Demographic extrapolations: how far can/should we go?

Just because you can (extrapolate models using the available demographic data in COMPADRE and COMADRE, and other sources) doesn’t mean you should. Shaun Coutts and colleagues have published a work in Ecology Letters asking how far can one extrapolate demographic outputs within and across species based on demographic knowledge, geographic and phylogenetic distance.

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The academic answer is here: SR Coutts, R Salguero‐Gómez, AM Csergő, Buckley YM (2016) Extrapolating demography with climate, proximity and phylogeny: approach with caution. Ecology Letters. doi: 10.1111/ele.12691

The lay summary is here: Shaun Coutts’ Research Site

The power of comparative demography: booms and busts

Jenni McDonald’s work on transient dynamics using COMPADRE was recently recognized with the Postdoctoral Excellence Award of the Plant Population Ecology of the Ecological Society of America. Congrats Jenni! Here we leave you with a short summary of her work.

 

The natural world is not static and populations don’t exist in a vacuum. Environmental variation is inevitable for wild populations. Consequently, the vital rates, stage structures and dynamics of every wild population will change through time. Earlier this year our paper linking stochastic dynamics into contributions from transient dynamics (driven by non-stable stage structures) and asymptotic dynamics (caused by changes in vital rates) was published in Journal of Ecology.

The idea of transients being important within stochastic environments was not a new one. However, we built on previous work by exploring absolute dynamics, which accounts for the strength of opposing asymptotic and transient effects. We also used a large-scale comparative database to test this hypothesis, using data from 277 plant populations across 132 species from the COMPADRE Plant Matrix Database. This comparative framework opened up exploration of evolutionary and ecological patterns. Our key result was that transients are ubiquitous in plant populations, contributing to half the dynamics in stochastic environments.

Understanding transients is vital for management of both pest species and those of conservation concern. Perturbations in the environment, such as fire, harvesting, disease epidemics and weather changes, will mean that populations are rarely at stable stage structure. Given the contribution of transients to population growth, ignoring non-stable population structure will have implications for management as population growth will be different from that predicted by the long term population growth rate. Consequently, an understanding of transient boom (accelerated population growth) and bust (reduced population growth) could be exploited by managers and conservationists to maintain persistence (or cause extinction) of wild populations. Transients may also provide an explanation as to how some species thrive in a variable landscape, whereas others suffer population declines, for example endangered species potentially may be those who respond poorly to demographic disturbance. Harnessing the power of comparative analysis enabled us to explore evolutionary and ecological patterns and start to shed light on these possibilities.

The COMPADRE Plant Matrix Database provides open access to thousands of plant population projection matrices parameterised from empirical data previously dispersed throughout peer-reviewed and grey literature. COMPADRE is the ideal resource to explore transients across populations varying in evolutionary history, growth form and life stage complexity. We found that both transient contributions and asymptotic contributions are influenced heavily by the number of life stages modelled. This could mean that species with complex life histories are able to bounce back from demographic disturbances; alternatively, this observation may be an artefact of modelling design. We found no phylogenetic signal in the contribution of transients to stochastic growth, nor clear patterns related to growth form. Plant populations have a tendency to boom rather than bust in response to variable environments. This raises the future question; have populations evolved to bounce back from disturbance?

Our research also highlights the value of large-scale databases. The power of comparative demography allowed us to ask questions regarding the impact of non-equilibrium stage structure on stochastic population dynamics and reveal patterns that would not have been deduced from other means. Empirical data on the life histories of living organisms stored in COMPADRE can contribute to a diverse spectrum of research areas and is of relevance to scientists working in the fields of conservation, ecology and evolution. In addition to the ability to ask new questions, the free and instant access of the database removes any logistical obstacles that many researchers may face in terms of field work and laboratory studies. Such a resource has the potential to inspire new scientific insights, while also embracing the diversity of work life patterns of scientists – undoubtedly a powerful resource.

Jenni McDonald

Postdoctoral researcher at Exeter University

 

New COMPADRE & COMADRE versions are out!

Yesterday, coinciding with the symposium “Landscape demography: Population dynamics across spatial scales” at the 2016 Ecological Society of America annual meeting, where we gave the talk “Global plant and animal demography: tearing the curtain and filling up the gap“, we released the new two versions of the sister databases: COMPADRE version 4.0.0 and COMADRE version 2.0.0. These can be downloaded fully open-access at www.compadre-db.org.

