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Distributions of Extinction Times from Fossil Ages and Tree Topologies: the Example of Some Mid-Permian Synapsid Extinctions Gilles Didier, Michel Laurin
Distributions of extinction times from fossil ages and tree topologies: the example of some mid-Permian synapsid extinctions Gilles Didier, Michel Laurin To cite this version: Gilles Didier, Michel Laurin. Distributions of extinction times from fossil ages and tree topologies: the example of some mid-Permian synapsid extinctions. 2021. hal-03258099v2 HAL Id: hal-03258099 https://hal.archives-ouvertes.fr/hal-03258099v2 Preprint submitted on 20 Sep 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributions of extinction times from fossil ages and tree topologies: the example of some mid-Permian synapsid extinctions Gilles Didier1 and Michel Laurin2 1 IMAG, Univ Montpellier, CNRS, Montpellier, France 2 CR2P (\Centre de Pal´eontologie { Paris"; UMR 7207), CNRS/MNHN/SU, Mus´eumNational d'Histoire Naturelle, Paris, France September 16, 2021 Abstract Given a phylogenetic tree that includes only extinct, or a mix of extinct and extant taxa, where at least some fossil data are available, we present a method to compute the distribution of the extinction time of a given set of taxa under the Fossilized-Birth-Death model. Our approach differs from the previous ones in that it takes into account (i) the possibility that the taxa or the clade considered may diversify before going extinct and (ii) the whole phylogenetic tree to estimate extinction times, whilst previous methods do not consider the diversification process and deal with each branch independently. -
Alfred Romer – Wikipedia
Alfred Romer – Wikipedia https://de.wikipedia.org/wiki/Alfred_Romer aus Wikipedia, der freien Enzyklopädie Alfred Sherwood Romer (* 28. Dezember 1894 in White Plains, New York; † 5. November 1973) war ein US-amerikanischer Paläontologe. Sein Fachgebiet war die Evolution der Wirbeltiere. Inhaltsverzeichnis 1 Leben 2 Romer-Lücke 3 Auszeichnungen und Ehrungen 4 Schriften 5 Weblinks 6 Einzelnachweise Leben Alfred Sherwood Romer wurde in White Plains, New York geboren, wo er seinen High-School-Abschluss machte. Danach arbeitete er ein Jahr lang als Angestellter bei der Eisenbahn und entschloss sich dann doch für den Besuch eines College. Mit Hilfe eines Stipendiums vom Amherst College konnte er dort Geschichte und deutsche Literatur studieren. Durch häufige Besuche des American Museum of Natural History entdeckte er seine Begeisterung für naturkundliche Fossilien. Bei Ausbruch des Ersten Weltkriegs meldete er sich als Freiwilliger zum Kriegsdienst und wurde sofort in Frankreich eingesetzt. 1919 kam er zurück nach New York und nahm das Studium der Biologie an der Columbia University auf, das er bereits zwei Jahre später mit der Promotion abschloss. Danach war er als wissenschaftliche Hilfskraft an der Bellevue Medical School der New York University beschäftigt und lehrte insbesondere Histologie, Embryologie und Allgemeine Anatomie. 1923 erhielt er einen Ruf von der Universität Chicago, wo er seine spätere Ehefrau Ruth kennenlernte, mit der er drei Kinder hatte. In Chicago fand er Bedingungen vor, die es ihm ermöglichten, sein Hauptinteresse zu intensivieren - die Paläontologie. So entstanden in den Jahren von 1925 bis 1935 37 Fachartikel, die sich mit diesem Thema befassten. 1934 wurde er zum Professor für Biologie an der Harvard University ernannt. -
Distributions of Extinction Times from Fossil Ages and Tree Topologies: the Example of Some Mid-Permian Synapsid Extinctions
