| 1. |
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- 2019
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Journal article (peer-reviewed)
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| 2. |
- Bengtsson-Palme, Johan, 1985, et al.
(author)
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Strategies to improve usability and preserve accuracy in biological sequence databases
- 2016
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In: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 16:18, s. 2454-2460
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Journal article (peer-reviewed)abstract
- Biology is increasingly dependent on large-scale analysis, such as proteomics, creating a requirement for efficient bioinformatics. Bioinformatic predictions of biological functions rely upon correctly annotated database sequences, and the presence of inaccurately annotated or otherwise poorly described sequences introduces noise and bias to biological analyses. Accurate annotations are, for example, pivotal for correct identifications of polypeptide fragments. However, standards for how sequence databases are organized and presented are currently insufficient. Here, we propose five strategies to address fundamental issues in the annotation of sequence databases: (i) to clearly separate experimentally verified and unverified sequence entries; (ii) to enable a system for tracing the origins of annotations; (iii) to separate entries with high-quality, informative annotation from less useful ones; (iv) to integrate automated quality-control software whenever such tools exist; and (v) to facilitate post-submission editing of annotations and metadata associated with sequences. We believe that implementation of these strategies, for example as requirements for publication of database papers, would enable biology to better take advantage of large-scale data.
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| 3. |
- Palme, Anna, 1986, et al.
(author)
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Development of an efficient route for combined recycling of PET and cotton from mixed fabrics
- 2017
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In: Textiles and Clothing Sustainability. - : Springer Science and Business Media LLC. - 2197-9936. ; 3:4
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Journal article (peer-reviewed)abstract
- Most textile waste is either incinerated or landfilled today, yet, the material could instead be recycled through chemical recycling to new high-quality textiles. A first important step is separation since chemical recycling of textiles requires pure streams. The focus of this paper is on the separation of cotton and PET (poly(ethylene terephthalate), polyester) from mixed textiles, so called polycotton. Polycotton is one of the most common materials in service textiles used in sheets and towels at hospitals and hotels. A straightforward process using 5–15 wt% NaOH in water and temperature in the range between 70 and 90 °C for the hydrolysis of PET was evaluated on the lab-scale. In the process, the PET was degraded to terephthalic acid (TPA) and ethylene glycol (EG). Three product streams were generated from the process. First is the cotton; second, the TPA; and, third, the filtrate containing EG and the process chemicals. The end products and the extent of PET degradation were characterized using light microscopy, UV-spectroscopy, and ATR FT-IR spectroscopy, as well as solution and solid-state NMR spectroscopy. Furthermore, the cotton cellulose degradation was evaluated by analyzing the intrinsic viscosity of the cotton cellulose. The findings show that with the addition of a phase transfer catalyst (benzyltributylammonium chloride (BTBAC)), PET hydrolysis in 10% NaOH solution at 90 °C can be completed within 40 min. Analysis of the degraded PET with NMR spectroscopy showed that no contaminants remained in the recovered TPA, and that the filtrate mainly contained EG and BTBAC (when added). The yield of the cotton cellulose was high, up to 97%, depending on how long the samples were treated. The findings also showed that the separation can be performed without the phase transfer catalyst; however, this requires longer treatment times, which results in more cellulose degradation.
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| 4. |
- Abramova, Anna, 1990, et al.
(author)
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A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments
- 2023
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In: Environment International. - 0160-4120 .- 1873-6750. ; 178
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Journal article (peer-reviewed)abstract
- The environment is an important component in the emergence and transmission of antimicrobial resistance (AMR). Despite that, little effort has been made to monitor AMR outside of clinical and veterinary settings. Partially, this is caused by a lack of comprehensive reference data for the vast majority of environments. To enable monitoring to detect deviations from the normal background resistance levels in the environment, it is necessary to establish a baseline of AMR in a variety of settings. In an attempt to establish this baseline level, we here performed a comprehensive literature survey, identifying 150 scientific papers containing relevant qPCR data on antimicrobial resistance genes (ARGs) in environments associated with potential routes for AMR dissemination. The collected data included 1594 samples distributed across 30 different countries and 12 sample types, in a time span from 2001 to 2020. We found that for most ARGs, the typically reported abundances in human impacted environments fell in an interval from 10-5 to 10-3 copies per 16S rRNA, roughly corresponding to one ARG copy in a thousand bacteria. Altogether these data represent a comprehensive overview of the occurrence and levels of ARGs in different environments, providing background data for risk assessment models within current and future AMR monitoring frameworks.
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| 5. |
- Abramova, Anna, 1990, et al.
(author)
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CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data
- 2021
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In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1460-2059. ; 37:1, s. 121-122
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Journal article (peer-reviewed)abstract
- Sequencing of transposon insertion libraries is used to determine the relative fitness of individual mutants at a large scale. However, there is a lack of tools for specifically analyzing data from such experiments with paired sample designs. Here, we introduce CAFE-Coefficient-based Analysis of Fitness by read Enrichment-a software package that can analyze data from paired transposon mutant sequencing experiments, generate fitness coefficients for each gene and condition and perform appropriate statistical testing on these fitness coefficients.
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| 6. |
- Abramova, Anna, 1990, et al.
(author)
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Meta-analysis reveals the global picture of antibiotic resistance gene prevalence across environments
- 2022
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In: bioRXIV. - : Cold Spring Harbor Laboratory.
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Journal article (other academic/artistic)abstract
- The environment is an important component in the emergence and transmission of antimicrobial resistance (AMR). Despite that, current AMR monitoring initiatives lack comprehensive reference data for the vast majority of environments. To enable monitoring to detect deviations from the normal background resistance levels in the environment, it is necessary to establish the typical baseline of AMR in a variety of settings. In an attempt to establish this baseline level, we here performed a comprehensive literature survey across 2516 scientific papers, 150 of which contained relevant qPCR data on antibiotic resistance genes (ARGs) in environments associated with potential routes of AMR dissemination. The collected data include 1487 samples distributed across 30 different countries and 17 environmental types, in a time span from 2005 to 2018. More than 330 different genes were identified from the collected studies. Most surveyed environments contained a diverse set of ARGs, but generally at low abundances. We used linear mixed models and overrepresentation analysis to identify time trends and associations between ARGs and specific environments. Altogether these data represent a comprehensive overview of the occurrence and levels of ARGs in different environments, providing background data for risk assessment models within current and future AMR monitoring frameworks.
