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Matthey-Doret C, Colp MJ, Escoll P, Thierry A, Moreau P, Curtis B, Sahr T, Sarrasin M, Gray MW, Lang BF, Archibald JM, Buchrieser C, Koszul R. Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection-related chromatin reorganization. Genome Res 2022; 32:gr.276375.121. [PMID: 36109147 PMCID: PMC9528979 DOI: 10.1101/gr.276375.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 07/25/2022] [Indexed: 11/24/2022]
Abstract
The unicellular amoeba Acanthamoeba castellanii is ubiquitous in aquatic environments, where it preys on bacteria. The organism also hosts bacterial endosymbionts, some of which are parasitic, including human pathogens such as Chlamydia and Legionella spp. Here we report complete, high-quality genome sequences for two extensively studied A. castellanii strains, Neff and C3. Combining long- and short-read data with Hi-C, we generated near chromosome-level assemblies for both strains with 90% of the genome contained in 29 scaffolds for the Neff strain and 31 for the C3 strain. Comparative genomics revealed strain-specific functional enrichment, most notably genes related to signal transduction in the C3 strain and to viral replication in Neff. Furthermore, we characterized the spatial organization of the A. castellanii genome and showed that it is reorganized during infection by Legionella pneumophila Infection-dependent chromatin loops were found to be enriched in genes for signal transduction and phosphorylation processes. In genomic regions where chromatin organization changed during Legionella infection, we found functional enrichment for genes associated with metabolism, organelle assembly, and cytoskeleton organization. Given Legionella infection is known to alter its host's cell cycle, to exploit the host's organelles, and to modulate the host's metabolism in its favor, these changes in chromatin organization may partly be related to mechanisms of host control during Legionella infection.
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Affiliation(s)
- Cyril Matthey-Doret
- Institut Pasteur, CNRS UMR 3525, Université de Paris, Unité Régulation Spatiale des Génomes, F-75015 Paris, France
- Collège Doctoral, Sorbonne Université, F-75005 Paris, France
| | - Morgan J Colp
- Department of Biochemistry and Molecular Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Pedro Escoll
- Institut Pasteur, Université de Paris, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, F-75015 Paris, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université de Paris, Unité Régulation Spatiale des Génomes, F-75015 Paris, France
| | - Pierrick Moreau
- Institut Pasteur, CNRS UMR 3525, Université de Paris, Unité Régulation Spatiale des Génomes, F-75015 Paris, France
| | - Bruce Curtis
- Department of Biochemistry and Molecular Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Tobias Sahr
- Institut Pasteur, Université de Paris, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, F-75015 Paris, France
| | - Matt Sarrasin
- Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - B Franz Lang
- Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Carmen Buchrieser
- Institut Pasteur, Université de Paris, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, F-75015 Paris, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université de Paris, Unité Régulation Spatiale des Génomes, F-75015 Paris, France
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2
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Bae J, Zheng J, Zhang H, Foster PJ, Needleman DJ, Vlassak JJ. A Micromachined Picocalorimeter Sensor for Liquid Samples with Application to Chemical Reactions and Biochemistry. Adv Sci (Weinh) 2021; 8:2003415. [PMID: 33717854 PMCID: PMC7927623 DOI: 10.1002/advs.202003415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/04/2020] [Indexed: 05/28/2023]
Abstract
Calorimetry has long been used to probe the physical state of a system by measuring the heat exchanged with the environment as a result of chemical reactions or phase transitions. Application of calorimetry to microscale biological samples, however, is hampered by insufficient sensitivity and the difficulty of handling liquid samples at this scale. Here, a micromachined calorimeter sensor that is capable of resolving picowatt levels of power is described. The sensor consists of low-noise thermopiles on a thin silicon nitride membrane that allow direct differential temperature measurements between a sample and four coplanar references, which significantly reduces thermal drift. The partial pressure of water in the ambient around the sample is maintained at saturation level using a small hydrogel-lined enclosure. The materials used in the sensor and its geometry are optimized to minimize the noise equivalent power generated by the sensor in response to the temperature field that develops around a typical sample. The experimental response of the sensor is characterized as a function of thermopile dimensions and sample volume, and its capability is demonstrated by measuring the heat dissipated during an enzymatically catalyzed biochemical reaction in a microliter-sized liquid droplet. The sensor offers particular promise for quantitative measurements on biological systems.
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Affiliation(s)
- Jinhye Bae
- Department of NanoEngineeringUniversity of California San DiegoLa JollaCA92093USA
| | - Juanjuan Zheng
- John A. Paulson School of Engineering and Applied SciencesHarvard UniversityCambridgeMA02138USA
| | - Haitao Zhang
- John A. Paulson School of Engineering and Applied SciencesHarvard UniversityCambridgeMA02138USA
| | - Peter J. Foster
- Physics of Living SystemsDepartment of PhysicsMassachusetts Institute of TechnologyCambridgeMA02139USA
| | - Daniel J. Needleman
- Department of Molecular and Cellular BiologyHarvard UniversityCambridgeMA02138USA
- Center for Computational BiologyFlatiron InstituteNew YorkNY10010USA
| | - Joost J. Vlassak
- John A. Paulson School of Engineering and Applied SciencesHarvard UniversityCambridgeMA02138USA
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3
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Pelusi A, De Luca P, Manfellotto F, Thamatrakoln K, Bidle KD, Montresor M. Virus-induced spore formation as a defense mechanism in marine diatoms. New Phytol 2021; 229:2251-2259. [PMID: 32978816 PMCID: PMC7894508 DOI: 10.1111/nph.16951] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/09/2020] [Indexed: 05/03/2023]
Abstract
Algal viruses are important contributors to carbon cycling, recycling nutrients and organic material through host lysis. Although viral infection has been described as a primary mechanism of phytoplankton mortality, little is known about host defense responses. We show that viral infection of the bloom-forming, planktonic diatom Chaetoceros socialis induces the mass formation of resting spores, a heavily silicified life cycle stage associated with carbon export due to rapid sinking. Although viral RNA was detected within spores, mature virions were not observed. 'Infected' spores were capable of germinating, but did not propagate or transmit infectious viruses. These results demonstrate that diatom spore formation is an effective defense strategy against viral-mediated mortality. They provide a possible mechanistic link between viral infection, bloom termination, and mass carbon export events and highlight an unappreciated role of viruses in regulating diatom life cycle transitions and ecological success.
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Affiliation(s)
- Angela Pelusi
- Department of Integrative Marine EcologyStazione Zoologica Anton DohrnVilla ComunaleNaples80121Italy
| | - Pasquale De Luca
- Research Infrastructures for Marine Biological ResourcesStazione Zoologica Anton DohrnVilla ComunaleNaples80121Italy
| | - Francesco Manfellotto
- Department of Integrative Marine EcologyStazione Zoologica Anton DohrnVilla ComunaleNaples80121Italy
| | | | - Kay D. Bidle
- Department of Marine and Coastal SciencesRutgers UniversityNew BrunswickNJ08901‐8520USA
| | - Marina Montresor
- Department of Integrative Marine EcologyStazione Zoologica Anton DohrnVilla ComunaleNaples80121Italy
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4
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Laroche O, Kersten O, Smith CR, Goetze E. Environmental DNA surveys detect distinct metazoan communities across abyssal plains and seamounts in the western Clarion Clipperton Zone. Mol Ecol 2020; 29:4588-4604. [PMID: 32452072 PMCID: PMC7754508 DOI: 10.1111/mec.15484] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/08/2020] [Accepted: 05/18/2020] [Indexed: 01/13/2023]
Abstract
The deep seafloor serves as a reservoir of biodiversity in the global ocean, with >80% of invertebrates at abyssal depths still undescribed. These diverse and remote deep-sea communities are critically under-sampled and increasingly threatened by anthropogenic impacts, including future polymetallic nodule mining. Using a multigene environmental DNA (eDNA) metabarcoding approach, we characterized metazoan communities sampled from sediments, polymetallic nodules and seawater in the western Clarion Clipperton Zone (CCZ) to test the hypotheses that deep seamounts (a) are species richness hotspots in the abyss, (b) have structurally distinct communities in comparison to other deep-sea habitats, and (c) that seafloor particulate organic carbon (POC) flux and polymetallic nodule density are positively correlated with metazoan diversity. eDNA metabarcoding was effective at characterizing distinct biotas known to occur in association with different abyssal substrate types (e.g., nodule- and sediment-specific fauna), with distinct community composition and few taxa shared across substrates. Seamount faunas had higher overall taxonomic richness, and different community composition and biogeography than adjacent abyssal plains, with seamount communities displaying less connectivity between regions than comparable assemblages on the abyssal plains. Across an estimated gradient of low to moderate POC flux, we find lowest taxon richness at the lowest POC flux, as well as an effect of nodule size on community composition. Our results suggest that while abyssal seamounts are important reservoirs of metazoan diversity in the CCZ, given limited taxonomic overlap between seamount and plains fauna, conservation of seamount assemblages will be insufficient to protect biodiversity and ecosystem function in regions targeted for mining.
