Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model

Food webs, networks of feeding relationships among organisms, provide fundamental insights into mechanisms that determine ecosystem stability and persistence. Despite long-standing interest in the compartmental structure of food webs, past network analyses of food webs have been constrained by a standard definition of compartments, or modules, that requires many links within compartments and few links between them. Empirical analyses have been further limited by low-resolution data for primary producers. In this paper, we present a Bayesian computational method for identifying group structure in food webs using a flexible definition of a group that can describe both functional roles and standard compartments. The Serengeti ecosystem provides an opportunity to examine structure in a newly compiled food web that includes species-level resolution among plants, allowing us to address whether groups in the food web correspond to tightly-connected compartments or functional groups, and whether network structure reflects spatial or trophic organization, or a combination of the two. We have compiled the major mammalian and plant components of the Serengeti food web from published literature, and we infer its group structure using our method. We find that network structure corresponds to spatially distinct plant groups coupled at higher trophic levels by groups of herbivores, which are in turn coupled by carnivore groups. Thus the group structure of the Serengeti web represents a mixture of trophic guild structure and spatial patterns, in contrast to the standard compartments typically identified in ecological networks. From data consisting only of nodes and links, the group structure that emerges supports recent ideas on spatial coupling and energy channels in ecosystems that have been proposed as important for persistence.Comment: 28 pages, 6 figures (+ 3 supporting), 2 tables (+ 4 supporting

Rochechouart 2017-Drilling Campaign: First Results

No abstract available

Gene content evolution in the arthropods

Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity

JBrowse: a dynamic web platform for genome visualization and analysis

BACKGROUND: JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page. RESULTS: Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication. CONCLUSIONS: JBrowse is a mature web application suitable for genome visualization and analysis

Drilling-induced and logging-related features illustrated from IODP-ICDP Expedition 364 downhole logs and borehole imaging tools

Expedition 364 was a joint IODP and ICDP mission-specific platform (MSP) expedition to explore the Chicxulub impact crater buried below the surface of the Yucatán continental shelf seafloor. In April and May 2016, this expedition drilled a single borehole at Site M0077 into the crater's peak ring. Excellent quality cores were recovered from ~ 505 to ~1335m below seafloor (m b.s.f.), and high-resolution open hole logs were acquired between the surface and total drill depth. Downhole logs are used to image the borehole wall, measure the physical properties of rocks that surround the borehole, and assess borehole quality during drilling and coring operations. When making geological interpretations of downhole logs, it is essential to be able to distinguish between features that are geological and those that are operation-related. During Expedition 364 some drilling-induced and logging-related features were observed and include the following: effects caused by the presence of casing and metal debris in the hole, logging-tool eccentering, drilling-induced corkscrew shape of the hole, possible re-magnetization of low-coercivity grains within sedimentary rocks, markings on the borehole wall, and drilling-induced changes in the borehole diameter and trajectory

Molecular Evolutionary Trends and Feeding Ecology Diversification in the Hemiptera, Anchored by the Milkweed Bug Genome

Background: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. Results: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. Conclusions: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus’s strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes

Early paleocene paleoceanography and export productivity in the Chicxulub crater

The Chicxulub impact caused a crash in productivity in the world''s oceans which contributed to the extinction of ~75% of marine species. In the immediate aftermath of the extinction, export productivity was locally highly variable, with some sites, including the Chicxulub crater, recording elevated export production. The long-term transition back to more stable export productivity regimes has been poorly documented. Here, we present elemental abundances, foraminifer and calcareous nannoplankton assemblage counts, total organic carbon, and bulk carbonate carbon isotope data from the Chicxulub crater to reconstruct changes in export productivity during the first 3 Myr of the Paleocene. We show that export production was elevated for the first 320 kyr of the Paleocene, declined from 320 kyr to 1.2 Myr, and then remained low thereafter. A key interval in this long decline occurred 900 kyr to 1.2 Myr post impact, as calcareous nannoplankton assemblages began to diversify. This interval is associated with fluctuations in water column stratification and terrigenous flux, but these variables are uncorrelated to export productivity. Instead, we postulate that the turnover in the phytoplankton community from a post-extinction assemblage dominated by picoplankton (which promoted nutrient recycling in the euphotic zone) to a Paleocene pelagic community dominated by relatively larger primary producers like calcareous nannoplankton (which more efficiently removed nutrients from surface waters, leading to oligotrophy) is responsible for the decline in export production in the southern Gulf of Mexico. © 2021. American Geophysical Union. All Rights Reserved

Ocean Drilling Perspectives on Meteorite Impacts

Extraterrestrial impacts that reshape the surfaces of rocky bodies are ubiquitous in the solar system. On early Earth, impact structures may have nurtured the evolution of life. More recently, a large meteorite impact off the Yucatán Peninsula in Mexico at the end of the Cretaceous caused the disappearance of 75% of species known from the fossil record, including non-avian dinosaurs, and cleared the way for the dominance of mammals and the eventual evolution of humans. Understanding the fundamental processes associated with impact events is critical to understanding the history of life on Earth, and the potential for life in our solar system and beyond. Scientific ocean drilling has generated a large amount of unique data on impact pro- cesses. In particular, the Yucatán Chicxulub impact is the single largest and most sig- nificant impact event that can be studied by sampling in modern ocean basins, and marine sediment cores have been instrumental in quantifying its environmental, cli- matological, and biological effects. Drilling in the Chicxulub crater has significantly advanced our understanding of fundamental impact processes, notably the formation of peak rings in large impact craters, but these data have also raised new questions to be addressed with future drilling. Within the Chicxulub crater, the nature and thickness of the melt sheet in the central basin is unknown, and an expanded Paleocene hemipelagic section would provide insights to both the recovery of life and the climatic changes that followed the impact. Globally, new cores collected from today’s central Pacific could directly sample the downrange ejecta of this northeast-southwest trending impact. Extraterrestrial impacts have been controversially suggested as primary drivers for many important paleoclimatic and environmental events throughout Earth history. However, marine sediment archives collected via scientific ocean drilling and geo- chemical proxies (e.g., osmium isotopes) provide a long-term archive of major impact events in recent Earth history and show that, other than the end-Cretaceous, impacts do not appear to drive significant environmental changes

Probing the hydrothermal system of the Chicxulub impact crater

The ~180-km-diameter Chicxulub peak-ring crater and ~240-km multiring basin, produced by the impact that terminated the Cretaceous, is the largest remaining intact impact basin on Earth. International Ocean Discovery Program (IODP) and International Continental Scientific Drilling Program (ICDP) Expedition 364 drilled to a depth of 1335 m below the sea floor into the peak ring, providing a unique opportunity to study the thermal and chemical modification of Earth’s crust caused by the impact. The recovered core shows the crater hosted a spatially extensive hydrothermal system that chemically and mineralogically modified ~1.4 × 105 km3 of Earth’s crust, a volume more than nine times that of the Yellowstone Caldera system. Initially, high temperatures of 300° to 400°C and an independent geomagnetic polarity clock indicate the hydrothermal system was long lived, in excess of 106 years