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| 7. |
- Andersson, Stefan, et al.
(author)
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Quantitative genetic effects of bottlenecks : experimental evidence from a wild plant species, Nigella degenii
- 2010
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In: Journal of Heredity. - : Oxford University Press (OUP). - 0022-1503 .- 1465-7333. ; 101:3, s. 298-307
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Journal article (peer-reviewed)abstract
- Understanding the genetic consequences of changes in population size is fundamental in a variety of contexts, such as adaptation and conservation biology. In the study presented here, we have performed a replicated experiment with the plant Nigella degenii to explore the quantitative genetic effects of a single-founder bottleneck. In agreement with adetive theory, the bottleneck reduced the mean (co)variance within lines and caused stochastic, line-specific changes in the genetic (co)variance structure. However, a significant portion of the (co)variance structure was conserved, and 2 characters—leaf and flower (sepal) size—turned out to be positively correlated in all data sets, indicating a potential for correlated evolution in these characters, even after a severe bottleneck. The hierarchical partitioning of genetic variance for flower size was in good agreement with predictions from additive theory, whereas the remaining characters showed an excess of within-line variance and a deficiency of among-line variance. The latter discrepancies were most likely a result of selection, given the small proportion of lines (23%) that remained viable until the end of the experiment. Our results suggest that bottlenecked populations of N. degenii generally have a lower adaptive potential than the ancentral population but also highlight the idiosyncratic nature of bottleneck effects.
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| 8. |
- Bengtsson-Palme, Johan, 1985, et al.
(author)
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Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
- 2013
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In: Methods in Ecology and Evolution. - 2041-210X. ; 4:10, s. 914-919
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Journal article (peer-reviewed)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.
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| 9. |
- Bengtsson-Palme, Johan, 1985, et al.
(author)
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Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets
- 2011
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In: Antonie van Leeuwenhoek: international journal of general and molecular microbiology. - : Springer Science and Business Media LLC. - 0003-6072 .- 1572-9699. ; 100:3, s. 471-475
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Journal article (peer-reviewed)abstract
- The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. In addition to being present in the nucleus of eukaryotes and the core genome of prokaryotes, the gene is also found in the mitochondria of eukaryotes and in the chloroplasts of photosynthetic eukaryotes. These three sets of genes are conceptually paralogous and should in most situations not be aligned and analyzed jointly. To identify the origin of SSU sequences in complex sequence datasets has hitherto been a time-consuming and largely manual undertaking. However, the present study introduces Metaxa (http://microbiology.se/software/metaxa/), an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacterial, nuclear eukaryote, mitochondrial, or chloroplast origin. Using data from reference databases and from full-length organelle and organism genomes, we show that Metaxa detects and scores SSU sequences for origin with very low proportions of false positives and negatives. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.
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| 10. |
- Bengtsson-Palme, Johan, 1985, et al.
(author)
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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
-
In: Environment International. - 0160-4120 .- 1873-6750. ; 178
-
Journal article (peer-reviewed)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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| 11. |
- Charlier, Johan, et al.
(author)
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Census (NC) and genetically effective (Ne) population size in a lake-resident population of brown trout Salmo trutta
- 2011
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In: Journal of Fish Biology. - : Wiley. - 0022-1112 .- 1095-8649. ; 79:7, s. 2074-2082
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Journal article (peer-reviewed)abstract
- Census (NC) and effective population size (Ne) were estimated for a lake-resident population of brown trout Salmo trutta as 576 and 63, respectively. The point estimate of the ratio of effective to census population size (Ne:NC) for this population is 0·11 with a range of 0·06–0·26, suggesting that Ne:NC ratio for lake-resident populations agree more with estimates for fishes with anadromous life histories than the small ratios observed in many marine fishes
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| 12. |
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| 13. |
- Hagenblad, Jenny, et al.
(author)
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Limited genetic changes observed during in situ and ex situ conservation in Nordic populations of red clover (Trifolium pratense)
- 2023
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In: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
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Journal article (peer-reviewed)abstract
- Introduction: In situ and ex situ conservation are the two main approaches for preserving genetic diversity. The advantages and disadvantages of the two approaches have been discussed but their genetic effects have not been fully evaluated.Methods: In this study we investigate the effects of the two conservation approaches on genetic diversity in red clover. Seed samples collected from wild populations in Sweden and Norway in 1980, their subsequent generations created during seed regeneration at the gene bank and samples recollected from the same location as the original samples, were analyzed with microsatellite markers, alongside reference samples from cultivars.Results: Overall, there was a differentiation between cultivars and the wild material and between wild material from Sweden and Norway. In general, the original collections clustered together with the later generations of the same accession in the gene bank, and with the recollected samples from the same location, and the level of diversity remained the same among samples of the same accession. Limited gene flow from cultivated varieties to the wild populations was detected; however, some wild individuals are likely to be escapees or affected by gene flow.Discussion: In conclusion, there were examples of genetic changes within individual accessions both in situ and ex situ, as is also to be expected in any living population. However, we observed only limited genetic changes in both in situ and ex situ conservation over the generations included in this study and with the relatively large populations used in the ex situ conservation in the gene bank at NordGen.
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| 14. |
- Inda Diaz, Juan Salvador, 1984, et al.
(author)
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Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes
- 2023
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In: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 11:1, s. 44-
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Journal article (peer-reviewed)abstract
- BACKGROUND: Bacterial communities in humans, animals, and the external environment maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs are well-characterized and thus established in existing resistance gene databases. In contrast, the remaining latent ARGs are typically unknown and overlooked in most sequencing-based studies. Our view of the resistome and its diversity is therefore incomplete, which hampers our ability to assess risk for promotion and spread of yet undiscovered resistance determinants. RESULTS: A reference database consisting of both established and latent ARGs (ARGs not present in current resistance gene repositories) was created. By analyzing more than 10,000 metagenomic samples, we showed that latent ARGs were more abundant and diverse than established ARGs in all studied environments, including the human- and animal-associated microbiomes. The pan-resistomes, i.e., all ARGs present in an environment, were heavily dominated by latent ARGs. In comparison, the core-resistome, i.e., ARGs that were commonly encountered, comprised both latent and established ARGs. We identified several latent ARGs shared between environments and/or present in human pathogens. Context analysis of these genes showed that they were located on mobile genetic elements, including conjugative elements. We, furthermore, identified that wastewater microbiomes had a surprisingly large pan- and core-resistome, which makes it a potentially high-risk environment for the mobilization and promotion of latent ARGs. CONCLUSIONS: Our results show that latent ARGs are ubiquitously present in all environments and constitute a diverse reservoir from which new resistance determinants can be recruited to pathogens. Several latent ARGs already had high mobile potential and were present in human pathogens, suggesting that they may constitute emerging threats to human health. We conclude that the full resistome-including both latent and established ARGs-needs to be considered to properly assess the risks associated with antibiotic selection pressures. Video Abstract.
