uu.seUppsala universitets publikasjoner
Endre søk
Begrens søket
3456789 251 - 300 of 539
RefereraExporteraLink til resultatlisten
Permanent link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
Treff pr side
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sortering
  • Standard (Relevans)
  • Forfatter A-Ø
  • Forfatter Ø-A
  • Tittel A-Ø
  • Tittel Ø-A
  • Type publikasjon A-Ø
  • Type publikasjon Ø-A
  • Eldste først
  • Nyeste først
  • Skapad (Eldste først)
  • Skapad (Nyeste først)
  • Senast uppdaterad (Eldste først)
  • Senast uppdaterad (Nyeste først)
  • Disputationsdatum (tidligste først)
  • Disputationsdatum (siste først)
  • Standard (Relevans)
  • Forfatter A-Ø
  • Forfatter Ø-A
  • Tittel A-Ø
  • Tittel Ø-A
  • Type publikasjon A-Ø
  • Type publikasjon Ø-A
  • Eldste først
  • Nyeste først
  • Skapad (Eldste først)
  • Skapad (Nyeste først)
  • Senast uppdaterad (Eldste først)
  • Senast uppdaterad (Nyeste først)
  • Disputationsdatum (tidligste først)
  • Disputationsdatum (siste først)
Merk
Maxantalet träffar du kan exportera från sökgränssnittet är 250. Vid större uttag använd dig av utsökningar.
  • 251.
    Larsson, Hanna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    De Paoli, Emanuele
    Dipartimento di Scienze Agrarie e Ambientali, Universita di Udine, Italy.
    Morgante, Michele
    Dipartimento di Scienze Agrarie e Ambientali, Universita di Udine, Italy.
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Gyllenstrand, Niclas
    Dept. of Plant Biology and Forest Genetics, Swedish Agricultural University, Uppsala, Sweden.
    The HypoMethylated Partial Restriction (HMPR) method reduces the repetitive content of genomic libraries in Norway spruce (Picea abies)2013Inngår i: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 9, nr 2, s. 601-612Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To evaluate the usefulness of Reduced Representation Libraries (RRL) in species with large and highly repetitive genomes such as conifers, we employed Hypomethylated Partial Restriction (HMPR) on the genome of Norway spruce (Picea abies). The HMPR method preferentially removes the commonly hypermethylated, repetitive fraction of the genome. Hence, RRLs should be enriched for the hypomethylated gene space. For comparison, a standard shotgun library was constructed and samples of the respective libraries were obtained through Sanger sequencing. We obtained a 9-fold gene enrichment, a value which is slightly higher than for other plant species. The amount of repetitive DNA was reduced by 45 % in the RRLs, demonstrating the ability to efficiently remove hypermethylated DNA. Annotating sequences in an uncharacterized genome remains challenging and a large number of sequences could not be classified as either repetitive DNA or as belonging to the gene space. Upon further investigation, we found that some of these uncharacterized fragments were expressed, and in most cases the expression was spatially differentiated, indicating that they might have a function. Full-length transcripts of a subset of expressed fragments also revealed that these could be long non-coding RNAs. In conclusion, our study shows that the HMPR method is effective in constructing libraries enriched for the genic fraction of the genome, while simultaneously reducing the repetitive fraction, in P. abies and may prove a valuable tool for the discovery, validation, and assessment of genetic markers in population studies and breeding efforts when combined with next-generation sequencing technology.

  • 252.
    Larsson, Hanna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Kallman, Thomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Gyllenstrand, Niclas
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Distribution of Long-Range Linkage Disequilibrium and Tajima's D Values in Scandinavian Populations of Norway Spruce (Picea abies)2013Inngår i: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 3, nr 5, s. 795-806Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The site frequency spectrum of mutations (SFS) and linkage disequilibrium (LD) are the two major sources of information in population genetics studies. In this study we focus on the levels of LD and the SFS and on the effect of sample size on summary statistics in 10 Scandinavian populations of Norway spruce. We found that previous estimates of a low level of LD were highly influenced by both sampling strategy and the fact that data from multiple loci were analyzed jointly. Estimates of LD were in fact heterogeneous across loci and increased within individual populations compared with the estimate from the total data. The variation in levels of LD among populations most likely reflects different demographic histories, although we were unable to detect population structure by using standard approaches. As in previous studies, we also found that the SFS-based test Tajima's D was highly sensitive to sample size, revealing that care should be taken to draw strong conclusions from this test when sample size is small. In conclusion, the results from this study are in line with recent studies in other conifers that have revealed a more complex and variable pattern of LD than earlier studies suggested and with studies in trees and humans that suggest that Tajima's D is sensitive to sample size. This has large consequences for the design of future association and population genetic studies in Norway spruce.

  • 253.
    Larsson, Hanna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Källman, Thomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Gyllenstrand, Niclas
    Dept. of Plant Biology and Forest Genetics, Swedish Agricultural University, Uppsala, Sweden.
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Distribution of long-range Linkage Disequilibrium and Tajima's D in Scandinavian populations of Norway spruce (Picea abies)Manuskript (preprint) (Annet vitenskapelig)
  • 254.
    Lascoux, Martin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Glémin, Sylvain
    Savolainen, Outi
    Local adaptation in plants2016Inngår i: Encyclopedia of Life Sciences, ISSN 1476-9506, E-ISSN 1476-9506, artikkel-id 0025270Artikkel i tidsskrift (Fagfellevurdert)
  • 255.
    Lascoux, Martin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Suyama, Yoshihisa
    Inferring forest tree population and species histories from genetic variation2012Inngår i: Molecular ecology of forest trees / [ed] Yoshihisa Suyama, Tokyo: bun-ichi sogo shuppan , 2012Kapittel i bok, del av antologi (Fagfellevurdert)
  • 256. Lazaro, Amparo
    et al.
    Jakobsson, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Totland, Orjan
    How do pollinator visitation rate and seed set relate to species' floral traits and community context?2013Inngår i: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 173, nr 3, s. 881-893Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Differences among plant species in visitation rate and seed set within a community may be explained both by the species' floral traits and the community context. Additionally, the importance of species' floral traits vs. community context on visitation rate and seed set may vary among communities. In communities where the pollinator-to-flower ratio is low, floral traits may be more important than community context, as pollinators may have the opportunity to be choosier when visiting plant species. In this study we investigated whether species' floral traits (flower shape, size and number, and flowering duration) and community context (conspecific and heterospecific flower density, and pollinator abundance) could explain among-species variation in visitation rate and seed set. For this, we used data on 47 plant species from two Norwegian plant communities differing in pollinator-to-flower ratio. Differences among species in visitation rate and seed set within a community could be explained by similar variables as those explaining visitation rate and seed set within species. As expected, we found floral traits to be more important than community context in the community with a lower pollinator-to-flower ratio; whereas in the community with a higher pollinator-to-flower ratio, community context played a bigger role. Our study gives significant insights into the relative importance of floral traits on species' visitation rate and seed set, and contributes to our understanding of the role of the community context on the fitness of plant species.

