COMADRE: a global data base of animal demography

Summary The open‐data scientific philosophy is being widely adopted and proving to promote considerable progress in ecology and evolution. Open‐data global data bases now exist on animal migration, species distribution, conservation status, etc. However, a gap exists for data on population dynamics spanning the rich diversity of the animal kingdom world‐wide. This information is fundamental to our understanding of the conditions that have shaped variation in animal life histories and their relationships with the environment, as well as the determinants of invasion and extinction. Matrix population models (MPMs) are among the most widely used demographic tools by animal ecologists. MPMs project population dynamics based on the reproduction, survival and development of individuals in a population over their life cycle. The outputs from MPMs have direct biological interpretations, facilitating comparisons among animal species as different as Caenorhabditis elegans, Loxodonta africana and Homo sapiens. Thousands of animal demographic records exist in the form of MPMs, but they are dispersed throughout the literature, rendering comparative analyses difficult. Here, we introduce the COMADRE Animal Matrix Database, an open‐data online repository, which in its version 1.0.0 contains data on 345 species world‐wide, from 402 studies with a total of 1625 population projection matrices. COMADRE also contains ancillary information (e.g. ecoregion, taxonomy, biogeography, etc.) that facilitates interpretation of the numerous demographic metrics that can be derived from its MPMs. We provide R code to some of these examples. Synthesis: We introduce the COMADRE Animal Matrix Database, a resource for animal demography. Its open‐data nature, together with its ancillary information, will facilitate comparative analysis, as will the growing availability of databases focusing on other aspects of the rich animal diversity, and tools to query and combine them. Through future frequent updates of COMADRE, and its integration with other online resources, we encourage animal ecologists to tackle global ecological and evolutionary questions with unprecedented sample size.

[1]  J. Gaillard,et al.  Linking demographic responses and life history tactics from longitudinal data in mammals , 2016 .

[2]  Y. Buckley,et al.  Fast–slow continuum and reproductive strategies structure plant life-history variation worldwide , 2015, Proceedings of the National Academy of Sciences.

[3]  F. Villalobos,et al.  letsR: a new R package for data handling and analysis in macroecology , 2015 .

[4]  P. Edmunds A quarter‐century demographic analysis of the Caribbean coral, Orbicella annularis, and projections of population size over the next century , 2015 .

[5]  Ming Dong,et al.  The compadre Plant Matrix Database: an open online repository for plant demography , 2015 .

[6]  Nigel G Yoccoz,et al.  Demographic effects of extreme weather events: snow storms, breeding success, and population growth rate in a long-lived Antarctic seabird , 2014, Ecology and evolution.

[7]  Sudhir Kumar,et al.  Tree of Life Reveals Clock-Like Speciation and Diversification , 2014, Molecular biology and evolution.

[8]  J. Clobert,et al.  A database of life-history traits of European amphibians , 2014, Biodiversity data journal.

[9]  J. Gaillard,et al.  Influence of Life-History Tactics on Transient Dynamics: A Comparative Analysis across Mammalian Populations , 2014, The American Naturalist.

[10]  H. Possingham,et al.  Impediments to the Success of Management Actions for Species Recovery , 2014, PloS one.

[11]  Florian Wetzel,et al.  The need for an integrated biodiversity policy support process – Building the European contribution to a global Biodiversity Observation Network (EU BON) , 2014 .

[12]  F. Barraquand,et al.  Demographic responses of a site-faithful and territorial predator to its fluctuating prey: long-tailed skuas and arctic lemmings. , 2014, The Journal of animal ecology.

[13]  J. Vaupel,et al.  Diversity of ageing across the tree of life , 2013, Nature.

[14]  Peter B. Adler,et al.  Functional traits explain variation in plant life history strategies , 2013, Proceedings of the National Academy of Sciences.

[15]  Dalia A. Conde,et al.  Carnivora Population Dynamics Are as Slow and as Fast as Those of Other Mammals: Implications for Their Conservation , 2013, PloS one.

[16]  R. A. Pyron,et al.  A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes , 2013, BMC Evolutionary Biology.

[17]  H. Weimerskirch,et al.  Fisheries Bycatch as an Inadvertent Human-Induced Evolutionary Mechanism , 2013, PloS one.

[18]  M. McCarthy,et al.  Incorporating Uncertainty of Management Costs in Sensitivity Analyses of Matrix Population Models , 2013, Conservation biology : the journal of the Society for Conservation Biology.

[19]  Sean M. McMahon,et al.  IPMpack: an R package for integral projection models , 2013 .

[20]  Eduard Szöcs,et al.  taxize: taxonomic search and retrieval in R , 2013, F1000Research.

[21]  W. Jetz,et al.  The global diversity of birds in space and time , 2012, Nature.

