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  • 1. Alvarez-Castro, J.M.
    et al.
    Carlborg, Ö.
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics.
    Estimation and interpretation of genetic effects with epistasis using the NOIA model2012In: Quantitative trait loci (QTL): Methods and Protocols / [ed] Scott A. Rifkin, Humana Press, 2012, p. 191-204Chapter in book (Other academic)
    Abstract [en]

    We introduce this communication with a brief outline of the historical landmarks in genetic modeling, especially concerning epistasis. Then, we present methods for the use of genetic modeling in QTL analyses. In particular, we summarize the essential expressions of the natural and orthogonal interactions (NOIA) model of genetic effects. Our motivation for reviewing that theory here is twofold. First, this review presents a digest of the expressions for the application of the NOIA model, which are often mixed with intermediate and additional formulae in the original articles. Second, we make the required theory handy for the reader to relate the genetic concepts to the particular mathematical expressions underlying them. We illustrate those relations by providing graphical interpretations and a diagram summarizing the key features for applying genetic modeling with epistasis in comprehensive QTL analyses. Finally, we briefly review some examples of the application of NOIA to real data and the way it improves the interpretability of the results.

  • 2. Armbruster, W. S.
    Pélabon, C
    Pérez-Barrales, R.
    Maad, Johanne
    Department of Biology, NTNU, NO-7491, Trondheim, Norway.
    The adaptive accuracy of flowers: Measurement and microevolutionary patterns2009In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 103, no 9, p. 1529-1545Article in journal (Refereed)
  • 3. Besnier, Francois
    et al.
    Wahlberg, Per
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics.
    Ek, Weronika
    Andersson, Leif
    Siegel, Paul
    Carlborg, Örjan
    Fine mapping and replication of QTL in outbred chicken advanced intercross lines2011In: Genetics Selection Evolution, ISSN 0999-193X, E-ISSN 1297-9686, Vol. 43, article id 3Article in journal (Refereed)
    Abstract [en]

    Background: Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F2 populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL), the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL) are produced by repeated intercrossing of F2 animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature.

    Methods: We have produced a nine-generation AIL pedigree (n = 1529) from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F2 population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight.

    Results: Five of the nine QTL detected with the original F2 population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL.

    Conclusions: Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that the statistical methods we have developed to efficiently study outbred AIL populations will increase the number of organisms for which in-depth complex traits can be analyzed.

  • 4. Boberg, E.
    Jonsson, M.
    Maad, Johanne
    Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
    Ågren, J.
    Nilsson, L. A.
    Pollinator shifts and the evolution of spur length in the moth-pollinated orchid Platanthera bifolia2014In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 113, no 2, p. 267-275Article in journal (Refereed)
  • 5. Eriksson, Ronnie
    et al.
    Jobs, Magnus
    Dalarna University, School of Education, Health and Social Studies, Medical Science.
    Ekstrand, Charlotta
    Ullberg, Måns
    Hermann, Björn
    Landegren, Ulf
    Nilsson, Mats
    Blomberg, Jonas
    Multiplex and quantifiable detection of nucleic acid from pathogenic fungi using padlock probes, generic real-time PCR and specific suspension array readout2009In: Journal of Microbiological Methods, ISSN 0167-7012, E-ISSN 1872-8359, Vol. 78, no 2, p. 195-202Article in journal (Refereed)
    Abstract [en]

    A new concept for multiplex detection and quantification of microbes is here demonstrated on a range of infectious fungal species. Padlock probe methodology in conjunction with qPCR and Luminex™ technology was used for simultaneous detection of ten fungal species in one single experiment. By combining the multiplexing properties of padlock probes and Luminex™ detection with the well established quantitative characteristics of qPCR, quantitative microbe detection was done in 10-plex mode. A padlock probe is an oligonucleotide that via a ligation reaction forms circular DNA when hybridizing to specific target DNA. The region of the padlock probe that does not participate in target DNA hybridization contains generic primer sequences for amplification and a tag sequence for Luminex™ detection. This was the fundament for well performing multiplexing. Circularized padlock probes were initially amplified by rolling circle amplification (RCA), followed by a SybrGreen™ real time PCR which allowed an additive quantitative assessment of target DNA in the sample. Detection and quantification of amplified padlock probes were then done on color coded Luminex™ microspheres carrying anti-tag sequences. A novel technique, using labeled oligonucleotides to prevent reannealing of amplimers by covering the flanks of the address sequence, improved the signal to noise ratio in the detection step considerably. The method correctly detected fungi in a variety of clinical samples and offered quantitative information on fungal nucleic acid.

  • 6. Espeland, Marianne
    et al.
    Irestedt, Martin
    Johanson, Kjell Arne
    Akerlund, Monika
    Bergh, Jan-Erik
    Dalarna University, School of Education, Health and Social Studies, Biology.
    Kallersjo, Mari
    Dichlorvos exposure impedes extraction and amplification of DNA from insects in museum collections2010In: Frontiers in Zoology, ISSN 1742-9994, E-ISSN 1742-9994, Vol. 7, article id 2Article in journal (Refereed)
    Abstract [en]

    Background: The insecticides dichlorvos, paradichlorobenzene and naphthalene have been commonly used to eradicate pest insects from natural history collections. However, it is not known how these chemicals affect the DNA of the specimens in the collections. We thus tested the effect of dichlorvos, paradichlorobenzene and naphthalene on DNA of insects (Musca domestica) by extracting and amplifying DNA from specimens exposed to insecticides in two different concentrations over increasing time intervals. Results: The results clearly show that dichlorvos impedes both extraction and amplification of mitochondrial and nuclear DNA after relatively short time, whereas paradichlorobenzene and naphthalene do not. Conclusion: Collections treated with paradichlorobenzene and naphthalene, are better preserved concerning DNA, than those treated with dichlorvos. Non toxic pest control methods should, however, be preferred due to physical damage of specimens and putative health risks by chemicals.

  • 7. Gullstrand, Lennart
    et al.
    Nilsson, Johnny
    Gymnastik- och idrottshögskolan, GIH, Laboratoriet för biomekanik och motorisk kontroll (BMC).
    A new method for recording the temporal pattern of stride during treadmill running2009In: Sports Engineering, ISSN 1369-7072, E-ISSN 1460-2687, no 11, p. 195-200Article in journal (Refereed)
    Abstract [en]

    The aim of this study was to investigate the reliability of a new infrared light based method (IR40) for recording temporal stride patterns during treadmill running. The IR40 device, emitting a tight web of 40 infrared light beams 10 mm above the treadmill running surface, was compared to a previously validated electro-pneumatic contact shoe (CS) method while nine well-trained athletes ran at 2.8, 3.3, 3.9, 4.4, 5.0, and 5.6 m s−1. Disconnection and reconnection of the IR beams marked the stance phase. The sampling rate was 500 Hz for both methods. The stance phase duration was on average 11.5 (±8.4) ms longer with the IR40 than with the CS depending on earlier touch down (8.3 ± 6.2 ms) and delayed toe off (3.2 ± 5.3 ms) registrations. Significantly different stance phases were recorded between all velocities and for both methods. Thus, despite the fact that the IR40 systematically measured a somewhat longer stance phase duration than CS, the IR40 is nonetheless useful for temporal stride analysis during treadmill running.      

