The compadre Plant Matrix Database: an open online repository for plant demography

Schedules of survival, growth and reproduction are key life‐history traits. Data on how these traits vary among species and populations are fundamental to our understanding of the ecological conditions that have shaped plant evolution. Because these demographic schedules determine population growth or decline, such data help us understand how different biomes shape plant ecology, how plant populations and communities respond to global change and how to develop successful management tools for endangered or invasive species. Matrix population models summarize the life cycle components of survival, growth and reproduction, while explicitly acknowledging heterogeneity among classes of individuals in the population. Matrix models have comparable structures, and their emergent measures of population dynamics, such as population growth rate or mean life expectancy, have direct biological interpretations, facilitating comparisons among populations and species. Thousands of plant matrix population models have been parameterized from empirical data, but they are largely dispersed through peer‐reviewed and grey literature, and thus remain inaccessible for synthetic analysis. Here, we introduce the compadre Plant Matrix Database version 3.0, an open‐source online repository containing 468 studies from 598 species world‐wide (672 species hits, when accounting for species studied in more than one source), with a total of 5621 matrices. compadre also contains relevant ancillary information (e.g. ecoregion, growth form, taxonomy, phylogeny) that facilitates interpretation of the numerous demographic metrics that can be derived from the matrices. Synthesis. Large collections of data allow broad questions to be addressed at the global scale, for example, in genetics (genbank), functional plant ecology (try, bien, d3) and grassland community ecology (nutnet). Here, we present compadre, a similarly data‐rich and ecologically relevant resource for plant demography. Open access to this information, its frequent updates and its integration with other online resources will allow researchers to address timely and important ecological and evolutionary questions.

[1]  Matthew W. Pennell,et al.  How much of the world is woody? , 2014 .

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

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

[4]  S. Zeigler,et al.  Actual and Potential Use of Population Viability Analyses in Recovery of Plant Species Listed under the U.S. Endangered Species Act , 2013, Conservation biology : the journal of the Society for Conservation Biology.

[5]  H. Caswell,et al.  A seasonal, density-dependent model for the management of an invasive weed. , 2013, Ecological applications : a publication of the Ecological Society of America.

[6]  Martha M. Ellis,et al.  Ability of Matrix Models to Explain the Past and Predict the Future of Plant Populations , 2013, Conservation biology : the journal of the Society for Conservation Biology.

[7]  M. Franco,et al.  The time distribution of reproductive value measures the pace of life , 2013 .

[8]  Sarah Cunze,et al.  D3: The Dispersal and Diaspore Database – Baseline data and statistics on seed dispersal , 2013 .

[9]  O. Jones,et al.  The pace and shape of senescence in angiosperms , 2013 .

[10]  H. Caswell,et al.  Age, stage and senescence in plants , 2013, The Journal of ecology.

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

[12]  Roberto Salguero-Gómez,et al.  A demographic approach to study effects of climate change in desert plants , 2012, Philosophical Transactions of the Royal Society B: Biological Sciences.

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

[14]  Y. Buckley,et al.  Increased population growth rate in invasive polyploid Centaurea stoebe in a common garden. , 2012, Ecology letters.

[15]  Richard Van Noorden Europe joins UK open-access bid , 2012, Nature.

[16]  R. Laskowski,et al.  Decomposition analysis of LTREs may facilitate the design of short-term ecotoxicological tests , 2012, Ecotoxicology.

[17]  Martha M. Ellis,et al.  Matrix population models from 20 studies of perennial plant populations , 2012 .

[18]  Ran Nathan,et al.  Seed terminal velocity, wind turbulence, and demography drive the spread of an invasive tree in an analytical model. , 2012, Ecology.

[19]  Danny A. P. Hooftman,et al.  Modelling spread of British wind‐dispersed plants under future wind speeds in a changing climate , 2012 .

[20]  S. Higgins,et al.  TRY – a global database of plant traits , 2011, Global Change Biology.

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

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

[23]  Elizabeth E Crone,et al.  How do plant ecologists use matrix population models? , 2011, Ecology letters.

[24]  Roberto Salguero-Gómez,et al.  Matrix Dimensions Bias Demographic Inferences: Implications for Comparative Plant Demography , 2010, The American Naturalist.

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

[26]  Elizabeth E Crone,et al.  Causes and consequences of variation in plant population growth rate: a synthesis of matrix population models in a phylogenetic context. , 2010, Ecology letters.

[27]  J. Peñuelas,et al.  Potentially immortal? , 2010, The New phytologist.

[28]  Brian Huntley,et al.  Beyond bioclimatic envelopes: dynamic species' range and abundance modelling in the context of climatic change , 2010 .

[29]  S. Townley,et al.  Boom or bust? A comparative analysis of transient population dynamics in plants , 2010 .

[30]  Johan Ehrlén,et al.  Empirical tests of life‐history evolution theory using phylogenetic analysis of plant demography , 2010 .

[31]  H. de Kroon,et al.  Region versus site variation in the population dynamics of three short‐lived perennials , 2010 .

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

[33]  A. Griffith Positive effects of native shrubs on Bromus tectorum demography. , 2010, Ecology.

