| 1. |
- Aagaard, Sunniva M.D. 1977-, et al.
(författare)
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Homoploid hybridization in Central European Diphasiastrum (Lycopodiaceae).
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Three species of homoploid hybrid origin are commonly recognized among Central European Diphasiastrum, and reticulate evolutionary events have for a long time been acknowledged as an important factor contributing to the species count in the genus. Presented evidence obtained from molecular data has until recently been scarce and inconclusive. Recent studies have, however, documented reticulate phylogenetic patterns involving all putative parental combinations reported from Central Europe. Reciprocal crosses involving the same parental combinations have also been confirmed. In order to further explore these putative reticulate events, admixture analyses using a Bayesian approach as implemented in the program NewHybrids are conducted on an expanded dataset obtained from six Central European populations from where putative hybrid taxa are reported. A majority of the accessions included in the analyses were inferred to represent pure bred D. alpinum, D. complanatum, D. tristachyum, F1 hybrids, F2 hybrids or backcrosses with one of the parent species. Accessions displaying ambiguous classification were found in both allopatric parent populations as well as in Central European hybrid populations. Presented results indicate the presence of frequently occurring hybrid zones with first and second generation hybrids as well as backcrosses.
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| 2. |
- Berlin Kolm, Sofia, et al.
(författare)
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Genetic diversity, population structure and phenotypic variation in European Salix viminalis L. (Salicaceae)
- 2014
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Ingår i: Tree Genetics & Genomes. - : Springer Science and Business Media LLC. - 1614-2942 .- 1614-2950. ; 10:6, s. 1595-1610
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Tidskriftsartikel (refereegranskat)abstract
- To investigate the potential of association genetics for willow breeding, Salix viminalis germplasm was assembled from UK and Swedish collections (comprising accessions from several European countries) and new samples collected from nature. A subset of the germplasm was planted at two sites (UK and Sweden), genotyped using 38 SSR markers and assessed for phenological and biomass traits. Population structure, genetic differentiation (F-ST) and quantitative trait differentiation (Q(ST)) were investigated. The extent and patterns of trait adaptation were assessed by comparing F-ST and Q(ST) parameters. Of the 505 genotyped diploid accessions, 27 % were not unique. Genetic diversity was high: 471 alleles was amplified; the mean number of alleles per locus was 13.46, mean observed heterozygosity was 0.55 and mean expected heterozygosity was 0.62. Bayesian clustering identified four subpopulations which generally corresponded to Western Russia, Western Europe, Eastern Europe and Sweden. All pairwise F-ST values were highly significant (p<0.001) with the greatest genetic differentiation detected between the Western Russian and the Western European subpopulations (F-ST = 0.12), and the smallest between the Swedish and Eastern European populations (F-ST = 0.04). The Swedish population also had the highest number of identical accessions, supporting the view that S. viminalis was introduced into this country and has been heavily influenced by humans. Q(ST) values were high for growth cessation and leaf senescence, and to some extent stem diameter, but low for bud burst time and shoot number. Overall negative clines between longitudinal coordinates and leaf senescence, bud burst and stem diameter were also found.
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| 3. |
- Chen, Jun, et al.
(författare)
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Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce (Picea abies)
- 2012
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Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 191:3, s. 865-881
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the genetic basis of local adaptation is challenging due to the subtle balance among conflicting evolutionary forces that are involved in its establishment and maintenance. One system with which to tease apart these difficulties is clines in adaptive characters. Here we analyzed genetic and phenotypic variation in bud set, a highly heritable and adaptive trait, among 18 populations of Norway spruce (Picea abies), arrayed along a latitudinal gradient ranging from 47°N to 68°N. We confirmed that variation in bud set is strongly clinal, using a subset of five populations. Genotypes for 137 single-nucleotide polymorphisms (SNPs) chosen from 18 candidate genes putatively affecting bud set and 308 control SNPs chosen from 264 random genes were analyzed for patterns of genetic structure and correlation to environment. Population genetic structure was low (F(ST) = 0.05), but latitudinal patterns were apparent among Scandinavian populations. Hence, part of the observed clinal variation should be attributable to population demography. Conditional on patterns of genetic structure, there was enrichment of SNPs within candidate genes for correlations with latitude. Twenty-nine SNPs were also outliers with respect to F(ST). The enrichment for clinal variation at SNPs within candidate genes (i.e., SNPs in PaGI, PaPhyP, PaPhyN, PaPRR7, and PaFTL2) indicated that local selection in the 18 populations, and/or selection in the ancestral populations from which they were recently derived, shaped the observed cline. Validation of these genes using expression studies also revealed that PaFTL2 expression is significantly associated with latitude, thereby confirming the central role played by this gene in the control of phenology in plants.
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| 4. |
- Chen, Jun, et al.
