Taphonomic biases in the insect fossil record: shifts in articulation over geologic time

Insect taphonomy is a topic that has drawn interest because of its potential biases on diversity patterns and the ecological information recorded by ancient insect faunas. Other than the onset of common amber fossilization in the Cretaceous, very little is known about long-term trends in the nature and quality of insect preservation and, as a result, the effects of taphonomic biases are poorly constrained. We assembled a database of nearly 7000 Carboniferous-Pliocene insect adpression (compression and impression) species from the primary literature to assess changes in insect taphonomy over time and test biotic and environmental controls on preservation. We grouped the fossils into 10-Myr bins and scored preservation of holotype specimens as either articulated bodies or isolated wings; articulated specimens with a body implied a generally higher quality of preservation. Paleozoic and Triassic insect holotypes are known overwhelmingly from isolated wings (only 12% articulated bodies), but our database shows a significant increase in the percentage preserved as articulated bodies, to more than 70%, beginning about 160 Myr ago in the Late Jurassic. This transition could reflect variations in the robustness of different insect orders and shifts in the taxonomic composition of insect faunas, but all the major orders in the database exhibit significant increases in articulation. Instead, a shift to increased preservation in lacustrine paleoenvironments, which contain a greater proportion of articulated body fossils, explains most of the trend. The pronounced Late Jurassic increase in articulation has implications for evolutionary and ecological reconstructions, for example, suggesting that preserved insect diversity may be biased downward in the earlier part of their history when articulation was poor

Canopy Flow Analysis Reveals the Advantage of Size in the Oldest Communities of Multicellular Eukaryotes

SummaryAt Mistaken Point, Newfoundland, Canada, rangeomorph “fronds” dominate the earliest (579–565 million years ago) fossil communities of large (0.1 to 2 m height) multicellular benthic eukaryotes. They lived in low-flow environments, fueled by uptake [1–3] of dissolved reactants (osmotrophy). However, prokaryotes are effective osmotrophs, and the advantage of taller eukaryotic osmotrophs in this deep-water community context has not been addressed. We reconstructed flow-velocity profiles and vertical mixing using canopy flow models appropriate to the densities of the observed communities. Further modeling of processes at organismal surfaces documents increasing uptake with height in the community as a function of thinning of the diffusive boundary layer with increased velocity. The velocity profile, produced by canopy flow in the community, generates this advantage of upward growth. Alternative models of upward growth advantage based on redox/resource gradients fail, given the efficiency of vertical mixing. In benthic communities of osmotrophs of sufficient density, access to flow in low-flow settings provides an advantage to taller architecture, providing a selectional driver for communities of tall eukaryotes in contexts where phototropism cannot contribute to upward growth. These Ediacaran deep-sea fossils were preserved during the increasing oxygenation prior to the Cambrian radiation of animals and likely represent an important phase in the ecological and evolutionary transition to more complex eukaryotic forms.Video Abstrac

Arthropods in modern resins reveal if amber accurately recorded forest arthropod communities

Amber is an organic multicompound derivative from the polymerization of resin of diverse higher plants. Compared with other modes of fossil preservation, amber records the anatomy of and ecological interactions between ancient soft-bodied organisms with exceptional fidelity. However, it is currently suggested that ambers do not accurately record the composition of arthropod forest paleocommunities, due to crucial taphonomic biases. We evaluated the effects of taphonomic processes on arthropod entrapment by resin from the plant Hymenaea, one of the most important resin-producing trees and a producer of tropical Cenozoic ambers and Anthropocene (or subfossil) resins. We statistically compared natural entrapment by Hymenaea verrucosa tree resin with the ensemble of arthropods trapped by standardized entomological traps around the same tree species. Our results demonstrate that assemblages in resin are more similar to those from sticky traps than from malaise traps, providing an accurate representation of the arthropod fauna living in or near the resiniferous tree, but not of entire arthropod forest communities. Particularly, arthropod groups such as Lepidoptera, Collembola, and some Diptera are underrepresented in resins. However, resin assemblages differed slightly from sticky traps, perhaps because chemical compounds in the resins attract or repel specific insect groups. Ground-dwelling or flying arthropods that use the treetrunk habitat for feeding or reproduction are also well represented in the resin assemblages, implying that fossil inclusions in amber can reveal fundamental information about biology of the past. These biases have implications for the paleoecological interpretation of the fossil record, principally of Cenozoic amber with angiosperm origin

