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  • 1301.
    Récapet, Charlotte
    et al.
    Univ Lyon, Univ Claude Bernard Lyon 1, Lab Biometr & Biol Evolut, CNRS,UMR 5558, 43 Bd 11 Novembre 1918, F-69622 Villeurbanne, France.;Univ Lausanne Sorge, Dept Ecol & Evolut, CH-1015 Lausanne, Switzerland..
    Bize, Pierre
    Univ Aberdeen, Sch Biol Sci, Tillydrone Ave, Aberdeen AB24 2TZ, Scotland..
    Doligez, Blandine
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Univ Lyon, Univ Claude Bernard Lyon 1, Lab Biometr & Biol Evolut, CNRS,UMR 5558, 43 Bd 11 Novembre 1918, F-69622 Villeurbanne, France..
    Food availability modulates differences in parental effort between dispersing and philopatric birds2017Inngår i: Behavioral Ecology, ISSN 1045-2249, E-ISSN 1465-7279, Vol. 28, nr 3, s. 688-697Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Dispersal entails costs and might have to be traded off against other life-history traits. Dispersing and philopatric individuals may thus exhibit alternative life-history strategies. Importantly, these differences could also partly be modulated by environmental variation. Our previous results in a patchy population of a small passerine, the collared flycatcher, suggest that, as breeding density, a proxy of habitat quality, decreases, dispersing individuals invest less in reproduction but maintain a stable oxidative balance, whereas philopatric individuals maintain a high reproductive investment at the expense of increased oxidative stress. In this study, we aimed at experimentally testing whether these observed differences between dispersing and philopatric individuals across a habitat quality gradient were due to food availability, a major component of habitat quality in this system. We provided additional food for the parents to use during the nestling rearing period and we measured subsequent parental reproductive effort (through provisioning rate, adult body mass, and plasmatic markers of oxidative balance) and reproductive output. Density-dependent differences between dispersing and philopatric parents in body mass and fledging success were observed in control nests but not in supplemented nests. However, density-dependent differences in oxidative state were not altered by the supplementation. Altogether, our results support our hypothesis that food availability is responsible for some of the density-dependent differences observed in our population between dispersing and philopatric individuals but other mechanisms are also at play. Our study further emphasizes the need to account for environmental variation when studying the association between dispersal and other traits.

  • 1302.
    Rózsa, Jani
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Strand, Tanja
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik.
    Montadert, Marc
    Univ Franche Comte, UC INRA, MRT, Lab Ecol & Ecophysiol,EA 3184, Pl Leclercq, F-25300 Besancon, France.
    Kozma, Radoslav
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Effects of a range expansion on adaptive and neutral genetic diversity in dispersal limited Hazel grouse (Bonasa bonasia) in the French Alps2016Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 17, nr 2, s. 401-412Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Biogeographic range expansions, when related to dispersal limitation, may have counter intuitive effects on genetic diversity. At range margins the relative roles of demographic changes, connectivity and genetic diversity need to be integrated for a successful assessment of population viability. Historically the Hazel grouse (Bonasa bonasia) in France was found in the north of the French Alps and also in a disjunct population in the nearby Jura Mountains. The species has recently undergone a range expansion in a north to south axis in the Alps. Local population size estimates and migration patterns during expansion have previously been studied. In this study, we performed genotyping at neutral (microsatellite) and adaptive (MHC) genetic markers in Hazel grouse. We compared diversity and differentiation (FST and DEST) at three sampling localities along the expansion axis in the French Alps and Jura, as well as at two sampling localities in Sweden, where the population has had a long-term continuous and stable distribution. Strong serial founder effects were found between the French localities, resulting in stronger isolation further south, with a relatively high neutral differentiation (pair-wise FST = 0.117). However, the loss of adaptive diversity MHC was slight. No adaptive differentiation (MHC DEST = −0.015) was observed, thus, the French localities can be considered uniform units with regard to MHC diversity, a criterion to treat populations in these localities as a management unit.

  • 1303.
    Rödin Mörch, Patrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Recombination, Diversity and Differentiation at the MHC-B Region in Two Populations of Black Grouse (Tetrao tetrix)2014Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Abstract [en]

    The genes of the major histocompatibility complex (MHC) encode proteins that are involved in the adaptive immune system. They are among the most polymorphic genes known in vertebrates and are mainly responsible for the presentation of antigens to T-cells in order to initiate an immune response. Evidence indicates that balancing selection is behind this extraordinary polymorphism. Known for it’s more compact and streamlined organization black grouse and other galliform birds have what is called a minimal essential MHC. Here, I investigate the patterns of recombination and linkage disequilibrium, genetic diversity, differentiation and signs of positive natural selection in two demographically distinct populations of black grouse (Tetrao tetrix). Using MHC linked microsatellites and MHC-BLB single locus sequences I showed that a small isolated population from the Netherlands is significantly differentiated from a large population from Finland , that the Dutch population has lower levels of genetic variation and a smaller number, but more divergent BLB alleles. Both populations also show signs of historical balancing selection acting on the codons responsible for the antigen binding site of the BLB genes. Lastly, the Dutch population shows overall signs of higher linkage disequilibrium resulting in lower population recombination rates compared to the Finnish population. Based on the estimated ratio between the population recombination rate and the population mutation rate I showed that mutations have been more prevalent in shaping diversity at the black grouse MHC-B region than recombination has been. The differences in variation, selection and recombination between the Dutch and Finnish population are likely a reflection of their very different demographic histories.

