Angiosperm phylogeny: 17 genes, 640 taxa Soltis, Douglas E.; Smith, Stephen A.; Cellinese, Nico ...
American journal of botany,
April 2011, Volume:
98, Issue:
4
Journal Article
Peer reviewed
Open access
Premise of the study. Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the ...hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. Methods: We conducted two primary analyses based on 640 species representing 330 families. The first included 25260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i. e., nucleus, plastid, and mitochondrion). The second included 19846 aligned bp from 13 genes (representing only the nucleus and plastid). Key results: Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms (Mesangiospermae), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + Ceratophyllaceae + Eudicotyledoneae. Eudicotyledoneae contains a basal grade subtending Gunneridae. Within Gunneridae, Gunnerales are sister to the remainder (Pentapetalae), which comprises (1) Superrosidae, consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae, comprising Berberidopsidales, Santalales, CaryophyHales, Asteridae, and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae, most deep-level relationships are resolved with strong support. Conclusions: Our analyses confirm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.
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Methane emissions from the U.S. oil and natural gas supply chain were estimated by using ground-based, facility-scale measurements and validated with aircraft observations in areas accounting for ...~30% of U.S. gas production. When scaled up nationally, our facility-based estimate of 2015 supply chain emissions is 13 ± 2 teragrams per year, equivalent to 2.3% of gross U.S. gas production. This value is ~60% higher than the U.S. Environmental Protection Agency inventory estimate, likely because existing inventory methods miss emissions released during abnormal operating conditions. Methane emissions of this magnitude, per unit of natural gas consumed, produce radiative forcing over a 20-year time horizon comparable to the CO
from natural gas combustion. Substantial emission reductions are feasible through rapid detection of the root causes of high emissions and deployment of less failure-prone systems.
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The eudicot order Malpighiales contains ~16000 species and is the most poorly resolved large rosid clade. To clarify phylogenetic relationships in the order, we used maximum likelihood, Bayesian, and ...parsimony analyses of DNA sequence data from 13 gene regions, totaling 15604 bp, and representing all three genomic compartments (i.e., plastid: atpB, matK, ndhF, and rbcL; mitochondrial: ccmB, cob, matR, nad1B-C, nad6, and rps3; and nuclear: 18S rDNA, PHYC, and newly developed low-copy EMB2765). Our sampling of 190 taxa includes representatives from all families of Malpighiales. These data provide greatly increased support for the recent additions of Aneulophus, Bhesa, Centroplacus, Ploiarium, and Rafflesiaceae to Malpighiales; sister relations of Phyllanthaceae + Picrodendraceae, monophyly of Hypericaceae, and polyphyly of Clusiaceae. Oxalidales + Huaceae, followed by Celastrales are successive sisters to Malpighiales. Parasitic Rafflesiaceae, which produce the world's largest flowers, are confirmed as embedded within a paraphyletic Euphorbiaceae. Novel findings show a well-supported placement of Ctenolophonaceae with Erythroxylaceae + Rhizophoraceae, sister-group relationships of Bhesa + Centroplacus, and the exclusion of Medusandra from Malpighiales. New taxonomic circumscriptions include the addition of Bhesa to Centroplacaceae, Medusandra to Peridiscaceae (Saxifragales), Calophyllaceae applied to Clusiaceae subfamily Kielmeyeroideae, Peraceae applied to Euphorbiaceae subfamily Peroideae, and Huaceae included in Oxalidales.
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Based on a uniquely dense network of surface towers measuring continuously the atmospheric concentrations of greenhouse gases (GHGs), we developed the first comprehensive monitoring systems of CO2 ...emissions at high resolution over the city of Indianapolis. The urban inversion evaluated over the 2012–2013 dormant season showed a statistically significant increase of about 20% (from 4.5 to 5.7 MtC ± 0.23 MtC) compared to the Hestia CO2 emission estimate, a state‐of‐the‐art building‐level emission product. Spatial structures in prior emission errors, mostly undetermined, appeared to affect the spatial pattern in the inverse solution and the total carbon budget over the entire area by up to 15%, while the inverse solution remains fairly insensitive to the CO2 boundary inflow and to the different prior emissions (i.e., ODIAC). Preceding the surface emission optimization, we improved the atmospheric simulations using a meteorological data assimilation system also informing our Bayesian inversion system through updated observations error variances. Finally, we estimated the uncertainties associated with undetermined parameters using an ensemble of inversions. The total CO2 emissions based on the ensemble mean and quartiles (5.26–5.91 MtC) were statistically different compared to the prior total emissions (4.1 to 4.5 MtC). Considering the relatively small sensitivity to the different parameters, we conclude that atmospheric inversions are potentially able to constrain the carbon budget of the city, assuming sufficient data to measure the inflow of GHG over the city, but additional information on prior emission error structures are required to determine the spatial structures of urban emissions at high resolution.
