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

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Protecting Habitat Connectivity for Endangered Vultures: Identifying Priorities with Network Analysis

Post provided by Juliana Pereira, Santiago Saura and Ferenc Jordán

The endangered Egyptian vulture. ©Carlos Delgado

The endangered Egyptian vulture. ©Carlos Delgado

One of the main causes behind biodiversity loss is the reduction and fragmentation of natural habitats. The conversion of natural areas into agricultural, urban or other human-modified landscapes often leaves wild species confined to small and isolated areas of habitat, which can only support small local populations. The problem with small, isolated populations is that they are highly vulnerable to extinction caused by chance events (such as an epidemic or a natural disaster in the area), or by genetic erosion (dramatic loss of genetic diversity that weakens species and takes away their ability to adapt to new conditions).

On top of that, we now have the added concern of climate change, which is altering environmental conditions and shifting habitats to different latitudes and altitudes. To survive in the face of these changes, many species need to modify their geographical distribution and reach new areas with suitable conditions. The combination of mobility (a biological property of species) and the possibility of spatial movement (a physical property of the landscape) is critically important for this. Continue reading

Mark-Recapture and Metapopulation Structure: Using Study Design to Minimize Heterogeneity

Post provided by Delphine Chabanne

Pod of bottlenose dolphins observed in Cockburn Sound, Perth, Western Australia.

Pod of bottlenose dolphins observed in Cockburn Sound, Perth, Western Australia.

Wildlife isn’t usually uniformly or randomly distributed across land- or sea-scapes. It’s typically distributed across a series of subpopulations (or communities). The subpopulations combined constitute a metapopulation. Identifying the size, demography and connectivity between the subpopulations gives us information that is vital to local-species conservation efforts.

What is a Metapopulation?

Richard Levins developed the concept of a metapopulation to describe “a population of populations”. More specifically, the term metapopulation has been used to describe a spatially structured population that persists over time as a set of local populations (or subpopulations; or communities).  Emigration and immigration between subpopulations can happen permanently (through additions or subtractions) or temporarily (through the short-term presence or absence of individuals).

How individuals could distribute themselves within an area.

How individuals could distribute themselves within an area.

Continue reading

Reptile DNA Sexing: Easier Than You Ever Thought

Post provided by Lukáš Kratochvíl and Michail Rovatsos

The sand lizard (Lacerta agilis).

The sand lizard (Lacerta agilis).

Many researchers, breeders and hobbyists need to know sex of their animals. Sometimes it’s easy – in sexually dimorphic species you only have to look. In other species or juveniles it’s often not so straightforward though. And it’s often impossible – but sometimes essential – in embryos or in tissue samples. Determining sex from DNA is the most practical option, or sometimes even the only possibility, in these cases.

Molecular sexing is routinely used in mammals and birds, but until now it has only been available for a handful of reptile species. Many people didn’t believe that this situation would improve considerably any time soon. But why? Continue reading

Birds and Climate in Space and Time: Separating Spatial and Temporal Effects of Climate Change on Wildlife

Post provided by Cornelia Oedekoven

The Standard Method

When trying to understand how wildlife, for example a bird species, may react to climate change scientists generally study how species numbers vary in relation to climatic or weather variables (e.g. Renwick et al. 2012, Johnston et al. 2013). The way this tends to be done is by gathering information (data!) about bird numbers as well as the weather variables (for example temperature) in several locations (i.e. in space) and fitting a regression model to these data to detect and illustrate how bird numbers go up or down with temperature.

Data on bird numbers and temperatures in several locations lets researchers see the relationship between the two.

Data on bird numbers and temperatures in several locations lets researchers see the relationship between the two.

This relationship is then used to forecast how bird numbers may change along with potential temperature changes in the future (i.e. in time), for example due to climate change.

Relationships between bird numbers and temperature in a given location are often used to forecast changes in bird numbers with expected changes in temperatures over time.

Relationships between bird numbers and temperature in a given location are often used to forecast changes in bird numbers with expected changes in temperatures over time.

Continue reading

Oxford Research Sheds Light on the Secret Life of Badgers

Below is a press release about the Methods paper ‘An active-radio-frequency-identification system capable of identifying co-locations and social-structure: Validation with a wild free-ranging animal‘ taken from the University of Oxford.