  • 8.
    Hernandez Velasco, Marco
    et al.
    Dalarna University, School of Technology and Business Studies, Energy Technology.
    Mattsson, Anders
    Dalarna University, School of Technology and Business Studies, Forest and Wood Technology.
    Light quality and intensity of light-emitting diodes during pre-cultivation of Picea abies (L.) Karst. and Pinus sylvestris L. seedlings - impact on growth performance, seedling quality and energy consumption2019In: Scandinavian Journal of Forest Research, ISSN 0282-7581, E-ISSN 1651-1891, Vol. 34, no 3, p. 159-177Article in journal (Refereed)
    Abstract [en]

    Three different LED lamps with continuous spectra were compared against commonly used fluorescent lights. The lamps were characterized by light output, energy consumption and spectral quality for plant growth. The biological effects of light quality were compared by pre-cultivating seedlings of Picea abies (L.) Karst. and Pinus sylvestris L. under each spectrum for 35 days in a growth chamber with controlled temperature, humidity and photoperiod. The seedlings were then transplanted and cultivated for one vegetation period at the nursery, then planted outdoors on a forest field trial and followed for three years. The seedlings showed similar growth performance for all spectra tested. LED lamps have several advantages to fluorescent light such as energy consumption, longer life span and adjustable light intensity. Regarding light intensity the effects on growth performance were studied for both species using the most promising LED spectra. The photosynthetically active radiation (PAR) was maintained at 50, 100, 200 and 400 mu mol m(-2) s(-1). Unlike energy consumption, seedling development did not display a linear relationship to light intensity. Instead, the results show an optimum light level between 100 and 200 mu mol m(-2) s(-1) for the shade tolerant Picea abies seedlings and a level of around 200 mu mol m(-2) s(-1) for the more shade intolerant Pinus sylvestris seedlings.

  • 9. Husby, Arild
    et al.
    Kawakami, Takeshi
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics. SLU.
    Smeds, Linnéa
    Ellegren, Hans
    Qvarnström, Anna
    Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait2015In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 282, no 1806Article in journal (Refereed)
    Abstract [en]

    Understanding the genetic basis of traits involved in adaptation is a major challenge in evolutionary biology but remains poorly understood. Here, we use genome-wide association mapping using a custom 50 k single nucleotide polymorphism (SNP) array in a natural population of collared flycatchers to examine the genetic basis of clutch size, an important life-history trait in many animal species. We found evidence for an association on chromosome 18 where one SNP significant at the genome-wide level explained 3.9% of the phenotypic variance. We also detected two suggestive quantitative trait loci (QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were generally weak and not significant, although there was some indication of a sex-by-genotype interaction for lifetime reproductive success at the suggestive QTL on chromosome 26. This implies that sexual antagonism may play a role in maintaining genetic variation at this QTL. Our findings provide candidate regions for a classic avian life-history trait that will be useful for future studies examining the molecular and cellular function of, as well as evolutionary mechanisms operating at, these loci.

  • 10.
    Johansson, Sverker
    Högskolan för lärande och kommunikation, Högskolan i Jönköping, HLK, Ämnesforskning.
    Origins of language: Constraints on hypotheses2005Book (Other academic)
    Abstract [en]

    Sverker Johansson has written an unusual book on language origins, with its emphasis on empirical evidence rather than theory-building. This is a book for the student or researcher who prefers solid data and well-supported conclusions, over speculative scenarios. Much that has been written on the origins of language is characterized by hypothesizing largely unconstrained by evidence. But empirical data do exist, and the purpose of this book is to integrate and review the available evidence from all relevant disciplines, not only linguistics but also, e.g., neurology, primatology, paleoanthropology, and evolutionary biology. The evidence is then used to constrain the multitude of scenarios for language origins, demonstrating that many popular hypotheses are untenable. Among the issues covered: (1) Human evolutionary history, (2) Anatomical prerequisites for language, (3) Animal communication and ape "language", (4) Mind and language, (5) The role of gesture, (6) Innateness, (7) Selective advantage of language, (8) Proto-language.

  • 11.
    Johansson, Sverker
    Högskolan för lärande och kommunikation, Högskolan i Jönköping, HLK, Ämnesforskning.
    Sagan om hur livet kom till Jorden1996Other (Other (popular science, discussion, etc.))
  • 12.
    Johansson, Sverker
    Högskolan för lärande och kommunikation, Högskolan i Jönköping, HLK, Ämnesforskning.
    The Monkey Trail: On the Fossil Record of Non-Human Primates1999Report (Other (popular science, discussion, etc.))
  • 13.
    Johansson, Sverker
    Högskolan i Jönköping, Högskolan för lärande och kommunikation.
    What constraints does animal communication place on human language origins?2010Conference paper (Other academic)
  • 14.
    Johansson, Sverker
    Högskolan för lärande och kommunikation, Högskolan i Jönköping, HLK, Ämnesforskning.
    Är kreationismen vetenskapligt hållbar?1992In: Svensk Teologisk Kvartalsskrift, no 68, p. 19-28Article in journal (Refereed)
  • 15. Lankinen, Å.
    et al.
    Maad, Johanne
    orwegian Univ Sci & Technol, Dept Biol, N-7491 Trondheim, Norway; Uppsala Univ, Dept Ecol Evolut & Plant Ecol, S-75236 Uppsala, Sweden.
    Armbruster, W. S.
    Pollen-tube growth rates in Collinsia heterophylla (Plantaginaceae): One-donor crosses reveal heritability but no effect on sporophytic-offspring fitness.2009In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 103, no 6, p. 941-950Article in journal (Refereed)
  • 16.
    Maad, Johanne
    Norwegian Univ Sci & Technol, Dept Biol, NO-7491 Trondheim, Norway; Uppsala Univ, EBC, Dept Plant Ecol, SE-75236 Uppsala, Sweden.
    Fenster, C. B.
    Floral size variation in Campanula rotundifolia (Campanulaceae) along altitudinal gradients: patterns and possible selective mechanisms2013In: Nordic Journal of Botany, ISSN 0107-055X, E-ISSN 1756-1051, Vol. 31, no 3, p. 361-371Article in journal (Refereed)
  • 17.
    Maad, Johanne
    Norwegian Univ Sci & Technol, Dept Biol, NO-7491 Trondheim, Norway.
    Incidence of geitonogamy differs between two populations in the hawkmoth-pollinated Platanthera bifolia (Orchidaceae)2004In: Canadian Journal of Botany, ISSN 0008-4026, E-ISSN 1480-3305, Vol. 82, no 11, p. 1586-1593Article in journal (Refereed)
  • 18.
    Maad, Johanne
    Norwegian Univ Sci & Technol, Dept Biol, NO-7491 Trondheim, Norway.
    On the mechanism of floral shifts in speciation: gained pollination efficiency from tongue- to eye-attachment of pollinia in Platanthera (Orchidaceae)2004In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 83, no 4, p. 481-495Article in journal (Refereed)
  • 19.
    Maad, Johanne
    Uppsala Univ, Evolutionary Biol Ctr, Dept Systemat Bot, Norbyvagen 18D, SE-75236 Uppsala, Sweden.
    Phenotypic selection in hawkmoth-pollinated Platanthera bifolia: Targets and fitness surfaces2000In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 54, no 1, p. 112-123Article in journal (Refereed)
  • 20.
    Maad, Johanne
    Uppsala universitet, Institutionen för evolutionsbiologi.
    Selection and Floral Evolution in Platanthera bifolia and P. chlorantha (Orchidaceae)2002Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Natural selection mediated by pollinators has influenced the evolution of floral diversity of the flowering plants (angiosperms). The scope of this thesis was to study: 1) phenotypic selection, 2) mating systems, and 3) floral shifts involved in plant speciation. Model plant species were Platanthera bifolia and P. chlorantha (Orchidaceae). These orchids are moth-pollinated, strictly co-sexual (bisexual flowers), and produce a spike that displays 10-20 white flowers.

