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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Lagerholm, Vendela K., et al.
(författare)
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Range shifts or extinction? Ancient DNA and distribution modelling reveal past and future responses to climate warming in cold-adapted birds
- 2017
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 23:4, s. 1425-1435
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Tidskriftsartikel (refereegranskat)abstract
- Global warming is predicted to cause substantial habitat rearrangements, with the most severe effects expected to occur in high-latitude biomes. However, one major uncertainty is whether species will be able to shift their ranges to keep pace with climate-driven environmental changes. Many recent studies on mammals have shown that past range contractions have been associated with local extinctions rather than survival by habitat tracking. Here, we have used an interdisciplinary approach that combines ancient DNA techniques, coalescent simulations and species distribution modelling, to investigate how two common cold-adapted bird species, willow and rock ptarmigan (Lagopus lagopus and Lagopus muta), respond to long-term climate warming. Contrary to previous findings in mammals, we demonstrate a genetic continuity in Europe over the last 20 millennia. Results from back-casted species distribution models suggest that this continuity may have been facilitated by uninterrupted habitat availability and potentially also the greater dispersal ability of birds. However, our predictions show that in the near future, some isolated regions will have little suitable habitat left, implying a future decrease in local populations at a scale unprecedented since the last glacial maximum.
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| 3. |
- Brace, Selina, et al.
(författare)
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Serial population extinctions in a small mammal indicate Late Pleistocene ecosystem instability
- 2012
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:50, s. 20532-20536
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Tidskriftsartikel (refereegranskat)abstract
- The Late Pleistocene global extinction of many terrestrial mammal species has been a subject of intensive scientific study for over a century, yet the relative contributions of environmental changes and the global expansion of humans remain unresolved. A defining component of these extinctions is a bias toward large species, with the majority of small-mammal taxa apparently surviving into the present. Here, we investigate the population-level history of a key tundra-specialist small mammal, the collared lemming (Dicrostonyx torquatus), to explore whether events during the Late Pleistocene had a discernible effect beyond the large mammal fauna. Using ancient DNA techniques to sample across three sites in North-West Europe, we observe a dramatic reduction in genetic diversity in this species over the last 50,000 y. We further identify a series of extinction-recolonization events, indicating a previously unrecognized instability in Late Pleistocene small-mammal populations, which we link with climatic fluctuations. Our results reveal climate-associated, repeated regional extinctions in a keystone prey species across the Late Pleistocene, a pattern likely to have had an impact on the wider steppe-tundra community, and one that is concordant with environmental change as a major force in structuring Late Pleistocene biodiversity.
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| 4. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 5. |
- Giménez-García, Angel, et al.
(författare)
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Pollination supply models from a local to global scale
- 2023
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Ingår i: Web Ecology. - 1399-1183. ; 23:2, s. 99-129
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Tidskriftsartikel (refereegranskat)abstract
- Ecological intensification has been embraced with great interest by the academic sector but is still rarely taken up by farmers because monitoring the state of different ecological functions is not straightforward. Modelling tools can represent a more accessible alternative of measuring ecological functions, which could help promote their use amongst farmers and other decision-makers. In the case of crop pollination, modelling has traditionally followed either a mechanistic or a data-driven approach. Mechanistic models simulate the habitat preferences and foraging behaviour of pollinators, while data-driven models associate georeferenced variables with real observations. Here, we test these two approaches to predict pollination supply and validate these predictions using data from a newly released global dataset on pollinator visitation rates to different crops. We use one of the most extensively used models for the mechanistic approach, while for the data-driven approach, we select from among a comprehensive set of state-of-The-Art machine-learning models. Moreover, we explore a mixed approach, where data-derived inputs, rather than expert assessment, inform the mechanistic model. We find that, at a global scale, machine-learning models work best, offering a rank correlation coefficient between predictions and observations of pollinator visitation rates of 0.56. In turn, the mechanistic model works moderately well at a global scale for wild bees other than bumblebees. Biomes characterized by temperate or Mediterranean forests show a better agreement between mechanistic model predictions and observations, probably due to more comprehensive ecological knowledge and therefore better parameterization of input variables for these biomes. This study highlights the challenges of transferring input variables across multiple biomes, as expected given the different composition of species in different biomes. Our results provide clear guidance on which pollination supply models perform best at different spatial scales-the first step towards bridging the stakeholder-Academia gap in modelling ecosystem service delivery under ecological intensification.
