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The international river interface cooperative: Public domain flow and morphodynamics software for education and applications

This paper describes a new, public-domain interface for modeling flow, sediment transport and morphodynamics in rivers and other geophysical flows. The interface is named after the International River Interface Cooperative (iRIC), the group that constructed the interface and many of the current solvers included in iRIC. The interface is entirely free to any user and currently houses thirteen models ranging from simple one-dimensional models through three-dimensional large-eddy simulation models. Solvers are only loosely coupled to the interface so it is straightforward to modify existing solvers or to introduce other solvers into the system. Six of the most widely-used solvers are described in detail including example calculations to serve as an aid for users choosing what approach might be most appropriate for their own applications. The example calculations range from practical computations of bed evolution in natural rivers to highly detailed predictions of the development of small-scale bedforms on an initially flat bed. The remaining solvers are also briefly described. Although the focus of most solvers is coupled flow and morphodynamics, several of the solvers are also specifically aimed at providing flood inundation predictions over large spatial domains. Potential users can download the application, solvers, manuals, and educational materials including detailed tutorials at www.-i-ric.org . The iRIC development group encourages scientists and engineers to use the tool and to consider adding their own methods to the iRIC suite of tools.

Advances in Water Resources↗

Net alkalinity and net acidity 1: Theoretical considerations

Net acidity and net alkalinity are widely used, poorly defined, and commonly misunderstood parameters for the characterization of mine drainage. The authors explain theoretical expressions of 3 types of alkalinity (caustic, phenolphthalein, and total) and acidity (mineral, CO2, and total). Except for rarely-invoked negative alkalinity, theoretically defined total alkalinity is closely analogous to measured alkalinity and presents few practical interpretation problems. Theoretically defined "CO 2-acidity" is closely related to most standard titration methods with an endpoint pH of 8.3 used for determining acidity in mine drainage, but it is unfortunately named because CO2 is intentionally driven off during titration of mine-drainage samples. Using the proton condition/mass- action approach and employing graphs to illustrate speciation with changes in pH, the authors explore the concept of principal components and how to assign acidity contributions to aqueous species commonly present in mine drainage. Acidity is defined in mine drainage based on aqueous speciation at the sample pH and on the capacity of these species to undergo hydrolysis to pH 8.3. Application of this definition shows that the computed acidity in mg L -1 as CaCO3 (based on pH and analytical concentrations of dissolved FeII, FeIII, Mn, and Al in mg L -1):aciditycalculated=50{1000(10-pH)+[2(FeII)+3(FeIII)]/56+2(Mn)/ 55+3(Al)/27}underestimates contributions from HSO4- and H+, but overestimates the acidity due to Fe3+ and Al3+. However, these errors tend to approximately cancel each other. It is demonstrated that "net alkalinity" is a valid mathematical construction based on theoretical definitions of alkalinity and acidity. Further, it is shown that, for most mine-drainage solutions, a useful net alkalinity value can be derived from: (1) alkalinity and acidity values based on aqueous speciation, (2) measured alkalinity minus calculated acidity, or (3) taking the negative of the value obtained in a standard method "hot peroxide" acidity titration, provided that labs report negative values. The authors recommend the third approach; i.e., net alkalinity = -Hot Acidity. ?? 2005 Elsevier Ltd. All rights reserved.

Applied Geochemistry↗

Na+/K+/2Cl- cotransporter and CFTR gill expression after seawater transfer in smolts (0+) of different Atlantic salmon (Salmo salar) families

