38124 Braunschweig, Germany.
    Jarek, Michael
    Helmholtz Ctr Infect Res, Dept Genome Analyt, D-38124 Braunschweig, Germany.
    Meyer, Axel
    Univ Konstanz, Dept Biol, Lehrstuhl Zool & Evolut Biol, Univ Str 10, D-78464 Constance, Germany.
    Vences, Miguel
    Braunschweig Univ Technol, Zool Inst, D-38106 Braunschweig, Germany.
    Philippe, Hervé
    Ctr Biodivers Theory & Modelling, UMR CNRS 5321, Stn Theoret & Expt Ecol, F-09200 Moulis, France; Univ Montreal, Dept Biochim, Montreal, PQ H3C 3J7, Canada.
    Phylotranscriptomic consolidation of the jawed vertebrate timetree2017Inngår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 1, nr 9, s. 1370-1378Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on ‘standards’ for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as a model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes, and some relationships remain controversial. We tested a new bioinformatic pipeline to assemble large and accu- rate phylogenomic datasets from RNA sequencing and found this phylotranscriptomic approach to be successful and highly cost- effective. Increased sequencing effort up to about 10 Gbp allows more genes to be recovered, but shallower sequencing (1.5 Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large, curated, nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.

  • 5.
    Jerlström-Hultqvist, Joel
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
    Warsi, Omar
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Söderholm, Annika
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Strukturbiologi.
    Knopp, Michael
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Eckhard, Ulrich
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Vorontsov, Egor
    Proteomics Core Facility at Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden.
    Selmer, Maria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Andersson, Dan I
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function2018Inngår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 2, nr 8, s. 1321-1330Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    One key concept in the evolution of new functions is the ability of enzymes to perform promiscuous side-reactions that serve as a source of novelty that may become beneficial under certain conditions. Here, we identify a mechanism where a bacteriophage-encoded enzyme introduces novelty by inducing expression of a promiscuous bacterial enzyme. By screening for bacteriophage DNA that rescued an auxotrophic Escherichia coli mutant carrying a deletion of the ilvA gene, we show that bacteriophage-encoded S-adenosylmethionine (SAM) hydrolases reduce SAM levels. Through this perturbation of bacterial metabolism, expression of the promiscuous bacterial enzyme MetB is increased, which in turn complements the absence of IlvA. These results demonstrate how foreign DNA can increase the metabolic capacity of bacteria, not only by transfer of bona fide new genes, but also by bringing cryptic bacterial functions to light via perturbations of cellular physiology.

  • 6.
    Kardos, Marty
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Åkesson, Mikael
    Swedish Univ Agr Sci, Grimso Wildlife Res Stn, Dept Ecol, SE-73091 Riddarhyttan, Sweden..
    Fountain, Toby
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Flagstad, Oystein
    Norwegian Inst Nat Res, POB 5685, NO-7485 Trondheim, Norway..
    Liberg, Olof
    Swedish Univ Agr Sci, Grimso Wildlife Res Stn, Dept Ecol, SE-73091 Riddarhyttan, Sweden..
    Olason, Pall
    Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Sand, Hakan
    Swedish Univ Agr Sci, Grimso Wildlife Res Stn, Dept Ecol, SE-73091 Riddarhyttan, Sweden..
    Wabakken, Petter
    Inland Norway Univ Appl Sci, Fac Appl Ecol & Agr Sci, Campus Evenstad, N-2480 Elverum, Norway..
    Wikenros, Camilla
    Swedish Univ Agr Sci, Grimso Wildlife Res Stn, Dept Ecol, SE-73091 Riddarhyttan, Sweden..
    Ellegren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Genomic consequences of intensive inbreeding in an isolated wolf population2018Inngår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 2, nr 1, s. 124-131Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Inbreeding (mating between relatives) is a major concern for conservation as it decreases individual fitness and can increase the risk of population extinction. We used whole-genome resequencing of 97 grey wolves (Canis lupus) from the highly inbred Scandinavian wolf population to identify 'identical-by-descent' (IBD) chromosome segments as runs of homozygosity (ROH). This gave the high resolution required to precisely measure realized inbreeding as the IBD fraction of the genome in ROH (F-ROH). We found a striking pattern of complete or near-complete homozygosity of entire chromosomes in many individuals. The majority of individual inbreeding was due to long IBD segments (>5 cM) originating from ancestors <= 10 generations ago, with 10 genomic regions showing very few ROH and forming candidate regions for containing loci contributing strongly to inbreeding depression. Inbreeding estimated with an extensive pedigree (F-P) was strongly correlated with realized inbreeding measured with the entire genome (r(2) = 0.86). However, inbreeding measured with the whole genome was more strongly correlated with multi-locus heterozygosity estimated with as few as 500 single nucleotide polymorphisms, and with F-ROH estimated with as few as 10,000 single nucleotide polymorphisms, than with F-P. These results document in fine detail the genomic consequences of intensive inbreeding in a population of conservation concern.

