Tiny Grains, Big Data: The Global Pollen Project

Post Provided by Andrew Martin

A drawer from the Oxford Long-Term Ecology Lab (OxLEL) pollen reference collections, which has been digitised into the Global Pollen Project reference set.

A drawer from the Oxford Long-Term Ecology Lab (OxLEL) pollen reference collections, which has been digitised into the Global Pollen Project reference set.

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

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

New Associate Editors

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 an evolutionary ecologist with broad interests in behavioural and population ecology. My research has explored reproductive strategies and the evolution of male and female reproductive traits in mammals and insects and I have used a range of techniques to study the behaviour and welfare of wildlife. I have just started to explore interdisciplinary approaches with the aim to improve our understanding of the value and role of ecosystem services in human health, specifically for antimicrobial resistance.”

Graziella’s most recent paper – Micropyle number is associated with elevated female promiscuity in Lepidoptera – investigates the evolution of the micropyle, a tiny canal which sperm use to fertilise eggs in insects. This is the first study to show that micropylar variation is driven by female promiscuity – the more micropyles her eggs have, the more choice she is likely to have over which male fathers her offspring. Also, Graziella currently holds a NERC Valuing Nature placement which aims to combine perspectives from evolutionary ecology, microbial ecology, epidemiology, ecosystem science and public health to develop a new, holistic way of understanding antimicrobial resistance

Simon Jarman

“Methods employing epigenetics, environmental DNA analysis or bioinformatics for ecological research are improving rapidly and have clear potential for future development. My research focuses on creating new methods in these areas and using them to study population biology and biodiversity. Epigenetic markers for physiological features such as biological age can be used to determine key features of population biology such as age class distribution. Environmental DNA can be used to measure species distributions; biodiversity in environmental samples; and animal diet composition. I am interested in the molecular biology and computational approaches that are required to implement these methods; as well as how they can be used to study specific ecological questions.”

In November 2016, Simon published an Open Access article in Methods in Ecology and Evolution. ‘Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates‘ explains how to collect scat samples to optimise the detection of food DNA in vertebrate scat samples. More recently, Simon was the last author of ‘KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba)‘ – which introduces the most advanced genetic database on Euphausia superba, KrillDB, and includes comprehensive data sets of former and present transcriptome projects.

Theoni Photopoulou

“I am interested in the way biological and ecological phenomena change in space and over time. My special interest is animal movement ecology and the mechanisms behind the patterns of movement we observe. Most of the time I work on ecological questions about how animals use their environment and the resources in it, using data collected remotely with animal-attached instruments. Marine biology was my first love so I will always have a soft spot for marine systems, especially movement of large marine vertebrates, but I work on all sorts of tracking data and also some non-tracking data.”

Theoni has also recently been published in Methods in Ecology and Evolution. Her article ‘Analysis of animal accelerometer data using hidden Markov model‘ appeared in the February issue of the journal (and provided the cover image). In the paper, the authors provide the details necessary to implement and assess a hidden Markov Model in both the supervised and unsupervised learning contexts and discuss the data requirements of each case. Another of Theoni’s articles has just been accepted for publication in Frontiers in Zoology. ‘Evidence for a postreproductive phase in female false killer whales (Pseudorca crassidens)‘ investigates the evidence for postreproductive lifespan (PRLS) in the false killer whale, using a quantitative measure of PRLS and morphological evidence from reproductive tissue.

Daniele Silvestro

“I am a computational biologist and my research focuses on (macro)evolution and the development of new probabilistic models to better understand it. I am interested in the implementation of Bayesian algorithms to model evolutionary processes such as phenotypic trait evolution and species diversification and extinction. I am also interested in historical biogeography and in particular in the estimation of dispersal rates and biotic connectivity between geographic areas. A lot of my work involves developing new models and algorithms and implementing them in computer programs. I have been using both phylogenetic data and fossil occurrences to infer deep time evolutionary dynamics and I am keen to see an improved integration between paleontological and neontological data in evolutionary research.”

In his most recent article – ‘Bayesian estimation of multiple clade competition from fossil data‘ – Daniele and his co-authors explore the properties of the existing Multiple Clade Diversity Dependence implementation, which is based on Bayesian variable selection, and introduce an alternative parameterisation based on the Horseshoe prior. He was also one of the authors of ‘Mammal body size evolution in North America and Europe over 20 Myr: similar trends generated by different processes‘, published in Proceedings of the Royal Society B earlier this year.

We are thrilled to welcome Simon, Graziella, Theoni and Daniele to the Associate Editor Board and we look forward to working with them over the coming years.