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Affiliation(s)
- Olivier Laroche
- Department of OceanographySchool of Ocean and Earth Science and TechnologyUniversity of Hawaii at MānoaHonoluluHIUSA
| | - Oliver Kersten
- Centre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| | - Craig R. Smith
- Department of OceanographySchool of Ocean and Earth Science and TechnologyUniversity of Hawaii at MānoaHonoluluHIUSA
| | - Erica Goetze
- Department of OceanographySchool of Ocean and Earth Science and TechnologyUniversity of Hawaii at MānoaHonoluluHIUSA
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5
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Chen Y, Randerson JT, Coffield SR, Foufoula‐Georgiou E, Smyth P, Graff CA, Morton DC, Andela N, van der Werf GR, Giglio L, Ott LE. Forecasting Global Fire Emissions on Subseasonal to Seasonal (S2S) Time Scales. J Adv Model Earth Syst 2020; 12:e2019MS001955. [PMID: 33042387 PMCID: PMC7540459 DOI: 10.1029/2019ms001955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 07/02/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
Fire emissions of gases and aerosols alter atmospheric composition and have substantial impacts on climate, ecosystem function, and human health. Warming climate and human expansion in fire-prone landscapes exacerbate fire impacts and call for more effective management tools. Here we developed a global fire forecasting system that predicts monthly emissions using past fire data and climate variables for lead times of 1 to 6 months. Using monthly fire emissions from the Global Fire Emissions Database (GFED) as the prediction target, we fit a statistical time series model, the Autoregressive Integrated Moving Average model with eXogenous variables (ARIMAX), in over 1,300 different fire regions. Optimized parameters were then used to forecast future emissions. The forecast system took into account information about region-specific seasonality, long-term trends, recent fire observations, and climate drivers representing both large-scale climate variability and local fire weather. We cross-validated the forecast skill of the system with different combinations of predictors and forecast lead times. The reference model, which combined endogenous and exogenous predictors with a 1 month forecast lead time, explained 52% of the variability in the global fire emissions anomaly, considerably exceeding the performance of a reference model that assumed persistent emissions during the forecast period. The system also successfully resolved detailed spatial patterns of fire emissions anomalies in regions with significant fire activity. This study bridges the gap between the efforts of near-real-time fire forecasts and seasonal fire outlooks and represents a step toward establishing an operational global fire, smoke, and carbon cycle forecasting system.
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Affiliation(s)
- Yang Chen
- Department of Earth System ScienceUniversity of CaliforniaIrvineCAUSA
| | - James T. Randerson
- Department of Earth System ScienceUniversity of CaliforniaIrvineCAUSA
- Department of Civil and Environmental EngineeringUniversity of CaliforniaIrvineCAUSA
| | - Shane R. Coffield
- Department of Earth System ScienceUniversity of CaliforniaIrvineCAUSA
| | - Efi Foufoula‐Georgiou
- Department of Earth System ScienceUniversity of CaliforniaIrvineCAUSA
- Department of Civil and Environmental EngineeringUniversity of CaliforniaIrvineCAUSA
| | - Padhraic Smyth
- Department of Computer ScienceUniversity of CaliforniaIrvineCAUSA
- Department of StatisticsUniversity of CaliforniaIrvineUSA
| | - Casey A. Graff
- Department of Computer ScienceUniversity of CaliforniaIrvineCAUSA
| | - Douglas C. Morton
- Biospheric Sciences LaboratoryNASA Goddard Space Flight CenterGreenbeltMDUSA
| | - Niels Andela
- Biospheric Sciences LaboratoryNASA Goddard Space Flight CenterGreenbeltMDUSA
| | | | - Louis Giglio
- Department of Geographical SciencesUniversity of MarylandCollege ParkMDUSA
| | - Lesley E. Ott
- Global Modeling and Assimilation OfficeNASA Goddard Space Flight CenterGreenbeltMDUSA
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Merzel RL, Purser L, Soucy TL, Olszewski M, Colón‐Bernal I, Duhaime M, Elgin AK, Banaszak Holl MM. Uptake and Retention of Nanoplastics in Quagga Mussels. Glob Chall 2020; 4:1800104. [PMID: 32685193 PMCID: PMC7268195 DOI: 10.1002/gch2.201800104] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 05/03/2019] [Indexed: 06/11/2023]
Abstract
Here, a set of experiments to assess the feasibility of using an invasive and widespread freshwater mussel (Dreissena rostrformis bugensis) as a sentinel species for nanoplastic detection is reported. Under laboratory experimental conditions, mussels ingest and retain fluorescent polystyrene (PS) beads with carboxylic acid (-COOH) termination over a size range of 200-2000 nm. The number of beads the mussels ingested is quantified using fluorescence spectroscopy and the location of the beads in the mussels is imaged using fluorescence microscopy. PS beads of similar size (1000-2000 nm) to mussels' preferred food are trafficked in the ciliated food grooves of the gills. Beads of all sizes are observed in the mussels' digestive tracts, indicating that the mussels do not efficiently reject the beads as unwanted foreign material, regardless of size. Fluorescence microscopy shows all sizes of beads are concentrated in the siphons and are retained there for longer than one month postexposure. Combined atomic force microscopy-infrared spectroscopy and photothermal infrared spectroscopy are used to locate, image, and chemically identify the beads in the mussel siphons. In sum, these experiments demonstrate the potential for using mussels, specifically their siphons, to monitor environmental accumulation of aquatic nanoplastics.
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Affiliation(s)
| | - Lauren Purser
- Chemistry DepartmentUniversity of MichiganAnn ArborMI48109USA
| | - Taylor L. Soucy
- Chemistry DepartmentUniversity of MichiganAnn ArborMI48109USA
| | | | | | - Melissa Duhaime
- Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMI48109USA
| | - Ashley K. Elgin
- NOAA Great Lakes Environmental Research LaboratoryLake Michigan Field StationMuskegonMI49441USA
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Oberosler V, Tenan S, Zipkin EF, Rovero F. When parks work: Effect of anthropogenic disturbance on occupancy of tropical forest mammals. Ecol Evol 2020; 10:3881-3894. [PMID: 32489618 PMCID: PMC7244893 DOI: 10.1002/ece3.6048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 11/20/2019] [Accepted: 01/03/2020] [Indexed: 11/11/2022] Open
Abstract
Protected areas (PAs) in the tropics are vulnerable to human encroachment, and, despite formal protection, they do not fully mitigate anthropogenic threats to habitats and biodiversity. However, attempts to quantify the effectiveness of PAs and to understand the status and changes of wildlife populations in relation to protection efficiency remain limited. Here, we used camera-trapping data collected over 8 consecutive years (2009-2016) to investigate the yearly occurrences of medium-to-large mammals within the Udzungwa Mountains National Park (Tanzania), an area of outstanding importance for biological endemism and conservation. Specifically, we evaluated the effects of habitat and proxies of human disturbance, namely illegal hunting with snares and firewood collection (a practice that was banned in 2011 in the park), on species' occurrence probabilities. Our results showed variability in species' responses to disturbance: The only species that showed a negative effect of the number of snares found on occurrence probability was the Harvey's duiker, a relatively widespread forest antelope. Similarly, we found a moderate positive effect of the firewood collection ban on only the suni, another common antelope, and a negative effect on a large opportunistic rodent, the giant-pouched rat. Importantly, we found evidence of temporal stability in occurrence probability for all species over the 8-year study period. Our findings suggest that well-managed PAs can sustain mammal populations in tropical forests. However, variability among species in their responses to anthropogenic disturbance necessitates consideration in the design of conservation action plans for multiple taxa.
