Biological invasions, life histories, and COMPADRE

The diversity of life on Earth is amazing, and just as species have evolved all sorts of interesting physical adaptations to cope with their surroundings, so have they evolved a dazzling array of life histories (patterns of birth, growth, reproduction and survival rates) that allow individuals to pass on their genes to future generations. And as it turns out, a subset of these life histories may confer an additional benefit: an inherent ability to establish new populations.

In a paper recently accepted in Journal of Ecology, we harnessed the power of the COMPADRE Plant Matrix Database to ask the question: “which plant life histories should be the best invaders?” The process of biological invasion is devilishly complicated, involving many phases occurring at different scales. We focused our attention on the early part of the establishment phase, when a new population has just taken root with only a few colonizers and is easily wiped out. Early on, small invading populations are strongly affected by the vagaries of chance events known as “demographic stochasticity”. We used computer simulations of plant population models for 105 species to see which populations, starting as seeds, were best able to persist while dealing with these chance events.

We found that life histories that 1) avoid short-term declines in abundance (e.g., by maintaining high seed and seedling survival, and rapidly reaching maturity) and 2) grow rapidly over the long-term were best able to cope with demographic stochasticity. Our most interesting finding, however, was that species capable of producing many seeds are especially good invaders because they have disproportionately favorable short-term and long-term population growth rates. This may help explain why species that escape their native ranges and become truly “invasive” generally have high fecundity: they are especially good at coping with chance events and avoiding extinction.

 

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Dave Iles in the field. He is a PhD candidate at Utah State University, and lead author of a recent publication in Journal of Ecology using COMPADRE to explore life history traits that pose plant species more likely to establish successful invasions

Of course, there remains much more to be learned about the demography of invasive species and of the invasion process in general – for example, our predictions need to be tested by directly comparing invasive and non-invasive species, both in their native and invasive ranges. Open access data, like that in the COMPADRE and COMADRE databases, will almost certainly play an important role in future discoveries. Free and instant access to massive online data repositories will greatly speed up the rate at which exciting questions can be addressed. Open access also guarantees that many other researchers will be familiar with the ins and outs of the data used in analyses, improving the overall quality of research and peer review. I will certainly use open access data again (and likely the COMPADRE/COMADRE databases themselves), and am excited to see what other insights will be gained from these incredible sources of information.

David Iles

Iles, D. T., Salguero‐Gómez, R., Adler, P. B., & Koons, D. N. (2015). Linking transient dynamics and life history to biological invasion success. Journal of Ecology. DOI: 10.1111/1365-2745.12516

Salguero-Gómez, R. et al. (2015). The COMPADRE Plant Matrix Database: an open online repository of plant demography. Journal of Ecology 103, 202-218

Learning opportunities on macroecology

The core committee of COMPADRE and COMADRE believe strongly in not just open-access and open-data, but also in providing tools and concepts to advance comparative biology. Consequently, we run workshops on comparative demography and macro-ecology rather frequently. Below, some of the upcoming opportunities:

The COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database will be integral part, together with other open-access repositories (IUCN, GBIF, Clo-Pla, BIEN, BIDDABA, MALDABA, FetchClimate), in the week-long workshop that will take place during the 25th-29th of April 2016 at the Max Planck Institute for Demographic Research, in Rostock, Germany. Details on the content, application format and deadline can be found here.

In addition to this intense course, Rob Salguero-Gomez will be conducting a one-day workshop on the newly launched COMADRE Animal Matrix Datbase at the University of Queensland (Australia) on the 9th Nov 2015, and Owen Jones will be running a short workshop at the BES meeting in Edinburgh.

We hope you consider participating and help us spread the word!

Rob S-G

Connecting data for research

On October 19th 2015, one of our science committee members, Eelke Jongejans,  attended a symposium in Amsterdam on “Connecting data for research”. Here are Eelke’s impressions about the meeting:

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Scientists and a board member of the Dutch Science Foundation all stressed the importance of shared data for progress in scientific research. Engaging examples like the data-driven management of the 2014 Ebola crisis, and coastal oceanography based on the combination of opened-up data sources (to find out whether our dunes and dikes will continue to keep us dry), clearly show the advantages of open data. But also ecological research benefits from open data, allowing analyses at a wider geographic and taxonomic scale, as shown in the presentation by Cees Hof on the Global Biodiversity Information Facility (GBIF) and in Rob Salguero-Gómez’ slides on COMPADRE and COMADRE that I used in my presentation.

