Demographic Methods across the Tree of Life

About this book

Demography is everywhere in our lives: from birth to death. Indeed, the universal currencies of survival, development, reproduction, and recruitment shape the performance of all species, from microbes to humans. The number of techniques for demographic data acquisition and analyses across the entire tree of life (microbes, fungi, plants, and animals) has drastically increased in recent decades. These developments have been partially facilitated by the advent of technologies such as GIS and drones, as well as analytical methods including Bayesian statistics and high-throughput molecular analyses. However, despite the universality of demography and the significant research potential that could emerge from unifying: (i) questions across taxa, (ii) data collection protocols, and (iii) analytical tools, demographic methods to date have remained taxonomically siloed and methodologically disintegrated. This is the first book to attempt a truly unified approach to demography and population ecology in order to address a wide range of questions in ecology, evolution, and conservation biology across the entire spectrum of life.

This novel book provides the reader with the fundamentals of data collection, model construction, analyses, and interpretation across a wide repertoire of demographic techniques and protocols. It introduces the novice demographer to a broad range of demographic methods, including abundance-based models, life tables, matrix population models, integral projection models, integrated population models, individual based models, and more. Through the careful integration of data collection methods, analytical approaches, and applications, clearly guided throughout with fully reproducible R scripts, Demographic Methods across the Tree of Life provides an up-to-date and authoritative overview of the most popular and effective demographic tools.

Demographic Methods across the Tree of Life is aimed at graduate students and professional researchers in the fields of demography, ecology, animal behaviour, genetics, evolutionary biology, mathematical biology, and wildlife management.

Contents

Foreword / Tim Coulson
Introduction: From Lions, to Lion's Manes, and Dandelions: Why Using (which types of) Demographic Data and Methods / Roberto Salguero-Gómez and Marlène Gamelon

Part I. Demographic Data Collection: From Genes to Environment
1. Genetic Data Collection, Pedigrees and Phylogenies / Emily G. Simmonds, Henrik Jensen, Alina Niskanen and Steven Smith
2. Biochemical and Physiological Data Collection / Oldrich Tomasek, Alan A. Cohen, Erola Fenollosa, Maurizio Mencuccini, Sergi Munné-Bosch and Fanie Pelletier
3. Social Data Collection and Analyses / Marie J.E. Charpentier, Marie Pelé, Julien P. Renoult and Cédric Sueur
4. Growth Rings across the Tree of Life: Demographic Insights from Biogenic Time Series Data / Margaret E. K. Evans, Bryan A. Black, Donald A. Falk, Courtney L. Giebink and Emily L. Schultz
5. Longitudinal Demographic Data Collection / Marlène Gamelon, Josh A. Firth, Mathilde Le Moullec, William K. Petry and Roberto Salguero-Gómez
6. Drivers of Demography: Past Challenges and a Promise for a Changed Future / Pedro F. Quintana-Ascencio, Eric S. Menges, Geoffrey S. Cook, Johan Ehrlén and Michelle E. Afkhami

Part II. Data and Research Question-Driven Methods
7. Abundance Based Approaches / Jonas Knape and Andreas Lindén
8. Life Tables: Construction and Interpretation / Owen R. Jones
9. Introduction to Matrix Population Models / Yngvild Vindenesa, Christie Le Coeura and Hal Caswell
10. Integral Projection Models / Edgar J. González, Dylan Z. Childs, Pedro F. Quintana-Ascencio and Roberto Salguero-Gómez
11. Transient Analyses of Population Dynamics Using Matrix Projection Models / David N. Koons, David T. Iles and Iain Stott
12. Individual-Based Models / Viktoriia Radchuk, Stephanie Kramer-Schadt, Uta Berger, Cédric Scherer, Pia Backmann and Volker Grimm
13. Survival Analyses / Sarah Cubaynes, Simon Galas, Myriam Richaud, Ana Sanz Aguilar, Roger Pradel, Giacomo Tavecchia, Fernando Colchero, Sebastien Roques, Richard Shefferson and Carlo Giovanni Camarda
14. Efficient use of demographic Data: Integrated Population Models / Marlène Gamelon, Stefan J.G. Vriend, Marcel E. Visser, Caspar A. Hallmann, Suzanne T.E. Lommen and Eelke Jongejans