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| 15. |
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| 16. |
- Järvinen, Pia, et al.
(author)
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Phylogenetic relationships of Betula species (Betulaceae) based on nuclear Adh and chloroplast matK sequences
- 2004
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In: American Journal of Botany. - : John Wiley & Sons. - 0002-9122 .- 1537-2197. ; 91:11, s. 1834-1845
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Journal article (peer-reviewed)abstract
- The phylogenetic relationships within the genus Betula (Betulaceae) were investigated using a part of the nuclear ADH gene and DNA sequences of the chloroplast matK gene with parts of its flanking regions. Two well‐supported phylogenetic groups could be identified in the chloroplast DNA sequence: one containing the three American species B. lenta, B. alleghaniensis, and B. papyrifera and the other including all the other species studied. The ADH gene displayed more variation, and three main groups could be identified. In disagreement with the classical division of the genus Betula, B. schmidtii and B. nana grouped with the species in subgenus Betula, and B. ermanii grouped with species in subgenus Chamaebetula, including B. humilis and B. fruticosa. The ADH phylogeny suggests that several independent polyploidizations within the genus Betula could have taken place. The ADH and chloroplast phylogenies were in part incongruent due to the placement of B. papyrifera. The most likely reason for this seems to be cytoplasmic introgression.
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| 17. |
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| 18. |
- Laikre, Linda, et al.
(author)
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Effekter av spridning av genetiskt främmande populationer : En kartläggning av förutsättningarna för uppföljande studier av utsättningar av djur och växter i Sverige
- 2008
-
Reports (other academic/artistic)abstract
- Förord Spridning av främmande arter utgör ett av de stora hoten mot biologisk mångfald. En viktig del i arbetet med att verkställa Förenta nationernas konvention om biologisk mångfald (Convention on Biological Diversity – CBD) är därför att öka kunskapen kring, och förhindra fortsatt spridning av, sådana arter. Begreppet ”art” har en vid definition inom konventionsarbetet – även lägre taxonomiska enheter så som underarter och genetiskt särpräglade populationer omfattas. Spridning av genetiskt främmande populationer utgör alltså ett internationellt erkänt hot mot biologisk mångfald. Framför allt är det diversiteten på gennivå som kan drabbas negativt av sådan spridning. Vetenskapliga rådet för biologisk mångfald utses av Sveriges regering och ska bistå regeringen med råd i samband med internationellt och nationellt arbete med frågor som rör biologisk mångfald. Rådet har länge påtalat vikten av att öka kunskapen kring den genetiska nivån av biologisk mångfald och inte minst effekterna på denna mångfald av storskaliga utsättningar av genetiskt främmande populationer. Sådana utsättningar är vanliga inom skogsbruket, fiskevården och viltvården. Från min egen mångåriga erfarenhet av fiskevårdsfrågor har jag praktisk erfarenhet av att introduktion och spridning av främmande arter och populationer kan få högst påtagliga negativa konsekvenser.Vetenskapliga rådet för biologisk mångfald har i samband med konventionens tillämpning tagit upp frågor med koppling till den genetiska variationens betydelse – särskilt de vetenskapliga aspekterna kring detta. Rådet har också arrangerat en workshop som för första gången samlade experter och intressenter från de tre områden inom vilka storskaliga utsättningar bedrivs (skogsbruket, fisk- och viltvården). De intressanta och givande diskussionerna finns refererade i Rapport 5683 i Naturvårdsverkets serie. I den nu föreliggande rapporten fortsätter kartläggningen av vad vi egentligen vet om de storskaliga utsättningarna i Sverige och vilka effekter de har på biologisk mångfald. Ett gediget arbete har gjorts för att försöka bringa reda i detta område där dokumentation till stora delar saknas. Bristen på registrering och uppföljning av dessa stora spridningar, som riskerar att förändra den genetiska sammansättning som under årtusenden mejslats fram hos våra vilda fisk-, träd- och fågelpopulationer, är skrämmande. Här behövs en snabb och påtaglig förändring. Vetenskapliga rådet för biologisk mångfald kommer att fortsätta ägna denna fråga stor uppmärksamhet. Det är angeläget att Sverige bedriver ett starkt och engagerat arbete som ligger i internationell framkant när det gäller att slå vakt om den grundläggande, och för fortsatt evolution nödvändiga, mångfalden på gennivå. Stockholm den 10 september 2008 Per Wramner Professor i tillämpad miljövetenskap Ordförande för Vetenskapliga rådet för biologisk mångfald Förord 2 Utsättning av främmande populationer eller provenienser av växter och djur sker i stor skala i svenska marker och vattendrag. Spridningen av främmande populationer har stora ekonomiska värden men vi vet väldigt lite om vilka effekter den har på biologisk mångfald. Etablering av främmande genotyper kan leda till förlust och förändringar av, i första hand, mångfalden på gennivå hos mottagande naturliga populationer. I förlängningen kan sådana effekter även drabba art- och ekosystemnivåerna negativt. Det är mycket angeläget att öka kunskaperna inom detta område. Regeringen har uppdragit åt naturvårdsverket att ta fram en nationell strategi och handlingsplan för främmande arter och genotyper. Denna rapport utgör ett underlag i detta arbete. Uppdraget gavs med anledning av uppföljningen av miljökvalitetsmålen och implementering av artikel 8 h i Konventionen om biologisk mångfald som särskilt berör främmande arter och populationer och deras effekter på biologisk mångfalden. Rapporten utgör en uppföljning av den första kartläggningen av spridning av genetiskt främmande populationer inom fiske- och viltvården samt skogsbruk i Sverige som genomfördes under 2004–2005. Syftet med rapporten är en fördjupad granskning av den information som är möjlig att få fram när det gäller spridningen av främmande populationer eller genotyper i Sverige, samt i vilken utsträckning effekterna av sådana utsättningar kan kartläggas. Författarna är ensamma ansvariga för rapportens innehåll.Stockholm den 7 oktober 2008Naturvårdsverket
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| 19. |
- Laikre, Linda, et al.