  • 1304.
    Sagitov, Serik
    et al.
    Chalmers University of Technology and the University of Gothenburg.
    Bartoszek, Krzysztof
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg.
    Interspecies correlation for neutrally evolving traits2012Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 309, s. 11-19Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A simple way to model phenotypic evolution is to assume that after splitting, the trait values of the sister species diverge as independent Brownian motions. Relying only on a prior distribution for the underlying species tree (conditioned on the number, n, of extant species) we study the random vector (X1,…,Xn) of the observed trait values. In this paper we derive compact formulae for the variance of the sample mean and the mean of the sample variance for the vector (X1,…,Xn).

    The key ingredient of these formulae is the correlation coefficient between two trait values randomly chosen from (X1,…,Xn). This interspecies correlation coefficient takes into account not only variation due to the random sampling of two species out of n and the stochastic nature of Brownian motion but also the uncertainty in the phylogenetic tree. The latter is modeled by a (supercritical or critical) conditioned branching process. In the critical case we modify the Aldous-Popovic model by assuming a proper prior for the time of origin.

  • 1305.
    Sagitov, Serik
    et al.
    Chalmers University of Technology and the University of Gothenburg.
    Bartoszek, Krzysztof
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg.
    Interspecies correlation for neutrally evolving traits2012Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 309, s. 11-19Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A simple way to model phenotypic evolution is to assume that after splitting, the trait values of the sister species diverge as independent Brownian motions. Relying only on a prior distribution for the underlying species tree (conditioned on the number, n, of extant species) we study the random vector (X1,…,Xn) of the observed trait values. In this paper we derive compact formulae for the variance of the sample mean and the mean of the sample variance for the vector (X1,…,Xn).

    The key ingredient of these formulae is the correlation coefficient between two trait values randomly chosen from (X1,…,Xn). This interspecies correlation coefficient takes into account not only variation due to the random sampling of two species out of n and the stochastic nature of Brownian motion but also the uncertainty in the phylogenetic tree. The latter is modeled by a (supercritical or critical) conditioned branching process. In the critical case we modify the Aldous-Popovic model by assuming a proper prior for the time of origin.

  • 1306.
    Salakka, Seela
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Geovetenskapliga sektionen, Institutionen för geovetenskaper, Paleobiologi.
    Tooth Replacement of Euhelopus zdanskyi (Dinosauria: Sauropoda) and the Evolution of Titanosaurian Tooth Morphology2014Independent thesis Advanced level (degree of Master (Two Years)), 80 poäng / 120 hpOppgave
    Abstract [en]

    Sauropod tooth morphologies and tooth replacement patterns bear important information on feeding habits and sauropod evolution. Euhelopus zdanskyi is an Early Cretaceous neosauropod, and belongs to the group Euhelopodidae, which is the sister group of Titanosauria. Euhelopus is a key taxon in the evolution of sauropod teeth, because it displays a very conservative tooth morphology compared to that seen in Titanosauria, despite being a close relative. The teeth of Euhelopus resemble those of Camarasaurus, as well as many basal sauropods that are not closely related to Euhelopus. The teeth of Euhelopus are spoon-shaped, and they have approximately two replacement teeth for each functional tooth. Their robust morphology and low number of replacement teeth suggest that they were worn down a lot more slowly than the pencil-shaped teeth of Titanosauria and Diplodocoidea. Diplodocoids, whose teeth have been studied widely, especially show very rapid tooth replacement rates, and the tooth morphology of titanosaurs suggests that they might have had similar replacement rates. On the contrary, Euhelopus was likely to have replacement rates similar to the relatively low rates of Camarasaurus, whose tooth battery is much like that of Euhelopus. Furthermore, some euhelopodids are known to have had pencil-shaped teeth, which indicates that there was a strong evolutionary pressure towards the development of narrow teeth during the Late Cretaceous. This pressure may have been caused by a change in vegetation or may merely represent somphospondylans occupying the niches vacated by the diplodocoids, which appear to have gone extinct before the end of the Cretaceous. This study uses 3D modelling for inspecting tooth replacement of Euhelopus and evolution of sauropod teeth.

  • 1307. Samils, Nicklas
    et al.
    Oliva, Jonas
    Johannesson, Hanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Nuclear interactions in a heterokaryon: insight from the model Neurospora tetrasperma2014Inngår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 281, nr 1786, s. UNSP 20140084-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A heterokaryon is a tissue type composed of cells containing genetically different nuclei. Although heterokaryosis is commonly found in nature, an understanding of the evolutionary implications of this phenomenon is largely lacking. Here, we use the filamentous ascomycete Neurospora tetrasperma to study the interplay between nuclei in heterokaryons across vegetative and sexual developmental stages. This fungus harbours nuclei of two opposite mating types (mat A and mat a) in the same cell and is thereby self-fertile. We used pyrosequencing of mat-linked SNPs of three heterokaryons to demonstrate that the nuclear ratio is consistently biased for mat A-nuclei during mycelial growth (mean mat A/mat a ratio 87%), but evens out during sexual development (ratio ranging from 40 to 57%). Furthermore, we investigated the association between nuclear ratio and expression of alleles of mat-linked genes and found that expression is coregulated to obtain a tissue-specific bias in expression ratio: during mycelial extension, we found a strong bias in expression for mat A-linked genes, that was independent of nuclear ratio, whereas at the sexual stage we found an expression bias for genes of the mat a nuclei. Taken together, our data indicate that nuclei cooperate to optimize the fitness of the heterokaryon, via both altering their nuclear ratios and coregulation genes expressed in the different nuclei.

