Using Dual RNA-seq to Investigate Host-Pathogen Systems When Genomic Resources are Limited

Post provided by KAYLEIGH O’KEEFFE

Tall fescue infected with fungal pathogen, Rhizoctonia solani. ©Brooklynn Newberry — Tall fescue infected with fungal pathogen, *Rhizoctonia solani*. ©Brooklynn Newberry

Pathogens and the infectious diseases that they cause can have devastating impacts on host individuals and populations. To better understand how pathogens are able to cause disease, we can investigate the genetic mechanisms underlying the infection process. Hosts may respond to infection by upregulating defence pathways. Pathogens, in turn, evade these host immune responses as they infect and cause disease. As this process unfolds and each organism responds to the other, gene expression changes in both the host and the pathogen. These gene expression changes can be captured by dual RNA‐seq, which simultaneously captures the gene expression profiles of a host and of a pathogen during infection. Continue reading “Using Dual RNA-seq to Investigate Host-Pathogen Systems When Genomic Resources are Limited”

India StephensonFebruary 20, 2019February 20, 20191 Comment

‘Eavesdropping’ Technology used to Protect one of New Zealand’s Rarest Birds

Below is a press release about the Methods in Ecology and Evolution article ‘A novel method for using ecoacoustics to monitor post‐translocation behaviour in an endangered passerine‘ taken from the Zoological Society of London.

Scientists from international conservation charity ZSL (Zoological Society of London), Imperial College London and conservationists from the Rotokare Scenic Reserve Trust used acoustic monitoring devices to listen in on the ‘conversations’ of New Zealand’s endemic hihi bird, allowing them to assess the success of the reintroduction without impacting the group.

For the first time ZSL scientists were able to use the calls of a species as a proxy for their movement. A happy hihi call sounds like two marbles clanging together in what is known as the ‘stitch’ call. Scientists saw the calls change from an initial random distribution to a more settled home range – marking the hihi reintroduction and the new method a success. Continue reading “‘Eavesdropping’ Technology used to Protect one of New Zealand’s Rarest Birds”

India StephensonFebruary 15, 2019Leave a comment

Journal updates

BES Journal Blogs Round Up: January 2019

It’s already been a busy 2019 for the six BES journal blogs. We’ve covered topics from leaving the nest to sustainable food production, stress in academia to climate change. On Relational Thinking we learned that cats can’t trespass. And Animal Ecology in Focus taught us that some crabs steal food from plants.

Today we’re having a look back at some of last month’s highlights from across the blogs:

Relational Thinking – PEOPLE AND NATURE

Cats Can’t Trespass
This post was created by the author of one of our published papers. It’s a really creative and funny illustrated summary of their paper.

BES 2018: Field Notes from Birmingham
This post was written by our Associate Editor Andrea Belgrano and is his conference report on BES2018. It is an evocative and sensitive reflection on the meeting, where he compares the spiritual energy of the community to that of the Zen Buddhist Daruma Doll. Continue reading “BES Journal Blogs Round Up: January 2019”

India StephensonFebruary 11, 2019February 8, 20192 Comments

Methods papers, Statistical methods, Uncategorized

Advances in Modelling Demographic Processes: A New Cross-Journal Special Feature

Analysis of datasets collected on marked individuals has spurred the development of statistical methodology to account for imperfect detection. This has relevance beyond the dynamics of marked populations. A couple of great examples of this are determining site occupancy or disease infection state.

EURING Meetings

The regular series of EURING-sponsored meetings (which began in 1986) have been key to this development. They’ve brought together biological practitioners, applied modellers and theoretical statisticians to encourage an exchange of ideas, data and methods.