(author)
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Internationellt fokus på laxgener
- 2012
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In: HavsUtsikt. - Stockholm : Stockholms universitet. - 1104-0513. ; :1
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Journal article (pop. science, debate, etc.)
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| 20. |
- Laikre, Linda, et al.
(author)
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Potentials for monitoring gene level biodiversity : using Sweden as an example
- 2008
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In: Biodiversity and Conservation. - : Springer Science and Business Media LLC. - 0960-3115 .- 1572-9710. ; 17:4, s. 893-910
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Journal article (peer-reviewed)abstract
- Programs for monitoring biological diversity over time are needed to detect changes that can constitute threats to biological resources. The convention on biological diversity regards effective monitoring as necessary to halt the ongoing erosion of biological variation, and such programs at the ecosystem and species levels are enforced in several countries. However, at the level of genetic biodiversity, little has been accomplished, and monitoring programs need to be developed. We define “conservation genetic monitoring” to imply the systematic, temporal study of genetic variation within particular species/populations with the aim to detect changes that indicate compromise or loss of such diversity. We also (i) identify basic starting points for conservation genetic monitoring, (ii) review the availability of such information using Sweden as an example, (iii) suggest categories of species for pilot monitoring programs, and (iv) identify some scientific and logistic issues that need to be addressed in the context of conservation genetic monitoring. We suggest that such programs are particularly warranted for species subject to large scale enhancement and harvest—operations that are known to potentially alter the genetic composition and reduce the variability of populations.
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| 21. |
- Laikre, Linda, et al.
(author)
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Release of alien populations in Sweden
- 2006
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In: Ambio. - 0044-7447 .- 1654-7209. ; 35:5, s. 255-261
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Journal article (peer-reviewed)abstract
- Introduction of alien species is a major threat to biological diversity. Although public attention typically focuses on the species level, guidelines from the Convention of Biological Diversity define alien species to include entities below species level. This inclusion recognizes that release of nonlocal populations of native species may also result in negative effects on biodiversity. In practice, little is known about the extent, degree of establishment, or the effects on natural gene pools of such releases. Existing information on the releases in Sweden shows that alien populations are spread to a great extent. The most commonly released species include brown trout, Atlantic salmon, Arctic char, common whitefish, Scots pine, Norway spruce, mallard duck, gray partridge, and pheasant. Although millions of forest trees, fish, and birds are released annually, poor documentation makes the geographic and genetic origin of these populations, as well as the sites where they have been released, largely unclear. We provide recommendations for urgently needed first steps relating to the risks and problems associated with release of alien populations.
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| 22. |
- Laikre, Linda, et al.
(author)
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Spatial genetic structure of northern pike (Esox lucius) in the Baltic Sea
- 2005
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In: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 14:7, s. 1955-1964
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Journal article (peer-reviewed)abstract
- The genetic relationships among 337 northern pike (Esox lucius) collected from the coastal zone of the central Baltic region and the Finnish islands of Åland were analysed using five microsatellite loci. Spatial structure was delineated using both traditional F-statistics and individually based approaches including spatial autocorrelation analysis. Our results indicate that the observed genotypic distribution is incompatible with that of a single, panmictic population. Isolation by distance appears important for shaping the genetic structure of pike in this region resulting in a largely continuous genetic change over the study area. Spatial autocorrelation analysis (Moran’s I) of individual pairwise genotypic data show significant positive genetic correlation among pike collected within geographical distances of less than c. 100–150 km (genetic patch size). We suggest that the genetic patch size may be used as a preliminary basis for identifying management units for pike in the Baltic Sea.
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| 23. |
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| 24. |
- Lindahl, Mikael, et al.
(author)
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A Test of the Becker-Tomes Model of Human Capital Transmission Using Microdata on Four Generations
- 2014
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In: Journal of Human Capital. - : University of Chicago Press. - 1932-8575 .- 1932-8664. ; 8:1, s. 80-96
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Journal article (peer-reviewed)abstract
- We estimate the well-known Becker-Tomes model of intergenerational transmission of human capital. A Swedish data set, which links individual measures on educational attainments of four generations, enables us to use great-grandparents' education as an instrumental variable. The identifying assumption, which holds within the Becker-Tomes framework, is that great-grandparents' education is unrelated to great-grandchildren's education, conditional on the education of the parent and grandparent. We test the model's prediction that the structural parameter for grandparents' education enters with a negative sign in an intergenerational regression model.
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| 25. |
- Lindahl, Mikael, et al.
(author)
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Long-Term Intergenerational Persistence of Human Capital : An Empirical Analysis of Four Generations
- 2015
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In: The Journal of human resources. - : University of Wisconsin Press. - 0022-166X .- 1548-8004. ; 50:1, s. 1-33
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Journal article (peer-reviewed)abstract
- Most previous studies of intergenerational transmission of human capital are restricted to two generations: how parents influence their children. In this study, we use a Swedish data set that links individual measures of lifetime earnings for three generations and data on educational attainment for four generations. We find that estimates obtained from data on two generations severely underestimate long-run intergenerational persistence in both labor earnings and educational attainments. Long-run social mobility is hence much lower than previously thought. We attribute this additional persistence to dynastic human capital-the influence on human capital of more distant family members than parents.
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| 26. |
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| 27. |
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| 28. |
- Lindahl, Mikael, et al.
(author)
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Transmission of Human Capital across Four Generations : Intergenerational Correlations and a Test of the Becker-Tomes Model
- 2011
-
Reports (other academic/artistic)abstract
- Most previous studies on intergenerational transmission of human capital are restricted to two generations - between the parent and the child generation. In this paper we investigate if there is an independent effect of the grandparent and the great grandparent generations in this process. We use a dataset where we are able to link individual measures of life time earnings for three generation and data on educational attainments of four generations. We first do conventional regressions and transition matrices for life time earnings measures and educational attainments adding variables for the grandparent and great grandparent generations, respectively. We find that grandparents and even great grandparents significantly influence earnings and education. We then estimate the so called Becker-Tomes model using the educational attainment of the great grandparent generation as an instrumental variable. We fail to find support for the model's predictions.
