| 1. |
- Plomion, Christophe, et al.
(författare)
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Oak genome reveals facets of long lifespan
- 2018
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Ingår i: NATURE PLANTS. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 4:7, s. 440-452
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Tidskriftsartikel (refereegranskat)abstract
- Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes' but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times(2). With 450 species spread throughout Asia, Europe and America(3), oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical(4) and modelling(5) approaches have shown that intra-organismal genetic heterogeneity can be selected for(6) and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes(7). However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.
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| 2. |
- Benavides, Raquel, et al.
(författare)
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The GenTree Leaf Collection : Inter- and intraspecific leaf variation in seven forest tree species in Europe
- 2021
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Ingår i: Global Ecology and Biogeography. - : John Wiley & Sons. - 1466-822X .- 1466-8238. ; 30:3, s. 590-597
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Tidskriftsartikel (refereegranskat)abstract
- Motivation Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide variation in leaf traits from seven of the most ecologically and economically important tree species in Europe. Sample collection and trait assessment are embedded in the GenTree project (EU-Horizon 2020), which aims at characterizing the genetic and phenotypic variability of forest tree species to optimize the management and sustainable use of forest genetic resources. Our dataset captures substantial intra- and interspecific leaf phenotypic variability, and provides valuable information for studying the relationship between ecosystem functioning and trait variability of individuals, and the response and resilience of species to environmental changes. Main types of variable contained We chose morphological and chemical characters linked to trade-offs between acquisition and conservation of resources and water use, namely specific leaf area, leaf size, carbon and nitrogen content and their ratio, and the isotopic signature of stable isotope C-13 and N-15 in leaves. Spatial location and grain We surveyed between 18 and 22 populations per species, 141 in total, across Europe. Time period Leaf sampling took place between 2016 and 2017. Major taxa and level of measurement We sampled at least 25 individuals in each population, 3,569 trees in total, and measured traits in 35,755 leaves from seven European tree species, i.e. the conifers Picea abies, Pinus pinaster and Pinus sylvestris, and the broadleaves Betula pendula, Fagus sylvatica, Populus nigra and Quercus petraea. Software format The data files are in ASCII text, tab delimited, not compressed.
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| 3. |
- Culina, Antica, et al.
(författare)
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Connecting the data landscape of long-term ecological studies : The SPI-Birds data hub
- 2021
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Ingår i: Journal of Animal Ecology. - : John Wiley & Sons. - 0021-8790 .- 1365-2656. ; 90:9, s. 2147-2160
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Tidskriftsartikel (refereegranskat)abstract
- The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change). To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database ()-a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting. SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language). The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration.
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| 4. |
- Guillemain, Matthieu, et al.
(författare)
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Predation risk constrains the plasticity of foraging behaviour in teals, Anas crecca : a flyway-level circumannual approach
- 2007
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Ingår i: Animal Behaviour. - 0003-3472 .- 1095-8282. - 0003-3472 ; 73:5, s. 845-854
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Tidskriftsartikel (refereegranskat)abstract
- The trade-off foragers make between predation risk and feeding efficiency is readily studied in dabbling ducks, which have stereotyped feeding methods, some of which prevent predator detection while others do not. Teals forage mostly with only the bill submerged (eyes above the water surface) in winter, but use a broader foraging repertoire in summer. Given the different environments used by teals over the year, it is likely that such a shift is due to changes in diet, but it may also be caused by differences in predation risk between habitats. However, neither predation risk nor teal behaviour has been studied with consistent methods around the year or throughout any of its flyways. Covering wintering, spring-staging, breeding and moulting sites, we combined focal observations of teals and predator flyover data from seven regions ranging from southern France to northern Sweden. Although not apparent at the scale of days within sites, teals indeed relied more on shallow foraging where predation risk was higher, i.e. at wintering sites. Average foraging depth increased gradually from September to August, i.e. from wintering to breeding sites. Foraging bout length of deeply foraging teals did not decrease over the year, suggesting that it is through selection of foraging technique, rather than by the balance between foraging and interruptions, that birds adjust to predation risk. This study highlights behavioural plasticity in response to contrasting selection regimes within a flyway, in dabbling ducks as well as long-distance migrants in general.
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| 5. |
- Guillemain, Matthieu, et al.
(författare)
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Predation risk constrains the plasticity of foraging behaviour in teals, Anas crecca : a flyway-level circumannual approach
- 2007
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Ingår i: Animal Behaviour. - : Academic Press Inc.. - 0003-3472 .- 1095-8282. ; 73:5, s. 845-854
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Tidskriftsartikel (refereegranskat)abstract
- The trade-off foragers make between predation risk and feeding efficiency is readily studied in dabbling ducks, which have stereotyped feeding methods, some of which prevent predator detection while others do not. Teals forage mostly with only the bill submerged (eyes above the water surface) in winter, but use a broader foraging repertoire in summer. Given the different environments used by teals over the year, it is likely that such a shift is due to changes in diet, but it may also be caused by differences in predation risk between habitats. However, neither predation risk nor teal behaviour has been studied with consistent methods around the year or throughout any of its flyways. Covering wintering, spring-staging, breeding and moulting sites, we combined focal observations of teals and predator flyover data from seven regions ranging from southern France to northern Sweden. Although not apparent at the scale of days within sites, teals indeed relied more on shallow foraging where predation risk was higher, i.e. at wintering sites. Average foraging depth increased gradually from September to August, i.e. from wintering to breeding sites. Foraging bout length of deeply foraging teals did not decrease over the year, suggesting that it is through selection of foraging technique, rather than by the balance between foraging and interruptions, that birds adjust to predation risk. This study highlights behavioural plasticity in response to contrasting selection regimes within a flyway, in dabbling ducks as well as long-distance migrants in general.
