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Deon de Jager

@ddj-sa.bsky.social
812 followers 443 following 60 posts

Postdoc at Globe Institute, University of Copenhagen | Wildlife genetics | Ancient DNA | Conservation | Birding | Sport. He/him. Opinions my own.

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Reposted by Deon de Jager
Mick Westbury @mick2474.bsky.social · 30/09/2026
New preprint out by PhD student @madshartmann.bsky.social 🥳 We present SCAR, the perfect tool for assessing the impact of #ancientDNA damage on analyses Validation tests show how damage massively impacts heterozygosity estimates 😨 Check it out here www.biorxiv.org/content/10.6...
biorxiv.org
SCAR: Controlled mutations, ancient DNA damage, and fragmentation of fasta and fastq sequences
Summary: Controlled modification of sequencing data is important for reproducible benchmarking, particularly when evaluating analyses affected by read fragmentation, divergent reference genomes and an...
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AaRC @aarc-community.bsky.social · 17/09/2026
We have new TikTalks next week already! Join us next Friday to hear about sheep and pipelines!
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AaRC @aarc-community.bsky.social · 10/09/2026
Okay a week left! Don't forget to sign up for the workshop! All about #metAaRCive with @anders-bergstrom.bsky.social and @ddj-sa.bsky.social
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Miren Iraeta Orbegozo @mireniraorb.bsky.social · 09/09/2026
Happy to share our new paper on DNA preservation in the Caribbean: Open access: doi.org/10.1098/rsos... 🌎 Summaries in Español, Français, Kreyòl Ayisyen and Kréyòl Gwadloup: shorturl.at/FMHNI 🧵👇 @jazminrm.bsky.social @bitesizedna.bsky.social
doi.org
Ancient DNA preservation in the Caribbean
Abstract. Ancient DNA (aDNA) analysis has transformed how we study human migration, species dispersals and environmental change, but poor preservation rema
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Deon de Jager @ddj-sa.bsky.social · 03/08/2026
Come join us to learn how to contribute to, and use, metAaRCive, a community-curated database of published ancient animal genomes! We'll also cover best-practises for metadata reporting in #aDNA studies and how to archive sequence data on the ENA! Sign up here: docs.google.com/forms/d/1E4k...
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Deon de Jager @ddj-sa.bsky.social · 06/09/2026
Some casual reading for your Sunday evening, or Monday morning coffee ☕ about our recent paper testing the limits of #ancientDNA recovery in #Africa. Courtesy of @africa.theconversation.com, myself and Eline Lorenzen. theconversation.com/discovery-of...
theconversation.com
Discovery of ancient DNA from antelope fossils in South Africa opens a new window on the past
Researchers managed to extract DNA from African fossils dating back to the last ice age.
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Dr Nicholas Freymueller @smilodontology.bsky.social · 03/09/2026
Interested in pursuing a #PhD or #MPhil on #ancientDNA in #Antarctica? Check out this fully-funded research position based here at #AdelaideUniversity here in South Australia! Full details attached below. Applications close 30 September. Please repost and share widely!
A flyer advertising a fully-funded PhD or MPhil position on Antarctic Ancient DNA.
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Jess da Silva @jess-dasilva.bsky.social · 15/08/2026
Proud to share my latest paper on genetic indicators. Aligning with existing processes such as Red Listing, truly enables these indicators to be mainstreamed en masse. www.sciencedirect.com/science/arti... #consgen #monitoring #gbf #genetic-indicators @cgsg.bsky.social
sciencedirect.com
Mainstreaming genetic diversity indicators through the IUCN Red List process: A national-scale assessment of South African mammals
Parties to the Convention on Biological Diversity are required to report on progress towards the Kunming–Montreal Global Biodiversity Framework (KMGBF…
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Alex Hübner @alexhbnr.bsky.social · 13/08/2026
🚨 Paper alert: if you are working on #metagenomics, particularly from #ancientDNA, and want to get into de novo #assembly, check out our latest work: 📄 De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag (journals.plos.org/ploscompbiol...) (1/4)
journals.plos.org
De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag
Author summary Advancements in genomic sequencing analyses are increasingly allowing researchers to reconstruct the genomes of microbial ‘dark matter’—those microbial species that are difficult to iso...