[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]  Y. Buckley,et al.  Multiple life stages with multiple replicated density levels are required to estimate density dependence for plants. , 2009 .

[37]  Nicolas Bacaër,et al.  Periodic Matrix Population Models: Growth Rate, Basic Reproduction Number, and Entropy , 2009, Bulletin of mathematical biology.

[38]  Yvonne M. Buckley,et al.  General guidelines for invasive plant management based on comparative demography of invasive and native plant populations , 2008 .

[39]  S. Tuljapurkar,et al.  Stage Dynamics, Period Survival, and Mortality Plateaus , 2008, The American Naturalist.

[40]  Richard W. Lucas,et al.  Using rainout shelters to evaluate climate change effects on the demography of Cryptantha flava , 2008 .

[41]  H. Caswell,et al.  Sensitivity Analysis of Reactive Ecological Dynamics , 2008, Bulletin of mathematical biology.

[42]  Robert K. Colwell,et al.  Correlates of extinction proneness in tropical angiosperms , 2008 .

[43]  Kiwako S. Araki,et al.  Matrix models using fine size classes and their application to the population dynamics of tree species: Bayesian non-parametric estimation , 2007 .

[44]  S. Pavard,et al.  All paths to fitness lead through demography , 2007 .

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

[46]  C. Bradshaw,et al.  Minimum viable population size: A meta-analysis of 30 years of published estimates , 2007 .

[47]  T. Yamakura,et al.  Strong habitat preference of a tropical rain forest tree does not imply large differences in population dynamics across habitats , 2007 .

[48]  Richard Fox,et al.  Direct and indirect effects of climate and habitat factors on butterfly diversity. , 2007, Ecology.

[49]  Shripad Tuljapurkar,et al.  From stage to age in variable environments: life expectancy and survivorship. , 2006, Ecology.

[50]  S. Ellner,et al.  Integral Projection Models for Species with Complex Demography , 2006, The American Naturalist.

[51]  Y. Kubota Demographic traits of understory trees and population dynamics of aPicea-Abies forest in Taisetsuzan National Park, northern Japan , 1997, Ecological Research.

[52]  Heather North,et al.  Slowing down a pine invasion despite uncertainty in demography and dispersal , 2005 .

[53]  S. Tuljapurkar,et al.  PLANT-ANIMAL INTERACTIONS IN RANDOM ENVIRONMENTS: HABITAT-STAGE ELASTICITY, SEED PREDATORS, AND HURRICANES , 2005 .

[54]  J. Lebreton Age, stages, and the role of generation time in matrix models , 2005 .

[55]  C. Horvitz,et al.  Population growth versus population spread of an ant-dispersed neotropical herb with a mixed reproductive strategy , 2005 .

[56]  Hans de Kroon,et al.  Space versus time variation in the population dynamics of three co‐occurring perennial herbs , 2005 .

[57]  H. Caswell,et al.  STOCHASTIC FLOOD AND PRECIPITATION REGIMES AND THE POPULATION DYNAMICS OF A THREATENED FLOODPLAIN PLANT , 2005 .

[58]  C. C. Barton,et al.  Where in the world are my field plots? Using GPS effectively in environmental field studies , 2004 .

[59]  J. Silvertown,et al.  A COMPARATIVE DEMOGRAPHY OF PLANTS BASED UPON ELASTICITIES OF VITAL RATES , 2004 .

[60]  P. Werner Predictions of fate from rosette size in teasel (Dipsacus fullonum L.) , 1975, Oecologia.

[61]  D. Doak,et al.  Book Review: Quantitative Conservation biology: Theory and Practice of Population Viability analysis , 2004, Landscape Ecology.

[62]  John Vandermeer,et al.  Choosing category size in a stage projection matrix , 2004, Oecologia.

[63]  John Sabo,et al.  Morris, W. F., and D. F. Doak. 2003. Quantitative Conservation Biology: Theory and Practice of Population Viability Analysis. Sinauer Associates, Sunderland, Massachusetts, USA , 2003 .

[64]  E. Menges,et al.  A Fire‐Explicit Population Viability Analysis of Hypericum cumulicola in Florida Rosemary Scrub , 2003 .

[65]  H. Kroon,et al.  AN EXTENDED FLOWERING AND FRUITING SEASON HAS FEW DEMOGRAPHIC EFFECTS IN A MEDITERRANEAN PERENNIAL HERB , 2002 .

[66]  R. Thorne How many species of seed plants are there , 2001 .

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

[68]  H. Caswell Matrix population models : construction, analysis, and interpretation , 2001 .

[69]  H. Caswell,et al.  Stochastic demography and conservation of an endangered perennial plant (Lomatium bradshawii) in a dynamic fire regime , 2001 .

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

[71]  Antoine Guisan,et al.  Predictive habitat distribution models in ecology , 2000 .

[72]  Hal Caswell,et al.  DEMOGRAPHY AND DISPERSAL: CALCULATION AND SENSITIVITY ANALYSIS OF INVASION SPEED FOR STRUCTURED POPULATIONS , 2000 .

[73]  H. Kroon,et al.  ELASTICITIES: A REVIEW OF METHODS AND MODEL LIMITATIONS , 2000 .

