Pressing environmental research questions demand the integration of increasingly diverse and large-scale ecological datasets as well as complex analytical methods, which require specialized tools and resources. Computational training for ecological and evolutionary sciences has become more abundant and accessible over the past decade, but tool development has outpaced the availability of specialized training. Most training for scripted analyses focuses on individual analysis steps in one script rather than creating a scripted pipeline, where modular functions comprise an ecosystem of interdependent steps. Although current computational training creates an excellent starting place, linear styles of scripting can risk becoming labor- and time-intensive and less reproducible by often requiring manual execution. Pipelines, however, can be easily automated or tracked by software to increase efficiency and reduce potential errors. Ecology and evolution would benefit from techniques that reduce these risks by managing analytical pipelines in a modular, readily parallelizable format with clear documentation of dependencies. Workflow management software (WMS) can aid in the reproducibility, intelligibility and computational efficiency of complex pipelines. To date, WMS adoption in ecology and evolutionary research has been slow. We discuss the benefits and challenges of implementing WMS and illustrate its use through a case study with the targets r package to further highlight WMS benefits through workflow automation, dependency tracking and improved clarity for reviewers. Although WMS requires familiarity with function-oriented programming and careful planning for more advanced applications and pipeline sharing, investment in training will enable access to the benefits of WMS and impart transferable computing skills that can facilitate ecological and evolutionary data science at large scales.

Detrital chromites are commonly reported within Archean metasedimentary rocks, but have thus far garnered little attention for use in provenance studies. Systematic variations of Cr-Fe spinel mineral chemistry with changing tectonic setting have resulted in the extensive use of chromite as a petrogenetic indicator, and so detrital chromites represent good candidates to investigate the petrogenesis of eroded Archean mafic and ultramafic crust. Here, we report the compositions of detrital chromites within fuchsitic (Cr-muscovite rich) metasedimentary rocks from the Jack Hills, situated within the Narryer Terrane, Yilgarn Craton, Western Australia, which are geologically renowned for hosting Hadean (>4000 Ma) zircons. We highlight signatures of metamorphism, including highly elevated ZnO and MnO, coupled with lowered Mg# in comparison with magmatic chromites, development of pitted domains, and replacement of primary inclusions by phases that are part of the metamorphic assemblages within host metasedimentary rocks. Oxygen isotope compositions of detrital chromites record variable exchange with host metasedimentary rocks. The variability of metamorphic signatures between chromites sampled only meters apart further indicates that modification occurred in situ by interaction of detrital chromites with metamorphic fluids and secondary mineral assemblages. Alteration probably occurred during upper greenschist to lower amphibolite facies metamorphism and deformation of host metasedimentary rocks at similar to 2650 Ma. Regardless of metamorphic signatures, sampling location or grain shape, chromite cores yield a consistent range in Cr#. Although other key petrogenetic indices, such as Fe2O3 and TiO2 contents, are complicated in Jack Hills chromites by mineral non-stoichiometry and secondary mobility within metasedimentary rocks, we demonstrate that the Cr# of chromite yields significant insights into their provenance. Importantly, moderate Cr# (typically 55-70) precludes a komatiitic origin for the bulk of chromites, reflecting a dearth of komatiites and intrusive equivalents within the erosional catchment of the Jack Hills metasedimentary units. We suggest that the Cr# of Jack Hills chromite fits well with chromites derived from layered intrusions, and that a single layered intrusion may account for the observed chemical compositions of Jack Hills detrital chromites. Where detailed characterization of key metamorphic signatures is undertaken, detrital chromites preserved within Archean metasedimentary rocks may therefore yield valuable information on the petrogenesis and geodynamic setting of poorly preserved mafic and ultramafic crust.

The release of phosphorus (P) from crustal rocks during weathering plays a key role in determining the size of Earth's biosphere, yet the concentration of P in crustal rocks over time remains controversial. Here, we combine spatial, temporal, and chemical measurements of preserved rocks to reconstruct the lithological and chemical evolution of Earth's continental crust. We identify a threefold increase in average crustal P concentrations across the Neoproterozoic-Phanerozoic boundary (600 to 400 million years), showing that preferential biomass burial on shelves acted to progressively concentrate P within continental crust. Rapid compositional change was made possible by massive removal of ancient P-poor rock and deposition of young P-rich sediment during an episode of enhanced global erosion. Subsequent weathering of newly P-rich crust led to increased riverine P fluxes to the ocean. Our results suggest that global erosion coupled to sedimentary P-enrichment forged a markedly nutrient-rich crust at the dawn of the Phanerozoic.