Smoltification involves morphological and physiological changes in the gills that prepare anadromous salmonids to osmoregulate efficiently in seawater. In a previous study, we found that different families of Atlantic salmon (Salmo salar) smolts vary in their ability to osmoregulate when abruptly transferred to cold seawater and that these differences are correlated with gill Na+/K+ ATPase activity. Here we extend these findings to test whether other key transport proteins, namely Na+/K+/2Cl- contransporter (NKCC) and the Cl- channel or cystic fibrosis transmembrane conductance regulator (CFTR), play a significant role in osmoregulatory differences between families. To facilitate molecular analysis of NKCC, we first isolated a gill cDNA containing the complete coding region (1147 aa) of an isoform previously reported as a partial sequence. Phylogenetic analysis showed that this isoform is most closely related to isoforms of the NKCC1a subfamily found in European eel and Mozambique tilapia. In a second step, we quantified NKCC protein abundance as well as mRNA expression levels for NKCC1a and two CFTR isoforms (CFTRI and CFTRII) in 0+ smolts from three families prior to and following seawater transfer. The family with the lowest salinity tolerance also showed significant increases in gill NKCC1a mRNA after seawater transfer. Taken together with our previous study, these data indicate that family differences in expression of transport proteins are in part related to salinity tolerance, although the best indicator of osmoregulatory performance between families may be gill Na+/K+ ATPase activity and CFTR I mRNA levels, rather than Na+/K+ ATPase and NKCC1a mRNA levels or NKCC protein abundance. ?? 2007 Elsevier B.V. All rights reserved.

Aquaculture↗

Evaluation of analytical techniques to determine AQUI-S® 20E (eugenol) concentrations in water

There is a critical need in U.S. public aquaculture and fishery management programs for an immediate-release sedative, i.e. a compound that can be safely and effectively used to sedate fish and subsequently, allow for their immediate release. AQUI-S® 20E (10% active ingredient, eugenol; any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government) is being pursued for U.S. approval as an immediate-release sedative. As part of the approval process, data describing animal safety and efficacy are needed. Essential to conducting studies that generate those data, is a method to accurately and precisely determine AQUI-S® 20E concentrations in exposure baths. Spectrophotometric and solid phase extraction (SPE)–high pressure liquid chromatography (LC) methods were developed and evaluated as methods to determine AQUI-S® 20E (eugenol) concentrations in water, methods that could be applied to any situation where eugenol was being evaluated as a fish sedative. The spectrophotometric method was accurate and precise (accuracy, > 87%; precision, < 0.70 %CV) when determining eugenol concentrations in solutions of 50 to 1000 mg/L AQUI-S® 20E made with LC grade water and water with varying pH and hardness. The spectrophotometric method's accuracy was negatively affected when analyzing water containing fish feed. The SPE–LC method was also accurate and precise (accuracy > 86%; precision < 8.9 %CV) when determining eugenol concentrations in solutions of 50 to 1000 mg/L AQUI-S® 20E made with LC grade water and water with varying pH and hardness. The SPE–LC method was influenced to a lesser degree by the presence of fish feed indicating greater specificity for eugenol.

Aquaculture↗

Contaminants as viral cofactors: assessing indirect population effects

Current toxicological methods often miss contaminant effects, particularly when immune suppression is involved. The failure to recognize and evaluate indirect and sublethal effects severely limits the applicability of those methods at the population level. In this study, the Vitality model is used to evaluate the population level effects of a contaminant exerting only indirect, sublethal effects at the individual level. Juvenile rainbow trout ( Oncorhynchus mykiss ) were injected with 2.5 or 10.0 mg/kg doses of the model CYP1A inducer, &beta;-naphthoflavone (BNF) as a pre-stressor, then exposed to a challenge dose of 10 2 or 10 4 pfu/fish of infectious hematopoietic necrosis virus (IHNV), an important viral pathogen of salmonids in North America. At the end of the 28-d challenge, the mortality data were processed according to the Vitality model which indicated that the correlation between the average rate of vitality loss and the pre-stressor dose was strong: R 2 = 0.9944. Average time to death and cumulative mortality were dependent on the BNF dose, while no significant difference between the two viral dosages was shown, implying that the history of the organism at the time of stressor exposure is an important factor in determining the virulence or toxicity of the stressor. The conceptual framework of this model permits a smoother transfer of results to a more complex stratum, namely the population level, which allows the immunosuppressive results generated by doses of a CYP1A inducer that more accurately represent the effects elicited by environmentally-relevant contaminant concentrations to be extrapolated to target populations. The indirect effects of other environmental contaminants with similar biotransformation pathways, such as polycyclic aromatic hydrocarbons (PAH), could be assessed and quantified with this model and the results applied to a more complex biological hierarchy.

