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  • 1451.
    Schäfer, Martin A.
    et al.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland.
    Berger, David
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi. Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland.
    Rohner, Patrick T.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland.
    Kjaersgaard, Anders
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland.
    Bauerfeind, Stephanie S.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland.
    Guillaume, Frederic
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland.
    Fox, Charles W.
    Univ Kentucky, Dept Entomol, Lexington, KY 40506 USA.
    Blanckenhorn, Wolf U.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland.
    Geographic clines in wing morphology relate to colonization history in New World but not Old World populations of yellow dung flies2018Inngår i: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 72, nr 8, s. 1629-1644Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1452.
    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.

  • 1453.
    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.

  • 1454.
    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)
  • 1455. 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.

  • 1456. 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.

  • 1457.
    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.

  • 1458.
    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. 

  • 1459.
    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.

  • 1460.
    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.

  • 1461.
    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)
  • 1462.
    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.

  • 1463.
    Shefferson, Richard P.
    et al.
    Univ Tokyo, Org Programs Environm Sci, Meguro Ku, Tokyo, Japan.
    Kull, Tiiu
    Estonian Univ Life Sci, Tartu, Estonia.
    Hutchings, Michael J.
    Univ Sussex, Sch Life Sci, Brighton BN1 9QG, E Sussex, England.
    Selosse, Marc-Andre
    Sorbonne Univ, CNRS, Museum Natl Hist Nat, Inst Systemat Evolut Biodivers ISYEB,EPHE, 57 Rue Cuvier,CP39, F-75005 Paris, France;Univ Gdansk, Dept Plant Taxon & Nat Conservat, Gdansk, Poland.
    Jacquemyn, Hans
    Katholieke Univ Leuven, Dept Biol, Leuven, Belgium.
    Kellett, Kimberly M.
    Univ Georgia, Odum Sch Ecol, Athens, GA 30602 USA.
    Menges, Eric S.
    Archbold Biol Stn, Venus, FL USA.
    Primack, Richard B.
    Boston Univ, Dept Biol, 5 Cummington St, Boston, MA 02215 USA.
    Tuomi, Juha
    Univ Turku, Dept Biol, Turku, Finland.
    Alahuhta, Kirsi
    Univ Oulu, Dept Ecol & Genet, Oulu, Finland.
    Hurskainen, Sonja
    Univ Oulu, Dept Ecol & Genet, Oulu, Finland.
    Alexander, Helen M.
    Univ Kansas, Dept Ecol & Evolutionary Biol, Lawrence, KS 66045 USA.
    Anderson, Derek S.
    Dept Nat Resources, St Paul, MN USA.
    Brys, Rein
    Res Inst Nat & Forest, Brussels, Belgium.
    Brzosko, Emilia
    Univ Bialystok, Inst Biol, Bialystok, Poland.
    Dostalik, Slavomir
    Gregg, Katharine
    West Virginia Wesleyan Coll, Dept Biol, Buckhannon, WV USA.
    Ipser, Zdenek
    Univ South Bohemia, Fac Sci, Dept Biol Ecosyst, Ceske Budejovice, Czech Republic.
    Jakalaniemi, Anne
    Univ Oulu, Dept Ecol & Genet, Oulu, Finland.
    Jersakova, Jana
    Univ South Bohemia, Fac Sci, Dept Biol Ecosyst, Ceske Budejovice, Czech Republic.
    Kettle, W. Dean
    Univ Kansas, Kansas Biol Survey, Lawrence, KS USA.
    McCormick, Melissa K.
    Smithsonian Environm Res Ctr, POB 28, Edgewater, MD 21037 USA.
    Mendoza, Ana
    Univ Nacl Autonoma Mexico, Inst Ecol, Ciudad Univ, Mexico City, DF, Mexico.
    Miller, Michael T.
    LGL Ltd, Sidney, BC, Canada.
    Moen, Asbjorn
    NTNU Univ Museum, Dept Nat Hist, Trondheim, Norway.
    Oien, Dag-Inge
    NTNU Univ Museum, Dept Nat Hist, Trondheim, Norway.
    Puttsepp, Ulle
    Estonian Univ Life Sci, Tartu, Estonia.
    Roy, Melanie
    Univ Paul Sabatier, CNRS, Lab Evolut & Divers Biol, Toulouse, France.
    Sather, Nancy
    Dept Nat Resources, St Paul, MN USA.
    Sletvold, Nina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Stipkova, Zuzana
    Czech Acad Sci, Global Change Res Inst, Brno, Czech Republic.
    Tali, Kadri
    Estonian Univ Life Sci, Tartu, Estonia.
    Warren, Robert J., II
    SUNY Buffalo State, Dept Biol, Buffalo, NY USA.
    Whigham, Dennis F.
    Smithsonian Environm Res Ctr, POB 28, Edgewater, MD 21037 USA.
    Drivers of vegetative dormancy across herbaceous perennial plant species2018Inngår i: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 21, nr 5, s. 724-733Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1464.
    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
  • 1465. 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)
  • 1466.
    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.