(författare)
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Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms compared to angiosperms
- 2012
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 13, s. 589-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Background: A detailed knowledge about which genes are expressed in which tissues and at which developmental stage is important for understanding both the function of genes and their evolution. For the vast majority of species, transcriptomes are still largely uncharacterized and even in those where substantial information is available it is often in the form of partially sequenced transcriptomes. With the development of next generation sequencing, a single experiment can now give both a snap-shot of the transcribed part of a species genome and simultaneously estimate levels of gene expression.Results: mRNA from actively growing needles of Norway spruce (Picea abies) was sequenced using next generation sequencing technology. In total, close to 70 million fragments with a length of 76 bp were sequenced resulting in 5 Gbp of raw data. A de novo assembly of these reads were, together with publicly available expressed sequence tag (EST) data from Norway spruce, used to create a reference transcriptome. Of the 38,419 PUTs (putative unique transcripts) longer than 150 bp in this reference assembly, 59% show similarity to ESTs from other spruce species and of the remaining PUTs, 3,704 show similarity to protein sequences from other plant species, leaving 4,167 PUTs with limited similarity to currently available plant proteins. By predicting coding frames and comparing not only the Norway spruce PUTs, but also PUTs from the close relatives Picea glauca and Picea sitchensis to both Pinus taeda and Taxus mairei, we obtained estimates of synonymous and non-synonymous divergence among conifer species. In addition, we detected close to 15,000 SNPs of high quality and estimated gene expression difference between samples collected during dark and light conditions.Conclusions: Our study yielded a large number of single nucleotide polymorphisms as well as estimates of gene expression on transcriptome scale. In agreement with a recent study we find that the synonymous substitution rate per year (0.6 × 10-09 and 1.1 × 10-09) is an order of magnitude smaller than values reported for angiosperm herbs, but if one takes generation time in to account, most of this difference disappear. The estimates of the non-synonymous over the synonymous divergence (dN/dS ratio) reported here is in general much lower than 1 and only a few genes showed a ratio larger than 1.
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| 5. |
- Díez-del-Molino, David, et al.
(författare)
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Population genomics reveals lack of greater white-fronted introgression into the Swedish lesser white-fronted goose
- 2020
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Interspecific introgression is considered a potential threat to endangered taxa. One example where this has had a major impact on conservation policy is the lesser white-fronted goose (LWfG). After a dramatic decline in Sweden, captive breeding birds were released between 1981–1999 with the aim to reinforce the population. However, the detection of greater white-fronted goose (GWfG) mitochondrial DNA in the LWfG breeding stock led to the release program being dismantled, even though the presence of GWfG introgression in the actual wild Swedish LWfG population was never documented. To examine this, we sequenced the complete genomes of 21 LWfG birds from the Swedish, Russian and Norwegian populations, and compared these with genomes from other goose species, including the GWfG. We found no evidence of interspecific introgression into the wild Swedish LWfG population in either nuclear genomic or mitochondrial data. Moreover, Swedish LWfG birds are genetically distinct from the Russian and Norwegian populations and display comparatively low genomic diversity and high levels of inbreeding. Our findings highlight the utility of genomic approaches in providing scientific evidence that can help improve conservation management as well as policies for breeding and reinforcement programmes.
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| 6. |
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| 7. |
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| 8. |
- Ghelardini, Luisa, et al.
(författare)
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Genetic architecture of spring and autumn phenology in Salix
- 2014
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Ingår i: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 14, s. 31-
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Tidskriftsartikel (refereegranskat)abstract
- Background: In woody plants from temperate regions, adaptation to the local climate results in annual cycles of growth and dormancy, and optimal regulation of these cycles are critical for growth, long-term survival, and competitive success. In this study we have investigated the genetic background to growth phenology in a Salix pedigree by assessing genetic and phenotypic variation in growth cessation, leaf senescence and bud burst in different years and environments. A previously constructed linkage map using the same pedigree and anchored to the annotated genome of P. trichocarpa was improved in target regions and used for QTL analysis of the traits. The major aims in this study were to map QTLs for phenology traits in Salix, and to identify candidate genes in QTL hot spots through comparative mapping with the closely related Populus trichocarpa. Results: All traits varied significantly among genotypes and the broad-sense heritabilities ranged between 0.5 and 0.9, with the highest for leaf senescence. In total across experiment and years, 80 QTLs were detected. For individual traits, the QTLs explained together from 21.5 to 56.5% of the variation. Generally each individual QTL explained a low amount of the variation but three QTLs explained above 15% of the variation with one QTL for leaf senescence explaining 34% of the variation. The majority of the QTLs were recurrently identified across traits, years and environments. Two hotspots were identified on linkage group (LG) II and X where narrow QTLs for all traits co-localized. Conclusions: This study provides the most detailed analysis of QTL detection for phenology in Salix conducted so far. Several hotspot regions were found where QTLs for different traits and QTLs for the same trait but identified during different years co-localised. Many QTLs co-localised with QTLs found in poplar for similar traits that could indicate common pathways for these traits in Salicaceae. This study is an important first step in identifying QTLs and candidate genes for phenology traits in Salix.