Key Points
High resolution bottom‐up and top‐down fossil fuel emissions agree within 20% at the city scale
Inverse urban emissions and GHG boundary inflow are well constrained by dense tower observation network
Undefined error structures in prior emissions impact significantly the source attribution capability at high resolution
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Published estimates of methane emissions from atmospheric data (top-down approaches) exceed those from source-based inventories (bottom-up approaches), leading to conflicting claims about the climate ...implications of fuel switching from coal or petroleum to natural gas. Based on data from a coordinated campaign in the Barnett Shale oil and gas-producing region of Texas, we find that top-down and bottom-up estimates of both total and fossil methane emissions agree within statistical confidence intervals (relative differences are 10% for fossil methane and 0.1% for total methane). We reduced uncertainty in top-down estimates by using repeated mass balance measurements, as well as ethane as a fingerprint for source attribution. Similarly, our bottom-up estimate incorporates a more complete count of facilities than past inventories, which omitted a significant number of major sources, and more effectively accounts for the influence of large emission sources using a statistical estimator that integrates observations from multiple ground-based measurement datasets. Two percent of oil and gas facilities in the Barnett accounts for half of methane emissions at any given time, and high-emitting facilities appear to be spatiotemporally variable. Measured oil and gas methane emissions are 90% larger than estimates based on the US Environmental Protection Agency’s Greenhouse Gas Inventory and correspond to 1.5% of natural gas production. This rate of methane loss increases the 20-y climate impacts of natural gas consumed in the region by roughly 50%.
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Debates over public programs frequently focus on questions of effectiveness, equity, and efficiency and the tradeoff among these objectives. Missing from the literature is whether the general public ...cares about these tradeoffs, can perceive such differences, and will act on them. This article reports on two pre‐registered vignette experiments where the effectiveness, equity, and efficiency are assessed relative to experimental treatments focused on U.S. K‐12 education involving test scores, equality of test scores, and program costs. One experiment focuses on equity in race and the other on equity in income. The experiments show that the general public perceives differences in program effectiveness and equity, values both, and is unwilling to tradeoff one for the other. The public cares about program costs, but it lacks a sophisticated understanding of efficiency as a concept. Inequalities in income appear to influence equity concerns more than those involving race.
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The Indianapolis Flux Experiment (INFLUX) aims to develop and assess methods for quantifying urban greenhouse gas emissions. Here we use CO2, 14CO2, and CO measurements from tall towers around ...Indianapolis, USA, to determine urban total CO2, the fossil fuel derived CO2 component (CO2ff), and CO enhancements relative to background measurements. When a local background directly upwind of the urban area is used, the wintertime total CO2 enhancement over Indianapolis can be entirely explained by urban CO2ff emissions. Conversely, when a continental background is used, CO2ff enhancements are larger and account for only half the total CO2 enhancement, effectively representing the combined CO2ff enhancement from Indianapolis and the wider region. In summer, we find that diurnal variability in both background CO2 mole fraction and covarying vertical mixing makes it difficult to use a simple upwind‐downwind difference for a reliable determination of total CO2 urban enhancement. We use characteristic CO2ff source sector CO:CO2ff emission ratios to examine the contribution of the CO2ff source sectors to total CO2ff emissions. This method is strongly sensitive to the mobile sector, which produces most CO. We show that the inventory‐based emission product (“bottom up”) and atmospheric observations (“top down”) can be directly compared throughout the diurnal cycle using this ratio method. For Indianapolis, the top‐down observations are consistent with the bottom‐up Hestia data product emission sector patterns for most of the diurnal cycle but disagree during the nighttime hours. Further examination of both the top‐down and bottom‐up assumptions is needed to assess the exact cause of the discrepancy.