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Affiliation(s)
- Valentina Oberosler
- Tropical Biodiversity SectionMUSE – Museo delle ScienzeTrentoItaly
- Department of Earth and Environmental SciencesUniversity of PaviaPaviaItaly
| | - Simone Tenan
- Vertebrate Zoology SectionMUSE – Museo delle ScienzeTrentoItaly
| | - Elise F. Zipkin
- Department of Integrative Biology and EcologyEvolutionary Biology and Behavior ProgramMichigan State UniversityEast LansingMichigan
| | - Francesco Rovero
- Tropical Biodiversity SectionMUSE – Museo delle ScienzeTrentoItaly
- Department of BiologyUniversity of FlorenceSesto FiorentinoItaly
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Hunter‐Cevera KR, Neubert MG, Olson RJ, Shalapyonok A, Solow AR, Sosik HM. Seasons of Syn. Limnol Oceanogr 2020; 65:1085-1102. [PMID: 32612307 PMCID: PMC7319482 DOI: 10.1002/lno.11374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/17/2019] [Accepted: 09/30/2019] [Indexed: 06/11/2023]
Abstract
Synechococcus is a widespread and important marine primary producer. Time series provide critical information for identifying and understanding the factors that determine abundance patterns. Here, we present the results of analysis of a 16-yr hourly time series of Synechococcus at the Martha's Vineyard Coastal Observatory, obtained with an automated, in situ flow cytometer. We focus on understanding seasonal abundance patterns by examining relationships between cell division rate, loss rate, cellular properties (e.g., cell volume, phycoerythrin fluorescence), and environmental variables (e.g., temperature, light). We find that the drivers of cell division vary with season; cells are temperature-limited in winter and spring, but light-limited in the fall. Losses to the population also vary with season. Our results lead to testable hypotheses about Synechococcus ecophysiology and a working framework for understanding the seasonal controls of Synechococcus cell abundance in a temperate coastal system.
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Affiliation(s)
- Kristen R. Hunter‐Cevera
- Josephine Bay Paul CenterMarine Biological LaboratoryWoods HoleMassachusetts
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Michael G. Neubert
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Robert J. Olson
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Alexi Shalapyonok
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Andrew R. Solow
- Marine Policy CenterWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Heidi M. Sosik
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
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Ponisio LC, de Valpine P, Michaud N, Turek D. One size does not fit all: Customizing MCMC methods for hierarchical models using NIMBLE. Ecol Evol 2020; 10:2385-2416. [PMID: 32184989 PMCID: PMC7069319 DOI: 10.1002/ece3.6053] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 11/30/2022] Open
Abstract
Improved efficiency of Markov chain Monte Carlo facilitates all aspects of statistical analysis with Bayesian hierarchical models. Identifying strategies to improve MCMC performance is becoming increasingly crucial as the complexity of models, and the run times to fit them, increases. We evaluate different strategies for improving MCMC efficiency using the open-source software NIMBLE (R package nimble) using common ecological models of species occurrence and abundance as examples. We ask how MCMC efficiency depends on model formulation, model size, data, and sampling strategy. For multiseason and/or multispecies occupancy models and for N-mixture models, we compare the efficiency of sampling discrete latent states vs. integrating over them, including more vs. fewer hierarchical model components, and univariate vs. block-sampling methods. We include the common MCMC tool JAGS in comparisons. For simple models, there is little practical difference between computational approaches. As model complexity increases, there are strong interactions between model formulation and sampling strategy on MCMC efficiency. There is no one-size-fits-all best strategy, but rather problem-specific best strategies related to model structure and type. In all but the simplest cases, NIMBLE's default or customized performance achieves much higher efficiency than JAGS. In the two most complex examples, NIMBLE was 10-12 times more efficient than JAGS. We find NIMBLE is a valuable tool for many ecologists utilizing Bayesian inference, particularly for complex models where JAGS is prohibitively slow. Our results highlight the need for more guidelines and customizable approaches to fit hierarchical models to ensure practitioners can make the most of occupancy and other hierarchical models. By implementing model-generic MCMC procedures in open-source software, including the NIMBLE extensions for integrating over latent states (implemented in the R package nimbleEcology), we have made progress toward this aim.
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Affiliation(s)
| | - Perry de Valpine
- Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyCAUSA
| | - Nicholas Michaud
- Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyCAUSA
| | - Daniel Turek
- Department of Mathematics and StatisticsWilliams CollegeWilliamstownMAUSA
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10
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Wilken S, Choi CJ, Worden AZ. Contrasting Mixotrophic Lifestyles Reveal Different Ecological Niches in Two Closely Related Marine Protists. J Phycol 2020; 56:52-67. [PMID: 31529498 PMCID: PMC7065223 DOI: 10.1111/jpy.12920] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/13/2019] [Indexed: 05/13/2023]
Abstract
Many marine microbial eukaryotes combine photosynthetic with phagotrophic nutrition, but incomplete understanding of such mixotrophic protists, their functional diversity, and underlying physiological mechanisms limits the assessment and modeling of their roles in present and future ocean ecosystems. We developed an experimental system to study responses of mixotrophic protists to availability of living prey and light, and used it to characterize contrasting physiological strategies in two stramenopiles in the genus Ochromonas. We show that oceanic isolate CCMP1393 is an obligate mixotroph, requiring both light and prey as complementary resources. Interdependence of photosynthesis and heterotrophy in CCMP1393 comprises a significant role of mitochondrial respiration in photosynthetic electron transport. In contrast, coastal isolate CCMP2951 is a facultative mixotroph that can substitute photosynthesis by phagotrophy and hence grow purely heterotrophically in darkness. In contrast to CCMP1393, CCMP2951 also exhibits a marked photoprotection response that integrates non-photochemical quenching and mitochondrial respiration as electron sink for photosynthetically produced reducing equivalents. Facultative mixotrophs similar to CCMP2951 might be well adapted to variable environments, while obligate mixotrophs similar to CCMP1393 appear capable of resource efficient growth in oligotrophic ocean environments. Thus, the responses of these phylogenetically close protists to the availability of different resources reveals niche differentiation that influences impacts in food webs and leads to opposing carbon cycle roles.
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Affiliation(s)
- Susanne Wilken
- Monterey Bay Aquarium Research Institute7700 Sandholdt RoadMoss LandingCalifornia95039USA
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamScience Park 904Amsterdam1098 XHThe Netherlands
| | - Chang Jae Choi
- Monterey Bay Aquarium Research Institute7700 Sandholdt RoadMoss LandingCalifornia95039USA
- Ocean EcoSystems Biology UnitGEOMAR Helmholtz Centre for Ocean ResearchDüsternbrooker Weg 20Kiel24105Germany
| | - Alexandra Z. Worden
- Monterey Bay Aquarium Research Institute7700 Sandholdt RoadMoss LandingCalifornia95039USA
- Ocean EcoSystems Biology UnitGEOMAR Helmholtz Centre for Ocean ResearchDüsternbrooker Weg 20Kiel24105Germany
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11
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Satterfield K, Rubin JC, Yang D, Friedman CP. Understanding the roles of three academic communities in a prospective learning health ecosystem for diagnostic excellence. Learn Health Syst 2019; 4:e210204. [PMID: 31989032 PMCID: PMC6971119 DOI: 10.1002/lrh2.10204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 08/19/2019] [Accepted: 09/25/2019] [Indexed: 12/14/2022] Open
Abstract
Inaccurate, untimely, and miscommunicated medical diagnoses represent a wicked problem requiring comprehensive and coordinated approaches, such as those demonstrated in the characteristics of learning health systems (LHSs). To appreciate a vision for how LHS methods can optimize processes and outcomes in medical diagnosis (diagnostic excellence), we interviewed 32 individuals with relevant expertise: 18 who have studied diagnostic processes using traditional behavioral science and health services research methods, six focused on machine learning (ML) and artificial intelligence (AI) approaches, and eight multidisciplinary researchers experienced in advocating for and incorporating LHS methods, ie, scalable continuous learning in health care. We report on barriers and facilitators, identified by these subjects, to applying their methods toward optimizing medical diagnosis. We then employ their insights to envision the emergence of a learning ecosystem that leverages the tools of each of the three research groups to advance diagnostic excellence. We found that these communities represent a natural fit forward, in which together, they can better measure diagnostic processes and close the loop of putting insights into practice. Members of the three academic communities will need to network and bring in additional stakeholders before they can design and implement the necessary infrastructure that would support ongoing learning of diagnostic processes at an economy of scale and scope.
