| 1. |
|
|
| 2. |
- Hudson, Lawrence N, et al.
(författare)
-
The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
-
Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
-
Tidskriftsartikel (refereegranskat)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
|
|
| 3. |
- Aquila, A., et al.
(författare)
-
The linac coherent light source single particle imaging road map
- 2015
-
Ingår i: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 2:4
-
Tidskriftsartikel (refereegranskat)abstract
- Intense femtosecond x-ray pulses from free-electron laser sources allow the imag-ing of individual particles in a single shot. Early experiments at the Linac CoherentLight Source (LCLS) have led to rapid progress in the field and, so far, coherentdiffractive images have been recorded from biological specimens, aerosols, andquantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLSheld a workshop to discuss the scientific and technical challenges for reaching theultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap towardreaching atomic resolution, 3D imaging at free-electron laser sources.
|
|
| 4. |
- De Palma, Adriana, et al.
(författare)
-
Predicting bee community responses to land-use changes : effects of geographic and taxonomic biases
- 2016
-
Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 6, s. 1-14
-
Tidskriftsartikel (refereegranskat)abstract
- Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.
|
|
| 5. |
- Mooij, Wolf M., et al.
(författare)
-
Modeling water quality in the Anthropocene : directions for the next-generation aquatic ecosystem models
- 2019
-
Ingår i: Current Opinion in Environmental Sustainability. - : Elsevier BV. - 1877-3435 .- 1877-3443. ; 36, s. 85-95
-
Forskningsöversikt (refereegranskat)abstract
- Everything changes and nothing stands still (Heraclitus). Here we review three major improvements to freshwater aquatic ecosystem models - and ecological models in general - as water quality scenario analysis tools towards a sustainable future. To tackle the rapid and deeply connected dynamics characteristic of the Anthropocene, we argue for the inclusion of eco-evolutionary, novel ecosystem and social-ecological dynamics. These dynamics arise from adaptive responses in organisms and ecosystems to global environmental change and act at different integration levels and different time scales. We provide reasons and means to incorporate each improvement into aquatic ecosystem models. Throughout this study we refer to Lake Victoria as a microcosm of the evolving novel social-ecological systems of the Anthropocene. The Lake Victoria case clearly shows how interlinked eco-evolutionary, novel ecosystem and social-ecological dynamics are, and demonstrates the need for transdisciplinary research approaches towards global sustainability.
|
|
| 6. |
|
|
| 7. |
- Soranno, Patricia A., et al.
(författare)
-
LAGOS-NE : A multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of U.S. lakes
- 2017
-
Ingår i: GigaScience. - : Oxford University Press (OUP). - 2047-217X. ; 6:12, s. 1-22
-
Tidskriftsartikel (refereegranskat)abstract
- Understanding the factors that affect water quality and the ecological services provided by freshwater ecosystems is an urgent global environmental issue. Predicting how water quality will respond to global changes not only requires water quality data, but also information about the ecological context of individual water bodies across broad spatial extents. Because lake water quality is usually sampled in limited geographic regions, often for limited time periods, assessing the environmental controls of water quality requires compilation of many data sets across broad regions and across time into an integrated database. LAGOS-NE accomplishes this goal for lakes in the northeastern-most 17 US states. LAGOS-NE contains data for 51101 lakes and reservoirs larger than 4 ha in 17 lake-rich US states. The database includes 3 datamodules for: lake location and physical characteristics for all lakes; ecological context (i.e., the land use, geologic, climatic, and hydrologic setting of lakes) for all lakes; and in situmeasurements of lake water quality for a subset of the lakes fromthe past 3 decades for approximately 2600–12 000 lakes depending on the variable. The database contains approximately 150000 measures of total phosphorus, 200 000 measures of chlorophyll, and 900 000 measures of Secchi depth. The water quality data were compiled from87 lake water quality data sets fromfederal, state, tribal, and non-profit agencies, university researchers, and citizen scientists. This database is one of the largest andmost comprehensive databases of its type because it includes both in situmeasurements and ecological context data. Because ecological context can be used to study a variety of other questions about lakes, streams, and wetlands, this database can also be used as the foundation for other studies of freshwaters at broad spatial and ecological scales
|
|
| 8. |
- Bonet, Eulàlia, et al.