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| 9. |
- Gyllenstrand, Niclas, et al.
(författare)
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A Norway spruce FLOWERING LOCUS T homolog is implicated in control of growth rhythm in conifers
- 2007
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 144:1, s. 248-257
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Tidskriftsartikel (refereegranskat)abstract
- Growth in perennial plants possesses an annual cycle of active growth and dormancy that is controlled by environmental factors, mainly photoperiod and temperature. In conifers and other nonangiosperm species, the molecular mechanisms behind these responses are currently unknown. In Norway spruce (Picea abies L. Karst.) seedlings, growth cessation and bud set are induced by short days and plants from southern latitudes require at least 7 to 10 h of darkness, whereas plants from northern latitudes need only 2 to 3 h of darkness. Bud burst, on the other hand, is almost exclusively controlled by temperature. To test the possible role of Norway spruce FLOWERING LOCUS T (FT)-like genes in growth rhythm, we have studied expression patterns of four Norway spruce FT family genes in two populations with a divergent bud set response under various photoperiodic conditions. Our data show a significant and tight correlation between growth rhythm (both bud set and bud burst), and expression pattern of one of the four Norway spruce phosphatidylethanolamine-binding protein gene family members (PaFT4) over a variety of experimental conditions. This study strongly suggests that one Norway spruce homolog to the FT gene, which controls flowering in angiosperms, is also a key integrator of photoperiodic and thermal signals in the control of growth rhythms in gymnosperms. The data also indicate that the divergent adaptive bud set responses of northern and southern Norway spruce populations, both to photoperiod and light quality, are mediated through PaFT4. These results provide a major advance in our understanding of the molecular control of a major adaptive trait in conifers and a tool for further molecular studies of adaptive variation in plants.
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| 10. |
- Gyllenstrand, Niclas, 1969-
(författare)
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Effects of Social Organisation on Spatial Genetic Structures in Formica Ants
- 2002
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The social organization of social insect colonies can be broadly defined as monogynous, single reproductive female or polygynous, several reproductive females. Monogynous organization is genetically simple while polygynous is more complex and the two social forms differ commonly in mating and dispersal behaviour as well as in colony foundation. The aim of the thesis was to study how social organization affects spatial genetic structures. Formica wood ants are suitable study organisms as both intra- and interspecific variation in social organization can occur.A set of microsatellite loci were characterized from a small insert library in the ant Formica exsecta. The microsatellite loci cross amplified among other Formica species. In a population of F. exsecta containing both monogynous and polygynous colonies, genetic differentiation was stronger in the polygynous form at both nuclear and mitochondrial DNA (mtDNA) markers. The data further suggests that female dispersal is restricted in the polygynous form.Female gene flow between the social forms appears to be absent in the ant F. truncorum as the social forms contained non overlapping mtDNA haplotypes. Strong nuclear genetic differentiation and profound allele frequency differences further suggest that male interform gene flow is weak. The social forms evolve largely independently when found in sympatry though the forms do not represent separate evolutionary lineages within the species.Spatial intraspecific genetic differentiation was similar in the species F. polyctena and F. rufa though quantitative differences in the level of polygyny existed. In polygynous populations of the ant F. lugubris, female gene flow was restricted but male gene flow was strong and homogenized nuclear allele frequencies.
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| 11. |
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| 12. |
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| 13. |
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| 14. |
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| 15. |
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| 16. |
- Hallingbäck, Henrik, et al.
(författare)
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Association mapping in Salix viminalis L. (Salicaceae) - identification of candidate genes associated with growth and phenology
- 2016
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Ingår i: Global Change Biology Bioenergy. - : Wiley. - 1757-1693 .- 1757-1707. ; 8:3, s. 670-685
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Tidskriftsartikel (refereegranskat)abstract
- Willow species (Salix) are important as short-rotation biomass crops for bioenergy, which creates a demand for faster genetic improvement and breeding through deployment of molecular marker-assisted selection (MAS). To find markers associated with important adaptive traits, such as growth and phenology, for use in MAS, we genetically dissected the trait variation of a Salix viminalis (L.) population of 323 accessions. The accessions were sampled throughout northern Europe and were established at two field sites in Pustnas, Sweden, and at Woburn, UK, offering the opportunity to assess the impact of genotype-by-environment interactions (GxE) on trait-marker associations. Field measurements were recorded for growth and phenology traits. The accessions were genotyped using 1536 SNP markers developed from phenology candidate genes and from genes previously observed to be differentially expressed in contrasting environments. Association mapping between 1233 of these SNPs and the measured traits was performed taking into account population structure and threshold selection bias. At a false discovery rate (FDR) of 0.2, 29 SNPs were associated with bud burst, leaf senescence, number of shoots or shoot diameter. The percentage of accession variation explained by these associations ranged from 0.3% to 4.4%, suggesting that the studied traits are controlled by many loci of limited individual impact. Despite this, a SNP in the EARLY FLOWERING 3 gene was repeatedly associated (FDR<0.2) with bud burst. The rare homozygous genotype exhibited 0.4-1.0 lower bud burst scores than the other genotype classes on a five-grade scale. Consequently, this marker could be promising for use in MAS and the gene deserves further study. Otherwise, associations were less consistent across sites, likely due to their small estimates and to considerable GxE interactions indicated by multivariate association analyses and modest trait accession correlations across sites (0.32-0.61).