    I explored the influence of characters on plant fitness by using multiple linear regressions. Pollen removal (male fitness) and fruit set (female fitness) increased with more flowers per plant in three P. bifolia populations. There was selection towards longer spurs in a dry year when average spur length was shorter than in normal-wet years. Female function was sensitive to drought, which enabled an application of the male function hypothesis of floral evolution (Bateman's principle). The results show that selection may vary between populations, years, and sex-functions.

    I examined inbreeding by estimating levels of geitonogamy (self-pollination between flowers of an individual) with an emasculation method in two P. bifolia populations. Geitonogamy did not vary with inflorescence size. Levels of geitonogamy was 20-40% in the smaller, but non-significant in the larger population. This may relate to lower number of possible mates and pollinator activity in the smaller population.

    Platanthera bifolia exhibits the ancestral character state of tongue-attachment of pollinia on the pollinator. Its close relative P. chlorantha attaches its pollinia onto the pollinator's eyes. To explore the mechanism of a floral shift, pollination efficiency and speed was compared between the two species. The results showed no differences in pollination efficiency, but P. chlorantha had faster pollen export and import. Efficiency of pollination in terms of speed may cause floral shifts, and thus speciation.

  • 21.
    Maad, Johanne
    et al.
    Norwegian Univ Sci & Technol, Dept Biol, NO-7491 Trondheim, Norway.
    Alexandersson, R.
    Variable selection in Platanthera bifolia (Orchidaceae): phenotypic selection differed between sex functions in a drought year2004In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 17, no 3, p. 642-650Article in journal (Refereed)
  • 22. Marjanovic, Jovana
    et al.
    Mulder, Han A
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics. SLU.
    Bijma, Piter
    Modelling the co-evolution of indirect genetic effects and inherited variability2018In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 121, p. 631-647Article in journal (Refereed)
    Abstract [en]

    When individuals interact, their phenotypes may be affected not only by their own genes but also by genes in their social partners. This phenomenon is known as Indirect Genetic Effects (IGEs). In aquaculture species and some plants, however, competition not only affects trait levels of individuals, but also inflates variability of trait values among individuals. In the field of quantitative genetics, the variability of trait values has been studied as a quantitative trait in itself, and is often referred to as inherited variability. Such studies, however, consider only the genetic effect of the focal individual on trait variability and do not make a connection to competition. Although the observed phenotypic relationship between competition and variability suggests an underlying genetic relationship, the current quantitative genetic models of IGE and inherited variability do not allow for such a relationship. The lack of quantitative genetic models that connect IGEs to inherited variability limits our understanding of the potential of variability to respond to selection, both in nature and agriculture. Models of trait levels, for example, show that IGEs may considerably change heritable variation in trait values. Currently, we lack the tools to investigate whether this result extends to variability of trait values. Here we present a model that integrates IGEs and inherited variability. In this model, the target phenotype, say growth rate, is a function of the genetic and environmental effects of the focal individual and of the difference in trait value between the social partner and the focal individual, multiplied by a regression coefficient. The regression coefficient is a genetic trait, which is a measure of cooperation; a negative value indicates competition, a positive value cooperation, and an increasing value due to selection indicates the evolution of cooperation. In contrast to the existing quantitative genetic models, our model allows for co-evolution of IGEs and variability, as the regression coefficient can respond to selection. Our simulations show that the model results in increased variability of body weight with increasing competition. When competition decreases, i.e., cooperation evolves, variability becomes significantly smaller. Hence, our model facilitates quantitative genetic studies on the relationship between IGEs and inherited variability. Moreover, our findings suggest that we may have been overlooking an entire level of genetic variation in variability, the one due to IGEs.

  • 23. Mulder, Han A.
    et al.
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics.
    Fikse, W Freddy
    Veerkamp, R F
    Strandberg, E
    Estimation of genetic variance for macro- and micro-environmental sensitivity using double hierarchical generalized linear models2013In: Genetics Selection Evolution, ISSN 0999-193X, E-ISSN 1297-9686, Vol. 45, article id 23Article in journal (Refereed)
    Abstract [en]

    Background: Genetic variation for environmental sensitivity indicates that animals are genetically different in their response to environmental factors. Environmental factors are either identifiable (e.g. temperature) and called macro-environmental or unknown and called micro-environmental. The objectives of this study were to develop a statistical method to estimate genetic parameters for macro- and micro-environmental sensitivities simultaneously, to investigate bias and precision of resulting estimates of genetic parameters and to develop and evaluate use of Akaike’s information criterion using h-likelihood to select the best fitting model.

    Methods: We assumed that genetic variation in macro- and micro-environmental sensitivities is expressed as genetic variance in the slope of a linear reaction norm and environmental variance, respectively. A reaction norm model to estimate genetic variance for macro-environmental sensitivity was combined with a structural model for residual variance to estimate genetic variance for micro-environmental sensitivity using a double hierarchical generalized linear model in ASReml. Akaike’s information criterion was constructed as model selection criterion using approximated h-likelihood. Populations of sires with large half-sib offspring groups were simulated to investigate bias and precision of estimated genetic parameters.

