Alex Hübner

www.nature.com/articles/s41...

Kava drinking and its role in cultural evolution A new study tests the hypothesis that the consumption of the mind-altering beverage kava facilitated the emergence of complex, hierarchical societies in Oceania

#Kava drinking & its role in cultural #evolution. Did the consumption of the mind-altering beverage facilitate the emergence of complex, hierarchical #societies in #Oceania? New study @pnas.org by an intl. team led by @vaclavhrncir.bsky.social. See tinyurl.com/4jt8vy3d & www.pnas.org/doi/10.1073/...

A large mass grave from the Early Iron Age indicates selective violence towards women and children in the Carpathian Basin - Nature Human Behaviour In this analysis of biomolecular and archaeological data from a ninth-century BCE mass grave in the Carpathian Basin, Fibiger et al. find evidence for the targeted killing of mostly unrelated women an...

Really excited to share our new paper on the Early Iron Age mass grave at Gomolava (9th c. BCE), a study I had the pleasure to work on during my PhD with an amazing group of co-authors across multiple disciplines. Open access link: www.nature.com/articles/s41... 🧵👇

Ancient mass grave in Serbia seen as a grisly show of power Women and children were executed in an elaborate prehistoric ritual

When archaeologists found the bodies of 77 women and children in an Iron Age grave, they pinned it on a prehistoric plague outbreak. A new analysis reveals it was actually a mass execution. Most bizarre? @mireniraorb.bsky.social's look at their genes shows the victims weren't related. @science.org

Assuming that coding agents will build you great software because they can follow a spec written and reviewed by world-class engineers is a bit like assuming that following Michael Phelps’ diet will make you great at swimming.

I used Claude Opus 4.5/4.6 (and a bit of Codex GPT-5.3) to port edgeR to Python. See edgePython github.com/pachterlab/e...
This allowed me to develop a single-cell DE method that extends NEBULA with edgeR Empirical Bayes. All in one week. Details in doi.org/10.64898/202...

We are looking for an enthusiast and motivated postdoc to join the Paleogenomics and Evolutionary Biology group at @liigh-unam.bsky.social, to lead a project working with human pre-hispanic samples. Interested candidates send a CV and letter of intent to fsanchez@liigh.unam.mx. Please #RT

CARTA: Human Microbiome Evolution with Christina Warinner YouTube video by University of California Television (UCTV)

New video of talk by @christinawarinner.bsky.social given at Center for Academic Research and Training in Anthropogeny posted by @ucsandiego.bsky.social explaining how advances in #aDNA and #proteomics can investigate the complex and diverse microbial communities from dental calculus

Point of no returns: researchers are crossing a threshold in the fight for funding With so little money to go round, the costs of competing for grants can exceed what the grants are worth. When that happens, nobody wins.

This report in Nature on the costs of competing for & administering scientific grants is shocking: "In other words, European taxpayers will have spent more on the funding process than on the funding itself, and the scientific ecosystem has been drained." www.nature.com/articles/d41... 🧪

Esther Lederberg in the laboratory in the 1950's. Credit: Estherlederberg.com

Born #OnThisDay in 1922, Esther Lederberg was the first to isolate the lambda phage in 1951. She characterised the lysogenic phase, whereby the phage are able to integrate into the bacterial genome, staying dormant. This discovery made them a model tool of study, leading to many more breakthroughs.

Actifensin Evolution in the Human Oral Cavity over the Past 100,000 Years Bacterially produced antimicrobial peptides (AMPs), or bacteriocins, play key roles in shaping microbial communities via interspecies competition. Unlike the more temporally dynamic gut microbiome, the oral microbiome exhibits long-term stability and is preserved into deep time in dental calculus, enabling evolutionary analysis across time. Here, we combine metagenomics, structural modeling, and experimental validation to investigate AMP diversity in ancient and modern dental biofilms from humans, Neanderthals, and nonhuman primates spanning 100,000 years. Using our newly developed platform, AMPcombi, we uncover evolutionary trajectories of bacteriocins and elucidate their ecological functions. Among these, we identify a conserved family of Actinomyces-derived defensin-like peptides, termed actifensins, present across all time periods. Phylogenetic, structural, and functional analyses revealed shared ancestry and adaptive diversification between ancient (paleo-) and modern actifensins, with evidence of positive selection and maintained antimicrobial activity. Our findings position the oral microbiome as a valuable reservoir for natural product discovery. In the face of rising antimicrobial resistance, evolutionary insights into AMP function open a door to next-generation therapeutics. AMPcombi streamlines this process, linking ancient biomolecules with biotechnology.

Wonderful @microverse.bsky.social collaboration led by Stallforth lab on the diversity of AMPs in ancient and modern dental biofilms from humans, Neanderthals, and nonhuman primates spanning 100,000 years 🧪🥳
We'll call it a paper wrap for 2025... maybe 😉
pubs.acs.org/doi/10.1021/...

Release v25.09: Site of Palmyra · SPAAM-community/AncientMetagenomeDir Release v25.09.0 includes 5 new publications, representing 33 new ancient host-associated metagenome samples, 40 new ancient microbial genomes, and 90 new ancient environmental samples. This brings...

🚨 New release of #AncientMetagenomeDir! (v25.09.0, Site of Palmyra)
github.com/SPAAM-commun...
It is a community resource of #metadata of >2K shotgun-sequenced #AncientMetagenome or ancient microbial genome enriched samples & >5K libraries. Stats below (🧵 1/4)

I'm very proud of being part of this team, @matejahajdi.bsky.social! Hopefully many more @eshesociety.bsky.social conferences will come!