[22]  Iain Stott,et al.  popdemo: an R package for population demography using projection matrix analysis , 2012 .

[23]  M. Holland,et al.  Effects of climate change on an emperor penguin population: analysis of coupled demographic and climate models , 2012, Global change biology.

[24]  M. Lima,et al.  Increased outbreak frequency associated with changes in the dynamic behaviour of populations of two aphid species , 2012 .

[25]  J. Dupuy,et al.  Assessing the Impact of Bycatch on Dolphin Populations: The Case of the Common Dolphin in the Eastern North Atlantic , 2012, PloS one.

[26]  Stuart Townley,et al.  A framework for studying transient dynamics of population projection matrix models. , 2011, Ecology letters.

[27]  The population projection as a matrix operator , 1964, Demography.

[28]  J. Gaillard,et al.  Towards a vertebrate demographic data bank , 2012, Journal of Ornithology.

[29]  Michael C Runge,et al.  Climate change threatens polar bear populations: a stochastic demographic analysis. , 2010, Ecology.

[30]  Hilmar Lapp,et al.  The Primate Life History Database: a unique shared ecological data resource , 2010, Methods in ecology and evolution.

[31]  O. Krüger,et al.  The return of the white-tailed eagle (Haliaeetus albicilla) to northern Germany: Modelling the past to predict the future , 2010 .

[32]  Roberto Salguero-Gómez,et al.  Matrix projection models meet variation in the real world , 2010 .

[33]  J. Grand,et al.  Contributions of vital rates to growth of a protected population of American black bears , 2009 .

[34]  H. Caswell Stage, age and individual stochasticity in demography , 2009 .

[35]  Kate E. Jones,et al.  PanTHERIA: a species‐level database of life history, ecology, and geography of extant and recently extinct mammals , 2009 .

[36]  J. de Magalhães,et al.  A database of vertebrate longevity records and their relation to other life‐history traits , 2009, Journal of evolutionary biology.

[37]  Ben Collen,et al.  Monitoring Change in Vertebrate Abundance: the Living Planet Index , 2009, Conservation biology : the journal of the Society for Conservation Biology.

[38]  Arpat Ozgul,et al.  Influence of Local Demography on Asymptotic and Transient Dynamics of a Yellow‐Bellied Marmot Metapopulation , 2009, The American Naturalist.

[39]  Hal Caswell,et al.  Demographic models and IPCC climate projections predict the decline of an emperor penguin population , 2009, Proceedings of the National Academy of Sciences.

[40]  M. Conroy,et al.  Modeling demographic processes in marked populations , 2009 .

[41]  S. Charles,et al.  Matrix Population Models as Relevant Modeling Tools in Ecotoxicology , 2009 .

[42]  S. Orzack,et al.  Dynamic heterogeneity in life histories. , 2009, Ecology letters.

[43]  D. Wake,et al.  Are we in the midst of the sixth mass extinction? A view from the world of amphibians , 2008, Proceedings of the National Academy of Sciences.

[44]  H. Caswell Perturbation analysis of nonlinear matrix population models , 2008 .

[45]  Brook G. Milligan,et al.  Estimating and Analyzing Demographic Models Using the popbio Package in R , 2007 .

[46]  María B. García,et al.  An extraordinary life span estimate for the clown anemonefish Amphiprion percula , 2007 .

[47]  C Jessica E Metcalf,et al.  Why evolutionary biologists should be demographers. , 2007, Trends in ecology & evolution.

[48]  Kate E. Jones,et al.  The delayed rise of present-day mammals , 1990, Nature.

[49]  Robert P. Guralnick,et al.  A web-based GIS tool for exploring the world's biodiversity: The Global Biodiversity Information Facility Mapping and Analysis Portal Application (GBIF-MAPA) , 2007, Ecol. Informatics.

[50]  Robert G. Clark,et al.  Lesser Scaup Population Dynamics: What Can Be Learned from Available Data? , 2006 .

[51]  L. Antonio Vélez-Espino,et al.  Characterization of elasticity patterns of North American freshwater fishes , 2006 .

[52]  Hugh P Possingham,et al.  Accounting for Management Costs in Sensitivity Analyses of Matrix Population Models , 2006, Conservation biology : the journal of the Society for Conservation Biology.

[53]  T. Beebee,et al.  The amphibian decline crisis: A watershed for conservation biology? , 2005 .

[54]  T. Flatt,et al.  Winter weather affects asp viper Vipera aspis population dynamics through susceptible juveniles , 2005 .

[55]  Jean-Dominique Lebreton,et al.  Using Demographic Invariants to Detect Overharvested Bird Populations from Incomplete Data , 2005 .

[56]  Jean-Michel Gaillard,et al.  Generation Time: A Reliable Metric to Measure Life‐History Variation among Mammalian Populations , 2005, The American Naturalist.