Key Points
Judicious background choice allows isolation of urban greenhouse gas emissions
In winter in Indianapolis, total CO2 can be used as a proxy for fossil fuel CO2
Multiple trace gas ratios can be used to examine diurnal cycle in emissions
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Accurately simulating gross primary productivity (GPP) in terrestrial ecosystem models is critical because errors in simulated GPP propagate through the model to introduce additional errors in ...simulated biomass and other fluxes. We evaluated simulated, daily average GPP from 26 models against estimated GPP at 39 eddy covariance flux tower sites across the United States and Canada. None of the models in this study match estimated GPP within observed uncertainty. On average, models overestimate GPP in winter, spring, and fall, and underestimate GPP in summer. Models overpredicted GPP under dry conditions and for temperatures below 0°C. Improvements in simulated soil moisture and ecosystem response to drought or humidity stress will improve simulated GPP under dry conditions. Adding a low‐temperature response to shut down GPP for temperatures below 0°C will reduce the positive bias in winter, spring, and fall and improve simulated phenology. The negative bias in summer and poor overall performance resulted from mismatches between simulated and observed light use efficiency (LUE). Improving simulated GPP requires better leaf‐to‐canopy scaling and better values of model parameters that control the maximum potential GPP, such asεmax (LUE), Vcmax (unstressed Rubisco catalytic capacity) or Jmax (the maximum electron transport rate).
Key Points
Gross primary productivity (GPP) from 26 models tested at 39 flux tower sites
Simulated light use efficiency controls model performance
Models overpredict GPP under dry conditions
The identification and quantification of methane emissions from natural gas production has become increasingly important owing to the increase in the natural gas component of the energy sector. An ...instrumented aircraft platform was used to identify large sources of methane and quantify emission rates in southwestern PA in June 2012. A large regional flux, 2.0–14 g CH ₄ s ⁻¹ km ⁻², was quantified for a ∼2,800-km ² area, which did not differ statistically from a bottom-up inventory, 2.3–4.6 g CH ₄ s ⁻¹ km ⁻². Large emissions averaging 34 g CH ₄/s per well were observed from seven well pads determined to be in the drilling phase, 2 to 3 orders of magnitude greater than US Environmental Protection Agency estimates for this operational phase. The emissions from these well pads, representing ∼1% of the total number of wells, account for 4–30% of the observed regional flux. More work is needed to determine all of the sources of methane emissions from natural gas production, to ascertain why these emissions occur and to evaluate their climate and atmospheric chemistry impacts.
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We show that transport differences between two commonly used global chemical transport models, GEOS‐Chem and TM5, lead to systematic space‐time differences in modeled distributions of carbon dioxide ...and sulfur hexafluoride. The distribution of differences suggests inconsistencies between the transport simulated by the models, most likely due to the representation of vertical motion. We further demonstrate that these transport differences result in systematic differences in surface CO2 flux estimated by a collection of global atmospheric inverse models using TM5 and GEOS‐Chem and constrained by in situ and satellite observations. While the impact on inferred surface fluxes is most easily illustrated in the magnitude of the seasonal cycle of surface CO2 exchange, it is the annual carbon budgets that are particularly relevant for carbon cycle science and policy. We show that inverse model flux estimates for large zonal bands can have systematic biases of up to 1.7 PgC/year due to large‐scale transport uncertainty. These uncertainties will propagate directly into analysis of the annual meridional CO2 flux gradient between the tropics and northern midlatitudes, a key metric for understanding the location, and more importantly the processes, responsible for the annual global carbon sink. The research suggests that variability among transport models remains the largest source of uncertainty across global flux inversion systems and highlights the importance both of using model ensembles and of using independent constraints to evaluate simulated transport.
Key Points
There are systematic differences in transport between two commonly used chemical transport models, TM5 and GEOS‐Chem
These systematic differences lead to significant and meaningful posterior flux uncertainties in atmospheric CO2 flux inversions
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