Extinction Event Factsheet Extinction Events Are Also Widely Known As Mass Extinctions
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A Late Methanogen Origin for Molybdenum-Dependent Nitrogenase E
Geobiology (2011), 9, 221–232 DOI: 10.1111/j.1472-4669.2011.00278.x A late methanogen origin for molybdenum-dependent nitrogenase E. S. BOYD,1 A. D. ANBAR,2 S. MILLER,3 T. L. HAMILTON,1 M. LAVIN4 ANDJ.W.PETERS1 1Department of Chemistry and Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT, USA 2School of Earth and Space Exploration and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, USA 3Department of Biological Sciences, University of Montana, Missoula, MT, USA 4Department of Plant Sciences, Montana State University, Bozeman, MT, USA ABSTRACT Mounting evidence indicates the presence of a near complete biological nitrogen cycle in redox-stratified oceans during the late Archean to early Proterozoic (c. 2.5–2.0 Ga). It has been suggested that the iron (Fe)- or vana- dium (V)-dependent nitrogenase rather than molybdenum (Mo)-dependent form was responsible for dinitrogen fixation during this time because oceans were depleted in Mo and rich in Fe. We evaluated this hypothesis by examining the phylogenetic relationships of proteins that are required for the biosynthesis of the active site cofactor of Mo-nitrogenase in relation to structural proteins required for Fe-, V- and Mo-nitrogenase. The results are highly suggestive that among extant nitrogen-fixing organisms for which genomic information exists, Mo-nitrogenase is unlikely to have been associated with the Last Universal Common Ancestor. Rather, the origin of Mo-nitrogenase can be traced to an ancestor of the anaerobic and hydrogenotrophic methanogens with acquisition in the bacterial domain via lateral gene transfer involving an anaerobic member of the Firmicutes.A comparison of substitution rates estimated for proteins required for the biosynthesis of the nitrogenase active site cofactor and for a set of paralogous proteins required for the biosynthesis of bacteriochlorophyll suggests that Nif emerged from a nitrogenase-like ancestor approximately 1.5–2.2 Ga. -
Climate Instability and Tipping Points in the Late Devonian
Archived version from NCDOCKS Institutional Repository – http://libres.uncg.edu/ir/asu/ Sarah K. Carmichael, Johnny A. Waters, Cameron J. Batchelor, Drew M. Coleman, Thomas J. Suttner, Erika Kido, L.M. Moore, and Leona Chadimová, (2015) Climate instability and tipping points in the Late Devonian: Detection of the Hangenberg Event in an open oceanic island arc in the Central Asian Orogenic Belt, Gondwana Research The copy of record is available from Elsevier (18 March 2015), ISSN 1342-937X, http://dx.doi.org/10.1016/j.gr.2015.02.009. Climate instability and tipping points in the Late Devonian: Detection of the Hangenberg Event in an open oceanic island arc in the Central Asian Orogenic Belt Sarah K. Carmichael a,*, Johnny A. Waters a, Cameron J. Batchelor a, Drew M. Coleman b, Thomas J. Suttner c, Erika Kido c, L. McCain Moore a, and Leona Chadimová d Article history: a Department of Geology, Appalachian State University, Boone, NC 28608, USA Received 31 October 2014 b Department of Geological Sciences, University of North Carolina - Chapel Hill, Received in revised form 6 Feb 2015 Chapel Hill, NC 27599-3315, USA Accepted 13 February 2015 Handling Editor: W.J. Xiao c Karl-Franzens-University of Graz, Institute for Earth Sciences (Geology & Paleontology), Heinrichstrasse 26, A-8010 Graz, Austria Keywords: d Institute of Geology ASCR, v.v.i., Rozvojova 269, 165 00 Prague 6, Czech Republic Devonian–Carboniferous Chemostratigraphy Central Asian Orogenic Belt * Corresponding author at: ASU Box 32067, Appalachian State University, Boone, NC 28608, USA. West Junggar Tel.: +1 828 262 8471. E-mail address: [email protected] (S.K. -
Cretaceous–Paleogene Extinction Event (End Cretaceous, K-T Extinction, Or K-Pg Extinction): 66 MYA At
