Jens Boenigk · Sabina Wodniok Edvard Glücksman Biodiversity and Earth History Biodiversity and Earth History Jens Boenigk • Sabina Wodniok • Edvard Glücksman Biodiversity and Earth History Jens Boenigk Sabina Wodniok Faculty of Biology Faculty of Biology Biodiversity Department Biodiversity Department University Duisburg-Essen University Duisburg-Essen Essen, Germany Essen, Germany Edvard Glücksman Environment & Sustainability Institute University of Exeter, Cornwall Campus Penryn, Cornwall, UK ISBN 978-3-662-46393-2 ISBN 978-3-662-46394-9 (eBook) DOI 10.1007/978-3-662-46394-9 Library of Congress Control Number: 2015936446 S pringer Heidelberg New York Dordrecht London © Springer-Verlag Berlin Heidelberg 2015 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Photo for Cover by Stuart Westmorland, Mill Creek, WA, USA Printed on acid-free paper Springer-Verlag GmbH Berlin Heildelberg is part of Springer Science+Business Media (www.springer.com) Foreword VV Foreword The detection of biological diversity and the understand- eukaryotes in the context of geological history. The focus ing of its underlying mechanisms – how it is generated and of this work, therefore, is to address areas not covered by maintained – has preoccupied humans since antiquity. Snap- conventional textbooks, specifically forging interdisciplinary shots of information about biodiversity were developed as links to develop new methods of understanding known con- early as in Ancient Greece, especially by the philosophers cepts. To that end, we address the overall diversity of eukary- Aristotle and Theophrastus. In the 18th century, Carl Lin- otes, avoiding the standard anthropocentric view of life as naeus proposed a classification system for plants and ani- mainly comprising animals and plants. We also cover, based mals, initially to understand the Divine Order of God’s crea- on highly advanced molecular studies, the phylogenetic de- tion. Roughly a century later, Charles Darwin published his velopment of species in the context of the planet’s geological canonical ideas about species variability; his theory of evo- development, weaving together the history of the Earth and lution continues to drive global research into the molecular the evolution of life. diversity of species, communities, and ecosystems, including We address classical biological and geosciences concepts the Human Genome Project or the Census of Marine Life. in a fresh and innovative manner. Our approach represents a Biodiversity is one of the most complex research topics. In definite break from the disciplinary segregation that charac- order to properly understand the mechanisms underpinning terises conventional textbooks; such a dramatic change could species distribution patterns, researchers must bring together not be avoided. However, in our opinion, this ‘interdiscipli- information from a range of different disciplines, mapping narity’ is one of the book’s great strengths, broadening the the evolution and development of organisms to their ecologi- context of biodiversity studies and presenting new insights cal adaptations and interactions, and linking physiological across century-old disciplines. and morphological diversity patterns to the interplay be- This book covers a range of concepts largely underrepre- tween Earth’s geological development and the evolution of sented in the literature. For example, we describe at length the planet’s life forms. the geological drivers behind the emergence of biodiversity Tools from a wide variety of disciplines, especially in the and current global species distribution patterns. We also life- and geosciences, are needed to address the various com- address in detail the enormous diversity of eukaryotes, em- ponents relating to biodiversity. Maintaining and developing phasising their massive but often overlooked microscopic this interdisciplinary framework is the key to understanding component. Therefore, at the very least, the content of this the emergence and preservation of species. Despite these book draws from geology and palaeontology, morphology unique advantages of such a broad-based approach, such and physiology, chemistry and physics, biology and ecology, work continues to face significant opposition, including from as well as from the most cutting-edge biological systematics. more conventional, single-discipline methods. Although to Our hope is that the truely transdisciplinary focus of this a certain extent valuable as independent research strands, book will resonate with researchers, teachers, and students such frameworks restrain and restrict our understanding of alike, as well as with members of the general public curious the more multifaceted aspects inherent in global biodiversity to learn more about biodiversity – one of nature’s most fun- studies. damental and awe-inspiring phenomena. In this book we provide a balancing act between the geo- sciences and biosciences, aiming to examine the diversity of VI Acknowledgements Acknowledgements We thank Susann Schiwy and Julia Nuy for their great We thank everyone at Springer-Spektrum, in particular support in all aspects of this book’s design. In particular, we Meike Barth, Merlet Behncke-Braunbeck, Barbara Lühker, thank Susann for her tremendous effort in compiling and and Andreas Held for the proofreading as well as everyone managing the image database and Julia for her invaluable at Springer, in particular Stephan Klapp and Ulrike Strick- contributions to the book’s layout and graphics through her er-Komba. For proofreading and editing, we also thank the mastery of Adobe InDesign. staff from proof-reading-service.com and Deutsche Hochs- We also thank Wolfgang Boenigk and Lars Großmann for chulverband, and specifically Frederic Bartlett and Gabriele their critical comments and editorial help in earlier versions Berberich. of the manuscript. Finally, we are particularly grateful to our families and We thank the late Michael Neugebauer and the rest of loved ones. In particular, JB thanks his wife, Stephanie, for the Boenigk working group for their patience and support, her infinite patience throughout the countless hours of re- especially during the increasingly stressful periods leading up search, creation of figures, and during the writing process. to the submission of both manuscripts. Her understanding gave him the time to bring this project We are also grateful to many colleagues and photogra- to fruition. SW thanks her partner, Thomas, and the rest of phers for making the many images featured in this book her family for their loving support, patience, and encourage- available to us. Without them, this project would not have ment. EG thanks his partner, Antonia, for all her love and been possible. inspiration, and his parents, Jerzy and Soulla, for a lifetime of support. Content VII Table of contents 1 Introduction ..................................................................................................................................... 1 1.1 How do I use this book? .............................................................................................................. 2 1.2 Biodiversity ..................................................................................................................................... 4 1.3 Life .................................................................................................................................................... 