Evidence of neutral transcriptome evolution in plants

The transcriptome of an organism is its set of gene transcripts (mRNAs) at a defined spatial and temporal locus. Because gene expression is affected markedly by environmental and developmental perturbations, it is widely assumed that transcriptome divergence among taxa represents adaptive phenotypic selection. This assumption has been challenged by neutral theories which propose that stochastic processes drive transcriptome evolution. To test for evidence of neutral transcriptome evolution in plants, we quantified 18 494 gene transcripts in nonsenescent leaves of 14 taxa of Brassicaceae using robust cross-species transcriptomics which includes a two-step physical and in silicobased normalization procedure based on DNA similarity among taxa. Transcriptome divergence correlates positively with evolutionary distance between taxa and with variation in gene expression among samples. Results are similar for pseudogenes and chloroplast genes evolving at different rates. Remarkably, variation in transcript abundance among root-cell samples correlates positively with transcriptome divergence among root tissues and among taxa. Because neutral processes affect transcriptome evolution in plants, many differences in gene expression among or within taxa may be nonfunctional, reflecting ancestral plasticity and founder effects. Appropriate null models are required when comparing transcriptomes in space and time

Sub-sampling a large physical soil archive for additional analyses to support spatial mapping; a pre-registered experiment in the Southern Nations, Nationalities, and Peoples Region (SNNPR) of Ethiopia

The value of physical archives of soil material from field sampling activities has been widely recognized. If we want to use archive material for new destructive analyses to support a task, such as spatial mapping, then an efficient sub-sampling strategy is needed, both to manage analytical costs and to conserve the archive material. In this paper we present an approach to this problem when the objective is spatial mapping by ordinary kriging. Our objective was to subsample the physical archive from the Ethiopia Soil Information System (EthioSIS) survey of the Southern Nations, Nationalities and Peoples Region (SNNPR) for spatial mapping of two variables, concentrations of particular fractions of selenium and iodine in the soil, which had not been measured there. We used data from cognate parts of surrounding regions of Ethiopia to estimate variograms of these properties, and then computed prediction error variances for maps in SNNPR based on proposed subsets of the archive of different size, selected to optimize a spatial coverage criterion (with some close sample pairs included). On this basis a subsample was selected. This is a preregistered experiment in that we have proposed criteria for evaluating the success of our approach, and are publishing that in advance of receiving analytical data on the subsampled material from the laboratories where they are being processed. A subsequent short report will publish the outcome. The use of preregistered trials is widely recommended and used in areas of science including public health, and we believe that it is a sound strategy to promote reproducible research in soil science

An evaluation of the C/N ratio of the mantle from natural CO2-rich gas analysis: Geochemical and cosmochemical implications

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Marty, B., Almayrac, M., Barry, P. H., Bekaert, D., V., Broadley, M. W., Byrne, D. J., Ballentine, C. J., & Caracausi, A. An evaluation of the C/N ratio of the mantle from natural CO2-rich gas analysis: Geochemical and cosmochemical implications. Earth and Planetary Science Letters, 551, (2020): 116574, doi:10.1016/j.epsl.2020.116574.The terrestrial carbon to nitrogen ratio is a key geochemical parameter that can provide information on the nature of Earth's precursors, accretion/differentiation processes of our planet, as well as on the volatile budget of Earth. In principle, this ratio can be determined from the analysis of volatile elements trapped in mantle-derived rocks like mid-ocean ridge basalts (MORB), corrected for fractional degassing during eruption. However, this correction is critical and previous attempts have adopted different approaches which led to contrasting C/N estimates for the bulk silicate Earth (BSE) (Marty and Zimmermann, 1999; Bergin et al., 2015). Here we consider the analysis of CO2-rich gases worldwide for which a mantle origin has been determined using noble gas isotopes in order to evaluate the C/N ratio of the mantle source regions. These gases experienced little fractionation due to degassing, as indicated by radiogenic 4He / 40Ar* values (where 4He and 40Ar* are produced by the decay of U+Th, and 40K isotopes, respectively) close to the mantle production/accumulation values. The C/N and C/3 He ratios of gases investigated here are within the range of values previously observed in oceanic basalts. They point to an elevated mantle C/N ratio (∼350-470, molar) higher than those of potential cosmochemical accretionary endmembers. For example, the BSE C/N and 36 Ar / N ratios (160-220 and 75 x 10-7, respectively) are higher than those of CM-CI chondrites but within the range of CV-CO groups. This similarity suggests that the Earth accreted from evolved planetary precursors depleted in volatile and moderately volatile elements. Hence the high C / N composition of the BSE may be an inherited feature rather than the result of terrestrial differentiation. The C / N and 36 Ar / N ratios of the surface (atmosphere plus crust) and of the mantle cannot be easily linked to any known chondritic composition. However, these compositions are consistent with early sequestration of carbon into the mantle (but not N and noble gases), permitting the establishment of clement temperatures at the surface of our planet.M.A, D.V.B, M.W.B, D.J.B and B.M were supported by the European Research Council (PHOTONIS project, grant agreement No. 695618 to B.M.). Samples were collected as part of Study # YELL-08056 - Xenon anomalies in the Yellowstone Hotspot. We would like to thank Annie Carlson and all of the rangers at the Yellowstone National Park for providing invaluable advice and help when collecting the samples. This work was partially supported by a grant (G-2016-7206) from the Alfred P. Sloan Foundation and the Deep Carbon Observatory to P.H.B as well as NSF award 2015789 to P.H.B.. Sampling at Mt. Etna and gas analysis was supported by Instituto Nazionale di Geofisica e Vulcanologia Palermo. Fruitful discussions with Marc Hirschmann helped us to shape the ideas presented in this work. We acknowledge detailed and insightful reviews by Sami Mikhail and an anonymous reviewer, and efficient editing by Frederic Moynier. This is CRPG contribution 2741