  • 1467. 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)
  • 1468.
    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.

  • 1469.
    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.

  • 1470.
    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.

  • 1471.
    Silva, C. N. S.
    et al.
    Univ Helsinki, Dept Biosci, Metapopulat Res Ctr, Helsinki, Finland;James Cook Univ, Coll Marine & Environm Sci, Ctr Sustainable Trop Fisheries & Aquaculture, Townsville, Qld, Australia.
    McFarlane, S. Eryn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Hagen, I. J.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Ronnegard, L.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden;Dalarna Univ, Sch Technol & Business Studies, Falun, Sweden.
    Billing, A. M.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Kvalnes, T.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Kemppainen, P.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Ronning, B.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Ringsby, T. H.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Saether, B-E
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Qvarnström, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Ellegren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Jensen, H.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Husby, A.
    Univ Helsinki, Dept Biosci, Metapopulat Res Ctr, Helsinki, Finland;Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Insights into the genetic architecture of morphological traits in two passerine bird species2017Inngår i: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 119, nr 3, s. 197-205Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1472.
    Silva, Willian T. A. F.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Non-genetic processes in development and heredity2018Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

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

  • 1473.
    Silva, Willian T. A. F.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Jolly, Cécile
    Alavioon, Ghazal
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Kiehl, Berrit
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Immler, Simone
    Social environment of fathers affects gene expression patterns in early offspringManuskript (preprint) (Annet vitenskapelig)
  • 1474.
    Silva, Willian T. A. F.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Otto, Sarah P.
    Immler, Simone
    Evolution of small RNA production under fluctuating environmental conditionsManuskript (preprint) (Annet vitenskapelig)
  • 1475.
    Silva, Willian T. A. F.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Sáez-Espinosa, Paula
    Torrijo-Boix, Stéphanie
    Romero, Alejandro
    Devaux, Caroline
    Durieux, Mathilde
    Gómez-Torres, María José
    Immler, Simone
    The effects of male social environment on sperm phenotype and genome integrityManuskript (preprint) (Annet vitenskapelig)
  • 1476.
    Sirkiä, Päivi M
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    McFarlane, S. Eryn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Jones, William
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Wheatcroft, David
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Ålund, Murielle
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Rybinski, Jakub
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Qvarnström, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Climate-driven build-up of temporal isolation within a recently formed avian hybrid zone.2018Inngår i: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 72, nr 2, s. 363-374Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1477.
    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)
  • 1478.
    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).

  • 1479.
    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.

  • 1480. 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.].

  • 1481.
    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.
    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.

  • 1482. 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.

  • 1483.
    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.