But how to enable and encourage researchers to make their data freely available? Information law Professor Mireille van Eechoud explained that ‘open data’ have several legal challenges, for instance concerning intellectual properties and data protection. Law-making is unlikely to be the driver of an open-data revolution. Other speakers also emphasized the carrots and sticks that could encourage researchers. Funding agencies and journals requiring open access to research data can be seen as sticks that push researcher over the hill top that needs to be climbed to actually archive data in the open. Representatives of DANS-easy and 3TU, Dutch data repositories, were also present at the symposium, claiming that that perceived hill isn’t so steep and high at all.

Even more interesting are the carrots. How rewarding is it when your archived data are reusable and citable (DOI)? How can institutes profit (e.g. international visibility and esteem?) when they host (expertise on) large amounts of open data? Do search committees acknowledge the value of the data publications? In that light, it is interesting to think about what COMPADRE and COMADRE can do to further encourage researchers to want to archive their population matrices and accompanying metadata in the Plant and Animal Matrix Databases. Plans to provide DOI’s to (new) data entries are currently being explored by the core committee of these databases, and would have several advantages. Researchers could then mention the DOI, that they received after archiving their matrices, in their manuscripts, showing that data openness and permanency is ensured. Separate DOI’s would make their data more visible and citable within big databases like COMPADRE and COMADRE, although it is not standardized yet how that should be done in comparative demography studies. Another important advantage could be that these developments could encourage researchers to enter their new matrices and metadata themselves (also currently being discussed as a future step in these databases), taking an important burden from the digitization team that then ‘only’ needs to check whether new entries are in order.

At the same time it is important to maintain the policy of embargoes. Giving researchers enough time to milk their own data likely takes away a big part of the hesitation to make one’s data freely available.

Eelke Jongejans

Assistant Professor of Animal Ecology & Physiology @ Radboud University, The Netherlands

Introducing the COMADRE Animal Matrix Database

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Coinciding with the 3rd annual Evolutionary Demography Society conference, in Lunteren (the Netherlands), we announce the release of COMADRE v.1.0.0, an open-access database for animal demography. COMADRE comes online nearly a year after the release of its sister database, the COMPADRE Plant Matrix Database.

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COMADRE contains 345 animal species from 402 studies and 1,625 matrix population models of global distribution, ranging organisms as different as sponges, birds or mammals, including humans. The preprint of the manuscript introducing COMADRE is available in bioRxiv, and the manuscript is currently in review at Journal of Animal Ecology.

Together with the release of COMADRE, we also release the new version of COMPADRE: v. 3.2.1. This version contains 637 plant species from 735 studies containing a total of 6,242 matrix population models.

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These are the updated user guides for COMPADRE and COMADRE. In an effort to remain as transparent as possible in the data digitalisation and error-checks effected in the database, we also make available the internal data entry protocols.

The release COMADRE coincides too with a new look to the portal for both databases. The main aspect of this portal is that user registration is no longer required, making these databases fully open data and open access.

Upcoming workshops on the usage of these resources are planned for EvoDemoS (Oct 2015), BES (Dec 2015) and a weeklong course at the Max Planck Institute for Demographic Research (April 2016, exact week TBA).

We hope that the research community will use these databases for exciting ecological and evolutionary questions!

Dr Rob Salguero-Gomez & Dr Owen Jones
on behalf of the core committee

PS: this is how our students (the COMPADRinos) feel about the release of COMADRE:

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COMPADRE 3.2.0 is here!

Dear COMPADRE and COMADRE users,

After several months, and following some important decisions made at the second annual COMPADRE/COMADRE core committee meeting (Denmark, March 2015), we are happy to announce the launching of the second open-access version of COMPADRE: COMPADRE 3.2.0 (why the number versioning? See here). This version contains more studies, more plant matrix population models, and new variables (e.g. “MatrixFec” in our user’s guide), as well as corrected typos. The previous version (3.0.0) will soon be archived in our GitHub repository for user access and replicability. [edit: this has now happened!]

