| 1. |
- Ellegren, Hans, et al.
(författare)
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The genomic landscape of species divergence in Ficedula flycatchers
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7426, s. 756-760
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Tidskriftsartikel (refereegranskat)abstract
- Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied flycatcher are important avian speciation models that show pre-as well as postzygotic isolation. We sequenced and assembled the 1.1-Gb flycatcher genome, physically mapped the assembly to chromosomes using a low-density linkage map and re-sequenced population samples of each species. Here we show that the genomic landscape of species differentiation is highly heterogeneous with approximately 50 'divergence islands' showing up to 50-fold higher sequence divergence than the genomic background. These non-randomly distributed islands, with between one and three regions of elevated divergence per chromosome irrespective of chromosome size, are characterized by reduced levels of nucleotide diversity, skewed allele-frequency spectra, elevated levels of linkage disequilibrium and reduced proportions of shared polymorphisms in both species, indicative of parallel episodes of selection. Proximity of divergence peaks to genomic regions resistant to sequence assembly, potentially including centromeres and telomeres, indicate that complex repeat structures may drive species divergence. A much higher background level of species divergence of the Z chromosome, and a lower proportion of shared polymorphisms, indicate that sex chromosomes and autosomes are at different stages of speciation. This study provides a roadmap to the emerging field of speciation genomics.
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| 2. |
- Helama, Samuli, et al.
(författare)
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Disentangling the Evidence of Milankovitch Forcing From Tree-Ring and Sedimentary Records
- 2022
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Ingår i: Frontiers in Earth Science. - : Frontiers Media SA. - 2296-6463. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Tree-ring records constitute excellent high-resolution data and provide valuable information for climate science and paleoclimatology. Tree-ring reconstructions of past temperature variations agree to show evidence for annual-to-centennial anomalies in past climate and place the industrial-era warming in the context of the late Holocene climate patterns and regimes. Despite their wide use in paleoclimate research, however, tree rings have also been deemed unsuitable as low-frequency indicators of past climate. The arising debate concerns whether the millennia-long tree-ring records show signals of orbital forcing due to the Milankovitch cycles. Here, we produce a summer-temperature reconstruction from tree-ring chronology running through mid- and late-Holocene times (since 5486 BCE) comprising minimum blue channel light intensity (BI). The BI reconstruction correlates with existing and new tree-ring chronologies built from maximum latewood density (MXD) and, unlike the MXD data, shows temperature trends on Milankovitch scales comparable to various types of sedimentary proxy across the circumpolar Arctic. Our results demonstrate an unrevealed potential of novel, unconventional tree-ring variables to contribute to geoscience and climate research by their capability to provide paleoclimate estimates from inter-annual scales up to those relevant to orbital forcing.
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| 3. |
- Kuklane, Kalev, et al.
(författare)
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Subzero project: Thermal insulation measurement of cold protective clothing using thermal manikins - Physiological tests
- 2003
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Ingår i: 2nd European Conference on Protective Clothing (ECPC) and NOKOBETEF 7 : Challenges for Protective Clothing - Challenges for Protective Clothing.
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Konferensbidrag (refereegranskat)abstract
- Wearer trials with human subjects were included in the Subzero project in order to validate the manikins' data against practice. Physiological tests of the project were aimed to study hu-man subjects at thermal comfort or being slightly warm in cold: 0, -10, -25 and wind-chill temperature –50 ºC. Wind-chill temperature –50 was achieved by combination of 2 tempera-tures and wind velocities: -40 ºC and 3 m/s, and -23 ºC and 10 m/s. Moderate activity to keep subjects at thermal comfort without sweating was chosen according to IREQ-neutral (ISO/CD 11079, 2001). High activity was decided to be 50 W/m2 higher than during moderate activity in order to generate considerably more sweat. Walking speeds for moderate activity were 3.5 (0 and -10 °C) and 3.8 (-25 °C), and for high activity 4.9 (0 and -10 °C) and 5.0 km/h (-25 °C). At wind-chill temperature of -50 the walking speed was the same for both wind speeds: 5.0 km/h with 0.5° inclination. Tests involved walking on a treadmill for 90 minutes. Clothing systems without and with water vapour barrier were tested. Wearer trials with human test subjects were carried out at 4 test institutes (study partners 2 (P2), 4 (P4), 5 (P5) and 6 (P6)). P2 and P4 carried out tests at 0 and -10 °C corresponding to ensembles A and B, P5 at -25 °C and -50 wind-chill temperature corresponding to ensembles C and D, and P6 at -10 and -25 °C. 8 young healthy men served as test subjects at each insti-tute. In total 256 single tests were performed. The subjects reached steady state in all clothing systems and stayed at comfort. Conditions with low sweat accumulation can be used to validate manikin measurements. Consideration of ensemble weight distribution, additional energy costs due to thicker clothing and wind veloc-ity and direction could increase prediction accuracy. Manikin tests lead to realistic results that can be used in practice.