  • 257.
    Leal, Luis
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Talla, Venkat
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Källman, Thomas
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Friberg, Magne
    Lund Univ, Biodivers Unit, Dept Biol, Lund, Sweden..
    Wiklund, Christer
    Stockholm Univ, Div Ecol, Dept Zool, Stockholm, Sweden..
    Dinca, Vlad
    Univ Oulu, Dept Ecol & Genet, Oulu, Finland..
    Vila, Roger
    Inst Biol Evolut CSIC UPF, Barcelona, Spain..
    Backström, Niclas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation2018Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, nr 4, s. 935-948Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In temperate latitudes, many insects enter diapause (dormancy) during the cold season, a period during which developmental processes come to a standstill. The wood white (Leptidea sinapis) is a butterfly species distributed across western Eurasia that shows photoperiod-induced diapause with variation in critical day-length across populations at different latitudes. We assembled transcriptomes and estimated gene expression levels at different developmental stages in experimentally induced directly developing and diapausing cohorts of a single Swedish population of L. sinapis to investigate the regulatory mechanisms underpinning diapause initiation. Different day lengths resulted in expression changes of developmental genes and affected the rate of accumulation of signal molecules, suggesting that diapause induction might be controlled by increased activity of monoamine neurotransmitters in larvae reared under short-day light conditions. Expression differences between light treatment groups of two monoamine regulator genes (DDC and ST) were observed already in instar III larvae. Once developmental pathways were irreversibly set at instar V, a handful of genes related to dopamine production were differentially expressed leading to a significant decrease in expression of global metabolic genes and increase in expression of genes related to fatty acid synthesis and sequestration. This is in line with a time-dependent (hour-glass) model of diapause regulation where a gradual shift in the concentration of monoamine neurotransmitters and their metabolites during development of larvae under short-day conditions leads to increased storage of fat, decreased energy expenditures, and ultimately developmental stasis at the pupal stage.

  • 258.
    Lee, Cheng-Ruei
    et al.
    Duke Univ, Dept Biol, Box 90338, Durham, NH 27708 USA.;Natl Taiwan Univ, Inst Ecol & Evolutionary Biol, Taipei 10617, Taiwan.;Natl Taiwan Univ, Inst Plant Biol, Taipei 10617, Taiwan..
    Wang, Baosheng
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Duke Univ, Dept Biol, Box 90338, Durham, NH 27708 USA.
    Mojica, Julius P.
    Duke Univ, Dept Biol, Box 90338, Durham, NH 27708 USA..
    Mandakova, Terezie
    Masaryk Univ, Cent European Inst Technol, Plant Cytogen Grp, Kamenice 5, CZ-62500 Brno, Czech Republic..
    Prasad, Kasavajhala Y. S. K.
    Colorado State Univ, Dept Biol, Ft Collins, CO 80523 USA..
    Goicoechea, Jose Luis
    Univ Arizona, Sch Plant Sci, Arizona Genom Inst, Tucson, AZ 85721 USA.;Univ Arizona, Sch Plant Sci, Inst BIO5, Tucson, AZ 85721 USA..
    Perera, Nadeesha
    Duke Univ, Dept Biol, Box 90338, Durham, NH 27708 USA..
    Hellsten, Uffe
    Joint Genome Inst, Dept Energy, Walnut Creek, CA 94598 USA..
    Hundley, Hope N.
    Joint Genome Inst, Dept Energy, Walnut Creek, CA 94598 USA..
    Johnson, Jenifer
    Joint Genome Inst, Dept Energy, Walnut Creek, CA 94598 USA..
    Grimwood, Jane
    HudsonApha Inst Biotechnol, Huntsville, AL 35806 USA..
    Barry, Kerrie
    Joint Genome Inst, Dept Energy, Walnut Creek, CA 94598 USA..
    Fairclough, Stephen
    Joint Genome Inst, Dept Energy, Walnut Creek, CA 94598 USA..
    Jenkins, Jerry W.
    Joint Genome Inst, Dept Energy, Walnut Creek, CA 94598 USA..
    Yu, Yeisoo
    Phyzen Inc, Phyzen Genom Inst, Seoul 151836, South Korea..
    Kudrna, Dave
    Univ Arizona, Sch Plant Sci, Arizona Genom Inst, Tucson, AZ 85721 USA.;Univ Arizona, Sch Plant Sci, Inst BIO5, Tucson, AZ 85721 USA..
    Zhang, Jianwei
    Univ Arizona, Sch Plant Sci, Arizona Genom Inst, Tucson, AZ 85721 USA.;Univ Arizona, Sch Plant Sci, Inst BIO5, Tucson, AZ 85721 USA..
    Talag, Jayson
    Univ Arizona, Sch Plant Sci, Arizona Genom Inst, Tucson, AZ 85721 USA.;Univ Arizona, Sch Plant Sci, Inst BIO5, Tucson, AZ 85721 USA..
    Golser, Wolfgang
    Univ Arizona, Sch Plant Sci, Arizona Genom Inst, Tucson, AZ 85721 USA.;Univ Arizona, Sch Plant Sci, Inst BIO5, Tucson, AZ 85721 USA..
    Ghattas, Kathryn
    Duke Univ, Dept Biol, Box 90338, Durham, NH 27708 USA..
    Schranz, M. Eric
    Wageningen Univ & Res Ctr, Biosystemat Grp, Droevendaalsesteeg 1, NL-6708 PB Wageningen, Netherlands..
    Wing, Rod
    HudsonApha Inst Biotechnol, Huntsville, AL 35806 USA..
    Lysak, Martin A.
    Univ Arizona, Sch Plant Sci, Arizona Genom Inst, Tucson, AZ 85721 USA.;Univ Arizona, Sch Plant Sci, Inst BIO5, Tucson, AZ 85721 USA..
    Schmutz, Jeremy
    Joint Genome Inst, Dept Energy, Walnut Creek, CA 94598 USA..
    Rokhsar, Daniel S.
    Joint Genome Inst, Dept Energy, Walnut Creek, CA 94598 USA..
    Mitchell-Olds, Thomas
    Duke Univ, Dept Biol, Box 90338, Durham, NH 27708 USA..
    Young inversion with multiple linked QTLs under selection in a hybrid zone2017Inngår i: NATURE ECOLOGY & EVOLUTION, ISSN 2397-334X, Vol. 1, nr 5, artikkel-id UNSP 0119Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose since the last glaciation and subsequently reached local high frequency in a hybrid speciation zone. Furthermore, the inversion shows signs of positive directional selection. To test whether the inversion could have captured existing, linked QTLs, we crossed standard, collinear haplotypes from the hybrid zone and found multiple linked phenology QTLs within the inversion region. These findings provide the first direct evidence that linked, locally adapted QTLs may be captured by young inversions during incipient speciation.

  • 259.
    Lehndal, Lina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Ecological and Evolutionary Consequences of Herbivory in the Perennial Herb Lythrum salicaria2015Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    In this thesis, I combined field, common-garden and greenhouse experiments to examine the ecological and evolutionary consequences of plant-herbivore interactions in the perennial herb Lythrum salicaria. More specifically I examined (1) whether resistance and tolerance to damage from herbivores vary with latitude and are positively related to the intensity of herbivory in natural populations, (2) whether effects of herbivory on plant fitness vary with latitude, (3) whether populations are locally adapted and whether herbivory influences the relative fitness of populations, and (4) whether the intensity and effects of insect herbivory on reproductive output vary locally along a disturbance gradient and are associated with differences in plant resistance.

    A common-garden and a greenhouse experiment demonstrated that plant resistance decreased whereas plant tolerance increased with latitude of origin among populations sampled along a latitudinal gradient in Sweden. Oviposition and feeding preference in the greenhouse and leaf damage in the common-garden experiment were negatively related to natural damage in the source populations.

    Experimental removal of insect herbivores in three populations sampled along the latitudinal gradient demonstrated that intensity of herbivory and its effects on plant fitness decreased towards the north. A reciprocal transplant experiment among the same three populations showed that herbivory affected the relative fitness of the three populations, but did not detect any evidence of local adaptation. Instead the southernmost population had the highest relative fitness at all three sites.

    A herbivore-removal experiment conducted in nine populations in an archipelago in northern Sweden demonstrated that insect herbivory strongly influenced among-population variation in reproductive output. However, variation in resistance was not related to differences in intensity of herbivory at this spatial scale.

    Taken together, the results demonstrate that resistance and tolerance to herbivory vary with latitude but in opposite directions, that intensity of herbivory is a major determinant of flowering and seed output, and that the strength of herbivore-mediated selection varies among populations in Lythrum salicaria. They further indicate that both physical disturbance regime and latitudinal variation in abiotic conditions may strongly influence the performance and abundance of perennial herbs because of their effects on interactions with specialized herbivores.