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.11.448028; this version posted June 11, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Distributions of extinction times from fossil ages and tree topologies: the example of some mid-Permian synapsid extinctions Gilles Didier1 and Michel Laurin2 1IMAG, Univ Montpellier, CNRS, Montpellier, France 2CR2P (“Centre de Recherches sur la Paléobiodiversité et les Paléoenvironnements”; UMR 7207), CNRS/MNHN/UPMC, Sorbonne Université, Muséum National d’Histoire Naturelle, Paris, France June 11, 2021 Abstract Given a phylogenetic tree of extinct and extant taxa with fossils where the only temporal infor- mation stands in the fossil ages, we devise a method to compute the distribution of the extinction time of a given set of taxa under the Fossilized-Birth-Death model. Our approach differs from the previous ones in that it takes into account the possibility that the taxa or the clade considered may diversify before going extinct, whilst previous methods just rely on the fossil recovery rate to estimate confidence intervals. We assess and compare our new approach with a standard previous one using simulated data. Results show that our method provides more accurate confidence intervals. This new approach is applied to the study of the extinction time of three Permo-Carboniferous synapsid taxa (Ophiacodontidae, Edaphosauridae, and Sphenacodontidae) that are thought to have disappeared toward the end of the Cisuralian, or possibly shortly thereafter. The timing of extinctions of these three taxa and of their component lineages supports the idea that a biological crisis occurred in the late Kungurian/early Roadian. -
Early Tetrapod Relationships Revisited
Biol. Rev. (2003), 78, pp. 251–345. f Cambridge Philosophical Society 251 DOI: 10.1017/S1464793102006103 Printed in the United Kingdom Early tetrapod relationships revisited MARCELLO RUTA1*, MICHAEL I. COATES1 and DONALD L. J. QUICKE2 1 The Department of Organismal Biology and Anatomy, The University of Chicago, 1027 East 57th Street, Chicago, IL 60637-1508, USA ([email protected]; [email protected]) 2 Department of Biology, Imperial College at Silwood Park, Ascot, Berkshire SL57PY, UK and Department of Entomology, The Natural History Museum, Cromwell Road, London SW75BD, UK ([email protected]) (Received 29 November 2001; revised 28 August 2002; accepted 2 September 2002) ABSTRACT In an attempt to investigate differences between the most widely discussed hypotheses of early tetrapod relation- ships, we assembled a new data matrix including 90 taxa coded for 319 cranial and postcranial characters. We have incorporated, where possible, original observations of numerous taxa spread throughout the major tetrapod clades. A stem-based (total-group) definition of Tetrapoda is preferred over apomorphy- and node-based (crown-group) definitions. This definition is operational, since it is based on a formal character analysis. A PAUP* search using a recently implemented version of the parsimony ratchet method yields 64 shortest trees. Differ- ences between these trees concern: (1) the internal relationships of aı¨stopods, the three selected species of which form a trichotomy; (2) the internal relationships of embolomeres, with Archeria -
Dashankou Fauna: a Unique Window on the Early Evolution of Therapsids
Vol.24 No.2 2010 Paleoherpetology Dashankou Fauna: A Unique Window on the Early Evolution of Therapsids LIU Jun* Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China n the 1980s, the Institute of Geology, Chinese Academy of IGeological Sciences (IGCAGS) sent an expedition to the area north of the Qilian Mountains to study the local terrestrial Permian and Triassic deposits. A new vertebrate fossil locality, later named Dashankou Fauna, was discovered by Prof. CHENG Zhengwu in Dashankou, Yumen, Gansu Province in 1981. Small-scale excavations in 1981, 1982 and 1985 demonstrated that this locality was a source of abundant and diverse vertebrate fossils. In the 1990s, supported by the National Natural Science Foundation of China, the Fig. 1 Prof. LI Jinling in the excavation of 1995. She first summarized the known IGCAGS, the Institute of Vertebrate members of the Dashankou Fauna and brought it to light as the most primitive and abundant Chinese tetrapod fauna. Paleontology and Paleoanthropology (IVPP) under CAS, and the Geological Museum of China formed a joint team IVPP were productive and have since investigations were first disseminated to work on this fauna. Three large- unveiled an interesting episode in the to the public in 1995. In 2001, Prof. scale excavations, undertaken in transition from reptiles to mammals in LI Jinling summarized the known 1991, 1992, and 1995 respectively, as evolutionary history. members of the fauna and discussed well as the subsequent ones held by The results from these their features. She pointed out that * To whom correspondence should be addressed at [email protected]. -