    Results: Designs with 100 sires, each with at least 100 offspring, are required to have standard deviations of estimated variances lower than 50% of the true value. When the number of offspring increased, standard deviations of estimates across replicates decreased substantially, especially for genetic variances of macro- and micro-environmental sensitivities. Standard deviations of estimated genetic correlations across replicates were quite large (between 0.1 and 0.4), especially when sires had few offspring. Practically, no bias was observed for estimates of any of the parameters. Using Akaike’s information criterion the true genetic model was selected as the best statistical model in at least 90% of 100 replicates when the number of offspring per sire was 100. Application of the model to lactation milk yield in dairy cattle showed that genetic variance for micro- and macro-environmental sensitivities existed.

    Conclusion: The algorithm and model selection criterion presented here can contribute to better understand genetic control of macro- and micro-environmental sensitivities. Designs or datasets should have at least 100 sires each with 100 offspring.

  • 24. Nelson, Ronald M
    et al.
    Temnykh, Svetlana V
    Johnson, Jennifer L
    Kharlamova, Anastasiya V
    Vladimirova, Anastasiya V
    Shepeleva, Darya V
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics.
    Trut, Lyudmila N
    Carlborg, Örjan
    Kukekova, Anna V
    Genetics of interactive behavior in silver foxes (Vulpes vulpes)2017In: Behavior Genetics, ISSN 0001-8244, E-ISSN 1573-3297, Vol. 47, no 1, p. 88-101Article in journal (Refereed)
    Abstract [en]

    Individuals involved in a social interaction exhibit different behavioral traits that, in combination, form the individual's behavioral responses. Selectively bred strains of silver foxes (Vulpes vulpes) demonstrate markedly different behaviors in their response to humans. To identify the genetic basis of these behavioral differences we constructed a large F2 population including 537 individuals by cross-breeding tame and aggressive fox strains. 98 fox behavioral traits were recorded during social interaction with a human experimenter in a standard four-step test. Patterns of fox behaviors during the test were evaluated using principal component (PC) analysis. Genetic mapping identified eight unique significant and suggestive QTL. Mapping results for the PC phenotypes from different test steps showed little overlap suggesting that different QTL are involved in regulation of behaviors exhibited in different behavioral contexts. Many individual behavioral traits mapped to the same genomic regions as PC phenotypes. This provides additional information about specific behaviors regulated by these loci. Further, three pairs of epistatic loci were also identified for PC phenotypes suggesting more complex genetic architecture of the behavioral differences between the two strains than what has previously been observed.

  • 25.
    Nilsson, Johnny
    et al.
    Gymnastik- och idrottshögskolan, GIH, Laboratoriet för biomekanik och motorisk kontroll (BMC).
    Tinmark, Fredrik
    Gymnastik- och idrottshögskolan, GIH, Laboratoriet för biomekanik och motorisk kontroll (BMC).
    Halvorsen, Kjartan
    Arndt, Anton
    Gymnastik- och idrottshögskolan, GIH, Laboratoriet för biomekanik och motorisk kontroll (BMC).
    Kinematic, kinetic and electromyographic adaptation to speed and resistance in double poling cross country skiing2013In: European Journal of Applied Physiology, ISSN 1439-6319, E-ISSN 1439-6327, Vol. 113, no 6, p. 1385-1394Article in journal (Refereed)
    Abstract [en]

    This study incorporated variations in speed and the horizontal resistance acting upon elite female skiers during double poling (DP) on a treadmill and specifically analyzed biomechanical adaptations to these variations. Whole body kinematics and pole force data were recorded and used to calculate the moment of force acting on the shoulder and elbow joints. Data were obtained with a 3D optoelectronic system using reflective markers at given anatomical landmarks. Forces along the long axis of the right pole were measured with a piezoelectric force transducer. Surface electrodes were used to record EMG activity in the rectus femoris, rectus abdominis, latissimus dorsi and triceps brachii muscles. In a first set of recordings, the participants double poled with zero elevation at five different speeds from 8 to 17 km h−1. In a second set of recordings, horizontal resistance was added by weights (0.4–1.9 kg) attached to a pulley system pulling the skier posteriorly during DP at 14 km h−1. Results showed increasing relative duration of the thrust phase with increasing resistance, but not with speed. Significant kinematic differences occurred with increase in both speed and resistance. The mean (±SD) horizontal force components ranged between 1.7 (±1.3) and 2.8 (±1.1) percent (%) bodyweight (BW) in the speed adaptation and 3.1 (±0.6) and 4.0 (±1.3) % BW in the adaptation to horizontal resistance. Peak muscle activity showed a central to peripheral (proximo-distal) activation sequence. The temporal cycle phase pattern in the adaptation to speed and horizontal resistance differed.

  • 26.
    Nyberg, Roger G.
    et al.
    Dalarna University, School of Technology and Business Studies, Computer Engineering. School of Engineering and the Built Environment, Edinburgh Napier University, EH10 5DT Edinburgh, UK.
    Gupta, Narendra K.
    School of Engineering and the Built Environment, Edinburgh Napier University, EH10 5DT Edinburgh, UK.
    Yella, Siril
    Dalarna University, School of Technology and Business Studies, Computer Engineering.
    Dougherty, Mark
    Dalarna University, School of Technology and Business Studies, Computer Engineering.
    Monitoring vegetation on railway embankments: supporting maintenance decisions2013In: Proceedings of the 2013 International Conference on Ecology and Transportation, 2013, p. 1-18Conference paper (Refereed)
    Abstract [en]

    The national railway administrations in Scandinavia, Germany, and Austria mainly resort to manual inspections to control vegetation growth along railway embankments. Manually inspecting railways is slow and time consuming. A more worrying aspect concerns the fact that human observers are often unable to estimate the true cover of vegetation on railway embankments. Further human observers often tend to disagree with each other when more than one observer is engaged for inspection. Lack of proper techniques to identify the true cover of vegetation even result in the excess usage of herbicides; seriously harming the environment and threating the ecology. Hence work in this study has investigated aspects relevant to human variationand agreement to be able to report better inspection routines. This was studied by mainly carrying out two separate yet relevant investigations.First, thirteen observers were separately asked to estimate the vegetation cover in nine imagesacquired (in nadir view) over the railway tracks. All such estimates were compared relatively and an analysis of variance resulted in a significant difference on the observers’ cover estimates (p<0.05). Bearing in difference between the observers, a second follow-up field-study on the railway tracks was initiated and properly investigated. Two railway segments (strata) representingdifferent levels of vegetationwere carefully selected. Five sample plots (each covering an area of one-by-one meter) were randomizedfrom each stratumalong the rails from the aforementioned segments and ten images were acquired in nadir view. Further three observers (with knowledge in the railway maintenance domain) were separately asked to estimate the plant cover by visually examining theplots. Again an analysis of variance resulted in a significant difference on the observers’ cover estimates (p<0.05) confirming the result from the first investigation.The differences in observations are compared against a computer vision algorithm which detects the "true" cover of vegetation in a given image. The true cover is defined as the amount of greenish pixels in each image as detected by the computer vision algorithm. Results achieved through comparison strongly indicate that inconsistency is prevalent among the estimates reported by the observers. Hence, an automated approach reporting the use of computer vision is suggested, thus transferring the manual inspections into objective monitored inspections