This new cross-journal Special Feature between Methods in Ecology and Evolution and Ecology and Evolution, edited by Rob Robinson and Beth Gardner, brings together a collection of papers from the most recent EURING meeting. That meeting was held in Barcelona, Spain, 2017, and was hosted by the Museu de Ciènces Naturals de Barcelona. Although birds have provided a convenient focus, the methods are applicable to a wide range of taxa, from plants to large mammals. Continue reading “Advances in Modelling Demographic Processes: A New Cross-Journal Special Feature”

India StephensonFebruary 5, 20191 Comment

General, Publishing Tips & Tricks

Managing Stress in Academia: Tools and Suggestions

Post provided by Holly Langridge

Stress in academia is increasingly recognised, but knowing about an issue and solving it are very different things. ©Christopher Sweeney

Sometimes stress can be anticipated, avoided or mitigated. Other times, it sneaks up on you and sucker punches you in the face. A quick google search turns up loads of articles and op-eds on the topic – this, this and this are just three of the first examples I found. Stats abound on the negative effect it can have on students, staff and productivity. Mental health problems and stress in academia are increasingly recognised, but knowing about an issue and solving it are very different things.

My lab at the University of Manchester is fairly big and busy. Headed by the current BES president, and with over 30 people, and many millions of pounds in funding, it can be a stressful place. I am by no means an expert in stress, but I can tell you about my personal experiences and some of the ways that the University of Manchester helps staff and students deal with stress here. Continue reading “Managing Stress in Academia: Tools and Suggestions”

India StephensonJanuary 30, 2019January 30, 20193 Comments

Conservation and management, Field Methods, Methods papers

Map of Chemicals in Jellyfish Could be the Future to Protecting UK Waters and Marine Life

Below is a press release about the Methods in Ecology and Evolution article ‘Spatial models of carbon, nitrogen and sulphur stable isotope distributions (isoscapes) across a shelf sea: An INLA approach‘ taken from the University of Southampton.

Jellyfish opportunistically caught in UK waters are used to map chemical variations across marine space. ©University of Southampton

Scientists at the University of Southampton have developed maps of chemicals found in jellyfish which could offer a new tool for conservation in British waters and fisheries. The maps will also be able to detect fraudulently labelled food in retail outlets by helping to trace the origins of seafood.

The Southampton based research team including Dr Clive Trueman, Dr Katie St. John Glew and Dr Laura Graham, built maps of the chemical variations in jellyfish caught in an area of approximately 1 million km2 of the UK shelf seas. These chemical signals vary according to where the fish has been feeding due to differences in the marine environment’s chemistry, biology and physical processes. Continue reading “Map of Chemicals in Jellyfish Could be the Future to Protecting UK Waters and Marine Life”

India StephensonJanuary 22, 2019January 22, 2019Leave a comment

Conservation and management, Methods papers, Second Language Post

Limitations and Benefits of the Unmatched Count Technique: Considering How We Use New Methods in Conservation

Post provided by Amy Hinsley and Ana Nuno

Esta publicação no blogue também está disponível em português

A New Conservation Toolbox

It is widely accepted that many conservation challenges are directly related to human behaviour. Whether it is the over-collection of a rare orchid by harvesters in Southeast Asia, or the decisions by collectors in Europe to buy and smuggle these orchids home, understanding the extent and nature of these behaviours is essential to addressing the threats they might cause. This has led conservation researchers and practitioners to start looking outside of their discipline, to find methods and approaches from across the social sciences to improve our understanding of these complex issues.

A research assistant carrying out a UCT survey about the use of Traditional Medicine products containing bear bile in China. © Chen Haochun.

While this interdisciplinarity is a positive move for conservation, it is important that we treat these ‘new’ methods carefully and understand their limitations. If we don’t, there is a risk that our new toolbox full of exciting methods that sound great on a funding application, may in fact not be making what we do any better, or in extreme cases they may even be making it worse.

With this in mind, a group of conservation social scientists, led by researchers at the Universities of Oxford and Exeter, decided to look in depth into one of these ‘new’ methods, to provide recommendations on when and how it should be used, and when it shouldn’t. Our Open Access article – ‘Asking sensitive questions using the unmatched count technique: Applications and guidelines for conservation‘ – looks at the Unmatched Count Technique (UCT – also called the list experiment), which is increasingly being used in conservation to ask questions about ‘sensitive’ topics. Continue reading “Limitations and Benefits of the Unmatched Count Technique: Considering How We Use New Methods in Conservation”