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| 17. |
- Heuertz, Myriam, et al.
(författare)
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Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]
- 2006
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Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 174:4, s. 2095-2105
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Tidskriftsartikel (refereegranskat)abstract
- DNA polymorphism at 22 loci was studied in an average of 47 Norway spruce [Picea abies (L.) Karst.] haplotypes sampled in seven populations representative of the natural range. The overall nucleotide variation was limited, being lower than that observed in most plant species so far studied. Linkage disequilibrium was also restricted and did not extend beyond a few hundred base pairs. All populations, with the exception of the Romanian population, could be divided into two main domains, a Baltico-Nordic and an Alpine one. Mean Tajima's D and Fay and Wu's H across loci were both negative, indicating the presence of an excess of both rare and high-frequency-derived variants compared to the expected frequency spectrum in a standard neutral model. Multilocus neutrality tests based on D and H led to the rejection of the standard neutral model and exponential growth in the whole population as well as in the two main domains. On the other hand, in all three cases the data are compatible with a severe bottleneck occurring some hundreds of thousands of years ago. Hence, demographic departures from equilibrium expectations and population structure will have to be accounted for when detecting selection at candidate genes and in association mapping studies, respectively.
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| 18. |
- Holm, Karl, et al.
(författare)
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Does the core circadian clock in the moss Physcomitrella patens (Bryophyta) comprise a single loop?
- 2010
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Ingår i: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 10, s. 109-
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Tidskriftsartikel (refereegranskat)abstract
- Background: The endogenous circadian clock allows the organism to synchronize processes both to daily and seasonal changes. In plants, many metabolic processes such as photosynthesis, as well as photoperiodic responses, are under the control of a circadian clock. Comparative studies with the moss Physcomitrella patens provide the opportunity to study many aspects of land plant evolution. Here we present a comparative overview of clock-associated components and the circadian network in the moss P. patens.Results: The moss P. patens has a set of conserved circadian core components that share genetic relationship and gene expression patterns with clock genes of vascular plants. These genes include Myb-like transcription factors PpCCA1a and PpCCA1b, pseudo-response regulators PpPRR1-4, and regulatory elements PpELF3, PpLUX and possibly PpELF4. However, the moss lacks homologs of AtTOC1, AtGI and the AtZTL-family of genes, which can be found in all vascular plants studied here. These three genes constitute essential components of two of the three integrated feed-back loops in the current model of the Arabidopsis circadian clock mechanism. Consequently, our results suggest instead a single loop circadian clock in the moss. Possibly as a result of this, temperature compensation of core clock gene expression appears to be decreased in P. patens.Conclusions: This study is the first comparative overview of the circadian clock mechanism in a basal land plant, the moss P. patens. Our results indicate that the moss clock mechanism may represent an ancestral state in contrast to the more complex and partly duplicated structure of subsequent land plants. These findings may provide insights into the understanding of the evolution of circadian network topology.
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| 19. |
- Karlgren, Anna, et al.
(författare)
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Conserved function of core clock proteins in the gymnosperm Norway spruce (Picea abies L. Karst)
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:3, s. e60110-
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Tidskriftsartikel (refereegranskat)abstract
- From studies of the circadian clock in the plant model species Arabidopsis (Arabidopsis thaliana), a number of important properties and components have emerged. These include the genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), GIGANTEA (GI), ZEITLUPE (ZTL) and TIMING OF CAB EXPRESSION 1 (TOC1 also known as PSEUDO-RESPONSE REGULATOR 1 (PRR1)) that via gene expression feedback loops participate in the circadian clock. Here, we present results from ectopic expression of four Norway spruce (Picea abies) putative homologs (PaCCA1, PaGI, PaZTL and PaPRR1) in Arabidopsis, their flowering time, circadian period length, red light response phenotypes and their effect on endogenous clock genes were assessed. For PaCCA1-ox and PaZTL-ox the results were consistent with Arabidopsis lines overexpressing the corresponding Arabidopsis genes. For PaGI consistent results were obtained when expressed in the gi2 mutant, while PaGI and PaPRR1 expressed in wild type did not display the expected phenotypes. These results suggest that protein function of PaCCA1, PaGI and PaZTL are at least partlyconserved compared to Arabidopsis homologs, however further studies are needed to reveal the protein function of PaPRR1. Our data suggest that components of thethree-loop network typical of the circadian clock in angiosperms were present beforethe split of gymnosperms and angiosperms.