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Our goals, at COMPADRE & COMADRE: to digitise and standardise matrix population models published and communicated to us by population ecologists, to error-check, fix and complement the information with metadata (e.g. taxonomy, phylogeny, biogeography), and to make it open access. In other words: to bring the field demographic data to your computer.

What’s new in them? More matrix population models, more species, more metadata! The COMPADRE Plant Matrix Database now contains 695 unique taxonomically accepted plant species from 819 published or personally communicated studies, adding up to a total of over 7,000 population matrix models. Similarly, the COMADRE Animal Matrix Database now contains 405 taxonomically accepted animal species outsourced from 508 studies, with a total of 1,927 matrix models.

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Summary statistics of the new versions of COMPADRE and COMADRE: more species, more matrix population models, and more metadata.

The increase in species and number matrices adds up to an unprecedented geographic cover. Clearly, however, geographic and taxonomic biases do exist in the databases, and we encourage users to carry out demographic research using matrix population models in under-explored areas (e.g. Belgium, Ireland, Italy, Greece, Russia, Morocco, Ecuador, Philippines, etc)

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Geographic location of the studies where GPS information was provided in the publications, showing the global coverage of COMPADRE and COMADRE (Salguero-Gómez et al. in prep.)

In addition to the new species and matrix models, we have also archived new variables. For instance, the latitudes and longitudes are no longer provided as separate degrees, minutes and seconds, but rather provided as two vectors (Lat and Lon), which is a more manageable format. For instance, try the following in your R console, after you have downloaded the Rdata objects and loaded them onto R:

load("~/WhereverYouSaveYourStuff/COMPADRE_v.4.0.0.RData")
map("world",col="white",fill=T,bg="white",xlim=c(-175,176),ylim=c(-60,85),border="gray",mar=rep(0,4))
points(compadre$metadata[,c("Lon","Lat")])

We’ve also renamed some other variables to unify the organization of plants and animals, for instance:

load("~/WhereverYouSaveYourStuff/COMADRE_v.2.0.0.RData")
table(comadre$metadata$OrganismType)

load("~/WhereverYouSaveYourStuff/COMPADRE_v.4.0.0.RData")
table(compadre$metadata$OrganismType)

 

More information about the databases, their organisation, the way we digitise, complement, error-check and release information, and some useful workshop materials and R functions (incoming R package… stay tuned!) can be found here.

Happy COM(P)ADRE-ing!

The COMPADRE & COMADRE core committee

     Rob Salguero-Gomez – The University of Sheffield & Max Planck Institute for Demographic Research (MPIDR)

     Owen Jones – Southern Denmark University (SDU), MaxO

     Ruth Archer – Exeter University

     Yvonne Buckley – Trinity College Dublin

     Judy Che-Castaldo – Lincoln Zoo

     Hal Caswell – University of Amsterdam

     Tom Ezard – University of Southampton

     Dave Hodgson – Exeter University

     Alex Scheuerlein – MPIDR

     Jim Vaupel – MPIDR & SDU, MaxO

 

 

 

 

Drivers of realized population dynamics and COM(P)ADRE

In a paper recently published in Ecology Letters, our brand new COM(P)ADRE science committee member Dave Koons, together with David Iles, Michael Schaub and our core committee member Hal Caswell, present a set of transient life table response experiments (LTREs) for decomposing realized population growth rates into contributions from specific vital rates and components of population structure. Unlike previous LTREs, the transient versions do not require assumptions about a constant environment or stationary environmental variation. Rather, they embrace the non-stationary environmental conditions (changing mean, variance, or both) created by climate and landscape change.

By applying their transient LTREs to a diverse array of simulated life histories, the authors reveal that established concepts in population biology will require revision because of reliance on asymptotic approaches that do not address the influence of unstable population structure on population growth and mean fitness in time-varying environments. Going forward, the repository of longitudinal demographic studies in COMPADRE and COMADRE will be necessary for testing these predictions, and applying transient LTREs to real-world conservation and management problems.

For popular press coverage of our paper, see here.

