Stage-dependent Demographic Modelling at Your Finger Tips

Post provided by EELKE JONGEJANS and ROB SALGUERO- GÓMEZ

Soay sheep: an organism that can be modelled with two-sex dynamics. ©Julian Paren

Soay sheep: an organism that can be modelled with two-sex dynamics. ©Julian Paren

Typically, ecology courses contain at least a day of matrix population models. So most ecologists are somewhat familiar with how simple life cycles (and complex ones) can be depicted and analysed using matrix models. Briefly, these models represent what happens to individuals over a certain time interval (do they die? do they reproduce? if so, how much?). What individuals do in the context of these models can then be used to study the dynamics of a population.

Often, individuals are classified by size in matrix models, as small individuals tend to have different survival, growth and reproduction rates than large ones. But how many classes do you need to model the dynamics of a size-structured population properly? Instead of choosing arbitrary size class boundaries, Easterling, Ellner and Dixon (2000) came up with the idea of using continuous size variables and integrals to define a population model… and that’s how the first Integral Projection Model (‘IPM’ for us friends) came to be.

Naturally, for the development of a new demographic tool to prove useful to the scientific community, it must be flexible enough to be ‘one-size-fits-all’… and the needs of ecologists, evolutionary biologists and conservation biologists – who have to date used extensively size-based matrix models – are rather variable in size, colour and shape. Continue reading

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Demography and Big Data

Post provided by BRITTANY TELLER, KRISTIN HULVEY and ELISE GORNISH

Follow Brittany (@BRITTZINATOR) and Elise (@RESTORECAL) on Twitter

To understand how species survive in nature, demographers pair field-collected life history data on survival, growth and reproduction with statistical inference. Demographic approaches have significantly contributed to our understanding of population biology, invasive species dynamics, community ecology, evolutionary biology and much more.

As ecologists begin to ask questions about demography at broader spatial and temporal scales and collect data at higher resolutions, demographic analyses and new statistical methods are likely to shed even more light on important ecological mechanisms.

Population Processes

Midsummer Opuntia cactus in eastern Idaho, USA. © B. Teller.

Midsummer Opuntia cactus in eastern Idaho, USA. © B. Teller.

Traditionally, demographers collect life history data on species in the field under one or more environmental conditions. This approach has significantly improved our understanding of basic biological processes. For example, rosette size is a significant predictor of survival for plants like wild teasel (Werner 1975 – links to all articles are at the end of the post), and desert annual plants hedge their bets against poor years by optimizing germination strategies (Gremer & Venable 2014).

Demographers also include temporal and spatial variability in their models to help make realistic predictions of population dynamics. We now know that temporal variability in carrying capacity dramatically improves population growth rates for perennial grasses and provides a better fit to data than models with varying growth rates because of this (Fowler & Pease 2010). Moreover, spatial heterogeneity and environmental stochasticity have similar consequences for plant populations (Crone 2016). Continue reading

New Associate Editors

Today we are welcoming three new Associate Editors to Methods in Ecology and Evolution: Nick Golding (University of Melbourne, Australia), Rachel McCrea (University of Kent, UK) and Francesca Parrini (University of the Witwatersrand, South Africa). They have all joined on a three-year term and you can find out more about them below.

Nick Golding

Nick Golding

Nick Golding

“I develop statistical models and software for mapping the distributions of species and diseases. I’m particularly interested in tools that make it easy for researchers to add more mechanistic structure into their correlative models (and vice versa) so that they can use all available information when making predictions. I also develop software and other tools to bring research communities together and help them advance ecology by enabling and incentivising reproducible and extensible research.”

Nick has recently had an article published in Methods in Ecology and Evolution (currently in Early View). In ‘Fast and flexible Bayesian species distribution modelling using Gaussian processes‘ Nick and his co-author (Bethan Purse) introduce Gaussian process (GP) models and their application to species distribution modelling (SDM), illustrate how ecological knowledge can be incorporated into GP SDMs via Bayesian priors and formulate a simple GP SDM that can be fitted efficiently. The article is Open Access, so it’s freely available to everyone.

Rachel McCrea

Rachel McCrea

Rachel McCrea

“I am a NERC research fellow and lecturer in statistics at the University of Kent.  My particular areas of interest include capture-recapture modelling, multistate models, modelling population dynamics and methods of model assessment.  My research is motivated by interesting discussions with ecologists and I strive to find innovative, but practical statistical solutions to ecological questions.”