Aquatic Toxicology↗

Merging integrated population models and individual-based models to project population dynamics of recolonizing species

Recolonizing species exhibit unique population dynamics, namely dispersal to and colonization of new areas, that have important implications for management. A resulting challenge is how to simultaneously model demographic and movement processes so that recolonizing species can be accurately projected over time and space. We introduce a framework for spatially explicit projection modeling that harnesses the rigorous parameter estimation made possible by an integrated population model (IPM) and the flexible movement modeling made possible by an individual-based model (IBM). Our framework has two components: [1] a Bayesian IPM-driven age- and state-structured population model that governs the population state process and estimation of demographic rates, and [2] an IBM-driven spatial model that allows for the projection of dispersal and habitat colonization. We applied this model framework to estimate current and project future dynamics of gray wolves ( Canis lupus ) in Washington State, USA. We used data from 74 telemetered wolves and yearly pup and pack counts to parameterize the model, and then projected statewide dynamics over 50 years. Mean population growth was 1.29 (95 % Bayesian Credible Interval = 1.26–1.33) during initial recolonization from 2009 to 2020 and decreased to 1.02 (95 % Prediction Interval = 0.98–1.04) in the projection period (2021–2070). Our results suggest that gray wolves have an ~100 % probability of colonizing the last of Washington State's three specified recovery regions by 2030, regardless of alternative assumptions about how dispersing wolves select new territories. Our spatially explicit projection model can be used to project the dynamics of any species for which spatial spread is an important driver of population dynamics.

Washington↗

Mineralization dynamics of metakaolin-based alkali-activated cements

This paper investigates the early-age dynamics of mineral formation in metakaolin-based alkali-activated cements. The effects of silica availability and alkali content on mineral formation were investigated via X-ray diffraction and solid-state 29 Si magic-angle spinning nuclear magnetic resonance spectroscopy at 2, 7, 14, and 28 days. Silica availability was controlled by using either liquid- (immediate) or solid-based (gradual) sodium silicate supplements. Mineral (zeolitic) and amorphous microstructural characteristics were correlated with observed changes in bulk physical properties, namely shrinkage, density, and porosity. Results demonstrate that, while alkali content controls the mineralization in immediately available silica systems, alkali content controls the silica availability in gradually available silica systems. Immediate silica availability generally leads to a more favorable mineral formation as demonstrated by correlated improvements in bulk physical properties.

Cement and Concrete Research↗

Gas geochemistry of a shallow submarine hydrothermal vent associated with the El Requesón fault zone, Bahía Concepción, Baja California Sur, México

We investigated hydrothermal gas venting associated with a coastal fault zone along the western margin of Bah&iacute;a Concepci&oacute;n, B.C.S., M&eacute;xico. Copious discharge of geothermal liquid (&asymp; 90 &deg;C) and gas is occurring in the intertidal and shallow subtidal zones (to a depth of 13 m) through soft sediments and fractures in rocks along a &sim;750 m linear trend generally sub-parallel to an onshore fault near Punta Santa Barbara. Hydrothermal activity shows negative correlation with tidal height; temperatures in the area of hydrothermal activity were up to 11.3 &deg;C higher at low tide than at high tide (measured tidal range &asymp; 120 cm). Gas samples were collected using SCUBA and analyzed for chemical composition and stable isotope values. The main components of the gas are N 2 (&asymp; 53%; 534 mmol/mol), CO 2 (&asymp; 43%; 435 mmol/mol), and CH 4 (&asymp; 2.2%; 22 mmol/mol). The &delta; 13 C values of the CH 4 (mean = &minus; 34.3&permil;), and the ratios of CH 4 to C 2 H 6 (mean = 89), indicate that the gas is thermogenic in origin. The carbon stable isotopes and the &delta; 15 N of the N 2 in the gas (mean = 1.7&permil;) suggest it may be partially derived from the thermal alteration of algal material in immature sedimentary organic matter. The He isotope ratios ( 3 He / 4 He = 1.32 R A ) indicate a significant mantle component (16.3%) in the gas. Here, we suggest the name El Reques&oacute;n fault zone for the faults that likely formed as a result of extension in the region during the late Miocene, and are currently serving as conduits for the observed hydrothermal activity.