Cretaceous–Paleogene extinction event (End Cretaceous, K-T extinction, or K-Pg extinction): 66 MYA at • About 17% of all families, 50% of all genera and 75% of all species became extinct. • In the seas it reduced the percentage of sessile animals to about 33%. • All non-avian dinosaurs became extinct during that time. • Iridium anomaly in sediments may indicate comet or asteroid induced extinctions Triassic–Jurassic extinction event (End Triassic): 200 Ma at the Triassic- Jurassic transition. • About 23% of all families, 48% of all genera (20% of marine families and 55% of marine genera) and 70-75% of all species went extinct. • Most non-dinosaurian archosaurs, most therapsids, and most of the large amphibians were eliminated • Dinosaurs had with little terrestrial competition in the Jurassic that followed. • Non-dinosaurian archosaurs continued to dominate aquatic environments • Theories on cause: 1.) Gradual climate change, perhaps with ocean acidification has been implicated, but not proven. 2.) Asteroid impact has been postulated but no site or evidence has been found. 3.) Massive volcanics, flood basalts and continental margin volcanoes might have damaged the atmosphere and warmed the planet. Permian–Triassic extinction event (End Permian): 251 Ma at the Permian-Triassic transition. Known as “The Great Dying” • Earth's largest extinction killed 57% of all families, 83% of all genera and 90% to 96% of all species (53% of marine families, 84% of marine genera, about 96% of all marine species and an estimated 70% of land species, • The evidence of plants is less clear, but new taxa became dominant after the extinction. -
Species Extinctions
http://www.iucn.org/about/union/commissions/wcpa/?7695/Multiple-ocean-stresses- threaten-globally-significant-marine-extinction Multiple ocean stresses threaten “globally significant” marine extinction 20 June 2011 | News story An international panel of experts warns in a report released today that marine species are at risk of entering a phase of extinction unprecedented in human history. The preliminary report arises from a ‘State of the Oceans’ workshop co-hosted by IUCN in April, the first ever to consider the cumulative impact of all pressures on the oceans. Considering the latest research across all areas of marine science, the workshop examined the combined effects of pollution, acidification, ocean warming, over-fishing and hypoxia (deoxygenation). The scientific panel concluded that the combination of stresses on the ocean is creating the conditions associated with every previous major extinction of species in Earth’s history. And the speed and rate of degeneration in the ocean is far greater than anyone has predicted. The panel concluded that many of the negative impacts previously identified are greater than the worst predictions. As a result, although difficult to assess, the first steps to globally significant extinction may have begun with a rise in the extinction threat to marine species such as reef- forming corals. “The world’s leading experts on oceans are surprised by the rate and magnitude of changes we are seeing,” says Dan Laffoley, Marine Chair of IUCN’s World Commission on Protected Areas, Senior Advisor on Marine Science and Conservation for IUCN and co-author of the report. “The challenges for the future of the ocean are vast, but unlike previous generations, we know what now needs to happen. -
Evaluating the Frasnian-Famennian Mass Extinction: Comparing Brachiopod Faunas
Evaluating the Frasnian-Famennian mass extinction: Comparing brachiopod faunas PAUL COPPER Copper, P. 1998. Evaluating the Frasnian-Famennian mass extinction: Comparing bra- chiopod faunas.- Acta Palaeontologica Polonica 43,2,137-154. The Frasnian-Famennian (F-F) mass extinctions saw the global loss of all genera belonging to the tropically confined order Atrypida (and Pentamerida): though Famen- nian forms have been reported in the literafure, none can be confirmed. Losses were more severe during the Givetian (including the extinction of the suborder Davidsoniidina, and the reduction of the suborder Lissatrypidina to a single genus),but ońgination rates in the remaining suborder surviving into the Frasnian kept the group alive, though much reduced in biodiversity from the late Earb and Middle Devonian. In the terminal phases of the late Palmatolepis rhenana and P linguifurmis zones at the end of the Frasnian, during which the last few Atrypidae dechned, no new genera originated, and thus the Atrypida were extĘated. There is no evidence for an abrupt termination of all lineages at the F-F