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| 29. |
- Linderoth, Anna, 1983-
(author)
-
Essays on Men's Preferences and Gender Inequality in the Labor Market
- 2023
-
Doctoral thesis (other academic/artistic)abstract
- Reference Points for Men’s Parental Leave-Taking Behavior:Evidence from Swedish ReformsThis paper tests the hypothesis of reference dependence in men's parental leave takeup. Using register data, I leverage two reforms introducing earmarked provision for fathers. A key empirical challenge in separating reference point behavior arises from the fact that the earmark provisions also altered men's financial incentives to bunch around the value of the provision. To address this issue, I net out behavioral responses to the financial incentives by calculating and controlling for their size and exploiting the fact that financial incentives remained unchanged for sub-groups of households. The findings reveal that introducing reference points through earmark provisions led to a substantial increase in the average number of parental leave days taken per man (the intensive margin) and an elevated likelihood that men would take any parental leave (the extensive margin). In comparison, responses to the financial incentives are modest. The effect of reference dependence was most pronounced immediately after the reforms but gradually declined as men's parental leave takeup increasingly exceeded the earmarked provision.Too Many Female Colleagues For Comfort? Men’s Tipping Behavior and Gender Segregation Across Workplaces.Women and men tend to work in different workplaces, and this gender segregation is an important contributor to the gender wage gap. This paper studies a new explanation for workplace gender segregation, namely that men leave the workplace when the share of women reaches a certain point. I draw on past research on occupation-level tipping to detect potential composition levels—tipping points—where the share of men in a workplace starts dropping discontinuously over time. This analysis uses Swedish register data for all small- and medium-size workplaces from 1986 to 2009 and is carried out separately by men's level of education (high or low). I find strong non-linear patterns for high-skilled men but not for low-skilled ones. The distribution of candidate tipping points for high-skilled workplaces is centered around 25% to 35% female. Using enlistment data, I find a significant decrease in men's cognitive and non-cognitive skills at tipping point. I draw on my empirical findings to show how compositional preferences can be built into a simple model of self-selection. The model explains the observed negative selection of men after a workplace has exceeded a critical tipping point. The result of this paper emphasizes the potential importance of the preferences of the dominant group.Occupational Gender Segregation and Men's Tipping Behavior: the Swedish Case.The division of occupations along gender lines seems to be a common and persistent feature between countries, despite differences in social norms and institutional settings across time. The aim of this paper is to investigate one possible explanation, namely tipping behaviour in occupations. It studies the non-linear dynamics of occupation segregation, applying an approach similar to regression discontinuity design. This paper studies tipping behaviour in the Swedish labour market from 1960 to 1990 and compares it to the results for the U.S. using an analogous methodology. The graphical approach exhibits a highly non-linear relationship in female share. I find candidate tipping points that range between 9 to 32 percent in female share. The results indicate discontinuous changes in net male employment growth at candidate tipping point.
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| 30. |
- Maliouchenko, O., et al.
(author)
-
Comparative phylogeography and population structure of European Betula species, with particular focus on B. pendula and B. pubescens
- 2007
-
In: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 34:9, s. 1601-1610
-
Journal article (peer-reviewed)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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| 31. |
- Nilsson, R. Henrik, 1976, et al.
(author)
-
Improving ITS sequence data for identification of plant pathogenic fungi
- 2014
-
In: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 11-19
-
Journal article (peer-reviewed)abstract
- Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.
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| 32. |
- Palme, Anna, 1986, et al.
(author)
-
Acid hydrolysis of cellulosic fibres: Comparison of bleached kraft pulp, dissolving pulps and cotton textile cellulose
- 2016
-
In: Carbohydrate Polymers. - : Elsevier BV. - 0144-8617. ; 136, s. 1281-1287
-
Journal article (peer-reviewed)abstract
- The behaviour of different cellulosic fibres during acid hydrolysis has been investigated and the levelling-off degree of polymerisation (LODP) has been determined. The study included a bleached kraft pulp (both never-dried and once-dried) and two dissolving pulps (once-dried). Additionally, cotton cellulose from new cotton sheets and sheets discarded after long-time use was studied. Experimental results from the investigation, together with results found in literature, imply that ultrastructural differences between different fibres affect their susceptibility towards acid hydrolysis. Drying of a bleached kraft pulp was found to enhance the rate of acid hydrolysis and also result in a decrease in LODP. This implies that the susceptibility of cellulosic fibres towards acid hydrolysis is affected by drying-induced stresses in the cellulose chains. In cotton cellulose, it was found that use and laundering gave a substantial loss in the degree of polymerisation (DP), but that the LODP was only marginally affected.
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| 33. |
- Palmé, Anna, 1975-
(author)
-
Assessing and monitoring genetic patterns for conservation purposes with special emphasis on Scandinavia
- 2010
-
Doctoral thesis (other academic/artistic)abstract
- Genetic variation is essential for biological evolution, for maintaining viability of populations, and to ensure ecosystem resilience. Increased human exploitation and environmental change result in rapid loss of biological variation, including genetic diversity. Measures to halt this trend require that biological diversity is assessed and monitored. Assessment of biodiversity includes identifying patterns of distribution of genetic variation within individual species. This thesis focuses on spatial genetic structure and assessment of units for conservation in continuous environments without apparent migration barriers. Empirical data refer to Scandinavia and the model species are northern pike (Esox lucius), brown trout (Salmo trutta), and harbour porpoise (Phocoena phocoena). Questions regarding monitoring genetic diversity and releases of alien populations are also addressed. The spatial genetic structure of the northern pike in the Baltic Sea is characterized by isolation by distance and continuous genetic change. Positive genetic correlation was found among pike within geographical distances of less than 150 km. This distance may be used to suggest management units in this area. For the brown trout, genetic monitoring identified two sympatric populations within a small mountain lake system. The situation is characterized by a clear genetic but no apparent phenotypic dichotomy. Scientific support for a genetically distinct Baltic harbour porpoise population is limited, and the spatial genetic structure of the harbour porpoise in Swedish waters needs to be clarified. Data for launching conservation genetic monitoring programs is available for only a few Swedish species. Millions of forest trees, fish, and birds are released annually in Sweden and the documentation on these releases is poor. To meet responsibilities of safeguarding biodiversity and surveying biological effects of releases, there is an urgent need for studies aimed at evaluating genetic diversity.
