The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species

Genes in durophage intersection set at 15 dpf. This is a comma separated table of the genes in the 15 dpf durophage intersection set. Given are edgeR results for each pairwise comparison. Columns indicating whether a gene is included in the intersection set at a threshold of 1.5 or 2 fold are provided. (CSV 13 kb

Long‐term phosphorus accumulation and removal efficiency in a land‐based wastewater treatment system in the UK

The study aims to assess the long‐term phosphorus (P) removal in a land treatment system (LTS) in the UK. Different sections of the site have been irrigated with wastewater effluent for different periods of time for up to 85 years. The amounts of P discharged and accumulated were calculated from historical data, estimations of water consumption, composition and soil measurement. The total P input during the study period was estimated to be 90 010 kg, the average P removal was 4% and there was no significant difference in the total P accumulated between plots irrigated for different periods, indicating that the sorption capacity of the soil might be saturated. Despite the low P retention rates in the LTS, there is no evidence that emissions from this system are affecting P concentrations in either the nearby river or the local chalk aquifer. Gaps remain, however, in performance optimisation and longevity forecasting

Molecular and cellular mechanisms underlying the evolution of form and function in the amniote jaw.

The amniote jaw complex is a remarkable amalgamation of derivatives from distinct embryonic cell lineages. During development, the cells in these lineages experience concerted movements, migrations, and signaling interactions that take them from their initial origins to their final destinations and imbue their derivatives with aspects of form including their axial orientation, anatomical identity, size, and shape. Perturbations along the way can produce defects and disease, but also generate the variation necessary for jaw evolution and adaptation. We focus on molecular and cellular mechanisms that regulate form in the amniote jaw complex, and that enable structural and functional integration. Special emphasis is placed on the role of cranial neural crest mesenchyme (NCM) during the species-specific patterning of bone, cartilage, tendon, muscle, and other jaw tissues. We also address the effects of biomechanical forces during jaw development and discuss ways in which certain molecular and cellular responses add adaptive and evolutionary plasticity to jaw morphology. Overall, we highlight how variation in molecular and cellular programs can promote the phenomenal diversity and functional morphology achieved during amniote jaw evolution or lead to the range of jaw defects and disease that affect the human condition

Thermal properties comparison of hybrid CF/FF and BF/FF cyanate ester-based composites

[EN] Insights within thermal expansion, conductivity, and decomposition dependencies with temperature on symmetrical and unsymmetrical layered carbon (CF) or basalt (BF) fabrics in combination with flax fibers (FF) were approached. Driven by commercial application and environmental concerns, the paper draws attention on a modified formula of cyanate ester with a common epoxy resin under an optimized ratio of 70:30 (vol%) as well as on the hybrid reinforcements stacking sequences. Synergetic effects were debated in terms of the CF and BF stacking sequences and corresponding volume fraction followed by comparisons with values predicted by the deployment of hybrid mixtures rules (RoHM/iRoHM). CF hybrid architectures revealed enhanced effective thermophysical properties over their BF counterparts and both over the FF-reinforced polymer composite considered as a reference. Thermal conductivities spread between 0.116 and 0.299 W m-1 K-1 from room temperature up to 250 C on all hybrid specimens, giving rise to an insulator character. Concerning the coefficient of thermal expansion, CF hybrid architectures disclosed values of 1.236 10-6 K-1 and 3.102 10-6 K-1 compared with BF affine exhibiting 4.794 10-6 K-1 and 6.245 10-6 K-1, respectively, with an increase in their volume fraction.The corresponding author gratefully acknowledges the financial assistance of German Academic Exchange Service-DAAD that enabled and supported the internship with Fraunhofer Research Institution for Polymeric Materials and Composites-PYCO, Germany. Many thanks go to Dr. Christian Dreyer and Dr. Maciej Gwiazda for the resin formula and access to the composite manufacturing technology.Motoc, DL.; Ferrándiz Bou, S.; Balart, R. (2018). Thermal properties comparison of hybrid CF/FF and BF/FF cyanate ester-based composites. 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North Andean origin and diversification of the largest ithomiine butterfly genus