boundary, nor that the Atrypida were abundant at this time, since all groups were in decline and impoverished. Atypida were well established in dysaerobic, muddy substrate, reef lagoonal and off-reef deeper water settings in the late Givetian and Frasnian, alongside a range of brachiopod orders which sailed through the F-F boundary: tropical shelf anoxia or hypońa seems implausible as a cause for aĘpid extinction. Glacial-interglacial climate cycles recorded in South Ameńca for the Late Devonian, and their synchronous global cooling effect in low latitudes, as well as loss of the reef habitat and shelf area reduction, remain as the most likely combined scenarios for the mass extinction events. -
METHANOGENS AS MODELS for LIFE on MARS. R. L. Mickol1, W. H. Waddell2, and T
Eighth International Conference on Mars (2014) 1005.pdf METHANOGENS AS MODELS FOR LIFE ON MARS. R. L. Mickol1, W. H. Waddell2, and T. A. Kral1,3, 1Arkansas Center for Space and Planetary Sciences, 202 Old Museum Building, University of Arkansas, Fayetteville, Arkansas, 72701, USA, [[email protected]], 2Dept. of Health, Human Performance, and Recreation, HPER 308, University of Arkansas, Fayetteville, Arkansas, 72701, USA, 3Dept. of Biological Sciences, SCEN 632, University of Arkansas, Fayetteville, Arkansas, 72701, USA. Introduction: The discovery of methane in the Sciences, University of Arkansas, Fayetteville, Arkan- martian atmosphere [1-4] has fueled the study of meth- sas. All four methanogen species were tested in these anogens as ideal candidates for life on Mars. Methano- experiments. Methanogens were grown in their respec- gens are chemoautotrophs from the domain Archaea. tive anaerobic growth media and placed into the cham- These microorganisms utilize hydrogen as an energy ber with a palladium catalyst box to remove residual source and carbon dioxide as a carbon source to pro- oxygen. The chamber was evacuated to a pre- duce methane. Methanogens can be considered ideal determined pressure and filled with 80:20 H2:CO2 gas. candidates for life on Mars because they are anaerobic, This procedure was repeated three times to ensure re- they do not require organic nutrients and are non- moval of the atmosphere. The chamber was then main- photosynthetic, indicating they could exist in sub- tained at the desired pressure (133-143 mbar, 67-72 surface environments. mbar, 33-38 mbar, 6-10 mbar, 7-20 mbar) for the dura- Our lab has studied methanogens as models for life tion of the experiments. -
Methanogenic Burst in the End-Permian Carbon Cycle
Methanogenic burst in the end-Permian carbon cycle Daniel H. Rothmana,b,1, Gregory P. Fournierc, Katherine L. Frenchb, Eric J. Almc, Edward A. Boyleb, Changqun Caod, and Roger E. Summonsb aLorenz Center, bDepartment of Earth, Atmospheric, and Planetary Sciences, and cDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; and dState Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China Edited by John M. Hayes, Woods Hole Oceanographic Institution, Woods Hole, MA, and approved February 4, 2014 (received for review September 27, 2013) The end-Permian extinction is associated with a mysterious disrup- and its perturbation to the carbon cycle but also to amplify the tion to Earth’s carbon cycle. Here we identify causal mechanisms via development of marine anoxia. Taken as a whole, these results three observations. First, we show that geochemical signals indicate reconcile an array of apparently disparate observations about the superexponential growth of the marine inorganic carbon reservoir, end-Permian event. coincident with the extinction and consistent with the expansion of a new microbial metabolic pathway. Second, we show that the effi- Growth of the Marine Carbon Reservoir cient acetoclastic pathway in Methanosarcina emerged at a time sta- Fig. 1A displays the carbon-isotopic record in Meishan, China tistically indistinguishable from the extinction. Finally, we show that (5). Immediately preceding the extinction event, the isotopic com- nickel concentrations in South China sediments increased sharply at position δ1 of carbonate carbon declines by about 7‰ during the extinction, probably as a consequence of massive Siberian volca- a period of about 100 thousand years (Kyr), first slowly, and sub- nism, enabling a methanogenic expansion by removal of nickel lim- sequently rapidly. -