Agronomic biofortification increases grain zinc concentration of maize grown under contrasting soil types in Malawi

Zinc (Zn) deficiency remains a public health problem in Malawi, especially among poor and marginalized rural populations, linked with low dietary intake of Zn due to consumption of staple foods that are low in Zn content. The concentration of Zn in staple cereal grain can be increased through application of Zn-enriched fertilizers, a process called agronomic biofortification or agro-fortification. Field experiments were conducted at three Agricultural Research Station sites to assess the potential of agronomic biofortification to improve Zn concentration in maize grain in Malawi as described in registered report published previously. The hypotheses of the study were (i) that application of Zn-enriched fertilizers would increase in the concentration of Zn in maize grain to benefit dietary requirements of Zn and (ii) that Zn concentration in maize grain and the effectiveness of agronomic biofortification would be different between soil types. At each site two different subsites were used, each corresponding to one of two agriculturally important soil types of Malawi, Lixisols and Vertisols. Within each subsite, three Zn fertilizer rates (1, 30, and 90 kg ha−1) were applied to experimental plots, using standard soil application methods, in a randomized complete block design. The experiment had 10 replicates at each of the three sites as informed by a power analysis from a pilot study, published in the registered report for this experiment, designed to detect a 10% increase in grain Zn concentration at 90 kg ha−1, relative to the concentration at 1 kg ha−1. At harvest, maize grain yield and Zn concentration in grain were measured, and Zn uptake by maize grain and Zn harvest index were calculated. At 30 kg ha−1, Zn fertilizer increased maize grain yields by 11% compared with nationally recommended application rate of 1 kg ha−1. Grain Zn concentration increased by 15% and uptake by 23% at the application rate of 30 kg ha−1 relative to the national recommendation rate. The effects of Zn fertilizer application rate on the response variables were not dependent on soil type. The current study demonstrates the importance of increasing the national recommendation rate of Zn fertilizer to improve maize yield and increase the Zn nutritional value of the staple crop

Communication Biophysics

Contains reports on five research projects.National Institutes of Health (Grant 5 RO1 NB-05462-02)National Aeronautics and Space Administration (Grant NsG-496)National Science Foundation (Grant GP-2495)National Institutes of Health (Grant MH-04737-05

