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  • Wiley  (20)
  • American Association for the Advancement of Science (AAAS)  (5)
  • 2015-2019  (25)
  • 1
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    Convergent regulatory evolution and loss of flight in paleognathous birds (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉A core question in evolutionary biology is whether convergent phenotypic evolution is driven by convergent molecular changes in proteins or regulatory regions. We combined phylogenomic, developmental, and epigenomic analysis of 11 new genomes of paleognathous birds, including an extinct moa, to show that convergent evolution of regulatory regions, more so than protein-coding genes, is prevalent among developmental pathways associated with independent losses of flight. A Bayesian analysis of 284,001 conserved noncoding elements, 60,665 of which are corroborated as enhancers by open chromatin states during development, identified 2355 independent accelerations along lineages of flightless paleognaths, with functional consequences for driving gene expression in the developing forelimb. Our results suggest that the genomic landscape associated with morphological convergence in ratites has a substantial shared regulatory component.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Natural selection shaped the rise and fall of passenger pigeon genomic diversity (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-11-17
    Description: The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. Although theory predicts that large populations will be more genetically diverse, passenger pigeon genetic diversity was surprisingly low. To investigate this disconnect, we analyzed 41 mitochondrial and 4 nuclear genomes from passenger pigeons and 2 genomes from band-tailed pigeons, which are passenger pigeons’ closest living relatives. Passenger pigeons’ large population size appears to have allowed for faster adaptive evolution and removal of harmful mutations, driving a huge loss in their neutral genetic diversity. These results demonstrate the effect that selection can have on a vertebrate genome and contradict results that suggested that population instability contributed to this species’s surprisingly rapid extinction.
    Keywords: Evolution, Genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Convergence in nitrogen deposition and cryptic isotopic variation across urban and agricultural valleys in northern Utah (2016)
    Wiley
    Details
    Publication Date: 2016-08-27
    Description: The extent to which atmospheric nitrogen (N) deposition reflects land use differences and biogenic vs. fossil fuel reactive N sources remains unclear, yet represents a critical uncertainty in ecosystem N budgets. We compared N concentrations and isotopes in precipitation-event bulk (wet + dry) deposition across nearby valleys in northern Utah with contrasting land use (highly urban vs. intensive agriculture/low-density urban). We predicted greater nitrate (NO 3 - ) vs. ammonium (NH 4 + ) and higher δ 15 N of NO 3 - and NH 4 + in urban valley sites. Contrary to expectations, annual N deposition (3.5–5.1 kg N ha -1 y -1 ) and inorganic N concentrations were similar within and between valleys. Significant summertime decreases in δ 15 N of NO 3 - possibly reflected increasing biogenic emissions in the agricultural valley. Organic N was a relatively minor component of deposition (~13%). Nearby paired wildland sites had similar bulk deposition N concentrations as the urban and agricultural sites. Weighted bulk deposition δ 15 N was similar to natural ecosystems (-0.6 ± 0.7‰). Fine atmospheric particulate matter (PM 2.5 ) had consistently high values of bulk δ 15 N (15.6 ± 1.4‰), δ 15 N in NH 4 + (22.5 ± 1.6‰), and NO 3 - (8.8 ± 0.7‰), consistent with equilibrium fractionation with gaseous species. δ 15 N in bulk deposition NH 4 + varied by more than 40‰, and spatial variation in δ 15 N within storms exceeded 10‰. Sporadically high values of δ 15 N were thus consistent with increased particulate N contributions as well as potential N source variation. Despite large differences in reactive N sources, urban and agricultural landscapes are not always strongly reflected in the composition and fluxes of local N deposition—an important consideration for regional-scale ecosystem models.
