The Self-Preserving eDNA Filter: How It Works and Why You Should Use It

Researchers at Washington State University and Smith-Root recently invented an environmental DNA (eDNA) filter housing that automatically preserves captured eDNA by desiccation. This eliminates the need for filter handling in the field and/or liquid DNA preservatives. The new material is also biodegradable, helping to reduce long-lasting plastic waste associated with eDNA sampling.

This video explains their new innovation in the field of eDNA sampling technology:

To find out more about the self-preserving eDNA filter, read the full, Open Access Methods in Ecology and Evolution article ‘A self‐preserving, partially biodegradable eDNA filter
(No Subscription Required).

If you’re using interesting new field techniques like this, why not submit a Practical Tools manuscript about them? You can find out more about Practical Tools manuscripts here.

Mosquitoes, Climate Change and Disease Transmission: How the Suitability Index P Can Help Improve Public Health and Contribute to Education

Post Provided by JOSÉ LOURENÇO

Esta publicação no blogue também está disponível em português

©BARILLET-PORTAL David

©BARILLET-PORTAL David

Vector-borne viruses (like those transmitted by mosquitoes) are (re)emerging and they’re hurting local economies and public health. Some typical examples are the West Nile, Zika, dengue, chikungunya and yellow fever viruses. The eco-evolutionary and epidemiological histories of these viruses differ massively. But they share one important factor: their transmission potential is highly dependent on the underlying mosquito population dynamics.

An ultimate challenge in infectious disease control is to prevent the start of an outbreak or alter the course of an ongoing outbreak. To achieve this, understanding the ecological, demographic and epidemiological factors driving a pathogen’s transmission success is essential. Without this information, public health planning is immensely difficult. To get this information, dynamic mathematical models of pathogen transmission have been successfully applied since the mid-20th century (e.g. malaria and dengue). Continue reading

Mosquitos, o clima e a transmissão de patógenos: como o índice P pode contribuir para saúde pública e educação

PUBLICAÇÃO NO BLOGUE FORNECIDO POR JOSÉ LOURENÇO

This blog post is also available in English

©BARILLET-PORTAL David

©BARILLET-PORTAL David

Vírus transmitidos por vetores (ex. mosquitos, carraças) estão a (re)emergir e a ter consequências negativas para a saúde pública e para as economias locais. Exemplos típicos recentes de vírus transmitidos por mosquitos incluem o vírus West Nile na América do Norte, Israel e Europa, e os vírus Zika, dengue, chikungunya, Mayaro e febre amarela na América do Sul e África. A epidemiologia, ecologia, e evolução destes vírus são altamente diversas,  mas todos eles partilham um fator crítico: o seus potenciais de transmissão são altamente dependentes da dinâmica de população das espécies de mosquitos envolvidas.

Um dos objetivos principais do controlo de doenças infeciosas é prevenir o inicio (ou alterar o curso) de  epidemias. Para esse fim, modelos dinâmicos de transmissão têm sido usados com sucesso desde meados do século XX (ex. no contexto de malaria). Esses modelos são aproximações computacionais dos sistemas biológicos reais, permitindo simular uma multitude de cenários nos nossos computadores pessoais, e com tal testar, reconstruir e projetar o potencial e comportamento epidemiológico de patógenos. Quando tais simulações são comparadas com observações reais (ex. número de casos reportados por um sistema de vigilância), os modelos oferecem respostas sobre a mecânica de transmissão e os fatores epidemiológicos ou demográficos que terão contribuído para determinados padrões observados nos dados. Enquanto que modelos dinâmicos são uma das peças fundamentais da epidemiologia contemporânea, dados imperfeitos ou a falta deles pode tornar difícil (se não impossível) a conceção, implementação e utilidade esses modelos. As razões pelas quais dados podem ser imperfeitos são várias, desde sistemas de vigilância fracos, erros humanos, falta de investimento, etc. Continue reading

Issue 10.7: Aquatic Ecology, Zeroes, Sequencing and More

The July issue of Methods is now online!

We’ve got a bumper issue of Methods in Ecology and Evolution this month. In the 200+ pages, you’ll find articles about measuring species distributions and abundances, integrated population models, and working at the whole-plant scale.

We’ve got six papers that are freely available to absolutely everyone this month too. You can find out about two of the Open Access papers in the Applications and Practical Tools section below. In the third, Chen et al. show that tree assemblages in tropical forest ecosystems can present a strong signal of extensive distributional interspersion.

Find out a little more about the new issue of Methods in Ecology and Evolution below. Continue reading

Making a Self-Preserving eDNA Filter

Below is a press release about the Methods in Ecology and Evolution article ‘A self‐preserving, partially biodegradable eDNA filter‘ taken from the Smith-Root.

A new self-preserving filter housing automatically preserves eDNA, while reducing the risk of contamination, and creating less plastic waste.

Researcher collecting an eDNA sample using the self-preserving filter housing.