  • 1308.
    Sanchez, Sophie
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Dupret, Vincent
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Ryll, Bettina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Trinajstic, Kate
    Curtin University, Western Australia.
    Wretman, Lovisa
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Zylberberg, Louise
    Université Pierre et Marie Curie, UPMC, Paris, France.
    Tafforeau, Paul
    European Synchrotron Radiation Facility, Grenoble, France.
    Ahlberg, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Fossil bone histology revealed in 3D thanks to the synchrotron light: palaeobiological implications2011Konferansepaper (Fagfellevurdert)
  • 1309.
    Sanchez, Sophie
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Dupret, Vincent
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Ryll, Bettina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Trinajstic, Kate
    Curti University, Western Australia.
    Wretman, Lovisa
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Zylberberg, Louise
    Université Pierre et Marie Curie, UPMC, Paris, France.
    Tafforeau, Paul
    European Synchrotron Radiation Facility, Grenoble, France.
    Ahlberg, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Synchrotron virtual palaeohistology: a new tool for studying the evolution of bone microstructures in 3D2011Konferansepaper (Fagfellevurdert)
  • 1310.
    Sanchez, Sophie
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi.
    Schoch, Rainer
    Environmental and metabolic plasticity revealed by bonehistology as a successful evolutionary strategy in a long-lived homeostatic triassic temnospondyl2013Konferansepaper (Annet vitenskapelig)
  • 1311.
    Sanchez, Sophie
    et al.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. European Synchrotron Radiat Facil, 71 Ave Martyrs,CS 40220, F-38043 Grenoble, France..
    Tafforeau, Paul
    European Synchrotron Radiat Facil, 71 Ave Martyrs,CS 40220, F-38043 Grenoble, France..
    Clack, Jennifer A.
    Univ Cambridge, Univ Museum Zool, Dept Zool, Downing St, Cambridge CB2 3EJ, England..
    Ahlberg, Per E.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Life history of the stem tetrapod Acanthostega revealed by synchrotron microtomography2016Inngår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 537, nr 7620, s. 408-+Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1312.
    Sangster, George
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk systematik och evolutionsforskning.
    Review of: Festschrift for Ned Johnson: Geographic variation and evolution in birds by C Cicero and J V Remsen.2008Inngår i: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 150, s. 843-Artikkel, omtale (Annet vitenskapelig)
  • 1313.
    Sangster, George
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk systematik och evolutionsforskning.
    The ring species concept revisitedManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Ring species may offer important insights into the role of isolation by distance in speciation. In recent years, the study of ring species has been revigorated by the application of phylogeographic methods. The concept of ring species, however, has received little attention since its original formulation in the first half of the twentieth century. A review of the two best-documented cases of putative ring species suggests that different evolutionary patterns have been referred to by the term ‘ring species’. These putative ring species share a circular colonization pattern but have fundamentally different evolutionary histories and patterns of geographic variation. Because these patterns cannot be explained by a single evolutionary model, a terminological distinction is warranted. It is suggested that the term ‘ring species’ be restricted to taxa which form a single evolutionary unit and in which the end-points have diverged as a result of isolation by distance. The new evolutionary term ‘taxon chain’ is suggested for a clade consisting of multiple evolutionary units separated by secondary contact zones. The study of ring species and taxon chains requires an integrative approach, including the description of geographic variation, phylogeographic study of historical divergence, assessment of gene flow, and study of interactions in contact zones.

  • 1314.
    Sangster, George
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk systematik och evolutionsforskning. Swedish Museum of Natural History.
    Collinson, J. Martin
    Crochet, Pierre-Andre
    Knox, Alan G.
    Parkin, David T.
    Votier, Stephen C.
    Taxonomic recommendations for Western Palearcticbirds: ninth report2013Inngår i: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 155, nr 4, s. 898-907Artikkel i tidsskrift (Annet vitenskapelig)
  • 1315. Sanudo-Restrepo, Claudia P.
    et al.
    Dinca, Vlad
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Talavera, Gerard
    Vila, Roger
    Biogeography and systematics of Aricia butterflies (Lepidoptera, Lycaenidae)2013Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 66, nr 1, s. 369-379Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Butterflies of the Aricia species group represent a paradigm of unresolved taxonomy, both at the genus and species levels. We studied phylogenetic relationships, biogeography, and systematics based on genetic - nuclear and mitochondrial - and morphometric - external (wings) and internal (genitalia) data. We show that Aricia is a monophyletic genus comprising the taxa Pseudoaricia, Ultraaricia and Umpria, which are here considered junior synonyms of Aricia. The taxa allous, inhonora, issekutzi, mandzhuriana, myrmecias and transalaica, which have often been raised to species rank, are shown to probably represent subspecies or synonyms. We show that montensis is likely a good species that is sister to all A. artaxerxes populations across the Palearctic region. The species A. anteros and A. morronensis are shown to display deep intraspecific divergences and they may harbor cryptic species. We also discovered that A. cramera and A. agestis exhibit a pattern of mutual exclusion on islands, and a parapatric distribution in mainland with a narrow contact zone where potential hybrids were detected. The lack of a prezygotic barrier that prevents their coexistence could explain this phenomenon. This study will hopefully contribute to the stability of the systematics of Aricia, a group with potential for the study of the link between speciation and biogeography.