    Print ISSN: 0148-0227
    Topics: Biology , Geosciences
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 4
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    The power of environmental observatories for advancing multidisciplinary research, outreach, and decision support: the case of the Minnesota River Basin (2019)
    Wiley
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    Publication Date: 2019
    Description: Abstract Observatory‐scale data collection efforts allow unprecedented opportunities for integrative, multidisciplinary investigations in large, complex watersheds which can affect management decisions and policy. Through the National Science Foundation‐funded REACH (REsilience under Accelerated CHange) project, in collaboration with the Intensively Managed Landscapes‐Critical Zone Observatory, we have collected a series of multidisciplinary datasets throughout the Minnesota River Basin in south‐central Minnesota, USA, a 43,400 km2 tributary to the Upper Mississippi River. Post‐glacial incision within the Minnesota River valley created an erosional landscape highly responsive to hydrologic change, allowing for transdisciplinary research into the complex cascade of environmental changes that occur due to hydrology and land use alterations from intensive agricultural management and climate change. Datasets collected include water chemistry and biogeochemical data; geochemical fingerprinting of major sediment sources; high resolution monitoring of river bluff erosion; and repeat channel cross‐sectional and bathymetry data following major floods. The data collection efforts led to development of a series of integrative reduced complexity models that provide deeper insight into how water, sediment, and nutrients route and transform through a large channel network and respond to change. These models represent the culmination of efforts to integrate interdisciplinary datasets and science to gain new insights into watershed‐scale processes in order to advance management and decision making. The purpose of this paper is to present a synthesis of the data sets and models, disseminate them to the community for further research, and identify mechanisms used to expand the temporal and spatial extent of short‐term observatory‐scale data collection efforts.
    Print ISSN: 0043-1397
    Electronic ISSN: 1944-7973
    Topics: Architecture, Civil Engineering, Surveying , Geography
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 5
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    Scaling Dissolved Nutrient Removal in River Networks: A Comparative Modeling Investigation (2017)
    Wiley
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    Publication Date: 2017-10-31
    Description: Along the river network, water, sediment, and nutrients are transported, cycled, and altered by coupled hydrological and biogeochemical processes. Our current understanding of the rates and processes controlling the cycling and removal of dissolved inorganic nutrients in river networks is limited due to a lack of empirical measurements in large, (non-wadeable), rivers. The goal of this paper was to develop a coupled hydrological and biogeochemical process model to simulate nutrient uptake at the network scale during summer baseflow conditions. The model was parameterized with literature values from headwater streams, and empirical measurements made in 15 rivers with varying hydrological, biological, and topographic characteristics, to simulate nutrient uptake at the network scale. We applied the coupled model to 15 catchments describing patterns in uptake for three different solutes to determine the role of rivers in network-scale nutrient cycling. Model simulation results, constrained by empirical data, suggested that rivers contributed proportionally more to nutrient removal than headwater streams given the fraction of their length represented in a network. In addition, variability of nutrient removal patterns among catchments was varied among solutes, and as expected, was influenced by nutrient concentration and discharge. Net ammonium uptake was not significantly correlated with any environmental descriptor. In contrast, net daily nitrate removal was linked to suspended chlorophyll a (an indicator of primary producers) and land use characteristics. Finally, suspended sediment characteristics and agricultural land use were correlated with net daily removal of soluble reactive phosphorus, likely reflecting abiotic sorption dynamics. Rivers are understudied relative to streams, and our model suggests that rivers can contribute more to network-scale nutrient removal than would be expected based upon their representative fraction of network channel length.
    Print ISSN: 0043-1397
    Electronic ISSN: 1944-7973
    Topics: Architecture, Civil Engineering, Surveying , Geography
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 6
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    Landscape-level wolf space use is correlated with prey abundance, ease of mobility, and the distribution of prey habitat (2017)
    Wiley
    In: Ecosphere
    Details
    Publication Date: 2017-04-27
    Description: Predator space use influences ecosystem dynamics, and a fundamental goal assumed for a foraging predator is to maximize encounter rate with prey. This can be achieved by disproportionately utilizing areas of high prey density or, where prey are mobile and therefore spatially unpredictable, utilizing patches of their prey's preferred resources. A third, potentially complementary strategy is to increase mobility by using linear features like roads and/or frozen waterways. Here, we used novel population-level predator utilization distributions (termed “localized density distributions”) in a single-predator (wolf), two-prey (moose and caribou) system to evaluate these space-use hypotheses. The study was conducted in contrasting sections of a large boreal forest area in northern Ontario, Canada, with a spatial gradient of human disturbances and predator and prey densities. Our results indicated that wolves consistently used forest stands preferred by moose, their main prey species in this part of Ontario. Direct use of prey-rich areas was also significant but restricted to where there was a high local density of moose, whereas use of linear features was pronounced where local moose density was lower. These behaviors suggest that wolf foraging decisions, while consistently influenced by spatially anchored patches of prey forage resources, were also determined by local ecological conditions, specifically prey density. Wolves appeared to utilize prey-rich areas when regional preferred prey density exceeded a threshold that made this profitable, whereas they disproportionately used linear features that promoted mobility when low prey density made directly tracking prey distribution unprofitable.