Supplementary Information
Retroconversion of estrogens into androgens by bacteria via a cobalamin-mediated methylation Po-Hsiang Wang, Yi-Lung Chen, Sean Ting-Shyang Wei, Kan Wu, Tzong-Huei Lee, Tien-Yu Wu, and Yin-Ru Chiang Supplementary Information Table of Contents Dataset Dataset S1. Genome annotation of strain DHT3 and transcriptomic analysis (RNA-Seq) of bacterial cells grown anaerobically with testosterone or estradiol. SI Tables Table S1. Oligonucleotides used in this study. Table S2. Selection of housekeeping genes of strain DHT3 used for constructing the linear regression line in the global gene expression profiles (RNA-Seq). Table S3. Selection of the cobalamin-dependent methyltransferases used for the un-rooted maximum likelihood tree construction. Table S4. UPLC–APCI–HRMS data of the intermediates involved in anaerobic estrone catabolism by strain DHT3. Table S5. 1H- (600 MHz) and 13C-NMR (150 MHz) spectral data of the HPLC-purified metabolite (AND2) and the authentic standard 5-androstan-3,17-diol Table S6. Selection of the bacteria used for comparative analysis of the gene organization for HIP degradation. SI Figures Fig. S1 Scanning electron micrographs of strain DHT3 cells. Fig. S2 Cobalamin as an essential vitamin during the anaerobic growth of strain DHT3 on estradiol. Fig. S3 Arrangement and expression analysis of the emt genes in strain DHT3. Fig. S4 The anaerobic growth of the wild type (A) and the emtA-disrupted mutant (B) of strain DHT3 with testosterone and estradiol. Fig. S5 APCI–HRMS spectrum of the HIP produced by estrone-fed strain DHT3. 1 Fig. S6 UPLC–APCI–HRMS spectra of two TLC-purified androgen metabolites, 17β-hydroxyandrostan-3-one (A) and 3β,17β-dihydroxyandrostane (B). -
A Genomic Timescale of Prokaryote Evolution: Insights Into the Origin of Methanogenesis, Phototrophy, and the Colonization of Land
BMC Evolutionary Biology BioMed Central Research article Open Access A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land Fabia U Battistuzzi1, Andreia Feijao2 and S Blair Hedges*1 Address: 1NASA Astrobiology Institute and Department of Biology, 208 Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802, USA and 2European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany Email: Fabia U Battistuzzi - [email protected]; Andreia Feijao - [email protected]; S Blair Hedges* - [email protected] * Corresponding author Published: 09 November 2004 Received: 07 August 2004 Accepted: 09 November 2004 BMC Evolutionary Biology 2004, 4:44 doi:10.1186/1471-2148-4-44 This article is available from: http://www.biomedcentral.com/1471-2148/4/44 © 2004 Battistuzzi et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. However, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. We assembled a data set of sequences from 32 proteins (~7600 amino acids) common to 72 species and estimated phylogenetic relationships and divergence times with a local clock method. Results: Our phylogenetic results support most of the currently recognized higher-level groupings of prokaryotes. -
The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts
biomolecules Review The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts Laura Matarredona ,Mónica Camacho, Basilio Zafrilla , María-José Bonete and Julia Esclapez * Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain; [email protected] (L.M.); [email protected] (M.C.); [email protected] (B.Z.); [email protected] (M.-J.B.) * Correspondence: [email protected]; Tel.: +34-965-903-880 Received: 31 July 2020; Accepted: 24 September 2020; Published: 29 September 2020 Abstract: Over the years, in order to survive in their natural environment, microbial communities have acquired adaptations to nonoptimal growth conditions. These shifts are usually related to stress conditions such as low/high solar radiation, extreme temperatures, oxidative stress, pH variations, changes in salinity, or a high concentration of heavy metals. In addition, climate change is resulting in these stress conditions becoming more significant due to the frequency and intensity of extreme weather events. The most relevant damaging effect of these stressors is protein denaturation. To cope with this effect, organisms have developed different mechanisms, wherein the stress genes play an important role in deciding which of them survive. Each organism has different responses that involve the activation of many genes and molecules as well as downregulation of other genes and pathways. Focused on salinity stress, the archaeal domain encompasses the most significant extremophiles living in high-salinity environments. To have the capacity to withstand this high salinity without losing protein structure and function, the microorganisms have distinct adaptations. -
