Rodrigo Domingues

Plotting phylogenetic trees in R: alternating clade highlights A guide to highlighting clades in phylogenetic trees in R

💬 "There’s already plenty of documentation out there for how to use #ggtree, but there is the odd thing I come up against that I haven’t seen explicitly demonstrated before." - @rowenahill.bsky.social.

A guide to plotting #phylogenetictrees in #R, and automating clade highlights
buff.ly/Vd5b61a

🧬💻

An image of the cover of the IPBES Transformative Change Assessment Report. Overlay text reads: “Transformative Change Assessment Report. Laid-out report in English available now.”

OUT NOW: The laid-out version of the FULL @ipbes.net #TransformativeChange Report 💥

Explore how fundamental change can halt biodiversity loss and secure just and sustainable futures for all. 🌏🧪

Access the full report in English⬇️
https://www.ipbes.net/transformative-change-assessment

Decoding eagle rays in the lab Like all work in the field of Molecular Ecology, our Save Our Seas Foundation funded eagle ray research comprises three broad components: Fieldwork, Labwork, and Bioinformatics (data analysis) Our fir...

How does one unveil kinship, survival, and evolution in eagle rays? Using a few drops of liquid, magnets, and light, John Swenson describes how molecular ecology can be used to uncover these stories.

More here: saveourseas.com/update/decod...

Synthesis of Population Trends Reveals Seascape‐Wide Reorganisation of Biodiversity From Microalgae to Birds

🔗 buff.ly/OrBu9Xm
@anikahappe.bsky.social @kasperjmeijer.bsky.social @hillebr1.bsky.social @hanolff.bsky.social

An integrative taxonomy investigation unravels a cryptic species of Mobula Rafinesque, 1810 (Mobulidae, Myliobatiformes), from the Atlantic Ocean - Environmental Biology of Fishes Manta and devil rays comprise a vulnerable animal group with a complex nomenclatural history and a somewhat unresolved taxonomy. The existence of a putative undescribed species of manta ray in the Atl...

𝑀𝑜𝑏𝑢𝑙𝑎 𝑦𝑎𝑟𝑎, a new cryptic species of Manta Ray, is described from the Western Atlantic Ocean. The existence of an undescribed manta ray species has been suggested for over 15 years and is now formally described. 🐟🧪

link.springer.com/article/10.1...

Ever wondered how to analyse your experimental data? 🌊🧪🌍

We’ve developed a series of tutorials in R to guide you through analysing & visualising data from single & multiple driver experiments.

Beginners and experts, we've got something for all of you.

Please share!

meddle-scor149.org/vignettes/

There are recordings, but unfortunately due to privacy reasons @physaliacourses.bsky.social is unable to make them available for downloading (even to participants).

My material is all available on github though: github.com/BertvanderVe....

A Metadata Checklist and Data Formatting Guidelines to Make eDNA FAIR (Findable, Accessible, Interoperable, and Reusable) Environmental DNA (eDNA) has emerged as a transformative tool for biodiversity monitoring and species detection, yet inconsistent metadata practices hinder data interoperability and reuse. To address...

🚨 Out now in #EnvironmentalDNA led by #MiwaTakahashi: Results of a huge, global effort to facilitate the publication of raw and processed #eDNA data & ensure that dataset we are currently generating, adhere to the #FAIR principles & won't be lost. @gbif.org, #ENA,
doi.org/10.1002/edn3...

Accounting for functionality in the identification of global conservation priorities: promises and pitfalls | Philosophical Transactions of the Royal Society B: Biological Sciences Whereas preventing species extinctions remains a central objective of conservation efforts, it must be complemented by the long-term preservation of functional ecosystems and of the benefits humans de...

I’ve grown wary of using metrics of functional diversity and rarity to guide conservation planning. In this paper I explain why, and discuss three promising approaches for accounting for functionality in the identification of global conservation priorities. (1/7) 🌐

Biodiversity–ecosystem function research must consider abundance and not just diversity Nature Reviews Biodiversity, Published online: 11 April 2025; doi:10.1038/s44358-025-00040-1Maintaining human well-being in an era of biodiversity loss requires understanding the role of biodiversity in ecosystem function. We argue that absolute abundance can drive ecosystem function and that this measure should be considered alongside traditional measures of biodiversity.

New online! Biodiversity–ecosystem function research must consider abundance and not just diversity

Rethinking Darwin’s coral reef paradox and the ubiquity of “marine oases” Morais et al. evaluate the history of Darwin’s paradox and the prevalence of oligotrophic conditions among coral reefs. They find no link between Darwin and the marine oasis concept. Most coral reefs ...

Our new paper in @currentbiology.bsky.social, led by @renatoamorais.bsky.social, examined the history and veracity of the alleged paradox and its patron Charles Darwin.

www.cell.com/current-biol...