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Katia Bougiouri @katiabou.bsky.social · 13/08/2026
The next AaRCademy workshop is coming up on Thursday September 17th! This time @anders-bergstrom.bsky.social and @ddj-sa.bsky.social will dive into #aDNA metadata reporting, archiving data in the ENA and the metAaRCive database, a community-led initiative of curating ancient animal genomes.
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J. Camilo Chacón-Duque @jcchacond.bsky.social · 05/08/2026
🧵 New preprint: Have you ever tried to perform molecular clock dating of ancient mitogenomes using BEAST? Have you struggled using manual tools to create your input files, run your analyses and extract your results? We hope our pipeline provides a solution to this: www.biorxiv.org/content/10.6...
biorxiv.org
MitoDate: a Nextflow pipeline for molecular clock dating and phylogenetic inference using ancient mitogenomes
Summary Ancient DNA studies are increasingly targeting samples that are beyond the limit of radiocarbon dating (>50 thousand years old) and are often difficult or impossible to date using other geochr...
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Deon de Jager @ddj-sa.bsky.social · 03/08/2026
Come join us to learn how to contribute to, and use, metAaRCive, a community-curated database of published ancient animal genomes! We'll also cover best-practises for metadata reporting in #aDNA studies and how to archive sequence data on the ENA! Sign up here: docs.google.com/forms/d/1E4k...
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Deon de Jager @ddj-sa.bsky.social · 15/07/2026
Excellent article about our recent paper by @killgrove.bsky.social in @livescience.com, covering our exciting finding that DNA can be recovered from Late Pleistocene remains in Africa! #aDNA #Africa #genetics #palaeontology
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Laboratory of Paleogenetics and Conservation Genetics @lpcg.bsky.social · 16/06/2026
New aDNA paper on Eurasian moose 🫎 @popovicdani.bsky.social @mateuszbaca.bsky.social www.nature.com/articles/s41...
nature.com
Phylogeographic and demographic responses of Eurasian moose to climate change since the Late Pleistocene - Heredity
Heredity - Phylogeographic and demographic responses of Eurasian moose to climate change since the Late Pleistocene
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Deon de Jager @ddj-sa.bsky.social · 17/06/2026
Beautiful work, congrats!
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Torsten Günther @trstngnthr.bsky.social · 16/06/2026
I am recruiting a PhD student (fully funded, 4yrs) to analyze modern 🧬 and ancient 🦴 genomic data from humans and domestic animals 🐑 Please share, I am happy to chat at #ICP2026 or #SMBE2026 this summer www.uu.se/en/about-uu/...
uu.se
PhD student position in Population Genomics - Uppsala University
PhD student position in Population Genomics , Department of Organismal Biology, Uppsala University
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Deon de Jager @ddj-sa.bsky.social · 04/06/2026
Super cool resource! Something I wish existed a couple of years ago, so thanks for making it happen @anders-bergstrom.bsky.social & members of @aarc-community.bsky.social! There are still many more ancient animal genomes to add & we need more hands! If you're keen to help us out, see below 😊✌️
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Deon de Jager @ddj-sa.bsky.social · 04/06/2026
I am unable to DM you: your name is faded out when I search for you under DMs. Is it perhaps a privacy setting?
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Deon de Jager @ddj-sa.bsky.social · 04/06/2026
Thanks Cecilia! Ah I suspect it is because I am in contact with the publisher to fix a section-numbering issue in the paper that wasn't caught in the proofs. It should be online again in a day or two hopefully, but will send via DM too!
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Deon de Jager @ddj-sa.bsky.social · 04/06/2026
I'm excited by where this research is leading & I'd like to thank the Iziko Museum, our funders @ec.europa.eu MSCA, @villumfonden.bsky.social, @carlsbergfondet.dk) & my collaborators, without whom this could not have been done! @deadbovids.bsky.social @drandiwilson.bsky.social & those not on BlueSky
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Deon de Jager @ddj-sa.bsky.social · 04/06/2026
A final thing I am proud of is the fact that we helped the Iziko museum digitize the part of the collection we worked on with 3D scans on MorphoSource, photos on Zenodo & occurrence records on GBIF, before any destructive sampling was done. (e.g. 3D models: doi.org/10.17602/M2/...)
A screenshot of a 3D model of a Cape grysbok fossil mandible with teeth.
