Assessment of Stream Health with DNA Metabarcoding

Following on from last week’s press release ‘How Clean are Finnish Rivers?’, Vasco Elbrecht et al. have produced a video to explain the methods in ‘Assessing strengths and weaknesses of DNA metabarcoding-based macroinvertebrate identification for routine stream monitoring‘.

In this video, the authors explore the potential of DNA metabarcoding to access stream health using macroinvertebrates. They compared DNA and morphology-based identification of bulk monitoring samples from 18 Finnish stream ecosystems. DNA-based methods show higher taxonomic resolution and similar assessment results as currently used morphology-based methods. Their study shows that the tested DNA-based methods integrate well with current approaches, but further optimisation and validation of DNA metabarcoding methods is encouraged.

This video is based on the article ‘Assessing strengths and weaknesses of DNA metabarcoding-based macroinvertebrate identification for routine stream monitoring‘ by Elbrecht et al.

 

Issue 8.3

Issue 8.3 is now online!

The March issue of Methods is now online!

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

 Solo: Solo audio recorders are inexpensive, easy to construct and record audible sound continuously for around 40 days. The paper also has a video tutorial explaining how to assemble the required hardware and comes with a companion website with more information.

 The third dimension: A novel design to obtain three-dimensional data on the movements of aquatic organisms at depths of up to 140m. The set-up consists of two synchronised high-speed cameras fixed to two articulated arms and can be used for any underwater applications that require synchronized video recordings of medium- to large-sized animals.

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Issue 7.12

Issue 7.12 is now online!

The final 2016 issue of Methods is now online!

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

– iNEXT: The R package iNEXT (iNterpolation/EXTrapolation) provides simple functions to compute and plot the seamless rarefaction and extrapolation sampling curves for the three most widely used members of the Hill number family (species richness, Shannon diversity and Simpson diversity).

– camtrapR: A new toolbox for flexible and efficient management of data generated in camera trap-based wildlife studies. The package implements a complete workflow for processing camera trapping data.

– rotl: An R package to search and download data from the Open Tree of Life directly in R. It uses common data structures allowing researchers to take advantage of the rich set of tools and methods that are available in R to manipulate, analyse and visualize phylogenies.

– Fluctuating-temperature chamber: A design for economical, programmable fluctuating-temperature chambers based on a relatively small commercially manufactured constant temperature chamber modified with a customized, user-friendly microcontroller.

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Issue 7.11

Issue 7.11 is now online!

The November issue of Methods is now online!

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

– moveHMM: This R package allows ecologists to process GPS tracking data into series of step lengths and turning angles, and to fit a hidden Markov model to these data, allowing, in particular, for the incorporation of environmental covariates.

– BORIS: An open-source and multiplatform standalone program that allows a user-specific coding environment to be set for a computer-based review of previously recorded videos or live observations. Being open to user-specific settings, the program allows a project-based ethogram to be defined that can then be shared with collaborators, or can be imported or modified.

– inbreedR: An R package that provides functions to measure variance in inbreeding – through the strength of correlation in heterozygosity across marker loci – based on microsatellite and SNP markers with associated P-values and confidence intervals. Within the framework of Heterozygosity–fitness correlation theory, inbreedR also estimates the impact of inbreeding on marker heterozygosity and fitness.

– Terrestrial Precipitation Analysis: This package is comprised of the Precipitation Trends (P-Trend), Precipitation Attributes (P-Att) and Precipitation Manipulation (P-Man) tools. Combined, these web tools allow researchers to easily calculate fundamental precipitation statistics for past, present and projected future precipitation regimes for any terrestrial location in the world.

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Automatic Camera Monitoring: A Window into the Daily Life of Pollinators

Post provided by Ronny Steen

Image from the Canon PowerShot camera with CHDK script ‘Motion Detect Plus’. The thistle flower being visited by ♀ honeybee Apis mellifera L.

Image from the Canon PowerShot camera with CHDK script ‘Motion Detect Plus’. The thistle flower being visited by ♀ honeybee Apis mellifera L.

Pollinators have fascinated ecologists for decades, and they have traditionally been monitored by on-site human observations. This can be a time-consuming enterprise and – more importantly – species identification and recordings of behaviour have to be registered at the time of observation. This has two complications:

  1. While writing notes, or recording them electronically, the observer cannot continue focusing on the animal or behaviour in question.
  2. Such data then have to be transcribed, with the risk of making transcription errors.

Bringing Monitoring into the 21st Century

Although on-site human observations have predominated, today’s widespread availability of digital monitoring equipment has enabled unique data on flower visitors to be collected. In my research, I have used a time-efficient automated procedure for monitoring flower-visiting animals – namely foraging bumblebees visiting focal white clovers and honeybees visiting thistles.