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| 6. |
- Li, Zhongqiang, et al.
(författare)
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Heat Waves Alter Macrophyte-Derived Detrital Nutrients Release under Future Climate Warming Scenarios
- 2021
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 55:8, s. 5272-5281
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Tidskriftsartikel (refereegranskat)abstract
- In addition to a rise in global air and water mean temperatures, extreme climate events such as heat waves are increasing in frequency, intensity, and duration in many regions of the globe. Developing a mechanistic understanding of the impacts of heat waves on key ecosystem processes and how they differ from just an increase in mean temperatures is therefore of utmost importance for adaptive management against effects of global change. However, little is known about the impact of extreme events on freshwater ecosystem processes, particularly the decomposition of macrophyte detritus. We performed a mesocosm experiment to evaluate the impact of warming and heat waves on macrophyte detrital decomposition, applied as a fixed increment (+4 °C) above ambient and a fluctuating treatment with similar energy input, ranging from 0 to 6 °C above ambient (i.e., simulating heat waves). We showed that both warming and heat waves significantly accelerate dry mass loss of the detritus and carbon (C) release but found no significant differences between the two heated treatments on the effects on detritus dry mass loss and C release amount. This suggests that moderate warming indirectly enhanced macrophyte detritus dry mass loss and C release mainly by the amount of energy input rather than by the way in which warming was provided (i.e., by a fixed increment or in heat waves). However, we found significantly different amounts of nitrogen (N) and phosphorus (P) released between the two warming treatments, and there was an asymmetric response of N and P release patterns to the two warming treatments, possibly due to species-specific responses of decomposers to short-term temperature fluctuations and litter quality. Our results conclude that future climate scenarios can significantly accelerate organic matter decomposition and C, N, and P release from decaying macrophytes, and more importantly, there are asymmetric alterations in macrophyte-derived detrital N and P release dynamic. Therefore, future climate change scenarios could lead to alterations in N/P ratios in the water column via macrophyte decomposition processes and ultimately affect the structure and function of aquatic ecosystems, especially in the plankton community.
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| 7. |
- Ersmark, Erik, et al.
(författare)
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Genetic turnovers and northern survival during the last glacial maximum in European brown bears
- 2019
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 9:10, s. 5891-5905
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Tidskriftsartikel (refereegranskat)abstract
- The current phylogeographic pattern of European brown bears (Ursus arctos) has commonly been explained by postglacial recolonization out of geographically distinct refugia in southern Europe, a pattern well in accordance with the expansion/contraction model. Studies of ancient DNA from brown bear remains have questioned this pattern, but have failed to explain the glacial distribution of mitochondrial brown bear clades and their subsequent expansion across the European continent. We here present 136 new mitochondrial sequences generated from 346 remains from Europe, ranging in age between the Late Pleistocene and historical times. The genetic data show a high Late Pleistocene diversity across the continent and challenge the strict confinement of bears to traditional southern refugia during the last glacial maximum (LGM). The mitochondrial data further suggest a genetic turnover just before this time, as well as a steep demographic decline starting in the mid-Holocene. Levels of stable nitrogen isotopes from the remains confirm a previously proposed shift toward increasing herbivory around the LGM in Europe. Overall, these results suggest that in addition to climate, anthropogenic impact and inter-specific competition may have had more important effects on the brown bear's ecology, demography, and genetic structure than previously thought.
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| 8. |
- Frantz, Laurent A. F., et al.