    Delarbeid
    1. Latitudinal variation in resistance and tolerance to herbivory in the perennial herb Lythrum salicaria is related to intensity of herbivory and plant phenology
    Åpne denne publikasjonen i ny fane eller vindu >>Latitudinal variation in resistance and tolerance to herbivory in the perennial herb Lythrum salicaria is related to intensity of herbivory and plant phenology
    2015 (engelsk)Inngår i: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 28, nr 3, s. 576-589Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Both the length of the growing season and the intensity of herbivory often vary along climatic gradients, which may result in divergent selection on plant phenology, and on resistance and tolerance to herbivory. In Sweden, the length of the growing season and the number of insect herbivore species feeding on the perennial herb Lythrum salicaria decrease from south to north. Previous common-garden experiments have shown that northern L. salicaria populations develop aboveground shoots earlier in the summer, and finish growth before southern populations do. We tested the hypotheses that resistance and tolerance to damage vary with latitude in L. salicaria, and are positively related to the intensity of herbivory in natural populations. We quantified resistance and tolerance of populations sampled along a latitudinal gradient by scoring damage from natural herbivores and fitness in a common-garden experiment in the field, and by documenting oviposition and feeding preference by specialist leaf beetles in a greenhouse experiment. Plant resistance decreased with latitude of origin, whereas plant tolerance increased. Oviposition and feeding preference in the greenhouse, and leaf damage in the common-garden experiment were negatively related to damage in the source populations. The latitudinal variation in resistance was thus consistent with reduced selection from herbivores towards the northern range margin of L. salicaria. Variation in tolerance may be related to differences in the timing of damage in relation to the seasonal pattern of plant growth, as northern genotypes have developed further than southern have when herbivores emerge in early summer.

    Emneord
    Galerucella calmariensis, Galerucella pusilla, herbivore removal, latitude, Lythrum salicaria, Nanophyes marmoratus, plant resistance, plant tolerance, plant–herbivore interactions
    HSV kategori
    Forskningsprogram
    Biologi med inriktning mot ekologisk botanik
    Identifikatorer
    urn:nbn:se:uu:diva-247082 (URN)10.1111/jeb.12589 (DOI)000352628400006 ()
    Forskningsfinansiär
    Swedish Research Council
    Tilgjengelig fra: 2015-03-13 Laget: 2015-03-13 Sist oppdatert: 2017-12-04bibliografisk kontrollert
    2. Herbivory Differentially Affects Plant Fitness in Three Populations of the Perennial Herb Lythrum salicaria along a Latitudinal Gradient
    Åpne denne publikasjonen i ny fane eller vindu >>Herbivory Differentially Affects Plant Fitness in Three Populations of the Perennial Herb Lythrum salicaria along a Latitudinal Gradient
    2015 (engelsk)Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, nr 9, artikkel-id e0135939Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Herbivory can negatively and selectively affect plant fitness by reducing growth, survival and reproductive output, thereby influencing plant population dynamics and evolution. We documented intensity of herbivory and experimentally examined its effect on survival, growth and reproductive output in three natural populations of the perennial herb Lythrum salicaria along a latitudinal gradient from southern to northernmost Sweden over two years. The intensity of herbivory and the effects of herbivory on plant fitness were strongest in the southern population and intermediate in the central population. The mean proportion of the leaf area removed ranged from 11% in the southern to 3% in the northern population. Herbivore removal increased plant height 1.5-fold in the southern and 1.2-fold in the central population, the proportion plants flowering 4-fold in the southern and 2-fold in the central population, and seed production per flower 1.6-fold in the southern and 1.2-fold in the central population, but did not affect plant fitness in the northern population. Herbivore removal thus affected the relative fecundity of plants in the three populations: In the control, seed output per plant was 8.6 times higher in the northern population compared to the southern population, whereas after herbivore removal it was 2.5 times higher in the southern population compared to the northern. Proportion of leaf area removed increased with plant size, but tolerance to damage did not vary with size. The results demonstrate that native herbivores may strongly affect the demographic structure of L. salicaria populations, and thereby shape geographic patterns of seed production. They further suggest that the strength of herbivore-mediated selection varies among populations and decreases towards the north.

    Emneord
    Galerucella calmariensis, Galerucella pusilla, Herbivore removal, Nanophyes marmoratus, Plant-herbivore interactions, Plant resistance, Plant size, Plant tolerance, Seed production
    HSV kategori
    Forskningsprogram
    Biologi med inriktning mot ekologisk botanik
    Identifikatorer
    urn:nbn:se:uu:diva-247084 (URN)10.1371/journal.pone.0135939 (DOI)000360437700025 ()
    Forskningsfinansiär
    Swedish Research Council
    Tilgjengelig fra: 2015-03-13 Laget: 2015-03-13 Sist oppdatert: 2017-12-04bibliografisk kontrollert
    3. Herbivory influences the relative fitness of three native Lythrum salicaria populations, but no evidence of local adaptation along a latitudinal gradient
    Åpne denne publikasjonen i ny fane eller vindu >>Herbivory influences the relative fitness of three native Lythrum salicaria populations, but no evidence of local adaptation along a latitudinal gradient
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Local adaptation along environmental gradients has been documented in many plant species, but the extent to which biotic interactions influence the relative fitness of local and non-local genotypes has rarely been examined experimentally. Previous common-garden experiments detected clinal variation in life history, phenology and resistance to herbivory in the perennial herb Lythrum salicaria along a latitudinal gradient in Sweden, which coincides with a decrease in the length of the growing season and intensity of herbivory from south to north. Here, we included a herbivore-removal treatment in a reciprocal transplant experiment to test whether three populations sampled along the latitudinal gradient are locally adapted, whether differences in resistance and tolerance are consistent across sites and whether herbivory influences the relative performance of the study populations. The results did not reveal any evidence of local adaptation. Instead the southernmost population had the highest relative fitness at all three sites and was consistently less damaged by herbivores than were the other populations. The intensity of herbivory was greatest at the southern site and very low at the northernmost site. The removal of insect herbivores positively affected plant growth and fecundity at the southern and central sites. Herbivore removal also affected the relative fitness of the study populations at the southern site, and tended to do so at the central site. However, the relative ranking of the three populations did not change, indicating that herbivores influenced the strength but not the direction of selection. Genetic drift, recent climatic warming and intermittent strong selection against southern genotypes at northern latitudes may all contribute to the documented patterns of among-population variation in fitness, while similarity in the behaviour and preferences of herbivore populations along the studied gradient may explain the consistent differences in resistance.

    Emneord
    Female reproductive success, Galerucella calmariensis, Galerucella pusilla, Nanophyes marmoratus, Plant-herbivore interactions, Reciprocal transplant, Plant resistance, Tolerance to herbivory
    HSV kategori
    Forskningsprogram
    Biologi med inriktning mot ekologisk botanik
    Identifikatorer
    urn:nbn:se:uu:diva-247252 (URN)
    Forskningsfinansiär
    Swedish Research Council
    Tilgjengelig fra: 2015-03-16 Laget: 2015-03-16 Sist oppdatert: 2015-07-07
    4. Herbivory strongly influences among-population variation in reproductive output of Lythrum salicaria in its native range
    Åpne denne publikasjonen i ny fane eller vindu >>Herbivory strongly influences among-population variation in reproductive output of Lythrum salicaria in its native range
    2016 (engelsk)Inngår i: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 180, nr 4, s. 1159-1171Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Herbivory can negatively affect several components of plant reproduction. Yet, because of a lack of experimental studies involving multiple populations, the extent to which differences in herbivory contribute to among-population variation in plant reproductive success is poorly known. We determined experimentally the effects of insect herbivory on reproductive output in nine natural populations of the perennial herb Lythrum salicaria along a disturbance gradient in an archipelago in northern Sweden, and we quantified among-population differentiation in resistance to herbivory in a common-garden experiment in the same area. The intensity of leaf herbivory varied >500-fold and mean female reproductive success >400-fold among the study populations. The intensity of herbivory was lowest in populations subject to strong disturbance from ice and wave action. Experimental removal of insect herbivores showed that the effect of herbivory on female reproductive success was correlated with the intensity of herbivory and that differences in insect herbivory could explain much of among-population variation in the proportion of plants flowering and seed production. Population differentiation in resistance to herbivory was limited. The results demonstrate that the intensity of herbivory is a major determinant of flowering and seed output in L. salicaria, but that differences in herbivory are not associated with differences in plant resistance at the spatial scale examined. They further suggest that the physical disturbance regime may strongly influence the performance and abundance of perennial herbs not only because of its effect on interspecific competition, but also because of effects on interactions with specialized herbivores.

