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Databases Cluster

MaxO Research Cluster on the Innovative apporaches for dealing with problematic population data

MaxO is leading the way in collating nonhuman demographic data into several databases. Of these, the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database are the most fully-developed. These databases include demographic information in the form of published matrix population models (MPMs) obtained from the literature. An MPM describes the dynamics of a population in discrete time using discrete stages (e.g. age, size classes and developmental stages). From them, a myriad of demographic outputs can be obtained, including rates of senescence, mean and variance of life expectancy, degree of iteroparity (number of reproductive cycles), population growth rates, etc. and they are therefore useful to address a wide range of demographic topics. The latest versions of these sister-databases contain demographic information in the form of over 9,000 matrix population models for 695 plant species and 405 animal species – matrices for a further ~800 plant and >1,000 animal species are in the process of being digitized. We have made these databases Open Access at www.compadre-db.org. The work to compile the databases was overseen by Salguero-Gómez and Jones; the data compilation effort was undertaken by student assistants working in Vaupel’s department at MPIDR in Rostock.


To complement these MPM databases the Databases Cluster is collaborating with other researchers to develop an analogous pair of databases known as PADRINO and MADRINA, which collate data on published Integral Projection Models (IPMs). IPMs are discrete time, continuous state (e.g. size, weight and parasite load) demographic models that incorporate rates of survival and fertility of individuals. They are therefore conceptually similar to MPMs.

DATLife (Demography Across the Tree of Life) is a data source for the comparative analysis of age-trajectories of mortality and fertility for many species, currently mostly vertebrates. The database, which is being compiled at MPIDR under the direction of Scheuerlein, is functional but still in test form. The data pertain to:

  1. Age-specific mortality, mostly in lifetables that are published or that we created from published data smoothed by the method of Rizzi et al. (2016). DATLife currently holds 2955 lifetables of 364 species, of which 263 are vertebrates.

  2. Age-specific fertility in 297 fertility tables of 90 species, all of which have corresponding mortality data.

  3. Stage-specific mortality usually describes annual juvenile and annual adult mortality of animals. DATLife currently includes 4394 values on 496 species.

  4. Maximum observed lifespan: 5437 values on 2859 species.

  5. Age at sexual maturity:  9269 values for  2620 species.

    For each of these databases an infrastructure for sharing data is provided. Published data are used, but an embargo option allows the inclusion of data before publication. For each data type we record study location, study duration, sex, the end of the study and the number of organisms in the study.

Steiner and Jouvet collect demographic data on E. coli using high throughput cutting-edge microfluidic technology that permits tracking of thousands of individual bacteria cells throughout their lives. Demographic data include division rate, survival, cell elongation rate, and size at cell division for each individual under tightly controlled environmental conditions. The data provide unprecedented insights into effects of genetics (species to single gene), the environment (temperature, nutrients), and intrinsic stochastic processes on demographic parameters.


An additional database, DISKo, was described in Section II.F of the MaxO report 2016.

Collectively, these databases offer unrivalled information for biodemographic research.

 

 

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