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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs?
- 2023
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Ingår i: Environment International. - 0160-4120 .- 1873-6750. ; 178
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Tidskriftsartikel (refereegranskat)abstract
- Antimicrobial resistance (AMR) is a global threat to human and animal health and well-being. To understand AMR dynamics, it is important to monitor resistant bacteria and resistance genes in all relevant settings. How-ever, while monitoring of AMR has been implemented in clinical and veterinary settings, comprehensive monitoring of AMR in the environment is almost completely lacking. Yet, the environmental dimension of AMR is critical for understanding the dissemination routes and selection of resistant microorganisms, as well as the human health risks related to environmental AMR. Here, we outline important knowledge gaps that impede implementation of environmental AMR monitoring. These include lack of knowledge of the 'normal' background levels of environmental AMR, definition of high-risk environments for transmission, and a poor understanding of the concentrations of antibiotics and other chemical agents that promote resistance selection. Furthermore, there is a lack of methods to detect resistance genes that are not already circulating among pathogens. We conclude that these knowledge gaps need to be addressed before routine monitoring for AMR in the environment can be implemented on a large scale. Yet, AMR monitoring data bridging different sectors is needed in order to fill these knowledge gaps, which means that some level of national, regional and global AMR surveillance in the envi-ronment must happen even without all scientific questions answered. With the possibilities opened up by rapidly advancing technologies, it is time to fill these knowledge gaps. Doing so will allow for specific actions against environmental AMR development and spread to pathogens and thereby safeguard the health and wellbeing of humans and animals.
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- Maliouchenko, O., et al.
(författare)
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Comparative phylogeography and population structure of European Betula species, with particular focus on B. pendula and B. pubescens
- 2007
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 34:9, s. 1601-1610
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Tidskriftsartikel (refereegranskat)abstract
- Aim To compare the population genetic structures of the haplotype-sharing species Betula pendula and B. pubescens and to draw phylogeographic inferences using chloroplast DNA markers. In particular, we tested whether B. pendula and B. pubescens exhibited the same or different phylogeographic structures. Location Western Europe and Russia. Methods In this study we used both chloroplast DNA polymerase chain reaction-restriction fragment length polymorphism and microsatellites to genotype B. pendula, B. pubescens and, to a limited extent, B. nana, in 53 populations across Eurasia. A spatialamova(samova) was used to identify major clusters within each species. Results The low level of phylogeographic structure previously observed in B. pendula was confirmed, and thesamovaanalysis retrieved only two major clusters. In contrast, seven clusters were observed in B. pubescens, although the overall level of population differentiation was similar to that of B. pendula. Main conclusions We detected a difference in the population genetic structure between the two species, despite extensive haplotype sharing. It is difficult to ascribe this finding to a single factor, but divergence in ecology between the two species may provide part of the explanation. For both species, the contribution of southern western populations to the recolonization after the Last Glacial Maximum seems to have been limited, and eastern and western European populations apparently had different histories.
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| 4. |
- Palmé, Amma E, et al.
(författare)
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SNP Markers and Evaluation of Duplicate Holdings of Brassica oleracea in Two European Genebanks
- 2020
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Ingår i: PLANTS. - : MDPI AG. - 2223-7747. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Around the world, there are more than 1500 genebanks storing plant genetic resources tobe used in breeding and research. Such resources are essential for future food security, but many genebanks experience backlogs in their conservation work, often combined with limited budgets. Therefore, avoiding duplicate holdings is on the agenda. A process of coordination has started, aiming at sharing the responsibility of maintaining the unique accessions while allowing access according to the international treaty for plant genetic resources. Identifying duplicate holdings based on passport data has been one component of this. In the past, and especially in vegetables, different selections within the same varieties were common and the naming practices of cultivars/selections were flexible. Here, we examined 10 accession pairs/groups of cabbage (Brassica oleracea var. capitata) with similar names maintained in the Russian and Nordic genebanks. The accessions were analyzed for 11 morphological traits and with a SNP (Single Nucleotide Polymorphism) array developed for B. napus. Both proved to be useful tools for understanding the genetic structure among the accessions and for identifying duplicates, and a subset of 500 SNP markers are suggested for futureBrassica oleracea genetic characterization. Within five out of 10 pairs/groups, we detected clear genetic differences among the accessions, and three of these were confirmed by significant differences in one or several morphological traits. In one case, a white cabbage and a red cabbage had similar accession names. The study highlights the necessity to be careful when identifying duplicate accessions based solely on the name, especially in older cross-pollinated species such as cabbage.
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- St.Onge, Kate, 1982-, et al.
(författare)
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The impact of sampling schemes on demographic inference : an empirical study in two species with different mating systems and demographic histories
- 2012
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Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 2:7, s. 803-814
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Tidskriftsartikel (refereegranskat)abstract
- Most species have at least some level of genetic structure. Recent simulation studies have shown that it is important to consider population structure when sampling individuals to infer past population history. This is because different sampling strategies will introduce biases in the site frequency spectrum (SFS), which is generally the basic information used to infer population history. The relevance of the results of these computer simulations for empirical studies, however, remains unclear. In the present study we use DNA sequence datasets collected in two closely related species with very different histories, the selfing species Capsella rubella and its outcrossing relative C. grandiflora, to assess the impact of different sampling strategies on summary statistics and the inference of historical demography. Sampling strategy did affect values of Tajima’s D in both species but differences were not significant, and the general conclusions about demographic history were comparable across sampling schemes even when re-sampled data were analysed with Approximate Bayesian Computation. We explore the effects of sampling scheme when a limited number of loci are analysed, and in models that include population expansion within demes and hierarchical structure. While we observe a less severe effect of sampling than predicted under some simulation models, our results should not be seen as an encouragement to neglect this issue. In general, a good coverage of the natural range, both within and between populations, will be needed to obtain a reliable reconstruction of a species demographic history.
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- Wachowiak, Witold, et al.
(författare)
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Speciation history of three closely related pines Pinus mugo (T.), P. uliginosa (N.) and P. sylvestris (L.)
- 2011
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 20:8, s. 1729-1743
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Tidskriftsartikel (refereegranskat)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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