@oclaripv.bsky.social
@paulinenarvaez.bsky.social
@utaustin.bsky.social
@psl-univ.bsky.social

#JFB: Aquatic eDNA outperforms sedimentary eDNA for the detection of estuarine fish communities in sub-tropical coastal vegetated ecosystems doi.org/10.1111/jfb.70056 #FishSci

Biodiversity Genomics Research Practices Require Harmonising to Meet Stakeholder Needs in Conservation Biodiversity resilience relies on genetic diversity, which sustains the evolutionary potential of organisms in dynamic ecosystems. Genomics is a powerful tool for accurately estimating genetic divers....

Biodiversity Genomics Research Practices Require Harmonising to Meet Stakeholder Needs in Conservation
onlinelibrary.wiley.com/doi/10.1111/...

Fear and fascination: has Jaws shaped how we talk about sharks? It’s been 50 years since fear gripped the fictional beaches of Amity Island and fixated in swimmers’ minds at public beaches and in concrete swimming pools. We ask what the enduring legacy of this sto...

In the end? Two things can be true at once. Fear and fascination as the enduring legacy of Jaws have both amplified any fear, loathing or misunderstanding that we had of sharks, and inspired some people to follow a career in shark conservation.

saveourseas.com/fear-and-fas...

A small cunner (Tautogolabrus adspersus) peers through strands of sugar kelp (Saccharina latissima) in a lush kelp forest ecosystem on Cashes Ledge in the Gulf of Maine.

Kelp forests on the coast of Maine are in decline owing to rapid ocean warming and are being replaced by turf algae, which alter the ecosystem’s chemistry, hindering the recovery of kelp forests.

Learn more in this week's issue of Science: scim.ag/4dwzl8j

Three years ago, #SpringerNature invited us to lead a book series inspired by our courses. We called it "Decoding Evolution", and the first volume is nearly ready—thanks to the amazing work of Filippo and Nelson!
#DeepLearning

Global phylogenetic and functional structure of rodent assemblages vist.ly/3n42ht2 #BigData #Rodents #Phylogeny

Utilizing aquatic environmental DNA to address global biodiversity targets - Nature Reviews Biodiversity Aquatic eDNA-based technologies offer the potential for universal and standardized biodiversity monitoring. In this Perspective, Altermatt et al. discuss how these technologies can help to achiev...

🌊🧬Revolutionizing Biodiversity Monitoring?🧪

Could aquatic #eDNA be a game-changer for tracking biodiversity loss? From detecting invasive species to restoring ecosystems...🌍

Study by Altermatt, F., Couton, M., Carraro, L. et al.: www.nature.com/articles/s44...

The what, how, and why of trait-based analyses in ecology vist.ly/3n3vkiy #FunctionalDiversity #Patterns #Processes

Survey on the use of DNA metabarcoding In order to strengthen the standardization and use of DNA metabarcoding in Neotropical biodiversity monitoring, it is essential to understand how the results and analyses of this approach have been us...

🧬Have you used DNA metabarcoding in your research or work?

We want to understand how this tool can help monitor neotropical biodiversity and gather insights into the experiences, challenges, and needs of those using it, including researchers and environmental managers.

forms.gle/osk8T7gGyabq...

A scientific figure showing a species ecological interaction network derived from environmental DNA for a marine ecosystem. The trophic levels span zooplankton to whales and other large predators.

Can #eDNA recover biotic interactions? Our new study says Yes sometimes! Co-occurrence network analyses with data for the Moray Firth marine ecosystem recovered subsets of known food web trophic links but methodological issues are still a challenge ⤵️ 🧪🧬🌍🐳🦭🐟
onlinelibrary.wiley.com/doi/10.1111/...

Biodiversity–ecosystem function research must consider abundance and not just diversity Nature Reviews Biodiversity, Published online: 11 April 2025; doi:10.1038/s44358-025-00040-1Maintaining human well-being in an era of biodiversity loss requires understanding the role of biodiversity in ecosystem function. We argue that absolute abundance can drive ecosystem function and that this measure should be considered alongside traditional measures of biodiversity.

ICYMI: New online! Biodiversity–ecosystem function research must consider abundance and not just diversity

Interested in current & upcoming #standardization practices to accelerate discoveries of #heatstress impacts on #marine life?

Review paper @annualreviews.bsky.social
—> shorturl.at/kVuh9

@reefgenomics.bsky.social @amyapprill.bsky.social @uni-konstanz.de

Are sharks outside protected areas adapted to higher stress?

Local song: adaptative potential of endemic southwest Atlantic guitarfish to anthropogenic stressors. Check out my SOSF project blog

saveourseas.com/project/are-...