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- Clark, Andrew G., et al.
(author)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Journal article (peer-reviewed)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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- Grossmann, Igor, et al.
(author)
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Insights into the accuracy of social scientists' forecasts of societal change
- 2023
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In: Nature Human Behaviour. - : Springer Nature. - 2397-3374. ; 7, s. 484-501
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Journal article (peer-reviewed)abstract
- How well can social scientists predict societal change, and what processes underlie their predictions? To answer these questions, we ran two forecasting tournaments testing the accuracy of predictions of societal change in domains commonly studied in the social sciences: ideological preferences, political polarization, life satisfaction, sentiment on social media, and gender-career and racial bias. After we provided them with historical trend data on the relevant domain, social scientists submitted pre-registered monthly forecasts for a year (Tournament 1; N = 86 teams and 359 forecasts), with an opportunity to update forecasts on the basis of new data six months later (Tournament 2; N = 120 teams and 546 forecasts). Benchmarking forecasting accuracy revealed that social scientists' forecasts were on average no more accurate than those of simple statistical models (historical means, random walks or linear regressions) or the aggregate forecasts of a sample from the general public (N = 802). However, scientists were more accurate if they had scientific expertise in a prediction domain, were interdisciplinary, used simpler models and based predictions on prior data. How accurate are social scientists in predicting societal change, and what processes underlie their predictions? Grossmann et al. report the findings of two forecasting tournaments. Social scientists' forecasts were on average no more accurate than those of simple statistical models.
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- Lindblad-Toh, Kerstin, et al.
(author)
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Genome sequence, comparative analysis and haplotype structure of the domestic dog.
- 2005
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19
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Journal article (peer-reviewed)abstract
- Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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- López-Blanco, Efrén, et al.
(author)
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Evaluation of terrestrial pan-Arctic carbon cycling using a data-assimilation system
- 2019
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In: Earth System Dynamics. - : Copernicus GmbH. - 2190-4979 .- 2190-4987. ; 10:2, s. 233-255
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Journal article (peer-reviewed)abstract
- There is a significant knowledge gap in the current state of the terrestrial carbon (C) budget. Recent studies have highlighted a poor understanding particularly of C pool transit times and of whether productivity or biomass dominate these biases. The Arctic, accounting for approximately 50 % of the global soil organic C stocks, has an important role in the global C cycle. Here, we use the CARbon DAta MOdel (CARDAMOM) data-assimilation system to produce pan-Arctic terrestrial C cycle analyses for 2000-2015. This approach avoids using traditional plant functional type or steady-state assumptions. We integrate a range of data (soil organic C, leaf area index, biomass, and climate) to determine the most likely state of the high-latitude C cycle at a 1 degrees x 1 degrees resolution and also to provide general guidance about the controlling biases in transit times. On average, CARDAMOM estimates regional mean rates of photosynthesis of 565 g C m(-2) yr (-1) (90 % confidence interval between the 5th and 95th percentiles: 428, 741), autotrophic respiration of 270 g Cm-2 yr(-1) (182, 397) and heterotrophic respiration of 219 g Cm-2 yr(-1) (31, 1458), suggesting a pan-Arctic sink of -67 (-287, 1160) g Cm-2 yr(-1), weaker in tundra and stronger in taiga. However, our confidence intervals remain large (and so the region could be a source of C), reflecting uncertainty assigned to the regional data products. We show a clear spatial and temporal agreement between CARDAMOM analyses and different sources of assimilated and independent data at both pan-Arctic and local scales but also identify consistent biases between CARDAMOM and validation data. The assimilation process requires clearer error quantification for leaf area index (LAI) and biomass products to resolve these biases. Mapping of vegetation C stocks and change over time and soil C ages linked to soil C stocks is required for better analytical constraint. Comparing CARDAMOM analyses to global vegetation models (GVMs) for the same period, we conclude that transit times of vegetation C are inconsistently simulated in GVMs due to a combination of uncertainties from productivity and biomass calculations. Our findings highlight that GVMs need to focus on constraining both current vegetation C stocks and net primary production to improve a process-based understanding of C cycle dynamics in the Arctic.
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- Madani, Nima, et al.
(author)
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Below-surface water mediates the response of African forests to reduced rainfall
- 2020
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In: Environmental Research Letters. - : IOP Publishing. - 1748-9318 .- 1748-9326. ; 15:3
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Journal article (peer-reviewed)abstract
- Terrestrial ecosystem gross primary productivity (GPP) is the largest land-atmosphere carbon flux and the primary mechanism of photosynthetic fixation of atmospheric CO2 into plant biomass. Anomalous rainfall events have been shown to have a great impact on the global carbon cycle. However, less is known about the impact of these events on GPP, especially in Africa, where in situ observations are sparse. Here, we use a suite of satellite and other geospatial data to examine the responses of major ecosystems in Africa to anomalous rainfall events from 2003 to 2017. Our results reveal that higher-than-average groundwater storage in tropical ecosystems offsets the rainfall deficit during the dry years. While the inter-annual variations in GPP in semi-arid ecosystems are controlled by near surface soil water, deeper soil moisture and groundwater control the inter-annual variability of the GPP in dense tropical forests. Our study highlights the critical role of groundwater in buffering rainfall shortages and continued availability of near-surface water to plants through dry spells.
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- White, Christopher J., et al.
(author)
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SLOW-SPEED SUPERNOVAE FROM THE PALOMAR TRANSIENT FACTORY : TWO CHANNELS
- 2015
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In: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 799:1
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Journal article (peer-reviewed)abstract
- Since the discovery of the unusual prototype SN 2002cx, the eponymous class of Type I (hydrogen-poor) supernovae with low ejecta speeds has grown to include approximately two dozen members identified from several heterogeneous surveys, in some cases ambiguously. Here we present the results of a systematic study of 1077 Type I supernovae discovered by the Palomar Transient Factory, leading to nine new members of this peculiar class. Moreover, we find there are two distinct subclasses based on their spectroscopic, photometric, and host galaxy properties: SN 2002cx-like supernovae tend to be in later-type or more irregular hosts, have more varied and generally dimmer luminosities, have longer rise times, and lack a Ti II trough when compared to SN 2002es-like supernovae. None of our objects show helium, and we counter a previous claim of two such events. We also find that the occurrence rate of these transients relative to Type Ia supernovae is 5.6(-3.8)(+22) % (90% confidence), lower compared to earlier estimates. Combining our objects with the literature sample, we propose that these subclasses have two distinct physical origins.
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