| 1. |
- Avia, Komlan, et al.
(author)
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Association of FLOWERING LOCUS T/TERMINAL FLOWER 1-like gene FTL2 expression with growth rhythm in Scots pine (Pinus sylvestris)
- 2014
-
In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 204:1, s. 159-170
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Journal article (peer-reviewed)abstract
- Understanding the genetic basis of the timing of bud set, an important trait in conifers, is relevant for adaptation and forestry practice. In common garden experiments, both Scots pine (Pinus sylvestris) and Norway spruce (Picea abies) show a latitudinal cline in the trait. We compared the regulation of their bud set biology by examining the expression of PsFTL2, a Pinus sylvestris homolog to PaFTL2, a FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1)-like gene, the expression levels of which have been found previously to be associated with the timing of bud set in Norway spruce. In a common garden study, we analyzed the relationship of bud phenology under natural and artificial photoperiods and the expression of PsFTL2 in a set of Scots pine populations from different latitudes. The expression of PsFTL2 increased in the needles preceding bud set and decreased during bud burst. In the northernmost population, even short night periods were efficient to trigger this expression, which also increased earlier under all photoperiodic regimes compared with the southern populations. Despite the different biology, with few limitations, the two conifers that diverged 140 million yr ago probably share an association of FTL2 with bud set, pointing to a common mechanism for the timing of growth cessation in conifers.
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| 2. |
- Benavides, Raquel, et al.
(author)
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The GenTree Leaf Collection : Inter- and intraspecific leaf variation in seven forest tree species in Europe
- 2021
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In: Global Ecology and Biogeography. - : John Wiley & Sons. - 1466-822X .- 1466-8238. ; 30:3, s. 590-597
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Journal article (peer-reviewed)abstract
- Motivation Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide variation in leaf traits from seven of the most ecologically and economically important tree species in Europe. Sample collection and trait assessment are embedded in the GenTree project (EU-Horizon 2020), which aims at characterizing the genetic and phenotypic variability of forest tree species to optimize the management and sustainable use of forest genetic resources. Our dataset captures substantial intra- and interspecific leaf phenotypic variability, and provides valuable information for studying the relationship between ecosystem functioning and trait variability of individuals, and the response and resilience of species to environmental changes. Main types of variable contained We chose morphological and chemical characters linked to trade-offs between acquisition and conservation of resources and water use, namely specific leaf area, leaf size, carbon and nitrogen content and their ratio, and the isotopic signature of stable isotope C-13 and N-15 in leaves. Spatial location and grain We surveyed between 18 and 22 populations per species, 141 in total, across Europe. Time period Leaf sampling took place between 2016 and 2017. Major taxa and level of measurement We sampled at least 25 individuals in each population, 3,569 trees in total, and measured traits in 35,755 leaves from seven European tree species, i.e. the conifers Picea abies, Pinus pinaster and Pinus sylvestris, and the broadleaves Betula pendula, Fagus sylvatica, Populus nigra and Quercus petraea. Software format The data files are in ASCII text, tab delimited, not compressed.
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| 3. |
- Fogelqvist, Johan, et al.
(author)
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Cryptic population genetic structure : the number of inferred clusters depends on sample size
- 2010
-
In: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:2, s. 314-323
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Journal article (peer-reviewed)abstract
- Clustering methods have been used extensively to unravel cryptic population genetic structure. We investigated the effect of the number of individuals sampled in each location on the resulting number of clusters. Our study was motivated by recent results in Arabidopsis thaliana: studies in which more than one individual was sampled per location apparently have led to a much higher number of clusters than studies where only one individual was sampled in each location, as is generally done in this species. We show, using computer simulations and microsatellite data in A. thaliana, that the number of sampled individuals indeed has a strong impact on the number of resulting clusters. This effect is smaller if the sampled populations have a hierarchical structure. In most cases, sampling 5-10 individuals per population should be enough. The results argue for abandoning the concept of 'accessions' in partially selfing organisms.
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| 4. |
- Karpale, Mikko, et al.