Dave Koons

Assoc Prof Utah State University

COMPADRE & COMADRE science committee member

Koons, D.N., D.T. Iles, M. Schaub, and H. Caswell. 2016. A life history perspective on the demographic drivers of structured population dynamics in changing environments. Ecology Letters. DOI: 10.1111/ele.12628

 

A Cornish demographic extravaganza

It was a rainy summers day in Cornwall, when a rare occurrence took place: comparative demographers gathered in the masses. They brought ideas, laughter, heaps of data, and collaborative thoughts and, despite some uncooperative travel troubles, they got their heads down and began to tackle the demographic problems of the 21st century.

The 10-day Cornish demographic extravaganza began with an introductory workshop where early career academics working with the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database educated the ‘scientists of the future’, aka MRes, PhD students and postdocs, about the importance of vital rates for conservation success. Vital rates you say? These rates describe how individuals within a population grow, reproduce and die; this information can be used to determine how likely a population is to expand, shrink, invade or even become extinct. Although encouraging scientists early on their career that mathematical ecology and comparative (desk-base!) studies are the key to our conservation problems is challenging at times, the workshop went swimmingly and the lecturers empowered the protégé demographers to follow in their academic footsteps.

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Ruth Archer, Jenni McDonald, Owen Jones (left photo) and Rob Salguero-Gomez ran a 3-day workshop on the comparative power of the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database at the Cornwall campus of the University of Exeter for some ca. 20 graduate students and postdocs.

This 3-day demographic teaser was followed by the main event. A thrilling international opportunity funded by the European research council, to bring together a world-class set of researchers with a focus on comparative demography and life history evolution, to work together for a full week.

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The group of international researchers (Left-to-right, top: Phil Wilson, Raymond Tremblay, Danny Buss, Eelke Jongejans. Bottom: Brigitte Tenhumberg, Drew Tyre, Elizabeth Crone, Rob Salguero-Gomez, Yvonne Buckley, Dave Hodgson, Judy Che-Castaldo, Veronica Sommer, Satu Ramula, Owen Jones, Simon Rolph and Iain Stott) on a day out in the field appreciating the local flora and fauna of Cornwall while discussing future directions of plant and animal demography.

The agenda was set by the SPAND_EX king, der Hodgsonmeister, who, in collaboration with the international researchers, discussed the need to highlight the “sins” found throughout the demographic literature, and demonstrated them to the scientific community. Gluttony, greed, sloth spilled onto the blank canvas…..wrath, envy, pride, shortly followed by lust…….. 7 sins turned into 10, than 12, 13 and even more……. this posed a big problem for the team. Seven sins…….. 14 crimes, 7 sins……. 14 crimes. The team pondered about this, the facts did not match the catchy title…… a testing problem to be solved by one of the newest members of the team COMPADRINO Simon Rolph (see photo above).

Day 2 began with the CDO duo – Computing Development Officers, Francesca Sargeant and Danny Buss, at the COMPADRE Exeter node, spilling the beans on the transformation of the COMPADRE database into a modern, speedy, query-able SQL storage machine. This raised much discussion: who was going to secure the funding? is the database going to transform into something more?  will COMADRE follow the same footsteps as COMPADRE? will the CDO team really go back down to nil by October this year?… All of these conversations were then taken by the COMPADRE core committee to the 3rd annual committee, which took place in Odense, Denmark, the week after.

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Danny Buss (left) and Francesca Sargent (right) discuss with the group of international demographers the latest developments that they have championed during the last year at the COMPADRE Exeter node: COMPADRE is currently undergoing an internal re-make, with SQL capabilities, and graphical displays for teaching purposes, with interactivity with IUCN and other open-access repositories.

The excitement began in the final days, where the mathematical challenges, unanswered ecological questions and exciting comparative techniques spilled from the minds and onto the whiteboards……. could the team come up with some solutions to……. Phylogenetic gap analysis for ecological traits……… a better understanding of the complex relationship between environmental drivers and demographic rates…….. or even, the burning answer to why does phylogenetic signal differ for demographic traits between fauna and flora, are plants and animals really that different?

After plenty of discussions, food, Cornish dolphins, botany and statistical analysis…….. the team was ready to begin their outputs. I hope you are all looking forward to some highly interesting publications to be released over the next year or two – I know I am!