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| 20. |
- Karlgren, Anna, et al.
(författare)
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Evolution of the PEBP Gene Family in Plants : Functional Diversification in Seed Plant Evolution
- 2011
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 156:4, s. 1967-1977
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Tidskriftsartikel (refereegranskat)abstract
- The phosphatidyl ethanolamine-binding protein (PEBP) gene family is present in all eukaryote kingdoms, with three subfamilies identified in angiosperms (FLOWERING LOCUS T [FT], MOTHER OF FT AND TFL1 [MFT], and TERMINAL FLOWER1 [TFL1] like). In angiosperms, PEBP genes have been shown to function both as promoters and suppressors of flowering and to control plant architecture. In this study, we focus on previously uncharacterized PEBP genes from gymnosperms. Extensive database searches suggest that gymnosperms possess only two types of PEBP genes, MFT-like and a group that occupies an intermediate phylogenetic position between the FT-like and TFL1-like (FT/TFL1-like). Overexpression of Picea abies PEBP genes in Arabidopsis (Arabidopsis thaliana) suggests that the FT/TFL1-like genes (PaFTL1 and PaFTL2) code for proteins with a TFL1-like function. However, PaFTL1 and PaFTL2 also show highly divergent expression patterns. While the expression of PaFTL2 is correlated with annual growth rhythm and mainly confined to needles and vegetative and reproductive buds, the expression of PaFTL1 is largely restricted to microsporophylls of male cones. The P. abies MFT-like genes (PaMFT1 and PaMFT2) show a predominant expression during embryo development, a pattern that is also found for many MFT-like genes from angiosperms. P. abies PEBP gene expression is primarily detected in tissues undergoing physiological changes related to growth arrest and dormancy. A first duplication event resulting in two families of plant PEBP genes (MFT-like and FT/TFL1-like) seems to coincide with the evolution of seed plants, in which independent control of bud and seed dormancy was required, and the second duplication resulting in the FT-like and TFL1-like clades probably coincided with the evolution of angiosperms.
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| 21. |
- Karlgren, Anna, et al.
(författare)
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FLOWERING LOCUS T/TERMINAL FLOWER1-Like Genes Affect Growth Rhythm and Bud Set in Norway Spruce
- 2013
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 163:2, s. 792-803
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Tidskriftsartikel (refereegranskat)abstract
- The timing of bud set, as one determinant of the annual growth rhythm, is critical for local adaptation of the conifer Norway spruce (Picea abies). Previous gene expression and population genetic studies have suggested a role for P. abies FLOWERING LOCUS T/TERMINAL FLOWER1-Like2 (PaFTL2) in the control of growth cessation and bud set in Norway spruce as well as in local adaptation resulting in clinal variation for timing of bud set. Using transgenic plants with PaFTL2 driven by an inducible promoter, we found that PaFTL2 indeed induces bud set and most probably also growth cessation. PaFTL2 shows high expression around the procambium and vascular tissue and in the crown region in buds of both seedlings and older trees. Furthermore, PaFTL2 expression is induced in vegetative shoots and all bud types in late summer, when growth cessation occurs. This supports the notion that PaFTL2 is involved in growth cessation. A close paralog to PaFTL2, PaFTL1, is strongly expressed in meristems during the summer, possibly to repress meristem activity and the formation of needle primordia during this period. The temporal and spatial expression of PaFTL1 and PaFTL2 largely complement each other, which suggests that they act in concert to control perennial growth in Norway spruce.
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| 22. |
- Karlgren, Anna, 1982-
(författare)
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Genetic Control of Annual Growth Rhythm in the Conifer Norway Spruce (Picea Abies L. Karst)
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Norway spruce (Picea abies L. Karst) is a conifer belonging to the group gymnosperms and is an ecologically and economically important species in several parts of Europe. It is crucial for trees like Norway spruce to adapt timing of events such as bud set and growth cessation to the local environment in order to maximize the growth period while avoiding frost damage.This thesis aims at widening the knowledge about genetic control of annual growth rhythm in Norway spruce and particularly the control of bud set. Using spruce transformants ectopically expressing PaFT/TFL1-LIKE 2 (PaFTL2) the prior hypothesis that PaFTL2 induces bud set is confirmed. This is further supported by spatial and temporal expression patterns in seedlings and adult trees. It is further shown that gymnosperms possess at least two FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1)-like genes with TFL1-like function, suggesting the ancestor of FT and TFL1 to be more TFL1-like. PaFTL1 appears to have complementary expression patterns to that of PaFTL2 both spatially and temporally indicating they may act together to control growth in Norway spruce.Since bud set is controlled by photoperiod and circadian clock genes are implicated in this process, putative clock homologs were studied to gain insight into the circadian clock in gymnosperms. Several clock homologs were identified and their expression showed a diurnal pattern but the expression was rapidly damped in constant conditions. Transgenic Arabidopsis expressing putative core clock genes from spruce indicate that at least three genes, PaCCA1, PaGI and PaZTL, appear to have a conserved function between angiosperms and gymnosperms. Taken together these results suggest that gymnosperms have a similar core clock structure as angiosperms even though fundamental differences might exist since the cycling of the clock genes were rapidly damped in free-running conditions.The studies presented in this thesis support substantial conservation of pathway components controlling photoperiodic responses in angiosperms and gymnosperms and identify PaFTL2 as a component of growth rhythm control. However, important changes in these processes are also evident. The results provide a solid basis for future research on molecular mechanisms controlling an adaptive trait in an important non-model organism.