(author)
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Activation of nuclear receptor PXR induces atherogenic lipids and PCSK9 through SREBP2-mediated mechanism
- 2021
-
In: British Journal of Pharmacology. - : Macmillan Publishers Ltd.. - 0007-1188 .- 1476-5381. ; 178:12, s. 2461-2481
-
Journal article (peer-reviewed)abstract
- BACKGROUND AND PURPOSE: Many drugs and environmental contaminants induce hypercholesterolemia and promote the risk of atherosclerotic cardiovascular disease. The mechanisms involved are poorly defined precluding efficient prediction and prevention. We tested the hypothesis that pregnane X receptor (PXR), a xenobiotic-sensing nuclear receptor, regulates the level of circulating atherogenic lipids in humans and utilized mouse experiments to identify the mechanisms involved.EXPERIMENTAL APPROACH: We performed serum NMR metabolomics in healthy volunteers administered rifampicin, a prototypical human PXR ligand, or placebo in a crossover setting. Furthermore, we used high-fat diet fed wildtype and PXR knockout mice to investigate the mechanisms and pathways mediating the PXR-induced alterations in cholesterol homeostasis.KEY RESULTS: Activation of PXR induced cholesterogenesis both in pre-clinical and clinical settings. In human volunteers, rifampicin increased IDL, LDL and total cholesterol and lathosterol-cholesterol ratio, a marker of cholesterol synthesis, suggesting increased cholesterol synthesis. Mechanistic studies in mice indicated that PXR activation launches widespread induction of the cholesterol synthesis genes including the rate-limiting Hmgcr and upregulates the intermediates in the Kandutsch-Russell cholesterol synthesis pathway in the liver. Additionally, PXR activation induced plasma PCSK9, a negative regulator of hepatic LDL uptake, in both mice and humans. We propose that these effects were mediated through increased proteolytic activation of SREBP2 in response to PXR activation.CONCLUSION AND IMPLICATIONS: PXR activation induces cholesterol synthesis and elevates LDL and total cholesterol in humans. The PXR-SREBP2 pathway is a novel regulator of the cholesterol and PCSK9 synthesis, and a molecular mechanism for drug- and chemical-induced hypercholesterolemia.
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| 5. |
- Kastally, Chedly, et al.
(author)
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Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research
- 2022
-
In: The Plant Journal. - : John Wiley & Sons. - 0960-7412 .- 1365-313X. ; 109:5, s. 1337-1350
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Journal article (peer-reviewed)abstract
- Pinus sylvestris (Scots pine) is the most widespread coniferous tree in the boreal forests of Eurasia, with major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies, genetic mapping and genomic selection. We present a new 50K single-nucleotide polymorphism (SNP) genotyping array for Scots pine research, breeding and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array and identified 47 712 high-quality SNPs for the final array (called 'PiSy50k'). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissue-specific expression patterns and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.9%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the level of Mendelian error was negligible. In addition, array genotypes successfully discriminate between Scots pine populations of Finnish and Scottish origins. The PiSy50k SNP array will be a valuable tool for a wide variety of future genetic studies and forestry applications.
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| 6. |
- Kemi, Ulla, et al.
(author)
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Role of vernalization and of duplicated Flowering Locus C in the perennial Arabidopsis lyrata
- 2013
-
In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 197:1, s. 323-335
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Journal article (peer-reviewed)abstract
- FLOWERING LOCUS C (FLC) is one of the main genes influencing the vernalization requirement and natural flowering time variation in the annual Arabidopsis thaliana. Here we studied the effects of vernalization on flowering and its genetic basis in the perennial Arabidopsis lyrata. Two tandemly duplicated FLC genes (FLC1 and FLC2) were compared with respect to expression and DNA sequence. The effect of vernalization on flowering and on the expression of FLC1 was studied in three European populations. The genetic basis of the FLC1 expression difference between two of the populations was further studied by expression quantitative trait locus (eQTL) mapping and sequence analysis. FLC1 was shown to have a likely role in the vernalization requirement for flowering in A. lyrata. Vernalization decreased its expression and the northern study populations showed higher FLC1 expression than the southern one. eQTL mapping between two of the populations revealed one eQTL affecting FLC1 expression in the genomic region containing the FLC genes. Most FLC1 sequence differences between the study populations were found in the promoter region and in the first intron. Variation in the FLC1 sequence may cause differences in FLC1 expression between late- and early-flowering A. lyrata populations.
