Can Opportunistically Collected Citizen Science Data Create Reliable Habitat Suitability Models for Less Common Species?

Post provided by Ute Bradter, Mari Jönsson and Tord Snäll

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Opportunistically collected species observation data, or citizen science data, are increasingly available. Importantly, they’re also becoming available for regions of the world and species for which few other data are available, and they may be able to fill a data gap.

Siberian jay ©Ute Bradter

Siberian jay ©Ute Bradter

In Sweden, over 60 million citizen science observations have been collected – an impressive number given that Sweden has a population of about 10 million people and that the Swedish Species Observation System, Artportalen, was created in 2000. For bird-watchers (or plant, fungi, or other animal enthusiasts), this is a good website to bookmark. It will give you a bit of help in finding species and as a bonus, has a lot of pretty pictures of interesting species. Given the amount of data citizen science can provide in areas with few other data, it’s important to evaluate whether they can be used reliably to answer questions in applied ecology or conservation. Continue reading

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ANDe™: High‐Throughput eDNA Sampling in a Fully Integrated System

Current eDNA sampling technologies consist mainly of do‐it‐yourself solutions. The lack of purpose‐built sampling equipment is limiting the efficiency and standardization of eDNA studies. So, Thomas et al. (a team of molecular ecologists and engineers) designed ANDe™.

In this video, the authors highlight the key features and benefits of ANDe™. This integrated system includes a backpack-portable pump that integrates sensor feedback, a pole extension with remote pump controller, custom‐made filter housings in single‐use packets for each sampling site and on-board sample storage. 

This video is based on the article ‘ANDe: A fully integrated environmental DNA sampling system‘ by Thomas et al.

Remote Sensing for Counting Animals: Polar Bears, Sheep and Everything In-Between

Post provided by Tracey Hollings

In an age of rapid technological advances, ecologists need to keep abreast of how we can improve or reinvent the way we do things. Remote sensing technology and image analysis have been developing rapidly and have the potential to revolutionise how we count and estimate animal populations.

Using remotely sensed imagery isn’t new in ecology, but recent innovations mean we can use it for more things. Land use change and vegetation mapping are among the areas of ecology where remote sensing has been used extensively for some time. Estimating animal populations with remotely sensed imagery was also demonstrated more than 40 years ago by detecting indirect signs of an animal with some success: think wombat burrows and penguin poop.

A polar bear from a helicopter

A polar bear from a helicopter

Thanks to improved spatial and spectral resolution (see the text box at the bottom of the post for a definition), accessibility, cost and coverage of remotely sensed data, and software development we have now reached a point where we can detect and count individual animals in imagery. Many of the first studies to demonstrate automated and semi-automated techniques have taken computer algorithms from other disciplines, such as engineering or biomedical sciences, and applied them to automate counting of animals in remotely sensed imagery. It turns out that detecting submarines is not so different to detecting whales! And finding abnormal cells in medical imaging is surprisingly similar to locating polar bears in the arctic! Continue reading

Methods in Ecology and Evolution 2017: The Year in Review

Happy New Year! We hope that you all had a wonderful Winter Break and that you’re ready to start 2018. We’re beginning the year with a look back at some of our highlights of 2017. Here’s how last year looked at Methods in Ecology and Evolution.

The Articles

We published some amazing articles in 2017, too many to mention them all here. However, we would like to take a moment to thank all of the Authors, Reviewers and Editors who contributed to the journal last year. Your time and effort make the journal what it is and we are incredibly grateful. THANK YOU for all of your hard work!

Technological Advances at the Interface between Ecology and Statistics

Our first Special Feature of the year came in the April issue of the journal. The idea for Technological Advances at the Interface between Ecology and Statistics  came from the 2015 Eco-Stats Symposium at the University of New South Wales and the feature was guest edited by Associate Editor David Warton. It consists of five articles based on talks from that conference and shows how interdisciplinary collaboration help to solve problems around estimating biodiversity and how it changes over space and time.

Continue reading

Refined DNA Tool Tracks Native and Invasive Fish

Below is a press release about the Methods paper ‘Long-range PCR allows sequencing of mitochondrial genomes from environmental DNA‘ taken from the Cornell University.

©Nick Hobgood

Rather than conduct an aquatic roll call with nets to know which fish reside in a particular body of water, scientists can now use DNA fragments suspended in water to catalog invasive or native species.

The research from Cornell University, the University of Notre Dame and Hawaii Pacific University was published July 14 in Methods in Ecology and Evolution.

“We’ve sharpened the environmental DNA (eDNA) tool, so that if a river or a lake has threatened, endangered or invasive species, we can ascertain genetic detail of the species there,” said senior author David Lodge, the Francis J. DiSalvo Director of the Atkinson Center for a Sustainable Future at Cornell, and professor of ecology and evolutionary biology. “Using eDNA, scientists can better design management options for eradicating invasive species, or saving and restoring endangered species.” Continue reading

New Associate Editors

Today we are welcoming two new people to the Methods in Ecology and Evolution Associate Editor Board. Pierre Durand is joining us from the University of the Witwatersrand (South Africa) and Andrew Mahon joins from Central Michigan University (USA). You can find out more about Pierre and Andrew below.

Pierre Durand

Pierre Durand

“My research is broadly focussed on the evolution of complexity. Many of my projects are related to the evolutionary ecology of programmed cell death (PCD) in unicellular organisms; how PCD impacts microbial communities; and how the philosophy of levels of selection informs our understanding of PCD evolution. I have also examined other aspects of complexity evolution such as the origin of life and group formation in unicellular chlorophytes in response to predation. The model organisms I typically use are phytoplankton. With specific reference to submissions to Methods in Ecology and Evolution, I have used a range of methods in my research, including general cell and molecular biology tools, biochemical assays, microscopy, flow cytometry, bioinformatics and computational algorithms.”