There are no planets intermediate in size between Earth and Neptune in our Solar System, yet these objects are found around a substantial fraction of other stars1. Population statistics show that close-in planets in this size range bifurcate into two classes on the basis of their radii2,3. It is proposed that the group with larger radii (referred to as 'sub-Neptunes') is distinguished by having hydrogen-dominated atmospheres that are a few percent of the total mass of the planets4. GJ 1214b is an archetype sub-Neptune that has been observed extensively using transmission spectroscopy to test this hypothesis5-14. However, the measured spectra are featureless, and thus inconclusive, due to the presence of high-altitude aerosols in the planet's atmosphere. Here we report a spectroscopic thermal phase curve of GJ 1214b obtained with the James Webb Space Telescope (JWST) in the mid-infrared. The dayside and nightside spectra (average brightness temperatures of 553±9 and 437±19K, respectively) each show more than 3sigma evidence of absorption features, with H2O as the most likely cause in both. The measured global thermal emission implies that GJ 1214b's Bond albedo is 0.51±0.06. Comparison between the spectroscopic phase curve data and three-dimensional models of GJ 1214b reveal a planet with a high metallicity atmosphere blanketed by a thick and highly reflective layer of clouds or haze.

The urban heat island (UHI) effect is an important topic for many cities across the globe. Previous studies, however, have mostly focused on UHI changes along either the spatial or temporal dimension. A simultaneous evaluation of the spatial and temporal variations is essential for understanding the long-term impacts of land cover on the UHI. This study presents the first evaluation and application of a newly developed spatiotemporal weighted regression framework (STWR), the performance of which was tested against conventional models including the ordinary least squares (OLS) and the geographically weighted regression (GWR) models. We conducted a series of simulation tests followed by an empirical study over central Phoenix, AZ. The results show that the STWR model achieves better parameter estimation and response prediction results with significantly smaller errors than the OLS and GWR models. This finding holds true when the regression coefficients are constant, spatially heterogeneous, and spatiotemporally heterogeneous. The empirical study reveals that the STWR model provides better model fit than the OLS and GWR models. The LST has a negative relationship with GNDVI and LNDVI and a positive relationship with GNDBI for the three years studied. Over the last 20 years, the cooling effect from green vegetation has weakened and the warming effect from built-up features has intensified. We suggest the wide adoption of the STWR model for spatiotemporal studies, as it uses past observations to reduce uncertainty and improve estimation and prediction results.

Plants often adapt to adverse or stress conditions via differential growth. The trans-Golgi Network (TGN) has been implicated in stress responses, but it is not clear in what capacity it mediates adaptive growth decisions. In this study, we assess the role of the TGN in stress responses by exploring the interactome of the Transport Protein Particle II (TRAPPII) complex, required for TGN structure and function. We identified physical and genetic interactions between TRAPPII and shaggy-like kinases (GSK3/AtSKs). Kinase assays and pharmacological inhibition provided in vitro and in vivo evidence that AtSKs target the TRAPPII-specific subunit AtTRS120/TRAPPC9. GSK3/AtSK phosphorylation sites in AtTRS120/TRAPPC9 were mutated, and the resulting AtTRS120 phosphovariants subjected to a variety of single and multiple stress conditions in planta. The non-phosphorylatable TRS120 mutant exhibited enhanced adaptation to multiple stress conditions and to osmotic stress whereas the phosphomimetic version was less resilient. Higher order inducible trappii atsk mutants had a synthetically enhanced defect in root gravitropism. Our results suggest that the TRAPPII phosphostatus mediates adaptive responses to abiotic cues. AtSKs are multifunctional kinases that integrate a broad range of signals. Similarly, the TRAPPII interactome is vast and considerably enriched in signaling components. An AtSKTRAPPII interaction would integrate all levels of cellular organization and instruct the TGN, a central and highly discriminate cellular hub, as to how to mobilize and allocate resources to optimize growth and survival under limiting or adverse conditions.

When brassinosteroid levels are low, the GSK3-like kinase BIN2 phosphorylates and in activates the BZR1 transcription factor to inhibit growth in plants. Brassinosteroid promotes growth by inducing dephosphorylation of BZR1, but the phosphatase that dephosphorylates BZR1 has remained unknown. Here, using tandem affinity purification, we identified protein phosphatase 2A (PP2A) as a BZR1-interacting protein. Genetic analyses demonstrated a positive role for PP2A in brassinosteroid signalling an BZR1 dephosphorylation. Members of the B' regulatory subunits of PP2A directly interact with BZR1's putative PEST domain containing the site of the bzr1-1D mutation. Interaction with and dephosphorylation by PP2A are enhanced by the bzr1-1D mutation, reduced by two intragenic bzr1-1D suppress or mutations, and abolished by deletion of the PEST domain. This study reveals a crucial function for PP2A in dephosphorylating and activating BZR1 and completes the set of core components of the brassinosteroid-signalling cascade from cell surface receptor kinase to gene regulation in the nucleus.

