Category: Methods papers

Conservation and management, Methods papers

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

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Conservation and management, Lab Methods, Methods papers

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 “Reptile DNA Sexing: Easier Than You Ever Thought”

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Conservation and management, Methods papers

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

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Conservation and management, Methods papers, Practical Tools

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 “Oxford Research Sheds Light on the Secret Life of Badgers”

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Methods papers, Online extras

Conditional Occupancy Design Explained

Occupancy surveys are widely used in ecology to study wildlife and plant habitat use. To account for imperfect detection probability many researchers use occupancy models. But occupancy probability estimates for rare species tend to be biased because we’re unlikely to observe the animals at all and as a result, the data aren’t very informative. In their new article – ‘Occupancy surveys with conditional replicates: An … Continue reading Conditional Occupancy Design Explained

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Methods papers

Refined DNA Tool Tracks Native and Invasive Fish

Below is a press release about the Methods paper ‘Long-range PCR allows sequencing of mitochondrial genomes from environmental DNA‘ taken from the Cornell University.

©Nick Hobgood

Rather than conduct an aquatic roll call with nets to know which fish reside in a particular body of water, scientists can now use DNA fragments suspended in water to catalog invasive or native species.

The research from Cornell University, the University of Notre Dame and Hawaii Pacific University was published July 14 in Methods in Ecology and Evolution.

“We’ve sharpened the environmental DNA (eDNA) tool, so that if a river or a lake has threatened, endangered or invasive species, we can ascertain genetic detail of the species there,” said senior author David Lodge, the Francis J. DiSalvo Director of the Atkinson Center for a Sustainable Future at Cornell, and professor of ecology and evolutionary biology. “Using eDNA, scientists can better design management options for eradicating invasive species, or saving and restoring endangered species.” Continue reading “Refined DNA Tool Tracks Native and Invasive Fish”

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Methods papers

Drones used to assess health of Antarctic vegetation

Below is a press release about the Methods paper ‘Unmanned aircraft system advances health mapping of fragile polar vegetation‘ taken from the University of Wollongong.

New method faster, more efficient and less damaging to the environment

A team of researchers from the University of Wollongong (UOW) and the University of Tasmania has developed a new method for assessing the health of fragile Antarctic vegetation using drones, which they say could be used to improve the efficiency of ecological monitoring in other environments as well.

The researchers have written about their method in an article published in Methods in Ecology and Evolution, a scientific journal of the British Ecological Society.

Continue reading “Drones used to assess health of Antarctic vegetation”

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Evolution, Methods papers

Getting Serious About Transposable Elements

Post Provided by: Gabriel Rech and José Luis Villanueva-Cañas

So Simple yet so Complex

A long standing research topic in evolutionary biology is the genetic basis of adaptation. In other words, how does a novel trait appear (or spread) in response to an environmental change? Despite the rapid advances in sequencing over the last two decades, we have only been able to fully characterize a few adaptations.

As stated by Richard Dawkins in Climbing Mount Improbable, while natural selection is a very simple process, modeling natural selection and determining its causes, effects and consequences is an extremely difficult task. Also, most of our efforts so far have been focused on just one type of genetic variation: single nucleotide polymorphisms (SNPs). Other types of variations such as transposable element (TE) insertions have received much less attention. Paradoxically, some great examples of the role of TEs in adaptation have been right under our noses the whole time, in basic biology textbooks. Continue reading “Getting Serious About Transposable Elements”

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Methods papers, Online extras

Why Soft Sweeps from Standing Genetic Variation are More Likely than You May Think

We coined the term “soft sweeps” in 2005. The term has since become widely used, though not everyone uses the term in the same way. As part of the ‘How to Measure Natural Selection‘ Special Feature in Methods in Ecology and Evolution, we attempt to clarify what “soft sweep” means and doesn’t mean. For example, not every sweep from standing genetic variation is necessarily a … Continue reading Why Soft Sweeps from Standing Genetic Variation are More Likely than You May Think

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Evolution, Methods papers, Virtual Issues

Evolutionary Quantitative Genetics: Virtual Issue

Post provided by Michael Morrissey

©Dr. Jane Ogilvie, Rocky Mountain Biological Laboratory

Evolutionary quantitative genetics provides formal theoretical frameworks for quantitatively linking natural selection, genetic variation, and the rate and direction of adaptive evolution. This strong theoretical foundation has been key to guiding empirical work for a long time. For example, rather than generally understanding selection to be merely an association of traits and fitness in some general way, theory tells us that specific quantities, such as the change in mean phenotype within generations (the selection differential; Lush 1937), or the partial regressions of relative fitness on traits (direct selection gradients; Lande 1979, Lande and Arnold 1983) will relate to genetic variation and evolution in specific, informative ways.

These specific examples highlight the importance of the theoretical foundation of evolutionary quantitative genetics for informing the study of natural selection. However, this foundation also supports the study other critical (quantification of genetic variation and evolution) and complimentary (e.g., interpretation when environments, change, the role of plasticity and genetic variation in plasticity) aspects of understanding the nuts and bolts of evolutionary change. Continue reading “Evolutionary Quantitative Genetics: Virtual Issue”

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