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Affiliation(s)
- Katherine Satterfield
- Department of Learning Health SciencesUniversity of Michigan Medical SchoolAnn ArborMichigan
| | - Joshua C. Rubin
- Department of Learning Health SciencesUniversity of Michigan Medical SchoolAnn ArborMichigan
| | - Daniel Yang
- The Gordon and Betty Moore FoundationPalo AltoCalifornia
| | - Charles P. Friedman
- Department of Learning Health SciencesUniversity of Michigan Medical SchoolAnn ArborMichigan
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12
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Rutt CL, Jirinec V, Cohn‐Haft M, Laurance WF, Stouffer PC. Avian ecological succession in the Amazon: A long-term case study following experimental deforestation. Ecol Evol 2019; 9:13850-13861. [PMID: 31938486 PMCID: PMC6953691 DOI: 10.1002/ece3.5822] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/14/2019] [Accepted: 10/14/2019] [Indexed: 11/06/2022] Open
Abstract
Approximately 20% of the Brazilian Amazon has now been deforested, and the Amazon is currently experiencing the highest rates of deforestation in a decade, leading to large-scale land-use changes. Roads have consistently been implicated as drivers of ongoing Amazon deforestation and may act as corridors to facilitate species invasions. Long-term data, however, are necessary to determine how ecological succession alters avian communities following deforestation and whether established roads lead to a constant influx of new species.We used data across nearly 40 years from a large-scale deforestation experiment in the central Amazon to examine the avian colonization process in a spatial and temporal framework, considering the role that roads may play in facilitating colonization.Since 1979, 139 species that are not part of the original forest avifauna have been recorded, including more secondary forest species than expected based on the regional species pool. Among the 35 species considered to have colonized and become established, a disproportionate number were secondary forest birds (63%), almost all of which first appeared during the 1980s. These new residents comprise about 13% of the current community of permanent residents.Widespread generalists associated with secondary forest colonized quickly following deforestation, with few new species added after the first decade, despite a stable road connection. Few species associated with riverine forest or specialized habitats colonized, despite road connection to their preferred source habitat. Colonizing species remained restricted to anthropogenic habitats and did not infiltrate old-growth forests nor displace forest birds.Deforestation and expansion of road networks into terra firme rainforest will continue to create degraded anthropogenic habitat. Even so, the initial pulse of colonization by nonprimary forest bird species was not the beginning of a protracted series of invasions in this study, and the process appears to be reversible by forest succession.
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Affiliation(s)
- Cameron L. Rutt
- Biological Dynamics of Forest Fragments ProjectInstituto Nacional de Pesquisas da Amazônia (INPA)ManausBrazil
- School of Renewable Natural ResourcesLouisiana State University and Louisiana State University AgCenterBaton RougeLAUSA
| | - Vitek Jirinec
- Biological Dynamics of Forest Fragments ProjectInstituto Nacional de Pesquisas da Amazônia (INPA)ManausBrazil
- School of Renewable Natural ResourcesLouisiana State University and Louisiana State University AgCenterBaton RougeLAUSA
| | - Mario Cohn‐Haft
- Biological Dynamics of Forest Fragments ProjectInstituto Nacional de Pesquisas da Amazônia (INPA)ManausBrazil
- Coleções Zoológicas – INPAManausBrazil
| | - William F. Laurance
- Biological Dynamics of Forest Fragments ProjectInstituto Nacional de Pesquisas da Amazônia (INPA)ManausBrazil
- Centre for Tropical Environmental and Sustainability ScienceCollege of Science and EngineeringJames Cook UniversityCairnsQldAustralia
| | - Philip C Stouffer
- Biological Dynamics of Forest Fragments ProjectInstituto Nacional de Pesquisas da Amazônia (INPA)ManausBrazil
- School of Renewable Natural ResourcesLouisiana State University and Louisiana State University AgCenterBaton RougeLAUSA
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Requena Suarez D, Rozendaal DMA, De Sy V, Phillips OL, Alvarez‐Dávila E, Anderson‐Teixeira K, Araujo‐Murakami A, Arroyo L, Baker TR, Bongers F, Brienen RJW, Carter S, Cook‐Patton SC, Feldpausch TR, Griscom BW, Harris N, Hérault B, Honorio Coronado EN, Leavitt SM, Lewis SL, Marimon BS, Monteagudo Mendoza A, Kassi N'dja J, N'Guessan AE, Poorter L, Qie L, Rutishauser E, Sist P, Sonké B, Sullivan MJP, Vilanova E, Wang MMH, Martius C, Herold M. Estimating aboveground net biomass change for tropical and subtropical forests: Refinement of IPCC default rates using forest plot data. Glob Chang Biol 2019; 25:3609-3624. [PMID: 31310673 PMCID: PMC6852081 DOI: 10.1111/gcb.14767] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/06/2019] [Indexed: 05/17/2023]
Abstract
As countries advance in greenhouse gas (GHG) accounting for climate change mitigation, consistent estimates of aboveground net biomass change (∆AGB) are needed. Countries with limited forest monitoring capabilities in the tropics and subtropics rely on IPCC 2006 default ∆AGB rates, which are values per ecological zone, per continent. Similarly, research into forest biomass change at a large scale also makes use of these rates. IPCC 2006 default rates come from a handful of studies, provide no uncertainty indications and do not distinguish between older secondary forests and old-growth forests. As part of the 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, we incorporate ∆AGB data available from 2006 onwards, comprising 176 chronosequences in secondary forests and 536 permanent plots in old-growth and managed/logged forests located in 42 countries in Africa, North and South America and Asia. We generated ∆AGB rate estimates for younger secondary forests (≤20 years), older secondary forests (>20 years and up to 100 years) and old-growth forests, and accounted for uncertainties in our estimates. In tropical rainforests, for which data availability was the highest, our ∆AGB rate estimates ranged from 3.4 (Asia) to 7.6 (Africa) Mg ha-1 year-1 in younger secondary forests, from 2.3 (North and South America) to 3.5 (Africa) Mg ha-1 year-1 in older secondary forests, and 0.7 (Asia) to 1.3 (Africa) Mg ha-1 year-1 in old-growth forests. We provide a rigorous and traceable refinement of the IPCC 2006 default rates in tropical and subtropical ecological zones, and identify which areas require more research on ∆AGB. In this respect, this study should be considered as an important step towards quantifying the role of tropical and subtropical forests as carbon sinks with higher accuracy; our new rates can be used for large-scale GHG accounting by governmental bodies, nongovernmental organizations and in scientific research.
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Affiliation(s)
- Daniela Requena Suarez
- Laboratory of Geo‐Information Science and Remote SensingWageningen University and ResearchWageningenThe Netherlands
| | - Danaë M. A. Rozendaal
- Laboratory of Geo‐Information Science and Remote SensingWageningen University and ResearchWageningenThe Netherlands
- Plant Production Systems GroupWageningen University and ResearchWageningenThe Netherlands
- Centre for Crop Systems AnalysisWageningen University and ResearchWageningenThe Netherlands
| | - Veronique De Sy
- Laboratory of Geo‐Information Science and Remote SensingWageningen University and ResearchWageningenThe Netherlands
| | | | - Esteban Alvarez‐Dávila
- Escuela de Ciencias agrícolas, pecuarias y ambientalesUniversidad Nacional Abierta y a DistanciaBogotaColombia
- Fundación ConVidaMedellínColombia
| | - Kristina Anderson‐Teixeira
- Conservation Ecology CenterSmithsonian Conservation Biology InstituteFront RoyalVRUSA
- Center for Tropical Forest Science‐Forest Global Earth ObservatorySmithsonian Tropical Research InstitutePanamaRepublic of Panama
| | - Alejandro Araujo‐Murakami
- Museo de Historia Natural Noel Kempff MercadoUniversidad Autónoma Gabriel René MorenoSanta CruzBolivia
| | - Luzmila Arroyo
- Universidad Autónoma Gabriel René MorenoSanta CruzBolivia
| | | | - Frans Bongers
- Forest Ecology and Forest Management GroupWageningen University and ResearchWageningenThe Netherlands
| | | | - Sarah Carter
- Laboratory of Geo‐Information Science and Remote SensingWageningen University and ResearchWageningenThe Netherlands
| | | | - Ted R. Feldpausch
- GeographyCollege of Life and Environmental SciencesUniversity of ExeterExeterUK
| | | | | | - Bruno Hérault
- CIRAD, UR Forests & SocietiesUniversity of MontpellierMontpellierFrance
- Institut National Polytechnique Félix Houphouet‐BoignyYamoussoukroIvory Coast
| | | | | | - Simon L. Lewis
- School of GeographyUniversity of LeedsLeedsUK
- Department of GeographyUniversity College LondonLondonUK
| | - Beatriz S. Marimon
- Campus de Nova XavantinaUniversidade do Estado de Mato GrossoNova XavantinaBrazil
| | - Abel Monteagudo Mendoza
- Jardín Botánico de MissouriOxapampaPeru
- Universidad Nacional de San Antonio Abad del CuscoCuscoPeru
| | - Justin Kassi N'dja
- UFR BiosciencesLaboratoire de BotaniqueUniversité Félix Houphouet‐BoignyAbidjanIvory Coast
| | - Anny Estelle N'Guessan
- UFR BiosciencesLaboratoire de BotaniqueUniversité Félix Houphouet‐BoignyAbidjanIvory Coast
| | - Lourens Poorter
- Forest Ecology and Forest Management GroupWageningen University and ResearchWageningenThe Netherlands
| | - Lan Qie
- School of Life SciencesUniversity of LincolnLincolnUK
| | - Ervan Rutishauser
- Center for Tropical Forest Science‐Forest Global Earth ObservatorySmithsonian Tropical Research InstitutePanamaRepublic of Panama
| | - Plinio Sist
- CIRAD, UR Forests & SocietiesUniversity of MontpellierMontpellierFrance
| | - Bonaventure Sonké
- Plant Systematic and Ecology LaboratoryUniversity of YaoundéYaoundéCameroon
| | | | - Emilio Vilanova
- Universidad de Los AndesMéridaVenezuela
- School of Environmental and Forest SciencesUniversity of WashingtonSeattleWAUSA
| | - Maria M. H. Wang
- Department of Animal & Plant SciencesUniversity of SheffieldSheffieldUK
| | | | - Martin Herold
- Laboratory of Geo‐Information Science and Remote SensingWageningen University and ResearchWageningenThe Netherlands
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14
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Gorris ME, Treseder KK, Zender CS, Randerson JT. Expansion of Coccidioidomycosis Endemic Regions in the United States in Response to Climate Change. Geohealth 2019; 3:308-327. [PMID: 32159021 PMCID: PMC7007157 DOI: 10.1029/2019gh000209] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/16/2019] [Accepted: 08/20/2019] [Indexed: 05/21/2023]
Abstract
Coccidioidomycosis (Valley fever) is a fungal disease endemic to the southwestern United States. Across this region, temperature and precipitation influence the extent of the endemic region and number of Valley fever cases. Climate projections for the western United States indicate that temperatures will increase and precipitation patterns will shift, which may alter disease dynamics. We estimated the area potentially endemic to Valley fever using a climate niche model derived from contemporary climate and disease incidence data. We then used our model with projections of climate from Earth system models to assess how endemic areas will change during the 21st century. By 2100 in a high warming scenario, our model predicts that the area of climate-limited endemicity will more than double, the number of affected states will increase from 12 to 17, and the number of Valley fever cases will increase by 50%. The Valley fever endemic region will expand north into dry western states, including Idaho, Wyoming, Montana, Nebraska, South Dakota, and North Dakota. Precipitation will limit the disease from spreading into states farther east and along the central and northern Pacific coast. This is the first quantitative estimate of how climate change may influence Valley fever in the United States. Our predictive model of Valley fever endemicity may provide guidance to public health officials to establish disease surveillance programs and design mitigation efforts to limit the impacts of this disease.