Chemical Geology↗

Controls on biochemical oxygen demand in the upper Klamath River, Oregon

A series of 30-day biochemical oxygen demand (BOD) experiments were conducted on water column samples from a reach of the upper Klamath River that experiences hypoxia and anoxia in summer. Samples were incubated with added nitrification inhibitor to measure carbonaceous BOD (CBOD), untreated to measure total BOD, which included demand from nitrogenous BOD (NBOD), and coarse-filtered to examine the effect of removing large particulate matter. All BOD data were fit well with a two-group model, so named because it considered contributions from both labile and refractory pools of carbon: BOD t = a 1 (1 − e − a 0 t ) + a 2 t . Site-average labile first-order decay rates a 0 ranged from 0.15 to 0.22/day for CBOD and 0.11 to 0.29/day for BOD. Site-average values of refractory zero-order decay rates a 2 ranged from 0.13 to 0.25 mg/L/day for CBOD and 0.01 to 0.45 mg/L/day for BOD; the zero-order CBOD decay rate increased from early- to mid-summer. Values of ultimate CBOD for the labile component a 1 ranged from 5.5 to 28.8 mg/L for CBOD, and 7.6 to 30.8 mg/L for BOD. Two upstream sites had higher CBOD compared to those downstream. Maximum measured total BOD 5 and BOD 30 during the study were 26.5 and 55.4 mg/L; minimums were 4.2 and 13.6 mg/L. For most samples, the oxygen demand from the three components considered here were: labile CBOD > NBOD > refractory CBOD, though the relative importance of refractory CBOD to oxygen demand increased over time. Coarse-filtering reduced CBOD for samples with high particulate carbon and high biovolumes of Aphanizomenon flos-aquae . There was a strong positive correlation between BOD, CBOD, and the labile component of CBOD to particulate C and N, with weaker positive correlation to field pH, field dissolved oxygen, and total N. The refractory component of CBOD was not correlated to particulate matter, instead showing weak but statistically significant correlation to dissolved organic carbon, UV absorbance at 254 nm, and total N. Particulate organic matter, especially the alga A. flos-aquae , is an important component of oxygen demand in this reach of the Klamath River, though refractory dissolved organic matter would continue to exert an oxygen demand over longer time periods and as water travels downstream.

Oregon↗

Introduction to the special issue on ‘Frontiers in gas geochemistry’

The study of the geochemistry of gases pervades the Earth and Environmental Sciences. This is due in no small measure to the well-established thermodynamic properties of gases which allow their application to a variety of processes occurring over a wide spectrum of natural conditions. In this respect, both major and associated minor gases have been proven useful: indeed, the trace gases have been particularly important given their role as sensitive geochemical tracers. Examples where gas geochemistry places key constraints on geochemical processes include the degassing history of the solid Earth to form the atmosphere and oceans, the origin and migration characteristics of hydrocarbon deposits, the scale of climate variability, the P–T characteristics of geothermal reservoirs, and the dynamics of the earthquake cycle and volcanic activity, to name but a few. This volume continues this rich tradition with an eclectic selection of papers aimed at exploring and exploiting gas geochemistry over a myriad set of research themes.

Chemical Geology↗

Splint coals of the Central Appalachians: Petrographic and geochemical facies of the Peach Orchard No. 3 split coal bed, southern Magoffin County, Kentucky

The Bolsovian (Middle Pennsylvanian) Peach Orchard coal bed is one of the splint coals of the Central Appalachians. Splint coal is a name for the dull, inertinite-rich lithologies typical of coals of the region. The No. 3 Split was sampled at five locations in Magoffin County, Kentucky and analyzed for petrography and major and minor elements. The No. 3 Split coals contain semifusinite-rich lithologies, up to 48% (mineral-free basis) in one case. The nature of the semifusinite varies with position in the coal bed, containing more mineral matter of detrital origin in the uppermost durain. The maceral assemblage of these terminal durains is dominated by detrital fusinite and semifusinite, suggesting reworking of the maceral assemblage coincident with the deposition of the detrital minerals. However, a durain in the middle of the coal bed, while lithologically similar to the uppermost durains, has a degraded, macrinite-rich, texture. The inertinite macerals in the middle durain have less distinct edges than semifusinites in the uppermost terminal durains, suggesting degradation as a possible path to inertinite formation. The uppermost durain has higher ash and semifusinite contents at the eastern sites than at the western sites. The difference in the microscopic petrology indicates that megascopic petrology alone can be a deceptive indicator of depositional environments and that close attention must be paid to the individual macerals and their implications for the depositional setting, especially within the inertinite group.

