Coupled Active Systems Encode an Emergent Hunting Behavior in the Unicellular Predator Lacrymaria olor

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Using spatially explicit commodity flow and truck activity data to map urban material flows

To analyze and promote resource efficiency in urban areas, it is important to characterize urban metabolism and particularly, material flows. Material flow analysis (MFA) offers a means to capture the dynamism of cities and their activities. Urban‐scale MFAs have been conducted in many cities, usually employing variants of the Eurostat methodology. However, current methodologies generally reduce the study area into a “black box,” masking details of the complex processes within the city's metabolism. Therefore, besides the aggregated stocks and flows of materials, the movement of materials—often embedded in goods or commodities—should also be highlighted. Understanding the movement and dispersion of goods and commodities can allow for more detailed analysis of material flows. We highlight the potential benefits of using high‐resolution urban commodity flows in the context of understanding material resource use and opportunities for conservation. Through the use of geographic information systems and visualizations, we analyze two spatially explicit datasets: (1) commodity flow data in the United States, and (2) Global Positioning System‐based commercial vehicle (truck) driver activity data in Singapore. In the age of “big data,” we bring advancements in freight data collection to the field of urban metabolism, uncovering the secondary sourcing of materials that would otherwise have been masked in typical MFA studies. This brings us closer to a consumption‐based, finer‐resolution approach to MFA, which more effectively captures human activities and its impact on urban environments.     

Global ammonia emissions from synthetic nitrogen fertilizer applications in agricultural systems: Empirical and process‐based estimates and uncertainty

Excessive ammonia (NH₃) emitted from nitrogen (N) fertilizer applications in global croplands plays an important role in atmospheric aerosol production, resulting in visibility reduction and regional haze. However, large uncertainty exists in the estimates of NH₃ emissions from global and regional croplands, which utilize different data and methods. In this study, we have coupled a process‐based Dynamic Land Ecosystem Model (DLEM) with the bidirectional NH₃ exchange module in the Community Multiscale Air‐Quality (CMAQ) model (DLEM‐Bi‐NH₃) to quantify NH₃ emissions at the global and regional scale, and crop‐specific NH₃ emissions globally at a spatial resolution of 0.5° × 0.5° during 1961–2010. Results indicate that global NH₃ emissions from N fertilizer use have increased from 1.9 ± 0.03 to 16.7 ± 0.5 Tg N/year between 1961 and 2010. The annual increase of NH₃ emissions shows large spatial variations across the global land surface. Southern Asia, including China and India, has accounted for more than 50% of total global NH₃ emissions since the 1980s, followed by North America and Europe. Rice cultivation has been the largest contributor to total global NH₃ emissions since the 1990s, followed by corn and wheat. In addition, results show that empirical methods without considering environmental factors (constant emission factor in the IPCC Tier 1 guideline) could underestimate NH₃ emissions in context of climate change, with the highest difference (i.e., 6.9 Tg N/year) occurring in 2010. This study provides a robust estimate on global and regional NH₃ emissions over the past 50 years, which offers a reference for assessing air quality consequences of future nitrogen enrichment as well as nitrogen use efficiency improvement.     

Epibenthic predators control mobile macrofauna associated with a foundation species in a subarctic subtidal community

Foundation species (FS) are strong facilitators providing habitat for numerous dependent organisms. The communities shaped by FS are commonly structured by interplay of facilitation and consumer control. Predators or grazers often indirectly determine community structure eliminating either FS or their principal competitors. Alternatively, they can prey on the dependent taxa directly, which is generally buffered by FS via forming complex habitats with numerous refuges. The latter case has been never investigated at high latitudes, where consumer control is widely considered weak. We manipulated the presence of common epibenthic crustacean predators to assess their effect on mobile macrofauna of the clusters developed by a FS (barnacle Balanus crenatus and its empty tests) in the White Sea shallow subtidal (65° N). While predation pressure on the FS itself here is low, the direct effects of a spider crab Hyas araneus and a shrimp Spirontocaris phippsii on the associated assemblages were unexpectedly strong. Removing the predators did not change species diversity, but tripled total abundance and altered multivariate community structure specifically increasing the numbers of amphipods, isopods (only affected by shrimp), and bivalves. Consumer control in the communities shaped by FS may not strictly follow the latitudinal predation gradient rule.     

PyMINEr Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq

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The role of infectious disease in the evolution of females: Evidence from anther‐smut disease on a gynodioecious alpine carnation*

In flowering plants, the evolution of females is widely hypothesized to be the first step in the evolutionary pathway to separate male and female sexes, or dioecy. Natural enemies have the potential to drive this evolution if they preferentially attack hermaphrodites over females. We studied sex‐based differences in exposure to anther‐smut (Microbotryum), a sterilizing pollinator‐transmitted disease, in Dianthus pavonius, a gynodioecious perennial herb. We found that within a heavily diseased population, females consistently had lower levels of Microbotryum spore deposition relative to hermaphrodites and that this difference was driven by rapid floral closing in females following successful pollination. We further show that this protective closing behavior is frequency dependent; females close faster when they are rare. These results indicate that anther‐smut disease is an important source of selection for females, especially since we found in a common garden experiment no evidence that females have any inherent fecundity advantages over hermaphrodites. Finally, we show that among populations, those where anther‐smut is present have a significantly higher frequency of females than those where the disease is absent. Taken together our results indicate that anther‐smut disease is likely an important biotic factor driving the evolution and maintenance of females in this gynodioecious species.     

Use of genotyping by sequencing data to develop a high‐throughput and multifunctional SNP panel for conservation applications in Pacific lamprey

Next‐generation sequencing data can be mined for highly informative single nucleotide polymorphisms (SNPs) to develop high‐throughput genomic assays for nonmodel organisms. However, choosing a set of SNPs to address a variety of objectives can be difficult because SNPs are often not equally informative. We developed an optimal combination of 96 high‐throughput SNP assays from a total of 4439 SNPs identified in a previous study of Pacific lamprey (Entosphenus tridentatus) and used them to address four disparate objectives: parentage analysis, species identification and characterization of neutral and adaptive variation. Nine of these SNPs are F_ST outliers, and five of these outliers are localized within genes and significantly associated with geography, run‐timing and dwarf life history. Two of the 96 SNPs were diagnostic for two other lamprey species that were morphologically indistinguishable at early larval stages and were sympatric in the Pacific Northwest. The majority (85) of SNPs in the panel were highly informative for parentage analysis, that is, putatively neutral with high minor allele frequency across the species’ range. Results from three case studies are presented to demonstrate the broad utility of this panel of SNP markers in this species. As Pacific lamprey populations are undergoing rapid decline, these SNPs provide an important resource to address critical uncertainties associated with the conservation and recovery of this imperiled species.