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| 4. |
- Künstner, Axel, et al.
(författare)
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Gene content and patterns of gene expression in the flycatcher genome
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Phenotypic evolution may be driven by changes in the sequence of protein-coding genes or by the way (when, where, at what level) proteins are expressed. Generally, our knowledge about the evolution of gene expression is relatively limited, and this is particularly so for wild populations. Collared flycatcher (Ficedula albicollis) and pied flycatcher (F. hypoleuca) are two recently diverged passerine birds, which have been subject to extensive ecological research, including aspects of speciation. We obtained RNA-seq data with Illumina technology from 10 adult individuals per species (five females and five males) using brain, kidney, liver, lung, muscle, skin, ovary, and testis tissue (plus eight embryos of each species). A total of more than 1 billion sequencing reads were assembled into >15.000 gene models for each species. The proportion of differentially expressed genes between species ranged from 8% to 18% per adult tissue. Very few GO categories were found to be overrepresented among differentially expressed genes, which at least in part might reflect that orphan and not yet annotated genes are prone to evolve more rapidly in gene expression level. However, in testis, the category olfactory receptor activity was significantly overrepresented among differentially expressed genes and it is of interest to note that this category of genes is involved in sperm-egg communication and thereby potentially may contribute to reproductive incompatibility between the two species. Genes with a high degree of differentiation in gene expression between species tended to have high rates of sequence evolution (high dN/dS). Overall, this study illustrates both the feasibility and usefulness of deep transcriptome sequencing in non-model organisms.
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| 5. |
- Lundregan, Sarah L., et al.
(författare)
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Infection by a helminth parasite is associated with changes in DNA methylation in the house sparrow
- 2022
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Ingår i: Ecology and Evolution. - : Wiley-Blackwell. - 2045-7758. ; 12:11
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Tidskriftsartikel (refereegranskat)abstract
- Parasites can exert strong selective pressures on their hosts and influence the evolution of host immunity. While several studies have examined the genetic basis for parasite resistance, the role of epigenetics in the immune response to parasites is less understood. Yet, epigenetic modifications, such as changes in DNA methylation, may allow species to respond rapidly to parasite prevalence or virulence. To test the role of DNA methylation in relation to parasite infection, we examined genome-wide DNA methylation before and during infection by a parasitic nematode, Syngamus trachea, in a natural population of house sparrows (Passer domesticus) using reduced representation bisulfite sequencing (RRBS). We found that DNA methylation levels were slightly lower in infected house sparrows, and we identified candidate genes relating to the initial immune response, activation of innate and adaptive immunity, and mucus membrane functional integrity that were differentially methylated between infected and control birds. Subsequently, we used methylation-sensitive high-resolution melting (MS-HRM) analyses to verify the relationship between methylation proportion and S. trachea infection status at two candidate genes in a larger sample dataset. We found that methylation level at NR1D1, but not CLDN22, remained related to infection status and that juvenile recruitment probability was positively related to methylation level at NR1D1. This underscores the importance of performing follow-up studies on candidate genes. Our findings demonstrate that plasticity in the immune response to parasites can be epigenetically mediated and highlight the potential for epigenetic studies in natural populations to provide further mechanistic insight into host-parasite interactions.
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| 6. |
- Mäkinen, Hannu, et al.