International Journal of Coal Geology↗

Review and update of the applications of organic petrology: Part 1, geological applications

Organic petrology developed as coal petrology at the beginning of the 20th century dedicated mainly to the study of coals because of their utilization in industry. Coal petrology was then considered a branch of coal science. Later, with the development of specialized nomenclature, classification of coal components, and the standardization and improvement of analytical (microscopical) methods, this discipline expanded in interests and name, becoming organic petrology. Organic petrology carries a broader context, being as well a tool applied in the study of dispersed organic matter in sedimentary rocks due to its importance in exploration for fossil fuel resources. At present, organic petrology is a discipline widely recognized for its role in fundamental and applied research with respect to both coal utilization and in geosciences. Throughout the 20th century several important monographs have been published on the discipline of organic petrology, including “Stach's textbook of coal petrology” (1st edition 1935, 2nd 1975, 3rd 1982), updated as the more general “Organic petrology” by Taylor et al. (1998). More recently, the text “Applied coal petrology: the role of petrology in coal utilization” was published by Suárez-Ruiz and Crelling (2008). This review is the first in a two-part review series that describes and updates the role of organic petrology in geosciences. A second part complementing this one and focused on the applications of organic petrology to other scientific fields will follow.

International Journal of Coal Geology↗

Relating systematic molecular and textural properties of graptolite pyrolyzed via gold tube hydrous pyrolysis: Implications for thermal proxies in lower Paleozoic marine shales

A series of gold tube pyrolysis experiments (72 h, 300–550 °C, 50 MPa) conducted on a graptolite-rich lower Paleozoic marine shale generated pyrolysis residues for a comprehensive evaluation of the molecular and structural variability of three types of graptolite periderm. Organic petrology, Raman spectroscopy, and field emission scanning electron microscopy (FE-SEM) with energy dispersive spectroscopy (EDS) were combined to evaluate the thermal evolution process. The three types of graptolite periderm, namely granular, non-granular, and nodular graptolite, were analyzed by Raman spectroscopy wherein point measurements were obtained after the maceral was identified and the location verified by organic petrology. Distinct thermal evolution pathways among non-granular, granular, and nodular graptolite periderms were recorded. The evolution patterns of the Raman parameters, particularly D1 and G bands, highlight the differences in geochemical composition of the graptolite periderm types and the alteration of molecular structure with increasing thermal maturity. Raman parameters D1 (position of the D1 peak), G-FWHM (full width at half maximum of the G peak), and ratios D1-FWHM/G-FWHM (full width at half maximum of the D1 peak ratioed to G-FWHM) and A D1 /A G (ratio of D1 and G peak intensities) showed effectiveness in assessing thermal maturity. Bireflectance with increasing gold tube pyrolysis temperature followed a hierarchy: non-granular > granular > nodular, reflecting different molecular alignment intensities. Qualitative FE-SEM evaluation showed that fine-grained mineral inclusions (primarily Fe-sulfide as determined via EDS) were associated with the graptolite populations, with granular graptolite containing greater amounts of coarser-grained (e.g., ∼300–1400 nm) mineral inclusions relative to non-granular and nodular graptolite, which contain finer-grained (e.g., ∼100–200 nm) inclusions difficult to resolve with optical microscopy. These findings are investigated to highlight the mechanisms that drive organic matter evolution within graptolite during thermal maturation, as well as to explore some of the limitations of using spectroscopic parameters as thermal maturity proxies.