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| 7. |
- Lascoux, Martin, et al.
(author)
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Local adaptation in plants
- 2016
-
In: Encyclopedia of Life Sciences. - : John Wiley & Sons. - 1476-9506.
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Journal article (peer-reviewed)
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| 8. |
- Lascoux, Martin, et al.
(author)
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Past demography in forest trees : what can we learn from nuclear DNA sequences that we do not already know?
- 2008
-
In: Plant Ecology & Diversity. - : Informa UK Limited. - 1755-0874 .- 1755-1668. ; 1:2, s. 209-215
-
Journal article (peer-reviewed)abstract
- Acquiring nuclear DNA sequences in forest tree species is becoming easier as molecular tools are developing rapidly and we now have at our disposal an array of theoretical methods to carry out statistical inferences from multilocus sequence variation. In the present article we use results from two recent studies of nuclear DNA sequence polymorphism in Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) to illustrate what additional insights to each species' history can be gained compared with classical phylogeographic studies based on chloroplast or mitochondrial DNA. The sampling schemes and statistical analyses used in these two studies were similar facilitating a comparison between them. In both cases we inferred the presence of a rather severe bottleneck predating the Last Glacial Maximum (∌18,000 years ago). This result is discussed in relation to recent reassessments of the fossil pollen record and to its implication for our understanding of adaptation. Finally we briefly outline some suggestions for future research.
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| 9. |
- Leinonen, Päivi H., et al.
(author)
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Local adaptation in European populations of Arabidopsis lyrata (Brassicaceae)
- 2009
-
In: American Journal of Botany. - : Wiley. - 0002-9122 .- 1537-2197. ; 96:6, s. 1129-1137
-
Journal article (peer-reviewed)abstract
- We studied local adaptation to contrasting environments usingan organism that is emerging as a model for evolutionary plantbiology—the outcrossing, perennial herb Arabidopsis lyratasubsp. petraea (Brassicaceae). With reciprocal transplant experiments,we found variation in cumulative fitness, indicating adaptivedifferentiation among populations. Nonlocal populations didnot have significantly higher fitness than the local population.Experimental sites were located in Norway (alpine), Sweden (coastal),and Germany (continental). At all sites after one year, thelocal population had higher cumulative fitness, as quantifiedby survival combined with rosette area, than at least one ofthe nonlocal populations. At the Norwegian site, measurementswere done for two additional years, and fitness differencespersisted. The fitness components that contributed most to differencesin cumulative fitness varied among sites. Relatively small rosettearea combined with a large number of inflorescences producedby German plants may reflect differentiation in life history.The results of the current study demonstrate adaptive populationdifferentiation in A. lyrata along a climatic gradient in Europe.The studied populations harbor considerable variation in severalcharacters contributing to adaptive population differentiation.The wealth of genetic information available makes A. lyrataa highly attractive system also for examining the functionaland genetic basis of local adaptation in plants.
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| 10. |
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| 11. |
- Leppälä, Johanna, et al.
(author)
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Investigating incipient speciation in Arabidopsis lyrata from patterns of transmission ratio distortion
- 2013
-
In: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 194:3, s. 697-708
-
Journal article (peer-reviewed)abstract
- Our understanding of the development of intrinsic reproductive isolation is still largely based on theoretical models and thorough empirical studies on a small number of species. Theory suggests that reproductive isolation develops through accumulation of epistatic genic incompatibilities, also known as Bateson-Dobzhansky-Muller (BDM) incompatibilities. We can detect these from marker transmission ratio distortion (TRD) in hybrid progenies of crosses between species or populations, where TRD is expected to result from selection against heterospecific allele combinations in hybrids. TRD may also manifest itself because of intragenomic conflicts or competition between gametes or zygotes. We studied early stage speciation in Arabidopsis lyrata by investigating patterns of TRD across the genome in F-2 progenies of three reciprocal crosses between four natural populations. We found that the degree of TRD increases with genetic distance between crossed populations, but also that reciprocal progenies may differ substantially in their degree of TRD. Chromosomes AL6 and especially AL1 appear to be involved in many single- and two-locus distortions, but the location and source of TRD vary between crosses and between reciprocal progenies. We also found that the majority of single- and two-locus TRD appears to have a gametic, as opposed to zygotic, origin. Thus, while theory on BDM incompatibilities is typically illustrated with derived nuclear alleles proving incompatible in hybrid zygotes, our results suggest a prominent role for distortions emerging before zygote formation.