The Neotropics harbour the most diverse flora and fauna on Earth. The Andes are a major centre of diversification and source of diversity for adjacent areas in plants and vertebrates, but studies on insects remain scarce, even though they constitute the largest fraction of terrestrial biodiversity. Here, we combine molecular and morphological characters to generate a dated phylogeny of the butterfly genus $\textit{Pteronymia}$ (Nymphalidae: Danainae), which we use to infer spatial, elevational and temporal diversification patterns. We first propose six taxonomic changes that raise the generic species total to 53, making $\textit{Pteronymia}$ the most diverse genus of the tribe Ithomiini. Our biogeographic reconstruction shows that $\textit{Pteronymia}$ originated in the Northern Andes, where it diversified extensively. Some lineages colonized lowlands and adjacent montane areas, but diversification in those areas remained scarce. The recent colonization of lowland areas was reflected by an increase in the rate of evolution of species' elevational ranges towards present. By contrast, speciation rate decelerated with time, with no extinction. The geological history of the Andes and adjacent regions have likely contributed to $\textit{Pteronymia}$ diversification by providing compartmentalized habitats and an array of biotic and abiotic conditions, and by limiting dispersal between some areas while promoting interchange across others.ME acknowledges financial support from ANR SPECREP and CNRS (France) and the Leverhulme trust (UK). LDS’s postdoc was funded by an ATIP (CNRS, France) grant awarded to ME. NC was funded by a doctoral grant from the Doctoral School 227 (Sciences de la Nature et de l’Homme: Evolution et Ecologie, France). KW acknowledges funding from NSF (DEB-0639861, DEB-0103746), the National Geographic Society, the Darwin Initiative and the Leverhulme Trust. A.V.L.F. thanks CNPq (fellowships 302585/2011-7 and 303834/2015-3), RedeLep-SISBIOTABrasil/CNPq (563332/2010-7), BR-BoL (MCT/CNPq/FNDCT 50/2010) and FAPESP (BIOTA-FAPESP Programs 2011/50225-3, 2012/50260-6 and 2013/50297-0). KLSB acknowledges support by FAPESP (2012/16266-6). Support for components of this work was provided through a collaborative grant, Dimensions US-Biota-São Paulo, supported by the US National Science Foundation (NSF DEB 1241056), National Aeronautics and Space Administration (NASA), and the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP Grant 2012/50260-6). Molecular work was performed at the GenePool (University of Edinburgh, UK), UCL (UK) and the Service of Molecular Systematics UMS2700 of the MNHN (France). Work by SK and TS to construct the original Solanaceae phylogeny was funded by the National Science Foundation (DEB-0316614)

Agronomic and Economic Performance Characteristics of Conventional and Low-External-Input Cropping Systems in the Central Corn Belt

We conducted a 9-ha field experiment near Boone, IA, to test the hypothesis that yield, weed suppression, and profit characteristics of low-external-input (LEI) cropping systems can match or exceed those of conventional systems. Over a 4-yr period, we compared a conventionally managed 2-yr rotation system {corn (Zea mays L.)/soybean [Glycine max (L.) Merr.]} with two LEI systems: a 3-yr corn/soybean/small grain + red clover (Trifolium pratense L.) rotation, and a 4-yr corn/soybean/small grain + alfalfa (Medicago sativa L.)/alfalfa rotation. Synthetic N fertilizer use was 59 and 74% lower in the 3- and 4-yr systems, respectively, than in the 2-yr system; similarly, herbicide use was reduced 76 and 82% in the 3- and 4-yr systems. Corn and soybean yields were as high or higher in the LEI systems as in the conventional system, and weed biomass in corn and soybean was low (≤4.2 g m−2) in all systems. Experimentally supplemented giant foxtail (Setaria faberi Herrm.) seed densities in the surface 20 cm of soil declined in all systems; supplemented velvetleaf (Abutilon theophrasti Medik.) seed densities declined in the 2- and 4-yr systems and remained unchanged in the 3-yr system. Without subsidy payments, net returns were highest for the 4-yr system ($540 ha−1 yr−1), lowest for the 3-yr system ($475 ha−1 yr−1), and intermediate for the 2-yr system ($504 ha−1 yr−1). With subsidies, differences among systems in net returns were smaller, as subsidies favored the 2-yr system, but rank order of the systems was maintained

Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle

As top predators, falcons possess unique morphological, physiological and behavioral adaptations that allow them to be successful hunters: for example, the peregrine is renowned as the world's fastest animal. To examine the evolutionary basis of predatory adaptations, we sequenced the genomes of both the peregrine (Falco peregrinus) and saker falcon (Falco cherrug), and we present parallel, genome-wide evidence for evolutionary innovation and selection for a predatory lifestyle. The genomes, assembled using Illumina deep sequencing with greater than 100-fold coverage, are both approximately 1.2 Gb in length, with transcriptome-assisted prediction of approximately 16,200 genes for both species. Analysis of 8,424 orthologs in both falcons, chicken, zebra finch and turkey identified consistent evidence for genome-wide rapid evolution in these raptors. SNP-based inference showed contrasting recent demographic trajectories for the two falcons, and gene-based analysis highlighted falcon-specific evolutionary novelties for beak development and olfaction and specifically for homeostasis-related genes in the arid environment–adapted saker

A Cross-Species Analysis of MicroRNAs in the Developing Avian Face

Higher vertebrates use similar genetic tools to derive very different facial features. This diversity is believed to occur through temporal, spatial and species-specific changes in gene expression within cranial neural crest (NC) cells. These contribute to the facial skeleton and contain species-specific information that drives morphological variation. A few signaling molecules and transcription factors are known to play important roles in these processes, but little is known regarding the role of micro-RNAs (miRNAs). We have identified and compared all miRNAs expressed in cranial NC cells from three avian species (chicken, duck, and quail) before and after species-specific facial distinctions occur. We identified 170 differentially expressed miRNAs. These include thirty-five novel chicken orthologs of previously described miRNAs, and six avian-specific miRNAs. Five of these avian-specific miRNAs are conserved over 120 million years of avian evolution, from ratites to galliforms, and their predicted target mRNAs include many components of Wnt signaling. Previous work indicates that mRNA gene expression in NC cells is relatively static during stages when the beak acquires species-specific morphologies. However, miRNA expression is remarkably dynamic within this timeframe, suggesting that the timing of specific developmental transitions is altered in birds with different beak shapes. We evaluated one miRNA:mRNA target pair and found that the cell cycle regulator p27KIP1 is a likely target of miR-222 in frontonasal NC cells, and that the timing of this interaction correlates with the onset of phenotypic variation. Our comparative genomic approach is the first comprehensive analysis of miRNAs in the developing facial primordial, and in species-specific facial development

Genome-Wide Genotype-Expression Relationships Reveal Both Copy Number and Single Nucleotide Differentiation Contribute to Differential Gene Expression between Stickleback Ecotypes

Repeated and independent emergence of trait divergence that matches habitat differences is a sign of parallel evolution by natural selection. Yet, the molecular underpinnings that are targeted by adaptive evolution often remain elusive. We investigate this question by combining genome-wide analyses of copy number variants (CNVs), single nucleotide polymorphisms (SNPs), and gene expression across four pairs of lake and river populations of the three-spined stickleback (Gasterosteus aculeatus). We tested whether CNVs that span entire genes and SNPs occurring in putative cis-regulatory regions contribute to gene expression differences between sticklebacks from lake and river origins. We found 135 gene CNVs that showed a significant positive association between gene copy number and gene expression, suggesting that CNVs result in dosage effects that can fuel phenotypic variation and serve as substrates for habitat-specific selection. Copy number differentiation between lake and river sticklebacks also contributed to expression differences of two immune-related genes in immune tissues, cathepsin A and GIMAP7. In addition, we identified SNPs in cis-regulatory regions (eSNPs) associated with the expression of 1,865 genes, including one eSNP upstream of a carboxypeptidase gene where both the SNP alleles differentiated and the gene was differentially expressed between lake and river populations. Our study highlights two types of mutations as important sources of genetic variation involved in the evolution of gene expression and in potentially facilitating repeated adaptation to novel environments