International Journal of Coal Geology↗

Strong nonlinear photonic responses from microbiologically synthesized tellurium nanocomposites

A new class of nanomaterials, namely microbiologically-formed nanorods composed of elemental tellurium [Te(0)] that forms unusual nanocomposites when combined with poly(m-phenylenevinylene-co-2,5-dioctoxy-phenylenevinylene) (PmPV) is described. These bio-nanocomposites exhibit excellent broadband optical limiting at 532 and 1064 nm. Nonlinear scattering, originating from the laser induced solvent bubbles and microplasmas, is responsible for this nonlinear behavior. The use of bacterially-formed Te(0) when combined with an organic chemical host (e.g., PmPV) is a new green method of nanoparticle syntheses. This opens the possibilities of using unique, biologically synthesized materials to advance future nanoelectronic and nanophotonic applications.

Chemical Physics Letters↗

The Cretaceous Tetori biota in Japan and its evolutionary significance for terrestrial ecosystems in Asia

Cretaceous nonmarine deposits are widely distributed on the Asian continent and include various kinds of zoo- and phyto-assemblages. The Tetori Group is one of the most important Mesozoic terrestrial deposits in East Asia, and for this reason its geology, stratigraphy, and biota have been studied intensively by our group for more than a decade. We present the main results herein. We confirm that formations as lithostratigraphic units are the best geological correlation tools for the Tetori Group and the best tools for a geological mapping of the group. Although subgroups have previously been used for correlation, proper designation and evaluation of subgroups is required if they are to be used effectively, and we show that previous geological correlation of the Tetori Group has been confused by inappropriate definition of these subgroups. We located fossil localities including reported zoo- and phyto-assemblages in the framework of formations correlated by our stratigraphy. The occurrence of zoo-assemblages was probably controlled by environments (i.e., most are in situ), but phyto-assemblages were mostly transported and rapidly buried by high-energy river systems. Although two distinct dinosaur faunas and four floras have been named for the zoo- and phyto-assemblages in the Tetori Group, in reality there is only one Tetori Dinosaur Fauna and one Tetori Flora, as proved by careful correlation. Two types of zoo-assemblages co-occur in the Tetori Group: vertebrate species whose ancestors flourished in the Jurassic (as found in China), and their descendants from the Late Cretaceous. As the latter modern type of assemblage is more abundant than the former, changeable environments at the continental margin probably accelerated evolution of more modern species. We can employ nonmarine molluscan species as geological correlation tools in some cases, i.e., when their taxon ranges are well-confirmed by independent evidence. However, because freshwater molluscan species and terrestrial vertebrate species had many opportunities to move to optimum habitat as environments changed through time on the Cretaceous Asian continent, their correlation potential is uncertain. Many nonmarine molluscan species from the Japanese and Chinese Cretaceous had their stratigraphic occurrences controlled by changing environments. ?? 2005 Elsevier Ltd. All rights reserved.

Cretaceous Research↗

New frontiers in bird migration research

Bird migrations are impressive behavioral phenomena, representing complex spatiotemporal strategies to balance costs of living while maximizing fitness. The field of bird migration research has made great strides over the past decades, yet fundamental gaps remain. Technologies have sparked a transformation in the study of bird migration research by revealing remarkable insights into the underlying behavioral, cognitive, physiological and evolutionary mechanisms of these diverse journeys. Here, we aim to encourage broad discussions and promote future studies by highlighting research fields that are characterized by major knowledge gaps or conflicting evidence, namely the fields of navigation, social learning, individual development, energetics and conservation. We approach each topic by summarizing the current state of knowledge and provide a future outlook of ideas and state-of-the-art methods to further advance the field. Integrating knowledge across these disciplines will allow us to understand the adaptive abilities of different species and to develop effective conservation strategies in a rapidly changing world.