  • 1316.
    Sanyal, Anushree
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. Univ Picardie Jules Verne, FRE CNRS 3498, Unite Ecol & Dynam Syst Anthropises EDYSAN, 1 Rue Louvels, FR-80037 Amiens, France..
    Decocq, Guillaume
    Univ Picardie Jules Verne, FRE CNRS 3498, Unite Ecol & Dynam Syst Anthropises EDYSAN, 1 Rue Louvels, FR-80037 Amiens, France..
    Adaptive evolution of seed oil content in angiosperms: accounting for the global patterns of seed oils2016Inngår i: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 16, artikkel-id 187Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1317.
    Savolainen, Outi
    et al.
    Univ Oulu, Dept Genet & Physiol, Oulu 90014, Finland.;Univ Oulu, Bioctr Oulu, Oulu 90014, Finland..
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    GENOMICS Geography matters for Arabidopsis2016Inngår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 537, nr 7620, s. 314-315Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

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

  • 1318.
    Sayadi, Ahmed
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Immonen, Elina
    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.
    Arnqvist, Göran
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    The Evolution of Dark Matter in the Mitogenome of Seed Beetles2017Inngår i: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, nr 10, s. 2697-2706Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1319. Sayadi, Ahmed
    et al.
    Immonen, Elina
    Tellgren-Roth, Christian
    Arnqvist, Göran
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    The Evolution of Dark Matter in the Mitogenome of Seed Beetles2017Inngår i: Genome biology and evolution, Vol. 9, nr 10, s. 2697-2706Artikkel i tidsskrift (Fagfellevurdert)
  • 1320. Schiller, Anja M.
    et al.
    Larson, Keith W.
    Klamath Bird Observatory, Ashland, Oregon.
    Alexander, John D.
    A White-crowned Sparrow with three legs2007Inngår i: Western Birds, ISSN 0160-1121, Vol. 38, nr 3, s. 222-223Artikkel i tidsskrift (Fagfellevurdert)
  • 1321.
    Schlebusch, Carina
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa..
    Malmström, Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa..
    Günther, Torsten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Sjödin, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Coutinho, Alexandra
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Edlund, Hanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Munters, Arielle R.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Vicente, Mário
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Steyn, Maryna
    Human Variation and Identification Research Unit, School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, South Africa..
    Soodyall, Himla
    Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa..
    Lombard, Marlize
    Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa.; Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Marais Street, Stellenbosch, 7600, South Africa. .
    Jakobsson, Mattias
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa..
    Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago2017Inngår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 358, nr 6363, s. 652-655Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1322. Schultz, Stewart T.
    et al.
    Scofield, Douglas
    Mutation Accumulation in Real Branches: Fitness Assays for Genomic Deleterious Mutation Rate and Effect in Large-Statured Plants2009Inngår i: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 174, nr 2, s. 163-175Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1323.
    Schuster, Astrid
    et al.
    Ludwig Maximilians Univ Munchen, Dept Earth & Environm Sci Palaeontol & Geobiol, Richard Wagner Str 10, D-80333 Munich, Germany..
    Lopez, Jose V.
    Nova Southeastern Univ, Halmos Coll Nat Sci & Oceanog, Dania, FL 33004 USA..
    Becking, Leontine E.
    Wageningen Univ & Res Ctr, Marine Anim Ecol, POB, NL-3700 AH Wageningen, Netherlands.;Naturalis Biodivers Ctr, Marine Zool Dept, POB 95172300RA, Leiden, Netherlands..
    Kelly, Michelle
    Natl Inst Water & Atmospher Res, Natl Ctr Aquat Biodivers & Biosecur, POB 109-695, Auckland, New Zealand..
    Pomponi, Shirley A.
    Florida Atlantic Univ, Harbor Branch Oceanog Inst, 5600 S 1 North, Ft Pierce, FL 34946 USA..
    Woerheide, Gert
    Ludwig Maximilians Univ Munchen, Dept Earth & Environm Sci Palaeontol & Geobiol, Richard Wagner Str 10, D-80333 Munich, Germany.;SNSB, Bavarian State Collect Palaeontol & Geol, Richard Wagner Str 10, D-80333 Munich, Germany.;Ludwig Maximilians Univ Munchen, GeoBio CenterLMU, Richard Wagner Str 10, D-80333 Munich, Germany..
    Erpenbeck, Dirk
    Ludwig Maximilians Univ Munchen, Dept Earth & Environm Sci Palaeontol & Geobiol, Richard Wagner Str 10, D-80333 Munich, Germany.;Ludwig Maximilians Univ Munchen, GeoBio CenterLMU, Richard Wagner Str 10, D-80333 Munich, Germany..
    Cárdenas, Paco
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi, Avdelningen för farmakognosi.
    Evolution of group I introns in Porifera: new evidence for intron mobility and implications for DNA barcoding2017Inngår i: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 17, artikkel-id 82Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1324.
    Schwander, Tanja
    et al.
    University of Groningen.
    Leimar, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Genes as leaders and followers in evolution2011Inngår i: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 26, nr 3, s. 143-151Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    A major question for the study of phenotypic evolution is whether intra- and interspecific diversity originates directly from genetic variation, or instead, as plastic responses to environmental influences initially, followed later by genetic change. In species with discrete alternative phenotypes, evolutionary sequences can be inferred from transitions between environmental and genetic phenotype control, and from losses of phenotypic alternatives. From the available evidence, sequences appear equally probable to start with genetic polymorphism as with polyphenism, with a possible dominance of one or the other for specific trait types. We argue in this review that to evaluate the prevalence of each route, an investigation of both genetic and environmental cues for phenotype determination in several related rather than in isolated species is required.