[57]  H. Caswell,et al.  Reactivity and transient dynamics of discrete-time ecological systems , 2005 .

[58]  T. Kawecki Demography of source—sink populations and the evolution of ecological niches , 2005, Evolutionary Ecology.

[59]  M. Neubert,et al.  Projecting Rates of Spread for Invasive Species , 2004, Risk analysis : an official publication of the Society for Risk Analysis.

[60]  S. K. Morgan Ernest,et al.  LIFE HISTORY CHARACTERISTICS OF PLACENTAL NONVOLANT MAMMALS , 2003 .

[61]  H. Caswell,et al.  Demography and dispersal : life table response experiments for invasion speed , 2003 .

[62]  J. Clobert,et al.  Mating behaviour influences extinction risk: insights from demographic modelling and comparative analysis of avian extinction risk , 2003 .

[63]  G. Cailliet,et al.  Comparative population demography of elasmobranchs using life history tables, Leslie matrices and stage-based matrix models , 2002 .

[64]  William F. Morris,et al.  Quantitative conservation biology , 2002 .

[65]  G. Powell,et al.  Terrestrial Ecoregions of the World: A New Map of Life on Earth , 2001 .

[66]  P. Inchausti,et al.  Investigating long-term ecological variability using the Global Population Dynamics Database. , 2001, Science.

[67]  Vikas Rai,et al.  Chaos in ecology , 2001 .

[68]  J. Silvertown,et al.  Evolution of senescence in iteroparous perennial plants , 2001 .

[69]  Hans de Kroon,et al.  Elasticity Analysis in Population Biology: Methods and Applications1 , 2000 .

[70]  L. Crowder,et al.  LIFE HISTORIES AND ELASTICITY PATTERNS: PERTURBATION ANALYSIS FOR SPECIES WITH MINIMAL DEMOGRAPHIC DATA , 2000 .

[71]  B. Sæther,et al.  AVIAN LIFE HISTORY VARIATION AND CONTRIBUTION OF DEMOGRAPHIC TRAITS TO THE POPULATION GROWTH RATE , 2000 .

[72]  Hal Caswell,et al.  HARBOR PORPOISE AND FISHERIES: AN UNCERTAINTY ANALYSIS OF INCIDENTAL MORTALITY , 1998 .

[73]  Hal Caswell,et al.  Matrix Methods for Population Analysis , 1997 .

[74]  Hal Caswell,et al.  Pod-specific demography of killer whales(Orcinus orca). , 1993 .

[75]  Kenneth H. Pollock,et al.  Estimating Transition Probabilities for Stage‐Based Population Projection Matrices Using Capture‐Recapture Data , 1992 .

[76]  Shripad Tuljapurkar,et al.  Population Dynamics in Variable Environments , 1990 .

[77]  P. Holgate,et al.  Matrix Population Models. , 1990 .

[78]  S. Stearns Trade-offs in life-history evolution , 1989 .

[79]  D. Hill Population dynamics of the avocet (Recurvirostra mavosetta) breeding in Britain , 1988 .

[80]  Larry B. Crowder,et al.  A Stage‐Based Population Model for Loggerhead Sea Turtles and Implications for Conservation , 1987 .

[81]  Hal Caswell,et al.  Elasticity: The Relative Contribution of Demographic Parameters to Population Growth Rate , 1986 .

[82]  O. Diekmann,et al.  The Dynamics of Physiologically Structured Populations , 1986 .

[83]  S. W. Christensen,et al.  A stochastic age-structured population model of striped bass (Morone saxatilis) in the Potomac River , 1983 .

[84]  S. Levin,et al.  Analysis of an age-structured fishery model , 1980 .

[85]  H. Caswell,et al.  A general formula for the sensitivity of population growth rate to changes in life history parameters. , 1978, Theoretical population biology.

[86]  R. Green,et al.  Animal Population Ecology , 1975 .

[87]  J. Rabinovich The Applicability of Some Population Growth Models to a Single-Species Laboratory Population , 1969 .

[88]  L. Pennycuick,et al.  A computer model of the Oxford great tit population. , 1969, Journal of theoretical biology.

[89]  N. Keyfitz,et al.  World Population: An Analysis of Vital Data. , 1969 .

[90]  L. Keith,et al.  Demographic Parameters of a Snowshoe Hare Population , 1968 .

[91]  Nathan Keyfitz,et al.  Introduction to the mathematics of population , 1968 .

[92]  R. C. Thompson On a class of matrix equations. , 1967 .

[93]  L. Lefkovitch The study of population growth in organisms grouped by stages , 1965 .

[94]  P. H. Leslie On the use of matrices in certain population mathematics. , 1945, Biometrika.