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| 34. |
- Palme, Anna, 1986
(author)
-
Characterization of cellulose in post-consumer cotton textiles
- 2015
-
Licentiate thesis (other academic/artistic)abstract
- The overall objective of this thesis is to provide a background to the recycling of cotton. Since cotton consists of pure cellulose, it might be possible to include used cotton, in the already existing viscose industry. In this thesis two aspects important to accomplishing this task have been studied; changes that occur in cotton fibres during service life, and comparison between cotton and dissolving pulp in terms of susceptibility to acid hydrolysis.During the service life of a cotton textile, it is laundered many times, exposing it to numerous drying and rewetting cycles. From research on paper recycling, it is well known that drying and rewetting induce hornification of cellulosic fibres, making the fibres stiff and less porous. However, no increase in the degree of hornification, during the service life of cotton fibres has been measured, probably due to the high initial hornification of cotton fibres. Laundering, however, decreases the mass average molecular mass of cellulose, down to 151 kDa, after more than 50 laundering cycles, from 1323 kDa in a never-laundered sheet.The second aspect studied was reactivity of different cellulosic fibres towards acid hydrolysis. It was found that laundering had no effect on the levelling off degree of polymerization (LODP). Despite the initial large difference between new sheets and discarded sheets, the molecular mass distributions were quite similar for the sheet samples, after only 60 min of hydrolysis (0.4 M HCl, 80 °C). With textile recycling in mind, this is promising, since textiles sent for recycling will have been though a different number of laundering cycles.
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| 35. |
- Palme, Anna, 1986, et al.
(author)
-
Chemical and ultrastructural changes in cotton cellulose induced by laundering and textile use
- 2014
-
In: Cellulose. - : Springer Science and Business Media LLC. - 0969-0239 .- 1572-882X. ; 21:6, s. 4681-4691
-
Journal article (peer-reviewed)abstract
- The textile industry is currently under pressure to decrease environmental load related to both the manufacture and the use of textiles. Material recycling may be one of many ways to accomplish such a decrease. Age-induced property changes in cotton textiles are important to understand in order to facilitate the recycling of cotton textiles. Consequently, this study investigates ultrastructural and chemical changes that take place in the cellulose of cotton sheets over a long time period of use and laundering. Ultrastructural changes were studied using water retention value (WRV), specific surface area measurement, scanning electron microscopy and solid state NMR spectroscopy. Chemical changes through measurement of intrinsic viscosity with and without reductive treatment, molecular mass distribution and carboxylate group content. A substantial decrease in mass average molecular mass from 1,320 to 151 kDa was observed when subjecting the sheets to more than 50 launderings. In contrast, only small differences in WRV, in fibril dimensions and crystallinity estimated using solid state NMR spectra, were observed between sheets laundered 2-4 times and more than 50 times. On one hand, the combination of minor laundering effects of WRV and solid state NMR spectra, together with the large decrease in molecular mass are positive indications for the possibility of recycling cotton into regenerated cellulosic fibres. On the other hand, results show that the specific surface area decreased, which implies that the reactivity of cotton cellulose may decrease during long-term use and laundering.
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| 36. |
- Palmé, Anna, et al.
(author)
-
Compromising Baltic salmon genetic diversity : conservation genetic risks associated with compensatory releases of salmon in the Baltic Sea
- 2012
-
Reports (other academic/artistic)abstract
- Many aspects need to be considered when evaluating the consequences of halting compensatory releases of salmon in the Baltic area. The present report focuses strictly on genetic concerns associated with large scale salmon releases. A majority of the original wild Baltic salmon populations, i.e. populations of Atlantic salmon (Salmo salar) in the Baltic Sea, has gone extinct. Historically, 84 rivers flowing into the Baltic Sea have harbored Atlantic salmon, but currently only 10 of these maintain self sustaining wild natural populations in safe numbers (CCB 2012). Large scale releases of salmon are carried out in the Baltic region to increase productivity of separate populations and to compensate for natural reproduction that has been lost due to hydroelectric power plants that are blocking previous migratory routes. Already in the 1980s observations of pronounced genetic differentiation between populations inhabiting different rivers, coupled with indications that salmon hatchery stocks are genetically divergent from the wild populations they were meant to represent, have warranted conservation genetics researchers to warn against potential negative effects of large scale releases (Ståhl 1981, 1983, 1987). In brief, current large scale releases can cause the following four types of genetic risks for native populations: 1) loss of genetic variation, 2) loss of adaptations, 3) change of population composition, and 4) change of population structure (Laikre et al. 2010). These adverse genetic impacts have been recognized and documented for salmonid fishes for decades (Ryman 1981; Ryman & Utter 1987; Hindar et al.1991; Waples 1999; Naish et al. 2008; Nielsen & Hansen 2008). In 2011 these potential risks of large scale releases gained attention when the European Commission put forward a proposal of phasing out all compensatory releases of salmon in the Baltic area (European Commission 2011). We have compiled and reviewed information regarding compensatory releases of salmon in Swedish rivers including spatio-temporal genetic variability patterns of wild and hatchery salmon populations in the Baltic region. We review and synthesize scientific information from both peer-review and “gray” literature, and have used available genetic data from both published and unpublished studies to address the following main questions: What is currently known regarding the spatio-temporal genetic variability patterns of Atlantic salmon in the Baltic Sea? How has the loss of salmon populations affected the overall capacity for Baltic salmon to maintain genetic variation? What are the effects of releases on genetic variation between and within wild salmon populations? How much of the overall genetic variability of Baltic salmon exists exclusively in hatcheries or is maintained only through breedingrelease operations?Based on current genetic knowledge, what recommendations can be provided with respect to the proposal from the European Commission to halt compensatory releases of salmon in the Baltic? A total of 37 scientific studies on Baltic salmon genetic diversity have been identified. "Gray" genetic literature on Swedish salmon populations comprises seven additional reports. Together they cover genetic information from populations representing 35 Baltic river systems (Rivers Umeälven and Vindelälven counted separately) and c. 23 000 genotyped individuals. The main conclusions from these studies are that the Baltic salmon is genetically divergent from other Atlantic salmon populations and that there is a high degree of genetic