  • 27.
    Ohlsson, Anna B.
    et al.
    AlbaNova Univ Ctr, Dept Biochem, Royal Inst Technol, KTH,Sch Biotechnol, SE-10691 Stockholm, Sweden.
    Segerfeldt, Patrik
    Royal Inst Technol, KTH, Sch Chem Sci & Engn, Dept Chem, Ecol Chem Grp, SE-10044 Stockholm, Sweden.
    Lindström, Anders
    Dalarna University, School of Technology and Business Studies, Forest and Wood Technology.
    Borg-Karlson, Anna-Karin
    Royal Inst Technol, KTH, Sch Chem Sci & Engn, Dept Chem,Ecol Chem Grp, SE-10044 Stockholm, Sweden ; Univ Tartu, Inst Technol, EE-50090 Tartu, Estonia.
    Berglund, Torkel
    AlbaNova Univ Ctr, Dept Biochem, Royal Inst Technol, KTH,Sch Biotechnol, SE-10691 Stockholm, Sweden.
    UV-B exposure of indoor-grown Picea abies seedlings causes an epigenetic effect and selective emission of terpenes2013In: Zeitschrift für Naturforschung C - A Journal of Biosciences, ISSN 0939-5075, E-ISSN 1865-7125, Vol. 68, no 3-4, p. 139-147Article in journal (Refereed)
    Abstract [en]

    Abstract: Terpenoids are involved in various defensive functions in plants, especially conifers. Epigenetic mechanisms, for example DNA methylation, can influence plant defence systems. The purpose of the present study was to investigate the influence of UV-B exposure on the release of terpenoids from spruce seedlings and on needle DNA methylation. Ten-week-old seedlings grown indoors were exposed to UV-B radiation during 4 h, and the volatile compounds emitted from the seedlings were analysed. Analysis of the volatiles 1, 3, and 22 d after this UV-B exposure showed that bornyl acetate, borneol, myrcene, and limonene contents increased during the first 3 days, while at day 22 the level of emission had returned to the control level. UV-B exposure decreased the level of DNA methylation in needles of young seedlings, reflected in methylation changes in CCGG sequences. Exposure of young seedlings to UV-B radiation might be a way to potentiate the general defensive capacity, improving their ability to survive in outdoor conditions. UV-B-induced defence is discussed in the light of epigenetic mechanisms.

  • 28. Olsson, E. G. A.
    et al.
    Maad, Johanne
    Dalarna University, School of Education, Health and Social Studies, Natural Science.
    Myklebost, H. E.
    Variation in life history traits of Gentiana nivalis (Gentianaceae) in alpine and sub-alpine habitats in the Norwegian mountains and its implications for biodiversity in relation to environmental change2015In: Annales Botanici Fennici, ISSN 0003-3847, E-ISSN 1797-2442, Vol. 52, no 3-4, p. 149-159Article in journal (Refereed)
  • 29.
    Rosdahl, Hans
    et al.
    Gymnastik- och idrottshögskolan, GIH, Laboratoriet för biomekanik och motorisk kontroll (BMC).
    Lindberg, Thomas
    Gymnastik- och idrottshögskolan, GIH, Laboratoriet för tillämpad idrottsvetenskap (LTIV).
    Edin, Fredrik
    Nilsson, Johnny
    Gymnastik- och idrottshögskolan, GIH, Laboratoriet för biomekanik och motorisk kontroll (BMC).
    The Moxus Modular metabolic sustem evaluated with two sensors for ventilation against the Douglas bag method2013In: European Journal of Applied Physiology, ISSN 1439-6319, E-ISSN 1439-6327, Vol. 113, no 5, p. 1353-1367Article in journal (Refereed)
    Abstract [en]

    This study evaluated the Moxus metabolic system with the Douglas bag method (DBM) as criterion. Reliability and validity were investigated in a wide range of ventilation and oxygen uptake and two sensors for determining ventilation were included. Thirteen well-trained athletes participated in one pre-test and four tests for data collection, exercising on a cycle ergometer at five submaximal powers (50-263 W) and at [Formula: see text]. Gas exchange variables were measured simultaneously using a serial setup with data collected on different days in an order randomized between Moxus with pneumotachometer (MP) and turbine flowmeter (MT) sensors for ventilation. Reliability with both sensors was comparable to the DBM. Average CV (%) of all exercise intensities were with MP: 3.0 ± 1.3 for VO(2), 3.8 ± 1.5 for VCO(2), 3.1 ± 1.2 for the respiratory exchange ratio (RER) and 4.2 ± 0.8 for V (E). The corresponding values with MT were: 2.7 ± 0.3 for VO(2), 4.7 ± 0.4 for VCO(2), 3.3 ± 0.9 for RER and 4.8 ± 1.4 for V (E). Validity was acceptable except for small differences related to the determination of ventilation. The relative differences in relation to DBM at the powers including [Formula: see text] were similar for both sensors with the ranges being: +4 to -2 % for V (E), +5 to -3 % for VO(2) and +5 to -4 % for VCO(2) while RER did not differ at any power. The Moxus metabolic system shows high and adequate reliability and reasonable validity over a wide measurement range. At a few exercise levels, V (E) differed slightly from DBM, resulting in concomitant changes in VO(2) and VCO(2).

  • 30.
    Rönnegård, Lars
    et al.
    Dalarna University, School of Technology and Business Studies, Statistics.
    Sand, Håkan
    Andren, Henrik
    Månsson, Johan
    Pehrson, Åke
    Evaluation of four methods used to estimate population density of moose (Alces alces)2008In: Wildlife Biology, ISSN 0909-6396, E-ISSN 1903-220X, Vol. 14, no 3, p. 358-371Article in journal (Refereed)
    Abstract [en]

    Various survey methods are used to monitor and manage ungulate popualations. The choice of optimal method depends on estimation accuracy, management objective and financial constraints. Here we compare estimates produced by four different methods for estimating population size, i.e. aerial counts, hunter observations, pellet group counts and cohort analysis. A Swedish moose Alces alces population was studied during 1973-2005 in the Grimso Wildlife Research Area (135 km(2)). The highest correlation was found between cohort analysis and aerial counts (r = 0.69. P < 0.05). and the hunter observations and the aerial counts (r = 0.76. P < 0.10). The different methods produced relatively consistent trends in population estimates over years. Pellet group counts prior to 1997 were not significantly correlated with the other methods. probably due to unrepresentative spatial sampling. A comparison of the aerial and pellet group counts in 2002 and 2006, showed that the average defecation rate was estimated at approximately 14 pellet groups per day per moose. Our results show the importance of having representative spatial sampling in pellet group surveys and indicate that hunter observations can be a useful tool for estimating long-term population trends even in moderately sized areas.