Proceedings of the Open University Geological Society
Proceedings of the Open University Geological Society Volume 4 2018 Including lecture articles from the AGM 2017, the Milton Keynes Symposium 2017, OUGS Members’ field trip reports, the Annual Report for 2017, and the 2017 Moyra Eldridge Photographic Competition winning and highly commended photographs Edited and designed by: Dr David M. Jones 41 Blackburn Way, Godalming, Surrey GU7 1JY e-mail: [email protected] The Open University Geological Society (OUGS) and its Proceedings Editor accept no responsibility for breach of copyright. Copyright for the work remains with the authors, but copyright for the published articles is that of the OUGS. ISSN 2058-5209 © Copyright reserved Proceedings of the OUGS 4 2018; published 2018; printed by Hobbs the Printers Ltd, Totton, Hampshire Evolution of life on land: how new Scottish fossils are re-writing our under- standing of this important transition Dr Tim Kearsey BGS Edinburgh Romer’s gap — a hole in our understanding t has long been understood that at some point in the evolution Meanwhile at a quarry called East Kirkton Quarry near Iof vertebrates there was a transition point where they moved Edinburgh in Scotland vertebrate fossils were discovered that are from mainly subsiding in water to living on land. However, until 10 million years younger than the Greenland fossils. These include recently there had been no fossil evidence that documented how Westlothiana, which is thought to be the first amniote (egg-layer) vertebrate life stepped from water to land. This significant hole in or possibly early reptile (Smithson and Rolfe 1990) and scientific knowledge of evolution is referred to as Romer’s gap Balanerpeton an extinct genus of temnospondyl amphibian. -
Physical and Environmental Drivers of Paleozoic Tetrapod Dispersal Across Pangaea
ARTICLE https://doi.org/10.1038/s41467-018-07623-x OPEN Physical and environmental drivers of Paleozoic tetrapod dispersal across Pangaea Neil Brocklehurst1,2, Emma M. Dunne3, Daniel D. Cashmore3 &Jӧrg Frӧbisch2,4 The Carboniferous and Permian were crucial intervals in the establishment of terrestrial ecosystems, which occurred alongside substantial environmental and climate changes throughout the globe, as well as the final assembly of the supercontinent of Pangaea. The fl 1234567890():,; in uence of these changes on tetrapod biogeography is highly contentious, with some authors suggesting a cosmopolitan fauna resulting from a lack of barriers, and some iden- tifying provincialism. Here we carry out a detailed historical biogeographic analysis of late Paleozoic tetrapods to study the patterns of dispersal and vicariance. A likelihood-based approach to infer ancestral areas is combined with stochastic mapping to assess rates of vicariance and dispersal. Both the late Carboniferous and the end-Guadalupian are char- acterised by a decrease in dispersal and a vicariance peak in amniotes and amphibians. The first of these shifts is attributed to orogenic activity, the second to increasing climate heterogeneity. 1 Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK. 2 Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstraße 43, 10115 Berlin, Germany. 3 School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK. 4 Institut -
Paleozoic Geomagnetism Shapes Vertebrate Evolution