Dietary mineral supplies in Malawi: spatial and socioeconomic assessment

Background Dietary mineral deficiencies are widespread globally causing a large disease burden. However, estimates of deficiency prevalence are often only available at national scales or for small population sub-groups with limited relevance for policy makers. Methods This study combines food supply data from the Third Integrated Household Survey of Malawi with locally-generated food crop composition data to derive estimates of dietary mineral supplies and prevalence of inadequate intakes in Malawi. Results We estimate that >50 % of households in Malawi are at risk of energy, calcium (Ca), selenium (Se) and/or zinc (Zn) deficiencies due to inadequate dietary supplies, but supplies of iron (Fe), copper (Cu) and magnesium (Mg) are adequate for >80 % of households. Adequacy of iodine (I) is contingent on the use of iodised salt with 80 % of rural households living on low-pH soils had inadequate dietary Se supplies compared to 55 % on calcareous soils; concurrent inadequate supplies of Ca, Se and Zn were observed in >80 % of the poorest rural households living in areas with non-calcareous soils. Prevalence of inadequate dietary supplies was greater in rural than urban households for all nutrients except Fe. Interventions to address dietary mineral deficiencies were assessed. For example, an agronomic biofortification strategy could reduce the prevalence of inadequate dietary Se supplies from 82 to 14 % of households living in areas with low-pH soils, including from 95 to 21 % for the poorest subset of those households. If currently-used fertiliser alone were enriched with Se then the prevalence of inadequate supplies would fall from 82 to 57 % with a cost per alleviated case of dietary Se deficiency of ~ US$ 0.36 year−1. Conclusions Household surveys can provide useful insights into the prevalence and underlying causes of dietary mineral deficiencies, allowing disaggregation by spatial and socioeconomic criteria. Furthermore, impacts of potential interventions can be modelled

Assessing the residual benefit of soil-applied zinc on grain zinc nutritional quality of maize grown under contrasting soil types in Malawi.

A proper understanding of the residual value of zinc (Zn) is necessary for sustainable biofortification of food crops. This study aimed to establish the extent to which application of Zn at the national rate, plus two experimentally elevated rates, in one year provided any benefit to plant yield and nutritional quality in the following growing season. Residual effects of soil-applied Zn on grain Zn concentration and uptake were estimated by an experiment in which maize was grown in successive seasons at two agricultural research stations in Malawi, with Zn applied to the soil in the first season but not the second. At each site two common soil types were used: Lixisols and Vertisols. The study used three Zn fertilizer rates of 1, 30 and 90 kg Zn ha -1 applied to the soil in the previous cropping season, arranged in a randomized complete block design (RCBD) with 10 replications at each experimental site. At harvest, maize grain yield and Zn concentration in grain and stover were measured; Zn uptake by maize grain and stover were determined and Zn harvest index was calculated. Effects on grain yield and Zn uptake by the crop were assessed in relation to residual Zn fertilizer and soil type. Maize grain yield on plots in the second season where 30 kg Zn ha -1 had been applied exceeded that on second season plots where 1 kg Zn ha -1 had been applied by 25%. The grain Zn concentration and Zn uptake in the second season after fertilizer application were larger by 13% and 30% respectively on the plots which had received 30 kg Zn ha -1 than those which had received 1 kg Zn ha -1 . There was no evidence that applying Zn at 90 kg Zn ha -1 resulted in larger crop yield, grain Zn concentration, or Zn uptake the second year after application than was seen in plots the second year after application of 30 kg Zn ha -1 . The magnitude of the benefits attributed to residual effects of soil-applied Zn did not depend on soil type. Conclusively, the residual effects of 30 kg ha -1 of soil-applied Zn in the preceding season benefited the subsequent maize compared to the national recommendation of 1 kg Zn ha -1 . The benefits of larger applications of Zn than the current national recommendations should be considered across at least two seasons and for different crops

Topography-derived variables provide insight into habitat occupancy of a cryptic snake, Bitis atropos

Understanding species’ habitat use is fundamental for conservation and management. However, quantifying habitat use for small cryptic species is limited by imperfect detection during field surveys and the lack of habitat data at meaningful spatial scales. Topographically-derived habitat variables from digital elevation models (DEMs) have the potential to overcome these limitations. Here we used DEM-derived topographic variables as fine-scale proxies for abiotic conditions to study site-occupancy patterns of the berg adder (Bitis atropos), a small-bodied cryptic viper. We carried out seven repeated field surveys across 219 hectares in a mountainous protected area in north-eastern South Africa to estimate snake detection probability and occupancy using maximum likelihood methods. Although snakes occurred across a third of the surveyed habitat, they were only detected 40% of the time during the springtime when detection was highest. Results showed that these snakes preferred north-west facing, mid and upper slopes, which are exposed to afternoon sun and presumably higher ambient energy. Our results demonstrate the value of using DEM-derived topographic variables for ecological studies where habitat data are either unavailable or inappropriate, thereby providing valuable insights into habitat use of cryptic and difficult to detect species