(författare)
-
(In)Direct reference in the phonology-syntax interface under phase theory: a response to Modular PIC (D’Alessandro and Scheer 2015)
- 2019
-
Ingår i: Linguistic Inquiry. - : MIT Press. - 0024-3892 .- 1530-9150. ; 50:4, s. 751-777
-
Tidskriftsartikel (refereegranskat)abstract
- While the domains of phrasal phonological processes are, in many interface theories, defined in terms of prosodic constituents, D’Alessandro and Scheer (2015) argue that their proposed modification of phase theory, Modular PIC, renders prosodic constituents superfluous. Phrasal phonological domains can instead be defined directly in the syntax. In this response, we argue that Modular PIC does not provide a convincing new approach to the syntaxphonology interface, as it is both too powerful and too restrictive. We show that the analysis offered of Raddoppiamento fonosintattico in Eastern Abruzzese does not justify the loss of restrictiveness Modular PIC brings to phase theory. Modular PIC is also shown to be too restrictive to account for phenomena, from Bantu languages and others, which have received satisfactory analyses within interface theories that appeal to prosodic constituents. We conclude that Modular PIC does not successfully replace prosodic constituent approaches to the interface.
|
|
| 9. |
- Cheng, Lisa L.-S., et al.
(författare)
-
Phasal syntax = cyclic phonology?
- 2016
-
Ingår i: Syntax. - : Wiley. - 1368-0005 .- 1467-9612. ; 19:2, s. 159-191
-
Tidskriftsartikel (refereegranskat)abstract
- This paper addresses three central questions in the phonology–syntax interface: What does phonology know about syntax? Does phrasal phonology “know” about syntax directly or indirectly (i.e., mediated by prosodic constituents such as Intonation Phrase)? When does the phonology–syntax interaction take place? Most current phase-based theories of the interface assume a strict cyclic model of derivation, in which the output of each spell-out domain directly feeds the phonology. We argue instead for an indirect model in which phonology is mainly conditioned by phase edges and accesses syntax only when the syntactic derivation is complete. We motivate the model mainly with data from Bantu languages that have played a leading role in the development of current theories of the phonology–syntax interface.
|
|
| 10. |
- Cornwallis, Charlie K., et al.
(författare)
-
Cooperation facilitates the colonization of harsh environments
- 2017
-
Ingår i: Nature Ecology and Evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 1:3
-
Tidskriftsartikel (refereegranskat)abstract
- Animals living in harsh environments, where temperatures are hot and rainfall is unpredictable, are more likely to breed in cooperative groups. As a result, harsh environmental conditions have been accepted as a key factor explaining the evolution of cooperation. However, this is based on evidence that has not investigated the order of evolutionary events, so the inferred causality could be incorrect. We resolved this problem using phylogenetic analyses of 4,707 bird species and found that causation was in the opposite direction to that previously assumed. Rather than harsh environments favouring cooperation, cooperativebreeding has facilitated the colonization of harsh environments. Cooperative breeding was, in fact, more likely to evolve from ancestors occupying relatively cool environmental niches with predictable rainfall, which had low levels of polyandry and hence high within-group relatedness. We also found that polyandry increased after cooperative breeders invaded harsh environments,suggesting that when helpers have limited options to breed independently, polyandry no longer destabilizes cooperation. This provides an explanation for the puzzling cases of polyandrous cooperative breeding birds. More generally, this illustrates how cooperation can play a key role in invading ecological niches, a pattern observed across all levels of biological organization from cells to animal societies.
|
|
| 11. |
- Downing, Andrea S., et al.
(författare)
-
Matching scope, purpose and uses of planetary boundaries science
- 2019
-
Ingår i: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 14:7
-
Forskningsöversikt (refereegranskat)abstract
- Background: The Planetary Boundaries concept (PBc) has emerged as a key global sustainability concept in international sustainable development arenas. Initially presented as an agenda for global sustainability research, it now shows potential for sustainability governance. Weuse the fact that it is widely cited in scientific literature (>3500 citations) and an extensively studied concept to analyse how it has been used and developed since its first publication. Design: From the literature that cites the PBc, we select those articles that have the terms 'planetary boundaries' or 'safe operating space' in either title, abstract or keywords. Weassume that this literature substantively engages with and develops the PBc. Results: Wefind that 6% of the citing literature engages with the concept. Within this fraction of the literature we distinguish commentaries-that discuss the context and challenges to implementing the PBc, articles that develop the core biogeophysical concept and articles that apply the concept by translating to sub-global scales and by adding a human component to it. Applied literature adds to the concept by explicitly including society through perspectives of impacts, needs, aspirations and behaviours. Discussion: Literature applying the concept does not yet include the more complex, diverse, cultural and behavioural facet of humanity that is implied in commentary literature. Wesuggest there is need for a positive framing of sustainability goals-as a Safe Operating Space rather than boundaries. Key scientific challenges include distinguishing generalised from context-specific knowledge, clarifying which processes are generalizable and which are scalable, and explicitly applying complex systems' knowledge in the application and development of the PBc. We envisage that opportunities to address these challenges will arise when more human social dimensions are integrated, as we learn to feed the global sustainability vision with a plurality of bottom-up realisations of sustainability.