Brassinosteroid (BR) binding activates the receptor kinase BRI1 by inducing heterodimerization with its co-receptor kinase BAK1; however, the mechanisms that reversibly inactivate BRI1 remain unclear. Here we show that cytoplasm-localized protein phosphatase 2A (PP2A) B' regulatory subunits interact with BRI1 to mediate its dephosphorylation and inactivation. Loss-of-function and overexpression experiments showed that a group of PP2A B' regulatory subunits, represented by B'eta, negatively regulate BR signaling by decreasing BRI1 phosphorylation. BR increases the expression levels of these B' subunits, and B'eta interacts preferentially with phosphorylated BRI1, suggesting that the dynamics of BR signaling are modulated by the PP2A-mediated feedback inactivation of BRI1. Compared with PP2A B'alpha and B'beta, which promote BR responses by dephosphorylating the downstream transcription factor BZR1, the BRI1inactivating B' subunits showed similar binding to BRI1 and BZR1 but distinct subcellular localization. Alteration of the nuclear/ cytoplasmic localization of the B' subunits revealed that cytoplasmic PP2A dephosphorylates BRI1 and inhibits the BR response, whereas nuclear PP2A dephosphorylates BZR1 and activates the BR response. Our findings not only identify the PP2A regulatory B subunits that mediate the binding and dephosphorylation of BRI1, but also demonstrate that the subcellular localization of PP2A specifies its substrate selection and distinct effects on BR signaling.

The aim of this paper is to study the transport of nitrous oxide (N2O) from the Asian surface to the eastern Mediterranean Basin (MB). We used measurements from the spectrometer Thermal and Near infrared Sensor for carbon Observation Fourier transform spectrometer on board the Greenhouse gases Observing SATellite (GOSAT) over the period of 2010-2013. We also used the outputs from the chemical transport model LMDz-OR-INCA over the same period. By comparing GOSAT upper tropospheric retrievals to aircraft measurements from the High-performance Instrumented Airborne Platform for Environmental Research Pole-to-Pole Observations, we calculated a GOSAT High-performance Instrumented Airborne Platform for Environmental Research standard deviation (SD error) of similar to 2.0ppbv for a single pixel and a mean bias of approximately -1.3ppbv (approximately -0.4%). This SD error is reduced to similar to 0.1ppbv when we average the pixels regionally and monthly over the MB. The use of nitrogen fertilizer coupled with high soil humidity during the summer Asian monsoon produces high N2O emissions, which are transported from Asian surfaces to the eastern MB. This summertime enrichment over the eastern MB produces a maximum in the difference between the eastern and the western MB upper tropospheric N2O (east-west difference) in July in both the measurements and the model. N2O over the eastern MB can therefore be considered as a footprint of Asian summertime emissions. However, the peak-to-peak amplitude of the east-west difference observed by GOSAT (similar to 1.40.3ppbv) is larger than that calculated by LMDz-OR-INCA (similar to 0.8ppbv). This is due to an underestimation of N2O emissions in the model and to a relatively coarse spatial resolution of the model that tends to underestimate the N2O accumulation into the Asian monsoon anticyclone.

The existence of massive (10(11) solar masses) elliptical galaxies by redshift z approximate to 4 (refs 1-3; when the Universe was 1.5 billion years old) necessitates the presence of galaxies with star-formation rates exceeding 100 solar masses per year at z > 6 (corresponding to an age of the Universe of less than 1 billion years). Surveys have discovered hundreds of galaxies at these early cosmic epochs, but their star-formation rates are more than an order of magnitude lower(4). The only known galaxies with very high star-formation rates at z > 6 are, with one exception(5), the host galaxies of quasars(6-9), but these galaxies also host accreting supermassive (more than 10(9) solar masses) black holes, which probably affect the properties of the galaxies. Here we report observations of an emission line of singly ionized carbon ([C II] at a wavelength of 158 micrometres) in four galaxies at z > 6 that are companions of quasars, with velocity offsets of less than 600 kilometres per second and linear offsets of less than 100 kiloparsecs. The discovery of these four galaxies was serendipitous; they are close to their companion quasars and appear bright in the far-infrared. On the basis of the [C II] measurements, we estimate star-formation rates in the companions of more than 100 solar masses per year. These sources are similar to the host galaxies of the quasars in [C II] brightness, linewidth and implied dynamical mass, but do not show evidence for accreting supermassive black holes. Similar systems have previously been found at lower redshift(10-12). We find such close companions in four out of the twenty-five z > 6 quasars surveyed, a fraction that needs to be accounted for in simulations(13,14). If they are representative of the bright end of the [C II] luminosity function, then they can account for the population of massive elliptical galaxies at z approximate to 4 in terms of the density of cosmic space.