In 2015 the inventor of the Keurig disposable coffee cartridge (K-Cups) told reporters that sometimes he regrets ever inventing the technology. The single-use design simply produces too much non-recyclable trash. Well, that very same problem is what ultimately led to the creation of a self-preserving filter for environmental DNA (eDNA); a recently reported Practical Tool in Methods in Ecology and Evolution.

eDNA scientists rely on single-use sampling equipment because eDNA surveys are highly sensitive to potential contamination. “We started out simply looking for biodegradable plastics that could be molded into a filter housing, with the objective of reducing plastic waste.” says Dr. Austen Thomas who led the team of researchers and engineers who invented the Smith-Root eDNA Sampler. “That’s when we realized that some of the biodegradable compounds function by being highly hydrophilic.” Continue reading

Ultraconserved Elements are Widely Shared across the Tree of Life

Post provided by SILAS BOSSERT

Large-scale phylogenies are increasingly fueled by genomic-data from Ultraconserved Elements. ©Silas Bossert

Large-scale phylogenies are increasingly fuelled by genomic-data from Ultraconserved Elements. ©Silas Bossert

Sequencing ultraconserved DNA for phylogenetic research is a hot topic in evolution right now. As the name implies, Ultraconserved Elements (UCEs) are regions of the genome that are nearly identical among distantly related organisms. They can provide useful information for difficult phylogenetic questions. The list of advantages is long – among others, UCEs are:

A key reason for the method’s success is the developers’ commitment to full transparency, active tutoring, and willingness to help next-gen sequencing newbies like me to get started. Help is just a github-issue post away.

It took little to convince me that I wanted to use UCEs to reconstruct the phylogeny of one of my favourite groups of bees. I eventually met that objective but it won’t be part of this post. This blog post is about the journey to get there—the background story to the article ‘On the universality of target‐enrichment baits for phylogenomic research’. Continue reading

The Dark and Bright Sides of Phylogenetics and Comparative Methods

Five years ago at Evolution 2014, ‘The Dark Side of Phylogenetics’ symposium (organised by Natalie Cooper) explored some of the issues with phylogenetic comparative methods (PCMs). This year at Evolution 2019, Michael Landis and Rosana Zenil-Ferguson are organising a contrasting ‘Bright Side of Phylogenetics‘ spotlight session (featuring Michael Matschiner). They aim to promote research that has overcome these pitfalls and that explores innovations in phylogenetics. Clearly they found our lack of faith disturbing.

Natalie and Michael have created a Virtual Issue to complement the spotlight session: Phylogenetics and Comparative Methods: The Bright and Dark Sides. It highlights recent Methods in Ecology and Evolution papers that feature either the ‘Bright Side’ or ‘Dark Side’ of phylogenetics and comparative methods. This Virtual Issue also highlights the diversity of researchers around the world working on these exciting questions. We hope you have a good feeling about it! Continue reading

Stereo DOV: A Non-Invasive, Non-Destructive Way to Study Fish Populations

It’s more important than ever for us to have accurate information to help marine conservation efforts. Jordan Goetze and his colleagues have provided the first comprehensive guide for researchers using diver operated stereo-video methods (or stereo-DOVs) to survey fish assemblages and their associated habitat.

But what is Stereo DOV? What makes it a better method than the traditional UVC (Underwater Visual Census) method? And when should you use it? Find out in this video:

To find out more about stereo DOVs, read the full Methods in Ecology and Evolution article ‘A field and video analysis guide for diver operated stereo‐video
(No Subscription Required).

If you’re using interesting new field techniques like this, why not submit a Practical Tools manuscript about them? You can find out more about Practical Tools manuscripts here.

Using Molecular Power to Reconstruct Hyperdiverse Food Webs

Post provided by JORDAN CASEY

Coral Reefs: The Ocean’s Most Extravagant Buffet

Coral reefs are home to an incredibly diverse array of species ©Jordan Casey

Coral reefs are home to an incredibly diverse array of species ©Jordan Casey

There are an estimated 830,000 species on coral reefs worldwide. At some stage in their lives, nearly all of these species are consumed as prey items. In this super diverse buffet of fishes, corals, crabs, worms, and other critters, the number of possible interactions between predators and prey is nearly inexhaustible.

The extreme diversity of coral reefs has fascinated naturalists for centuries. Pinpointing predator-prey dynamics is essential to fully understand coral reef ecosystem dynamics, and visual analysis of gut contents has been a staple technique of coral reef ecologists. While the joy of spending copious hours looking through a microscope at half-digested marine mush is undeniable, this type of visual inspection has limitations. Even so, visual gut content analysis (along with stable isotope analysis and behavioural observations) has showcased a highly complex dietary network.

To digest this extreme complexity and surmount the hurdle of dietary unknowns, researchers frequently lump fishes into broad trophic categories, such as ‘mobile herbivores’. Broad generalisations are pragmatic and may be help us detect broad ecological trends, but they oversimplify species’ actual dietary preferences. As coral reefs are changing due to anthropogenic disturbances, it’s critical to thoroughly examine how well trophic groupings capture dietary linkages among reef organisms. Continue reading

Analysing Big Datasets while Answering Big Ecological Questions: #BESQuantMove2019

Post provided by LAURA GRAHAM and THEONI PHOTOPOULOU

Last week we heard about the importance of small conferences from Natalie Cooper. Hopefully she inspired you to look into smaller meetings going on this summer. If so, how about joining the Quantitative and Movement Special Interest Groups in Sheffield on 9 and 10 July for our back-to-back annual meetings?

This joint meeting will take advantage of shared strengths as well as shared challenges between the two groups and foster links between them. Both days will be a mix of keynotes, short contributed talks, poster sessions and discussion. Plus lots of all-important networking.

The meeting will be along the common theme of analysing big datasets while answering big ecological questions and the challenges associated with it. We welcome submissions of talks and posters. There will also be discussions on general issues with computation; integrating different datasets; and propagating uncertainty in ecological analyses.

The registration deadline is FRIDAY 7 JUNE – just three days away at the time of posting! Attendees will have the opportunity to attend one, or both annual meetings. A quick insider tip for registration: it’s cheaper to join the BES as a member and register for a BES member ticket, than to register for the non-BES member ticket. Continue reading