    Emneord
    Disturbance gradient, Flowering, Plant-herbivore interactions, Plant resistance, Seed production
    HSV kategori
    Forskningsprogram
    Biologi med inriktning mot ekologisk botanik
    Identifikatorer
    urn:nbn:se:uu:diva-247086 (URN)10.1007/s00442-015-3520-2 (DOI)000373186100022 ()26678991 (PubMedID)
    Forskningsfinansiär
    Swedish Research Council
    Merknad

    Erratum in: OECOLOGIA 180(4), pg. 1173-1174. DOI: 10.1007/s00442-016-3570-0

    Tilgjengelig fra: 2015-03-13 Laget: 2015-03-13 Sist oppdatert: 2017-12-04bibliografisk kontrollert
  • 260.
    Lehndal, Lina
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Hambäck, Peter
    Stockholm Univ, Dept Ecol Environm & Plant Sci, S-10691 Stockholm, Sweden.
    Ericson, Lars
    Umea Univ, Dept Ecol & Environm Sci, S-90187 Umea, Sweden.
    Ågren, Jon
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Herbivory strongly influences among-population variation in reproductive output of Lythrum salicaria in its native range2016Inngår i: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 180, nr 4, s. 1159-1171Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Herbivory can negatively affect several components of plant reproduction. Yet, because of a lack of experimental studies involving multiple populations, the extent to which differences in herbivory contribute to among-population variation in plant reproductive success is poorly known. We determined experimentally the effects of insect herbivory on reproductive output in nine natural populations of the perennial herb Lythrum salicaria along a disturbance gradient in an archipelago in northern Sweden, and we quantified among-population differentiation in resistance to herbivory in a common-garden experiment in the same area. The intensity of leaf herbivory varied >500-fold and mean female reproductive success >400-fold among the study populations. The intensity of herbivory was lowest in populations subject to strong disturbance from ice and wave action. Experimental removal of insect herbivores showed that the effect of herbivory on female reproductive success was correlated with the intensity of herbivory and that differences in insect herbivory could explain much of among-population variation in the proportion of plants flowering and seed production. Population differentiation in resistance to herbivory was limited. The results demonstrate that the intensity of herbivory is a major determinant of flowering and seed output in L. salicaria, but that differences in herbivory are not associated with differences in plant resistance at the spatial scale examined. They further suggest that the physical disturbance regime may strongly influence the performance and abundance of perennial herbs not only because of its effect on interspecific competition, but also because of effects on interactions with specialized herbivores.

  • 261.
    Lehndal, Lina
    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.
    Herbivory Differentially Affects Plant Fitness in Three Populations of the Perennial Herb Lythrum salicaria along a Latitudinal Gradient2015Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, nr 9, artikkel-id e0135939Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Herbivory can negatively and selectively affect plant fitness by reducing growth, survival and reproductive output, thereby influencing plant population dynamics and evolution. We documented intensity of herbivory and experimentally examined its effect on survival, growth and reproductive output in three natural populations of the perennial herb Lythrum salicaria along a latitudinal gradient from southern to northernmost Sweden over two years. The intensity of herbivory and the effects of herbivory on plant fitness were strongest in the southern population and intermediate in the central population. The mean proportion of the leaf area removed ranged from 11% in the southern to 3% in the northern population. Herbivore removal increased plant height 1.5-fold in the southern and 1.2-fold in the central population, the proportion plants flowering 4-fold in the southern and 2-fold in the central population, and seed production per flower 1.6-fold in the southern and 1.2-fold in the central population, but did not affect plant fitness in the northern population. Herbivore removal thus affected the relative fecundity of plants in the three populations: In the control, seed output per plant was 8.6 times higher in the northern population compared to the southern population, whereas after herbivore removal it was 2.5 times higher in the southern population compared to the northern. Proportion of leaf area removed increased with plant size, but tolerance to damage did not vary with size. The results demonstrate that native herbivores may strongly affect the demographic structure of L. salicaria populations, and thereby shape geographic patterns of seed production. They further suggest that the strength of herbivore-mediated selection varies among populations and decreases towards the north.

  • 262.
    Lehndal, Lina
    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.
    Herbivory influences the relative fitness of three native Lythrum salicaria populations, but no evidence of local adaptation along a latitudinal gradientManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Local adaptation along environmental gradients has been documented in many plant species, but the extent to which biotic interactions influence the relative fitness of local and non-local genotypes has rarely been examined experimentally. Previous common-garden experiments detected clinal variation in life history, phenology and resistance to herbivory in the perennial herb Lythrum salicaria along a latitudinal gradient in Sweden, which coincides with a decrease in the length of the growing season and intensity of herbivory from south to north. Here, we included a herbivore-removal treatment in a reciprocal transplant experiment to test whether three populations sampled along the latitudinal gradient are locally adapted, whether differences in resistance and tolerance are consistent across sites and whether herbivory influences the relative performance of the study populations. The results did not reveal any evidence of local adaptation. Instead the southernmost population had the highest relative fitness at all three sites and was consistently less damaged by herbivores than were the other populations. The intensity of herbivory was greatest at the southern site and very low at the northernmost site. The removal of insect herbivores positively affected plant growth and fecundity at the southern and central sites. Herbivore removal also affected the relative fitness of the study populations at the southern site, and tended to do so at the central site. However, the relative ranking of the three populations did not change, indicating that herbivores influenced the strength but not the direction of selection. Genetic drift, recent climatic warming and intermittent strong selection against southern genotypes at northern latitudes may all contribute to the documented patterns of among-population variation in fitness, while similarity in the behaviour and preferences of herbivore populations along the studied gradient may explain the consistent differences in resistance.

  • 263.
    Lehndal, Lina
    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.
    Latitudinal variation in resistance and tolerance to herbivory in the perennial herb Lythrum salicaria is related to intensity of herbivory and plant phenology2015Inngår i: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 28, nr 3, s. 576-589Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Both the length of the growing season and the intensity of herbivory often vary along climatic gradients, which may result in divergent selection on plant phenology, and on resistance and tolerance to herbivory. In Sweden, the length of the growing season and the number of insect herbivore species feeding on the perennial herb Lythrum salicaria decrease from south to north. Previous common-garden experiments have shown that northern L. salicaria populations develop aboveground shoots earlier in the summer, and finish growth before southern populations do. We tested the hypotheses that resistance and tolerance to damage vary with latitude in L. salicaria, and are positively related to the intensity of herbivory in natural populations. We quantified resistance and tolerance of populations sampled along a latitudinal gradient by scoring damage from natural herbivores and fitness in a common-garden experiment in the field, and by documenting oviposition and feeding preference by specialist leaf beetles in a greenhouse experiment. Plant resistance decreased with latitude of origin, whereas plant tolerance increased. Oviposition and feeding preference in the greenhouse, and leaf damage in the common-garden experiment were negatively related to damage in the source populations. The latitudinal variation in resistance was thus consistent with reduced selection from herbivores towards the northern range margin of L. salicaria. Variation in tolerance may be related to differences in the timing of damage in relation to the seasonal pattern of plant growth, as northern genotypes have developed further than southern have when herbivores emerge in early summer.