Movement Ecology: Stepping into the Mainstream

Post provided by Theoni Photopoulou

“Movement is the glue that ties ecological processes together”
from Francesca Cagnacci et al. 2010

CTD-SRDL telemetry tags being primed for deployment. ©Theoni Photopoulou

CTD-SRDL telemetry tags being primed for deployment. ©Theoni Photopoulou

Movement ecology is a cross-disciplinary field. Its main aim is to quantitatively describe and understand how movement relates to individual and population-level processes for resource acquisition and, ultimately, survival. Today the study of movement ecology hinges on two 21st century advances:

  1. Animal-borne devices/tags (biologging science, Hooker et al., 2007) and/or remote sensing technology to quantify movement and collect data from remote or otherwise challenging environments
  2. Computational power sufficient to manipulate, process and analyse substantial volumes of data

Although datasets often involve small numbers of individuals, each individual can have thousands – sometimes even millions – of data points associated with it. Study species have tended to be large birds and mammals, due to the ease of tag attachment. However, the trend for miniaturisation of tags and the development of remote detection technologies (such as radar, e.g. Capaldi et al., 2000), have allowed researchers to track and study ever smaller animals. Continue reading

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.

Continue reading

Issue 7.9

Issue 7.9 is now online!

The September issue of Methods is now online!

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

– Arborist Throw-Line Launcher: A cost-effective and simple alternative for collecting leaves and seeds from tall trees. The authors have also provided some tutorial videos on YouTube.

– ctmm: An R package which implements all of the continuous-time stochastic processes currently in use in the ecological literature and couples them with powerful statistical methods for autocorrelated data adapted from geostatistics and signal processing.

Continue reading

Estimating Shifts in Species Distribution: An Interview with James Thorson

David Warton (University of New South Wales) interviews James Thorson (NOAA) about his paper Model-based inference for estimating shifts in species distribution, area occupied and centre of gravity. The article is included in the August 2016 issue of Methods in Ecology and Evolution.  They discuss how to estimate changes in distribution shifts accounting for changes in the spatial distribution of sampling intensity, James’ current workplace NOAA, his academic background and what trouble he is planning to get up to next.

Continue reading

European Bison, Rewilding and Dung Fungal Spore

Post provided by AMBROISE BAKER

In the US, July is National Bison Month but most people in Europe are totally oblivious to it. I wasn’t even aware of it before being asked to write this blog post in connection with our recent Methods in Ecology and Evolution paper about quantifying population sizes of large herbivores. Some will argue that it is because we don’t ‘do’ day, month, state or national animals on this side of the Atlantic as much as the Americans do.

The European bison survived from extinction thanks to about 50 individuals kept in zoos. The species has been reintroduced in the wild in several European countries but remains ‘Vulnerable’ according to the IUCN criteria.

The European bison survived extinction thanks to ~50 individuals kept in zoos. It has been reintroduced in several countries but remains ‘Vulnerable’. ©4028mdk09

But another reason is that the European bison, Bison bonasus bonasus, is simply not sufficiently well-known or associated with European nature in the public’s mind. This is particularly true in Western Europe where this species has been extinct since medieval times.

Early European accounts from North America reported huge bison populations – with estimates of up to 60 million – moving to and fro in the great bison belt. These past migratory movements across the Great Plains are familiar well beyond the US and feed our view of untamed wilderness prior to the impact of European ’civilisation’. In contrast, there are hardly any records of European bison numbers until just before the last wild one was reported killed in Poland in 1921. Continue reading

Spatially-explicit Power Analysis: A First Step for Occupancy-Based Monitoring

Post provided by Martha Ellis and Jody Tucker

Where’s Waldo? Trying to find this fisher somewhere in a giant landscape is going to be tricky! ©Mike Schwartz

Where’s Waldo? Trying to find this little guy somewhere in a giant landscape is going to be tricky! © Mike Schwartz

The seemingly basic question of whether a population is increasing, decreasing, or stable can be one of the most difficult to answer. Collecting data on rare and elusive species is hard. Imagine trying to detect a handful of fisher or wolverine across hundreds of thousands of acres – it is physically demanding, time consuming and logistically complicated. And that’s just to do it once! To monitor a population for changes, you have to repeat these surveys regularly over many years. The long-term monitoring that is necessary for conservation requires careful planning and a substantial commitment of resources and funding. So before we spend these valuable resources, it’s critical to know whether the data we are collecting can help us to answer our questions. Continue reading

Issue 7.3

Issue 7.3 is now online!

The March 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.

METAGEAR: A comprehensive, multifunctional toolbox with capabilities aimed to cover much of the research synthesis taxonomy: from applying a systematic review approach to objectively assemble and screen the literature, to extracting data from studies, and to finally summarize and analyse these data with the statistics of meta-analysis.

Universal FQA Calculator: A free, open-source web-based Floristic Quality Assessment (FQA) Calculator. The calculator offers 30 FQA data bases (with more being added regularly) from across the United States and Canada and has been used to calculate thousands of assessments. Its growing repository for site inventory and transect data is accessible via a REST API and represents a valuable resource for data on the occurrence and abundance of plant species. Continue reading