  • 31.
    Shen, Xia
    et al.
    Dalarna University, School of Technology and Business Studies, Statistics.
    Alam, Moudud
    Dalarna University, School of Technology and Business Studies, Statistics.
    Fikse, Freddy
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala.
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics.
    A novel generalized ridge regression method for quantitative genetics2013In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 193, no 4, p. 1255-1268Article in journal (Refereed)
    Abstract [en]

    As the molecular marker density grows, there is a strong need in both genome-wide association studies and genomic selection to fit models with a large number of parameters. Here we present a computationally efficient generalized ridge regression (RR) algorithmfor situations where the number of parameters largely exceeds the number of observations. The computationally demanding parts of the method depend mainly on the number ofobservations and not the number of parameters. The algorithm was implemented in the R package bigRR based on the previously developed package hglm. Using such an approach, a heteroscedastic effects model (HEM) was also developed, implemented and tested. Theefficiency for different data sizes were evaluated via simulation. The method was tested for a bacteria-hypersensitive trait in a publicly available Arabidopsis dataset including 84 inbred lines and 216 130 SNPs. The computation of all the SNP effects required less than10 seconds using a single 2.7 GHz core. The advantage in run-time makes permutationtest feasible for such a whole-genome model, so that a genome-wide significance threshold can be obtained. HEM was found to be more robust than ordinary RR (a.k.a. SNPBLUP) in terms of QTL mapping, because SNP specific shrinkage was applied instead of acommon shrinkage. The proposed algorithm was also assessed for genomic evaluation and was shown to give better predictions than ordinary RR.

  • 32.
    Shen, Xia
    et al.
    Dalarna University, School of Technology and Business Studies, Statistics. Swedish University of Agricultural Sciences.
    Carlborg, Örjan
    Swedish University of Agricultural Sciences.
    Beware of risk for increased false positive rates in genome-wide association studies for phenotypic variability2013In: Frontiers in Genetics, ISSN 1664-8021, E-ISSN 1664-8021, no 4Article in journal (Refereed)
  • 33. Shen, Xia
    et al.
    Li, Ying
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics.
    Uden, Peter
    Carlborg, Orjan
    Application of a genomic model for high-dimensional chemometric analysis2014In: Journal of Chemometrics, ISSN 0886-9383, E-ISSN 1099-128X, Vol. 28, no 7, p. 548-557Article in journal (Refereed)
    Abstract [en]

    The rapid development of newtechnologies for large-scale analysis of genetic variation in the genomes of individuals and populations has presented statistical geneticists with a grand challenge to develop efficient methods for identifying the small proportion of all identified genetic polymorphisms that have effects on traits of interest. To address such a "large p small n" problem, we have developed a heteroscedastic effects model (HEM) that has been shown to be powerful in high-throughput genetic analyses. Here, we describe how this whole-genome model can also be utilized in chemometric analysis. As a proof of concept, we use HEM to predict analyte concentrations in silage using Fourier transform infrared spectroscopy signals. The results show that HEM often outperforms the classic methods and in addition to this presents a substantial computational advantage in the analyses of such high-dimensional data. The results thus show the value of taking an interdisciplinary approach to chemometric analysis and indicate that large-scale genomic models can be a promising new approach for chemometric analysis that deserve to be evaluated more by experts in the field. The software used for our analyses is freely available as an R package at http://cran.r-project.org/web/packages/bigRR/. Copyright (C) 2014 JohnWiley & Sons, Ltd.

  • 34.
    Shen, Xia
    et al.
    Dalarna University, School of Technology and Business Studies, Statistics.
    Pettersson, Mats
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics.
    Carlborg, Örjan
    Inheritance beyond plain heritability: variance-controlling genes in Arabidopsis thaliana2012In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 8, no 8, article id e1002839Article in journal (Refereed)
    Abstract [en]

    The phenotypic effect of a gene is normally described by the mean-difference between alternative genotypes. A gene may, however, also influence the phenotype by causing a difference in variance between genotypes. Here, we reanalyze a publicly available Arabidopsis thaliana dataset [1] and show that genetic variance heterogeneity appears to be as common as normal additive effects on a genomewide scale. The study also develops theory to estimate the contributions of variance differences between genotypes to the phenotypic variance, and this is used to show that individual loci can explain more than 20% of the phenotypic variance. Two well-studied systems, cellular control of molybdenum level by the ion-transporter MOT1 and flowering-time regulation by the FRI-FLC expression network, and a novel association for Leaf serration are used to illustrate the contribution of major individual loci, expression pathways, and gene-by-environment interactions to the genetic variance heterogeneity.

  • 35.
    Shen, Xia
    et al.
    SLUDivision of Computational Genetics, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala.
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics. Division of Quantitative Genetics, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala.
    Issues with data transformation in genome-wide association studies for phenotypic variability2013In: F1000Research, ISSN 2046-1402, Vol. 2, no 200Article in journal (Refereed)
    Abstract [en]

    The purpose of this correspondence is to discuss and clarify a few points about data transformation used in genome-wide association studies, especially for phenotypic variability. By commenting on the recent publication by Sun et al. in the American Journal of Human Genetics, we emphasize the importance of statistical power in detecting functional loci and the real meaning of the scale of the phenotype in practice.

  • 36. Silva, C. N. S
    et al.
    McFarlane, S. E
    Hagen, I. J
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics. Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala.
    Billing, A. M
    Kvalnes, T
    Kemppainen, P
    Rønning, B
    Ringsby, T. H
    Husby, A
    Insights into the genetic architecture of morphological traits in two passerine bird species2017In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 119, no 3, p. 197-205Article in journal (Refereed)
    Abstract [en]

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

  • 37. Sivertsen, Therese R.
    et al.
    Åhman, Birgitta
    Steyaert, Sam M. J. G.
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics.
    Frank, Jens
    Segerström, Peter
    Støen, Ole-Gunnar
    Skarin, Anna
    Reindeer habitat selection under the risk of brown bear predation during calving season2016In: Ecosphere, ISSN 2150-8925, E-ISSN 2150-8925, Vol. 7, no 11, article id e01583Article in journal (Refereed)
    Abstract [en]