The @nytimes.com has rarely felt as hopelessly out of its depth as in the past two days or so. There is still much I admire, many journalists I respect and trust, but on the Charlie Kirk assassination it simply hasn’t been very informative - not to mention some atrocious opinion “journalism”.

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

Ancient skeletons’ genes reveal origin of the Slavic people DNA connects modern Slavs to a wave of migration following the fall of the Roman Empire

A study led by @zhofmanova.bsky.social @mpi-eva-leipzig.bsky.social used ancient DNA to investigate the spread of Slavic language and culture 1,500 years ago. “This wasn’t a migration of elites, or a few male warriors,” 1 co-author says. “This was the migration of an entire population.” @science.org

A huge thanks to all the amazing speakers and participants at #SPAAM7 yesterday 🧬🙌

The sessions were full of inspiring talks and great discussions!✨

I am so thrilled for this opportunity and to talk about #ancient #pathogenomics!! There is still time to register for #SPAAM7, happening this 26th of August in Turin!! (also online!): join us for a day of #ancient #metagenomics with the welcoming community of @spaam-community.bsky.social

screenshot of the lyme regis fossil festival pamphlet, showcasing two workshops with a very serious dinosaur reconstruction right next to my really silly duckbilled dinosaur lineart. Text is: Saturday 14th June Paleoart Workshop 10.30-11.30 Dinosaur reconstructions Jay Balamurugan (Age 10+yrs) Have you ever wondered about how scientists and artists work together to bring extinct animals to life in illustrations, books, and documentaries? In this workshop, Jay will run through how paleoartists reconstruct dinosaurs and other prehistoric life - from looking at the original fossils and skeletal diagrams to referencing modern animals and their behaviours and ecologies. By the end of the session, we'll have illustrated an iconic local extinct species! Paleoart Workshop 13.30-14.30 Doodling and colouring corner Petra Korlevic (Ages 3-6yrs - accompanied) A relaxed workshop offering the opportunity to come colour a variety of dinosaurs and other extinct animal themed templates or draw and colour your own. Perfect for a sit down and some downtime in between the hustle and bustle of the event!

an absolutely chaotic scene with 15 different extinct critter prints strewn across my bed as I am trying to sort and cathegorize everything. we got dinosaurs, water reptiles, flying reptiles, almost birds, a t-rex with a crown, all in various states of horizontal/vertical upside-down, cut partially.

find me this weekend at the #LymeRegisFossilFestival Hub point for some chill #SciArt dinosaur coloring/doodling!

We just succeeded in formally linking a specific rodent species - the otherwise charming fire-footed rope squirrel - to the onset of a mpox outbreak in a primate species - sooty mangabeys. Here Kai’s report on the preprint we released yesterday 1/2

The next release is out!

Ancient DNA from the Green Sahara reveals ancestral North African lineage - Nature Pastoralism spread through cultural diffusion into the Green Sahara, where an isolated, distinct North African ancestry persisted.

I'm beyond excited to share our new paper in Nature! We sequenced the first ancient human autosomal genomes from the Central Sahara, two ~7,000-year-old individuals from Takarkori in Libya, revealing a long-isolated North African lineage: www.nature.com/articles/s41...
Here's a short thread: (1/n)

Just over 2 weeks left to apply for this 3-y position. It qualifies for the full UK visa sponsorship. Come work with us on a truly exciting project, with visits to different #museums #aDNA #popgen

Last week’s AncientMetagenomeDir hackathon was a great success 🚀. More than 20 participants added new studies, updated the documentation, fixed bugfixes, and added the first 14C dates to the study 💪!

The Tai Chimpanzee Project is making available microCT scans from their collections on human-fossil-record.org. All proceeds are used to support their mission of conservation and non-invasive research in Tai National Park (taichimpproject.org).

Caption by professor B Gronnow. Water color by Nuka Konrad Godtfredsen (2021). Copyright: The National Museum of Denmark. "Hunting a herd of swimming caribou from kayak at the site, Aasivissuit, in the early 18th century West Greenland as interpreted by the Greenlandic artist, Nuka Godtfredsen. Through communal drive hunts the Inuit secured large amounts of caribou meat and fat for consumption as well as hide and antler for raw materials and trade. Large heaps of bones from the butchering of the animals piled up as waste in the midden area of the settlement, Three centuries later archaeologists excavated the bones, which were analyzed, including studies of preservation conditions of ancient DNA contained in the bones and soil."

New paper out! 📄
My first adventures in (ancient) metagenomics. 🦠

“Exploring DNA degradation in situ and in museum storage through genomics and metagenomics” www.nature.com/articles/s42...

Curious about the water color painting (see ALT text)? 🦌

Thread (Bluetorial?) with findings!
🧶👇 (1/n)

Bronze Age Yersinia pestis genome from sheep sheds light on hosts and evolution of a prehistoric plague lineage Most human pathogens are of zoonotic origin. Many emerged during prehistory, coinciding with domestication providing more opportunities for spillover from original host species. However, we lack direc...

Many zoonotic diseases are believed to have emerged during prehistory, but can we actually identify their past host range using ancient DNA? In the first publication of the Key Lab we present a 4000y old Yersinia pestis genome reconstructed from domesticated sheep. 🧵 www.biorxiv.org/content/10.1...

Edmond Albius was just a 12-year-old boy, enslaved and without formal education, in 1841. He managed to develop an innovative technique to pollinate vanilla orchids quickly and profitably, solving an enigma that intrigued prominent botanists of the time. (The rest in comments)

If you like hearing about #aDNA of animals by Early Career Researchers - join us at AaRC for our seminar series, on the last Friday of every month!