  • 264.
    Lendvay, Bertalan
    et al.
    Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland..
    Hartmann, Martin
    Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland..
    Brodbeck, Sabine
    Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland..
    Nievergelt, Daniel
    Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland..
    Reinig, Frederick
    Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland..
    Zoller, Stefan
    ETH, Genet Divers Ctr, Univ Str 16, CH-8092 Zurich, Switzerland..
    Parducci, Laura
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Gugerli, Felix
    Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland..
    Buentgen, Ulf
    Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland.;Univ Cambridge, Dept Geog, Downing Pl, Cambridge CB2 3EN, England.;Masaryk Univ, Global Change Res Ctr, Brno 61300, Czech Republic..
    Sperisen, Christoph
    Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland..
    Improved recovery of ancient DNA from subfossil wood - application to the world's oldest Late Glacial pine forest2018Inngår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, nr 4, s. 1737-1748Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Ancient DNA from historical and subfossil wood has a great potential to provide new insights into the history of tree populations. However, its extraction and analysis have not become routine, mainly because contamination of the wood with modern plant material can complicate the verification of genetic information. Here, we used sapwood tissue from 22 subfossil pines that were growing c. 13000yr bp in Zurich, Switzerland. We developed and evaluated protocols to eliminate surface contamination, and we tested ancient DNA authenticity based on plastid DNA metabarcoding and the assessment of post-mortem DNA damage. A novel approach using laser irradiation coupled with bleaching and surface removal was most efficient in eliminating contaminating DNA. DNA metabarcoding confirmed which ancient DNA samples repeatedly amplified pine DNA and were free of exogenous plant taxa. Pine DNA sequences of these samples showed a high degree of cytosine to thymine mismatches, typical of post-mortem damage. Stringent decontamination of wood surfaces combined with DNA metabarcoding and assessment of post-mortem DNA damage allowed us to authenticate ancient DNA retrieved from the oldest Late Glacial pine forest. These techniques can be applied to any subfossil wood and are likely to improve the accessibility of relict wood for genome-scale ancient DNA studies.

  • 265. Lesur, I
    et al.
    Durand, J
    Sebastiani, F
    Gyllenstrand, N
    Bodénès, C
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Kremer, A
    Vendramin, GG
    Plomion, C
    A sample view of the pedunculate oak (Quercus robur) genome from the sequencing of hypomethylated and random genetic libraries2011Inngår i: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 7, nr 6, s. 1277-1285Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Genomic resources have recently been developed for a number of species of Fagaceae, with the purpose of identifying the genetic factors underlying the adaptation of these long-lived, biologically predominant, commercially and ecologically important species to their environment. The sequencing of genomes of the size of the oak genome (740 Mb/C) is now becoming both possible and affordable due to breakthroughs in sequencing technology. However, an understanding of the composition and structure of the oak genome is required before launching a sequencing initiative. We constructed random (Rd) and hypomethylated (Hp) genomic libraries for pedunculate oak (Quercus robur) and carried out a sample sequencing of 2.33 and 2.36 Mb of shotgun DNA from the Rd and Hp libraries, respectively, to provide a first insight into the repetitive element and gene content of the oak genome. We found striking similarities between Rd sequences and previously analyzed BAC end sequences of pedunculate oak, with a similar percentage of known repeat elements (5.56%), an almost identical simple sequence repeat density (i.e., 29 SSRs per 100 kb), an identical profile of SSR motifs (in descending order of frequency—dinucleotide, pentanucleotide, trinucleotide, tetranucleotide, and hexanucleotide motifs). Conversely, the Hp fraction was, as expected, enriched in nuclear genes (2.44-fold enrichment). This enrichment was associated with a lower frequency of retrotransposons than for Rd sequences. We also identified twice as many SSR motifs in the Rd library as in the Hp library. This work provides useful information before opening a new chapter in oak genome sequencing.

  • 266. Li, Junrui
    et al.
    Li, Haipeng
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Li, Sen
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Sjödin, Per
    Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Joint analysis of demography and selection in population genetics: where do we stand and where could we go?2012Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, nr 1, s. 28-44Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Teasing apart the effects of selection and demography on genetic polymorphism remains one of the major challenges in the analysis of population genomic data. The traditional approach has been to assume that demography would leave a genome-wide signature, whereas the effect of selection would be local. In the light of recent genomic surveys of sequence polymorphism, several authors have argued that this approach is questionable based on the evidence of the pervasive role of positive selection and that new approaches are needed. In the first part of this review, we give a few empirical and theoretical examples illustrating the difficulty in teasing apart the effects of selection and demography on genomic polymorphism patterns. In the second part, we review recent efforts to detect recent positive selection. Most available methods still rely on an a priori classification of sites in the genome but there are many promising new approaches. These new methods make use of the latest developments in statistics, explore aspects of the data that had been neglected hitherto or take advantage of the emerging population genomic data. A current and promising approach is based on first estimating demographic and genetic parameters, using, e.g., a likelihood or approximate Bayesian computation framework, focusing on extreme outlier regions, and then using an independent method to confirm these. Finally, especially for species where evidence of natural selection has been limited, more experimental and versatile approaches that contrast populations under varied environmental constraints might be more successful compared with species-wide genome scans in search of specific signatures.

  • 267.
    Li, Xidan
    et al.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Liu, Xiaodong
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Nadaf, Javad
    INRA, Rech Avicoles UR83, F-37380 Nouzilly, France.;Univ Edinburgh, Roslin Inst, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, R D SVS, Roslin EH25 9RG, Midlothian, Scotland..
    Le Bihan-Duval, Elisabeth
    INRA, Rech Avicoles UR83, F-37380 Nouzilly, France..
    Berri, Cecile
    INRA, Rech Avicoles UR83, F-37380 Nouzilly, France..
    Dunn, Ian
    Univ Edinburgh, Roslin Inst, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, R D SVS, Roslin EH25 9RG, Midlothian, Scotland..
    Talbot, Richard
    Univ Edinburgh, Roslin Inst, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, R D SVS, Roslin EH25 9RG, Midlothian, Scotland..
    De Koning, Dirk-Jan
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden.;Univ Edinburgh, Roslin Inst, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, R D SVS, Roslin EH25 9RG, Midlothian, Scotland..
    Using Targeted Resequencing for Identification of Candidate Genes and SNPs for a QTL Affecting the pH Value of Chicken Meat2015Inngår i: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 5, nr 10, s. 2085-2089Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Using targeted genetical genomics, a quantitative trait locus (QTL) affecting the initial postmortem pH value of chicken breast muscle (Pectoralis major) on chromosome 1 (GGA1) recently was fine-mapped. Thirteen genes were present in the QTL region of approximately 1 Mb. In this study, 10 birds that were inferred to be homozygous for either the high (QQ) or low (qq) QTL allele were selected for resequencing. After enrichment for 1 Mb around the QTL region, >500 x coverage for the QTL region in each of the 10 birds was obtained. In total 5056 single-nucleotide polymorphisms (SNPs) were identified for which the genotypes were consistent with one of the QTL genotypes. We used custom tools to identify putative causal mutations in the mapped QTL region from these SNPs. Four nonsynonymous SNPs differentiating the two QTL genotype groups were identified within four local genes (PRDX4, EIF2S3, PCYT1B, and E1BTD2). Although these are likely candidate SNPs to explain the QTL effect, 54 additional consensus SNPs were detected within gene-related regions (untranslated regions, splicing sites CpG island, and promoter regions) for the QQ birds and 71 for the qq birds. These could also play a role explaining the observed QTL effect. The results provide an important step for prioritizing among a large amount of candidate mutations and significantly contribute to the understanding of the genetic mechanisms affecting the initial postmortem pH value of chicken muscle.