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| 12. |
- Mackay, John, et al.
(author)
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Towards decoding the conifer giga-genome
- 2012
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In: Plant Molecular Biology. - : Springer. - 0167-4412 .- 1573-5028. ; 80:6, s. 555-569
-
Research review (peer-reviewed)abstract
- Several new initiatives have been launched recently to sequence conifer genomes including pines, spruces and Douglas-fir. Owing to the very large genome sizes ranging from 18 to 35 gigabases, sequencing even a single conifer genome had been considered unattainable until the recent throughput increases and cost reductions afforded by next generation sequencers. The purpose of this review is to describe the context for these new initiatives. A knowledge foundation has been acquired in several conifers of commercial and ecological interest through large-scale cDNA analyses, construction of genetic maps and gene mapping studies aiming to link phenotype and genotype. Exploratory sequencing in pines and spruces have pointed out some of the unique properties of these giga-genomes and suggested strategies that may be needed to extract value from their sequencing. The hope is that recent and pending developments in sequencing technology will contribute to rapidly filling the knowledge vacuum surrounding their structure, contents and evolution. Researchers are also making plans to use comparative analyses that will help to turn the data into a valuable resource for enhancing and protecting the world's conifer forests.
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| 13. |
- Martinez-Sancho, Elisabet, et al.
(author)
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The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe
- 2020
-
In: Scientific Data. - : NATURE PUBLISHING GROUP. - 2052-4463. ; 7
-
Journal article (peer-reviewed)abstract
- The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios.
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| 14. |
- Mattila, Tiina M., et al.
(author)
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Impact of demography on linked selection in two outcrossing Brassicaceae species
- 2019
-
In: Ecology and Evolution. - : Wiley. - 2045-7758. ; 9:17, s. 9532-9545
-
Journal article (peer-reviewed)abstract
- Genetic diversity is shaped by mutation, genetic drift, gene flow, recombination, and selection. The dynamics and interactions of these forces shape genetic diversity across different parts of the genome, between populations and species. Here, we have studied the effects of linked selection on nucleotide diversity in outcrossing populations of two Brassicaceae species, Arabidopsis lyrata and Capsella grandiflora, with contrasting demographic history. In agreement with previous estimates, we found evidence for a modest population size expansion thousands of generations ago, as well as efficient purifying selection in C. grandiflora. In contrast, the A. lyrata population exhibited evidence for very recent strong population size decline and weaker efficacy of purifying selection. Using multiple regression analyses with recombination rate and other genomic covariates as explanatory variables, we can explain 47% of the variance in neutral diversity in the C. grandiflora population, while in the A. lyrata population, only 11% of the variance was explained by the model. Recombination rate had a significant positive effect on neutral diversity in both species, suggesting that selection at linked sites has an effect on patterns of neutral variation. In line with this finding, we also found reduced neutral diversity in the vicinity of genes in the C. grandiflora population. However, in A. lyrata no such reduction in diversity was evident, a finding that is consistent with expectations of the impact of a recent bottleneck on patterns of neutral diversity near genes. This study thus empirically demonstrates how differences in demographic history modulate the impact of selection at linked sites in natural populations.
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| 15. |
- Opgenoorth, Lars, et al.
