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

How Clean are Finnish Rivers?

Below is a press release about the Methods paper ‘Assessing strengths and weaknesses of DNA metabarcoding-based macroinvertebrate identification for routine stream monitoring‘ taken from the University of Duisburg-Essen.

©Shanthanu Bhardwaj

©Shanthanu Bhardwaj

Dragonflies, mayflies and water beetles have one thing in common: They indicate how clean the streams are in which they live. Scientists from the University of Duisburg-Essen and the Finnish Environment Institute (SYKE) have developed a DNA-based method, which allows to assess the stream water quality with unprecedented speed and accuracy. The article – ‘Assessing strengths and weaknesses of DNA metabarcoding-based macroinvertebrate identification for routine stream monitoring‘ – was just released in the esteemed peer-reviewed journal Methods in Ecology and Evolution.

Traditional stream assessment using visual identification of indicator species is time-consuming, expensive and procedures are seldom standardised. Especially small organisms may look similar and misidentifications happen frequently. Using a genetic method to identify the species these concerns are not an issue, as even small organisms can be securely identified using a DNA marker. Continue reading

Editor Recommendation – HistMapR: Rapid Digitization of Historical Land-Use Maps in R

Post provided by Sarah Goslee

For an ecologist interested in long-term dynamics, one of the most thrilling experiences is discovering a legacy dataset stashed away somewhere.

For an ecologist interested in long-term dynamics, one of the most daunting experiences is figuring how to turn that box full of paper into usable data.

The new tool HistMapR, described in ’HistMapR: Rapid digitization of historical land-use maps in R’ by Alistair Auffret and colleagues, makes one part of that task much easier.

Examples of input (©Lantmäteriet) and output maps from (a–b) the District Economic map and (c–d) the Economic map.

Examples of input (©Lantmäteriet) and output maps from (a–b) the District Economic map and (c–d) the Economic map.

Historical maps with coloured areas denoting different land cover or use are a valuable record, but difficult to analyse. This R package automates much of the time-consuming and tedious process of turning paper maps into classified categorical raster maps.

A map is scanned, imported into R, and the software is trained by clicking in different areas of each category. It then automatically classifies pixels based on which colour they are most similar to. The resulting classification is assessed manually. The process can be repeated with slightly different parameters until a good fit is achieved.

The authors found 80-90% agreement between HistMapR classification and manual digitisation (sources of error included clarity of original maps and scan quality). Using HistMapR reduced the time needed for digitising a series of historical land cover maps from two months to two days. Ecologists interested in long-term dynamics should be cheering!

The HistMapR package is available on GitHub and you can find example scripts on Figshare, so you can get right to work.

HistMapR: Rapid digitization of historical land-use maps in R‘ by Auffret et al. is a freely available Applications article (no subscription required).

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

Building Universal PCR Primers for Aquatic Ecosystem Assessments

Post provided by Vasco Elbrecht

Many things can negatively affect stream ecosystems – water abstraction, eutrophication and fine sediment influx are just a few. However, only intact freshwater ecosystems can sustainably deliver the ecosystem services – such as particle filtration, food biomass production and the supply of drinking water – that we rely on. Because of this, stream management and restoration has often been in the focus of environmental legislation world-wide. Macrozoobenthic communities are often key biological components of stream ecosystems. As many taxa within these communities are sensitive to negative stressors introduced by humans, they’re ideal for assessing the quality of water.

Unfortunately, most macrozoobenthic taxa – such as stone-, may-, and caddisflies as well as most other invertebrates – are often found in juvenile larval life stages in these ecosystems, so they’re often difficult to identify based on morphology. With the DNA based metabarcoding method though, almost all taxa in a stream can be reliably identified up to species level using a standardised gene fragment. One key component of this strategy is the development of universal markers, which allow detection of the diverse macrozoobenthic groups.

Our new R package PrimerMiner provides a framework for obtaining sequence data from available reference databases and identifying suitable primer binding sites for marker amplification. The package makes this process quicker and easier. In the following pictures, we summarise the key steps of DNA metabarcoding.

To find out more about PrimerMiner, read our Methods in Ecology and Evolution article ‘PrimerMiner: an r package for development and in silico validation of DNA metabarcoding primers’. Like all Applications articles, this paper is freely available to everyone.