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Affiliation(s)
- Morgan E. Gorris
- Department of Earth System ScienceUniversity of CaliforniaIrvineCAUSA
| | - Kathleen K. Treseder
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaIrvineCAUSA
| | - Charles S. Zender
- Department of Earth System ScienceUniversity of CaliforniaIrvineCAUSA
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15
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Andersen JC, Oboyski P, Davies N, Charlat S, Ewing C, Meyer C, Krehenwinkel H, Lim JY, Noriyuki S, Ramage T, Gillespie RG, Roderick GK. Categorization of species as native or nonnative using DNA sequence signatures without a complete reference library. Ecol Appl 2019; 29:e01914. [PMID: 31050090 PMCID: PMC7079013 DOI: 10.1002/eap.1914] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 03/18/2019] [Accepted: 04/01/2019] [Indexed: 05/26/2023]
Abstract
New genetic diagnostic approaches have greatly aided efforts to document global biodiversity and improve biosecurity. This is especially true for organismal groups in which species diversity has been underestimated historically due to difficulties associated with sampling, the lack of clear morphological characteristics, and/or limited availability of taxonomic expertise. Among these methods, DNA sequence barcoding (also known as "DNA barcoding") and by extension, meta-barcoding for biological communities, has emerged as one of the most frequently utilized methods for DNA-based species identifications. Unfortunately, the use of DNA barcoding is limited by the availability of complete reference libraries (i.e., a collection of DNA sequences from morphologically identified species), and by the fact that the vast majority of species do not have sequences present in reference databases. Such conditions are critical especially in tropical locations that are simultaneously biodiversity rich and suffer from a lack of exploration and DNA characterization by trained taxonomic specialists. To facilitate efforts to document biodiversity in regions lacking complete reference libraries, we developed a novel statistical approach that categorizes unidentified species as being either likely native or likely nonnative based solely on measures of nucleotide diversity. We demonstrate the utility of this approach by categorizing a large sample of specimens of terrestrial insects and spiders (collected as part of the Moorea BioCode project) using a generalized linear mixed model (GLMM). Using a training data set of known endemic (n = 45) and known introduced species (n = 102), we then estimated the likely native/nonnative status for 4,663 specimens representing an estimated 1,288 species (412 identified species), including both those specimens that were either unidentified or whose endemic/introduced status was uncertain. Using this approach, we were able to increase the number of categorized specimens by a factor of 4.4 (from 794 to 3,497), and the number of categorized species by a factor of 4.8 from (147 to 707) at a rate much greater than chance (77.6% accuracy). The study identifies phylogenetic signatures of both native and nonnative species and suggests several practical applications for this approach including monitoring biodiversity and facilitating biosecurity.
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Affiliation(s)
- Jeremy C. Andersen
- Department of Environmental Science Policy and ManagementUniversity of California Berkeley130 Mulford HallBerkeleyCalifornia94720‐3114USA
| | - Peter Oboyski
- Essig Museum of EntomologyUniversity of California BerkeleyBerkeleyCalifornia94720USA
| | - Neil Davies
- Gump South Pacific Research StationUniversity of California BerkeleyMaharepaMooreaFrench Polynesia
| | - Sylvain Charlat
- Biométrie et Biologie ÉvolutiveUMR CNRS69622VilleurbanneFrance
| | - Curtis Ewing
- Komohana Research and Extension CenterUniversity of Hawai'i at MānoaHiloHawaii96720USA
| | | | | | - Jun Ying Lim
- Department of Integrated BiologyUniversity of California Berkeley3040 Valley Life Sciences BuildingBerkeleyCalifornia94720USA
| | - Suzuki Noriyuki
- Faculty of Agriculture and Marine ScienceKochi UniversityKochiJapan
| | | | - Rosemary G. Gillespie
- Department of Environmental Science Policy and ManagementUniversity of California Berkeley130 Mulford HallBerkeleyCalifornia94720‐3114USA
| | - George K. Roderick
- Department of Environmental Science Policy and ManagementUniversity of California Berkeley130 Mulford HallBerkeleyCalifornia94720‐3114USA
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16
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Marlier ME, Liu T, Yu K, Buonocore JJ, Koplitz SN, DeFries RS, Mickley LJ, Jacob DJ, Schwartz J, Wardhana BS, Myers SS. Fires, Smoke Exposure, and Public Health: An Integrative Framework to Maximize Health Benefits From Peatland Restoration. Geohealth 2019; 3:178-189. [PMID: 32159040 PMCID: PMC7007093 DOI: 10.1029/2019gh000191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/04/2019] [Accepted: 06/04/2019] [Indexed: 05/08/2023]
Abstract
Emissions of particulate matter from fires associated with land management practices in Indonesia contribute to regional air pollution and mortality. We assess the public health benefits in Indonesia, Malaysia, and Singapore from policies to reduce fires by integrating information on fire emissions, atmospheric transport patterns, and population exposure to fine particulate matter (PM2.5). We use adjoint sensitivities to relate fire emissions to PM2.5 for a range of meteorological conditions and find that a Business-As-Usual scenario of land use change leads, on average, to 36,000 excess deaths per year into the foreseeable future (the next several decades) across the region. These deaths are largely preventable with fire reduction strategies, such as blocking fires in peatlands, industrial concessions, or protected areas, which reduce the health burden by 66, 45, and 14%, respectively. The effectiveness of these different strategies in mitigating human health impacts depends on the location of fires relative to the population distribution. For example, protecting peatlands through eliminating all fires on such lands would prevent on average 24,000 excess deaths per year into the foreseeable future across the region because, in addition to storing large amounts of fuel, many peatlands are located directly upwind of densely populated areas. We also demonstrate how this framework can be used to prioritize restoration locations for the Indonesian Peatland Restoration Agency based on their ability to reduce pollution exposure and health burden. This scientific framework is publicly available through an online decision support tool that allows stakeholders to readily determine the public health benefits of different land management strategies.