6 1.4 Species ............................................................................................................................................. 8 2 Earth‘s History ................................................................................................................................ 11 2.1 Fundamentals of the geosciences ............................................................................................ 12 2.1.1 Construction and formation of the Earth .................................................................................. 14 2.1.1.1 Composition of the Earth’s layers .......................................................................................... 16 2.1.1.2 Plate tectonics ................................................................................................................... 18 2.1.2 Rock-forming processes ............................................................................................................ 20 2.1.2.1 Magmatism and igneous rocks .............................................................................................. 22 2.1.2.2 Weathering, erosion, sedimentation and sedimentary rocks ...................................................... 24 2.1.2.3 Carbonate balance and carbonates ....................................................................................... 26 2.1.3 Eons ........................................................................................................................................... 28 2.2 The Precambrian ........................................................................................................................... 30 2.2.1 The Archean eon ....................................................................................................................... 32 2.2.1.1 Chemical evolution and origin of life ...................................................................................... 34 2.2.1.2 ‘RNA world hypothesis’ and formation of cells during the Archean ............................................. 36 2.2.1.3 The Archean carbon metabolism: fermentation ....................................................................... 38 2.2.1.4 Evolution of the Archean photoautotrophy: energetics of the anoxygenic and oxygenic photosynthesis ....................................................... 40 2.2.1.5 Evolution of the Archean photoautotrophy: compartmentalisation ............................................ 42 2.2.2 The Proterozoic eon .................................................................................................................. 44 2.2.2.1 Biogenic and geochemical feedback loops of the Proterozoic oxygen evolution ............................ 46 2.2.2.2 Climatic effects of oxygen evolution: the Huronian glaciation (from 2.4 to 2.1 billion years) ........... 48 2.2.2.3 Metabolic effects of oxygen evolution: cytotoxic effect ............................................................. 50 2.2.2.4 Metabolic consequences of oxygen evolution: aerobic respiration ............................................. 52 2.2.2.5 Evolution of the eukaryotic cell in the Mesoproterozoic ............................................................ 54 2.2.2.6 Evolution of the eukaryotic algae in the Mesoproterozoic ......................................................... 56 2.2.2.7 The ‘boring billion’ years (1.85-0.85 billion years) .................................................................... 58 2.2.2.8 Evolution of complex multi-cellularity in the Neoproterozoic ..................................................... 60 2.2.2.9 Neoproterozoic glaciations (0.85–0.72 billion years) ................................................................. 62 VIII Content 2.3 The Phanerozoic eon ................................................................................................................... 64 2.3.1 The Phanerozoic eon: an overview ........................................................................................... 66 2.3.1.1 Plate tectonics and climate evolution during the Phanerozoic .................................................... 68 2.3.1.2 Lagerstätten....................................................................................................................... 70 2.3.1.3 Fossilisation – the formation of fossils .................................................................................... 72 2.3.1.4 Geochronology and stratigraphy ........................................................................................... 74 2.3.1.5 Termination and biostratigraphic definition of the Phanerozoic systems ...................................... 76 2.3.2 Fossil biodiversity ...................................................................................................................... 78 2.3.2.1 Foraminifers ...................................................................................................................... 80 2.3.2.2 Reef-builders ..................................................................................................................... 82 2.3.2.3 Cephalopods ...................................................................................................................... 84 2.3.2.4 Benthic filter-feeders: brachiopods and bivalves ...................................................................... 86 2.3.2.5 Trilobites ........................................................................................................................... 88 2.3.2.6 Echinoderms ...................................................................................................................... 90 2.3.2.7 Graptolites and Conodonts................................................................................................... 92 2.3.2.8 Vertebrates ........................................................................................................................ 94 2.3.2.9 Land plants ........................................................................................................................ 96 2.3.3 The Palaeozoic era .................................................................................................................... 98 2.3.3.1 The Ediacaran and Phanerozoic-Precambrian boundary ............................................................ 100 2.3.3.2 Evolution of skeletal elements .............................................................................................. 102 2.3.3.3 The Cambrian period........................................................................................................... 104 2.3.3.4 The Ordovician period ......................................................................................................... 106 2.3.3.5 The Silurian period .............................................................................................................. 108 2.3.3.6 Colonisation of terrestrial environments ................................................................................ 110 2.3.3.7 The Devonian period ........................................................................................................... 112 2.3.3.8 The Carboniferous period .................................................................................................... 114 2.3.3.9 The Permian period ............................................................................................................ 