  • 1484.
    Skoglund, Pontus
    et al.
    Stockholms universitet, Humanistiska fakulteten, Institutionen för arkeologi och antikens kultur. Harvard Medical School, USA; Broad Institute of Harvard and MIT, USA.
    Ersmark, Erik
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen. Swedish Museum of Natural History, Sweden.
    Palkopoulou, Eleftheria
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen. Swedish Museum of Natural History, Sweden.
    Dalen, Love
    Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds2015Inngår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 25, nr 11, s. 1515-1519Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The origin of domestic dogs is poorly understood [1-15], with suggested evidence of dog-like features in fossils that predate the Last Glacial Maximum [6, 9, 10, 14, 16] conflicting with genetic estimates of a more recent divergence between dogs and worldwide wolf populations [13, 15, 17-19]. Here, we present a draft genome sequence from a 35,000 year-old wolf from the Taimyr Peninsula in northern Siberia. We find that this individual belonged to a population that diverged from the common ancestor of present-day wolves and dogs very close in time to the appearance of the domestic dog lineage. We use the directly dated ancient wolf genome to recalibrate the molecular timescale of wolves and dogs and find that the mutation rate is substantially slower than assumed by most previous studies, suggesting that the ancestors of dogs were separated from present-day wolves before the Last Glacial Maximum. We also find evidence of introgression from the archaic Taimyr wolf lineage into present-day dog breeds from northeast Siberia and Greenland, contributing between 1.4% and 27.3% of their ancestry. This demonstrates that the ancestry of present-day dogs is derived from multiple regional wolf populations.

  • 1485.
    Skoglund, Pontus
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Jakobsson, Mattias
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Archaic human ancestry in East Asia2011Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 108, nr 45, s. 18301-18306Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1486.
    Skoglund, Pontus
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Malmstrom, Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Omrak, Ayca
    Raghavan, Maanasa
    Valdiosera, Cristina
    Günther, Torsten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Hall, Per
    Tambets, Kristiina
    Parik, Jueri
    Sjogren, Karl-Goran
    Apel, Jan
    Willerslev, Eske
    Stora, Jan
    Gotherstrom, Anders
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers2014Inngår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 344, nr 6185, s. 747-750Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1487. Sköld, H. N.
    et al.
    Amundsen, T.
    Svensson, P. Andreas
    Mayer, I.
    Bjelvenmark, J.
    Forsgren, E.
    Hormonal regulation of female nuptial coloration in a fish2008Inngår i: Hormones and Behavior, ISSN 0018-506X, E-ISSN 1095-6867, Vol. 54, nr 4, s. 549-556Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Physiological color change in camouflage and mating is widespread among fishes, but little is known about the regulation of such temporal changes in nuptial coloration and particularly concerning female coloration. To better understand regulation of nuptial coloration we investigated physiological color change in female two-spotted gobies (Gobiusculus flavescens). Females of this species develop an orange belly that acts as an ornament. The orange color is caused by the color of the gonads combined with the chromathophore based pigmentation and transparency of the skin. Often during courtship and female-female competition, a rapid increase in orange coloration, in combination with lighter sides and back that increases skin and body transparency, gives the belly an intense 'glowing' appearance. To understand how this increased orange coloration can be regulated we analysed chromatic and transparency effects of neurohumoral agents on abdominal skin biopsies in vitro. We found prolactin and alpha-melanocyte stimulating hormone (MSH) to increase orange coloration of the skin. By contrast, melatonin and noradrenaline increased skin transparency, but had a negative effect on orange coloration. However, mixtures of melatonin and MSH, or melatonin and prolactin, increased both orange coloration and transparency. This effect mimics the chromatic 'glow' effect that commonly takes place during courtship and intra sexual aggression. Notably, not only epidermal chromatophores but also internal chromatophores lining the peritoneum responded to hormone treatments. There were no chromatic effects of the sex steroids 17 beta-estradiol, testosterone or 11-ketotestosterone. We hypothesize that similar modulation of nuptial coloration by multiple hormones may be widespread in nature. (C) 2008 Elsevier Inc. All rights reserved.