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Deon de Jager @ddj-sa.bsky.social · 04/06/2026
Only a few African palaeogenetic studies exist, focusing mostly within the last 2000 years. Thus, we share the lessons learned along the way at the end of the article to help others get the most out of African specimens, like using ssDNA libraries that retrieve shorter reads & more endogenous DNA!
A two-panel plot showing the read length distribution obtained for two samples (A and B) by using two different DNA library building protocols: SCR and BEST. The graphs show that SCR (single-stranded) libraries contain a much higher proportion of shorter reads than the double-stranded BEST libraries. This is particularly important in contexts where DNA preservation is poor and ancient DNA fragments are very short, such as in Africa.
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Deon de Jager @ddj-sa.bsky.social · 04/06/2026
We also investigated collagen preservation in these fossils, and the correlation between collagen and DNA preservation. Collagen is used for direct radiocarbon dating of fossils, an NB data point for ancient DNA studies. We found a strong correlation when site was included: adj. R-sqrd = 0.72.
Biomolecular preservation. A Endogenous DNA proportion as a function of specimen age for the whole dataset (n = 144). The text inside the plot indicates the proportion of specimens that were genetically identifiable (“Yes”) in the Holocene and Pleistocene. B Collagen yield as a percentage of total dentine/bone powder, as a function of specimen age. C The relationship between DNA and collagen preservation, as represented by collagen yield in percentage and endogenous DNA proportion. Note that for B and C, only Phase 1 specimens (n = 54) are shown, for which we had both collagen and DNA data. D Mean length of endogenous reads as a function of specimen age (n = 65). Only genetically identifiable specimens are shown, as these have endogenous DNA from which to calculate read length. The vertical dashed line indicates the boundary between the Pleistocene and Holocene (11,700 years ago) in all plots. Species identifiable refers to whether the species could be genetically identified.
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Deon de Jager @ddj-sa.bsky.social · 04/06/2026
We are excited by these results, because it means we can probably do genetic studies of ancient animal populations in RSA, so long as they lived during the Holocene. And second, because this means we can do palaeogenetic studies of extinct like the giant long-horned buffalo! 🐃 So watch this space 👀
A photo of a skull with one horn of the extinct long-horned buffalo with a skull of the extant Cape buffalo for comparison. The long-horned buffalo horn is several times longer, and the skull much larger, than that of the Cape buffalo.
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Deon de Jager @ddj-sa.bsky.social · 04/06/2026
We found that 63% of the Holocene-aged fossils (younger than 11,700 years old) preserved DNA, while only 4 samples (9%) of the Pleistocene-aged fossils had ancient DNA. But this is still crazy to us, as it's the first time DNA has been retrieved from Pleistocene fossils in South Africa, v. exciting!
A plot showing endogenous DNA content on the y-axis and age of fossil specimens on the x-axis in log scale, from 0 to 100,000 years. Triangular points representing fossils are coloured green if DNA was retrieved and light grey if not. The trend shows that younger fossils, especially those from the Holocene (<11,700 years old) contain more endogenous, while older fossils tend to contain less DNA. Four Pleistocene fossil, older than 11,700 years, contain endogenous DNA, though at very low proportions.
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Deon de Jager @ddj-sa.bsky.social · 04/06/2026
In our paper, we screened 144 antelope & buffalo teeth & bones from #SouthAfrica spanning the last 100,000 years. The oldest DNA we retrieved was between 21,000 and 50,000 years old! 👀 This is the oldest for sub-Saharan #Africa & we're busy confirming the age of these fossils.
A 3-panel plot, where panels A and B show fossils collected in Phase 1 and 2 of the study, with species on the x-axis and age of fossils on the y-axis in six sub-panels corresponding to sampling sites. Panel C is a map of southern South Africa showing the location of the archaeological sites where the fossils originated.
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Deon de Jager @ddj-sa.bsky.social · 04/06/2026
The oldest DNA retrieved from an animal fossil is ~1.6 million years old - a mammoth from icy Siberia where cold temperatures preserve DNA well. But have you ever wondered how long #ancientDNA is preserved in animal remains from sunny & warm Africa? Well, wonder now more! doi.org/10.1016/j.qu...
A schematic where five circles are connected to a central bovid tooth with dotted lines. Each circle represents something done with the tooth: Photography, 3D scanning, DNA preseservation evaluation, collagen preservation evaluation , and recording of its occurrence on GBIF.