Current Biology↗

Secular trends in the geologic record and the supercontinent cycle

Geologic secular trends are used to refine the timetable of supercontinent assembly, tenure, and breakup. The analysis rests on what is meant by the term supercontinent, which here is defined broadly as a grouping of formerly dispersed continents. To avoid the artificial pitfall of an all-or-nothing definition, quantitative measures of “supercontinentality” are presented: the number of continents, and the area of the largest continent, which both can be gleaned from global paleogeographic maps for the Phanerozoic. For the secular trends approach to be viable in the deep past when the very existence of supercontinents is debatable and reconstructions are fraught with problems, it must first be calibrated in the Phanerozoic against the well-constrained Pangea supercontinent cycle. The most informative geologic variables covering both the Phanerozoic and Precambrian are the abundances of passive margins and of detrital zircons. Both fluctuated with size of the largest continent during the Pangea supercontinent cycle and can be quantified back to the Neoarchean. The tenure of Pangea was a time represented in the rock record by few zircons and few passive margins. Thus, previously documented minima in the abundance of detrital zircons (and orogenic granites) during the Precambrian (Condie et al., 2009a, Gondwana Research 15, 228–242) now can be more confidently interpreted as marking the tenures of supercontinents. The occurrences of carbonatites, granulites, eclogites, and greenstone-belt deformation events also appear to bear the imprint of Precambrian supercontinent cyclicity. Together, these secular records are consistent with the following scenario. The Neoarchean continental assemblies of Superia and Sclavia broke up at ca. 2300 and ca. 2090 Ma, respectively. Some of their fragments collided to form Nuna by about 1750 Ma; Nuna then grew by lateral accretion of juvenile arcs during the Mesoproterozoic, and was involved in a series of collisions at ca. 1000 Ma to form Rodinia. Rodinia broke up in stages from ca. 1000 to ca. 520 Ma. Before Rodinia had completely come apart, some of its pieces had already been reassembled in a new configuration, Gondwana, which was completed by 530 Ma. Gondwana later collided with Laurentia, Baltica, and Siberia to form Pangea by about 300 Ma. Breakup of Pangea began at about 180 Ma (Early Jurassic) and continues today. In the suggested scenario, no supercontinent cycle in Earth history corresponded to the ideal, in which all the continents were gathered together, then broke apart, then reassembled in a new configuration. Nuna and Gondwana ended their tenures not by breakup but by collision and name change; Rodinia's assembly overlapped in time with its disassembly; and Pangea spalled Tethyan microcontinents throughout much of its tenure. Many other secular trends show a weak or uneven imprint of the supercontinent cycle, no imprint at all. Instead, these secular trends together reveal aspects of the shifting background against which the supercontinents came and went, making each cycle unique. Global heat production declined; plate tectonics sped up through the Proterozoic and slowed down through the Phanerozoic; the atmosphere and oceans became oxidized; life emerged as a major geochemical agent; some rock types went extinct or nearly so (BIF, massif-type anorthosite, komatiite); and other rock types came into existence or became common (blueschists, bioclastic limestone, coal).

Earth-Science Reviews↗

A reporting format for leaf-level gas exchange data and metadata

Leaf-level gas exchange data support the mechanistic understanding of plant fluxes of carbon and water. These fluxes inform our understanding of ecosystem function, are an important constraint on parameterization of terrestrial biosphere models, are necessary to understand the response of plants to global environmental change, and are integral to efforts to improve crop production. Collection of these data using gas analyzers can be both technically challenging and time consuming, and individual studies generally focus on a small range of species, restricted time periods, or limited geographic regions. The high value of these data is exemplified by the many publications that reuse and synthesize gas exchange data, however the lack of metadata and data reporting conventions make full and efficient use of these data difficult. Here we propose a reporting format for leaf-level gas exchange data and metadata to provide guidance to data contributors on how to store data in repositories to maximize their discoverability, facilitate their efficient reuse, and add value to individual datasets. For data users, the reporting format will better allow data repositories to optimize data search and extraction, and more readily integrate similar data into harmonized synthesis products. The reporting format specifies data table variable naming and unit conventions, as well as metadata characterizing experimental conditions and protocols. For common data types that were the focus of this initial version of the reporting format, i.e., survey measurements, dark respiration, carbon dioxide and light response curves, and parameters derived from those measurements, we took a further step of defining required additional data and metadata that would maximize the potential reuse of those data types. To aid data contributors and the development of data ingest tools by data repositories we provided a translation table comparing the outputs of common gas exchange instruments. Extensive consultation with data collectors, data users, instrument manufacturers, and data scientists was undertaken in order to ensure that the reporting format met community needs. The reporting format presented here is intended to form a foundation for future development that will incorporate additional data types and variables as gas exchange systems and measurement approaches advance in the future. The reporting format is published in the U.S. Department of Energy's ESS-DIVE data repository, with documentation and future development efforts being maintained in a version control system.

Ecological Informatics↗