1 Paleozoic geomagnetism shapes vertebrate evolution 2 John Phillip Staub 3 Unaffiliated researcher 4 Corresponding Author: John P. Staub Email address: [email protected] 5 6 Background. Despite a fifty-year failure of paleontologists to find a viable connection between 7 geomagnetic polarity reversals and evolutionary patterns, recent databases show that the early 8 appearance, radiation, and diversification of Paleozoic vertebrates tends to occur during periods 9 having frequent collapses of the Earth’s geomagnetic field. The transition time during the 10 collapse of the Earth’s protective magnetic shield can last thousands of years, and the effects on 11 biota are unknown. Solar and cosmic radiation, volcanism, weather alteration, low-frequency 12 electromagnetic fields, depletion of ozone, and the stripping of atmospheric oxygen have been 13 proposed as possible causes, but previous studies have found no effects. 14 Methods. Using published databases, we compiled a spreadsheet that shows the first appearance 15 of 1809 age-dated genera with each genus assigned to one of 28 taxonomic groups. From 16 Gradstein’s Geologic Time Scale 2012, we delineated 17 Paleozoic zones with either high or low 17 levels of polarity reversals. 18 Results. From our compilation, we counted 508 Paleozoic vertebrates that first appeared within 19 20 million-years of the origin of their clade or natural group. These genera represent the initial 20 radiation and diversification of individual Paleozoic vertebrate clades. After compensating for 21 sample-size and external geologic biases, the resulting Pearson’s coefficient between these 22 genera and polarity zones equals 0.781. Using 11 commonly accepted clades and assuming a 23 natural competition existed between them, we counted each genus from a clade’s inception until 24 it was bypassed by a subsequent clade. -
3Systematics and Diversity of Extant Amphibians
Systematics and Diversity of 3 Extant Amphibians he three extant lissamphibian lineages (hereafter amples of classic systematics papers. We present widely referred to by the more common term amphibians) used common names of groups in addition to scientifi c Tare descendants of a common ancestor that lived names, noting also that herpetologists colloquially refer during (or soon after) the Late Carboniferous. Since the to most clades by their scientifi c name (e.g., ranids, am- three lineages diverged, each has evolved unique fea- bystomatids, typhlonectids). tures that defi ne the group; however, salamanders, frogs, A total of 7,303 species of amphibians are recognized and caecelians also share many traits that are evidence and new species—primarily tropical frogs and salaman- of their common ancestry. Two of the most defi nitive of ders—continue to be described. Frogs are far more di- these traits are: verse than salamanders and caecelians combined; more than 6,400 (~88%) of extant amphibian species are frogs, 1. Nearly all amphibians have complex life histories. almost 25% of which have been described in the past Most species undergo metamorphosis from an 15 years. Salamanders comprise more than 660 species, aquatic larva to a terrestrial adult, and even spe- and there are 200 species of caecilians. Amphibian diver- cies that lay terrestrial eggs require moist nest sity is not evenly distributed within families. For example, sites to prevent desiccation. Thus, regardless of more than 65% of extant salamanders are in the family the habitat of the adult, all species of amphibians Plethodontidae, and more than 50% of all frogs are in just are fundamentally tied to water. -
Bones, Molecules, and Crown- Tetrapod Origins
TTEC11 05/06/2003 11:47 AM Page 224 Chapter 11 Bones, molecules, and crown- tetrapod origins Marcello Ruta and Michael I. Coates ABSTRACT The timing of major events in the evolutionary history of early tetrapods is discussed in the light of a new cladistic analysis. The phylogenetic implications of this are com- pared with those of the most widely discussed, recent hypotheses of basal tetrapod interrelationships. Regardless of the sequence of cladogenetic events and positions of various Early Carboniferous taxa, these fossil-based analyses imply that the tetrapod crown-group had originated by the mid- to late Viséan. However, such estimates of the lissamphibian–amniote divergence fall short of the date implied by molecular studies. Uneven rates of molecular substitutions might be held responsible for the mismatch between molecular and morphological approaches, but the patchy quality of the fossil record also plays an important role. Morphology-based estimates of evolutionary chronology are highly sensitive to new fossil discoveries, the interpreta- tion and dating of such material, and the impact