The most current projects in Pierre’s laboratory concern: programmed cell death evolution and complexity in microbial communities; changes in phytoplankton abundance and diversity in harmful algal blooms, led by PhD candidate Andrew Ndhlovu (“A red tide forming dinoflagellate Prorocentrum triestinum: identification, phylogeny and impacts on St Helena Bay, South Africa” in review in Phycologia); and the genomics of the four-celled chlorophyte Tetrabaena socialis, led by PhD candidate Jonathan Featherson.

Andrew Mahon

Andrew Mahon

“I’m a molecular ecologist who uses genetic and genomic tools to ask questions ranging from surveillance and monitoring to biodiversity and phylogeography.  My work includes development of novel molecular detection tools and metabarcoding applications for aquatic invasive species.  I’m also interested in applying molecular tools to ask questions related to the evolution and biodiversity of benthic marine invertebrates in Antarctica.”

Andrew has recently been published in the journal Research Ideas and Outcomes (‘DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe‘) and in Environmental Science and Technology (‘Influence of Stream Bottom Substrate on Retention and Transport of Vertebrate Environmental DNA‘). He also has a manuscript in press with Ecology and Evolution (‘Geographic structure in the Southern Ocean circumpolar brittle star Ophionotus victoriae (Ophiuridae) revealed from mtDNA and single-nucleotide polymorphism data‘).

We are thrilled to welcome Pierre and Andrew to the Associate Editor Board and we look forward to working with them over the coming years.

Biogeography Virtual Issue

Photo © An-Yi Cheng

© An-Yi Cheng

To coincide with the International Biogeography Society’s 2017 conference in Tuscon, Arizona, we have compiled a Virtual Issue that shows off new Methods in Ecology and Evolution articles in the field from a diverse array of authors.

To truly understand how species’ distributions vary through space and time, biogeographers often have to make use of analytical techniques from a wide array of disciplines. As such, these papers cover advances in fields such as evolutionary analysis, biodiversity definitions, species distribution modelling, remote sensing and more. They also reflect the growing understanding that biogeography can include experiments and highlight the increasing number of software packages focused towards biogeography.

This Virtual Issue was compiled by Methods in Ecology and Evolution Associate Editors Pedro Peres-Neto and Will Pearse (both of whom are involved in the conference). All of the articles in this Virtual Issue are free for a limited time and we have a little bit more information about each of the papers included here: Continue reading

A New Modelling Strategy for Conservation Practice? Ensembles of Small Models (ESMS) for Modelling Rare Species

Post provided by FRANK BREINER, ARIEL BERGAMINI, MICHAEL NOBIS and ANTOINE GUISAN

Rare Species and their Protection

Erythronium dens-canis L. – a rare and threatened species used for modelling in Switzerland. ©Michael Nobis

Erythronium dens-canis L. – a rare and threatened species used for modelling in Switzerland. ©Michael Nobis

Rare species can be important for ecosystem functioning and there is also a high intrinsic interest to protect them as they are often the most original and unique components of local biodiversity. However, rare species are usually those most threatened with extinction.

In order to help prioritizing conservation efforts, the International Union for Conservation of Nature (IUCN) has published criteria to categorize the status of threatened species, which are then published in Red Lists. Changes in a species’ geographical distribution is one of the several criteria used to assign a threat status. For rare species, however, the exact distribution is often inadequately known. In conservation science, Species Distribution Models (SDMs) have recurrently been used to estimate the potential distribution of rare or insufficiently sampled species. Continue reading

What is Dark Diversity?

Post provided by ROB LEWIS & MEELIS PÄRTEL

Our understanding of how biological diversity works has been advanced by a long history of observing species and linking patterns to ecological processes. However, we generally don’t focus as much on those species that aren’t observed, or in other words ‘absent species’. But, can absent species provide valuable information?

Dark diversity – a set of species absent from a particular site but which belong to its species pool – has the potential to be as ecologically meaningful as observed diversity. Part of the species pool concept, understanding dark diversity is relatively straightforward.

The Basic Theory of Dark Diversity

To begin learning about dark diversity, there are two important terms that we need to define: ‘species pool’ and ‘focal community’. A ‘species pool’ is a set of species present in a particular region or landscape that can potentially inhabit a particular observed community because of suitable local ecological conditions.

A ‘focal community’ is the set of species that have been observed in a particular region or landscape (this is the ‘observed community’ and can also be referred to as alpha diversity). For a given focal community to become established, the species within it must have overcome dispersal pressures as well as environmental and biotic filters.

A

Continue reading

A Model Approach to Weed Management

Post provided by VANESSA ADAMS

Vanessa Adams in the field with gamba grass in the Batchelor region, NT. ©Amy Kimber (NERP Northern Australia Hub)

Vanessa Adams in the field with gamba grass in the Batchelor region, NT.
©Amy Kimber (NERP Northern Australia Hub)

Invasive weeds cause environmental and economic harm around the world. Land managers bear a heavy responsibility for the control of infestations in what is often a time-consuming and costly battle.

Fortunately, an increasing number of research-based solutions are giving land managers an advantage. This includes tools to determine the distribution of weeds and also the development of modelling approaches to predict their spread.

Understanding the current and future distribution of an invasive species allows managers to better direct their limited resources. However, the direct and strategic management of weeds is tricky and that’s why population models (in particular spatial dispersal models that can be applied without much data) are needed to inform and facilitate action on the ground. Continue reading