What silver fir aDNA can tell us about Neolithic forests

Below is a press release about the Methods paper ‘HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA‘ taken from Swiss Federal Institute for Forest, Snow and Landscape Research WSL (this press release is also available in French, German and Italian via the links below).

A new technique makes it possible to cost-effectively analyse genetic material from fossil plants and animals. Researchers from the Swiss Federal Institute for Forest, Snow and Landscape Research WSL and the universities of Lausanne and Bern have used this technique to examine the DNA of silver fir remains found in lake sediment in Ticino. They found clues as to how forests reacted to the emergence of agriculture.

The new process utilises the latest advances in DNA technology to isolate ancient DNA (aDNA) from prehistoric plants and animals. The techniques used to date are, however, expensive. “As population geneticists often need several dozens samples to make reliable statements, many research ideas are not currently financially viable,” says Nadir Alvarez, a professor at the University of Lausanne’s Department of Ecology and Evolution.

The research team led by Alvarez and his colleagues Christoph Sperisen (a population geneticist at the WSL), Willy Tinner (a professor of palaeoecology at the University of Bern) and Sarah Schmid (a biologist from the University of Lausanne) has now developed a cost-effective alternative and demonstrated its potential with subfossil silver fir needles found at Origlio lake in Ticino. The team showcased the results in the research journal Methods in Ecology and Evolution. 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.

What Can Penguins Tell Us About Mitochondria? And Vice-Versa!

Post provided by Antoine Stier

Why on earth would someone try to combine field ornithology and mitochondrial biology? They’re so different! However, as I have a general background in both ecology and physiology, I am deeply convinced that physiology can help us to better understand ecology. I also see ways that ecology can help us to better understand physiological processes.

Admittedly, my memories from lectures on the mitochondrial electron transport chain are a little fuzzy – many ecologists and evolutionary biologists might feel the same way. Yet, I discovered the importance of getting over this first negative feeling when realizing the importance of mitochondrial function in shaping both ecological and evolutionary processes. Continue reading

When Measuring Biodiversity, Do Individuals Matter?

Post provided by Samuel RP-J Ross

Close up of a black-capped babbler (Pellorneum capistratum), one of the species included in our study.

Close up of a black-capped babbler (Pellorneum capistratum), one of the species in our study.

Our newly-developed method simulates intraspecific trait variation when measuring biodiversity. This gives us an understanding of how individual variation affects ecosystem processes and functioning. We were able to show that accounting for within-species variation when measuring functional diversity can reveal details about ecological communities which would otherwise remain unseen. Namely, we found a negative impact of selective-logging on birds in Borneo when accounting for intraspecific variation which we could not detect when ignoring intraspecific variation.

Why Biodiversity Matters

Biodiversity is important for many reasons. One of the main reasons is its contribution to the range of goods and services provided by ecosystems (i.e. ecosystem services) that we can take advantage of, such as natural food resources or climatic regulation. It’s generally believed that biodiversity contributes to these services by increasing and maintaining ‘ecosystem functioning’ – often defined as the rate at which ecosystems are turning input energy (e.g. sunlight) into outputs (e.g. plant biomass). Continue reading

Capturing the Contribution of Rare and Common Species to Turnover: A Multi-Site Version of Generalised Dissimilarity Modelling

Post provided by Guillaume Latombe and Melodie A. McGeoch

Understanding how biodiversity is distributed and its relationship with the environment is crucial for conservation assessment. It also helps us to predict impacts of environmental changes and design appropriate management plans. Biodiversity across a network of local sites is typically described using three components:

  1. alpha (α) diversity, the average number of species in each specific site of the study area
  2. beta (β) diversity, the difference in species composition between sites
  3. gamma (γ) diversity, the total number of species in the study area.
Two tawny frogmouths, a species native to Australia. ©Marie Henriksen.

Two tawny frogmouths, a species native to Australia. ©Marie Henriksen.

Despite the many insights provided by the combination of alpha, beta and gamma diversity, the ability to describe species turnover has been limited by the fact that they do not consider more than two sites at a time. For more than two sites, the average beta diversity is typically used (multi-site measures have also been developed, but suffer shortcomings, including difficulties of interpretation). This makes it difficult for researchers to determine the likely environmental drivers of species turnover.

We have developed a new method that combines two pre-existing advances, zeta diversity and generalised dissimilarity modelling (both explained below). Our method allows the differences in the contributions of rare versus common species to be modelled to better understand what drives biodiversity responses to environmental gradients. Continue reading