India StephensonJanuary 9, 2019January 9, 20192 Comments

Conservation and management, Methods papers, Second Language Post

Limitações e benefícios da técnica de contagem de itens: considerações sobre o uso de novos métodos em Conservação

publicação no blogue FORNECIDO POR AMY HINSLEY E ANA NUNO

This blog post is also available in English

Novas ferramentas de conservação

Muitos desafios em conservação estão diretamente relacionados com o comportamento humano. Quer seja a recolha excessiva de uma orquídea rara no Sudeste Asiático, ou a compra e contrabando dessas orquídeas por colecionadores na Europa, entender a magnitude e a natureza desses comportamentos é essencial para lidar com as ameaças que eles podem causar. Isso levou os investigadores e profissionais da área de conservação a começarem a olhar para fora da sua própria disciplina, de modo a encontrar métodos e abordagens das ciências sociais para melhorar a nossa compreensão sobre estas questões complexas.

Assistente de investigação a realizar um estudo recorrendo a TCI sobre o uso de produtos de medicina tradicional com bílis de urso na China. © Chen Haochun.

Embora esta interdisciplinaridade seja um passo positivo para a conservação, é importante tratar esses “novos” métodos com cuidado e entender as suas limitações. Se não o fizermos, existe o risco da nossa nova caixa de ferramentas, repleta de métodos interessantes que soam bem em candidaturas a financiamento, na verdade não melhorar aquilo que nós geralmente já fazemos ou, em casos extremos, até piorá-lo.

Tendo isto em conta, um grupo de cientistas sociais em conservação, liderado por investigadores das Universidades de Oxford e Exeter, decidiu examinar em profundidade um desses “novos” métodos, fornecer recomendações sobre quando e como ele deveria ser usado, e quando não deveria. O artigo, disponível gratuitamente na revista científica Methods in Ecology and Evolution nesta semana, examina a Técnica de Contagem de Itens (TCI), que tem sido cada vez mais usada em conservação para fazer perguntas sobre tópicos “sensíveis”. Continue reading “Limitações e benefícios da técnica de contagem de itens: considerações sobre o uso de novos métodos em Conservação”

India StephensonJanuary 9, 2019January 9, 20192 Comments

Editor Profiles, Journal updates

New Associate Editor: Laura Graham

Today, we are pleased to announce the latest new member of the Methods in Ecology and Evolution Associate Editor Board. Laura Graham joins us from the University of Southampton, UK as an Applications Editor. You can find out a little more about her below.

Laura Graham

“I’m a quantitative ecologist interested in how anthropogenic changes such as climate change and habitat loss affect global ecosystems, and how this in turn affects human well-being. I develop computational methods for spatial ecology to facilitate the reproducible analysis of social-ecological systems and ecosystem services. I’m interested in using novel statistical methods and heterogeneous sources of data to answer applied and theoretical questions.” Continue reading “New Associate Editor: Laura Graham”

India StephensonJanuary 7, 2019January 7, 2019Leave a comment

Conservation and management, Meetings

Methods in Temporal Ecology

Post provided by Althea L. Davies & M. Jane Bunting

This post presents our reflections from two sessions at the first British Ecological Society Annual Meeting since the Palaeoecology Special Interest Group (SIG) was formed. Did the term “palaeoecology” make you want to stop reading? Then you’re not alone – our field of ecology seems to have drifted apart from neoecology over the last couple decades. We seem to have been separated by our choice of methods, rather than brought together by the fascinating, complex and essential challenges of better understanding ecosystem function that we share.

The diversity of talks at BES 2018 showed that ecologists working on time scales beyond the scope of direct study are researching the same urgent, exciting questions as other flavours of ecology. And that they are doing it by using an ever-growing range of methods and technologies. The Thematic Session ‘Advancing Our Understanding of Long-Term Ecology’ showcased advances in studies of long-term ecology. The Palaeoecology Oral Session demonstrated the diversity within this field. We don’t have room to mention all presenters, so we’d like to highlight contributions from two speakers in each session which demonstrate how strong the shared ground between palaeoecology and neoecology is. Continue reading “Methods in Temporal Ecology”

India StephensonDecember 20, 2018December 20, 2018Leave a comment