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Affiliation(s)
- Miriam E. Marlier
- The RAND CorporationSanta MonicaCAUSA
- Department of Ecology, Evolution, and Environmental BiologyColumbia UniversityNew YorkNYUSA
| | - Tianjia Liu
- Department of Earth and Planetary SciencesHarvard UniversityCambridgeMAUSA
| | - Karen Yu
- School of Engineering and Applied SciencesHarvard UniversityCambridgeMAUSA
| | - Jonathan J. Buonocore
- Center for Climate, Health, and the Global Environment, Harvard T.H. Chan School of Public HealthHarvard UniversityBostonMAUSA
| | - Shannon N. Koplitz
- Department of Earth and Planetary SciencesHarvard UniversityCambridgeMAUSA
| | - Ruth S. DeFries
- Department of Ecology, Evolution, and Environmental BiologyColumbia UniversityNew YorkNYUSA
| | - Loretta J. Mickley
- School of Engineering and Applied SciencesHarvard UniversityCambridgeMAUSA
| | - Daniel J. Jacob
- Department of Earth and Planetary SciencesHarvard UniversityCambridgeMAUSA
- School of Engineering and Applied SciencesHarvard UniversityCambridgeMAUSA
| | - Joel Schwartz
- Harvard T.H. Chan School of Public HealthHarvard UniversityBostonMAUSA
| | | | - Samuel S. Myers
- Harvard T.H. Chan School of Public HealthHarvard UniversityBostonMAUSA
- Harvard University Center for the EnvironmentHarvard UniversityCambridgeMAUSA
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17
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Zimmerman AE, Bachy C, Ma X, Roux S, Jang HB, Sullivan MB, Waldbauer JR, Worden AZ. Closely related viruses of the marine picoeukaryotic alga Ostreococcus lucimarinus exhibit different ecological strategies. Environ Microbiol 2019; 21:2148-2170. [PMID: 30924271 PMCID: PMC6851583 DOI: 10.1111/1462-2920.14608] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/16/2019] [Accepted: 03/23/2019] [Indexed: 01/01/2023]
Abstract
In marine ecosystems, viruses are major disrupters of the direct flow of carbon and nutrients to higher trophic levels. Although the genetic diversity of several eukaryotic phytoplankton virus groups has been characterized, their infection dynamics are less understood, such that the physiological and ecological implications of their diversity remain unclear. We compared genomes and infection phenotypes of the two most closely related cultured phycodnaviruses infecting the widespread picoprasinophyte Ostreococcus lucimarinus under standard- (1.3 divisions per day) and limited-light (0.41 divisions per day) nutrient replete conditions. OlV7 infection caused early arrest of the host cell cycle, coinciding with a significantly higher proportion of infected cells than OlV1-amended treatments, regardless of host growth rate. OlV7 treatments showed a near-50-fold increase of progeny virions at the higher host growth rate, contrasting with OlV1's 16-fold increase. However, production of OlV7 virions was more sensitive than OlV1 production to reduced host growth rate, suggesting fitness trade-offs between infection efficiency and resilience to host physiology. Moreover, although organic matter released from OlV1- and OlV7-infected hosts had broadly similar chemical composition, some distinct molecular signatures were observed. Collectively, these results suggest that current views on viral relatedness through marker and core gene analyses underplay operational divergence and consequences for host ecology.
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Affiliation(s)
| | - Charles Bachy
- Monterey Bay Aquarium Research InstituteMoss LandingCAUSA
| | - Xiufeng Ma
- Department of the Geophysical SciencesUniversity of ChicagoChicagoILUSA
| | - Simon Roux
- Department of MicrobiologyEnvironmental and Geodetic Engineering, The Ohio State UniversityColumbusOHUSA
| | - Ho Bin Jang
- Department of MicrobiologyEnvironmental and Geodetic Engineering, The Ohio State UniversityColumbusOHUSA
- Department of CivilEnvironmental and Geodetic Engineering, The Ohio State UniversityColumbusOHUSA
| | - Matthew B. Sullivan
- Department of MicrobiologyEnvironmental and Geodetic Engineering, The Ohio State UniversityColumbusOHUSA
- Department of CivilEnvironmental and Geodetic Engineering, The Ohio State UniversityColumbusOHUSA
| | | | - Alexandra Z. Worden
- Monterey Bay Aquarium Research InstituteMoss LandingCAUSA
- Ocean EcoSystems Biology Unit, Marine Ecology DivisionGEOMAR Helmholtz Centre for Ocean Research KielKielDE
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18
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Gorris ME, Cat LA, Zender CS, Treseder KK, Randerson JT. Coccidioidomycosis Dynamics in Relation to Climate in the Southwestern United States. Geohealth 2018; 2:6-24. [PMID: 32158997 PMCID: PMC7007142 DOI: 10.1002/2017gh000095] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/22/2017] [Accepted: 11/30/2017] [Indexed: 05/07/2023]
Abstract
Valley fever is endemic to the southwestern United States. Humans contract this fungal disease by inhaling spores of Coccidioides spp. Changes in the environment can influence the abundance and dispersal of Coccidioides spp., causing fluctuations in valley fever incidence. We combined county-level case records from state health agencies to create a regional valley fever database for the southwestern United States, including Arizona, California, Nevada, New Mexico, and Utah. We used this data set to explore how environmental factors influenced the spatial pattern and temporal dynamics of valley fever incidence during 2000-2015. We compiled climate and environmental geospatial data sets from multiple sources to compare with valley fever incidence. These variables included air temperature, precipitation, soil moisture, surface dust concentration, normalized difference vegetation index, and cropland area. We found that valley fever incidence was greater in areas with warmer air temperatures and drier soils. The mean annual cycle of incidence varied throughout the southwestern United States and peaked following periods of low precipitation and soil moisture. From year-to-year, however, autumn incidence was higher following cooler, wetter, and productive springs in the San Joaquin Valley of California. In southcentral Arizona, incidence increased significantly through time. By 2015, incidence in this region was more than double the rate in the San Joaquin Valley. Our analysis provides a framework for interpreting the influence of climate change on valley fever incidence dynamics. Our results may allow the U.S. Centers for Disease Control and Prevention to improve their estimates of the spatial pattern and intensity of valley fever endemicity.
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Affiliation(s)
- M. E. Gorris
- Department of Earth System ScienceUniversity of CaliforniaIrvineCAUSA
| | - L. A. Cat
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaIrvineCAUSA
| | - C. S. Zender
- Department of Earth System ScienceUniversity of CaliforniaIrvineCAUSA
| | - K. K. Treseder
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaIrvineCAUSA
| | - J. T. Randerson
- Department of Earth System ScienceUniversity of CaliforniaIrvineCAUSA
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19
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Roucoux K, Lawson I, Baker T, Del Castillo Torres D, Draper F, Lähteenoja O, Gilmore M, Honorio Coronado E, Kelly T, Mitchard E, Vriesendorp C. Threats to intact tropical peatlands and opportunities for their conservation. Conserv Biol 2017; 31:1283-1292. [PMID: 28272753 PMCID: PMC6849624 DOI: 10.1111/cobi.12925] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 12/06/2016] [Accepted: 03/03/2017] [Indexed: 06/06/2023]
Abstract
Large, intact areas of tropical peatland are highly threatened at a global scale by the expansion of commercial agriculture and other forms of economic development. Conserving peatlands on a landscape scale, with their hydrology intact, is of international conservation importance to preserve their distinctive biodiversity and ecosystem services and maintain their resilience to future environmental change. We explored threats to and opportunities for conserving remaining intact tropical peatlands; thus, we excluded peatlands of Indonesia and Malaysia, where extensive deforestation, drainage, and conversion to plantations means conservation in this region can protect only small fragments of the original ecosystem. We focused on a case study, the Pastaza-Marañón Foreland Basin (PMFB) in Peru, which is among the largest known intact tropical peatland landscapes in the world and is representative of peatland vulnerability. Maintenance of the hydrological conditions critical for carbon storage and ecosystem function of peatlands is, in the PMFB, primarily threatened by expansion of commercial agriculture linked to new transport infrastructure that is facilitating access to remote areas. There remain opportunities in the PMFB and elsewhere to develop alternative, more sustainable land-use practices. Although some of the peatlands in the PMFB fall within existing legally protected areas, this protection does not include the most carbon-dense (domed pole forest) areas. New carbon-based conservation instruments (e.g., REDD+, Green Climate Fund), developing markets for sustainable peatland products, transferring land title to local communities, and expanding protected areas offer pathways to increased protection for intact tropical peatlands in Amazonia and elsewhere, such as those in New Guinea and Central Africa which remain, for the moment, broadly beyond the frontier of commercial development.
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Affiliation(s)
- K.H. Roucoux
- School of Geography and Sustainable DevelopmentUniversity of St AndrewsIrvine Building, North StreetSt AndrewsFifeKY16 9ALU.K.
| | - I.T. Lawson
- School of Geography and Sustainable DevelopmentUniversity of St AndrewsIrvine Building, North StreetSt AndrewsFifeKY16 9ALU.K.
| | - T.R. Baker
- School of GeographyUniversity of LeedsLeedsLS6 9JTU.K.
| | - D. Del Castillo Torres
- Instituto de Investigaciones de la Amazonía PeruanaIquitos, Av. José A. Quiñones km. 2.5 ‐ Apartado Postal 784LoretoPeru
| | - F.C. Draper
- Department of Global EcologyCarnegie Institution for Science260 Panama StStanfordCA94305U.S.A.