    The depredation of semi-domesticated reindeer by large carnivores reflects an important human-wildlife conflict in Fennoscandia. Recent studies have revealed that brown bears (Ursus arctos) may kill substantial numbers of reindeer calves (Rangifer tarandus tarandus) in forest areas in Sweden. Several authors have suggested that predation risk is an important driver of habitat selection in wild Rangifer populations where predation is a limiting factor, but little is known about these mechanisms in semi-domesticated populations. We examined the habitat selection of female reindeer in relation to spatial and temporal variations in brown bear predation risk on the reindeer calving grounds and evaluated the simultaneous responses of brown bears and reindeer to landscape characteristics. We used GPS data from 110 reindeer years (97 individuals) and 29 brown bear years (19 individuals), from two reindeer herding districts in the forest area of northern Sweden. Our results did not indicate that reindeer alter their behavior in response to spatiotemporal variation in brown bear predation risk, on the scale of the calving range. Instead, we suggest that spatiotemporal behavioral adjustments by brown bears were the main driver of prey-predator interactions in our study system. Contrasting responses by brown bears and reindeer to clear-cuts and young forest indicate that forestry can influence species interactions and possibly yield negative consequences for the reindeer herd. Even if clear-cuts may be beneficial in terms of calf survival, logging activity will eventually cause greater abundance of young regenerating forest, reducing available reindeer habitats and increasing habitat preferred by brown bears. Domestication may have made semi-domesticated reindeer in Fennoscandia less adapted to cope with predators. Areal restrictions, limiting the opportunity for dispersion and escape, possibly make the calves more susceptible to predation. Also, a generally higher population density in semi-domesticated herds compared to wild populations can make dispersion a less efficient strategy and the reindeer calves easier prey. Overall, the lack of ability of the reindeer females to reduce brown bear encounter risk on the scale of the calving range is probably an important reason for the high brown bear predation rates on reindeer calves documented in our study areas. 

  • 38. Skarin, Anna
    et al.
    Helleman, Christian
    Sandström, Per
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics.
    Lundquist, Henrik
    Renar och vindkraft: Studie från anläggningen av två vindkraftparker i Malå sameby2013Report (Other academic)
    Abstract [sv]

    Studien undersöker hur renar påverkas under konstruktionsfasen när vindkraftverk byggs. Studien följer uppförandet av två nya vindparker i Malå kommun i Västerbotten. Sammanlagt byggdes 18 vindkraftverk i Malå samebys kalvnings- och försommarland. Inventering av renspillning samt positioner från renar med GPS-halsband visar att konstruktionen av vindkraftsparkerna har påverkat renarnas användning av området. Analysen visar att renarna under tiden för byggnationen har sökt sig bort från området. Spillningsinventeringen och GPS-data visar också att renarna undviker kraftledningar och större vägar när de ska beta.

    Rapport från kunskapsprogrammet Vindval.

  • 39.
    Skarin, Anna
    et al.
    Swedish Univ Agr Sci, Dept Anim Nutr & Management, Uppsala.
    Nellemann, Christian
    GRID Arendal, United Nations Environm Programme, Lillehammer, Norway..
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics.
    Sandstrom, Per
    Swedish Univ Agr Sci, Dept Forest Resource Management, Umea, Sweden.
    Lundqvist, Henrik
    Swedish Univ Agr Sci, Dept Anim Nutr & Management, Uppsala, Sweden.
    Wind farm construction impacts reindeer migration and movement corridors2015In: Landscape Ecology, ISSN 0921-2973, E-ISSN 1572-9761, Vol. 30, no 8, p. 1527-1540Article in journal (Refereed)
    Abstract [en]

    Over the last decade, we have seen a massive increase in the construction of wind farms in northern Fennoscandia. Wind farms comprising hundreds of wind turbines are being built, with little knowledge of the possible cumulative adverse effects on the habitat use and migration of semi-domesticated free-ranging reindeer. We assessed how reindeer responded to wind farm construction in an already fragmented landscape, with specific reference to the effects on use of movement corridors and reindeer habitat selection. We used GPS-data from reindeer during calving and post-calving in the MalAyen reindeer herding community in Sweden. We analysed data from the pre-development years compared to the construction years of two relatively small wind farms. During construction of the wind farms, use of original migration routes and movement corridors within 2 km of development declined by 76 %. This decline in use corresponded to an increase in activity of the reindeer measured by increased step lengths within 0-5 km. The step length was highest nearest the development and declining with distance, as animals moved towards migration corridors and turned around or were observed in holding patterns while not crossing. During construction, reindeer avoided the wind farms at both regional and landscape scale of selection. The combined construction activities associated with even a few wind turbines combined with power lines and roads in or close to central movement corridors caused a reduction in the use of such corridors and grazing habitat and increased the fragmentation of the reindeer calving ranges.

  • 40.
    Skarin, Anna
    et al.
    SLU.
    Sandström, Per
    SLU.
    Alam, Moudud
    Dalarna University, School of Technology and Business Studies, Statistics.
    Out of sight of wind turbines — Reindeer response to wind farms in operation2018In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 8, p. 9906-9919Article in journal (Refereed)
    Abstract [en]

    To meet the expanding land use required for wind energy development, a better understanding of the effects on terrestrial animals’ responses to such development is required. Using GPS-data from 50 freely ranging female reindeer (Rangifer tarandus) in the Malå reindeer herding community, Sweden, we determined reindeer calving sites and estimated reindeer habitat selection using resource selection functions (RSF). RSFs were estimated at both second- (selection of home range) and third-order (selection within home range) scale in relation to environmental variables, wind farm (WF) development phase (before construction, construction, and operation), distance to the WFs and at the second-order scale whether the wind turbines were in or out of sight of the reindeer. We found that the distance between reindeer calving site and WFs increased during the operation phase, compared to before construction. At both scales of selection, we found a significant decrease in habitat selection of areas in proximity of the WFs, in the same comparison. The results also revealed a shift in home range selection away from habitats where wind turbines became visible toward habitats where the wind turbines were obscured by topography (increase in use by 79% at 5 km). We interpret the reindeer shift in home range selection as an effect of the wind turbines per se. Using topography and land cover information together with the positions of wind turbines could therefore help identify sensitive habitats for reindeer and improve the planning and placement of WFs. In addition, we found that operation phase of these WFs had a stronger adverse impact on reindeer habitat selection than the construction phase. Thus, the continuous running of the wind turbines making a sound both day and night seemed to have disturbed the reindeer more than the sudden sounds and increased human activity during construction work.

  • 41. Sonesson, Anna K
    et al.
    Odegård, Jørgen
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics.
    Genetic heterogeneity of within-family variance of body weight in Atlantic salmon (Salmo salar)2013In: Genetics Selection Evolution, ISSN 0999-193X, E-ISSN 1297-9686, Vol. 45, article id 41Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Canalization is defined as the stability of a genotype against minor variations in both environment and genetics. Genetic variation in degree of canalization causes heterogeneity of within-family variance. The aims of this study are twofold: (1) quantify genetic heterogeneity of (within-family) residual variance in Atlantic salmon and (2) test whether the observed heterogeneity of (within-family) residual variance can be explained by simple scaling effects.

    RESULTS: Analysis of body weight in Atlantic salmon using a double hierarchical generalized linear model (DHGLM) revealed substantial heterogeneity of within-family variance. The 95% prediction interval for within-family variance ranged from ~0.4 to 1.2 kg2, implying that the within-family variance of the most extreme high families is expected to be approximately three times larger than the extreme low families. For cross-sectional data, DHGLM with an animal mean sub-model resulted in severe bias, while a corresponding sire-dam model was appropriate. Heterogeneity of variance was not sensitive to Box-Cox transformations of phenotypes, which implies that heterogeneity of variance exists beyond what would be expected from simple scaling effects.