To download the data, please go to our repository, and click on “Data”. We must note that the download of the data will provide you with the user’s guide to the 3.0.0 version (not the 3.1.0 – for that please click here). The Rdata object also seems to have lost its “.Rdata” extension. To open it in R, please change “COMPADRE_8_9_2015_version_3.1.0” to “COMPADRE_8_9_2015_version_3.1.0.RData”. We will fix this in the coming days.

Two other important announcements: (i) we are working on an updated version of the website. This will get rid of the need for users to register before accessing the data, and (ii) the upcoming release of the COMADRE Animal Matrix Database, scheduled for October 5th this year.

Have fun with those 6242 plant population matrix models!

Rob Salguero-Gómez and COMPADRE Core Committee

What is the COMPADRE/COMADRE core committee?

We love committees in academia – there’s a committee for everything and the plant and animal matrix databases COMPADRE & COMADRE are no exception. Ecology is increasingly collaborative and the resources we require are pulled together from numerous sources and make use of diverse knowledge and skill sets for their compilation and use so committee meetings are the best way to have short, intense and productive work sessions. I have been to two COMPADRE/COMADRE core committee meetings, exactly one year apart. The first one was in a way the most exciting, as we planned the release of the COMPADRE database with a coincident paper in Journal of Ecology. The most recent meeting was no less important as we planned the release of COMADRE (animal matrix database) later this year and two more papers, but given our experience with COMPADRE, there is less adrenaline involved than last year!

Our discussions this year revolved around the future and sustainability of COMPADRE and COMADRE. We are transitioning from several years of support from the Max Planck Institute for Demographic Research to a more distributed funding system and will be seeking new funding opportunities over the next couple of years. The MPIDR has been instrumental in getting the databases up and running and in the public domain. Our challenge now is to ensure the quality and ease of use of the current data and to continue to add new matrices as they are produced.

Finally – what do you do when you’re at a committee meeting and have three hours of unprepared lectures on herbivory to write for delivery the following week? You crowd-source your task and get everyone at dinner to give you their favourite herbivore story! We heard about bison saliva, the homing abilities of snails, plants with adaptations to extinct herbivores, an unexpected role of hairiness in grasses, digestibility of C4 vs. C3 plants and the aphid mustard bomb.

Yvonne Buckley

The Power of Global Databases

Dave Hodgson, University of Exeter

These are exciting times for the study of animal and plant demographies and life histories. Evolutionary ecologists seek to understand how evolutionary processes shape the distribution, abundance and dynamics of organisms in their environment. Only then can we confidently predict the future of biodiversity on our planet.

If we are to understand ecological fitness, or population dynamics, then we must consider the vital rates (birth, survival, growth) and the demographic rates (transition and numerical changes across life-stages) of organisms, integrated across the entire life cycle. A dog is a dog from the moment of conception right through to moment of death. A thistle is a thistle from the moment of pollination through to the moment of death. The mathematical methods to integrate these vital rates are well-established, but continue to develop. The empirical efforts of demographers, and life history biologists, worldwide and for several decades, have yielded projection matrix models, and integral projection models, for thousands of populations or genotypes of hundreds of plant and animal species, often replicated through time. The COMPADRE (Salguero‐Gómez et al. 2015) and COMADRE global databases bring these models together (Salguero-Gómez et al. in prep.), for the first time, and are available for use by all interested researchers.

The power of these databases was unveiled recently at the British Ecological Society symposium “Demography: Beyond the Population”, in Sheffield, organised by Alden Griffith, Rob Salguero-Gómez, Jessica Metcalf, Sean McMahon, Cory Merow and Dylan Childs. Here, several speakers used COMPADRE, the plant database, to perform comparative analyses of how plant life histories evolve and how plant populations fluctuate in their environments. Replication of demographic models across space and through time allows us to study the impacts of non-equilibrium conditions on optimal life histories and on population dynamics. Exciting developments include the matching of life history to climate envelopes; the adaptive value of life histories that boom in response to demographic disturbances; detecting the signal of shared ancestry on life history; linking demography to niche dimensions; understanding how environmental and demographic stochasticity shapes vital rates.