116 2.3.3.10 Development of the cormus ............................................................................................... 118 2.3.3.11 Towards a smaller and shorter-lived haploid generation (gametophyte) .................................... 120 2.3.3.12 Towards an increasingly dominant diploid generation (sporophyte) .......................................... 122 2.3.4 The Mesozoic era ...................................................................................................................... 124 2.3.4.1 The Triassic period .............................................................................................................. 126 2.3.4.2 Reproductive adaptations to terrestrial life ............................................................................. 128 2.3.4.3 The Jurassic period ............................................................................................................. 130 2.3.4.4 Sauria ............................................................................................................................... 132 2.3.4.5 The Cretaceous period ........................................................................................................ 134 2.3.4.6 EEvolution of pollination ...................................................................................................... 136 2.3.5 The Cenozoic era ....................................................................................................................... 138 2.3.5.1 The Palaeogene period ........................................................................................................ 140 2.3.5.2 The Neogene period ........................................................................................................... 142 2.3.5.3 Evolution of C photosynthesis .............................................................................................. 144 4 2.3.5.4 Physiological efficiency of C and CAM photosynthesis ............................................................. 146 4 2.3.5.5 The Quaternary period ........................................................................................................ 148 2.3.5.6 The Cenozoic Ice Age ........................................................................................................... 150 Content IX 2.3.5.7 Hominisation ..................................................................................................................... 152 2.3.5.8 The future ......................................................................................................................... 154 3 Distribution of present-day biodiversity ....................................................................... 157 3.1 Basics of the biogeographical distribution of taxa ............................................................... 158 3.1.1 Species descriptions .................................................................................................................. 160 3.1.2 The species concept .................................................................................................................. 162 3.1.3 Molecular diversity and OTUs ................................................................................................... 164 3.1.4 Biodiversity indices ................................................................................................................... 166 3.1.5 Spatial distribution of biodiversity ............................................................................................ 168 3.1.6 Species concept limitations: viruses ......................................................................................... 170 3.1.7 Species concept limitations: lichen ........................................................................................... 172 3.2 Biodiversity distribution .............................................................................................................. 174 3.2.1 Pattern and mechanisms .......................................................................................................... 176 3.2.1.1 Biodiversity hotspots ........................................................................................................... 178 3.2.1.2 Ecological niches ................................................................................................................ 180 3.2.1.3 Speciation mechanisms ....................................................................................................... 182 3.2.1.4 Island biogeography ............................................................................................................ 184 3.2.1.5 Global biodiversity gradients ................................................................................................ 186 3.2.1.6 Biogeography of microorganisms .......................................................................................... 188 3.2.1.7 Alien and invasive species .................................................................................................... 190 3.2.1.8 Cenozoic mass extinction ..................................................................................................... 192 3.2.2 Biogeographic regions ............................................................................................................... 194 3.2.2.1 Global precipitation and temperature distribution ................................................................... 196 3.2.2.2 Global wind systems and climate zones .................................................................................. 198 3.2.2.3 Tundra .............................................................................................................................. 200 3.2.2.4 Taiga ................................................................................................................................. 202 3.2.2.5 Temperate forests ............................................................................................................... 204 3.2.2.6 Temperate grasslands .......................................................................................................... 206 3.2.2.7 Montane and flooded grasslands .......................................................................................... 208 3.2.2.8 Mediterranean biome ......................................................................................................... 210 3.2.2.9 Hot and temperate deserts .................................................................................................. 212 3.2.2.10 Subtropical and tropical grasslands ...................................................................................... 214 3.2.2.11 Subtropical and tropical arid (xerophytic) forests ................................................................... 216 3.2.2.12 Tropical rainforest ............................................................................................................. 218 3.2.2.13 Lakes .............................................................................................................................. 220 3.2.2.14 Rivers .............................................................................................................................. 222 3.2.2.15 Oceans and seas ............................................................................................................... 224