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Issue 7.7

Issue 7.7 is now online!

The July issue of Methods is now online!

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

– MO-Phylogenetics: A software tool to infer phylogenetic trees optimising two reconstruction criteria simultaneously and integrating a framework for multi-objective optimisation with two phylogenetic software packages.

– PHYLOMETRICS: An efficient algorithm to construct the null distributions (by generating phylogenies under a trait state-dependent speciation and extinction model) and a pipeline for estimating the false-positive rate and the statistical power of tests on phylogenetic metrics..

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Canopy Camera Trapping: Heightening Our Knowledge of Arboreal Mammals

Post provided by FARAH CARRASCO-RUEDA and TREMAINE GREGORY

We wanted to test whether arboreal mammals were using natural canopy bridges – connections between tree branches over a clearing – to travel over a natural gas pipeline in the Peruvian Amazon. The challenge was figuring out how to monitor branches 100 feet up in the tree tops. In this case, the clearing was a 30-foot-wide pipeline path, and we expected arboreal mammals – like monkeys, squirrels and porcupines – to prefer crossing on the branches rather than on the ground. The ground is an unfamiliar and often dangerous place for an animal that’s spent its life way up in the canopy.

The path captured by the camera.

The yellow arrow shows the path captured by the camera trap.

In fact, we wondered if without branches, would arboreal mammals cross at all? How could we find out if animals were using the branches? There were 13 canopy bridges and finding a person to sit and wait all day (and night) under each of them for animals to cross wasn’t an option. With our goal of a year’s worth of monitoring, we had a conundrum. We needed a more efficient way to gather the data and concluded that camera traps – motion sensitive cameras – could be an excellent way to monitor the bridges continuously and remotely.

But, we discovered that no one had ever really used camera traps in the high canopy before. How were we going to get them all the way up there? If we were able to get up to the canopy, how could we make sure they were taking photos of the correct points where animals would potentially cross? Continue reading

Issue 7.1

Issue 7.1 is now online!

The January issue of Methods is now online!

As always, the first issue of the year is our sample issue. You can access all of the articles online free of charge. No subscription or membership is required!

We have two Open Access articles and two Applications papers in our January issue.

Recognizing False Positives: Environmental DNA (eDNA) is increasingly used for surveillance and detection of species of interest in aquatic and soil samples. A significant risk associated with eDNA methods is potential false-positive results due to laboratory contamination. To minimize and quantify this risk, Chris Wilson et al. designed and validated a set of synthetic oligonucleotides for use as species-specific positive PCR controls for several high-profile aquatic invasive species.

BiMat: An open-source MATLAB package for the study of the structure of bipartite ecological networks. BiMat enables both multiscale analysis of the structure of a bipartite ecological network – spanning global (i.e. entire network) to local (i.e. module-level) scales – and meta-analyses of many bipartite networks simultaneously. The authors have chosen to make this Applications article Open Access.

Gemma Murray et al. provide this month’s second Open Access article. In ‘The effect of genetic structure on molecular dating and tests for temporal signal‘ the authors use simulated data to investigate the performance of several tests of temporal signal, including some recently suggested modifications. The article shows that all of the standard tests of temporal signal are seriously misleading for data where temporal and genetic structures are confounded (i.e. where closely related sequences are more likely to have been sampled at similar times). This is not an artifact of genetic structure or tree shape per se, and can arise even when sequences have measurably evolved during the sampling period.

Our January issue also features articles on Monitoring, Population Ecology, Genetics, Evolution, Community Ecology, Diversity and more. 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 6.10

Issue 6.10 is now online!

The October 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.

letsR: A package for the R statistical computing environment, designed to handle and analyse macroecological data such as species’ geographic distributions and environmental variables. It also includes functions to obtain data on species’ habitat use, description year and current as well as temporal trends in conservation status.

Cleaning Oil from Seabirds: The authors assess the efficacy of sea water as an alternative to fresh water for cleaning oil from seabirds’ feathers. Results indicate that for oiled feathers, a sea water wash/rinse produced clean, low BAI/unclumped feathers with minimal particulate residue.

Stefano Canessa et al. provide this month’s only Open Access article. In ‘When do we need more data? A primer on calculating the value of information for applied ecologists‘ the authors guide readers through the calculation of Value of Information (VoI) using two case studies and illustrate the use of Bayesian updating to incorporate new information. Collecting information can require significant investments of resources; VoI analysis assists managers in deciding whether these investments are justified. The authors also wrote a blog post on VoI which you can find here.

Our October issue also features articles on Niche Modelling, Population Ecology, Spatial Ecology, Conservation, Monitoring and much more. Continue reading