  • 7.
    Knief, Ulrich
    et al.
    Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, Fac Biol, Munich, Germany.
    Bossu, Christen M.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Stockholm Univ, Dept Zool, Populat Genet, Stockholm, Sweden;Univ Calif Los Angeles, Ctr Trop Res, Inst Environm & Sustainabil, Los Angeles, CA USA.
    Saino, Nicola
    Univ Milan, Dept Environm Sci & Policy, Milan, Italy.
    Hansson, Bengt
    Lund Univ, Dept Biol, Lund, Sweden.
    Poelstra, Jelmer
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Duke Univ, Biol Dept, Durham, NC USA.
    Vijay, Nagarjun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Indian Inst Sci Educ & Res, Dept Biol Sci, Bhopal, India.
    Weissensteiner, Matthias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, Fac Biol, Munich, Germany.
    Wolf, Jochen B. W.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, Fac Biol, Munich, Germany.
    Epistatic mutations under divergent selection govern phenotypic variation in the crow hybrid zone2019Inngår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 3, nr 4, s. 570-576Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The evolution of genetic barriers opposing interspecific gene flow is key to the origin of new species. Drawing from information on over 400 admixed genomes sourced from replicate transects across the European hybrid zone between all-black carrion crows and grey-coated hooded crows, we decipher the interplay between phenotypic divergence and selection at the molecular level. Over 68% of plumage variation was explained by epistasis between the gene NDP and a similar to 2.8-megabase region on chromosome 18 with suppressed recombination. Both pigmentation loci showed evidence for divergent selection resisting introgression. This study reveals how few, large-effect loci can govern prezygotic isolation and shield phenotypic divergence from gene flow.

  • 8.
    Knopp, Michael
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Andersson, Dan I
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    No beneficial fitness effects of random peptides2018Inngår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 2, nr 7, s. 1046-1047Artikkel i tidsskrift (Annet vitenskapelig)
  • 9. Poorter, Lourens
    et al.
    Rozendaal, Danaë M. A.
    Bongers, Frans
    de Almeida-Cortez, Jarcilene S.
    Almeyda Zambrano, Angélica María
    Álvarez, Francisco S.
    Andrade, José Luís
    Villa, Luis Felipe Arreola
    Balvanera, Patricia
    Becknell, Justin M.
    Bentos, Tony V.
    Bhaskar, Radika
    Boukili, Vanessa
    Brancalion, Pedro H. S.
    Broadbent, Eben N.
    César, Ricardo G.
    Chave, Jerome
    Chazdon, Robin L.
    Colletta, Gabriel Dalla
    Craven, Dylan
    de Jong, Ben H. J.
    Denslow, Julie S.
    Dent, Daisy H.
    DeWalt, Saara J.
    García, Elisa Díaz
    Dupuy, Juan Manuel
    Durán, Sandra M.
    Espírito Santo, Mário M.
    Fandiño, María C.
    Fernandes, Geraldo Wilson
    Finegan, Bryan
    Moser, Vanessa Granda
    Hall, Jefferson S.
    Hernández-Stefanoni, José Luis
    Jakovac, Catarina C.
    Junqueira, André B.
    Kennard, Deborah
    Lebrija-Trejos, Edwin
    Letcher, Susan G.
    Lohbeck, Madelon
    Lopez, Omar R.
    Marín-Spiotta, Erika
    Martínez-Ramos, Miguel
    Martins, Sebastião V.
    Massoca, Paulo E. S.
    Meave, Jorge A.
    Mesquita, Rita
    Mora, Francisco
    de Souza Moreno, Vanessa
    Müller, Sandra C.
    Muñoz, Rodrigo
    Muscarella, Robert
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    de Oliveira Neto, Silvio Nolasco
    Nunes, Yule R. F.
    Ochoa-Gaona, Susana
    Paz, Horacio
    Peña-Claros, Marielos
    Piotto, Daniel
    Ruíz, Jorge
    Sanaphre-Villanueva, Lucía
    Sanchez-Azofeifa, Arturo
    Schwartz, Naomi B.
    Steininger, Marc K.
    Thomas, William Wayt
    Toledo, Marisol
    Uriarte, Maria
    Utrera, Luis P.
    van Breugel, Michiel
    van der Sande, Masha T.
    van der Wal, Hans
    Veloso, Maria D. M.
    Vester, Hans F. M.
    Vieira, Ima C. G.
    Villa, Pedro Manuel
    Williamson, G. Bruce
    Wright, S. Joseph
    Zanini, Kátia J.
    Zimmerman, Jess K.
    Westoby, Mark
    Wet and dry tropical forests show opposite successional pathways in wood density but converge over time2019Inngår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 3, nr 6, s. 928-934Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Tropical forests are converted at an alarming rate for agricultural use and pastureland, but also regrow naturally through secondary succession. For successful forest restoration, it is essential to understand the mechanisms of secondary succession. These mechanisms may vary across forest types, but analyses across broad spatial scales are lacking. Here, we analyse forest recovery using 1,403 plots that differ in age since agricultural abandonment from 50 sites across the Neotropics. We analyse changes in community composition using species-specific stem wood density (WD), which is a key trait for plant growth, survival and forest carbon storage. In wet forest, succession proceeds from low towards high community WD (acquisitive towards conservative trait values), in line with standard successional theory. However, in dry forest, succession proceeds from high towards low community WD (conservative towards acquisitive trait values), probably because high WD reflects drought tolerance in harsh early successional environments. Dry season intensity drives WD recovery by influencing the start and trajectory of succession, resulting in convergence of the community WD over time as vegetation cover builds up. These ecological insights can be used to improve species selection for reforestation. Reforestation species selected to establish a first protective canopy layer should, among other criteria, ideally have a similar WD to the early successional communities that dominate under the prevailing macroclimatic conditions.