  • 1325.
    Schwander, Tanja
    et al.
    University of Groningen.
    Leimar, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    The evolution of novel cues for ancestral phenotypes2011Inngår i: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 26, nr 9, s. 436-437Artikkel i tidsskrift (Fagfellevurdert)
  • 1326.
    Schäpers, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Evolutionary and mechanistic aspects of insect host plant preference2016Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Plant feeding insects comprise about 25% of all animal species on earth and play an important role in all ecosystems. Although we understand that their association with plants is a key-factor driving the diversification in this group, we still have large gaps in our knowledge of the underlying processes of this relationship. Female choice of host plant is an important event in the insect life-cycle, as it is a major determinant of the larval food plant. In this Thesis I studied different aspects of insect host plant choice and used butterflies from the family Nymphalidae as my study system. I found that butterflies have a well developed olfactory system and that they use odors when searching for food or host plants. However, the information obtained from the odor of host plants does not seem to be sufficient for the studied species to make a distinction between plants of different qualities. Interestingly, even when in full contact with the leaf they do not make optimal decisions. I show for example that a sub-optimal female choice may be mitigated by larval ability to cope with unfavorable situations. Moreover, species that utilize a broader set of host plants may not be very well adapted to all the hosts they use, but at the same time they may survive in areas where there is only a subset of the plants available. Lastly, differences in the evolution of life-history traits between species can account for differences in how each species realizes its lifestyle. Thus, by incorporating findings on mechanisms of host plant choice with the ecological and evolutionary context of a species, our ability to explain the dynamics of host plant choice and insect-plant interactions can be improved.

  • 1327.
    Schäpers, Alexander
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Petrén, Hampus
    Wheat, Christopher W.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Wiklund, Christer
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Friberg, Magne
    Female fecundity variation affects reproducibility of experiments on host plant preference and acceptance in a phytophagous insect2017Inngår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, nr 1849, artikkel-id 20162643Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Reproducibility is a scientific cornerstone. Many recent studies, however, describe a reproducibility crisis and call for assessments of reproducibility across scientific domains. Here, we explore the reproducibility of a classic ecological experiment—that of assessing female host plant preference and acceptance in phytophagous insects, a group in which host specialization is a key driver of diversification. We exposed multiple cohorts of Pieris napi butterflies from the same population to traditional host acceptance and preference tests on three Brassicaceae host species. Whereas the host plant rank order was highly reproducible, the propensity to oviposit on low-ranked hosts varied significantly even among cohorts exposed to similar conditions. Much variation could be attributed to among-cohort variation in female fecundity, a trait strongly correlated both to female size and to the size of the nuptial gift a female receives during mating. Small males provide small spermatophores, and in our experiment small females that mated with small males had a disproportionally low propensity to oviposit on low-ranked hosts. Hence, our results provide empirical support to the theoretical prediction that female host utilization is strongly affected by non-genetic, environmental variation, and that such variation can affect the reproducibility of ecological experiments even under seemingly identical conditions.

  • 1328.
    Scofield, Douglas G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    A definitive demonstration of fitness effects due to somatic mutation in a plant2014Inngår i: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 112, nr 4, s. 361-362Artikkel i tidsskrift (Annet vitenskapelig)
  • 1329. Scofield, Douglas
    et al.
    Lynch, Michael
    Evolutionary Diversification of the Sm Family of RNA-Associated Proteins2008Inngår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 25, nr 11, s. 2255-2267Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1330. Scofield, Douglas
    et al.
    Schultz, Stewart
    Mitosis, stature and evolution of plant mating systems: low-Phi and high-Phi plants2006Inngår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 273, nr 1584, s. 275-282Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1331.
    Segelbacher, Gernot
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Strand, Tanja M.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Quintela, Maria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Axelsson, Tomas
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Molekylär medicin.
    Jansman, Hugh A.H.
    Koelewijn, Hans-Peter
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Analyses of historical and current populations of black grouse in Central Europe reveal strong effects of genetic drift and loss of genetic diversity2014Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 15, nr 5, s. 1183-1195Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1332.
    Segelbacher, Gernot
    et al.
    Dept Wildlife Ecology and Management, University Freiburg.
    Strand, Tanja
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Populationsbiologi och naturvårdsbiologi.
    Quintela, Maria
    Dept of Animal Biology, Plant Biology and Ecology, Faculty of Science, University of A Coruña.
    Axelsson, Tomas
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten.
    Jansman, Hugh
    Alterra Wageningen UR.
    Koelewijn, Peter
    Nunhems BV.
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Historic and current populations of black grouse in central Europe – evidence for rapid loss of genetic diversity2011Artikkel i tidsskrift (Annet vitenskapelig)
    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. 