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| 6. |
- Guillemain, Matthieu, et al.
(författare)
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Risky foraging leads to cost-free mate guarding in male teal Anas crecca
- 2007
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Ingår i: Journal of Ornithology = Journal fur Ornithologie. - 0021-8375 .- 1439-0361. - 0021-8375 ; 148:2, s. 251-254
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Tidskriftsartikel (refereegranskat)abstract
- Mate guarding by males is common in species with long-lasting pair bonds. We tested if the need to guard females affected foraging depth in male teal (Anas crecca), and if they were more vigilant than females when foraging with submerged eyes (preventing monitoring of competing males and predators). These predictions were not supported, suggesting that foraging depth selection is primarily driven by other factors, presumably food related. A likely reason why deeply foraging males did not increase vigilance is that 37.5% of the foraging time was already dedicated to it. The apparent lack of guarding costs in foraging male teal may explain why such small ducks can maintain pair bonds for up to 7 months.
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| 7. |
- Guillemain, Matthieu, et al.
(författare)
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Risky foraging leads to cost-free mate guarding in male teal Anas crecca
- 2007
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Ingår i: Journal of Ornithology = Journal fur Ornithologie. - : Springer Science and Business Media LLC. - 0021-8375. ; 148:2, s. 251-254
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Tidskriftsartikel (refereegranskat)abstract
- Mate guarding by males is common in species with long-lasting pair bonds. We tested if the need to guard females affected foraging depth in male teal (Anas crecca), and if they were more vigilant than females when foraging with submerged eyes (preventing monitoring of competing males and predators). These predictions were not supported, suggesting that foraging depth selection is primarily driven by other factors, presumably food related. A likely reason why deeply foraging males did not increase vigilance is that 37.5% of the foraging time was already dedicated to it. The apparent lack of guarding costs in foraging male teal may explain why such small ducks can maintain pair bonds for up to 7 months.
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| 8. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 9. |
- Lambrechts, Marcel M., et al.
(författare)
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The design of artificial nestboxes for the study of secondary hole-nesting birds: a review of methodological inconsistencies and potential biases
- 2010
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Ingår i: Acta Ornithologica. - 0001-6454 .- 1734-8471. ; 45:1, s. 1-26
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Tidskriftsartikel (refereegranskat)abstract
- The widespread use of artificial nestboxes has led to significant advances in our knowledge of the ecology, behaviour and physiology of cavity nesting birds, especially small passerines Nestboxes have made it easier to perform routine monitoring and experimental manipulation of eggs or nestlings, and also repeatedly to capture, identify and manipulate the parents However, when comparing results across study sites the use of nestboxes may also Introduce a potentially significant confounding variable in the form of differences in nestbox design amongst studies, such as their physical dimensions, placement height, and the way in which they are constructed and maintained However, the use of nestboxes may also introduce an unconsidered and potentially significant confounding variable clue to differences in nestbox design amongst studies, such as their physical dimensions, placement height, and the way in which they are constructed and maintained Here we review to what extent the characteristics of artificial nestboxes (e g size, shape, construction material, colour) are documented in the 'methods' sections of publications involving hole-nesting passerine birds using natural or excavated cavities or artificial nestboxes for reproduction and roosting Despite explicit previous recommendations that authors describe in detail the characteristics of the nestboxes used, we found that the description of nestbox characteristics in most recent publications remains poor and insufficient We therefore list the types of descriptive data that should be included in the methods sections of relevant manuscripts and justify this by discussing how variation in nestbox characteristics can affect or confound conclusions from nestbox studies We also propose several recommendations to improve the reliability and usefulness of research based on long-term studies of any secondary hole-nesting species using artificial nestboxes for breeding or roosting.
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| 10. |
- Lemoine, Melissa, et al.
(författare)
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Low but contrasting neutral genetic differentiation shaped by winter temperature in European great tits
- 2016
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Ingår i: Biological Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4066 .- 1095-8312. ; 118:3, s. 668-685
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Tidskriftsartikel (refereegranskat)abstract
- Gene flow is usually thought to reduce genetic divergence and impede local adaptation by homogenising gene pools between populations. However, evidence for local adaptation and phenotypic differentiation in highly mobile species, experiencing high levels of gene flow, is emerging. Assessing population genetic structure at different spatial scales is thus a crucial step towards understanding mechanisms underlying intraspecific differentiation and diversification. Here, we studied the population genetic structure of a highly mobile species - the great tit Parus major - at different spatial scales. We analysed 884 individuals from 30 sites across Europe including 10 close-by sites (< 50 km), using 22 microsatellite markers. Overall we found a low but significant genetic differentiation among sites (F-ST = 0.008). Genetic differentiation was higher, and genetic diversity lower, in south-western Europe. These regional differences were statistically best explained by winter temperature. Overall, our results suggest that great tits form a single patchy metapopulation across Europe, in which genetic differentiation is independent of geographical distance and gene flow may be regulated by environmental factors via movements related to winter severity. This might have important implications for the evolutionary trajectories of sub-populations, especially in the context of climate change, and calls for future investigations of local differences in costs and benefits of philopatry at large scales.
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