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

[75]  S. Ellner,et al.  SIZE‐SPECIFIC SENSITIVITY: APPLYING A NEW STRUCTURED POPULATION MODEL , 2000 .

[76]  E. Menges,et al.  Population viability analyses in plants: challenges and opportunities. , 2000, Trends in ecology & evolution.

[77]  W. Gurney,et al.  Delays, demography and cycles : A forensic study , 1999 .

[78]  J. Silvertown,et al.  Plant Life Histories: Ecology, Phylogeny, and Evolution , 1999 .

[79]  C. Pfister,et al.  Patterns of variance in stage-structured populations: evolutionary predictions and ecological implications. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[80]  Shripad Tuljapurkar,et al.  Structured-Population Models in Marine, Terrestrial, and Freshwater Systems , 1997, Population and Community Biology Series.

[81]  R. Nisbet,et al.  Delay-Differential Equations for Structured Populations , 1997 .

[82]  J. Silvertown,et al.  Life history variation in plants: an exploration of the fast-slow continuum hypothesis , 1996 .

[83]  Eric S. Menges,et al.  Interpretation of elasticity matrices as an aid to the management of plant populations for conservation , 1996 .

[84]  J. Oostermeijer,et al.  Temporal and spatial variation in the demography of Gentiana pneumonanthe, a rare perennial herb , 1996 .

[85]  Robert H. Webb,et al.  Longevity, recruitment and mortality of desert plants in Grand Canyon, Arizona, USA , 1995 .

[86]  Hal Caswell,et al.  Sensitivity Analysis of Periodic Matrix Models , 1994 .

[87]  Miguel Franco,et al.  comparative plant demography - relative importance of life-cycle components to the finite rate of increase in woody and herbaceous perennials , 1993 .

[88]  D. Yamaguchi,et al.  The Oldest Known Rocky Mountain Bristlecone Pines (Pinus aristata Engelm.) , 1992, Arctic and Alpine Research.

[89]  Stephen P. Ellner,et al.  Simple Methods for Calculating Age‐Based Life History Parameters for Stage‐Structured Populations , 1992 .

[90]  K. McConway,et al.  A demographic interpretation of Grime's triangle , 1992 .

[91]  Hal Caswell,et al.  POPULATION RESPONSES TO FIRE IN A TROPICAL SAVANNA GRASS, ANDROPOGON SEMIBERBIS: A MATRIX MODEL APPROACH , 1991 .

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

[93]  M. Franco Plant demography : What do we know? , 1990 .

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

[95]  William Gurney,et al.  Stage Structure Models Applied in Evolutionary Ecology , 1989 .

[96]  Kirk A. Moloney,et al.  Fine‐Scale Spatial and Temporal Variation in the Demography of a Perennial Bunchgrass , 1988 .

[97]  H. Caswell Approaching Size and Age in Matrix Population Models , 1988 .

[98]  H. Kroon,et al.  Density dependent simulation of the population dynamics of a perennial grassland species, Hypochaeris radicata , 1987 .

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

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

[101]  Richard Law,et al.  A Model for the Dynamics of a Plant Population Containing Individuals Classified by Age and Size , 1983 .

[102]  R. Lande,et al.  A Quantitative Genetic Theory of Life History Evolution , 1982 .

[103]  Paulette Bierzychudek,et al.  The Demography of Jack‐in‐the‐Pulpit, a Forest Perennial that Changes Sex , 1982 .

[104]  S. Hubbell,et al.  On Measuring the Intrinsic Rate of Increase of Populations with Heterogeneous Life Histories , 1979, The American Naturalist.

[105]  J. Harper Population Biology of Plants , 1979 .

[106]  Hal Caswell,et al.  Population Growth Rates and Age Versus Stage-Distribution Models for Teasel (Dipsacus Sylvestris Huds.) , 1977 .

[107]  G. Hartshorn A Matrix Model of Tree Population Dynamics , 1975 .

[108]  M. Gadgil,et al.  Studies on Plant Demography: Ranunculus Repens L., R. Bulbosus L. and R. Acris L.: III. A Mathematical Model Incorporating Multiple Modes of Reproduction , 1974 .

[109]  J. Harper,et al.  The Demography of Plants , 1974 .

[110]  J. Harper A Darwinian Approach to Plant Ecology , 1967 .

[111]  N. Keyfitz Reconciliation of Population Models: Matrix, Integral Equation and Partial Fraction , 1967 .

[112]  M. Usher,et al.  A Matrix Approach to the Management of Renewable Resources, with Special Reference to Selection Forests , 1966 .

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

[114]  P. H. Leslie SOME FURTHER NOTES ON THE USE OF MATRICES IN POPULATION MATHEMATICS , 1948 .

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

[116]  W. O. Kermack,et al.  Contributions to the mathematical theory of epidemics: V. Analysis of experimental epidemics of mouse-typhoid; a bacterial disease conferring incomplete immunity , 1939, Journal of Hygiene.

[117]  Kendrick,et al.  Applications of Mathematics to Medical Problems , 1925, Proceedings of the Edinburgh Mathematical Society.