(author)
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The GenTree Platform : growth traits and tree-level environmental data in 12 European forest tree species
- 2021
-
In: GigaScience. - : Oxford University Press. - 2047-217X. ; 10:3
-
Journal article (peer-reviewed)abstract
- Background: Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information.Findings: The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecologically and economically important European forest tree species: Abies alba Mill. (silver fir), Betula pendula Roth. (silver birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra L. (Swiss stone pine), Pinus halepensis Mill. (Aleppo pine), Pinus nigra Arnold (European black pine), Pinus pinaster Aiton (maritime pine), Pinus sylvestris L. (Scots pine), Populus nigra L. (European black poplar), Taxus baccata L. (English yew), and Quercus petraea (Matt.) Liebl. (sessile oak). Phenotypic (height, diameter at breast height, crown size, bark thickness, biomass, straightness, forking, branch angle, fructification), regeneration, environmental in situ measurements (soil depth, vegetation cover, competition indices), and environmental modeling data extracted by using bilinear interpolation accounting for surrounding conditions of each tree (precipitation, temperature, insolation, drought indices) were obtained from trees in 194 sites covering the species' geographic ranges and reflecting local environmental gradients.Conclusion: The GenTree Platform is a new resource for investigating ecological and evolutionary processes in forest trees. The coherent phenotyping and environmental characterization across 12 species in their European ranges allow for a wide range of analyses from forest ecologists, conservationists, and macro-ecologists. Also, the data here presented can be linked to the GenTree Dendroecological collection, the GenTree Leaf Trait collection, and the GenTree Genomic collection presented elsewhere, which together build the largest evolutionary forest ecology data collection available.
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| 16. |
- Paananen, A, et al.
(author)
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Genetic and phenotypic diversity of echovirus 30 strains and pathogenesis of type 1 diabetes
- 2007
-
In: Journal of Medical Virology. - : Wiley. - 0146-6615 .- 1096-9071. ; 79:7, s. 945-955
-
Journal article (peer-reviewed)abstract
- Several enterovirus serotypes should be considered as potentially diabetogenic. The capacity of an enterovirus to kill or impair the functions of human -cells can vary among the strains within a given serotype as shown previously for echovirus 9 and 30 (E-30). The evolution of E-30 has also shown patterns correlating with the global increase of type 1 diabetes incidence. In the present study, antigenic properties of a set of E-30 isolates were investigated and the results correlated with the previously documented -cell destructive phenotype of the strains, or to genetic clustering of the strains. No simple correlation between the three properties was observed. A full-length infectious clone was constructed and sequenced from one of the isolates found to be most destructive to -cells (E-30/14916net87). Phylogenetic analyses demonstrated that this strain was closely related to the E-30 prototype strain at the capsid coding region while outside the capsid region prototype strains of several other human enterovirus B serotypes clustered more closely. This suggests that the relatively greater pathogenicity of the strain might be based on properties of the genome outside of the structural protein coding region. Neutralizing antibody assays on sera from 100 type 1 diabetic patients and 100 controls using three different E-30 strains did not reveal differences between the groups. This finding does not support a previous proposition of aberrant antibody responses to E-30 in diabetic patients. It is concluded that identification of the genetic counterparts of pathogenicity of E-30 strains requires further studies.
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| 17. |
- Palmé, Anna, 1973-, et al.
(author)
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Patterns of Divergence among Conifer ESTs and Polymorphism in Pinus sylvestris Identify Putative Selective Sweeps
- 2008
-
In: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 25:12, s. 2567-2577
-
Journal article (peer-reviewed)abstract
- Finding genes that are under positive selection is a difficult task, especially in non-model organisms. Here, we haveanalyzed expressed sequence tag (EST) data from 4 species (Pinus pinaster, Pinus taeda, Picea glauca, and Pseudotsugamenziesii) to investigate selection patterns during their evolution and to identify genes likely to be under positiveselection. To confirm selection, population samples of these genes have been sequenced in Pinus sylvestris, a species thatwas not included in the EST data set. The estimates of branch-specific Ka/Ks (nonsynonymous/synonymous substitutionrates) across all genes in the EST data set were similar or smaller than estimates from other higher plant species. Therewas no evidence for the traditional indication of positive selection, Ka/Ks above 1. However, several lines of evidencebased on polymorphism patterns suggest that genes with high Ka/Ks (0.20–0.52) in the EST data set are in fact moreaffected by positive selection in P. sylvestris than genes with low Ka/Ks (0.01–0.04). The high Ka/Ks genes have a lowerlevel of polymorphism and more negative Tajima’s D than the low Ka/Ks genes. Further, in the high Ka/Ks group, theHudson–Kreitman–Aguade test is significant. This suggests that the EST data set is a good starting point for findinggenes under positive selection in conifers and that even moderate Ka/Ks values could be indicative of selection. A groupof 5 genes with high Ka/Ks collectively show evidence for positive selection within P. sylvestris.
