Author: plydtanthera

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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Lab Methods

Reflecting on the past: developing hyperspectral reflectance spectroscopy for herbarium specimens

Post provided by Aaron Lee Complicated instruments and simple solutions It was an abnormally warm and balmy December in Minnesota, and Dr. Jeannine Cavender-Bares and I were in the lab. The lights were off, blinds were closed, and we had fashioned a makeshift stand to hold a large tungsten halogen lightbulb, angled perfectly to shine into the long fiber optic cable of a spectrometer connected … Continue reading Reflecting on the past: developing hyperspectral reflectance spectroscopy for herbarium specimens

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Ecology, Statistical methods, Theoretical methods

Hybrid Forest Models: integrating mechanistic knowledge and data

Post provided by Yannek Käber and Maximilian Pichler We met at YOMOS, a workshop for early-career researchers and young modelers in ecology supported by the German Society for Ecology, and we came at modeling from opposite ends. Yannek builds dynamic forest models, which are mechanistic models that integrate decades of ecological reasoning about how trees grow, compete, and die. Max builds machine learning models for … Continue reading Hybrid Forest Models: integrating mechanistic knowledge and data

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Ecology, Field Methods, Practical Tools

Goby gummies: the fish ‘lolly’ that provides a window to study predation underwater

Post provided by Christopher Hemingson Close your eyes and picture a predation event. Personally, I default to the Planet Earth series’ “Mountains” episode, in which a snow leopard acrobatically chases a mountain goat across near-vertical cliffs in an adrenaline-inducing pursuit. While iconic, predation sequences like this one generally represent the minority. More often than not, predation events occur on the order of split seconds – … Continue reading Goby gummies: the fish ‘lolly’ that provides a window to study predation underwater

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Code and Applications, Ecology

Processing visual survey data with sampley

Post provided by Jonathan Syme Picture this idyllic scene: You’re on a research vessel that is steadily making its way through the vast blue sea, surveying back and forth along a set of transect lines, its track recorded by a GPS. Through your binoculars, you see a column of spray, an arching back, a fluke that rises high above the water, then disappears. You call … Continue reading Processing visual survey data with sampley

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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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Practical Tools

The future of natural history specimen 3D digitization is here with COPIS

Post provided by Jeremy D. Pustilnik and Genevieve S. Rios Natural history museums around the world collectively hold over one billion specimens in their collections, from animal skins and fossils to pressed plants, minerals, and cultural heritage artifacts. Only a small fraction of these objects is ever placed on public display, while most remain in collection cabinets where they are studied by scientists, but rarely … Continue reading The future of natural history specimen 3D digitization is here with COPIS

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Ecology, Practical Tools

What a national marine dataset taught us about the power of quality control and collaboration

Post provided by Brooke Bond (Gibbons) Ecologists often dream about big datasets—Combining observations from multiple studies across space and time could reveal patterns that would otherwise be impossible to detect. But anyone who has tried to merge datasets from different sources knows the reality is often less glamorous. My first job involved synthesising Baited Remote Underwater Video (BRUV) datasets from across Australia. BRUV systems use … Continue reading What a national marine dataset taught us about the power of quality control and collaboration

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Ecology

Building the Infrastructure for Reproducible Biodiversity Science

BIEN 4.2: A Reproducible Standard for Global Plant Biodiversity Data Post provided by the BIEN Working Group For hundreds of years, biologists have carefully collected information on plants, animals, and other organisms and have created and maintained enormous libraries of physical specimens from all around the globe. Specimens are collected with all kinds of information– often there’s a physical example, but beyond that, scientists record … Continue reading Building the Infrastructure for Reproducible Biodiversity Science

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Conservation and management, Ecology

As above, so below: a perspective into the application of land-forest monitoring methods for the assessment of marine animal forests

Post provided by Torcuato Pulido Mantas I am a postdoctoral researcher in Marine Biology and Ecology at the Department of Life and Environmental Sciences (DiSVA), Polytechnic University of Marche, where I work in the Zoology Lab (link: https://www.instagram.com/zoomardisva/). We focus on understanding how climate change affects benthic marine organisms, developing new methods for marine environmental monitoring, and promoting effective conservation strategies for vulnerable habitats and … Continue reading As above, so below: a perspective into the application of land-forest monitoring methods for the assessment of marine animal forests

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