  • 10.
    Reger, Julia
    et al.
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England..
    Lind, Martin I.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Robinson, Matthew R.
    Univ Lausanne, Dept Computat Biol, CH-1015 Lausanne, Switzerland.;Swiss Inst Bioinformat, CH-1015 Lausanne, Switzerland..
    Beckerman, Andrew P.
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England..
    Predation drives local adaptation of phenotypic plasticity2018Inngår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 2, nr 1, s. 100-107Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Phenotypic plasticity is the ability of an individual genotype to alter aspects of its phenotype depending on the current environment. It is central to the persistence, resistance and resilience of populations facing variation in physical or biological factors. Genetic variation in plasticity is pervasive, which suggests its local adaptation is plausible. Existing studies on the adaptation of plasticity typically focus on single traits and a few populations, while theory about interactions among genes (for example, pleiotropy) suggests that a multi-trait, landscape scale (for example, multiple populations) perspective is required. We present data from a landscape scale, replicated, multi-trait experiment using a classic predator-prey system centred on the water flea Daphnia pulex. We find predator regime-driven differences in genetic variation of multivariate plasticity. These differences are associated with strong divergent selection linked to a predation regime. Our findings are evidence for local adaptation of plasticity, suggesting that responses of populations to environmental variation depend on the conditions in which they evolved in the past.