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| 23. |
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| 24. |
- Källman, Thomas, et al.
(författare)
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A significant fraction of 21-nucleotide small RNA originates from phased degradation of resistance genes in several perennial species
- 2013
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 162:2, s. 741-754
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Tidskriftsartikel (refereegranskat)abstract
- Small RNAs (sRNAs), including microRNA (miRNA) and short-interfering RNA (siRNA), are important in the regulation of diverse biological processes. Comparative studies of sRNAs from plants have mainly focused on miRNA, even though they constitute a mere fraction of the total sRNA diversity. In this study, we report results from an in-depth analysis of the sRNA population from the conifer spruce (Picea abies) and compared the results with those of a range of plant species. The vast majority of sRNA sequences in spruce can be assigned to 21-nucleotide-long siRNA sequences, of which a large fraction originate from the degradation of transcribed sequences related to nucleotide-binding site-leucine-rich repeat-type resistance genes. Over 90% of all genes predicted to contain either a Toll/interleukin-1 receptor or nucleotide-binding site domain showed evidence of siRNA degradation. The data further suggest that this phased degradation of resistance-related genes is initiated from miRNA-guided cleavage, often by an abundant 22-nucleotide miRNA. Comparative analysis over a range of plant species revealed a huge variation in the abundance of this phenomenon. The process seemed to be virtually absent in several species, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and nonvascular plants, while particularly high frequencies were observed in spruce, grape (Vitis vinifera), and poplar (Populus trichocarpa). This divergent pattern might reflect a mechanism to limit runaway transcription of these genes in species with rapidly expanding nucleotide-binding site-leucine-rich repeat gene families. Alternatively, it might reflect variation in a counter-counter defense mechanism between plant species.
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| 25. |
- Källman, Thomas, et al.
(författare)
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Major difference in short RNA populations among plants - the results of interaction with pathogen?
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Small RNA (sRNA) including miRNA and siRNA are important in the regulation of diverse biological processes. Comparative studies of sRNA from plants have mainly focused on miRNA even though this group in most cases is just a mere fraction of the total sRNA diversity. In the present study we report results from an in-depth analysis of the sRNA population from the conifer Picea abies and compared the results to those of a range of species from the plant kingdom. The vast majority of sRNA in P. abies was 21 nucleotides long siRNA, of which a large fraction originate from degradation of transcribed sequences related to TIR-NBS-LRR (Toll/Interleukin-1-Nucleotide Binding Site-Leucine Rich Repeats) type resistance genes. Over 90% of all genes predicted to contain either a TIR or an NBS domain showed evidence of siRNA degradation. Data further suggests that those phased siRNA are initiated from miRNA guided cleavage, often by an abundant 22 nt miRNA. Comparative analysis over a range of divergent plant species revealed a large variation between species in the abundance of this phenomenon. The process seemed to be virtually absent in several species, including Arabidopsis thaliana, Oryza sativa and non-vascular plants, while particularly high frequencies were observed in Vitis vinifera and Populus thrichocarpa. This divergent pattern between species might reflect a mechanism to limit runaway transcription of these genes in species with rapidly expanding NBS-LRR gene families. Alternatively it might reflect variation in a counter-counter defence mechanism partly affected by differences in life history traits, e.g. perennial versus annual life cycles. A major difference between annuals and perennials, affecting the evolution of resistance, is that perennials will with almost certainty encounter many different pathogens before reproduction, and that the long generation times confers problems in matching the evolutionary rates of the pathogens.
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| 26. |
- Källman, Thomas, et al.