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| 18. |
- Palmé, Anna, 1973-, et al.
(author)
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Selection on Nuclear Genes in a Pinus Phylogeny
- 2009
-
In: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 26:4, s. 893-905
-
Journal article (peer-reviewed)abstract
- In this study, we investigate natural selection in a pine phylogeny. DNA sequences from 18 nuclear genes were used toconstruct a very well-supported species tree including 10 pine species. This tree is in complete agreement witha previously reported supertree constructed from morphological and molecular data, but there are discrepancies withprevious chloroplast phylogenies within the section Pinus. A significant difference in evolutionary rate between Piceaand Pinus was found, which could potentially indicate a lower mutation rate in Picea, but other scenarios are alsopossible. Several approaches were used to study selection patterns in a set of 21 nuclear genes in pines and in some casesin Picea and Pseudotsuga. The overall pattern suggests efficient purifying selection resulting in low branch-specific dn/dsratios with an average of 0.22, which is similar to other higher plants. Evidence for purifying selection was common andfound on at least 55% of the branches. Evidence of positive selection at several sites was found in a phytocyanin homologand significant differences in dn/ds among the branches in the gene tree in dehydrin 1. Several genes suitable for furtherphylogenetic analysis at various levels of divergence were identified.
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| 19. |
- Quilot-Turion, Bénédicte, et al.
(author)
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Genetic changes in flowering and morphology in response to adaptation to a high-latitude environment in Arabidopsis lyrata
- 2013
-
In: Annals of Botany. - : Oxford University Press. - 0305-7364 .- 1095-8290. ; 111:5, s. 957-968
-
Journal article (peer-reviewed)abstract
- Background and Aims The adaptive plastic reactions of plant populations to changing climatic factors, such as winter temperatures and photoperiod, have changed during range shifts after the last glaciation. Timing of flowering is an adaptive trait regulated by environmental cues. Its genetics has been intensively studied in annual plants, but in perennials it is currently not well characterized. This study examined the genetic basis of differentiation in flowering time, morphology, and their plastic responses to vernalization in two locally adapted populations of the perennial Arabidopsis lyrata: (1) to determine whether the two populations differ in their vernalization responses for flowering phenology and morphology; and (2) to determine the genomic areas governing differentiation and vernalization responses.Methods Two A. lyrata populations, from central Europe and Scandinavia, were grown in growth-chamber conditions with and without cold treatment. A QTL analysis was performed to find genomic regions that interact with vernalization.Key Results The population from central Europe flowered more rapidly and invested more in inflorescence growth than the population from alpine Scandinavia, especially after vernalization. The alpine population had consistently a low number of inflorescences and few flowers, suggesting strong constraints due to a short growing season, but instead had longer leaves and higher leaf rosettes. QTL mapping in the F2 population revealed genomic regions governing differentiation in flowering time and morphology and, in some cases, the allelic effects from the two populations on a trait were influenced by vernalization (QTL × vernalization interactions).Conclusions The results indicate that many potentially adaptive genetic changes have occurred during colonization; the two populations have diverged in their plastic responses to vernalization in traits closely connected to fitness through changes in many genomic areas.
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| 20. |
- Sandring, Saskia, et al.
