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- Hudson, Lawrence N, et al.
(författare)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
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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.
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- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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- Jarvis, Erich D., et al.
(författare)
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Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
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Tidskriftsartikel (refereegranskat)abstract
- To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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- Saarela, Svetlana, et al.
(författare)
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Comparing frameworks for biomass prediction for the Global Ecosystem Dynamics Investigation
- 2022
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Ingår i: Remote Sensing of Environment. - : Elsevier. - 0034-4257 .- 1879-0704. ; 278
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Tidskriftsartikel (refereegranskat)abstract
- NASA's Global Ecosystem Dynamics Investigation (GEDI) mission offers data for temperate and pan-tropical estimates of aboveground forest biomass (AGB). The spaceborne, full-waveform LiDAR from GEDI provides sample footprints of canopy structure, expected to cover about 4% of the land area following two years of operation. Several options are available for estimating AGB at different geographical scales. Using GEDI sample data alone, gridded biomass predictions are based on hybrid inference which correctly propagates errors due to the modeling and accounts for sampling variability, but this method requires at least two GEDI tracks in the area of interest. However, there are significant gaps in GEDI coverage and in some areas of interest GEDI data may need to be combined with other wall-to-wall remotely sensed (RS) data, such as those from multispectral or SAR sensors. In these cases, we may employ hierarchical model-based (HMB) inference that correctly considers the additional model errors that result from relating GEDI data to the wall-to-wall data. Where predictions are possible from both hybrid and HMB inference the question arises which framework to choose, and under what circumstances? In this paper, we make progress towards answering these questions by comparing the performance of the two prediction frameworks under conditions relevant for the GEDI mission. Conventional model-based (MB) inference with wall-to-wall TanDEM-X data was applied as a baseline prediction framework, which does not involve GEDI data at all. An important feature of the study was the comparison of AGB predictors in terms of both standard deviation (SD: the square root of variance) and root mean square error (RMSE: the square root of mean square error – MSE). Since, in model-based inference, the true AGB in an area of interest is a random variable, comparisons of the performance of prediction frameworks should preferably be made in terms of their RMSEs. However, in practice only the SD can be estimated based on empirical survey data, and thus it is important also to study whether or not the difference between the two uncertainty measures is small or large under conditions relevant for the GEDI mission. Our main findings were that: (i) hybrid and HMB prediction typically resulted in smaller RMSEs than conventional MB prediction although the difference between the three frameworks in terms of SD often was small; (ii) in most cases the difference between hybrid and HMB inference was small in terms of both RMSE and SD; (iii) the RMSEs for all frameworks was substantially larger than the SDs in small study areas whereas the two uncertainty measures were similar in large study areas, and; (iv) spatial autocorrelation of model residual errors had a large effect on the RMSEs of AGB predictors, especially in small study areas. We conclude that hybrid inference is suitable in most GEDI applications for AGB assessment, due to its simplicity compared to HMB inference. However, where GEDI data are sparse HMB inference should be preferred.
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- Zhang, Guojie, et al.
(författare)
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Comparative genomics reveals insights into avian genome evolution and adaptation
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320
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Tidskriftsartikel (refereegranskat)abstract
- Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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