  • 1333.
    Shafer, Aaron B. A.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Miller, Joshua M.
    Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT USA..
    Kardos, Marty
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Cross-Species Application of SNP Chips is Not Suitable for Identifying Runs of Homozygosity2016Inngår i: Journal of Heredity, ISSN 0022-1503, E-ISSN 1465-7333, Vol. 107, nr 2, s. 193-195Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1334.
    Shafer, Aaron B. A.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Trent Univ, Forens Sci & Environm & Life Sci, 2014 East Bank Dr, Peterborough, ON K9J 7B8, Canada..
    Peart, Claire R.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Tusso, Sergio
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Maayan, Inbar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Brelsford, Alan
    Univ Lausanne, Dept Ecol & Evolut, CH-1015 Lausanne, Switzerland..
    Wheat, Christopher W.
    Stockholm Univ, Dept Zool, S-10691 Stockholm, Sweden..
    Wolf, Jochen B. W.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Ludwig Maximilians Univ Munchen, Div Evolutionary Biol, Fac Biol, Grosshaderner Str 2, D-82152 Planegg Martinsried, Germany..
    Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference2017Inngår i: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 8, nr 8, s. 907-917Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1335.
    Shafer, Aaron B. A.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Wolf, Jochen B. W.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Alves, Paulo C.
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, P-4485661 Oporto, Portugal.;Fac Ciencias, P-4485661 Oporto, Portugal..
    Bergström, Linnea
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Colling, Guy
    Musee Natl Hist Nat Luxembourg, Populat Biol, L-2160 Luxembourg, Luxembourg..
    Dalen, Love
    Swedish Museum Nat Hist, Bioinformat & Genet, S-10405 Stockholm, Sweden..
    De Meester, Luc
    KU Leuven Univ Leuven, Aquat Ecol Evolut & Conservat, B-3000 Leuven, Belgium..
    Ekblom, Robert
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Fior, Simone
    Swiss Fed Inst Technol, Integrat Biol, CH-8092 Zurich, Switzerland..
    Hajibabaei, Mehrdad
    Univ Guelph, Integrat Biol, Guelph, ON N1G 2W1, Canada..
    Hoezel, A. Rus
    Univ Durham, Biol & Biomed Sci, Durham DH1 3LE, England..
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Jensen, Evelyn L.
    Univ British Columbia Okanagan, Biol, Kelowna, BC V1V 1V7, Canada..
    Kruetzen, Michael
    Univ Zurich, Anthropol Inst & Museum, CH-8057 Zurich, Switzerland..
    Norman, Anita J.
    Swedish Univ Agr Sci, Wildlife Fish & Environm Studies, S-90183 Umea, Sweden..
    Osterling, E. Martin
    Karlstad Univ, Biol, S-65188 Karlstad, Sweden..
    Ouborg, N. Joop
    Radboud Univ Nijmegen, Expt Plant Ecol, NL-6500 GL Nijmegen, Netherlands..
    Piccolo, John
    Primmer, Craig R.
    Univ Turku, Biol, Turku 20014, Finland..
    Reed, Floyd A.
    Univ Hawaii Manoa, Biol, Honolulu, HI 96822 USA..
    Roumet, Marie
    Swiss Fed Inst Technol, Integrat Biol, CH-8092 Zurich, Switzerland..
    Salmona, Jordi
    Inst Gulbenkian Ciencias, Populat & Conservat Genet Grp, P-2780156 Oeiras, Portugal..
    Schwartz, Michael K.
    USDA, Forest Serv, Rocky Mt Res Stn, Missoula, MT 59801 USA..
    Segelbacher, Gernot
    Univ Freiburg, Wildlife Ecol & Management, D-79106 Freiburg, Germany..
    Thaulow, Jens
    Norwegian Inst Water Res, Freshwater Biol, N-0349 Oslo, Norway..
    Valtonen, Mia
    Univ Eastern Finland, Biol, Joensuu 80101, Finland..
    Vergeer, Philippine
    Wageningen Univ, Nat Conservat & Plant Ecol, NL-6708 PB Wageningen, Netherlands..
    Weissensteiner, Matthias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Wheat, Christopher W.
    Stockholm Univ, Zool, S-10691 Stockholm, Sweden..
    Vila, Carlese
    Estn Biol Donana, Conservat & Evolutionary Genet Grp, Seville 41092, Spain..
    Zielinski, Piotr
    Jagiellonian Univ, Inst Environm Sci, PL-30387 Krakow, Poland..
    Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application Reply2016Inngår i: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 31, nr 2, s. 83-84Artikkel i tidsskrift (Fagfellevurdert)
  • 1336.
    Sharwood, Robert
    et al.
    Australian Natl Univ, Res Sch Biol, Canberra, ACT 2601, Australia.; Australian Natl Univ, ARC Ctr Excellence Translat Photosynthesis, Canberra, ACT 2601, Australia..
    Ghannoum, Oula
    Australian Natl Univ, ARC Ctr Excellence Translat Photosynthesis, Canberra, ACT 2601, Australia.; Univ Western Sydney, Hawkesbury Inst Environm, Richmond, NSW 2753, Australia..
    Kapralov, Maxim
    Liverpool John Moores Univ, Sch Nat Sci & Psychol, Liverpool L3 3AF, Merseyside, England..
    Gunn, Laura
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. Australian Natl Univ, Res Sch Biol, Canberra, ACT 2601, Australia..
    Whitney, Spencer
    Australian Natl Univ, Res Sch Biol, Canberra, ACT 2601, Australia.; Australian Natl Univ, ARC Ctr Excellence Translat Photosynthesis, Canberra, ACT 2601, Australia..
    Temperature responses of Rubisco from Paniceae grasses provide opportunities for improving C3 photosynthesis2016Inngår i: Nature Plants, ISSN 2055-0278, Vol. 2, nr 12, artikkel-id 16186Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1337.
    Sheikh, Sanea
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Microsatellites in the Flycatcher Genome2012Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
  • 1338. Sheng, G.-L.
    et al.
    Soubrier, J.
    Liu, J.-Y.
    Werdelin, Lars
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Llamas, B.
    Thomson, V. A.
    Tuke, J.
    Wu, L.-W.
    Chen, Q.-L.
    Lai, X.-L.
    Cooper, A.
    Pleistocene cave hyenas and the recent Eurasian history of the spotted hyena, Crocuta crocuta2013Inngår i: Molecular Ecology, Vol. 23, s. 522-533Artikkel i tidsskrift (Fagfellevurdert)
  • 1339.
    Shipilina, Daria
    et al.
    Lomonosov Moscow State Univ, Dept Vertebrate Zool, Moscow, Russia..
    Serbyn, Maksym
    Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA..
    Ivanitskii, Vladimir
    Lomonosov Moscow State Univ, Dept Vertebrate Zool, Moscow, Russia..
    Marova, Irina
    Lomonosov Moscow State Univ, Dept Vertebrate Zool, Moscow, Russia..
    Backström, Niclas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Patterns of genetic, phenotypic, and acoustic variation across a chiffchaff (Phylloscopus collybita abietinus/tristis) hybrid zone2017Inngår i: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 7, nr 7, s. 2169-2180Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1340. Shoda-Kagaya, E.
    et al.
    Saito, S.
    Okada, M.
    Nozaki, A.
    Nunokawa, K.
    Tsuda, Yoshiaki
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionär funktionsgenomik.
    Genetic structure of the oak wilt vector beetle Platypus quercivorus: inferences toward the process of damaged area expansion2010Inngår i: BMC Ecology, ISSN 1472-6785, E-ISSN 1472-6785, Vol. 10, nr 21Artikkel i tidsskrift (Fagfellevurdert)
  • 1341.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och 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"2018Inngår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 359, nr 6374, artikkel-id eaan5760Artikkel i tidsskrift (Annet vitenskapelig)
    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.

