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 … Continue reading Assessment of Stream Health with DNA Metabarcoding
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”)
The Global Pollen Project is a new, online, freely available tool developed to help people identify and disseminate palynological resources. Palynology – the study of pollen grains and other spores – is used across many fields of study modern and fossil vegetation dynamics, forensic sciences, pollination, beekeeping, and much more. This platform helps to facilitate cross/multi-disciplinary integration and discussion, outsourcing identifications, expertise and the sharing of knowledge.
Pollen’s Role in Plant Conservation
Successful conservation of rare, threatened, and valuable plants is dependent on an understanding of the threats that they face. Also, conservationists must prioritise species and populations based on their value to humans, which may be cultural, economic, medicinal, etc. The study of fossil pollen (palaeoecology), deposited through time in sediments from lakes and bogs, can help inform the debate over which species to prioritise: which are native, and when did they arrive? How did humans impact species richness? By establishing such biodiversity baselines, policymakers can make more informed value judgements over which habitats and species to conserve, especially where conservation efforts are weighted in favour of native and/or endemic flora. Continue reading “Tiny Grains, Big Data: The Global Pollen Project”
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 “How Clean are Finnish Rivers?”
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 … Continue reading Editor Recommendation – HistMapR: Rapid Digitization of Historical Land-Use Maps in R
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 “Estimating the Size of Animal Populations from Camera Trap Surveys”
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 … Continue reading Building Universal PCR Primers for Aquatic Ecosystem Assessments
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.
Today we are welcoming four new Associate Editors to Methods in Ecology and Evolution. Graziella Iossa (University of Lincoln) and Theoni Photopoulou (Nelson Mandela Metropolitan University) are joining as regular Associate Editors and Simon Jarman (Unversity of Porto) and Daniele Silvestro (University of Gothenburg) will be working on Applications articles. You can find out more about all of our new Associate Editors below. Graziella Iossa “I am … Continue reading New Associate Editors
This issue contains three Applications articles and two Open Access articles. These five papers are freely available to everyone, no subscription required.
– MatlabHTK: A software interface to a popular speech recognition system making it possible for non-experts to implement hidden Markov models for bioacoustic signal processing.
–PrimerMiner: The R package PrimerMiner batch downloads DNA barcode gene sequences from BOLD and NCBI databases for specified target taxonomic groups and then applies sequence clustering into operational taxonomic units to reduce biases introduced by the different number of available sequences per species.
–BarcodingR: An integrated software package that provides a comprehensive implementation of species identification methods, including artificial intelligence, fuzzy-set, Bayesian and kmer-based methods, that are not readily available in other packages.
.jpg)
Methods Blog 