Biodiversity Monitoring by Plant Proxy is Cheap and Easy: Here’s How and Why

Post provided by Rasmus Ejrnæs, Ane Kirstine Brunbjerg & Hans Henrik Bruun

Could we use the plants in this swamp forest to predict the diversity of other species?

Local communities and regional biotas are built of hundreds, if not thousands, of species. Most of these species are small-bodied and discreet lifeforms. So it’s no wonder that naturalists have almost always focused their attention on conspicuous species of their particular liking. Why plants then? Well, plants are practical and efficient. They “stand still and wait to be counted”, as the eminent population biologist John Harper put it. No matter the weather, from spring to autumn. There are enough plant species to show contrasts between sites, and yet they can usually be identified to species level in the field.

You Can’t Predict the Diversity of Beetles from Lichens… Can You?

Unfortunately, the overwhelming scientific consensus seems to be that any particular taxonomic group won’t adequately represent the biodiversity of other taxonomic groups. The idea of surrogacy seems to hit the same hard wall as most attempts to provide generally working models for variation in biodiversity at local and regional scales. Biodiversity remains one of the largest scientific research questions without good general answers. Continue reading

The Future of Solar Geolocation Tracking is NOW

Post provided by Julia Karagicheva, Theunis Piersma and Eldar Rakhimberdiev

Black-tailed godwit with leg-mounted solar geolocator. ©Jan van de Kam

Black-tailed godwit with leg-mounted solar geolocator. ©Jan van de Kam

Working on FLightR, the package for analysis of data obtained from solar geolocation tracking devices, we were haunted by the unpleasant feeling of investing in technology which will soon be out of date. Until now solar geolocators have been popular in ornithological studies. This is because they’re small, light-weight (< 1/3 g) tracking devices that can be deployed even on miniature birds, such as swallows and warblers. They’ve also been the longest-lasting data loggers, with the most storage space and, of course, the most affordable ones.

Are Solar Geolocators Finished?

There are apparent drawbacks of using this technique though. To begin with, solar geolocation simply does not work for some species. You can’t use it to study birds living in dense tropical forests or in cavities, because of the light-pattern bias. For the same reason, it doesn’t provide fantastic results in light-polluted areas. Data from geolocators cannot be retrieved remotely, and this is why you need to have high recapture rates for the species you’re studying.   Continue reading

Remote Camera Network Tracks Antarctic Species at Low Cost

Below is a press release about the Methods in Ecology and Evolution article ‘Estimating nest‐level phenology and reproductive success of colonial seabirds using time‐lapse cameras‘ taken from NOAA Fisheries.

Camera system in place in an Adélie and gentoo penguin colony ©Jefferson Hinke, NOAA Fisheries

Camera system in place in an Adélie and gentoo penguin colony ©Jefferson Hinke, NOAA Fisheries

An international research team has developed a simple method for using a network of autonomous time-lapse cameras to track the breeding and population dynamics of Antarctic penguins, providing a new, low-cost window into the health and productivity of the Antarctic ecosystem.

The team of scientists from NOAA Fisheries and several other nations published in the journal Methods in Ecology and Evolution, descriptions of the camera system and a new method for turning static images into useful data on the timing and success of penguin reproduction. They say that the system monitors penguins as effectively as scientists could in person, for a fraction of the cost. Continue reading

Practical Tools: A New Article Type and a Virtual Issue

Today, we’re pleased to announce that we’re launching a new article type for Methods in Ecology and Evolution: Practical Tools. Like our Applications articles, Practical Tools will be short papers (up to 3000 words). They’ll focus on new field techniques, equipment or lab protocols. From this point forward, our Applications papers will solely focus on software and code.

Practical tools need to clearly demonstrate how tools designed for specific systems or problems can be adapted for more general use. Online supporting information can include specific instructions, especially for building equipment. You can find some examples of Applications that would now fit into this article type here and here.

To help launch our new article type, we asked four of our Associate Editors – Pierre Durand, Graziella Iossa, Nicolas Lecomte and Andrew Mahon – to put together a Virtual Issue of papers about Field Methods that have previously been published in the journal. All of the articles in ‘Practical Tools: A Field Methods Virtual Issue‘ will be free to everyone for the next month. You can find out a bit more about each of the four sections of the Virtual Issue below. Continue reading

Issue 8.8

Issue 8.10 is now online!

The October issue of Methods is now online!

This double-sized issue contains three Applications articles and two Open Access articles. These five papers are freely available to everyone, no subscription required.

 Phylogenetic TreesThe fields of phylogenetic tree and network inference have advanced independently, with only a few attempts to bridge them. Schliep et al. provide a framework, implemented in R, to transfer information between trees and networks.

 Emon: Studies, surveys and monitoring are often costly, so small investments in preliminary data collection and systematic planning of these activities can help to make best use of resources. To meet recognised needs for accessible tools to plan some aspects of studies, surveys and monitoring, Barry et al. developed the R package emon, which includes routines for study design through power analysis and feature detection.

 Haplostrips: A tool to visualise polymorphisms of a given region of the genome in the form of independently clustered and sorted haplotypes. Haplostrips is a command-line tool written in Python and R, that uses variant call format files as input and generates a heatmap view.

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Monitoring the Distribution and Abundance of Sea Otters

Post provided by Perry Williams

Sea otters (Enhydra lutris) are an apex predator of the nearshore marine ecosystem – the narrow band between terrestrial and oceanic habitat. During the commercial maritime fur trade in the 18th and 19th centuries, sea otters were nearly hunted to extinction across their range in the North Pacific Ocean. By 1911, only a handful of small isolated populations remained.

Sea otters resting in Glacier Bay National Park. © Jamie Womble, NPS. USFWS Permit #14762C-0, NPS Permit #GLBA-2016- SCI-0022.

Sea otters resting in Glacier Bay National Park. © Jamie Womble, NPS. USFWS Permit #14762C-0, NPS Permit #GLBA-2016- SCI-0022.

But sea otter populations have recovered in many areas due to a few changes. The International Fur Seal Treaty in 1911 and the Marine Mammal Protection Act (1972) protected sea otters from most human harvest. Wildlife agencies helped sea otter colonisation by transferring them to unoccupied areas. Eventually, sea otters began to increase in abundance and distribution, and they made their way to Glacier Bay, a tidewater glacier fjord and National Park in southeastern Alaska. 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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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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