© Peter Trimming

Detecting the movements and interactions of elusive, nocturnal wildlife is a perpetual challenge for wildlife biologists. But, with security tracking technology, more commonly used to protect museum artwork, new Oxford University research has revealed fresh insights into the social behaviour of badgers, with implications for disease transmission.

Previous studies have assumed that badgers are territorial and, at times, anti-social, living in tight-knit and exclusive family groups in dens termed ‘setts’. This led to the perception that badgers actively defend territorial borders and consequently rarely travel beyond their social-group boundaries.

This picture of the badger social system is so widely accepted that some badger culling and vaccination programmes rely on it – considering badger society as being divided up into discrete units, with badgers rarely venturing beyond their exclusive social-groups. But, the findings, newly published in Methods in Ecology and Evolution, have revealed that badgers travel more frequently beyond these notional boundaries than first thought, and appear to at least tolerate their neighbours. Continue reading

Britain’s Smallest Bird Affected by Cold Winters: New Analysis Methods Relate Wildlife Abundance to Weather

Below is a press release about the Methods paper ‘Attributing changes in the distribution of species abundance to weather variables using the example of British breeding birds‘ taken from the University of St Andrews.

©CJ Hughson

The goldcrest is being hit hard by cold winters. ©CJ Hughson

Britain’s smallest bird species, the goldcrest, is being hit hard by cold winters, new analysis methods developed by researchers at the University of St Andrews have revealed.

The data analysis techniques, published today in Methods in Ecology and Evolution, take a longer term view over multiple locations and for a period of several years, compared to previous studies.

They showed that the cold temperatures strongly affected breeding numbers of the goldcrest, while in contrast, the song thrush was not affected by the cold, but benefited from wet and mild summers. Continue reading

Fast-Moving Biodiversity Assessment: Are We Already in the Future?

Post provided by Carola Gómez-Rodríguez & Alfried P. Vogler

Time flies… in the blink of an eye! And even more so in science. The molecular lab work we were used to two decades ago seems like ancient history to today’s PhD students. The speed of change in sequencing technology is so overwhelming that imagination usually fails to foresee how our daily work will be in 10 years’ time. But in the field of biodiversity assessment, we have very good clues. Next Generation Sequencing is quickly becoming our workhorse for ambitious projects of species and genetic inventories.

One by One Approach to Studying Biodiversity

For decades, most initiatives measured biodiversity in the same way: collect a sample of many individuals in the field, sort the specimens, identify them to a Linnaean species one at a time (if there was a good taxonomist in the group which, unfortunately, it is kind of lucky these days!), and count them. Or, if identification was based on molecular data, the specimen was subject to DNA extraction, to sequence one (or several) short DNA markers. This involved countless hours of work that could be saved if, instead of inventorying biodiversity specimen-by-specimen, we followed a sample-by-sample approach. To do this now, we just have to make a “biodiversity soup”.

Biodiversity assessment based on morphological identification and/or Sanger sequencing (“The one-by-one approach”)

Biodiversity assessment based on morphological identification and/or Sanger sequencing (“The one-by-one approach”)

Continue reading

Estimating the Size of Animal Populations from Camera Trap Surveys

Below is a press release about the Methods paper ‘Distance sampling with camera traps‘ taken from the Max Planck Society.

A Maxwell's duiker photographed using a camera trap. Marie-Lyne Després-Einspenner

A Maxwell’s duiker photographed using a camera trap. ©Marie-Lyne Després-Einspenner

Camera traps are a useful means for researchers to observe the behaviour of animal populations in the wild or to assess biodiversity levels of remote locations like the tropical rain forest. Researchers from the University of St Andrews, the Max Planck Institute for Evolutionary Anthropology (MPI-EVA) and the German Centre for Integrative Biodiversity Research (iDiv) recently extended distance sampling analytical methods to accommodate data from camera traps. This new development allows abundances of multiple species to be estimated from camera trapping data collected over relatively short time intervals – information critical to effective wildlife management and conservation.

Remote motion-sensitive photography, or camera trapping, is revolutionising surveys of wild animal populations. Camera traps are an efficient means of detecting rare species, conducting species inventories and biodiversity assessments, estimating site occupancy, and observing behaviour. If individual animals can be identified from the images obtained, camera trapping data can also be used to estimate animal density and population size – information critical to effective wildlife management and conservation. 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.