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Deon de Jager @ddj-sa.bsky.social · 09/04/2026
Free online workshop for estimating relatedness from genomic data! Great opportunity especially for students and other early career researchers (but everyone is welcome)! #AaRCademy #popgen
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Laura Bertola @lauradbertola.bsky.social · 09/11/2025
Lessons learned: Recommendations for reproducible paleogenomic data analyses www.cell.com/ajhg/abstrac...
cell.com
Lessons learned: Recommendations for reproducible paleogenomic data analyses
Souilmi et al. propose essential guidelines to improve the reproducibility of paleogenomic data analysis. As ancient DNA research often relies on the destructive sampling of finite resources, these re...
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Genetics Society of America @genetics-gsa.bsky.social · 30/10/2025
The latest issue of #G3journal features work from @trstngnthr.bsky.social, @amygoldberg.bsky.social, @jgschraiber.bsky.social, where they benchmarked methods for estimating ancestry proportions under mapping bias and present adjusted genotype-likelihoods to mitigate its impact. buff.ly/9ET69CA
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AdMEXture ERC project @admexture.bsky.social · 16/10/2025
New job opportunity in our project! Want to join us — or know someone who could? More details coming soon. The PhD will be supervised by Cristina Valdiosera and Colin Smith #JobOpening #ERC #Spain #UBU #México #PhD #PhDposition #Mestizaje #stableisotopes
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Nikolay Oskolkov @oskolkov.bsky.social · 04/10/2025
Our method, GENome EXogenous (GENEX) sequence detection, for identifying microbial-like regions in eukaryotic reference genomes is online in GigaScience track.smtpsendmail.com/9032119/c?p=...
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Pedro Brandão-Dias F Pinto @pedrobd.bsky.social · 05/07/2025
I had an idea—just a hunch, really— on how to link #Popgen and #eDNA. I was lucky to be in a lab that embraced curiosity, open discussion, and let me run with it. One year, many equations, and a few too many simulations later, here’s the result: 🧬 Preprint now live: doi.org/10.1101/2025...
doi.org
Estimating Organism Abundance Using Within-Sample Haplotype Frequencies of eDNA Metabarcoding Data
Environmental DNA (eDNA) metabarcoding provides powerful insights into species presence and community composition, but remains limited in its ability to quantify species abundance or structure. Here, ...
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Elaine Ayers @eayers0.bsky.social · 03/07/2025
I use BHL every single day in my research and teaching. I could not write my books or articles without it, I don't know what my students would do without it, and I would have to radically rethink my career without it. This is more critical with funding cuts. Please, please someone support BHL.
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Trevor A. Branch @trevorabranch.bsky.social · 02/07/2025
In an unconscionable decision, the Smithsonian Institute has decided to no longer support the Biodiversity Heritage Library from 1 Jan 2026. Please someone step up and take it over.
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Deon de Jager @ddj-sa.bsky.social · 24/06/2025
Congratulations, Mikkel!
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Anna Brüniche-Olsen @annabruniche.bsky.social · 16/06/2025
GenDivRange: A global dataset of geo-referenced population genetic diversity across species ranges #popgen #consgen www.nature.com/articles/s41...
nature.com
GenDivRange: A global dataset of geo-referenced population genetic diversity across species ranges - Scientific Data
Scientific Data - GenDivRange: A global dataset of geo-referenced population genetic diversity across species ranges
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Alex Wild @alexwild.bsky.social · 21/04/2025
Everyone should know about GBIF. It's an international biodiversity data aggregator. Museum collections, apps like eBird and iNaturalist, published datasets from the technical literature, all in one place. www.gbif.org
gbif.org
GBIF
Global Biodiversity Information Facility. Free and Open Access to Biodiversity Data.
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Alt National Park Service @altnps.bsky.social · 20/04/2025
Today was truly inspiring. Something happened that we’ve never seen before, you made noise in places that rarely see protests like this. Communities across traditionally conservative areas hosted historic turnouts.
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Saganism @sagan.bsky.social · 19/04/2025
Right Now, most of the American can relate to this message from the 90's.
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Sherrilyn Ifill @sifill.bsky.social · 20/04/2025
If you have a public platform & spent years calming everyone down, telling us Trump was not a danger,was not racist, & arguing that the best way to deal w/Trump was to laugh at him, berated ppl who used the word fascist, insisted that the two parties are the same, admit YOU WERE WRONG.
