Multi-State Species Distribution Models: What to do When Species Need Multiple Habitats

Post provided by Jan Engler, Veronica Frans and Amélie Augé

The north, south, east, and west boundaries of a species’ range tell us very little about what is happening inside…

― Robert H. MacArthur (1972, p. 149)

When You Enter the Matrix, Things Become Difficult!

New Zealand sea lion mother and pup. © Amélie Augé

New Zealand sea lion mother and pup. © Amélie Augé

Protecting wildlife calls for a profound understanding of species’ habitat demands to guide concrete conservation actions. Quantifying the relationships between species and their environment using species distribution models (SDMs) has attracted tremendous attention over the past two decades. Usually these species-environment relationships are estimated on coarse spatial scales, using globally-interpolated long-term climate data sets. While they’re useful for studies on large-scale species distributions, these environmental predictors have limited applications for conservation management.

Climatic data were the first environmental information available with global coverage, but a wide range of Earth observation techniques have increased the availability of much finer environmental information. This allows us to quantify species-environment relationships in unprecedented detail. We can now shift the scale that SDMs operate at, resulting in more useful applications in conservation – SDMs now enter the matrix.

This shift in scale brings new challenges, especially for species using multiple distinct habitat types to survive. The landscape matrix, which has been negligible at the broad (global) scale, is hugely important at the fine (local) scale. It is not only that we need to quantify certain habitat types but also need to consider their arrangement in the landscape, which is basically what the landscape matrix is about. But as we enter the matrix, things become difficult. Continue reading


Digitizing Historical Land-use Maps with HistMapR

Habitat destruction and degradation represent serious threats to biodiversity, and quantification of land-use change over time is important for understanding the consequences of these changes to organisms and ecosystem service provision.

Historical land-use maps are important for documenting how habitat cover has changed over time, but digitizing these maps is a time consuming process. HistMapR is an R package designed to speed up the digitization process, and in this video we take an example map to show you how the method works.

Digitization is fast, and agreement with manually digitized maps of around 80–90% meets common targets for image classification. We hope that the ability to quickly classify large areas of historical land use will promote the inclusion of land-use change into analyses of biodiversity, species distributions and ecosystem services.

This video is based on the Applications article ‘HistMapR: Rapid digitization of historical land-use maps in R‘ by Auffret et al. This article is freely available to anyone (no subscription required).

The package is hosted on GitHub and example scripts can be downloaded from Figshare.

Can We Really Measure Habitat Condition From Space?

Post provided by Tom Harwood, Randall Donohue, Simon Ferrier, Tim McVicar, Graeme Newell, Matt White and Kristen Williams

Remotely sensing can see patterns of land cover, but how do we use this information to quantify human impact on biodiversity?

Remotely sensing can see patterns of land cover, but how do we use this information to quantify human impact on biodiversity? ©NASA/GSFC/Jeff Schmaltz/MODIS Land Rapid Response Team

It’s very hard to make sensible choices without sensible information. When it comes to actions around changing land use and its ecological impact though, this is often what we are forced to do. If we want to reduce the impact of human activities on natural ecosystems, we need to know how much change has already occurred and how altered an ecosystem might be from its “natural” state.

Working out which parts of the landscape have been changed and mapping the absence of natural vegetation is an achievable (though onerous) task. However, moving beyond this binary view of the world is a huge challenge. Pretty much all habitat has been modified by human influences to some extent – by, for example, wood extraction, the introduction of invasive species or livestock grazing. This means that a lot of the apparently native habitat is no longer capable of supporting its full complement of native biodiversity. Continue reading

Creating Bigger, Better and More Joined-up Habitat Networks

Below is a press release about the Methods paper ‘How to manipulate landscapes to improve the potential for range expansion‘ taken from the University of Liverpool.



Scientists at the University of Liverpool have developed a new ‘route planner’ tool that could help conservationists aid the movement of species as they adapt to a changing climate.

The environmental ranges of many animal and plant species are starting to alter with climate change, as temperatures change and force species to migrate to more suitable climes.

To be able to do this successfully, they will need sufficient habitat in their existing range, their future range, and any intermediate areas to enable populations to survive and thrive. Many conservation initiatives to restore habitats and increase connectivity are trying to address this issue. However, existing modelling tools mainly treat the landscape as static, and it is difficult to use these to plan restoration. Continue reading

State-and-Transition Models: An Interview with Marie-Josee Fortin

David Warton (University of New South Wales) interviews Marie-Josee Fortin (University of Toronto) about a recent article on state-and-transition models from her group in Methods in Ecology and Evolution. David and Marie-Josee also discuss what motivated her career to date in spatial ecology, and what she sees as the main advances in this area and current challenges in the field.

Continue reading

Issue 6.11

Issue 6.11 is now online!

The November issue of Methods is now online!

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

mvMORPH: A package of multivariate phylogenetic comparative methods for the R statistical environment which allows fitting a range of multivariate evolutionary models under a maximum-likelihood criterion. Its use can be extended to any biological data set with one or multiple covarying continuous traits.

Low-cost soil CO2 efflux and point concentration sensing systems: The authors use commercially available, low-cost and low-power non-dispersive infrared (NDIR) CO2 sensors to develop a soil CO2 efflux system and a point CO2 concentration system. Their methods enable terrestrial ecologists to substantially improve the characterization of CO2 fluxes and concentrations in heterogeneous environments.

This month’s Open Access article comes from Jolyon Troscianko and Martin Stevens. In ‘Image calibration and analysis toolbox – a free software suite for objectively measuring reflectance, colour and pattern‘ they introduce a toolbox that can convert images to correspond to the visual system (cone-catch values) of a wide range of animals, enabling human and non-human visual systems to be modelled. The toolbox is freely available as an addition to the open source ImageJ software and will considerably enhance the appropriate use of digital cameras across multiple areas of biology. In particular, researchers aiming to quantify animal and plant visual signals will find this useful. This article received some media attention upon Early View publication over the summer. You can read the Press Release about it here.

Our November issue also features articles on Population Genetics, Macroevolution, Modelling species turnover, Abundance modelling, Measuring stress and much more. Continue reading

Measuring functional connectivity using butterflies

Long-term datasets yield a great deal of information and are increasingly used to inform conservation measures.

In the first video of the new year, Gary Powney and Tom Oliver show how long-term monitoring data on the Speckled Wood butterfly (Pararge aegeria) from the UK monitoring butterfly scheme can be used to assess functional connectivity of the landscape.

In a paper recently published in Methods, Gary Powney, Tom Oliver and colleagues use synchrony between population counts as a new empirical method to assess functional connectivity – the permeability of landscapes given species dispersal attributes. Functional connectivity is important because well-connected metapopulations are expected to be more resistant to stochastic events causing extinction. They use long-term monitoring data on the Speckled Wood butterfly and find that population synchrony is positively correlated with landscape suitability, suggesting that synchrony might be used to measure functional connectivity.

A key finding is that relatively close populations may exchange sufficient migrants for synchronisation, regardless of the matrix suitability. In contrast, more separate populations are synchronised only where the landscape permits functional connectivity, most likely through dispersal between intermediate stepping-stone populations.

This technique might be used to test and prioritise the effectiveness of land management for conservation of species and to mitigate the effects of climate change.