Comparative size evolution of marine clades from the Late Permian through Middle Triassic

Abstract.-The small size of Early Triassic marine organisms has important implications for the ecological and environmental pressures operating during and after the end-Permian mass extinction. However, this "Lilliput Effect" has only been documented quantitatively in a few invertebrate clades. Moreover, the discovery of Early Triassic gastropod specimens larger than any previously known has called the extent and duration of the Early Triassic size reduction into question. Here, we document and compare Permian-Triassic body size trends globally in eight marine clades (gastropods, bivalves, calcitic and phosphatic brachiopods, ammonoids, ostracods, conodonts, and foraminiferans). Our database contains maximum size measurements for 11,224 specimens and 2,743 species spanning the Late Permian through the Middle to Late Triassic. The Permian/Triassic boundary (PTB) shows more size reduction among species than any other interval. For most higher taxa, maximum and median size among species decreased dramatically from the latest Permian (Changhsingian) to the earliest Triassic (Induan), and then increased during Olenekian (late Early Triassic) and Anisian (early Middle Triassic) time. During the Induan, the only higher taxon much larger than its long-term mean size was the ammonoids; they increased significantly in median size across the PTB, a response perhaps related to their comparatively rapid diversity recovery after the end-Permian extinction. The loss of large species in multiple clades across the PTB resulted from both selective extinction of larger species and evolution of surviving lineages toward smaller sizes. The within-lineage component of size decrease suggests that only part of the size decrease can be related to the end-Permian kill mechanism; in addition, Early Triassic environmental conditions or ecological pressures must have continued to favor small body size as well. After the end-Permian extinction, size decrease occurred across ecologically and physiologically disparate clades, but this size reduction was limited to the first part of the Early Triassic (Induan). Nektonic habitat or physiological buffering capacity may explain the contrast of Early Triassic size increase and diversification in ammonoids versus size reduction and slow recovery in benthic clades

Multiple episodes of extensive marine anoxia linked to global warming and continental weathering following the latest Permian mass extinction

Copyright © 2018 The Authors. Explaining the ∼5-million-year delay in marine biotic recovery following the latest Permian mass extinction, the largest biotic crisis of the Phanerozoic, is a fundamental challenge for both geological and biological sciences. Ocean redox perturbations may have played a critical role in this delayed recovery. However, the lack of quantitative constraints on the details of Early Triassic oceanic anoxia (for example, time, duration, and extent) leaves the links between oceanic conditions and the delayed biotic recovery ambiguous. We report high-resolution U-isotope (δ238U) data from carbonates of the uppermost Permian to lowermost Middle Triassic Zal section (Iran) to characterize the timing and global extent of ocean redox variation during the Early Triassic. Our δ238U record reveals multiple negative shifts during the Early Triassic. Isotope mass-balance modeling suggests that the global area of anoxic seafloor expanded substantially in the Early Triassic, peaking during the latest Permian to mid-Griesbachian, the late Griesbachian to mid-Dienerian, the Smithian-Spathian transition, and the Early/Middle Triassic transition. Comparisons of the U-, C-, and Sr-isotope records with a modeled seawater PO43- concentration curve for the Early Triassic suggest that elevated marine productivity and enhanced oceanic stratification were likely the immediate causes of expanded oceanic anoxia. The patterns of redox variation documented by the U-isotope record show a good first-order correspondence to peaks in ammonoid extinctions during the Early Triassic. Our results indicate that multiple oscillations in oceanic anoxia modulated the recovery of marine ecosystems following the latest Permian mass extinction

Paleoecology of brachiopod communities during the late Paleozoic ice age in Bolivia (Copacabana Formation, Pennsylvanian–Early Permian)

