Category: Methods papers

Ecology, Methods papers, Statistical methods

The Baby and the Teddy Bear: The Flash of Insight Behind the WAH-i Algorithm

Post Provided by Ravi Umadi On a sunny morning after heavy snowfall in the Bavarian winter, I stood by the door of an early train to Munich. Bright sunlight streamed through the glass and lit me up. I thought to myself: it was a good day. Moments later, the train screeched to a halt. The driver announced an unscheduled stop and possible disruptions due to … Continue reading The Baby and the Teddy Bear: The Flash of Insight Behind the WAH-i Algorithm

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Methods papers

From replicate detection to DNA concentration: What can ddPCR tell us about sedaDNA metabarcoding?

Post provided by Elena Baños Lara I am currently completing my PhD at the Centre for Advanced Studies of Blanes (CEAB-CSIC) in Spain, where I use environmental and sedimentary ancient DNA to explore past marine ecosystems. As part of my PhD, I had the opportunity to spend three months at the Globe Institute in Copenhagen, joining Kristine Bohmann’s group and working side by side with … Continue reading From replicate detection to DNA concentration: What can ddPCR tell us about sedaDNA metabarcoding?

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Methods papers

Fostering a network for creating and implementing open education resources in ecology

Blog post provided by Ann Russell The Need for Authentic, Open Educational Resources Given the rapid changes underway in undergraduate STEM education, the teaching community aspires to move beyond models that involve static content to develop agile, scalable ways to create authentic open educational resources (OERs). Researchers can provide authentic case studies, but they may lack the skills to create engaging OERs based on their … Continue reading Fostering a network for creating and implementing open education resources in ecology

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Methods papers

How to spot river-borne diseases with almost no data

Post provided by Pouria Ramazi When Alberta Environment and Parks brought this problem to our group in 2018, the question was practical. Whirling disease had been detected in Alberta, but testing every stretch of a river was impossible. Could a few scattered fish and worm tests show where the parasite Myxobolus cerebralis was most likely to occur across the Oldman River? I had just begun … Continue reading How to spot river-borne diseases with almost no data

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Methods papers

Make insect metabarcoding quantitative? Challenge accepted.

Post provided by Ela Iwaszkiewicz-Eggebrecht The journey from scepticism to abundance estimates When I moved to Sweden in 2019 to start a postdoc, I entered a completely new research field. My background was in evolutionary biology, but I knew very little about DNA metabarcoding (identifying many species at once by sequencing barcode DNA from mixed samples). I was joining a project that was developing methods … Continue reading Make insect metabarcoding quantitative? Challenge accepted.

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Methods papers

From pattern to process: estimating species interactions and driver-species relationships from count data

Post provided by Quinn Asena Uncovering signals from the past Understanding interactions among organisms, and between organisms and their environment, has been a cornerstone of ecology as long as we have been busying ourselves with the lives of other species. How do plants and animals facilitate or compete with each other? How do they respond to the continuous challenge of changing climates or new neighbors? … Continue reading From pattern to process: estimating species interactions and driver-species relationships from count data

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Methods papers

Forking anatomy: borrowing software’s best idea to build 3D atlases together

Post provided by A. Murat Maga Picture a graduate student who has just spent eighty hours tracing the individual bones of a fish skull, slice by slice, through a high-resolution microCT scan. The result is a beautiful, richly labelled 3D dataset. And then? Too often it lands on a hard drive, or gets flattened into a static 3D model that no one else can edit, … Continue reading Forking anatomy: borrowing software’s best idea to build 3D atlases together

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Ecology, Lab Methods, Methods papers

A longer read on microbes: Why bigger fragments matter in Earth’s harshest habitats

Post provided by Xi Peng When I first started analysing metagenomic data from cold seeps and hot springs, I didn’t expect to spend quite so much time staring at confusing lines of code and fragmented sequences. Yet these digital traces—broken fragments of DNA scattered across a matrix of microbial complexity—hold the fingerprints of life in Earth’s most extreme habitats. In this work, we developed an … Continue reading A longer read on microbes: Why bigger fragments matter in Earth’s harshest habitats

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Methods papers, Statistical methods

DImodelsMulti: Making Advanced DI Modelling Accessible.

Post provided by Laura Byrne. I am a researcher at University College Cork, Ireland, working with statistical models for use with biodiversity data. My research is driven by my interests in sustainability, the facilitation of natural ecosystems alongside necessary urbanisation, statistical modelling, and coding. You can find out more about our work on Diversity-Interactions models (including video introductions, maths and coding tutorials, and an archive … Continue reading DImodelsMulti: Making Advanced DI Modelling Accessible.

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Methods papers

Managing plant viral epidemics – linking insect transmission and epidemic risk

Post provided by Ruairí Donnelly, Israël Tankam, and Alison Scott-Brown Here in the Epidemiology and Modelling Group at the University of Cambridge, our work is driven by the need to secure food supplies for future generations, particularly for those living in areas of the world already under increasing pressure from climate change and extreme weather conditions, making it harder for small-holders to produce and trade … Continue reading Managing plant viral epidemics – linking insect transmission and epidemic risk

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