  • 268.
    Li, Yuan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik, Evolutionär funktionsgenomik.
    Stocks, Michael
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Hemmilä, Sofia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik, Evolutionär funktionsgenomik.
    Källman, Thomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik, Evolutionär funktionsgenomik.
    Zhu, Hongtao
    Zhou, Yongfeng
    Chen, Jun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik, Evolutionär funktionsgenomik.
    Liu, Jianquan
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci2010Inngår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 27, nr 5, s. 1001-1014Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 269. Li, Zhonghu
    et al.
    Zhang, Qian
    Liu, Jianquan
    Källman, Thomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    The Pleistocene demography of an alpine juniper of the Qinghai-Tibetan Plateau: tabula rasa, cryptic refugia or something else?2011Inngår i: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 38, nr 1, s. 31-43Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Aim Numerous palaeoecological and genetic studies have shown that different tree species responded in very different ways to Pleistocene climatic oscillations. Some were forced into small refugia far from their current range, while others were able to survive in small refugia close to, or even within, their current natural range. In this study we examine the Pleistocene demography of a juniper species (Juniperus przewalskii, Cupressaceae) from the Qinghai-Tibetan Plateau. Location The Qinghai-Tibetan Plateau (QTP). Methods Eight nuclear loci were sequenced in 141 individuals from 20 natural populations distributed across the entire natural range of J. przewalskii, and coalescent analysis was used to test demographic hypotheses. Results The overall nucleotide diversity in the sample was low (pi(sil) = 0.0029), with few rare alleles and pronounced population genetic structure (F-ST = 0.181). We detected a division previously found using chloroplast DNA markers: all segregating sites in populations from the central part of the QTP appear to be a subset of those found around the edge of the plateau, confirming the relatively young age of the former. In contrast to the middle Pleistocene bottlenecks detected in boreal tree species, the coalescent-based analyses failed to reject the standard neutral model for the juniper species considered here. Main conclusions Juniperus przewalskii did not undergo marked changes in population sizes during the Pleistocene, although this species seems to have experienced recent, post-glacial expansion. This finding is largely consistent with the limited number of previous studies on conifer species of the QTP, but contradicts findings of studies on boreal species. These findings have wide implications for understanding plant species' responses to past climatic oscillations on the high-elevation QTP.

  • 270. Li, Zhonghu
    et al.
    Zou, Jiabin
    Mao, Kangshan
    Lin, Kao
    Li, Haipeng
    Liu, Jianquan
    Källman, Thomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Population Genetic Evidence for Complex Evolutionary Histories of Four High Altitude Juniper Species in the Qinghai-Tibetan Plateau2012Inngår i: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 66, nr 3, s. 831-845Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Population genetics data based on multiple nuclear loci provide invaluable information to understand demographic, selective, and divergence histories of the current species. We studied nucleotide variation at 13 nuclear loci in 53 populations distributed among four closely related, but morphologically distinct juniper species of the QinghaiTibetan Plateau (QTP). We used a novel approach combining Approximate Bayesian Computation and a recently developed neutrality test based on the maximum frequency of derived mutations to examine the demographic and selective histories of individual species, and isolation-with-migration analyses to study the joint history of the species and detect gene flow between them. We found that (1) the four species, which diverged in response to the extensive QTP uplifts, have different demographic histories; (2) two loci, Pgi and CC0822, depart significantly from neutrality in one species and Pgi, is also marginally significant in another; and (3) shared polymorphisms are common, indicating both incomplete lineage sorting and gene flow after species divergence. In addition, the detected unidirectional gene flow provides indirect support for the theoretical prediction that introgression should mostly take place from local to invading species. Our results, together with previous studies, underscore complex evolutionary histories of plant diversification in the biodiversity-hotspot QTP.

  • 271. Limpens, J.
    et al.
    Granath, Gustaf
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Aerts, R.
    Heijmans, M. M. P. D.
    Sheppard, L. J.
    Bragazza, L.
    Williams, B. L.
    Rydin, Håkan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Bubier, J.
    Moore, T.
    Rochefort, L.
    Mitchell, E. A. D.
    Buttler, A.
    van den Berg, L. J. L.
    Gunnarsson, U.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Francez, A. -J
    Gerdol, R.
    Thormann, M.
    Grosvernier, P.
    Wiedermann, M. M.
    Nilsson, M. B.
    Hoosbeek, M. R.
    Bayley, S.
    Nordbakken, J. -F
    Paulissen, M. P. C. P.
    Hotes, S.
    Breeuwer, A.
    Ilomets, M.
    Tomassen, H. B. M.
    Leith, I.
    Xu, B.
    Glasshouse vs field experiments: do they yield ecologically similar results for assessing N impacts on peat mosses?2012Inngår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 195, nr 2, s. 408-418Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Peat bogs have accumulated more atmospheric carbon (C) than any other terrestrial ecosystem today. Most of this C is associated with peat moss (Sphagnum) litter. Atmospheric nitrogen (N) deposition can decrease Sphagnum production, compromising the C sequestration capacity of peat bogs. The mechanisms underlying the reduced production are uncertain, necessitating multifactorial experiments. We investigated whether glasshouse experiments are reliable proxies for field experiments for assessing interactions between N deposition and environment as controls on Sphagnum N concentration and production. We performed a meta-analysis over 115 glasshouse experiments and 107 field experiments. We found that glasshouse and field experiments gave similar qualitative and quantitative estimates of changes in Sphagnum N concentration in response to N application. However, glasshouse-based estimates of changes in production even qualitative assessments diverged from field experiments owing to a stronger N effect on production response in absence of vascular plants in the glasshouse, and a weaker N effect on production response in presence of vascular plants compared to field experiments. Thus, although we need glasshouse experiments to study how interacting environmental factors affect the response of Sphagnum to increased N deposition, we need field experiments to properly quantify these effects.

  • 272. Limpens, J.
    et al.
    Granath, Gustaf
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Gunnarsson, Urban
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Aerts, R.
    Bayley, S.
    Bragazza, L.
    Bubier, J.
    Buttler, A.
    van den Berg, L. J. L.
    Francez, A-J
    Gerdol, R.
    Grosvernier, P.
    Heijmans, M. M. P. D.
    Hoosbeek, M. R.
    Hotes, S.
    Ilomets, M.
    Leith, I.
    Mitchell, E. A. D.
    Moore, T.
    Nilsson, M. B.
    Nordbakken, J-F
    Rochefort, L.
    Rydin, Håkan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Sheppard, L. J.
    Thormann, M.
    Wiedermann, M. M.
    Williams, B. L.
    Xu, B.
    Climatic modifiers of the response to nitrogen deposition in peat-forming Sphagnum mosses: a meta-analysis2011Inngår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 191, nr 2, s. 496-507Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Peatlands in the northern hemisphere have accumulated more atmospheric carbon (C) during the Holocene than any other terrestrial ecosystem, making peatlands long-term C sinks of global importance. Projected increases in nitrogen (N) deposition and temperature make future accumulation rates uncertain. Here, we assessed the impact of N deposition on peatland C sequestration potential by investigating the effects of experimental N addition on Sphagnum moss. We employed meta-regressions to the results of 107 field experiments, accounting for sampling dependence in the data. We found that high N loading (comprising N application rate, experiment duration, background N deposition) depressed Sphagnum production relative to untreated controls. The interactive effects of presence of competitive vascular plants and high tissue N concentrations indicated intensified biotic interactions and altered nutrient stochiometry as mechanisms underlying the detrimental N effects. Importantly, a higher summer temperature (mean for July) and increased annual precipitation intensified the negative effects of N. The temperature effect was comparable to an experimental application of almost 4 g N m(-2) yr(-1) for each 1 degrees C increase. Our results indicate that current rates of N deposition in a warmer environment will strongly inhibit C sequestration by Sphagnum-dominated vegetation.