COMPADRE is now firmly established as a key database for evolutionary and ecological demography. COMADRE, its sister database that hosts demographic models for animals worldwide, is on the verge of release to a global scientific audience. These databases are ripe for exploitation, and we hope they will help reveal patterns and mechanisms that create the incredible diversity of life histories we observe in the world around us. The databases also reveal new opportunities: the next generation of computer-savvy ecologists should seek to combine the strengths of various global databases, to integrate information on life history, demography, genomics, phenotypic traits, climate, habitat, distribution and population dynamics FOR AS MANY SPECIES AS WE POSSIBLY CAN.

Read more at http://www.compadre-db.org/

Salguero‐Gómez R., Jones O.R., Archer C.R., Buckley Y.M., Che‐Castaldo J., Caswell H., Hodgson D., Scheuerlein A., Conde D.A. & Brinks E. (2015). The compadre Plant Matrix Database: an open online repository for plant demography. Journal of Ecology, 103, 202-218.

Promotional poster now available in Portuguese

With the generous help of Mariana Silva Ferreira, a PhD student based at the Federal University of Rio de Janeiro – Brazil, we now have a Portuguese version of our COMPADRE poster. Thank you Mariana!

Mariana’s translation is to Brazilian Portuguese, which I understand to be very similar to European Portuguese.

We hope that the poster will bring our matrix database to a new audience of researchers and students.

You can download the PDF by clicking on the image below.

COMPADRE Poster in Brazilian Portuguese

COMPADRE Poster in Brazilian Portuguese

You can find the poster in other languages including English (of course), Italian, German, French, Chinese, Japanese, Turkish, Hungarian and Afrikaans here.

 

 

Introducing new science committee member: Eelke Jongejans

We have recently increased the pool of science committee members of COMPADRE & COMADRE by one individual – a very prolific one –  who joins the group of researchers that help us make long-term decisions on the sister demographic databases, and obtain funding: Eelke Jongejans.

We have asked him to describe his research and his vision for COM(P)ADRE. This is what he says:

“How much do species differ in survival and reproduction rates? How much do these vital rates vary between populations within species? Can traits like seed mass, brood care and migration behavior explain variation in vital rates within and between species? Or do local environmental conditions have a larger effect than mean trait values? How much does life history variation affect the dynamics of populations of plants and animals? These interesting questions are key to population ecology. Answering them requires information about the life history traits, vital rates and dynamics of multiple populations and species. Bringing together this information for thousands of populations is exactly what the population matrix databases COMADRE and COMPADRE do.

As the goal of this post is to introduce my research, I will give some examples of comparative demography that I have been involved in. Together with various wonderful co-authors I have used data that is now archived in COMPADRE and COMADRE to explore several aspects of life history variation. For instance, we found that for herbs buffering mechanisms (that might have softened the impact of year-to-year climate variation on fluctuations in population size) appeared to be overwhelmed by the effects of positive correlations among vital rates (Jongejans et al. 2010a). Such comparative analyses can be used to explore what could happen in climate scenarios in which not only mean weather parameters change, but also their variability.

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Picture: Excursion with students near Nijmegen, The Netherlands, setting up mist nets to survey birds (Photo by M. Lampe)

We also used published matrix population models to study whether there is as much life history variation within the order of Carnivora as within all Mammalia (van de Kerk et al. 2013). Elasticity analyses showed that this was indeed the case, and that Carnivora span a very similar gradient over the slow-fast continuum. However, this study also showed that although there were major differences in e.g. the lifespan between e.g. stoats and grizzly bears, the individual variation within species is often very large and important for population dynamics.

The variability of life histories also becomes apparent in studies in which several populations of the same species are studied at the same time, as already showed by Oostermeijer et al. (1996). Vital rates not only vary considerably between regions of species distributions (e.g. between European countries), but also between localities within regions (Jongejans et al. 2010b). Furthermore, this spatial variation in life history variation appears to be qualitatively different from temporal variation in demography (Jongejans & de Kroon 2005, but see Ramula 2009), making it more difficult to borrow information between spatial and temporal replication for stochastic simulations. It has become clear that life history differences, as quantified by various forms of sensitivity and elasticity analyses do not only depend on species or population characteristics but also on the phase in which the population was during the study period: whether the population was growing, stable or declining.

Given this large life history variability at the individual and population levels, is it still sensible to attempt comparative demography across species? Yes, as long as these other sources of variation are acknowledges or, even better, as soon as novel methods are developed to incorporate these sources in the comparative analyses.