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Joyce White Vance @joycewhitevance.bsky.social · 20/04/2025
If you're struggling to keep all of the different immigration/deportation cases straight, I've got a post for you: open.substack.com/pub/joycevan...
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Dr Mark D. Scherz @markscherz.bsky.social · 10/04/2025
The Natural History Museum Denmark is hiring a new Tenure-Track Assistant Professor and Curator of (Vertebrate) Palaeontology! Could it be you or someone you know‽ spread the word! Really excited to have a new colleague to work on our amazing collections! 🧪🏛️ candidate.hr-manager.net/ApplicationI...
candidate.hr-manager.net
211-0238/25-2N Tenure-track Assistant Professor and Curator of Paleontology
Tenure-track Assistant Professor and Curator in Paleontology Natural History Museum Denmark Faculty of Science University of Copenhagen The Natural History Muse
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Deon de Jager @ddj-sa.bsky.social · 24/03/2025
Many, if not most, of us depend on open, accessible research infrastructure to do our work and improve the world around us. But political support for such systems is not always there, or can change rapidly - consider signing below mitigate some that risk. investinopen.org/blog/stateme...
investinopen.org
Statement of support for a global research ecosystem
Our global research ecosystem is at risk — it's time to invest in the tools and services that power research and scholarship.
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PLOS Biology @plosbiology.org · 19/03/2025
Analysis of #IUCNRedList data on 67,217 animal spp, by @ashsimkins.bsky.social @billsutherland.bsky.social &co, reveals that a range of #conservation actions successfully conserved species at greatest risk of extinction, but rarely resulted in full recovery 🧪 @plosbiology.org plos.io/3XUzEDd
Species that have improved status following conservation efforts. From top-left to bottom-right: Mauritian kestrel (Falco punctatus ©Josh Noseworthy CC BY 2.0), Pemba flying fox (Pteropus voeltzkowi ©Nigel Voaden CC BY 4.0), Little spotted kiwi (Apteryx owenii ©Kimberley_collins CC BY 2.0), Sierra Juarez Brook frog (Duellmanohyla ignicolor ©Medardo_Arreortua CC BY 4.0), Cook’s petrel (Pteroroma cookii ©sussexbirder CC BY 2.0), European bison (Bison bonasus ©Oleg Kosterin CC BY 4.0), Utahm’s bush frog (Raorchestes uthamani ©Ansil B.R. CC BY 4.0), Iberian lynx (Lynx pardinus ©http://www.lynxexsitu.es CC BY 3.0), Humpback whale (Megaptera novaeangliae ©Christopher.Michel CC BY 2.0).
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Juan Antonio Rodríguez @jrotwitguez.bsky.social · 07/03/2025
A fantastic, critical and accurate piece on the 🦣mammoth de-extinction claims from Colossal, sparked by the woolly mice we’ve been seeing these days on the news. Some sentences are gold 👇🏽 www.theguardian.com/commentisfre... ✍️ by @adamrutherford.bsky.social
theguardian.com
Reviving the woolly mammoth isn’t just unethical. It’s impossible | Adam Rutherford
At a time when US scientists are under attack from their own government, the illiteracy around these elephantine fantasies is dangerous, says geneticist Adam Rutherford
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AaRC @aarc-community.bsky.social · 07/03/2025
On 21st of March we'll have a feedback session with MInAS to talk about animal #aDNA metadata and reporting. If you are producing ancient animal data, please join @ddj-sa.bsky.social and Ophélie Lebrasseur on the conversation to set up proper metadata standards. www.animal-adna.org/events/2025/...
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Timothée Poisot @ctrlalttim.com · 23/11/2024
Ecology & biodiversity folks! Reply to this post to join the science feed! Checklist to help with verification ✅ Have posted a few times already ✅ Profile description not empty ✅ Have a profile picture ✅ Link to orcid, scholar, RG profile, etc, in the reply ℹ️ DM only if anonymous account 🧪🌏
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Deon de Jager @ddj-sa.bsky.social · 25/02/2025
Please :) orcid.org/0000-0003-43...
orcid.org
ORCID
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Alt National Park Service @altnps.bsky.social · 22/02/2025
“Operation Whirlwind” What’s Happening Now? In 2025, Operation Whirlwind was launched under Interim U.S. Attorney Ed Martin to investigate alleged threats against employees of the Department of Government Efficiency (DOGE).
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