(författare)
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Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe
- 2019
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116:35, s. 17231-17238
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Tidskriftsartikel (refereegranskat)abstract
- Archaeological evidence indicates that pig domestication had begun by similar to 10,500 y before the present ( BP) in the Near East, and mitochondrial DNA ( mtDNA) suggests that pigs arrived in Europe alongside farmers similar to 8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.
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| 9. |
- Smith, Steve, et al.
(författare)
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Nonreceding hare lines : genetic continuity since the Late Pleistocene in European mountain hares (Lepus timidus)
- 2017
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Ingår i: Biological Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4066 .- 1095-8312. ; 120:4, s. 891-908
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Tidskriftsartikel (refereegranskat)abstract
- Throughout time, climate changes have caused substantial rearrangements of habitats which have alternately promoted and disfavoured different types of taxa. At first glance, the mountain hare (Lepus timidus) shows the typical hallmarks of a cold-adapted species that has retreated to refugia since the onset of the current Holocene interglacial. In contrary to expectations, however, the species has a high contemporary genetic diversity with no clear differentiation between geographically isolated populations. In order to clarify the phylogeographic history of European mountain hares, we here analysed ancient DNA from the glacial populations that inhabited the previous midlatitude European tundra region. Our results reveal that the Ice Age hares had similar levels of genetic variation and lack of geographic structure as observed today, and the ancient samples were intermingled with modern individuals throughout the reconstructed evolutionary tree. This suggests a temporal genetic continuity in Europe, where the mountain hares were able to keep pace with the rapid changes at the last glacial/ interglacial transition and successfully track their shifting habitat to northern and alpine regions. Further, the temporal demographic analyses showed that the species' population size in Europe appears to have been tightly linked with palaeoclimatic fluctuations, with increases and declines occurring during periods of global cooling and warming, respectively. Taken together, our results suggest that neither habitat shifts nor demographic fluctuations have had any substantial impact on the genetic diversity of European mountain hares. This remarkable resilience, which contrasts to a majority of previously investigated cold-adapted species, is likely due to its generalist nature that makes it less vulnerable to environmental changes.
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| 10. |
- Allen-Perkins, Alfonso, et al.
(författare)
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CropPol : a dynamic, open and global database on crop pollination
- 2022
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Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 103:3
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Tidskriftsartikel (refereegranskat)abstract
- Seventy five percent of the world's food crops benefit from insect pollination. Hence, there has been increased interest in how global change drivers impact this critical ecosystem service. Because standardized data on crop pollination are rarely available, we are limited in our capacity to understand the variation in pollination benefits to crop yield, as well as to anticipate changes in this service, develop predictions, and inform management actions. Here, we present CropPol, a dynamic, open and global database on crop pollination. It contains measurements recorded from 202 crop studies, covering 3,394 field observations, 2,552 yield measurements (i.e. berry weight, number of fruits and kg per hectare, among others), and 47,752 insect records from 48 commercial crops distributed around the globe. CropPol comprises 32 of the 87 leading global crops and commodities that are pollinator dependent. Malus domestica is the most represented crop (32 studies), followed by Brassica napus (22 studies), Vaccinium corymbosum (13 studies), and Citrullus lanatus (12 studies). The most abundant pollinator guilds recorded are honey bees (34.22% counts), bumblebees (19.19%), flies other than Syrphidae and Bombyliidae (13.18%), other wild bees (13.13%), beetles (10.97%), Syrphidae (4.87%), and Bombyliidae (0.05%). Locations comprise 34 countries distributed among Europe (76 studies), Northern America (60), Latin America and the Caribbean (29), Asia (20), Oceania (10), and Africa (7). Sampling spans three decades and is concentrated on 2001-05 (21 studies), 2006-10 (40), 2011-15 (88), and 2016-20 (50). This is the most comprehensive open global data set on measurements of crop flower visitors, crop pollinators and pollination to date, and we encourage researchers to add more datasets to this database in the future. This data set is released for non-commercial use only. Credits should be given to this paper (i.e., proper citation), and the products generated with this database should be shared under the same license terms (CC BY-NC-SA). This article is protected by copyright. All rights reserved.
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