  • 1342.
    Sigurdardóttir, Sunniva Samson
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Hit and Miss: The Complexity of Admixture2014Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    With massive population declines all over the world, conservationists are faced with a serious threat of extinctions with a need to explore possibilities of translocations and interbreeding programs. While admixture, mixing of separate gene pools, can have beneficial effects, scientists have become aware of the risk of outbreeding depression. The aim of the present study was to investigate the symmetry in outcome in interbreeding population pairs and examine if there are any general patterns. A systematic review was conducted on 28 experimental studies about interbreeding and admixture in plants and animals with comparisons between purebred groups and hybrid groups. Three main types of traits were investigated, chosen to represent quantity, quality and body size of offspring. Overall, symmetrical outcomes were most frequent (62.8 ± 2.6 %), most commonly with a neutral outcome (i.e. none of the populations significantly affected by admixture) in both populations (40.6  ± 3.9 % of all outcome possibilities), which even might be an underestimate because of potential publication bias. Positive and negative outcomes were similar in frequency (11.5 and 11.2 %, respectively, in symmetrical outcomes; 18.1 and 14.4 % in asymmetrical outcomes). The results indicate that consequences of admixture differed between experiments conducted in the laboratory versus semi-natural or natural conditions, between plants and animals, and between the three types of traits. The effects of admixture depended on whether the response was measured in first, second, third generation hybrids, or backcrosses. However, there was no difference in outcome between first and second generation hybrids, which is not in agreement with theory where a more frequent and/or severe negative outcome is expected in later generations. The cause of positive or negative admixture could not be identified, although the heterogenous outcome might indicate that interactions in population pairs are unique. Accordingly, no translocation should be carried out into endangered populations before cautious investigation of possible admixture outcomes. Future research should aim to disentangle the cause and effect of admixture and, preferably, use genetic divergence as an explanatory variable.