(author)
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Selection on flowering time and floral display in an alpine and a lowland population of Arabidopsis lyrata
- 2007
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In: Journal of Evolutionary Biology. - : Wiley. - 1010-061X .- 1420-9101. ; 20:2, s. 558-567
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Journal article (peer-reviewed)abstract
- To determine whether population differentiation in flowering time is consistent with differences in current selection, we quantified phenotypic selection acting through female reproductive success on flowering phenology and floral display in two Scandinavian populations of the outcrossing, perennial herb Arabidopsis lyrata in two years. One population was located in an alpine environment strongly affected by grazing, whereas the other was close to sea level and only moderately affected by herbivory. Multiple regression models indicated directional selection for early end of flowering in one year in the lowland population, and directional selection for early start of flowering in one year in the alpine population. As expected, there was selection for more inflorescences in the lowland population. However, in the alpine population, plants with many inflorescences were selectively grazed and the number of inflorescences produced was negatively related to female fitness in one year and not significantly related to female fitness in the second year. The results are consistent with the hypothesis that genetic differentiation in flowering phenology between the study populations is adaptive, and indicate that interactions with selective grazers may strongly influence selection on floral display in A. lyrata.
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| 21. |
- Savolainen, Outi, et al.
(author)
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Adaptation of forest trees to climate change
- 2007
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In: Climate change and forest genetic diversity. - Rome : Bioversity International. - 9789290437499 ; , s. 19-30
-
Conference paper (peer-reviewed)
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| 22. |
- Savolainen, Outi, et al.
(author)
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Ecological genomics of local adaptation
- 2013
-
In: Nature reviews genetics. - : Springer Science and Business Media LLC. - 1471-0056 .- 1471-0064. ; 14:11, s. 807-820
-
Research review (peer-reviewed)abstract
- It is increasingly important to improve our understanding of the genetic basis of local adaptation because of its relevance to climate change, crop and animal production, and conservation of genetic resources. Phenotypic patterns that are generated by spatially varying selection have long been observed, and both genetic mapping and field experiments provided initial insights into the genetic architecture of adaptive traits. Genomic tools are now allowing genome-wide studies, and recent theoretical advances can help to design research strategies that combine genomics and field experiments to examine the genetics of local adaptation. These advances are also allowing research in non-model species, the adaptation patterns of which may differ from those of traditional model species.
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| 23. |
- Savolainen, Outi, et al.
(author)
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GENOMICS Geography matters for Arabidopsis
- 2016
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 537:7620, s. 314-315
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Journal article (other academic/artistic)abstract
- A free database describes genome sequences, gene expression and molecular modifications to DNA for more than 1,000 Arabidopsis thaliana plants, providing valuable information on the complex history and current variation of this species.
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| 24. |
- Wachowiak, Witold, et al.
(author)
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Speciation history of three closely related pines Pinus mugo (T.), P. uliginosa (N.) and P. sylvestris (L.)
- 2011
-
In: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 20:8, s. 1729-1743
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Journal article (peer-reviewed)abstract
- Nucleotide polymorphisms at genomic regions including 17 nuclear loci, two chloroplast and one mitochondrial DNA fragments were used to study the speciation history of three pine species: dwarf mountain pine (Pinus mugo), peat-bog pine (P. uliginosa) and Scots pine (P. sylvestris). We set out to investigate three specific speciation scenarios: (I) P. uliginosa is a homoploid hybrid between the other two, (II) the species have evolved without gene flow after divergence and (III) there has been substantial gene flow between the species since their divergence. Overall, the genetic data suggest that P. mugo and P. uliginosa share the same gene pool (average net divergence of 0.0001) and that the phenotypic differences (e.g. growth form) are most likely due to very limited areas of the genome. P. mugo and P. uliginosa are more diverged from P. sylvestris than from each other (average net divergence of 0.0027 and 0.0026, respectively). The nucleotide patterns can best be explained by the divergence with migration speciation scenario, although the hybrid speciation scenario with small genomic contribution from P. sylvestris cannot be completely ruled out. We suggest that the large amount of shared polymorphisms between the pine taxa and the lack of monophyly at all loci studied between P. sylvestris and P. mugo-P. uliginosa can largely be explained by relatively recent speciation history and large effective population sizes but also by interspecific gene flow. These closely related pine taxa form an excellent system for searching for loci involved in adaptive variation as they are differentiated in phenotype and ecology but have very similar genetic background.
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