Louis L'Hôte
@louis-lhote.bsky.social
PhD candidate at University College of Dublin. aDNA, Ancient pathogens🦠, small Ruminants and virology
Please have a look at our article on TheConversation.com about our recent work on ancient animal viruses found in parchment! Co-written with @gingerhowley.bsky.social and Mike Herd. (Cool pics of @gingerhowley.bsky.social making parchments in the article) theconversation.com/ancient-viru...
Ancient virus hunters: how we discovered sheeppox DNA hidden in medieval gospels
DNA can survive in parchment for well over a thousand years.
theconversation.com
🔬📜 “The recording of ancient DNA of pathogens has completely changed our understanding of infectious disease in the past, and here we show that parchment can also preserve animal pathogen DNA." - Louis L’Hôte, the study’s lead author and a PhD student at UCD School of Agriculture and Food Science
Scientists Extracted DNA From Medieval Parchment—and Found a Hidden Disease
The 3,500-year history of sheeppox was written into the books—quite literally.
gizmodo.com
I am opening a PhD position at the University of Vienna to work with me on ancient pathogen aDNA 🦠🧬 Please help spread the word to any relevant candidates or contact me if you are interested! Join us here in Vienna!
Thanks to @franceculture.fr for having me on! 🎙️ Absolutely thrilled to have had a little radio moment, in French, to talk about our new work on sheeppox virus found in medieval parchment🐑🦠📖 www.radiofrance.fr/francecultur...
3500 ans d'histoire de la variole ovine dévoilés par l'analyse de génomes cachés dans des manuscrits
La variole du mouton fait des ravages depuis des siècles et, pour reconstituer son histoire, des scientifiques du University Collège de Dublin ont analysé l'ADN caché dans des manuscrits du Moyen-Âge ...
radiofrance.fr
Our paper on the second plague pandemic is now finally published: www.pnas.org/doi/10.1073/... We present 11 new Y. pestis genomes from around Europe and introduce a new approach to refine the dating of ancient genomes that helped us to contextualize 75 plague genomes of the Second Pandemic.
New preprint for the Ruminant Paleogenomic group! PISGTI (Pathogen anImal Genome Sequence ToolkIt), a pipeline for host detection + ancient pathogen authentication. By using PISGTI on published domesticated animal datasets, we notably found ancient Rickettsia felis and Leptospira borgpetersenii.
bioRxiv Genomics@biorxiv-genomic.bsky.social · last mo.PIGSTI: a modular, reproducible pipeline for detecting species identity, pathogens, and microbes from animal palaeogenomic data https://www.biorxiv.org/content/10.64898/2026.09.01.748539v1
Our paper on archaic introgression in imputed ancient genomes is out. Imputation performs better in archaic regions, making Neanderthal and Denisovan segments detectable in low-coverage data. Thousands of archived genomes become usable. doi.org/10.1038/s414...
Archaic ancestry inference in imputed ancient human genomes - Nature Communications
Genotype imputation enables accurate detection of Neanderthal and Denisovan ancestry in low-coverage ancient genomes and allows the identification of introgressed haplotypes as well as candidate genes...
doi.org
Researchers have pinned the emergence of sheeppox to about 5000 years ago. The peek into the pathogen’s past came from an unusual source: dozens of medieval books and legal documents written on parchment, which is made from specially treated animal skins. Learn more: https://scim.ag/4iaLx30
Extremely happy to share our new study on Sheeppox virus (SPPV) ! We notably found many genomes in Medieval parchments🦠📖 A short thread about it : share.google/JqVOTB2lvxcO...
Three thousand five hundred years of sheeppox virus evolution inferred from archaeological and codicological genomes
Sheeppox virus (SPPV) is a major livestock pathogen causing economic hardship through reduced production and death of vulnerable sheep, with written descriptions of sheeppox-like disease recorded sinc...
share.google
Our paper on ancient sheeppox virus genomes, including many found from parchment samples, is now published af Science Advances. Congrats to all our co-authors and particularly first author Louis. #aDNA share.google/JqVOTB2lvxcO...