structuring between populations in different rivers within the Baltic area. Further, there is a hierarchical grouping of populations in the Baltic, and three larger genetic groups, corresponding to populations in the north, east and south Baltic Sea have been found. In Sweden, compensatory releases of salmon are performed in eight rivers flowing into the Baltic Sea and a total of more than 1.8 million salmon smolt are released annually in Sweden. Despite the hydropower companies’ policy to use local strains, fish of non-local origin is sometimes released. Further, in some hatcheries relatively few spawners are used, which may lead to an increased loss of genetic variation. Information regarding the number of released salmon, number of females and males used in rearing, and strains used for stocking is not easily accessible, and therefore assessment of genetic effects of large scale releases is not straightforward Our analyses of published and unpublished genetic data indicate that a large part of the original genetic variation in Baltic salmon has already been lost due to extinction of individual populations and reduction in population sizes. There is a clear pattern of isolation-by-distance among wild populations, whereas no such pattern is found among hatchery stocks. Further, hatchery stocks typically exhibit lower genetic variation and are less divergent from each other than wild populations. However, hatchery stocks can harbor unique genetic variation and may thus be important to conserve. The genetic effects of releases have not been monitored in the Baltic, but one scientific study indicates strong genetic homogenization of wild populations. Many of the changes of Baltic salmon gene pools occurred prior to the time when molecular genetic studies were possible. Thus, we are not likely to ever clarify exactly the changes that have occurred. Studies of salmonid releases in other parts of the world have in several cases documented altered genetic composition and reduced variability and viability. The extent of this threat needs further investigation. Until such data is available large scale releases should be stopped in line with the precautionary principle, provided that essential actions are implemented to protect remaining wild stocks from e.g. overharvest. Likewise, as many previous spawning areas as possible need to be restored, to safeguard the continued existence of Baltic salmon.
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| 37. |
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| 38. |
- Palmé, Anna, et al.
(author)
-
Conservation genetics without knowing what to conserve : the case of the Baltic harbour porpoise Phocoena phocoena
- 2008
-
In: Oryx. - 0030-6053 .- 1365-3008. ; 42:2, s. 305-308
-
Journal article (peer-reviewed)abstract
- Effective conservation requires that arguments for identifying units for preservation and management are based on scientifically sound information. There is a strong conservation concern for the harbour porpoise Phocoena phocoena of the Baltic Sea. This concern rests on the assumption that these porpoises represent a genetically distinct population reproductively separated from adjacent populations to the west. We argue that current scientific support for this claim is weak and to a large degree speculative. Current management of Baltic harbour porpoises as a genetically separate conservation unit is premature and we urge that high priority be given towards resolving this issue.
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| 39. |
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| 40. |
- Palme, Anna, 1986, et al.
(author)
-
Differences in swelling of chemical pulp fibers and cotton fibers-Effect of the supramolecular structure
- 2019
-
In: BioResources. - : North Carolina State University. - 1930-2126. ; 14:3, s. 5698-5715
-
Journal article (peer-reviewed)abstract
- The swelling and dissolution of cellulose are key parameters in the production of regenerated cellulose fibers. Since cotton is almost pure cellulose, it has been proposed that the recycling of cotton textiles may be accomplished through incorporating the cotton textiles into the production of regenerated cellulosic fibers. In this study, the supramolecular structure before and after pretreatment was characterized using solid-state carbon-13 nuclear magnetic resonance (13C NMR), and the findings related to the swelling of dissolving pulp and cotton were quantified with a fiber analyzer. The cotton and dissolving pulp samples were subjected to three different pretreatments: mild acid hydrolysis, acid hydrolysis in ethanol, and a hydrothermal treatment. The results showed that cotton was harder to swell than the dissolving pulp. This indicated that either waste cotton requires another type of activating pretreatment than those included in this study or very good solvents if it is to be included in the production of regenerated fibers.
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| 41. |
- Palmé, Amma E, et al.
(author)
-
SNP Markers and Evaluation of Duplicate Holdings of Brassica oleracea in Two European Genebanks
- 2020
-
In: PLANTS. - : MDPI AG. - 2223-7747. ; 9
-
Journal article (peer-reviewed)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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| 42. |
- Palmé, Anna, 1973-
(author)
-
Evolutionary history and chloroplast DNA variation in three plant genera: Betula, Corylus and Salix. : The impact of post-glacial colonisation and hybridisation.
- 2003
-
Doctoral thesis (other academic/artistic)abstract
- The great difference in the level of chloroplast variation and its geographic structure among the three main species studied here demonstrates that forest species do not form a homogeneous group. Hazel shows a genetic structure similar to many other thermophilous species and this structure, in combination with fossil evidence, indicates that the post-glacial colonisation of most of Europe originated in a refugium in western France while the Balkan and Italy were colonised from a south-eastern refugium.In sallow and silver birch the chloroplast DNA variation and its structure does not fit with a scenario of glacial restriction to southern refugia and survival at intermediate latitudes is suggested for both species. The chloroplast DNA variation in silver birch suggests the presence of one western and one eastern European post-glacial colonisation route and limited contribution of southern populations in the colonisation of the rest of Europe. Unique haplotypes by the Ural Mountains indicates the possibility of a separate glacial origin of these populations.The study of chloroplast DNA in species closely related to sallow and silver birch indicate that extensive hybridisation and cytoplasmic gene flow occurs within both the Salix and Betula genera in Europe. The nuclear and chloroplast phylogenies of 14 Betula species were not in complete agreement with each other or with the classical division of the Betula genus into subgenera or sections. The phylogenetic structure implies that hybridisation has played a role in the evolution of the Betula genus.This thesis focuses on the chloroplast DNA variation in three forest tree genera: Corylus, Betula and Salix. Chloroplast PCR-RFLP is used to evaluate the post-glacial history of hazel, Corylus avellana, silver birch, Betula pendula and sallow, Salix caprea and to explore the possibility of introgression in the Salix and Betula genera. In addition, the chloroplast matK gene, its flanking regions and the nuclear ADH gene were used to study the phylogenetic relationships within the Betula genus.
