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

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

How Many Animals are Infected with Chronic Wasting Disease?

Post provided by Hildegunn Viljugrein

©Alexandre Buisse

©Alexandre Buisse

The discovery of Chronic Wasting Disease (CWD) in Norway in 2016 has led to extensive measures and testing of deer in Norway. Since 2018 there have been similar measures within the EU. But how many deer need to be tested before we can be (almost) certain that a population is not infected by CWD?

In our article – ‘A method that accounts for differential detectability in mixed samples of long‐term infections with applications to the case of Chronic Wasting Disease in cervids’ – we provide important tools for estimation of prevalence and likelihood of finding infected animals in a given population. The paper is a result of a collaborative work between a multidisciplinary group of scientists from the Norwegian Veterinary Institute, Norwegian Institute for Nature Research and Prof. Atle Mysterud from Centre for Ecological and Evolutionary Synthesis at the University of Oslo. Continue reading

Statistical Ecology Virtual Issue

To celebrate the International Statistical Ecology Conference and British Ecological Society Quantitative Ecology Annual Meeting, Laura Graham and Susan Jarvis have compiled a virtual issue celebrating all things statistical and quantitative in ecology.

Statistical and quantitative methods within ecology have increased substantially in recent years. This rise can be attributed both to the growing need to address global environmental change issues, as well as the increase in data sources to address these challenges. Continue reading

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.

Issue 9.2

Issue 9.2 is now online!

The February issue of Methods is now online!

This double-size issue contains six Applications articles (one of which is Open Access) and two Open Access research articles. These eight papers are freely available to everyone, no subscription required.

 Temperature Manipulation: Welshofer et al. present a modified International Tundra Experiment (ITEX) chamber design for year-round outdoor use in warming taller-stature plant communities up to 1.5 m tall.This design is a valuable tool for examining the effects of in situ warming on understudied taller-stature plant communities

 ZoonThe disjointed nature of the current species distribution modelling (SDM) research environment hinders evaluation of new methods, synthesis of current knowledge and the dissemination of new methods to SDM users. The zoon R package aims to overcome these problems by providing a modular framework for constructing reproducible SDM workflows.

 BEIN R Package: The Botanical Information and Ecology Network (BIEN) database comprises an unprecedented wealth of cleaned and standardised botanical data. The bien r package allows users to access the multiple types of data in the BIEN database. This represents a significant achievement in biological data integration, cleaning and standardisation.

Continue reading

Imperfect Pathogen Detection: What to Do When Sampling and Diagnostic Tests Produce Inaccurate Results

Post Provided by Graziella DiRenzo

A salamander having its skin swabbed to test for Bsal infection.

A salamander having its skin swabbed to test for Bsal infection.

Imagine you’re at the doctor’s office. You’re waiting to hear back on a critical test result. With recent emerging infectious diseases in human populations, you are worried you may be infected after a sampling trip to a remote field site. The doctor walks in. You sit nervously, sensing a slight tremble in your left leg. The doctor confidently declares, “Well, your tests results came back negative.” In that moment, you let out a sigh of relief, the kind you feel throughout your body. Then, thoughts start flooding your mind. You wonder– what are the rates of false negatives associated with the test? How sensitive is the diagnostic test to low levels of infection? The doctor didn’t sample all of your blood, so how can they be sure I’m not infected? Is the doctor’s conclusion right?