  • 273. Lind, Marten
    et al.
    Kallman, Thomas
    Chen, Jun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Ma, Xiao-Fei
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Bousquet, Jean
    Morgante, Michele
    Zaina, Giusi
    Karlsson, Bo
    Elfstrand, Malin
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Stenlid, Jan
    A Picea abies Linkage Map Based on SNP Markers Identifies QTLs for Four Aspects of Resistance to Heterobasidion parviporum Infection2014Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, nr 7, s. e101049-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A consensus linkage map of Picea abies, an economically important conifer, was constructed based on the segregation of 686 SNP markers in a F-1 progeny population consisting of 247 individuals. The total length of 1889.2 cM covered 96.5% of the estimated genome length and comprised 12 large linkage groups, corresponding to the number of haploid P. abies chromosomes. The sizes of the groups (from 5.9 to 9.9% of the total map length) correlated well with previous estimates of chromosome sizes (from 5.8 to 10.8% of total genome size). Any locus in the genome has a 97% probability to be within 10 cM from a mapped marker, which makes the map suited for QTL mapping. Infecting the progeny trees with the root rot pathogen Heterobasidion parviporum allowed for mapping of four different resistance traits: lesion length at the inoculation site, fungal spread within the sapwood, exclusion of the pathogen from the host after initial infection, and ability to prevent the infection from establishing at all. These four traits were associated with two, four, four and three QTL regions respectively of which none overlapped between the traits. Each QTL explained between 4.6 and 10.1% of the respective traits phenotypic variation. Although the QTL regions contain many more genes than the ones represented by the SNP markers, at least four markers within the confidence intervals originated from genes with known function in conifer defence; a leucoanthocyanidine reductase, which has previously been shown to upregulate during H. parviporum infection, and three intermediates of the lignification process; a hydroxycinnamoyl CoA shikimate/quinate hydroxycinnamoyltransferase, a 4-coumarate CoA ligase, and a R2R3-MYB transcription factor.

  • 274.
    Linde, Anna-Malin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Rates and patterns of bryophyte molecular evolution2019Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Plants have been growing on land for at least 450 million years. The bryophytes comprising the three phyla liverworts, mosses and hornworts, are considered to be the closest extant relatives to the plants that colonized land. Bryophytes has been described as evolutionary “unchanging sphinxes of the past” regarding both morphological and genetic potential. This suggestion has some support in limited studies of molecular evolution within bryophytes, but has also been questioned based on e.g., studies of species diversification rates. To shed more light on this controversy, the overall aim of this thesis is to investigate rates and patterns of bryophyte molecular evolution.

    Our data suggest that the per nucleotide mutation rates in bryophytes are lower than those in angiosperms. Likewise, angiosperms are also more dynamic in terms of genome size, structural rearrangements, genome duplications and transposon activity. However, our data show that mutation rates of bryophytes are higher or at least on par with those of gymnosperms. Genome evolution in bryophytes is actually, in many aspects, similar to that of gymnosperms. Gymnosperms and bryophytes are both characterized by a low speciation rate, a low nucleotide mutation rate, low variation in chromosome numbers and relatively stable genome sizes. Studies have also suggested that macrosynteny is better conserved between conifer species compared with angiosperms, just as this study shows for bryophytes.

    Hybridization and introgression has been suggested to affect speciation and evolution. Recent genomic data shows that hybridization and introgression in angiosperms is more common then previously thought, but the question is less well studied in bryophytes. The present study gave some support to the occurrence of introgression between Marchantia polymorpha subspecies, but refute a previous hypothesis that M. polymorpha subsp. ruderalis is a new stabilized hybrid between M. polymorpha montivagans and polymorpha.

    An additional aspect of genome evolution and complexity is changes in gene regulatory networks. Gene regulatory networks generally appear more complex in angiosperms compared with bryophytes; also reflected in the circadian clock; with more gene components and more duplicated paralogous members, with possibly overlapping function, allowing a more robust and flexible system. Our studies of the plant circadian clock revealed that orthologs of most genes of the A. thaliana clock were present already in charophycean algae. Although gene numbers and complexity have generally increased during plant circadian clock evolution, our results suggest that gene loss has also been important in shaping the circadian clocks in the three bryophyte groups.

    Delarbeid
    1. Evolutionary history of the Marchantia polymorpha complex
    Åpne denne publikasjonen i ny fane eller vindu >>Evolutionary history of the Marchantia polymorpha complex
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-392455 (URN)
    Tilgjengelig fra: 2019-09-04 Laget: 2019-09-04 Sist oppdatert: 2019-09-05
    2. Rates and patterns of molecular evolution in liverwort genomes, with focus of Marchantiopsida.
    Åpne denne publikasjonen i ny fane eller vindu >>Rates and patterns of molecular evolution in liverwort genomes, with focus of Marchantiopsida.
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-392459 (URN)
    Tilgjengelig fra: 2019-09-05 Laget: 2019-09-05 Sist oppdatert: 2019-09-05
    3. Rates of structural changes in bryophyte genomes; exemplified by Marchantiopsida
    Åpne denne publikasjonen i ny fane eller vindu >>Rates of structural changes in bryophyte genomes; exemplified by Marchantiopsida
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-392461 (URN)
    Tilgjengelig fra: 2019-09-05 Laget: 2019-09-05 Sist oppdatert: 2019-09-05
    4. Early evolution of the land plant circadian clock
    Åpne denne publikasjonen i ny fane eller vindu >>Early evolution of the land plant circadian clock
    Vise andre…
    2017 (engelsk)Inngår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 216, nr 2, s. 576-590Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    While angiosperm clocks can be described as an intricate network of interlocked transcriptional feedback loops, clocks of green algae have been modelled as a loop of only two genes. To investigate the transition from a simple clock in algae to a complex one in angiosperms, we performed an inventory of circadian clock genes in bryophytes and charophytes. Additionally, we performed functional characterization of putative core clock genes in the liverwort Marchantia polymorpha and the hornwort Anthoceros agrestis. Phylogenetic construction was combined with studies of spatiotemporal expression patterns and analysis of M. polymorpha clock gene mutants. Homologues to core clock genes identified in Arabidopsis were found not only in bryophytes but also in charophytes, albeit in fewer copies. Circadian rhythms were detected for most identified genes in M. polymorpha and A. agrestis, and mutant analysis supports a role for putative clock genes in M. polymorpha. Our data are in line with a recent hypothesis that adaptation to terrestrial life occurred earlier than previously expected in the evolutionary history of charophyte algae. Both gene duplication and acquisition of new genes was important in the evolution of the plant circadian clock, but gene loss has also contributed to shaping the clock of bryophytes.

    Emneord
    Marchantia polymorpha, bryophyte, circadian clock, evolution, transcription factor
    HSV kategori
    Forskningsprogram
    Biologi med inriktning mot evolutionär funktionsgenomik
    Identifikatorer
    urn:nbn:se:uu:diva-317912 (URN)10.1111/nph.14487 (DOI)000427294000024 ()28244104 (PubMedID)
    Forskningsfinansiär
    Swedish Research Council, 2011-5609Swedish Research Council, 2014-522
    Tilgjengelig fra: 2017-03-22 Laget: 2017-03-22 Sist oppdatert: 2019-09-05bibliografisk kontrollert
  • 275.
    Linde, Anna-Malin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Linnean Ctr Plant Biol Uppsala, Uppsala, Sweden.
    Eklund, D. Magnus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Linnean Ctr Plant Biol Uppsala, Uppsala, Sweden.
    Kubota, Akane
    Kyoto Univ, Grad Sch Biostudies, Kyoto 6068502, Japan.
    Pederson, Eric R. A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Linnean Ctr Plant Biol Uppsala, Uppsala, Sweden.
    Holm, Karl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Linnean Ctr Plant Biol Uppsala, Uppsala, Sweden.
    Gyllenstrand, Niclas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Linnean Ctr Plant Biol Uppsala, Uppsala, Sweden.
    Nishihama, Ryuichi
    Kyoto Univ, Grad Sch Biostudies, Kyoto 6068502, Japan.
    Cronberg, Nils
    Lund Univ, Dept Biol, Ecol Bldg, SE-22362 Lund, Sweden.
    Muranaka, Tomoaki
    Kyoto Univ, Grad Sch Sci, Kyoto 6068502, Japan.
    Oyama, Tokitaka
    Kyoto Univ, Grad Sch Sci, Kyoto 6068502, Japan.
    Kohchi, Takayuki
    Kyoto Univ, Grad Sch Biostudies, Kyoto 6068502, Japan.
    Lagercrantz, Ulf
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Linnean Ctr Plant Biol Uppsala, Uppsala, Sweden.
    Early evolution of the land plant circadian clock2017Inngår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 216, nr 2, s. 576-590Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    While angiosperm clocks can be described as an intricate network of interlocked transcriptional feedback loops, clocks of green algae have been modelled as a loop of only two genes. To investigate the transition from a simple clock in algae to a complex one in angiosperms, we performed an inventory of circadian clock genes in bryophytes and charophytes. Additionally, we performed functional characterization of putative core clock genes in the liverwort Marchantia polymorpha and the hornwort Anthoceros agrestis. Phylogenetic construction was combined with studies of spatiotemporal expression patterns and analysis of M. polymorpha clock gene mutants. Homologues to core clock genes identified in Arabidopsis were found not only in bryophytes but also in charophytes, albeit in fewer copies. Circadian rhythms were detected for most identified genes in M. polymorpha and A. agrestis, and mutant analysis supports a role for putative clock genes in M. polymorpha. Our data are in line with a recent hypothesis that adaptation to terrestrial life occurred earlier than previously expected in the evolutionary history of charophyte algae. Both gene duplication and acquisition of new genes was important in the evolution of the plant circadian clock, but gene loss has also contributed to shaping the clock of bryophytes.