(författare)
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Patterns of nucleotide diversity at photoperiod related genes in the conifer Norway spruce [Picea abies (L.) (Karst)]
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:5, s. e95306-
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Tidskriftsartikel (refereegranskat)abstract
- The ability of plants to track seasonal changes is largely dependent on genes assigned to the photoperiod pathway, and variation in those genes is thereby important for adaptation to local day length conditions. Extensive physiological data in several temperate conifer species suggest that populations are adapted to local light conditions, but data on the genes underlying this adaptation are more limited. Here we present nucleotide diversity data from 19 genes putatively involved in photoperiodic response in Norway spruce (Picea abies). Based on similarity to model plants the genes were grouped into three categories according to their presumed position in the photoperiod pathway: photoreceptors, circadian clock genes, and downstream targets. An HKA (Hudson, Kreitman and Aquade) test showed a significant excess of diversity at photoreceptor genes, but no departure from neutrality at circadian genes and downstream targets. Departures from neutrality were also tested with Tajima's D and Fay and Wu's H statistics under three demographic scenarios: the standard neutral model, a population expansion model, and a more complex population split model. Only one gene, the circadian clock gene PaPRR3 with a highly positive Tajima's D value, deviates significantly from all tested demographic scenarios. As the PaPRR3 gene harbours multiple non-synonymous variants it appears as an excellent candidate gene for control of photoperiod response in Norway spruce
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| 27. |
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| 28. |
- Larsson, Hanna, et al.
(författare)
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Distribution of Long-Range Linkage Disequilibrium and Tajima's D Values in Scandinavian Populations of Norway Spruce (Picea abies)
- 2013
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Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 3:5, s. 795-806
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 29. |
- Larsson, Hanna, et al.
(författare)
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The HypoMethylated Partial Restriction (HMPR) method reduces the repetitive content of genomic libraries in Norway spruce (Picea abies)
- 2013
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Ingår i: Tree Genetics & Genomes. - : Springer Science and Business Media LLC. - 1614-2942 .- 1614-2950. ; 9:2, s. 601-612
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 30. |
- Lesur, I, et al.
(författare)
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A sample view of the pedunculate oak (Quercus robur) genome from the sequencing of hypomethylated and random genetic libraries
- 2011
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Ingår i: Tree Genetics & Genomes. - : Springer Science and Business Media LLC. - 1614-2942 .- 1614-2950. ; 7:6, s. 1277-1285
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 31. |
- Linde, Anna-Malin, et al.
(författare)
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Early evolution of the land plant circadian clock
- 2017
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 216:2, s. 576-590
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 32. |
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| 33. |
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| 34. |
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| 35. |
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| 36. |
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| 37. |
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| 38. |
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| 39. |
- Nilsson, Emil, et al.
(författare)
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Six polymorphic microsatellite markers for Plantago maritima
- 2006
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Ingår i: Molecular Ecology Notes. - : Wiley. - 1471-8278 .- 1471-8286. ; 6:4, s. 1093-1095
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Tidskriftsartikel (refereegranskat)abstract
- Plantago maritima displays an extraordinary variation in breeding system. In northern Europe, the species occurs as either self-incompatible or self-compatible, and as unisexual females or co-sexual hermaphrodites. The isolation of polymorphic codominant markers will provide the necessary tools to investigate the proportion of self-fertilized seeds and levels of inbreeding depression in natural populations of this species. Isolation of microsatellite loci was achieved using a membrane-enrichment method for four loci, and a streptavidin-coated-beads method for two loci. Primers were designed in microsatellite flanking sequences and were analysed using fluorescent labels.
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| 40. |
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| 41. |
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| 42. |
- Quang, Tran Ho, et al.
(författare)
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EVALUATING POPULATION STRUCTURE BY NEUTRAL MARKERS AND QUANTITATIVE GENETIC PARAMETERS IN A THINNED PROGENY TRIAL OF EUCALYPTUS UROPHYLLA
- 2013
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Ingår i: Journal of Tropical Forest Science. - 0128-1283. ; 25, s. 350-360
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this study was to estimate from microsatellite variation the levels of homozygote excess within nine populations comprising a combined population and progeny trial of Eucalyptus urophylla in northern Vietnam and to compare the population differentiation estimated by molecular markers with that estimated from growth traits. The material was thinned in year 2 (removing 75% of the trees) and year 5 (removing 37% of the remaining trees). Microsatellite variation was measured after the second thinning. Homozygote excess (F-IS) among populations ranged from 0.069 to 0.198. Most of the molecular variation was within populations (97.1% of the total variation), in agreement with the low FST value (0.023) of neutral molecular markers (F-ST) (0.023). Estimates of quantitative trait differentiation (Q(ST)) based on a univariate model among populations for height and diameter at breast height were low over the first eight years of the trial, at most 0.21. This presumably reflected selection for the same traits in a common environment. The differences between Q(ST) after the second thinning and F-ST, a measure of the effects of selection, were also small. Prospects for further breeding progress are bright, whether or not crosses are made among populations.
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| 43. |
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| 44. |
- Rogell, Björn, et al.