  • 1488.
    Sletvold, Nina
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Trunschke, Judith
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Smit, Mart
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Verbeek, Jeffrey
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Ågren, Jon
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Strong pollinator-mediated selection for increased flower brightness and contrast in a deceptive orchid2016Inngår i: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 70, nr 3, s. 716-724Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1489.
    Sletvold, Nina
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Ågren, Jon
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Uppsala Univ, EBC, Dept Ecol & Genet, Plant Ecol & Evolut, SE-75236 Uppsala, Sweden..
    Nonlinear costs of reproduction in a long-lived plant2015Inngår i: Journal of Ecology, ISSN 0022-0477, E-ISSN 1365-2745, Vol. 103, nr 5, s. 1205-1213Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1490.
    Sletvold, Nina
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Ågren, Jon
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    There is More to Pollinator-Mediated Selection than Pollen Limitation2014Inngår i: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 68, nr 7, s. 1907-1918Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1491.
    Slove, Jessica
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Eriksson, Torsten
    Department of Biodiversity informatics, Swedish Museum of Natural History.
    Nylin, Sören
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Janz, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Exploring a complex trait - the effect of larval feeding ability and unequal transition costs on the dynamics ofhost range evolution in two groups of related butterfliesManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Host plant use is a complex trait, better described as the combined outcome of many interrelated traits, such as female preference and larval ability to feed, grow and survive. The necessary co-adaptation of these traits would suggest that the host shifts should be difficult to accomplish. Still, even though a large-scale conservatism can be seen in most groups, frequent changes in host use are not uncommon, suggesting that under some circumstances adding new plants to the range might not be as difficult as one might expect. In a case study on two closelyr elated butterfly genera, we investigate the effect of unequal transition costs and of including available data on larval feeding ability as well as plants used in the field, and describe and compare the dynamics of host range evolution in these groups. We find that apparent independent colonisations are in many cases likely to be the result of non-independent processes such as multiple losses, recolonisation or parallel colonisations following some preadaptation. Host plants shifts and range expansions are likely important drivers of the exceptional diversity of herbivorousinsects. A better understanding of the dynamics of host range evolution will improve our understanding of the source of this diversity.

  • 1492.
    Smeds, Linnea
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Kawakami, Takeshi
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Burri, Reto
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Bolivar, Paulina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Husby, Arild
    Qvarnström, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Uebbing, Severin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Ellegren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes2014Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, s. 5448-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1493.
    Smeds, Linnea
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Qvarnström, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Ellegren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Direct estimate of the rate of germline mutation in a bird2016Inngår i: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 26, nr 9, s. 1211-1218Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1494. Smith, Felisa A
    et al.
    Boyer, Alison G
    Brown, James H
    Costa, Daniel P
    Dayan, Tamar
    Ernest, SK Morgan
    Evans, Alistair R
    Fortelius, Mikael
    Gittleman, John L
    Hamilton, Marcus J
    Harding, Larisa E
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Lintulaakso, Kari
    Lyons, S Kathleen
    McCain, Christy
    Okie, Jordan G
    Saarinen, Juha J
    Sibly, Richard M
    Stephens, Patrick R
    Theodor, Jessica
    Uhen, Mark D
    The evolution of maximum body size of terrestrial mammals2010Inngår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 330, nr 6008, s. 1216-1219Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The extinction of dinosaurs at the Cretaceous/Paleogene (K/Pg) boundary was the seminal event that opened the door for the subsequent diversification of terrestrial mammals. Our compilation of maximum body size at the ordinal level by sub-epoch shows a near-exponential increase after the K/Pg. On each continent, the maximum size of mammals leveled off after 40 million years ago and thereafter remained approximately constant. There was remarkable congruence in the rate, trajectory, and upper limit across continents, orders, and trophic guilds, despite differences in geological and climatic history, turnover of lineages, and ecological variation. Our analysis suggests that although the primary driver for the evolution of giant mammals was diversification to fill ecological niches, environmental temperature and land area may have ultimately constrained the maximum size achieved.

  • 1495.
    Sniegula, Szymon
    et al.
    Polish Acad Sci, Inst Nat Conservat, Dept Ecosyst Conservat, Al Mickiewicza 33, PL-31120 Krakow, Poland.
    Golab, Maria J.
    Polish Acad Sci, Inst Nat Conservat, Dept Ecosyst Conservat, Al Mickiewicza 33, PL-31120 Krakow, Poland.
    Drobniak, Szymon M.
    Jagiellonian Univ, Inst Environm Sci, Populat Ecol Grp, Krakow, Poland.
    Johansson, Frank
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    The genetic variance but not the genetic covariance of life-history traits changes towards the north in a time-constrained insect2018Inngår i: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 31, nr 6, s. 853-865Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1496.
    Sniegula, Szymon
    et al.
    Polish Acad Sci, Inst Nat Conservat, Dept Ecosyst Conservat, Al Mickiewicza 33, PL-31120 Krakow, Poland..
    Golab, Maria J.
    Polish Acad Sci, Inst Nat Conservat, Dept Ecosyst Conservat, Al Mickiewicza 33, PL-31120 Krakow, Poland..
    Johansson, Frank
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Cannibalism and activity rate in larval damselflies increase along a latitudinal gradient as a consequence of time constraints2017Inngår i: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 17, artikkel-id 167Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 1497. Sniegula, Szymon
    et al.
    Nilsson-Örtman, Viktor
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Johansson, Frank
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Growth Pattern Responses to Photoperiod across Latitudes in a Northern Damselfly2012Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, nr 9, s. e46024-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Latitudinal clines in temperature and seasonality impose strong seasonal constraints on ectotherms. Studies of population differentiation in phenotypic plasticity of life history traits along latitudinal gradients are important for understanding how organisms have adapted to seasonal environments and predict how they respond to climate changes. Such studies have been scarce for species with a northern distribution. Methodology/Principle Finding: Larvae of the northern damselfly Coenagrion johanssoni originating from semivoltine central, partivoltine northern, and partivoltine northernmost Swedish populations were reared in the laboratory. To investigate whether larvae use photoperiodic cues to induce compensatory growth along this latitudinal gradient, larvae were reared under two different photoperiods corresponding to a northern and southern latitude. In addition, field adult size was assessed to test the strength of possible compensatory growth mechanisms under natural conditions and hatchling size was measured to test for maternal effects. We hypothesized that populations originating from lower latitudes would be more time constrained than high-latitude populations because they have a shorter life cycle. The results showed that low-latitude populations had higher growth rates in summer/fall. In general northern photoperiods induced higher growth rates, but this plastic response to photoperiod was strongest in the southernmost populations and negligible in the northernmost population. During spring, central populations grew faster under the southern rather than the northern photoperiod. On the other hand, northern and northernmost populations did not differ between each other and grew faster in the northern rather than in the southern photoperiod. Field sampled adults did not differ in size across the studied regions. Conclusion/Significance: We found a significant differentiation in growth rate across latitudes and latitudinal difference in growth rate response to photoperiod. Importantly, growth responses measured at a single larval developmental stage in one season may not always generalize to other developmental stages or seasons.

  • 1498. Sniegula, Szymon
    et al.
    Prus, Monika A.
    Golab, Maria J.
    Outomuro, David
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Do males with higher mating success invest more in armaments?: An across-populations study in damselflies2017Inngår i: Ecological Entomology, ISSN 0307-6946, E-ISSN 1365-2311, Vol. 42, nr 4, s. 526-530Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

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

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

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

  • 1499.
    Sokolovskis, Kristaps
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Lund University, MEEL, Bensch group.
    Genetics of bird migration: Study on East Siberian willow warblers (Phylloscopus trochilus)2017Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Abstract [en]

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

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

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

  • 1500. Soliani, Carolina
    et al.
    Tsuda, Yoshiaki
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Bagnoli, Francesca
    Gallo, Leonardo A.
    Vendramin, Giovanni G.
    Marchelli, Paula
    Halfway encounters: Meeting points of colonization routes among the southern beeches Nothofagus pumilio and N. antarctica2015Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 85, s. 197-207Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

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