- International Center for Tropical BotanyFlorida International University11200 SW 8th StMiamiFL33199U.S.A.
| | - O. Lähteenoja
- School of Life SciencesArizona State UniversityTempeAZ85287U.S.A.
| | - M.P. Gilmore
- School of Integrative StudiesGeorge Mason UniversityFairfaxVA22030U.S.A.
| | - E.N. Honorio Coronado
- Instituto de Investigaciones de la Amazonía PeruanaIquitos, Av. José A. Quiñones km. 2.5 ‐ Apartado Postal 784LoretoPeru
| | - T.J. Kelly
- School of GeographyUniversity of LeedsLeedsLS6 9JTU.K.
| | - E.T.A. Mitchard
- School of GeoSciences,The University of Edinburgh Crew Building,The King's BuildingsEdinburghEH9 3FFU.K.
| | - C.F. Vriesendorp
- Science and EducationThe Field Museum of Natural History1400 S Lake Shore DrChicagoIL60605U.S.A.
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20
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Panchapakesan SSS, Ferguson ML, Hayden EJ, Chen X, Hoskins AA, Unrau PJ. Ribonucleoprotein purification and characterization using RNA Mango. RNA 2017; 23:1592-1599. [PMID: 28747322 PMCID: PMC5602116 DOI: 10.1261/rna.062166.117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/12/2017] [Indexed: 05/04/2023]
Abstract
The characterization of RNA-protein complexes (RNPs) is a difficult but increasingly important problem in modern biology. By combining the compact RNA Mango aptamer with a fluorogenic thiazole orange desthiobiotin (TO1-Dtb or TO3-Dtb) ligand, we have created an RNA tagging system that simplifies the purification and subsequent characterization of endogenous RNPs. Mango-tagged RNP complexes can be immobilized on a streptavidin solid support and recovered in their native state by the addition of free biotin. Furthermore, Mango-based RNP purification can be adapted to different scales of RNP isolation ranging from pull-down assays to the isolation of large amounts of biochemically defined cellular RNPs. We have incorporated the Mango aptamer into the S. cerevisiae U1 small nuclear RNA (snRNA), shown that the Mango-snRNA is functional in cells, and used the aptamer to pull down a U1 snRNA-associated protein. To demonstrate large-scale isolation of RNPs, we purified and characterized bacterial RNA polymerase holoenzyme (HE) in complex with a Mango-containing 6S RNA. We were able to use the combination of a red-shifted TO3-Dtb ligand and eGFP-tagged HE to follow the binding and release of the 6S RNA by two-color native gel analysis as well as by single-molecule fluorescence cross-correlation spectroscopy. Together these experiments demonstrate how the Mango aptamer in conjunction with simple derivatives of its flurophore ligands enables the purification and characterization of endogenous cellular RNPs in vitro.
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Affiliation(s)
- Shanker Shyam S Panchapakesan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Matthew L Ferguson
- Department of Physics, Boise State University, Boise, Idaho 83725, USA
- Department of Biological Science and Biomolecular Sciences Graduate Program, Boise State University, Boise, Idaho 83725, USA
| | - Eric J Hayden
- Department of Biological Science and Biomolecular Sciences Graduate Program, Boise State University, Boise, Idaho 83725, USA
| | - Xin Chen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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21
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Johnson MO, Galbraith D, Gloor M, De Deurwaerder H, Guimberteau M, Rammig A, Thonicke K, Verbeeck H, von Randow C, Monteagudo A, Phillips OL, Brienen RJW, Feldpausch TR, Lopez Gonzalez G, Fauset S, Quesada CA, Christoffersen B, Ciais P, Sampaio G, Kruijt B, Meir P, Moorcroft P, Zhang K, Alvarez‐Davila E, Alves de Oliveira A, Amaral I, Andrade A, Aragao LEOC, Araujo‐Murakami A, Arets EJMM, Arroyo L, Aymard GA, Baraloto C, Barroso J, Bonal D, Boot R, Camargo J, Chave J, Cogollo A, Cornejo Valverde F, Lola da Costa AC, Di Fiore A, Ferreira L, Higuchi N, Honorio EN, Killeen TJ, Laurance SG, Laurance WF, Licona J, Lovejoy T, Malhi Y, Marimon B, Marimon BH, Matos DCL, Mendoza C, Neill DA, Pardo G, Peña‐Claros M, Pitman NCA, Poorter L, Prieto A, Ramirez‐Angulo H, Roopsind A, Rudas A, Salomao RP, Silveira M, Stropp J, ter Steege H, Terborgh J, Thomas R, Toledo M, Torres‐Lezama A, van der Heijden GMF, Vasquez R, Guimarães Vieira IC, Vilanova E, Vos VA, Baker TR. Variation in stem mortality rates determines patterns of above-ground biomass in Amazonian forests: implications for dynamic global vegetation models. Glob Chang Biol 2016; 22:3996-4013. [PMID: 27082541 PMCID: PMC6849555 DOI: 10.1111/gcb.13315] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 02/05/2016] [Accepted: 03/01/2016] [Indexed: 05/05/2023]
Abstract
Understanding the processes that determine above-ground biomass (AGB) in Amazonian forests is important for predicting the sensitivity of these ecosystems to environmental change and for designing and evaluating dynamic global vegetation models (DGVMs). AGB is determined by inputs from woody productivity [woody net primary productivity (NPP)] and the rate at which carbon is lost through tree mortality. Here, we test whether two direct metrics of tree mortality (the absolute rate of woody biomass loss and the rate of stem mortality) and/or woody NPP, control variation in AGB among 167 plots in intact forest across Amazonia. We then compare these relationships and the observed variation in AGB and woody NPP with the predictions of four DGVMs. The observations show that stem mortality rates, rather than absolute rates of woody biomass loss, are the most important predictor of AGB, which is consistent with the importance of stand size structure for determining spatial variation in AGB. The relationship between stem mortality rates and AGB varies among different regions of Amazonia, indicating that variation in wood density and height/diameter relationships also influences AGB. In contrast to previous findings, we find that woody NPP is not correlated with stem mortality rates and is weakly positively correlated with AGB. Across the four models, basin-wide average AGB is similar to the mean of the observations. However, the models consistently overestimate woody NPP and poorly represent the spatial patterns of both AGB and woody NPP estimated using plot data. In marked contrast to the observations, DGVMs typically show strong positive relationships between woody NPP and AGB. Resolving these differences will require incorporating forest size structure, mechanistic models of stem mortality and variation in functional composition in DGVMs.