There certainly is a lot to gain from comparative demography, and not just for fundamental ecology. One of the promising applications of large-scale comparative demography is the trait-based interpolation of the life histories and population dynamics of endangered species for which there are none or little demographic data. Comparative demography can thus be used to assist progress towards the dearly needed ‘science- and evidence-based conservation biology’. COMADRE and COMPADRE should therefore also be used to inspire botanists, ornithologists, herpetologists, etc, to embark on the adventure called field demography. By showing what can be learned and achieved from systematic and constant-effort observations, and by providing a complete (!) overview of what species have been studied already (emphasizing the large gaps of demographic knowledge about many other species), these databases and analyses can help both professional and amateur biologists when starting new studies in the field. We wrote a book about how the life cycle of plants can be studied by biologists willing to devote some leisure time to discover the secret life history strategies of a plant species (in Dutch; Bremer et al. 2012) and other such resources and programs exist for plants. However, much can be learned in that respect from field ornithology, which can rely on a large number of volunteer birders to collect data on survival, dispersal and reproduction.”

Eelke Jongejans

Department of Animal Ecology and Ecophysiology. Institute for Water and Wetland Research. Radboud University Nijmegen. The Netherlands.

Cited works: 

Bremer P, Jongejans E, Oostermeijer G & Willems J (2012) Planten tellen. Over demografisch onderzoek. KNNV 160 pages (Dutch book on plant demography; now also available as digi-book for iPad, tablet or smartphone)

Jongejans E & de Kroon H (2005) Space versus time variation in the population dynamics of three co-occurring perennial herbs. Journal of Ecology 93:681-692

Jongejans E, de Kroon H, Tuljapurkar S & Shea K (2010a) Plant populations track rather than buffer climate fluctuations. Ecology Letters 13:736-743

Jongejans E, Jorritsma-Wienk LD, Becker U, Dostál P, Mildén M & de Kroon H (2010b) Region versus site variation in the population dynamics of three short-lived perennials. Journal of Ecology 98:279-289

Oostermeijer JGB, Brugman ML, de Boer ER & den Nijs HCM (1996) Temporal and spatial variation in the demography of Gentiana pneumonanthe, a rare perennial herb. Journal of Ecology 84:153-166

Ramula S, Dinnétz P, Lehtilä K (2009) Spatial data replacing temporal data in population viability analyses: An empirical investigation for plants. Basic and Applied Ecology 10:401–410. http://dx.doi.org/10.1016/j.baae.2008.10.007

van de Kerk M, de Kroon H, Conde DA & Jongejans E (2013) Carnivora population dynamics are as slow and as fast as those of other mammals: implications for their conservation. PLOS ONE 8:e70354

COMPADRE 3.0 is live!

November 11th 2014 marks what we anticipate as the beginning of a new era in plant population studies:

It is our pleasure to introduce the COMPADRE Plant Matrix Database (version 3.0). Work initiated in the late 80s by Miguel Franco and Jonathan Silvertown, and continued by multiple individuals with the support of several funding agencies from Germany, Australia, the UK, Mexico, and Ireland has finally resulted in the release of completely open-access demographic information for over 600 plant species of global distribution.

The release of this unprecedented global demographic effort, which can be accessed in the COMPADRE/COMADRE portal, has also been sync’ed with the publication of the manuscript that describes the database, the information within, and its potential. The publication saw the light as open-access early online view in Journal of Ecology on Nov 11th 2014 too. That very day, we also introduced the database and one of the lines of research we are developing using these data at the 2nd annual meeting of the Evolutionary Demography Society, held at Stanford.

The publication of COMPADRE has also been accompanied with press releases from some of the participating institutions:

Max Planck Institute for Demographic Reseach, Germany

Centre for Excellence in Environmental Decisions, Australia

Trinity College Dublin, Ireland

University of Southern Denmark, Denmark

COMPADRE has several extensions beyond the portal, such as R/MatLab routines and a fully resolved phylogenetic tree in our github repository, a facebook page, and a twitter account (@compadreDB).

We are currently working on the COMPADRE version 3.1, which will contain more species, more demographic and covariate information, and some minor error-checks. We also have several workshop proposals in review to teach students how to use COMPADRE for comparative demographic analyses in ecology and evolution. Stay tuned… this is but the beginning of what we have in store!

The COMPADRE team