Studies of modern ecological communities demonstrate that climate change may trigger changes in diversity and taxonomic composition; however, these studies are fundamentally limited to short timescales and therefore cannot demonstrate the full impact of major climate change. Understanding the ecological response of marine invertebrate communities to the Late Paleozoic Ice Age (LPIA), the last complete transition from icehouse to greenhouse, can establish a more complete picture of the climate-faunal relationship. We analyzed brachiopod community structure in Moscovian-Sakmarian (mid-Pennsylvanian to Early Permian) samples spanning the greatest extent of the LPIA, collected from four localities of the Copacabana Formation in Bolivia: Ancoraimes, Yaurichambi, Cuyavi, and Yampupata. Cluster analysis reveals three main groups that appear to coincide with pre-, syn-, and post-glacial times. Genus richness was significantly greater in samples during the Asselian glacial episode; however, the difference may be due to a combination of smaller body size and time averaged mixing of genera from different depths during more rapid glacioeustatic sea level change. Genera present in Bolivia consistently had warm-water affinities, even during the main glaciation, but warm-water taxa increased in abundance over time and the samples became increasingly dominated by characteristically North American genera. Overall mean body size and the size of particular genera were smaller in the Asselian cluster. These size changes likely reflect variations in substrate because marine invertebrates should be larger at cooler temperatures due to oxygen limitation at higher temperatures. The monotonic increase in abundance of warm-water genera and increasingly North American biogeographic affinity imply that community change was most likely the result of the northward drift of Bolivia rather than a response to late Paleozoic glacial-nonglacial cycles. This lack of climate related faunal change was probably a result of Bolivia's mid-latitude location during the late Paleozoic because both the rate of temperature change and its magnitude were likely smaller at lower latitudes, reducing the impact of climate change on marine communities. © 2013 Elsevier B.V

Endoplasmic reticulum and lysosomal Ca2+ stores are remodelled in GBA1-linked Parkinson disease patient fibroblasts.

Mutations in β-glucocerebrosidase (encoded by GBA1) cause Gaucher disease (GD), a lysosomal storage disorder, and increase the risk of developing Parkinson disease (PD). The pathogenetic relationship between the two disorders is unclear. Here, we characterised Ca2+ release in fibroblasts from type I GD and PD patients together with age-matched, asymptomatic carriers, all with the common N370S mutation in β-glucocerebrosidase. We show that endoplasmic reticulum (ER) Ca2+ release was potentiated in GD and PD patient fibroblasts but not in cells from asymptomatic carriers. ER Ca2+ signalling was also potentiated in fibroblasts from aged healthy subjects relative to younger individuals but not further increased in aged PD patient cells. Chemical or molecular inhibition of β-glucocerebrosidase in fibroblasts and a neuronal cell line did not affect ER Ca2+ signalling suggesting defects are independent of enzymatic activity loss. Conversely, lysosomal Ca2+ store content was reduced in PD fibroblasts and associated with age-dependent alterations in lysosomal morphology. Accelerated remodelling of Ca2+ stores by pathogenic GBA1 mutations may therefore feature in PD

Lives saved with vaccination for 10 pathogens across 112 countries in a pre-COVID-19 world.