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Affiliation(s)
| | | | - Manuel Gloor
- School of GeographyUniversity of LeedsLeedsLS6 2QTUK
| | - Hannes De Deurwaerder
- CAVElab Computational & Applied Vegetation EcologyFaculty of Bioscience EngineeringGhent UniversityCoupure Links 653B‐9000GentBelgium
| | - Matthieu Guimberteau
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA‐CNRS‐UVSQUniversité Paris‐SaclayF‐91191Gif‐sur‐YvetteFrance
- UMR 7619 METISIPSL, Sorbonne Universités, UPMC, CNRS, EPHE75252ParisFrance
| | - Anja Rammig
- TUM School of Life Sciences WeihenstephanTechnical University MunichHans‐Carl‐von‐Carlowitz‐Platz 285354FreisingGermany
- Potsdam Institute for Climate Impact Research (PIK)Telegrafenberg A62PO Box 60 12 03D‐14412PotsdamGermany
| | - Kirsten Thonicke
- Potsdam Institute for Climate Impact Research (PIK)Telegrafenberg A62PO Box 60 12 03D‐14412PotsdamGermany
| | - Hans Verbeeck
- CAVElab Computational & Applied Vegetation EcologyFaculty of Bioscience EngineeringGhent UniversityCoupure Links 653B‐9000GentBelgium
| | - Celso von Randow
- INPEAv. Dos Astronautas, 1.758, Jd. GranjaCEP: 12227‐010Sao Jose dos CamposSPBrazil
| | - Abel Monteagudo
- Jardín Botánico de MissouriProlongacion Bolognesi Mz.e, Lote 6Oxapampa, PascoPeru
| | | | | | - Ted R. Feldpausch
- GeographyCollege of Life and Environmental SciencesUniversity of ExeterRennes DriveExeterEX4 4RJUK
| | | | - Sophie Fauset
- School of GeographyUniversity of LeedsLeedsLS6 2QTUK
| | | | - Bradley Christoffersen
- School of GeosciencesUniversity of EdinburghEdinburghEH9 3FFUK
- Earth and Environmental Sciences DivisionLos Alamos National LaboratoryPO Box 1663Los AlamosNM 87545USA
| | - Philippe Ciais
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA‐CNRS‐UVSQUniversité Paris‐SaclayF‐91191Gif‐sur‐YvetteFrance
| | - Gilvan Sampaio
- INPEAv. Dos Astronautas, 1.758, Jd. GranjaCEP: 12227‐010Sao Jose dos CamposSPBrazil
| | - Bart Kruijt
- ALTERRAWageningen‐URPO Box 476700 AAWageningenThe Netherlands
| | - Patrick Meir
- School of GeosciencesUniversity of EdinburghEdinburghEH9 3FFUK
- Research School of BiologyAustralian National UniversityCanberraACT0200Australia
| | - Paul Moorcroft
- Department of Organismic and Evolutionary BiologyHarvard University26 Oxford StreetCambridgeMA 02138USA
| | - Ke Zhang
- Cooperative Institute for Mesoscale Meteorological StudiesUniversity of Oklahoma National Weather Center Suite 2100120 David L. Boren BlvdNormanOK73072USA
| | | | | | - Ieda Amaral
- INPAAv. André Araújo, 2.936CEP 69067‐375Petrópolis, ManausAMBrazil
| | - Ana Andrade
- INPAAv. André Araújo, 2.936CEP 69067‐375Petrópolis, ManausAMBrazil
| | - Luiz E. O. C. Aragao
- Jardín Botánico de MissouriProlongacion Bolognesi Mz.e, Lote 6Oxapampa, PascoPeru
| | - Alejandro Araujo‐Murakami
- Museo de Historia Natural Noel Kempff MercadoUniversidad Autonoma Gabriel Rene MorenoCasilla 2489, Av. Irala 565Santa CruzBolivia
| | | | - Luzmila Arroyo
- Museo de Historia Natural Noel Kempff MercadoUniversidad Autonoma Gabriel Rene MorenoCasilla 2489, Av. Irala 565Santa CruzBolivia
| | - Gerardo A. Aymard
- UNELLEZ‐Guanare, Programa de Ciencias del Agro y el Mar, Herbario Universitario (PORT)Mesa de CavacasEstado Portuguesa3350Venezuela
| | - Christopher Baraloto
- Department of Biological SciencesInternational Center for Tropical Botany (ICTB)Florida International University112200 SW 8th Street, OE 167MiamiFL33199USA
| | - Jocely Barroso
- Universidade Federal do AcreCampus de Cruzeiro do SulRio BrancoBrazil
| | - Damien Bonal
- INRAUMR 1137 “Ecologie et Ecophysiologie Forestiere”54280ChampenouxFrance
| | - Rene Boot
- Tropenbos InternationalPO Box 2326700 AEWageningenThe Netherlands
| | - Jose Camargo
- INPAAv. André Araújo, 2.936CEP 69067‐375Petrópolis, ManausAMBrazil
| | - Jerome Chave
- Université Paul Sabatier CNRSUMR 5174 Evolution et Diversité Biologiquebâtiment 4R131062ToulouseFrance
| | - Alvaro Cogollo
- Jardín Botánico de Medellín Joaquín Antonio Uribe Calle 73 # 51 D 14 MedellínCartagenaColombia
| | | | | | - Anthony Di Fiore
- Department of AnthropologyUniversity of Texas at AustinSAC Room 5.1502201 Speedway Stop C3200AustinTX78712USA
| | - Leandro Ferreira
- Museu Paraense Emilio GoeldiAv. Magalhães Barata, 376 ‐ São BrazCEP: 66040‐170BelémPABrazil
| | - Niro Higuchi
- INPAAv. André Araújo, 2.936CEP 69067‐375Petrópolis, ManausAMBrazil
| | - Euridice N. Honorio
- Instituto de Investigaciones de la Amazonía PeruanaAv. José Quiñones km 2.5IquitosPerú
| | | | - Susan G. Laurance
- Centre for Tropical Environmental and Sustainability Science (TESS) and College of Marine and Environmental SciencesJames Cook UniversityCairnsQld4878Australia
| | - William F. Laurance
- Centre for Tropical Environmental and Sustainability Science (TESS) and College of Marine and Environmental SciencesJames Cook UniversityCairnsQld4878Australia
| | - Juan Licona
- Instituto Boliviano de Investigación ForestalC.P. 6201Santa Cruz de la SierraBolivia
| | - Thomas Lovejoy
- Environmental Science and Policy Department and the Department of Public and International Affairs at George Mason University (GMU)3351 Fairfax DriveArlingtonWashingtonDCVA 22201USA
| | - Yadvinder Malhi
- Environmental Change InstituteSchool of Geography and the EnvironmentUniversity of OxfordSouth Parks RoadOxfordOX1 3QYUK
| | - Bia Marimon
- Universidade do Estado de Mato GrossoCampus de Nova XavantinaCaixa Postal 08CEP 78.690‐000Nova XavantinaMTBrazil
| | - Ben Hur Marimon
- Universidade do Estado de Mato GrossoCampus de Nova XavantinaCaixa Postal 08CEP 78.690‐000Nova XavantinaMTBrazil
| | - Darley C. L. Matos
- Museu Paraense Emilio GoeldiAv. Magalhães Barata, 376 ‐ São BrazCEP: 66040‐170BelémPABrazil
| | - Casimiro Mendoza
- Escuela de Ciencias Forestales (ESFOR)Av. Final Atahuallpa s/nCasilla 447CochabambaBolivia
| | - David A. Neill
- Facultad de Ingeniería AmbientalUniversidad Estatal AmazónicaPaso lateral km 2 1/2 via NapoPuyoPastazaEcuador
| | - Guido Pardo
- Universidad Autonoma del BeniCampus UniversitarioAv. Ejército Nacional, finalRiberaltaBeniBolivia
| | - Marielos Peña‐Claros
- Instituto Boliviano de Investigación ForestalC.P. 6201Santa Cruz de la SierraBolivia
- Forest Ecology and Forest Management GroupWageningen UniversityPO Box 47Wageningen6700 AAThe Netherlands
| | - Nigel C. A. Pitman
- Center for Tropical ConservationDuke UniversityBox 90381DurhamNC27708USA
| | - Lourens Poorter
- Forest Ecology and Forest Management GroupWageningen UniversityPO Box 47Wageningen6700 AAThe Netherlands
| | - Adriana Prieto
- Doctorado Instituto de Ciencias NaturalesUniversidad Nacional de ColombiaBogotáColombia
| | - Hirma Ramirez‐Angulo
- Instituto de Investigaciones para el Desarrollo ForestalUniversidad de Los AndesAvenida Principal Chorros de MillaCampus Universitario ForestalEdificio PrincipalMéridaVenezuela
| | - Anand Roopsind
- Iwokrama International Centre for Rainforest Conservation and Development77 High Street KingstonGeorgetownGuyana
| | - Agustin Rudas
- Doctorado Instituto de Ciencias NaturalesUniversidad Nacional de ColombiaBogotáColombia
| | - Rafael P. Salomao
- Museu Paraense Emilio GoeldiAv. Magalhães Barata, 376 ‐ São BrazCEP: 66040‐170BelémPABrazil
| | - Marcos Silveira
- Museu UniversitárioUniversidade Federal do AcreRio BrancoAC69910‐900Brazil
| | - Juliana Stropp
- Institute of Biological and Health SciencesFederal University of AlagoasAv. Lourival Melo Mota s/nTabuleiro do Martins, MaceióAL 57072‐900Brazil
| | - Hans ter Steege
- Naturalis Biodiversity CenterPO Box 95172300 RALeidenThe Netherlands
| | - John Terborgh
- Center for Tropical ConservationDuke UniversityBox 90381DurhamNC27708USA
| | - Raquel Thomas
- Iwokrama International Centre for Rainforest Conservation and Development77 High Street KingstonGeorgetownGuyana
| | - Marisol Toledo
- Instituto Boliviano de Investigación ForestalC.P. 6201Santa Cruz de la SierraBolivia
| | - Armando Torres‐Lezama
- Instituto de Investigaciones para el Desarrollo ForestalUniversidad de Los AndesAvenida Principal Chorros de MillaCampus Universitario ForestalEdificio PrincipalMéridaVenezuela
| | | | - Rodolfo Vasquez
- GeographyCollege of Life and Environmental SciencesUniversity of ExeterRennes DriveExeterEX4 4RJUK
| | | | - Emilio Vilanova
- Instituto de Investigaciones para el Desarrollo ForestalUniversidad de Los AndesAvenida Principal Chorros de MillaCampus Universitario ForestalEdificio PrincipalMéridaVenezuela
| | - Vincent A. Vos
- Centro de Investigación y Promoción del Campesinado, regional Norte AmazónicoC/Nicanor Gonzalo Salvatierra N° 362Casilla 16RiberaltaBolivia
- Universidad Autónoma del BeniAvenida 6 de Agosto N° 64RiberaltaBolivia
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