Three thousand five hundred years of sheeppox virus evolution inferred from archaeological and codicological genomes
Sheeppox virus (SPPV) is a major livestock pathogen causing economic hardship through reduced production and death of vulnerable sheep, with written descriptions of sheeppox-like disease recorded sinc...
share.google
Ancient parchments, covered in ancient disease DNA! Researchers led by @ucddublin.bsky.social's @gingerhowley.bsky.social recover the genes of a deadly animal pathogen from medieval manuscripts. @science.org
Ancient sheep virus found hiding in medieval parchment
Newly recovered sheeppox sequences reveal when and how the virus emerged
science.org
The first #ancient #smallpox genomes from the Americas! 🦠🧬#Genomes from two #Inca-Colonial individuals in Chile reveal an extinct #Variola lineage, providing direct evidence of smallpox during the early colonial period. www.science.org/doi/10.1126/... #MetagenomicsMonday #SPAAM #AncientDNA #aDNA
The genomic identity of early smallpox in South America
Smallpox was a major driver of population collapse in the Americas after European contact, yet the genetic identity of the causal strains remains unknown. Here, we report the first ancient smallpox…
science.org
📢 Registration for #CRABi 2026 is now open! 📍 Bordeaux, France 📆 12–13 November 2026 Find the programme and practical information here: crabi.sciencesconf.org 📝 Registration deadline: 4 September 2026, 5:00 PM (Paris time). #BiomolecularArchaeology #Proteomics #AncientDNA #Isotopes
Première conférence de la Communauté de Recherche en Archéologie Biomoléculaire et isotopique - Sciencesconf.org
crabi.sciencesconf.org
How did the rapid Mediterranean dispersal of Neolithic livestock shape their genomes? 16 Neolithic sheep & goat genomes from the Mediterranean Áine Halpin, @gingerhowley.bsky.social Roger Alcàntara Fors, Maria Saña-Segui, @brad-dan.bsky.social and others www.biorxiv.org/content/10.6... #aDNA
Mediterranean dispersal imposed bottlenecks in Neolithic sheep and goats
The Neolithic period in western Eurasia involved major dispersal events, including the translocation of livestock into Europe. These domestic animal translocations likely featured founder effects, fun...
biorxiv.org
Our recent study on a mass mortality assemblage of sheep, covered nicely in this article from Paris One.
Projet MALADI : Une maladie ovine identifiée grâce à l’ADN ancien - Recherche à l'université Paris 1 Panthéon-Sorbonne
Une étude interdisciplinaire menée par Annelise Binois-Roman, maîtresse de conférences à Paris 1 Panthéon-Sorbonne, en collaboration avec Kevin Daly de University College Dublin, a permis d’élucider l...
recherche.pantheonsorbonne.fr
@louis-lhote.bsky.social talks about a high-resolution analysis of the evolution of the sheepox virus from a surprising source... #Medieval #Parchment @palaeogenomics.bsky.social. www.biorxiv.org/content/10.6...
If ancient metagenomics is your jam, #SPAAM8, hosted by @spaam-community.bsky.social, will be one of three pre-conference workshops at #ICP2026 🧬 When: June 22nd, ~09:00-17:30 (exact times tba) Where: Frescati campus @stockholm-uni.bsky.social and online Register here: tinyurl.com/36rvwe4y
SPAAM8 · SPAAM Community
tinyurl.com
🚨 PhD Studentship Alert 🚨 4-year DPhil in Genomic Medicine and Statistics, funded by the Royal Society *Reconstructing the evolutionary history of pathogens using ancient DNA* ☠️🧬🦠🐕🐖🐇 🇬🇧 UK/home students 📍 Centre for Human Genetics, University of Oxford ⏰ Fri, 17 July tinyurl.com/gms-rs-dphil
GMS Royal Society Studentship
DPhil Studentship opportunity for the DPhil Genomic Medicine and Statistics programme
tinyurl.com
Our investigation of mass mortality burial of sheep is published at @royalsociety.org Open Science! Evidence of sheeppox in seventeenth- to nineteenth-century France: a multi-disciplinary investigation of a sheep mass mortality assemblage
Evidence of sheeppox in seventeenth- to nineteenth-century France: a multi-disciplinary investigation of a sheep mass mortality assemblage
Abstract. Epizootic outbreaks posed major threats to food security, economic stability and animal welfare in past communities. While these events and their
royalsocietypublishing.org
S13: Perspectives on paleo-omics: defining functional evolution of ancient viruses in the era of big data 🗓️ Wed Jul 1, 1:20pm 🔗 smbe2026.org/programme
Come join our aDNA community at Trinity College Dublin and explore medieval ruminant genomes! Funded PhD studentship in ancient animal genomics at Trinity College Dublin. Deadline 27th May 2026 Please see the information attached for full description and application process.