  • 1343.
    Siljestam, Mattias
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Östman, Örjan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    The combined effects of temporal autocorrelation and the costs of plasticity on the evolution of plasticity2017Inngår i: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 30, nr 7, s. 1361-1371Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 1344.
    Sjödin, Henrik
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Evolution and Ecology Program, International Institute for Applied Systems Analysis, 2361 Laxenburg, Austria.
    Brännström, Åke
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik. Evolution and Ecology Program, International Institute for Applied Systems Analysis, 2361 Laxenburg, Austria.
    Dieckmann, Ulf
    Evolution and Ecology Program, International Institute for Applied Systems Analysis, 2361 Laxenburg, Austria.
    Mazzucco, Rupert
    Evolution and Ecology Program, International Institute for Applied Systems Analysis, 2361 Laxenburg, Austria.
    Contingent dispersal and the formation of cooperative groupsManuskript (preprint) (Annet vitenskapelig)
  • 1345.
    Sjödin, Per
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Skoglund, Pontus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Assessing the Maximum Contribution from Ancient Populations2014Inngår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 31, nr 5, s. 1248-1260Artikkel i tidsskrift (Fagfellevurdert)
    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).

  • 1346.
    Sjöstrand, Agnès E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Origins and Adaptation in Humans: A Case Study of Taste and Lifestyle2015Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

  • 1347. Sjöstrand, Joel
    et al.
    Tofigh, Ali
    Daubin, Vincent
    Arvestad, Lars
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Sennblad, Bengt
    Lagergren, Jens
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    A Bayesian Method for Analyzing Lateral Gene Transfer2014Inngår i: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 63, nr 3, s. 409-420Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Lateral gene transfer (LGT)uwhich transfers DNA between two non-vertically related individuals belonging to the same or different speciesuis recognized as a major force in prokaryotic evolution, and evidence of its impact on eukaryotic evolution is ever increasing. LGT has attracted much public attention for its potential to transfer pathogenic elements and antibiotic resistance in bacteria, and to transfer pesticide resistance from genetically modified crops to other plants. In a wider perspective, there is a growing body of studies highlighting the role of LGT in enabling organisms to occupy new niches or adapt to environmental changes. The challenge LGT poses to the standard tree-based conception of evolution is also being debated. Studies of LGT have, however, been severely limited by a lack of computational tools. The best currently available LGT algorithms are parsimony-based phylogenetic methods, which require a pre-computed gene tree and cannot choose between sometimes wildly differing most parsimonious solutions. Moreover, in many studies, simple heuristics are applied that can only handle putative orthologs and completely disregard gene duplications (GDs). Consequently, proposed LGT among specific gene families, and the rate of LGT in general, remain debated. We present a Bayesian Markov-chain Monte Carlo-based method that integrates GD, gene loss, LGT, and sequence evolution, and apply the method in a genome-wide analysis of two groups of bacteria: Mollicutes and Cyanobacteria. Our analyses show that although the LGT rate between distant species is high, the net combined rate of duplication and close-species LGT is on average higher. We also show that the common practice of disregarding reconcilability in gene tree inference overestimates the number of LGT and duplication events. [Bayesian; gene duplication; gene loss; horizontal gene transfer; lateral gene transfer; MCMC; phylogenetics.].

  • 1348.
    Skar, Helena
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Tibell, Lena A E
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Linköpings universitet.
    The potential of the evolutionary tree as mediational means in museum exhibitions containing key evolutionary concepts2015Inngår i: Non-formal Learning Environments, 2015Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Diagrams have been used to visualize evolutionary relationships for more than 150 years, and are today readily found in many areas such as textbooks, media, museums and the scientific literature. The tree of life metaphor, where the diagram takes the form of an organic vertical tree has been used almost as long and is still used to a high degree in textbooks and at museums. Despite this high prevalence the instructional needed to develop tree-thinking abilities are often lacking, potentially leading to interpretational misconceptions of the evolutionary concepts presented.

    In this study 5 exhibitions with evolutionary content in natural science museums in the Nordic countries have been analysed in order to understand how evolutionary tree diagrams are incorporated in these exhibitions, what design is used and what instructional support is available to the visitor. A multi-modal social semiotic approach was used, where 3 functional levels were analysed together in order to assess the meaning making potential of the evolutionary trees in these exhibitions; i) content, representational process and design. ii) instruction and interactivity. iii) spatial and organizational composition. The analyses show a wide range of communication strategies; reaching from the evolutionary tree diagrams having a pivotal role in the exhibition narrative to being placed purely in the margin with no explicit connection to the overall evolutionary content. The instructional support is in many cases lacking but is sometimes incorporated in the presentational text of specific parts of the evolutionary tree, and the design ranges from tree of life type iconic visualisations to highly abstract renderings. Overall the evolutionary tree as a visual tool to communicate important evolutionary concepts seems to be used to a high degree but important aspects in order to better afford scientific correct interpretations of the trees are sometimes lacking.

  • 1349. Skarpe, C.
    et al.
    Bergström, R.
    Makhabu, S.
    Rooke, T.
    Hytteborn, Håkan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Danell, K.
    Plant-Herbivore Interactions2014Inngår i: 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, s. 189-206Kapittel i bok, del av antologi (Fagfellevurdert)
    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.

  • 1350.
    Skoglund, Pontus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Reconstructing the Human Past using Ancient and Modern Genomes2013Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

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