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More ecological inspirations for the research that took place on comparative animal and plant demography at the Cornwall campus of Uni Exeter. Left to right: dolphin! Danny Buss, Yvonne Buckley, Judy Che-Castaldo, Raymond Tremblay, Dave Hodgson, Eelke Jongejans, Veronica Sommer, Brigitte Tenhumberg, Drew Tyre, Elizabeth Crone & Owen Jones. Not shown individuals: Rob Salguero-Gomez (behind the camera), and Satu Ramula (top level of boat).

A huge thank you goes out to the team at NERC who provided the funding for such an extraordinary collaborative event, I really hope we can re-convene together again next year.

Danny Buss, Computer Development Officer

COMPADRE – Exeter node

COMPADRE & COMADRE in a world of big data and comparative science

A blog post by Maria Paniw

Take a look at recent publications in peer-reviewed journals or popular science magazines and you cannot miss the two big trends: big data and comparative analyses. Recent reviews suggest that future groundbreaking, socially relevant science will be achieved through large collaborative efforts bringing together multiple datasets for a global comparison of ecological phenomena. Recently (April 2016), a group of researchers working on various topics related to life-history strategies got a taste of how open-access outputs of such collaborative efforts can be used for comparative analyses. And using the COMPADRE and COMADRE databases, together with other (see below) open-access data repositories was a big part of the experience.

Young academics from around the world met in the Max Planck Institute for Demographic Research (MPIDR) in Rostock, Germany for a week-long workshop titled “Comparative Approaches in Ecology and Evolution” as part of the programme of International Advanced Studies in Demography. The course was a unique opportunity to learn how to extract information from various open-access databases. The teaching was done, via lectures and, importantly, lots of R code (!), by an impressive number of instructors – all experts in functional ecology, demography and/or phylogenetic analyses. All work had one goal: examining global drivers of life history strategies using robust statistical tools on large datasets. In the process, participants were introduced, among many others, to CLOPLA, a database on clonal traits in plants, or DATLife, providing mortality and fertility data for numerous species.

 

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Participants and instructors of the workshop “Comparative Approaches in Ecology and Evolution” organized by Rob Salguero-Gómez at the MPIDR in Rostock, Germany. Instructors included: Dr Scott Chamberlain (UC Berkeley, USA), Dr Kevin Healy (Trinity College Dublin, Ireland), Dr Owen Jones (Southern Denmark University, Denmark), Jean-François Lemaitre (CNRS, Lyon), Prof Bruce Kendall (UC Santa Barabara, USA), Prof Jitka Klimešová (Institute of Botany, Academy of Sciences of the Czech Republic), Prof Dmitrii Logofet (Russian Academy of Sciences, Moscow, Russia), Dr Alejandro Ordoñez (Aarhus University, Denmark), Dr Rob Salguero-Gomez (University of Sheffield, UK), Dr Alexander Scheuerlein (Max Planck Institute for Demographic Research), Dr Iain Stott (Max Planck Institute for Demographic Research, Germany) and Prof Jean-Michel Gaillard (CNRS, Lyon, France).

The COMPADRE Plant Matrix Database, along with COMADRE Animal Matrix Database, played a central role throughout the workshop. Of course, the fact that the core team of both databases organized the event played a part in this. At the same time, it was evident that the hard work put forth to make COM(P)ADRE easily accessible to researchers – including the ease to download the data and the detailed manuals – paid off. Working in groups, participants were encouraged to develop projects related to life-history analysis using open-access data – and several groups decided to work with COMPADRE/COMADRE. These projects included investigating environmental drivers behind demographic variability, correlating matrix projections of extinction probability with the IUCN Red List, or tracing phylogenetic signals in life-history traits. Preliminary outputs of these projects were promising – stay tuned to read about papers that will surely come out of these projects.

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The 24 participants (from a total of 20 countries!) and instructors working together on their group projects examining various aspects of life history variation among plants and animals worldwide.

To sum up, the workshop was a great success, despite the “spring weather” in Rostock, and will hopefully be repeated in the future.

Maria Paniw

PhD candidate at the Universidad de Cádiz, Spain

 

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