Ancient DNA from grape seeds spanning 4,000 years reveals the domestication, cultivation, and trade of grapes in France over this period, according to research in Nature Communications. The authors find that one Medieval sample is genetically identical to modern Pinot Noir grapes. 🧬 🏺 🧪
Ancient DNA reveals 4000 years of grapevine diversity, viticulture and clonal propagation in France - Nature Communications
Here, the authors present aDNA from 49 grape pips spanning the Bronze Age to Medieval period in France and surrounding areas. They find evidence of long-distance exchange of domestic varieties through vegetative clones and one Medieval sample that is nearly identical to modern Pinot Noir.
go.nature.com
I was on Mooney Goes Wild talking goats! Cannot describe how sleep deprived I was recording this. Mooney Goes Wild Monday 30 March 2026 - Mooney Goes Wild share.google/I4GNDt7kF2bF...
Mooney Goes Wild Monday 30 March 2026
Derek Mooney and guests explore the natural world in all its forms.
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Two upcoming events with one sign up! AaRC Online Conference – Tuesday, May 19 (virtual) ICP In-Person Meet-Up – Monday, June 22 in Stockholm (in person) Here is a link to register/submit an abstract forms.gle/Kse1kPYnpsVg...
Can safely way this is the craziest and coolest study I have led. We chart the evolution of sheeppox virus, finding it in the Eurasian steppe ~3700 years ago, and also in a LOT of parchment from medieval Europe (made from a range of animals skins!) #aDNA
bioRxiv Genetics@biorxiv-genetic.bsky.social · 8mo ago3,500 years of sheeppox virus evolution inferred from archaeological and codicological genomes https://www.biorxiv.org/content/10.64898/2026.02.23.707469v1
Biopathocodicology?? 🦠🧬🐑 (1/4) Check out this groundbreaking new #aDNA #pathology paper by @louis-lhote.bsky.social @gingerhowley.bsky.social and colleagues! www.biorxiv.org/content/10.6...
Another #aDNA preprint! We recovered DNA from 7,000 year old (!) goat leather from Cueva de los Murciélagos - and see a genetic link with Bermeya goats today! Credit to Francisco Martínez-Sevilla for seeing me on Youtube(?!) + reaching out to collaborate - there's still value in the internet.
Genetic analysis of 7,000 year old preserved goat leather from Cueva de los Murciélagos (Albuñol, Spain).
Advances in ancient DNA research have expanded the range of materials from which genetic information can be recovered, enabling the analysis of atypical materials. These often preserve both host and e...
biorxiv.org
After a four-year journey, my PhD work is out in @science.org Endless gratitude to the amazing @felix-erc.bsky.social team, all coauthors and collaborators, and my loved ones. Without you all this couldn't be real! 💛🐱✨ @erc.europa.eu @nationalgeographic.bsky.social www.science.org/doi/10.1126/...
The dispersal of domestic cats from North Africa to Europe around 2000 years ago
The domestic cat (Felis catus) descends from the African wildcat Felis lybica lybica. Its global distribution alongside humans testifies to its successful adaptation to anthropogenic environments. Unc...
science.org
Despite my insomnia, I'm very happy to share our preprint: a multi-disciplinary assessment of a sheep mass mortality event from ~18th century France. We report the first ancient sheeppox virus (think smallpox) and the Taenia hydatigena (nasty roundworm) genomes. #aDNA
Evidence of sheeppox in 17th-19th century France: a multi-disciplinary investigation of a sheep mass mortality assemblage
Epizootic outbreaks posed major threats to food security, economic stability, and animal welfare in past communities. While these events and their impacts are well documented in historical records, ve...
biorxiv.org