|
|
| 12. |
- Downing, Philip A., et al.
(författare)
-
How to make a sterile helper
- 2017
-
Ingår i: BioEssays. - : Wiley. - 0265-9247. ; 39:1
-
Tidskriftsartikel (refereegranskat)abstract
- The sterile worker castes found in the colonies of social insects are often cited as archetypal examples of altruism in nature. The challenge is to explain why losing the ability to mate has evolved as a superior strategy for transmitting genes into future generations. We propose that two conditions are necessary for the evolution of sterility: completely overlapping generations and monogamy. A review of the literature indicates that when these two conditions are met we consistently observe the evolution of sterile helpers. We explain the theory and evidence behind these ideas, and discuss the importance of ecology in predicting whether sterility will evolve using examples from social birds, mammals, and insects. In doing so, we offer an explanation for the extraordinary lifespans of some cooperative species which hint at ways in which we can unlock the secrets of long life.
|
|
| 13. |
- Downing, Philip A., et al.
(författare)
-
Sex differences in helping effort reveal the effect of future reproduction on cooperative behaviour in birds
- 2018
-
Ingår i: Royal Society of London. Proceedings B. Biological Sciences. - : The Royal Society. - 1471-2954. ; 285:1885
-
Tidskriftsartikel (refereegranskat)abstract
- The evolution of helping behaviour in species that breed cooperatively in family groups is typically attributed to kin selection alone. However, in many species, helpers go on to inherit breeding positions in their natal groups, but the extent to which this contributes to selection for helping is unclear as the future reproductive success of helpers is often unknown. To quantify the role of future reproduction in the evolution of helping, we compared the helping effort of female and male retained offspring across cooperative birds. The kin selected benefits of helping are equivalent between female and male helpers-they are equally related to the younger siblings they help raise-but the future reproductive benefits of helping differ because of sex differences in the likelihood of breeding in the natal group. We found that the sex which is more likely to breed in its natal group invests more in helping, suggesting that in addition to kin selection, helping in family groups is shaped by future reproduction.
|
|
| 14. |
- Downing, Philip, et al.
(författare)
-
Sex, long life and the evolutionary transition to cooperative breeding in birds.
- 2015
-
Ingår i: Royal Society of London. Proceedings B. Biological Sciences. - : The Royal Society. - 1471-2954. ; 282:1816
-
Tidskriftsartikel (refereegranskat)abstract
- Long life is a typical feature of individuals living in cooperative societies. One explanation is that group living lowers mortality, which selects for longer life. Alternatively, long life may make the evolution of cooperation more likely by ensuring a long breeding tenure, making helping behaviour and queuing for breeding positions worthwhile. The benefit of queuing will, however, depend on whether individuals gain indirect fitness benefits while helping, which is determined by female promiscuity. Where promiscuity is high and therefore the indirect fitness benefits of helping are low, cooperation can still be favoured by an even longer life span. We present the results of comparative analyses designed to test the likelihood of a causal relationship between longevity and cooperative breeding by reconstructing ancestral states of cooperative breeding across birds, and by examining the effect of female promiscuity on the relationship between these two traits. We found that long life makes the evolution of cooperation more likely and that promiscuous cooperative species are exceptionally long lived. These results make sense of promiscuity in cooperative breeders and clarify the importance of life-history traits in the evolution of cooperative breeding, illustrating that cooperation can evolve via the combination of indirect and direct fitness benefits.
|
|
| 15. |
- Edmonson, MN, et al.