Simple Stochastic Populations in Habi- Tats with Bounded, and Varying Carry- Ing Capacities
Simple Stochastic Populations in Habi- tats with Bounded, and Varying Carry- ing Capacities Master’s thesis in Complex Adaptive Systems EDWARD KORVEH Department of Mathematical Sciences CHALMERS UNIVERSITY OF TECHNOLOGY Gothenburg, Sweden 2016 Master’s thesis 2016:NN Simple Stochastic Populations in Habitats with Bounded, and Varying Carrying Capacities EDWARD KORVEH Department of Mathematical Sciences Division of Mathematical Statistics Chalmers University of Technology Gothenburg, Sweden 2016 Simple Stochastic Populations in Habitats with Bounded, and Varying Carrying Capacities EDWARD KORVEH © EDWARD KORVEH, 2016. Supervisor: Peter Jagers, Department of Mathematical Sciences Examiner: Peter Jagers, Department of Mathematical Sciences Master’s Thesis 2016:NN Department of Mathematical Sciences Division of Mathematical Statistics Chalmers University of Technology SE-412 96 Gothenburg Gothenburg, Sweden 2016 iv Simple Stochastic Populations in Habitats with Bounded, and Varying Carrying Capacities EDWARD KORVEH Department of Mathematical Sciences Chalmers University of Technology Abstract A population consisting of one single type of individuals where reproduction is sea- sonal, and by means of asexual binary-splitting with a probability, which depends on the carrying capacity of the habitat, K and the present population is considered. Current models for such binary-splitting populations do not explicitly capture the concepts of early and late extinctions. A new parameter v, called the ‘scaling pa- rameter’ is introduced to scale down the splitting probabilities in the first season, and also in subsequent generations in order to properly observe and record early and late extinctions. The modified model is used to estimate the probabilities of early and late extinctions, and the expected time to extinction in two main cases. -
The Late Ordovician Mass Extinction
P1: FXY/GBP P2: aaa February 24, 2001 19:23 Annual Reviews AR125-12 Annu. Rev. Earth Planet. Sci. 2001. 29:331–64 Copyright c 2001 by Annual Reviews. All rights reserved THE LATE ORDOVICIAN MASS EXTINCTION Peter M Sheehan Department of Geology, Milwaukee Public Museum, Milwaukee, Wisconsin 53233; e-mail: [email protected] Key Words extinction event, Silurian, glaciation, evolutionary recovery, ecologic evolutionary unit ■ Abstract Near the end of the Late Ordovician, in the first of five mass extinctions in the Phanerozoic, about 85% of marine species died. The cause was a brief glacial interval that produced two pulses of extinction. The first pulse was at the beginning of the glaciation, when sea-level decline drained epicontinental seaways, produced a harsh climate in low and mid-latitudes, and initiated active, deep-oceanic currents that aerated the deep oceans and brought nutrients and possibly toxic material up from oceanic depths. Following that initial pulse of extinction, surviving faunas adapted to the new ecologic setting. The glaciation ended suddenly, and as sea level rose, the climate moderated, and oceanic circulation stagnated, another pulse of extinction occurred. The second extinction marked the end of a long interval of ecologic stasis (an Ecologic-Evolutionary Unit). Recovery from the event took several million years, but the resulting fauna had ecologic patterns similar to the fauna that had become extinct. Other extinction events that eliminated similar or even smaller percentages of species had greater long-term ecologic effects. INTRODUCTION The Late Ordovician extinction was the first of five great extinction events of the by Universidad Nacional Autonoma de Mexico on 03/15/13.