    CONCLUSIONS: Substantial heterogeneity of within-family variance was found for body weight in Atlantic salmon. A tendency towards higher variance with higher means (scaling effects) was observed, but heterogeneity of within-family variance existed beyond what could be explained by simple scaling effects. For cross-sectional data, using the animal mean sub-model in the DHGLM resulted in biased estimates of variance components, which differed substantially both from a standard linear mean animal model and a sire-dam DHGLM model. Although genetic differences in canalization were observed, selection for increased canalization is difficult, because there is limited individual information for the variance sub-model, especially when based on cross-sectional data. Furthermore, potential macro-environmental changes (diet, climatic region, etc.) may make genetic heterogeneity of variance a less stable trait over time and space.

  • 42.
    Strandberg, E
    et al.
    SLU.
    Felleki, Majbritt
    Dalarna University, School of Technology and Business Studies, Statistics.
    Fikse, W F
    SLU.
    Franzén, J
    Stockholms Universitet.
    Mulder, H A
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics.
    Urioste, J I
    Windig, J J
    Statistical tools to select for robustness and milk quality2013In: Advances in Animal Biosciences, ISSN 2040-4719, Vol. 4, no 3, p. 606-611Article in journal (Refereed)
    Abstract [en]

    This work was part of the EU RobustMilk project. In this work package, we have focused on two aspects of robustness, micro- and macro-environmental sensitivity and applied these to somatic cell count (SCC), one aspect of milk quality. We showed that it is possible to combine both categorical and continuous descriptions of the environment in one analysis of genotype by environment interaction. We also developed a method to estimate genetic variation in residual variance and applied it to both simulated and a large field data set of dairy cattle. We showed that it is possible to estimate genetic variation in both micro- and macro-environmental sensitivity in the same data, but that there is a need for good data structure. In a dairy cattle example, this would mean at least 100 bulls with at least 100 daughters each. We also developed methods for improved genetic evaluation of SCC. We estimated genetic variance for some alternative SCC traits, both in an experimental herd data and in field data. Most of them were highly correlated with subclinical mastitis (>0.9) and clinical mastitis (0.7 to 0.8), and were also highly correlated with each other. We studied whether the fact that animals in different herds are differentially exposed to mastitis pathogens could be a reason for the low heritabilities for mastitis, but did not find strong evidence for that. We also created a new model to estimate breeding values not only for the probability of getting mastitis but also for recovering from it. In a progeny-testing situation, this approach resulted in accuracies of 0.75 and 0.4 for these two traits, respectively, which means that it is possible to also select for cows that recover more quickly if they get mastitis.

  • 43. Sundberg, S.
    Jonsell, L.
    Floraförändringar2010In: Upplands flora / [ed] Jonsell L., Uppsala: SBF-förlaget , 2010, p. 117-131-Chapter in book (Other academic)
  • 44.
    Wallin, Elisabeth
    et al.
    Dalarna University, School of Technology and Business Studies, Energy Technology. SLU.
    Gräns, Daniel
    Dalarna University, School of Technology and Business Studies, Forest and Wood Technology. SLU.
    Jacobs, Douglass F
    Purdue Univ, Dept Forestry & Nat Resources, W Lafayette, IN 47907 USA..
    Lindström, Anders
    Dalarna University, School of Technology and Business Studies, Forest and Wood Technology. SLU.
    Verhoef, Nathalie
    NSure, Binnenhaven 5, NL-6700 AA Wageningen, Netherlands..
    Short-day photoperiods affect expression of genes related to dormancy and freezing tolerance in Norway spruce seedlings2017In: Annals of Forest Science, ISSN 1286-4560, E-ISSN 1297-966X, Vol. 74, no 3, article id 59Article in journal (Refereed)
    Abstract [en]

    Key message: Gene expression analysis showed that prolonged short day (SD) treatment deepened dormancy and stimulated development of freezing tolerance of Picea abies seedlings. Prolonged SD treatment also caused later appearance of visible buds in autumn, reduced risks for reflushing, and promoted earlier spring bud break.

    Context: Short day (SD) treatment of seedlings is a common practice in boreal forest tree nurseries to regulate shoot growth and prepare the seedlings for autumn planting or frozen storage. Aims The aim of this study was to examine responses of Norway spruce (Picea abies (L.) Karst.) to a range of SD treatments of different length and evaluate gene expression related to dormancy induction and development of freezing tolerance.

    Methods: The seedlings were SD treated for 11 h a day during 7, 14, 21, or 28 days. Molecular tests were performed, and the expression profiles of dormancy and freezing tolerance- related genes were analyzed as well as determination of shoot growth, bud set, bud size, reflushing, dry matter content, and timing of spring bud break.

    Results: The 7-day SD treatment was as effective as longer SD treatments in terminating apical shoot growth. However, short (7 days) SD treatment resulted in later activation of dormancy-related genes and of genes related to freezing tolerance compared to the longer treatments which had an impact on seedling phenology.

    Conclusion: Gene expression analysis indicated an effective stimulus of dormancy-related genes when the SD treatment is prolonged for at least 1-2 weeks after shoot elongation has terminated and that seedlings thereafter are exposed to ambient outdoor climate conditions.

  • 45. Zan, Yanjun
    et al.
    Sheng, Zheya
    Lillie, Mette
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics. SLU.
    Honaker, Christa F
    Siegel, Paul B
    Carlborg, Örjan
    Artificial selection response due to polygenic adaptation from a multilocus, multiallelic genetic architecture2017In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 34, no 10, p. 2678-2689Article in journal (Refereed)
    Abstract [en]

    The ability of a population to adapt to changes in their living conditions, whether in nature or captivity, often depends on polymorphisms in multiple genes across the genome. In-depth studies of such polygenic adaptations are difficult in natural populations, but can be approached using the resources provided by artificial selection experiments. Here, we dissect the genetic mechanisms involved in long-term selection responses of the Virginia chicken lines, populations that after 40 generations of divergent selection for 56-day body weight display a 9-fold difference in the selected trait. In the F15 generation of an intercross between the divergent lines, 20 loci explained >60% of the additive genetic variance for the selected trait. We focused particularly on fine-mapping seven major QTL that replicated in this population and found that only two fine-mapped to single, bi-allelic loci; the other five contained linked loci, multiple alleles or were epistatic. This detailed dissection of the polygenic adaptations in the Virginia lines provides a deeper understanding of the range of different genome-wide mechanisms that have been involved in these long-term selection responses. The results illustrate that the genetic architecture of a highly polygenic trait can involve a broad range of genetic mechanisms, and that this can be the case even in a small population bred from founders with limited genetic diversity.

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