    Electronic ISSN: 2150-8925
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by Wiley on behalf of The Ecological Society of America (ESA).
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  • 7
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    Questioning the influence of sunspots on Amazon hydrology – even a broken clock tells the right time twice a day (2018)
    Wiley
    Details
    Publication Date: 2018-01-30
    Description: It was suggested in a recent article that sunspots drive decadal variation in Amazon River flow [ Antico and Torres , 2015]. This conclusion was based on a novel time series decomposition method used to extract a decadal signal from the Amazon River record. We have extended this analysis back in time, using a new hydrological proxy record of tree-ring oxygen isotopes (δ 18 O TR ). Consistent with the findings of Antico and Torres, we find a positive correlation between sunspots and the decadal δ 18 O TR cycle from 1903 to 2012 ( r =0.60, p 〈0.001). However, the relationship does not persist into the preceding century, and even becomes weakly negative ( r =–0.30, p =0.11, 1799–1902). This result casts considerable doubt over the mechanism by which sunspots are purported to influence Amazon hydrology.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 8
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    What drives interannual variation in tree ring oxygen isotopes in the Amazon? (2016)
    Wiley
    Details
    Publication Date: 2016-11-10
    Description: Oxygen isotope ratios in tree rings (δ 18 O TR ) from northern Bolivia record local precipitation δ 18 O and correlate strongly with Amazon basin-wide rainfall. While this is encouraging evidence that δ 18 O TR can be used for palaeoclimate reconstructions, it remains unclear whether variation in δ 18 O TR is truly driven by within-basin processes, thus recording Amazon climate directly, or if the isotope signal may already be imprinted on incoming vapour, perhaps reflecting a pan-tropical climate signal. We use atmospheric back-trajectories combined with satellite observations of precipitation, together with water vapour transport analysis to show that δ 18 O TR in Bolivia are indeed controlled by basin-intrinsic processes, with rainout over the basin the most important factor. Furthermore, interannual variation in basin-wide precipitation and atmospheric circulation are both shown to affect δ 18 O TR . These findings suggest δ 18 O TR can be reliably used to reconstruct Amazon precipitation, and have implications for the interpretation of other palaeoproxy records from the Amazon basin.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 9
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    Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉Necrotizing enterocolitis (NEC) is a devastating intestinal disease that occurs primarily in premature infants. We performed genome-resolved metagenomic analysis of 1163 fecal samples from premature infants to identify microbial features predictive of NEC. Features considered include genes, bacterial strain types, eukaryotes, bacteriophages, plasmids, and growth rates. A machine learning classifier found that samples collected before NEC diagnosis harbored significantly more 〈i〉Klebsiella〈/i〉, bacteria encoding fimbriae, and bacteria encoding secondary metabolite gene clusters related to quorum sensing and bacteriocin production. Notably, replication rates of all bacteria, especially Enterobacteriaceae, were significantly higher 2 days before NEC diagnosis. The findings uncover biomarkers that could lead to early detection of NEC and targets for microbiome-based therapeutics.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Slow Sinking Particulate Organic Carbon in the Atlantic Ocean: magnitude, flux and potential controls (2017)
    Wiley
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    Publication Date: 2017-06-18
    Description: The remineralization depth of particulate organic carbon (POC) fluxes exported from the surface ocean exert a major control over atmospheric CO₂ levels. According to a long held paradigm most of the POC exported to depth is associated with large particles. However, recent lines of evidence suggest that slow sinking POC (SS POC ) may be an important contributor to this flux. Here we assess the circumstances under which this occurs. Our study uses samples collected using the Marine Snow Catcher throughout the Atlantic Ocean, from high latitudes to mid latitudes. We find median SS POC concentrations of 5.5 μg L -1 , 13 times smaller than suspended POC concentrations and 75 times higher than median fast sinking POC (FS POC ) concentrations (0.07 μg L -1 ). Export fluxes of SS POC generally exceed FS POC flux, with the exception being during a spring bloom sampled in the Southern Ocean. In the Southern Ocean SS POC fluxes often increase with depth relative to FS POC flux, likely due to midwater fragmentation of FS POC , a process which may contribute to shallow mineralization of POC and hence to reduced carbon storage. Biogeochemical models do not generally reproduce this behaviour, meaning that they likely overestimate long term ocean carbon storage.
    Print ISSN: 0886-6236
    Electronic ISSN: 1944-9224
    Topics: Biology , Chemistry and Pharmacology , Geography , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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