(författare)
-
Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants
- 2019
-
Ingår i: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 29:9, s. 1555-1565
-
Tidskriftsartikel (refereegranskat)abstract
- Variant interpretation in the era of massively parallel sequencing is challenging. Although many resources and guidelines are available to assist with this task, few integrated end-to-end tools exist. Here, we present the Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE), a web- and cloud-based platform for annotation, identification, and classification of variations in known or putative disease genes. Starting from a set of variants in variant call format (VCF), variants are annotated, ranked by putative pathogenicity, and presented for formal classification using a decision-support interface based on published guidelines from the American College of Medical Genetics and Genomics (ACMG). The system can accept files containing millions of variants and handle single-nucleotide variants (SNVs), simple insertions/deletions (indels), multiple-nucleotide variants (MNVs), and complex substitutions. PeCanPIE has been applied to classify variant pathogenicity in cancer predisposition genes in two large-scale investigations involving >4000 pediatric cancer patients and serves as a repository for the expert-reviewed results. PeCanPIE was originally developed for pediatric cancer but can be easily extended for use for nonpediatric cancers and noncancer genetic diseases. Although PeCanPIE's web-based interface was designed to be accessible to non-bioinformaticians, its back-end pipelines may also be run independently on the cloud, facilitating direct integration and broader adoption. PeCanPIE is publicly available and free for research use.
|
|
| 16. |
- Faber, Zachary J, et al.
(författare)
-
The genomic landscape of core-binding factor acute myeloid leukemias
- 2016
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 48, s. 1551-1556
-
Tidskriftsartikel (refereegranskat)abstract
- Acute myeloid leukemia (AML) comprises a heterogeneous group of leukemias frequently defined by recurrent cytogenetic abnormalities, including rearrangements involving the core-binding factor (CBF) transcriptional complex. To better understand the genomic landscape of CBF-AMLs, we analyzed both pediatric (n = 87) and adult (n = 78) samples, including cases with RUNX1-RUNX1T1 (n = 85) or CBFB-MYH11 (n = 80) rearrangements, by whole-genome or whole-exome sequencing. In addition to known mutations in the Ras pathway, we identified recurrent stabilizing mutations in CCND2, suggesting a previously unappreciated cooperating pathway in CBF-AML. Outside of signaling alterations, RUNX1-RUNX1T1 and CBFB-MYH11 AMLs demonstrated remarkably different spectra of cooperating mutations, as RUNX1-RUNX1T1 cases harbored recurrent mutations in DHX15 and ZBTB7A, as well as an enrichment of mutations in epigenetic regulators, including ASXL2 and the cohesin complex. This detailed analysis provides insights into the pathogenesis and development of CBF-AML, while highlighting dramatic differences in the landscapes of cooperating mutations for these related AML subtypes.
|
|
| 17. |
- Griffiths, Jennifer R., et al.
(författare)
-
Phytoplankton community interactions and environmental sensitivity in coastal and offshore habitats
- 2016
-
Ingår i: Oikos. - : Wiley. - 0030-1299 .- 1600-0706. ; 125:8, s. 1134-1143
-
Tidskriftsartikel (refereegranskat)abstract
- Assessing the relative importance of environmental conditions and community interactions is necessary for evaluating the sensitivity of biological communities to anthropogenic change. Phytoplankton communities have a central role in aquatic food webs and biogeochemical cycles, therefore, consequences of differing community sensitivities may have broad ecosystem effects. Using two long-term time series (28 and 20 years) from the Baltic Sea, we evaluated coastal and offshore major phytoplankton taxonomic group biovolume patterns over annual and monthly time-scales and assessed their response to environmental drivers and biotic interactions. Overall, coastal phytoplankton responded more strongly to environmental anomalies than offshore phytoplankton, although the specific environmental driver changed with time scale. A trend indicating a state shift in annual biovolume anomalies occurred at both sites and the shift's timing at the coastal site closely tracked other long-term Baltic Sea ecosystem shifts. Cyanobacteria and the autotrophic ciliate Mesodinium rubrum were more strongly related than other groups to this trend with opposing relationships that were consistent across sites. On a monthly scale, biotic interactions within communities were rare and did not overlap between the coastal and offshore sites. Annual scales may be better able to assess general patterns across habitat types in the Baltic Sea, but monthly community dynamics may differ at relatively small spatial scales and consequently respond differently to future change.
|
|
| 18. |
- Hjerne, Olle, et al.
