Ficus insipida subsp. insipida (Moraceae) reveals the role of ecology in the phylogeography of widespread Neotropical rain forest tree species

Aim: To examine the phylogeography of Ficus insipida subsp. insipida in order to investigate patterns of spatial genetic structure across the Neotropics and within Amazonia. Location: Neotropics. Methods: Plastid DNA (trnH-psbA; 410 individuals from 54 populations) and nuclear ribosomal internal transcribed spacer (ITS; 85 individuals from 27 populations) sequences were sampled from Mexico to Bolivia, representing the full extent of the taxon's distribution. Divergence of plastid lineages was dated using a Bayesian coalescent approach. Genetic diversity was assessed with indices of haplotype and nucleotide diversities, and genetic structure was examined using spatial analysis of molecular variance (SAMOVA) and haplotype networks. Population expansion within Amazonia was tested using neutrality and mismatch distribution tests. Results: trnH-psbA sequences yielded 19 haplotypes restricted to either Mesoamerica or Amazonia; six haplotypes were found among ITS sequences. Diversification of the plastid DNA haplotypes began c. 14.6 Ma. Haplotype diversity for trnH-psbA was higher in Amazonia. Seven genetically differentiated SAMOVA groups were described for trnH-psbA, of which two were also supported by the presence of unique ITS sequences. Population expansion was suggested for both markers for the SAMOVA group that contains most Amazonian populations. Main conclusions: Our results show marked population genetic structure in F. insipida between Mesoamerica and Amazonia, implying that the Andes and seasonally dry areas of northern South America are eco-climatic barriers to its migration. This pattern is shared with other widespread pioneer species affiliated to wet habitats, indicating that the ecological characteristics of species may impact upon large-scale phylogeography. Ficus insipida also shows genetic structure in north-western Amazonia potentially related to pre-Pleistocene historical events. In contrast, evident population expansion elsewhere in Amazonia, in particular the presence of genetically uniform populations across the south-west, indicate recent colonization. Our findings are consistent with palaeoecological data that suggest recent post-glacial expansion of Amazonian forests in the south

Rochechouart 2017-Drilling Campaign: First Results

No abstract available

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

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

Unique Features of a Global Human Ectoparasite Identified Through Sequencing of the Bed Bug Genome

The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host-symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human-bed bug and symbiont-bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite

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

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

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