Part III. Applications
15. Spatial Demography / Guillaume Péron
16. Evolutionary Demography / Shripad Tuljapurkar and Wenyun Zuo
17. Reproductive value and analyses of population dynamics of age-structured populations / Bernt-Erik Sæther and Steinar Engen
18. Applying Comparative Methods to Different Databases: Lessons from Demographic Analyses Across Mammal Species / Jean-Michel Gaillard, Victor Ronget, Jean-François Lemaître, Christophe Bonenfant, Guillaume Péron, Pol Capdevila, M.arlène Gamelon and Roberto Salguero-Gómez
19. Adaptive Management: Making Recurrent Decisions in the Face of Uncertainty / James D. Nichols
20. Heritability, Polymorphism and Population Dynamics: Individual-Based Eco-Evolutionary Simulations / Anna Kuparinen
21. Demographic Processes in Socially Structured Populations / Maria Paniw, Gabriele Cozzi, Stefan Sommer and Arpat Ozgul
22. Demographic Methods in Epidemiology / Petra Klepac and C. Jessica E. Metcalf

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Biography

Roberto Salguero-Gómez is an Associate Professor in Ecology at the Department of Zoology and a Tutorial Fellow at Pembroke College at the University of Oxford, UK. He also holds research affiliations at the University of Sheffield, UK, the University of Queensland, Australia, and the Max Planck Institute for Demographic Research, Germany. He studies population responses to climate change, the evolution of senescence, and drivers of variation in life-history trait variation across plants and animals. He has authored over 80 peer-reviewed papers, including articles in Nature, PNAS, Nature Ecology and Evolution and Ecology Letters. He serves as Associate Editor at Ecology Letters, Journal of Ecology, Journal of Animal Ecology, and Theoretical Population Biology. He has also edited 10 special features and published the book The Evolution of Senescence in the Tree of Life (2017).

Marlène Gamelon is a Researcher at the Centre National de la Recherche Scientifique (CNRS) in Lyon, France. She is also a researcher at the Centre for Biodiversity Dynamics (CBD) at the University of Science and Technology (NTNU) in Trondheim, Norway. She is interested in understanding how free-ranging animal populations respond to environmental changes, including abiotic (climate conditions), anthropogenic (harvest), and biotic (intra- and interspecific interactions) factors. Her work mainly relies on individual long-term monitoring of birds and mammals. She has authored peer-reviewed papers, including articles in Trends in Ecology and Evolution, Ecology Letters, Evolution, Journal of Animal Ecology and the American Naturalist.


