Uncertainties in Species Occurrence Data: How to deal with False Positives and False Negatives

Post provided by Gurutzeta Guillera-Arroita

Species Surveys: New Opportunities and Ongoing Data Challenges

Technologies, such as drones, open new opportunities for wildlife monitoring ©J. Lahoz-Monfort, UMelb.

Technologies, such as drones, open new opportunities for wildlife monitoring ©J. Lahoz-Monfort, UMelb.

Monitoring is a fundamental step in the management of any species. The collection and careful analysis of species data allows us to make informed decisions about management priorities and to critically evaluate our actions. There are many aspects of a natural system that we can measure and, when it comes to monitoring the status of species, occurrence is a commonly used metric.

Ecologists have a long history of collecting species occurrence data from systematic surveys and our ability to gather species data is only going to grow! This is partly enabled by the fact that citizen science programs are starting to gain a prominent role in wildlife monitoring. There’s a growing recognition that well-managed citizen science surveys can produce useful data, while scaling up monitoring effort thanks to the increased human-power from large numbers of committed volunteers. Continue reading

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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.

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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

Listen Up! Using Passive Acoustic Monitoring to Help Forest Elephant Conservation

Post provided by Peter H. Wrege

Forest elephant in Gabon

Forest elephant in Gabon

Heard but not seen, populations of forest elephants (Loxodonta cyclotis) are rapidly declining due to ivory poaching. As one of the largest land mammals in the world, this species is surprisingly difficult to observe in the dense forests of Central Africa, but their low frequency rumbles can be recorded. With the autonomous recording afforded by passive acoustic monitoring (PAM) though, we have a window onto forest elephant ecology and behaviour that’s providing data critical to their conservation and survival.

The diverse ways that PAM can contribute to conservation outcomes is growing and while still underappreciated, the availability of relatively inexpensive recorders, increased power efficiency, and powerful techniques to automate the detection of signals have led to an explosion in use. In 2007 there were only about 20 published papers using PAM techniques, but since then over 400 papers have appeared in peer-reviewed journals.

Spectrogram of two forest elephant rumbles. Horizontal line shows the limit of human hearing.

Spectrogram of two forest elephant rumbles. Horizontal line shows the limit of human hearing.

Essentially, PAM is the automatic recording of sounds in a given environment, often for long periods. The trick, and often greatest challenge, is to find the signals of interest (bird calls, elephant rumbles, gunshots) within the recordings. With these signals we can quantify abundance, occupancy and spatial or temporal patterns of activity. Particularly in landscapes or ecosystems where visual observation is difficult (e.g. oceans, rainforests, nocturnal environments) PAM may be uniquely capable of delivering informative and unbiased data. Because PAM is a relatively new method but of considerable interest across the disciplines of ecology, behaviour and conservation, there is huge interest in refining the sampling and statistical methods needed to deal with the peculiarities of acoustic data. Continue reading

Issue 8.8

Issue 8.8 is now online!

The August issue of Methods is now online!

This issue contains two Applications articles and two Open Access articles. These four papers are freely available to everyone, no subscription required.

 Paco: An R package that assesses the phylogenetic congruence, or evolutionary dependence, of two groups of interacting species using both ecological interaction networks and their phylogenetic history.

 Open MEE: Open Meta-analyst for Ecology and Evolution (Open MEE) addresses the need for advanced, easy-to-use software for meta-analysis and meta-regression.It offers a suite of advanced meta-analysis and meta-regression methods for synthesizing continuous and categorical data, including meta-regression with multiple covariates and their interactions, phylogenetic analyses, and simple missing data imputation.

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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.

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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

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 alternative sampling design for rare species‘ – Specht et al. developed a new “conditional” occupancy survey design to improve occupancy estimates for rare species, They also compare it to standard and removal occupancy study designs. In this video two of the authors, Hannah Specht and Henry Reich, explain how their new conditional occupancy survey design works. 

This video is based on the article ‘Occupancy surveys with conditional replicates: An alternative sampling design for rare species‘ by Specht et al.

 

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

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.

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