| 1. |
- Lascoux, Martin, et al.
(författare)
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Past demography in forest trees : what can we learn from nuclear DNA sequences that we do not already know?
- 2008
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Ingår i: Plant Ecology & Diversity. - : Informa UK Limited. - 1755-0874 .- 1755-1668. ; 1:2, s. 209-215
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Tidskriftsartikel (refereegranskat)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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| 2. |
- Leinonen, Päivi H., et al.
(författare)
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Local adaptation in European populations of Arabidopsis lyrata (Brassicaceae)
- 2009
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Ingår i: American Journal of Botany. - : Wiley. - 0002-9122 .- 1537-2197. ; 96:6, s. 1129-1137
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Tidskriftsartikel (refereegranskat)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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| 3. |
- Paananen, A, et al.
(författare)
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Genetic and phenotypic diversity of echovirus 30 strains and pathogenesis of type 1 diabetes
- 2007
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Ingår i: Journal of Medical Virology. - : Wiley. - 0146-6615 .- 1096-9071. ; 79:7, s. 945-955
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Tidskriftsartikel (refereegranskat)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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| 4. |
- Palmé, Anna, 1973-, et al.
(författare)
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Patterns of Divergence among Conifer ESTs and Polymorphism in Pinus sylvestris Identify Putative Selective Sweeps
- 2008
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 25:12, s. 2567-2577
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Tidskriftsartikel (refereegranskat)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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| 5. |
- Palmé, Anna, 1973-, et al.
(författare)
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Selection on Nuclear Genes in a Pinus Phylogeny
- 2009
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 26:4, s. 893-905
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Tidskriftsartikel (refereegranskat)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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| 6. |
- Sandring, Saskia, et al.
(författare)
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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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Ingår i: Journal of Evolutionary Biology. - : Wiley. - 1010-061X .- 1420-9101. ; 20:2, s. 558-567
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Tidskriftsartikel (refereegranskat)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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| 7. |
- Savolainen, Outi, et al.
(författare)
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Adaptation of forest trees to climate change
- 2007
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Ingår i: Climate change and forest genetic diversity. - Rome : Bioversity International. - 9789290437499 ; , s. 19-30
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Konferensbidrag (refereegranskat)
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