Contributors:
- Michelle E. Afkhami, University of Miami, USA
- Pia Backmann, Technische Universität Dresden, Germany
- Uta Berger, Technische Universität Dresden, Germany
- Bryan A. Black, University of Arizona, USA
- Christophe Bonenfant, CNRS, University of Lyon, France
- Carlo Giovanni Camarda, Institut National d'Études Démographiques, France
- Pol Capdevila, University of Bristol, UK
- Hal Caswell, University of Amsterdam, The Netherlands
- Marie J. E. Charpentier, CNRS, France
- Dylan Z. Childs, University of Sheffield, UK
- Alan A. Cohen, University of Sherbrooke, Canada
- Fernando Colchero, University of Southern Denmark, Denmark
- Geoffrey S. Cook, University of Central Florida, USA
- Gabriele Cozzi, University of Zurich, Switzerland
- Sarah Cubaynes, University of Montpellier and University of Paul Valéry, France
- Johan Ehrlén, Stockholm University, Sweden
- Steinar Engen, Norwegian University of Science and Technology, Norway
- Margaret E. K. Evans, University of Arizona, USA
- Donald A. Falk, University of Arizona, USA
- Erola Fenollosa, University of Barcelona and IRBio (Institut de Recerca de la Biodiversitat), Spain
- Josh A. Firth, University of Oxford, UK
- Jean-Michel Gaillard, University of Lyon, France
- Simon Galas, University of Montpellier, France
- Marlène Gamelon, CNRS, University of Lyon, France; Norwegian University of Science and Technology, Norway
- Courtney L. Giebink, University of Arizona, USA
- Edgar J. González, Universidad Nacional Autónoma de México, Mexico
- Volker Grimm, University of Potsdam and Helmholtz Centre for Environmental Research-UFZ, Germany
- Caspar A. Hallmann, Radboud University Nijmegen, The Netherlands
- David T. Iles, Environment and Climate Change Canada, Canada
- Henrik Jensen, Norwegian University of Science and Technology, Norway
- Owen R. Jones, University of Southern Denmark, Denmark
- Eelke Jongejans, Radboud University Nijmegen, The Netherlands
- Petra Klepac, London School of Hygiene and Tropical Medicine, UK
- Jonas Knape, Swedish University of Agricultural Sciences, Sweden
- Stephanie Kramer-Schadt, Institute of Ecology, Technische Universität Berlin and Institute for Zoo and Wildlife Research, Germany
- David N. Koons, Colorado State University, USA
- Anna Kuparinen, University of Jyväskylä, Finland
- Christie Le Coeur, University of Oslo, Norway
- Andreas Lindén, Natural Resources Institute Finland (Luke), Finland
- Suzanne T. E. Lommen, Leiden University, the Netherlands and University of Fribourg, Germany
- Maurizio Mencuccini, ICREA (Catalan Institute for Research and Advances Studies); CREAF (Research Center in Ecology and Forestry Applications), Spain
- Eric S Menges, Archbold Biological Station, USA
- C. Jessica E. Metcalf, Princeton University, USA
- Mathilde Le Moullec, Norwegian University of Science and Technology, Norway
- Jean-François Lemaître, University of Lyon, France
- Sergi Munné-Bosch, University of Barcelona, Spain
- James D. Nichols, University of Florida, USA
- Alina Niskanen, University of Oulu, Finland
- Arpat Ozgul, University of Zurich, Switzerland
- Maria Paniw, University of Zurich, Switzerland
- Marie Pelé, Lille Catholic University, France
- Fanie Pelletier, University of Sherbrooke, Canada
- Guillaume Péron, University of Lyon, France
- William K. Petry, North Carolina State University, USA
- Roger Pradel, University of Montpellier and University of Paul Valéry, France
- Pedro F. Quintana-Ascencio, University of Central Florida, USA
- Viktoriia Radchuk, Leibniz Institute for Zoo and Wildlife Research, Austria
- Julien P. Renoult, CNRS and CEFE, France
- Myriam Richaud, University of Montpellier, France
- Victor Ronget, University of Paris, France
- Sebastien Roques, University of Montpellier and University of Paul Valéry, France
- Roberto Salguero-Gómez, University of Oxford, UK; Max Planck Institute for Demographic Research, Germany; University of Queensland, Australia
- Bernt-Erik Sæther, Norwegian University of Science and Technology, Norway
- Ana Sanz Aguilar Ramon y Cajal, University of the Balearic Islands and Animal Demography and Ecology Unit (GEDA), IMEDEA, CSIC-UIB, Spain
- Cédric Scherer, Leibniz Institute for Zoo and Wildlife Research, Austria
- Emily L. Schultz, University of Arizona, USA
- Richard Shefferson, University of Tokyo, Japan
- Emily G. Simmonds, Norwegian University of Science and Technology, Norway
- Steven Smith, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Austria
- Stefan Sommer, University of Zurich, Switzerland
- Iain Stott, University of Lincoln, UK
- Cédric Sueur, Université de Strasbourg and Institut Universitaire de France, France