  • 276.
    Linde, Anna-Malin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Eklund, Magnus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Cronberg, Nils
    Biodiversity, Department of Biology, Lund University.
    Lagercrantz, Ulf
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Rates and patterns of molecular evolution in liverwort genomes, with focus of Marchantiopsida.Manuskript (preprint) (Annet vitenskapelig)
  • 277.
    Linde, Anna-Malin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Eklund, Magnus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Cronberg, Nils
    Biodiversity, Department of Biology, Lund University.
    Lagercrantz, Ulf
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Rates of structural changes in bryophyte genomes; exemplified by MarchantiopsidaManuskript (preprint) (Annet vitenskapelig)
  • 278.
    Linde, Anna-Malin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Sawangproh, Weerachon
    Biodiversity, Department of Biology, Lund University.
    Cronberg, Nils
    Biodiversity, Department of Biology, Lund University.
    Lagercrantz, Ulf
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Evolutionary history of the Marchantia polymorpha complexManuskript (preprint) (Annet vitenskapelig)
  • 279. Liu, Chunping
    et al.
    Tsuda, Yoshiaki
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Shen, Hailong
    Hu, Lijiang
    Saito, Yoko
    Ide, Yuji
    Genetic Structure and Hierarchical Population Divergence History of Acer mono var. mono in South and Northeast China2014Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, nr 1, s. e87187-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species' evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (F-ST = 0.073; G(ST)' = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species' more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study.

  • 280.
    Liu, Xiaodong
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Mechanisms of speciation in Silene2018Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    A fundamental question in the field of evolutionary biology is how new species originate. Investigating speciation benefits from an integrated approach, which requires a solid understanding of ecology, reproductive biology, geographical distribution, underlying genetic architecture of reproductive isolation (RI), demographic history and genomic divergence. In this thesis, I studied the evolution of reproductive isolation in the sister species Silene dioica (L.) Clairv. and S. latifolia Poiret. The aims of the thesis are to investigate (1) the individual and cumulative contributions of extrinsic and intrinsic reproductive barriers between S. dioica and S. latifolia, (2) the genetic architecture of traits associated with reproductive barriers (3) the demographic history of lineage-split between the two species, (4) genomic patterns of divergence between the species.

    I found that multiple extrinsic pre- and postzygotic barriers resulting from ecological differentiation contributed most to total RI, while intrinsic barriers had substantial individual strength but contributed weakly to total RI. QTL mapping revealed evidence for genetic coupling of QTLs controlling traits associated with RI, although QTLs were overall widely distributed. QTLs related to sexually dimorphic traits were located on or near the pseudo-autosomal region of the sex chromosomes. The best-supported demographic model suggests heterogeneous population size and migration rates among genome-wide loci and points to the presence of barrier loci. Genomic divergence (measured using FST and dXY) was commonly accentuated around the middle of linkage groups and near QTLs for traits associated with reproductive barriers.

    In summary, the results in my thesis indicate that the speciation process is driven by multiple interacting and complex reproductive barriers. The genomic divergence landscape is shaped by interplay of the magnitude of gene flow, the strength and timing of selection, and other  confounding factors such as genomic features.

    Delarbeid
    1. Ecological divergence plays an important role in strong but complex reproductive isolation in campions (Silene).
    Åpne denne publikasjonen i ny fane eller vindu >>Ecological divergence plays an important role in strong but complex reproductive isolation in campions (Silene).
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    Emneord
    adaptation, germination, reproductive barrier, species distribution modeling, speciation
    HSV kategori
    Forskningsprogram
    Biologi med inriktning mot ekologisk botanik
    Identifikatorer
    urn:nbn:se:uu:diva-356985 (URN)
    Tilgjengelig fra: 2018-08-09 Laget: 2018-08-09 Sist oppdatert: 2019-03-11
    2. Genetic architecture of traits associated with reproductive barriers in Silene:: Coupling, sex chromosomes and variation
    Åpne denne publikasjonen i ny fane eller vindu >>Genetic architecture of traits associated with reproductive barriers in Silene:: Coupling, sex chromosomes and variation
    2018 (engelsk)Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, nr 19, s. 3889-3904Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    The evolution of reproductive barriers and their underlying genetic architecture is ofcentral importance for the formation of new species. Reproductive barriers can becontrolled either by few large-effect loci suggesting strong selection on key traits,or by many small-effect loci, consistent with gradual divergence or with selection onpolygenic or multiple traits. Genetic coupling between reproductive barrier loci fur-ther promotes divergence, particularly divergence with ongoing gene flow. In thisstudy, we investigated the genetic architectures of ten morphological, phenologicaland life history traits associated with reproductive barriers between the hybridizingsister species Silene dioica and S. latifolia; both are dioecious with XY-sex determina-tion. We used quantitative trait locus (QTL) mapping in two reciprocal F2crosses.One to six QTLs per trait, including nine major QTLs (PVE > 20%), were detectedon 11 of the 12 linkage groups. We found strong evidence for coupling of QTLs foruncorrelated traits and for an important role of sex chromosomes in the geneticarchitectures of reproductive barrier traits. Unexpectedly, QTLs detected in the twoF2crosses differed largely, despite limited phenotypic differences between themand sufficient statistical power. The widely dispersed genetic architectures of traitsassociated with reproductive barriers suggest gradual divergence or multifariousselection. Coupling of the underlying QTLs likely promoted divergence with geneflow in this system. The low congruence of QTLs between the two crosses furtherpoints to variable and possibly redundant genetic architectures of traits associatedwith reproductive barriers, with important implications for the evolutionary dynam-ics of divergence and speciation.

    Emneord
    adaptation, ddRAD-seq, genetic coupling, QTL, reproductive barrier, speciation
    HSV kategori
    Forskningsprogram
    Biologi med inriktning mot evolutionär genetik
    Identifikatorer
    urn:nbn:se:uu:diva-356980 (URN)10.1111/mec.14562 (DOI)000446838400012 ()29577481 (PubMedID)
    Forskningsfinansiär
    Swedish Research Council, 2012-03622
    Tilgjengelig fra: 2018-08-09 Laget: 2018-08-09 Sist oppdatert: 2019-03-11bibliografisk kontrollert
    3. Genomic divergence and reproductive isolation in Silene
    Åpne denne publikasjonen i ny fane eller vindu >>Genomic divergence and reproductive isolation in Silene
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Forskningsprogram
    Biologi med inriktning mot evolutionär genetik
    Identifikatorer
    urn:nbn:se:uu:diva-356986 (URN)