on tree topologies. Furthermore, the earliest and most primitive taxa are almost always known from very few fossil localities, with the result that these are likely to exert a disproportionate influence. Fossils and molecules should be treated as complementary approaches, rather than as conflicting and irreconcilable methods. Introduction Modern tetrapods have a long evolutionary history dating back to the Late Devonian. Their origins are rooted into a diverse, paraphyletic assemblage of lobe-finned bony fishes known as the ‘osteolepiforms’ (Cloutier and Ahlberg 1996; Janvier 1996; Ahlberg and Johanson 1998; Jeffery 2001; Johanson and Ahlberg 2001; Zhu and Schultze 2001). -
Biarmosuchus
Meet the Amniotes: The great terrestrial adaptation Pterosauria Archaic archosaurs Crocodiles Dinosauria Lepidosaurs Anapsids Synapsids Most ‘amphibians’ Most ‘fishes’ Assorted jawless fish Amniota Urochordata Tetrapoda Cephalochordata Gnathostomata Vertebrata Amniotic egg Chordata Thick skin Distinctive skulls The cleidoic egg: a private pond Eggshell: Semipermeable Calcareous or leathery Albumen: Egg cytoplasm Amnion: Protection / Gas transfer Yo l k Sac: Nutrient Pool Allantois: Waste Pool Synapsida Anapsida Lepidosauria Archosauria First amniotes Diapsida in record (!!) Eureptilia Amniotes Walking with Monsters Chapter 2 1:10-5:00 Evolution of Eggs? Some modern amphibians To deal with longer time Eggs became larger, lay eggs on land... why? periods on dry land, tougher. Large eggs can - One inner membrane tougher shells were produce larger babies, 1. escape predation selected for. Gas exchange which had a higher and waste devices evolved likelihood of survival in a for complete eggtonomy tough world. Evolution of Hair? Amniotes all have the gene for hair: alpha keratin In birds/lizards, it’s expressed in claws In mammals, it’s used in hair & nails 310 Ma Thrinaxodon Blood vessel channels on premaxillae, maxillae ~vibrassae (whiskers) (early Triassic) Castorcauda First direct fossil evidence of hair (mid-Jurassic) Meet the Amniotes No temporal fenestra Upper temporal fenestra Lower temporal fenestra Single temporal fenestra = ‘window’ fenestra The Permian 299-251 Ma The Permian 299-251 Ma Convergence of Pangaea The effects of the landscape on climate: Gondwana icecap disappeared Heat distributed more equally through fluids than solids as continent drifted north Oceans slower to warm/cool than continents Pangaea: Rapid warming/cooling ~ more intense than today Temperature extremes Our modern continents are ‘tempered’ by oceans between them. -
Alfred Romer to Hugh L
NATIONAL ACADEMY OF SCIENCES ALFRED SHERWOOD ROMER 1894—1973 A Biographical Memoir by EDWIN H. COLBERT Any opinions expressed in this memoir are those of the author(s) and do not necessarily reflect the views of the National Academy of Sciences. Biographical Memoir COPYRIGHT 1982 NATIONAL ACADEMY OF SCIENCES WASHINGTON D.C. ALFRED SHERWOOD ROMER December 28, 1894 -November 5, 1973 BY EDWIN H. COLBERT LFRED SHERWOOD ROMER was a man of many aspects: a A profound scholar whose studies of vertebrate evolution based upon the comparative anatomy of fossils established him throughout the world as an outstanding figure in his field; a gifted teacher who trained several generations of paleontologists and anatomists; an effective administrator who never allowed the burden of office to diminish his re- search activities; a lucid writer whose books and scientific papers were and are of inestimable value; and a warm per- son, loved and admired by family, friends, and colleagues. Al, as he was universally known to his friends, lived a full and rewarding life, during which he led and influenced paleon- tologists, anatomists, and evolutionists in many lands. His absence is keenly felt. A1 Romer was born in White Plains, New York on December 28, 1894, the son of a newspaper man who was editor, and sometimes owner, of several small-town news- papers in Connecticut and New York, and who later worked for the Associated Press. On the paternal side he was de- scended from Jacob Romer, an emigrant from Ziirich who settled among the Dutch residents of the Hudson River Val- ley about 1725.