(författare)
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Six polymorphic microsatellite loci in the Natterjack toad, Bufo calamita
- 2005
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Ingår i: Molecular Ecology Notes. - : Wiley. - 1471-8278 .- 1471-8286. ; 5:3, s. 639-640
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Tidskriftsartikel (refereegranskat)abstract
- The Natterjack toad, Bufo calamita, is a locally endangered anuran endemic to Europe. It has been used as a model organism in several ecological studies. When studying the genetic structure of marginalized populations of the species, there was a need to involve more loci in the study than those previously published. Here we present the development of six polymorphic microsatellite loci in the Natterjack. The loci will be used for studying population genetic structure and gene flow between populations.
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| 45. |
- Seppa, Perttu, et al.
(författare)
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Colony fission affects kinship in a social insect
- 2008
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Ingår i: Behavioral Ecology and Sociobiology. - : Springer Science and Business Media LLC. - 0340-5443 .- 1432-0762. ; 62:4, s. 589-597
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Tidskriftsartikel (refereegranskat)abstract
- Establishment of new groups is an important step in the life history of a social species. Fissioning is a common mode not only in group proliferation, for instance, as a regular part of the life cycle in the honey bee, but also when multiple females reproduce in the same group, as in multiple-queen ant societies. We studied the genetic consequences of fissioning in the ant Proformica longiseta, based on DNA microsatellites. In P. longiseta, new nests arise by fissioning from the old ones when they grow large, and the daughter nests consist of workers and queens or queen pupae but never both. Our results show that fissioning is not entirely random with respect to kinship. Workers tend to segregate along kin lines, but only when the initial relatedness in the parental nests is low. Workers in a daughter nest also tend to be associated with closely related adult queens, whereas such an association is not detected between workers and queen pupae. Most queens and workers are carried to the daughter nest by a specialized group of transporting workers, suggesting active kin discrimination by them. Fissioning pattern in P. longiseta is different from that found in other social insects with regular fission (e.g., the honey bee, swarm-founding wasps), where no fissioning along kin lines has been found. It does, however, resemble fissioning in another group of social animals: primates.
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| 46. |
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| 47. |
- Seppä, Perttu, et al.
(författare)
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Colony kin structure and breeding patterns in the social wasp, Polistes biglumis
- 2011
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Ingår i: Insectes Sociaux. - : Springer Science and Business Media LLC. - 0020-1812 .- 1420-9098. ; 58:3, s. 345-355
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Tidskriftsartikel (refereegranskat)abstract
- We used DNA microsatellites to study colony kin structure and breeding patterns in the primitively eusocial wasp Polistes biglumis. P. biglumis inhabits cool areas at high altitudes and, as a consequence, has a reduced colony cycle compared to more temperate Polistes. P. biglumis colonies are always founded and controlled by a single foundress, but nest failure is common and foundresses losing their nests do not have time to start new ones due to the short season. Instead, nests are characterized by frequent female turnover, in the form of females taking over (usurpation) other con-specific nests. Our results showed that most nests had offspring from multiple unrelated females, including some where multiple females were not observed in monitoring. Reconstruction of behavioural events from the genetic data revealed three types of multiple matriline nests: (a) nests that were usurped by another female, where the original nest owner disappeared following the usurpation event, (b) nests that were joined by another female, where the original nest owner stayed following the joining event, (c) nests that were both usurped and joined by other females. We also found, for the first time, a clear indication of multiple mating by Polistes females. Moreover, males mating with the same female were related, which may be explained by the lek mating system of P. biglumis. Finally, we analysed the nest sex ratios and how it changed during the season and found that sexes were produced sequentially, males before females.
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| 48. |
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| 49. |
- Seppä, Perttu, et al.
(författare)
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Obligatory female philopatry affects genetic population structure in the ant Proformica longiseta
- 2006
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Ingår i: Insectes Sociaux. - : Springer Science and Business Media LLC. - 0020-1812 .- 1420-9098. ; 53:3, s. 362-368
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Tidskriftsartikel (refereegranskat)abstract
- Evolution of sociality has instigated many changes in the biology of social insects. Particularly, evolution towards complex social systems in ants affects how individuals move in space, usually by making females philopatric. Proformica longisetais well-suited for studying the effects of female philopatry, because female sexuals are wingless and do not actively disperse. We studied genetic population structure in P. longiseta in local scale both as genetic viscosity within one subpopulation, and as differentiation between closely (0.1-1.5 km) located subpopulations, by using nuclear (microsatellites) and mitochondrial (SSCP) markers. Dependent colony founding by splitting old nests is the only known nest founding strategy in P. longiseta. However, no genetic viscosity was detected at the nuclear markers within the subpopulation studied, possibly due to the dynamic nature of P. longiseta populations. The extreme female philopatry showed as strong structure between closely located subpopulations in the mitochondrial genome, but there was no isolation by distance showing that the differentiation pattern was random. Genetic structure in the nuclear genome was much weaker, and there was an indication of isolation by distance. This suggests that male dispersal is strong but not totally free across the area. Finally, non-dispersing P. longiseta females necessarily mate locally raising the possibility of inbreeding, but inbreeding coefficients showed that mating is random.
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| 50. |
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