(författare)
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Temporally replicated DNA methylation patterns in great tit using reduced representation bisulfite sequencing
- 2019
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Ingår i: Scientific Data. - : NATURE PUBLISHING GROUP. - 2052-4463. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Seasonal timing of reproduction is an important fitness trait in many plants and animals but the underlying molecular mechanism for this trait is poorly known. DNA methylation is known to affect timing of reproduction in various organisms and is therefore a potential mechanism also in birds. Here we describe genome wide data aiming to detect temporal changes in methylation in relation to timing of breeding using artificial selection lines of great tits (Parus major) exposed to contrasting temperature treatments. Methylation levels of DNA extracted from erythrocytes were examined using reduced representation bisulfite sequencing (RRBS). In total, we obtained sequencing data from 63 libraries over four different time points from 16 birds with on average 20 million quality filtered reads per library. These data describe individual level temporal variation in DNA methylation throughout the breeding season under experimental temperature regimes and provides a resource for future studies investigating the role of temporal changes in DNA methylation in timing of reproduction.
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| 7. |
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| 8. |
- Sokka, Tuulikki, et al.
(författare)
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QUEST-RA : quantitative clinical assessment of patients with rheumatoid arthritis seen in standard rheumatology care in 15 countries
- 2007
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Ingår i: Annals of the Rheumatic Diseases. - : BMJ. - 0003-4967 .- 1468-2060. ; 66:11, s. 1491-1496
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE:To conduct a cross-sectional review of non-selected consecutive outpatients with rheumatoid arthritis (RA) as part of standard clinical care in 15 countries for an overview of the characteristics of patients with RA.METHODS:The review included current disease activity using data from clinical assessment and a patient self-report questionnaire, which was translated into each language. Data on demographic, disease and treatment-related variables were collected and analysed using descriptive statistics. Variation in disease activity on DAS28 (disease activity score on 28-joint count) within and between countries was graphically analysed. A median regression model was applied to analyse differences in disease activity between countries.RESULTS:Between January 2005 and October 2006, the QUEST-RA (Quantitative Patient Questionnaires in Standard Monitoring of Patients with Rheumatoid Arthritis) project included 4363 patients from 48 sites in 15 countries; 78% were female, >90% Caucasian, mean age was 57 years and mean disease duration was 11.5 years. More than 80% of patients had been treated with methotrexate in all but three countries. Overall, patients had an active disease with a median DAS28 of 4.0, with a significant variation between countries (p<0.001). Among 42 sites with >50 patients included, low disease activity of DAS28 50% of patients had high disease activity of DAS28 >5.1.CONCLUSIONS:This international multicentre cross-sectional database provides an overview of clinical status and treatments of patients with RA in standard clinical care in 2005-6 including countries that are infrequently involved in clinical research projects.
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| 9. |
- Uebbing, Severin, et al.
(författare)
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Divergence in gene expression within and between two closely related flycatcher species
- 2016
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 25:9, s. 2015-2028
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Tidskriftsartikel (refereegranskat)abstract
- Relatively little is known about the character of gene expression evolution as species diverge. It is for instance unclear if gene expression generally evolves in a clock-like manner (by stabilizing selection or neutral evolution) or if there are frequent episodes of directional selection. To gain insights into the evolutionary divergence of gene expression, we sequenced and compared the transcriptomes of multiple organs from population samples of collared (Ficedula albicollis) and pied flycatchers (F. hypoleuca), two species which diverged less than one million years ago. Ordination analysis separated samples by organ rather than by species. Organs differed in their degrees of expression variance within species and expression divergence between species. Variance was negatively correlated with expression breadth and protein interactivity, suggesting that pleiotropic constraints reduce gene expression variance within species. Variance was correlated with between-species divergence, consistent with a pattern expected from stabilizing selection and neutral evolution. Using an expression PST approach, we identified genes differentially expressed between species and found 16 genes uniquely expressed in one of the species. For one of these, DPP7, uniquely expressed in collared flycatcher, the absence of expression in pied flycatcher could be associated with a ≈ 20 kb deletion including 11 out of 13 exons. This study of a young vertebrate speciation model system expands our knowledge of how gene expression evolves as natural populations become reproductively isolated.
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