(författare)
-
Climate Driven Changes in Timing, Composition and Magnitude of the Baltic Sea Phytoplankton Spring Bloom
- 2019
-
Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 6
-
Tidskriftsartikel (refereegranskat)abstract
- Spring phytoplankton blooms contribute a substantial part to annual production, support pelagic and benthic secondary production and influence biogeochemical cycles in many temperate aquatic systems. Understanding environmental effects on spring bloom dynamics is important for predicting future climate responses and for managing aquatic systems. We analyzed long-term phytoplankton data from one coastal and one offshore station in the Baltic Sea to uncover trends in timing, composition and size of the spring bloom and its correlations to environmental variables. There was a general trend of earlier phytoplankton blooms by 1-2 weeks over the last 20 years, associated with more sunshine and less windy conditions. High water temperatures were associated with earlier blooms of diatoms and dinoflagellates that dominate the spring bloom, and decreased diatom bloom magnitude. Overall bloom timing, however, was buffered by a temperature and ice related shift in composition from early blooming diatoms to later blooming dinoflagellates and the autotrophic ciliate Mesodinium rubrum. Such counteracting responses to climate change highlight the importance of both general and taxon-specific investigations. We hypothesize that the predicted earlier blooms of diatoms and dinoflagellates as a response to the expected temperature increase in the Baltic Sea might also be counteracted by more clouds and stronger winds. A shift from early blooming and fast sedimenting diatoms to later blooming groups of dinoflagellates and M. rubrum at higher temperatures during the spring period is expected to increase energy transfers to pelagic secondary production and decrease spring bloom inputs to the benthic system, resulting in lower benthic production and reduced oxygen consumption.
|
|
| 19. |
- Janssen, Annette B. G., et al.
(författare)
-
Exploring, exploiting and evolving diversity of aquatic ecosystem models : a community perspective
- 2015
-
Ingår i: Aquatic Ecology. - : Springer Science and Business Media LLC. - 1386-2588 .- 1573-5125. ; 49:4, s. 513-548
-
Tidskriftsartikel (refereegranskat)abstract
- Here, we present a community perspective on how to explore, exploit and evolve the diversity in aquatic ecosystem models. These models play an important role in understanding the functioning of aquatic ecosystems, filling in observation gaps and developing effective strategies for water quality management. In this spirit, numerous models have been developed since the 1970s. We set off to explore model diversity by making an inventory among 42 aquatic ecosystem modellers, by categorizing the resulting set of models and by analysing them for diversity. We then focus on how to exploit model diversity by comparing and combining different aspects of existing models. Finally, we discuss how model diversity came about in the past and could evolve in the future. Throughout our study, we use analogies from biodiversity research to analyse and interpret model diversity. We recommend to make models publicly available through open-source policies, to standardize documentation and technical implementation of models, and to compare models through ensemble modelling and interdisciplinary approaches. We end with our perspective on how the field of aquatic ecosystem modelling might develop in the next 5-10 years. To strive for clarity and to improve readability for non-modellers, we include a glossary.
|
|
| 20. |
- Nanda, V, et al.
(författare)
-
Membership spotlight
- 2015
-
Ingår i: Vascular medicine (London, England). - 1477-0377. ; 20:3, s. 274-274
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)
|
|
| 21. |
- van Gerven, Luuk P. A., et al.
(författare)
-
Advantages of concurrent use of multiple software frameworks in water quality modelling using a database approach
- 2015
-
Ingår i: Fundamental and Applied Limnology. - : Schweizerbart. - 1863-9135. ; 186:1-2, s. 5-20
-
Tidskriftsartikel (refereegranskat)abstract
- Water quality modelling deals with multidisciplinary questions ranging from fundamental to applied. Addressing this broad range of questions requires multiple analysis techniques and therefore multiple frameworks. Through the recently developed database approach to modelling (DATM), it has become possible to run a model in multiple software frameworks without much overhead. Here we apply DATM to the ecosystem model for ditches PCDitch and its twin model for shallow lakes PCLake. Using DATM, we run these models in six frameworks (ACSL, DELWAQ, DUFLOW, GRIND for MATLAB, OSIRIS and R), and report on the possible model analyses with tools provided by each framework. We conclude that the dynamic link between frameworks and models resulting from DATM has the following main advantages: it allows one to use the framework one is familiar with for most model analyses and eases switching between frameworks for complementary model analyses, including the switch between a 0-D and 1-D to 3-D setting. Moreover, the strength of each framework - including runtime performance - can now be easily exploited. We envision that a community-based further development of the concept can contribute to the future development of water quality modelling, not only by addressing multidisciplinary questions but also by facilitating the exchange of models and process formulations within the community of water quality modellers.
|
|