  • 11.
    Sayadi, Ahmed
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Martínez Barrio, Álvaro
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Immonen, Elina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Dainat, Jacques
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Berger, David
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Tellgren-Roth, Christian
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Nystedt, Björn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Arnqvist, Göran
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi. Uppsala Univ, Dept Ecol & Genet, Anim Ecol, Uppsala, Sweden.
    The genomic footprint of sexual conflict2019Inngår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 3, nr 12, s. 1725-1730Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 12.
    Xu, Luohao
    et al.
    Zhejiang Univ, MOE Lab Biosyst Homeostasis & Protect, Life Sci Inst, Hangzhou, Zhejiang, Peoples R China;Univ Vienna, Dept Mol Evolut & Dev, Vienna, Austria.
    Auer, Gabriel
    Univ Vienna, Dept Mol Evolut & Dev, Vienna, Austria.
    Peona, Valentina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Suh, Alexander
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Deng, Yuan
    BGI Shenzhen, China Natl Genebank, Shenzhen, Peoples R China;BGI Shenzhen, Shenzhen, Peoples R China.
    Feng, Shaohong
    BGI Shenzhen, China Natl Genebank, Shenzhen, Peoples R China;BGI Shenzhen, Shenzhen, Peoples R China.
    Zhang, Guojie
    BGI Shenzhen, China Natl Genebank, Shenzhen, Peoples R China;Chinese Acad Sci, State Key Lab Genet Resources & Evolut, Kunming Inst Zool, Kunming, Yunnan, Peoples R China;Univ Copenhagen, Sect Ecol & Evolut, Dept Biol, Copenhagen, Denmark.
    Blom, Mozes P. K.
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden;Leibniz Inst Evolut & Biodiversitatsforsch, Museum Naturkunde, Berlin, Germany.
    Christidis, Les
    Southern Cross Univ, Natl Marin Sci Ctr, Coffs Harbour, NSW, Australia;Univ Melbourne, Sch Biosci, Victoria, Australia.
    Prost, Stefan
    Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA;Senckenberg, LOEWE Ctr Translat Biodivers Genom, Frankfurt, Germany.
    Irestedt, Martin
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden.
    Zhou, Qi
    Zhejiang Univ, MOE Lab Biosyst Homeostasis & Protect, Life Sci Inst, Hangzhou, Zhejiang, Peoples R China;Univ Vienna, Dept Mol Evolut & Dev, Vienna, Austria.
    Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds2019Inngår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 3, nr 5, s. 834-844Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 13.
    Zhu, Min
    et al.
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China.;Univ Chinese Acad Sci, Coll Earth Sci, Beijing 100049, Peoples R China..
    Ahlberg, Per E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Zhao, Wen-Jin
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China.;Univ Chinese Acad Sci, Coll Earth Sci, Beijing 100049, Peoples R China..
    Jia, Lian-Tao
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China..
    A Devonian tetrapod-like fish reveals substantial parallelism in stem tetrapod evolution2017Inngår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 1, nr 10, s. 1470-1476Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 14.
    Zumberge, J. Alex
    et al.
    Univ Calif Riverside, Dept Earth Sci, Riverside, CA 92521 USA.
    Love, Gordon D.
    Univ Calif Riverside, Dept Earth Sci, Riverside, CA 92521 USA.
    Cárdenas, Paco
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi, Farmakognosi.
    Sperling, Erik A.
    Stanford Univ, Dept Geol Sci, Stanford, CA 94305 USA.
    Gunasekera, Sunithi
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi, Farmakognosi.
    Rohrssen, Megan
    Cent Michigan Univ, Dept Earth & Atmospher Sci, Mt Pleast, MI USA.
    Grosjean, Emmanuelle
    Geosci Australia, Canberra, ACT, Australia.
    Grotzinger, John P.
    CALTECH, Div Geol & Planetary Sci, Pasadena, CA USA.
    Summons, Roger E.
    MIT, Dept Earth Atmospher & Planetary Sci, Cambridge, MA USA.
    Demosponge steroid biomarker 26-methylstigmastane provides evidence for Neoproterozoic animals2018Inngår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 2, nr 11, s. 1709-1714Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Sterane biomarkers preserved in ancient sedimentary rocks hold promise for tracking the diversification and ecological expansion of eukaryotes. The earliest proposed animal biomarkers from demosponges (Demospongiae) are recorded in a sequence around 100 Myr long of Neoproterozoic-Cambrian marine sedimentary strata from the Huqf Supergroup, South Oman Salt Basin. This C-30 sterane biomarker, informally known as 24-isopropylcholestane (24-ipc), possesses the same carbon skeleton as sterols found in some modern-day demosponges. However, this evidence is controversial because 24-ipc is not exclusive to demosponges since 24-ipc sterols are found in trace amounts in some pelagophyte algae. Here, we report a new fossil sterane biomarker that co-occurs with 24-ipc in a suite of late Neoproterozoic-Cambrian sedimentary rocks and oils, which possesses a rare hydrocarbon skeleton that is uniquely found within extant demosponge taxa. This sterane is informally designated as 26-methylstigmastane (26-mes), reflecting the very unusual methylation at the terminus of the steroid side chain. It is the first animal-specific sterane marker detected in the geological record that can be unambiguously linked to precursor sterols only reported from extant demosponges. These new findings strongly suggest that demosponges, and hence multicellular animals, were prominent in some late Neoproterozoic marine environments at least extending back to the Cryogenian period.

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