 Now, let’s say I’m the doctor and my patient is an amphibian. I don’t have an office where the amphibian can come in and listen to me explain the diagnosis or the progression of disease − BUT I do regularly test amphibians in the wild for a fatal fungal pathogen, known as Batrachochytrium dendrobatidis (commonly known as Bd). Diseases like Bd are among the leading causes of the approximately one-third of amphibian species that are threatened, near threatened, or vulnerable to extinction. To test for Bd, and the recently emerged sister taxon Batrachochytrium salamandrivorans (hereafter referred to as: Bsal), disease ecologists rely on non-invasive skin swabs. Continue reading

In Vivo Micro-CT Scanning: Studying Reptiles and Amphibians from the Inside Out

POST PROVIDED BY CHRIS BROECKHOVEN, ANTON DU PLESSIS, STEPHAN G. LE ROUX, P. LE FRAS N. MOUTON AND CANG HUI

Lizards, such as these South African armadillo lizards, serve an important role as model organisms for various ecological and evolutionary studies. © Chris Broeckhoven

Lizards, such as these South African armadillo lizards, serve an important role as model organisms for various ecological and evolutionary studies. © Chris Broeckhoven

X-ray micro-computed tomography – or µCT – is a technique that uses x-rays to create high resolution cross-sections of samples. Virtual 3D models can be made from these cross-sections without destroying the original samples. Micro-CT has important applications in medical imaging and, in the biomedical field, in vivo µCT allows researchers to make virtual 3D models of the skeleton and organs of live small animals. Three-dimensional models like these could provide insight into diseases and guide the development of medicines and therapies.

In vivo µCT holds three major advantages over other methods:

  1. It allows for repeated measurements of small live animals at different times without having to sacrifice them.
  2. It eliminates variation among individuals.
  3. It can reduce the number of animals required to obtain statistically meaningful data.

A variety of commercially available µCT scanners that are optimised for scanning live animals are now available. The use of in vivo µCT in ecological and evolutionary studies, however, has greatly lagged behind its use in biomedical studies. Continue reading

Predicting Disease Outbreaks Using Environmental Changes

Below is a press release about the Methods paper ‘Environmental-mechanistic modelling of the impact of global change on human zoonotic disease emergence: a case study of Lassa fever‘ taken from the University College London.

The multimammate rat (Mastomys natalensis) transmits Lassa virus to humans. ©Kelly, et al.

The multimammate rat transmits Lassa virus to humans. ©Kelly, et al.

A model that predicts outbreaks of zoonotic diseases – those originating in livestock or wildlife such as Ebola and Zika – based on changes in climate, population growth and land use has been developed by a UCL-led team of researchers.

“This model is a major improvement in our understanding of the spread of diseases from animals to people. We hope it can be used to help communities prepare and respond to disease outbreaks, as well as to make decisions about environmental change factors that may be within their control,” said lead author Professor Kate Jones, UCL Genetics, Evolution & Environment and the Zoological Society of London. Continue reading

Demography and Big Data

Post provided by BRITTANY TELLER, KRISTIN HULVEY and ELISE GORNISH

Follow Brittany (@BRITTZINATOR) and Elise (@RESTORECAL) on Twitter

To understand how species survive in nature, demographers pair field-collected life history data on survival, growth and reproduction with statistical inference. Demographic approaches have significantly contributed to our understanding of population biology, invasive species dynamics, community ecology, evolutionary biology and much more.

As ecologists begin to ask questions about demography at broader spatial and temporal scales and collect data at higher resolutions, demographic analyses and new statistical methods are likely to shed even more light on important ecological mechanisms.

Population Processes

Midsummer Opuntia cactus in eastern Idaho, USA. © B. Teller.

Midsummer Opuntia cactus in eastern Idaho, USA. © B. Teller.

Traditionally, demographers collect life history data on species in the field under one or more environmental conditions. This approach has significantly improved our understanding of basic biological processes. For example, rosette size is a significant predictor of survival for plants like wild teasel (Werner 1975 – links to all articles are at the end of the post), and desert annual plants hedge their bets against poor years by optimizing germination strategies (Gremer & Venable 2014).

Demographers also include temporal and spatial variability in their models to help make realistic predictions of population dynamics. We now know that temporal variability in carrying capacity dramatically improves population growth rates for perennial grasses and provides a better fit to data than models with varying growth rates because of this (Fowler & Pease 2010). Moreover, spatial heterogeneity and environmental stochasticity have similar consequences for plant populations (Crone 2016). Continue reading