Rachel is one of the authors of Analysis of Capture-Recapture Data (along with Byron Morgan). The book covers the many modern developments of capture-recapture (and related) methods and will be of interest to researchers and graduate students in statistics, ecology and demography. It contains 130 exercises designed to complement and extend the text and help readers to assimilate the material.

Francesca Parrini

Francesca Parrini

Francesca Parrini

“My broad research interests lie in the ecology and behaviour of mammalian herbivores, their interaction with biotic and abiotic factors and the integration of factors governing decisions at the small foraging scale and factors governing decisions at the landscape level. As such, my research lies at the interface of remote sensing, behavioural ecology and conservation. Recently I have become interested in the application of graph theory and network analysis to ecological settings, in particular to study the spatio-temporal structure of animal movement patterns.”

Last year Francesca had her article (co-authored with Maria Miranda) ‘Congruence between species phylogenetic and trophic distinctiveness‘ published in Biodiversity and Conservation. In this paper the authors investigate the relationship between species’ phylogenetic history and patterns of resource use. They show that there is congruence between species phylogenetics and interaction distinctiveness and propose that this relationship could provide a possible novel approach to the conservation of ecosystem diversity.

We are thrilled to welcome Nick, Rachel and Francesca to the Associate Editor Board and we look forward to working with them over the coming years.

Issue 7.2: Demography Beyond the Population

Issue 7.2 is now online!

Sagebrush steppe in eastern Idaho, USA

© Brittany J. Teller

The February issue of Methods is now online! As you may have seen already, it includes the BES cross-journal Special Feature: “Demography Beyond the Population“. There are also eight other wonderful articles to read.

We have four articles in the Demography Beyond the Symposium Special Feature. You can read an overview of them by two of the Feature’s Guest Editor Sean McMahon and Jessica Metcalf here (Sean and Jessica are also Associate Editors of Methods).

If you’d like to find out more about each of the individual papers before downloading them, we have blog posts about each one. Daniel Falster and Rich Fitzjohn discuss the development of plant and provide some advice on creating simulation models in Key Technologies Used to Build the plant Package (and Maybe Soon Some Other Big Simulation Models in R). There is a look back at the evolution of Integral Projection Models from Mark Rees and Steve Ellner in How Did We Get Here From There? A Brief History of Evolving Integral Projection Models. In Inverse Modelling and IPMs: Estimating Processes from Incomplete Information Edgar González explains how you can estimate process that you can’t observe. And keep an eye out for Brittany Teller’s blog post coming next week!

Don’t wait too long to get the Demography Beyond the Population Special Feature papers though, they’re freely available for a limited time only

Continue reading

Making the Most of Volunteer Data: Counting the birds and more…

Post provided by Rob Robinson

It’s 6am on a warm spring morning and I’m about to visit the second of my Breeding Bird Survey1 sites. Like 2,500 other volunteers in the UK, twice a year I get up early to record all the birds I see or hear on the two transects in my randomly selected 1km square. Each year I look forward to these mornings almost as much for the comparisons as the actual sightings. Will there be more or fewer sightings of our summer migrants this year? How will numbers in this rolling Norfolk farmland stack up against those I see in urban, central Norwich?

Dawn bird survey in arable farmland. © Rob Robinson/BTO

Dawn bird survey in arable farmland. © Rob Robinson/British Trust for Ornithology (BTO)

The importance of demography

But simply recording these changes is not enough; we need to understand why they occur if action is to be taken. This requires us to quantify the demographic rates (survival, productivity and movements) that underlie them, which in turn requires samples of marked individuals. Simply counting individuals is not enough. Continue reading

Issue 6.9

Issue 6.9 is now online!

The September issue of Methods is now online!

This month’s issue contains one Applications article and two Open Access articles, all of which are freely available.

POPART: An integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication-ready figure production. The package also provides a platform for the implementation and distribution of new network-based methods.

Michalis Vardakis et al. provide this month’s first Open Access article. In ‘Discrete choice modelling of natal dispersal: ‘Choosing’ where to breed from a finite set of available areas‘ the authors show how the dispersal discrete choice model can be used for analysing natal dispersal data in patchy environments given that the natal and the breeding area of the disperser are observed. This model can be used for any species or system that uses some form of discrete breeding location or a certain degree of discretization can be applied.

Our September issue also features articles on Animal Movement, Population Dynamics, Statistical Ecology, Biodiversity, Conservation Biology and much more. Continue reading