Could We Be Treating Invertebrates More Ethically?

Post provided by ELEANOR DRINKWATER

©Joaquim Alves Gaspar

For ecology to stay ethical and maintain public support, we need to revisit invertebrate ethics in research.  With our recent advances in understanding invertebrate cognition and shifts in public opinion, an ethical re-examination of currently used methodologies is needed. In our article – ‘Keeping invertebrate research ethical in a landscape of shifting public opinion’ – that’s exactly what we aim to do.

Invertebrate Cognition

Recent work, particularly on lobsters, has raised questions about whether invertebrates can experience suffering. In lobsters for example, noxious stimuli can induce long term changes in behaviour, and these changes can be inhibited by adding analgesic. While these findings can be interpreted as evidence for pain perception in crustaceans, the question of invertebrate suffering is still hotly debated, and a firm consensus is still to be reached. But these studies, coupled with recent public concern about the ethics of large-scale sampling projects, highlight the need for discussion on invertebrate ethics in ecology research. Continue reading

A More Reliable Method for Estimating Abundance: Close-Kin Mark-Recapture

Post provided by DANIEL RUZZANTE

Knowing how many individuals there are in a population is a fundamental objective in ecology and conservation biology. But estimating abundance is often extremely difficult. It’s particularly difficult in the management of exploited marine, anadromous and freshwater populations. In marine fisheries, abundance estimation traditionally relies on demographic models, costly and time consuming mark recapture (MR) approaches if they are feasible at all, and the relationship between fishery catches and effort (catch per unit effort or CPUE). CPUEs can be subject to bias and uncertainty. This is why they tend to be considered relatively unreliable and contentious.

Close-Kin Mark-Recapture: Reducing Bias and Uncertainty

There is an alternative method though. It’s known as “Close-Kin Mark-Recapture” (CKMR), and is grounded in genomics and was first proposed by Skaug in 2001. The method is based on the principle that an individual’s genotype can be considered a “recapture” of the genotypes of each of its parents. Assuming the sampling of offspring and parents is independent of each other, the number of Parent-Offspring pairs (POP) genetically identified in a large collection of both groups can be used to estimate abundance. Continue reading

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

Our 2019 Impact Factor: Now We are Seven

A bottle of cleaning fluid. Not JIF

Not an Impact Factor

Last week a few things happened in the world of science. One was the publication of the Journal Impact Factors (JIFs)… Followed by journals saying how wonderful their JIF is… And then everyone else saying how awful impact factors are.

Methods in Ecology and Evolution is a journal, so naturally we’re obliged to take journal point of view. Which means we need to get really excited about how amazing impact factors are1. Even though we know we shouldn’t, we are really really excited to say that our impact factor for 2018 is…

7.099

Last year it was a lowly 6.3. This increase is great, especially as we are still in the top 10 of Ecology journals (at no. 9, having risen to be a massive 0.05 above Molecular Ecology Resources). If we were listed in Evolution, we would be at number 7. And if we were a biology journal, we would be at number 5. There’s evidently not a lot of biology going on nowadays.

1 unless of course our impact factor decreases

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