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| 43. |
- Palmé, Anna, et al.
(author)
-
Genetic monitoring reveals two sympatric brown trout populations in a small mountain lake
-
Other publication (other academic/artistic)abstract
- It is contentious to what extent sympatric speciation represents a general and taxonomically widespread phenomenon. Documenting the occurrence of multiple, genetically distinct populations within areas lacking barriers to gene flow can increase our understanding of this type of speciation, because such populations are expected to represent the first steps of sympatric speciation. We analyzed the genetic relationships among over 4000 brown trout (Salmo trutta) collected during 19 sampling years from a series of small mountain lakes in northern Scandinavia. Our results clearly indicate the presence of two sympatric populations within these lakes. The populations are characterized by a high degree of genetic divergence coupled with a lack of apparent phenotypic dichotomy. The differentiation pattern appears stable over the two decades monitored, and the exchange of individuals between the two populations appears small. The existence of sympatric populations characterized by substantial genetic divergence may be a much more common phenomenon than anticipated, but difficult to detect in situations where morphological or ecological differentiation is missing. Larger samples than typically collected in a single sampling effort may be needed for revealing situations of sympatry, and for reliable estimation of the number of populations.
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| 44. |
- Palme, Anna, et al.
(author)
-
Monitoring reveals two genetically distinct brown trout populations remaining in stable sympatry over 20 years in tiny mountain lakes
- 2013
-
In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 14:4, s. 795-808
-
Journal article (peer-reviewed)abstract
- Detecting population subdivision when apparent barriers to gene flow are lacking is important in evolutionary and conservation biology. Recent research indicates that intraspecific population complexity can be crucial for maintaining a species' evolutionary potential, productivity, and ecological role. We monitored the genetic relationships at 14 allozyme loci among similar to 4,000 brown trout (Salmo trutta) collected during 19 years from two small interconnected mountain lakes (0.10 and 0.17 km(2), respectively) in central Sweden. There were no allele frequency differences between the lakes. However, heterozygote deficiencies within lakes became obvious after a few years of monitoring. Detailed analyses were then carried out without a priori grouping of samples, revealing unexpected differentiation patterns: (i) the same two genetically distinct (F (ST) a parts per thousand yen 0.10) populations occur sympatrically at about equal frequencies within both lakes, (ii) the genetic subdivision is not coupled with apparent phenotypical dichotomies, (iii) this cryptic structure remains stable over the two decades monitored, and (iv) the point estimates of effective population size are c. 120 and 190, respectively, indicating that genetic drift is important in this system. A subsample of 382 fish was also analyzed for seven microsatellites. The genetic pattern does not follow that of the allozymes, and in this subsample the presence of multiple populations would have gone undetected if only scoring microsatellites. Sympatric populations may be more common than anticipated, but difficult to detect when individuals cannot be grouped appropriately, or when markers or sample sizes are insufficient to provide adequate statistical power with approaches not requiring prior grouping.
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| 45. |
- Palmé, Anna, et al.
(author)
-
Nordic Crop Wild Relative conservation : A report from two collaborative projects 2015–2019
- 2019
-
Reports (other academic/artistic)abstract
- The report summarizes results from a cooperation among all the Nordic countries during the period 2015 – 2019 (two projects). The work has focused on the conservation of Crop Wild Relatives (CWR), i.e. wild plant species closely related to crops. They are of special importance to humanity since traits of potential value for food security and climate change adaptation can be transferred from CWR into crops. The projects represent the first joint action on the Nordic level regarding in situ conservation of CWR. Substantial progress has been made regarding CWR conservation planning, including development of a Nordic CWR checklist and identification of suitable sites for CWR conservation. A set of recommended future actions was developed, with the most important one being initiation of active in situ conservation of CWR in all Nordic countries.
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| 46. |
- Palmé, Anna, 1973-, et al.
(author)
-
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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| 47. |
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| 48. |
- Palme, Anna, 1986
(author)
-
Recycling of cotton textiles: Characterization, pretreatment, and purification
- 2016
-
Doctoral thesis (other academic/artistic)abstract
- In many parts of the world, there are well-established systems for material recycling of metal, glass, and paper. However, no large-scale chemical recycling of textiles currently exists. Since the collection of second hand textiles is established on a large-scale, one of the main barriers to obtaining chemical textile recycling is the development of recycling technology. Recently, it has been proposed that recycling cotton may be accomplished using post-consumer cotton to produce regenerated cellulose fibers, such as viscose and lyocell. These fibers are, today, made either from wood-derived dissolving pulp or cotton linters, both of which contain almost pure cellulose. The incorporation of used cotton fibers from textiles is an interesting possibility since cotton also contains almost pure cellulose. The most common textile material on the market contains a mix of polyester, i.e. poly(ethylene terephthalate) (PET), and cotton, referred to as polycotton, and the separation of the two components is necessary before recycling. This thesis investigates some important aspects of the chemical recycling of textiles. The focus is on four areas; property changes during laundering and use of cotton, acid pretreatment of cotton, swelling properties of cotton, and separation of cotton from polycotton textiles.The first part is based on that during the service life of cotton textiles, laundering is performed many times, and this may change the properties of cotton. When new cotton fibers are compared to cotton fibers from sheets that have been used in hospitals for a long period of time, findings show that laundering and use do not have a large impact on the supramolecular structure of cotton cellulose. However, the cellulose the degree of polymerization decrease greatly after long-term use.The second and third parts of the thesis investigate the pretreatment of cotton. Pretreatments of cellulose fibers are used to enhance susceptibility to dissolution before the production of regenerated fibers. Three different pretreatments were investigated, acid hydrolysis in water, acid hydrolysis in ethanol and hydrothermal treatment. Findings show that the degradation pattern is similar in cotton and dissolving pulp for all pretreatments.The last part of the thesis investigates the separation of the components in polycotton. In the process, polyester is hydrolyzed by the action of alkali while cotton is maintained. The process yields three product streams; two containing the two different monomers obtained when hydrolyzing the PET, and one with residual cotton. The yield of the process is high, and the fractions showed high purity.
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| 49. |
- Palmé, Anna, 1973-, et al.
(author)
-
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
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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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