BackgroundVaccination is one of the most effective public health interventions. We investigate the impact of vaccination activities for Haemophilus influenzae type b, hepatitis B, human papillomavirus, Japanese encephalitis, measles, Neisseria meningitidis serogroup A, rotavirus, rubella, Streptococcus pneumoniae, and yellow fever over the years 2000-2030 across 112 countries.MethodsTwenty-one mathematical models estimated disease burden using standardised demographic and immunisation data. Impact was attributed to the year of vaccination through vaccine-activity-stratified impact ratios.ResultsWe estimate 97 (95%CrI[80, 120]) million deaths would be averted due to vaccination activities over 2000-2030, with 50 (95%CrI[41, 62]) million deaths averted by activities between 2000 and 2019. For children under-5 born between 2000 and 2030, we estimate 52 (95%CrI[41, 69]) million more deaths would occur over their lifetimes without vaccination against these diseases.ConclusionsThis study represents the largest assessment of vaccine impact before COVID-19-related disruptions and provides motivation for sustaining and improving global vaccination coverage in the future.FundingVIMC is jointly funded by Gavi, the Vaccine Alliance, and the Bill and Melinda Gates Foundation (BMGF) (BMGF grant number: OPP1157270 / INV-009125). Funding from Gavi is channelled via VIMC to the Consortium's modelling groups (VIMC-funded institutions represented in this paper: Imperial College London, London School of Hygiene and Tropical Medicine, Oxford University Clinical Research Unit, Public Health England, Johns Hopkins University, The Pennsylvania State University, Center for Disease Analysis Foundation, Kaiser Permanente Washington, University of Cambridge, University of Notre Dame, Harvard University, Conservatoire National des Arts et Métiers, Emory University, National University of Singapore). Funding from BMGF was used for salaries of the Consortium secretariat (authors represented here: TBH, MJ, XL, SE-L, JT, KW, NMF, KAMG); and channelled via VIMC for travel and subsistence costs of all Consortium members (all authors). We also acknowledge funding from the UK Medical Research Council and Department for International Development, which supported aspects of VIMC's work (MRC grant number: MR/R015600/1).JHH acknowledges funding from National Science Foundation Graduate Research Fellowship; Richard and Peggy Notebaert Premier Fellowship from the University of Notre Dame. BAL acknowledges funding from NIH/NIGMS (grant number R01 GM124280) and NIH/NIAID (grant number R01 AI112970). The Lives Saved Tool (LiST) receives funding support from the Bill and Melinda Gates Foundation.This paper was compiled by all coauthors, including two coauthors from Gavi. Other funders had no role in study design, data collection, data analysis, data interpretation, or writing of the report. All authors had full access to all the data in the study and had final responsibility for the decision to submit for publication

Correction for Johansson et al., An open challenge to advance probabilistic forecasting for dengue epidemics.

Correction for “An open challenge to advance probabilistic forecasting for dengue epidemics,” by Michael A. Johansson, Karyn M. Apfeldorf, Scott Dobson, Jason Devita, Anna L. Buczak, Benjamin Baugher, Linda J. Moniz, Thomas Bagley, Steven M. Babin, Erhan Guven, Teresa K. Yamana, Jeffrey Shaman, Terry Moschou, Nick Lothian, Aaron Lane, Grant Osborne, Gao Jiang, Logan C. Brooks, David C. Farrow, Sangwon Hyun, Ryan J. Tibshirani, Roni Rosenfeld, Justin Lessler, Nicholas G. Reich, Derek A. T. Cummings, Stephen A. Lauer, Sean M. Moore, Hannah E. Clapham, Rachel Lowe, Trevor C. Bailey, Markel García-Díez, Marilia Sá Carvalho, Xavier Rodó, Tridip Sardar, Richard Paul, Evan L. Ray, Krzysztof Sakrejda, Alexandria C. Brown, Xi Meng, Osonde Osoba, Raffaele Vardavas, David Manheim, Melinda Moore, Dhananjai M. Rao, Travis C. Porco, Sarah Ackley, Fengchen Liu, Lee Worden, Matteo Convertino, Yang Liu, Abraham Reddy, Eloy Ortiz, Jorge Rivero, Humberto Brito, Alicia Juarrero, Leah R. Johnson, Robert B. Gramacy, Jeremy M. Cohen, Erin A. Mordecai, Courtney C. Murdock, Jason R. Rohr, Sadie J. Ryan, Anna M. Stewart-Ibarra, Daniel P. Weikel, Antarpreet Jutla, Rakibul Khan, Marissa Poultney, Rita R. Colwell, Brenda Rivera-García, Christopher M. Barker, Jesse E. Bell, Matthew Biggerstaff, David Swerdlow, Luis Mier-y-Teran-Romero, Brett M. Forshey, Juli Trtanj, Jason Asher, Matt Clay, Harold S. Margolis, Andrew M. Hebbeler, Dylan George, and Jean-Paul Chretien, which was first published November 11, 2019; 10.1073/pnas.1909865116. The authors note that the affiliation for Xavier Rodó should instead appear as Catalan Institution for Research and Advanced Studies (ICREA) and Climate and Health Program, Barcelona Institute for Global Health (ISGlobal). The corrected author and affiliation lines appear below. The online version has been corrected

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562 WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants