Thierry Grange
@thierrygrange.bsky.social
Biologist, geneticist, genomics & paleogenomics, molecular biologist
Institut Jacques Monod, Paris
Studying human and animal evolution from a biological and historical perspective using ancient genomes.
#paleogenomics, #aDNA, #genomics, #domestication
Institut Jacques Monod, Paris
Studying human and animal evolution from a biological and historical perspective using ancient genomes.
#paleogenomics, #aDNA, #genomics, #domestication
Do I understand properly that you imputed only variants that are common today, and thus none of the specific variants that are used to infer that they didn't contribute ancestry to the subsequent waves?
Ranis and Zlaty Kun still share the out-of-Africa bottleneck with modern groups! So while not directly ancestral, most coalescing is recent enough (<<100ky) for imputing common variants.
Similar to how one can impute modern East Asian genomes with European ref panels - despite the split 10kys ago.
Similar to how one can impute modern East Asian genomes with European ref panels - despite the split 10kys ago.
December 15, 2024 at 6:57 PM
Do I understand properly that you imputed only variants that are common today, and thus none of the specific variants that are used to infer that they didn't contribute ancestry to the subsequent waves?
How come imputation with modern genomes can be accurate if Ranis and Zlaty Kun have not contributed ancestry to later arriving anatomically modern humans as claimed in the paper? If they don't share their specific ancestry with modern humans, imputation should not work at these specific positions.
Fascinating technical aspect: Imputing & ancIBDing 45ky-old human genomes works well. With modern ref panels and down to 0.1x WGS coverage! We used downsampling of the two high coverage genomes to prove that. 🎯 That direct experiment showcases the application range of those tool. ✅️✅️ (3/3)
December 15, 2024 at 10:28 AM
How come imputation with modern genomes can be accurate if Ranis and Zlaty Kun have not contributed ancestry to later arriving anatomically modern humans as claimed in the paper? If they don't share their specific ancestry with modern humans, imputation should not work at these specific positions.
Reposted by Thierry Grange
📣Exposition AGRIPOP
📆 Jusqu'au 16 décembre 2024
📍 Hall A des Grands Moulins / Université Paris Cité
Il reste encore 1 semaine pour visiter AGRIPOP, une exposition mise en place par l'équipe "Épigénome & Paléogénome” (@thierrygrange.bsky.social) de l’@ijmonod.bsky.social !
🔗https://urls.fr/HPX142
📆 Jusqu'au 16 décembre 2024
📍 Hall A des Grands Moulins / Université Paris Cité
Il reste encore 1 semaine pour visiter AGRIPOP, une exposition mise en place par l'équipe "Épigénome & Paléogénome” (@thierrygrange.bsky.social) de l’@ijmonod.bsky.social !
🔗https://urls.fr/HPX142
December 9, 2024 at 1:00 PM
📣Exposition AGRIPOP
📆 Jusqu'au 16 décembre 2024
📍 Hall A des Grands Moulins / Université Paris Cité
Il reste encore 1 semaine pour visiter AGRIPOP, une exposition mise en place par l'équipe "Épigénome & Paléogénome” (@thierrygrange.bsky.social) de l’@ijmonod.bsky.social !
🔗https://urls.fr/HPX142
📆 Jusqu'au 16 décembre 2024
📍 Hall A des Grands Moulins / Université Paris Cité
Il reste encore 1 semaine pour visiter AGRIPOP, une exposition mise en place par l'équipe "Épigénome & Paléogénome” (@thierrygrange.bsky.social) de l’@ijmonod.bsky.social !
🔗https://urls.fr/HPX142
🧪 #aDNA 🧬🖥️ A very interesting paper by Gözde Atağ, Mehmet Somel and colleagues of METU showing how f-statistics results can be confounded by low-level admixture from an unaccounted source. academic.oup.com/genetics/art...
An explanation for the sister repulsion phenomenon in Patterson's f-statistics
Abstract. Patterson's f-statistics are among the most heavily utilized tools for analyzing genome-wide allele frequency data for demographic inference. Bey
academic.oup.com
December 1, 2024 at 8:29 PM
🧪 #aDNA 🧬🖥️ A very interesting paper by Gözde Atağ, Mehmet Somel and colleagues of METU showing how f-statistics results can be confounded by low-level admixture from an unaccounted source. academic.oup.com/genetics/art...
🏺🧪 #aDNA
#Evolution
🧬🖥️ Reposting a scientific exchange with a colleague who proposes paleospecies and who is not willing to be challenged about what he is doing and prefers to block posts to silence the disagreements.
#Evolution
🧬🖥️ Reposting a scientific exchange with a colleague who proposes paleospecies and who is not willing to be challenged about what he is doing and prefers to block posts to silence the disagreements.
I agree with your point and this is exactly why I am not convinced by many paleospecies, not talking about the very concept of paleospecies.
November 30, 2024 at 3:16 PM
🏺🧪 #aDNA
#Evolution
🧬🖥️ Reposting a scientific exchange with a colleague who proposes paleospecies and who is not willing to be challenged about what he is doing and prefers to block posts to silence the disagreements.
#Evolution
🧬🖥️ Reposting a scientific exchange with a colleague who proposes paleospecies and who is not willing to be challenged about what he is doing and prefers to block posts to silence the disagreements.
🏺🧪 #aDNA #Evolution 🧬🖥️ Just reread this excellent paper from @elliescery.bsky.social about the Ragsdale paper discussing the differences between species and stems in human evolution. www.nature.com/articles/s41...
November 30, 2024 at 10:27 AM
🏺🧪 #aDNA #Evolution 🧬🖥️ Just reread this excellent paper from @elliescery.bsky.social about the Ragsdale paper discussing the differences between species and stems in human evolution. www.nature.com/articles/s41...
"The return of the splitters" aka "The splitters strike back"!
November 30, 2024 at 9:47 AM
"The return of the splitters" aka "The splitters strike back"!
What should I do to post this in the #aDNA list?
#Evolution #aDNA 🧪⚱️🧬🖥️
If you are in Paris before December 16th and are interested in the #Neolithic and #Paleogenomics, you can visit the exhibition Eva-Maria Geigl and myself organized: AGRIPOP 1/10
culture.u-paris.fr/actualites/a...
If you are in Paris before December 16th and are interested in the #Neolithic and #Paleogenomics, you can visit the exhibition Eva-Maria Geigl and myself organized: AGRIPOP 1/10
culture.u-paris.fr/actualites/a...
Université Paris Cité| Culture | AGRIPOP
AGRIPOP | De l'Anatolie à la vallée de l’Aisne, les migrations néolithiques ont amené ce mode de vie sédentaire de producteurs-agriculteurs qui est toujours le nôtre.
culture.u-paris.fr
November 28, 2024 at 6:06 PM
What should I do to post this in the #aDNA list?
Some of the icons did not allow my post to reach the places I targeted 🏺🧪 and #aDNA
#Evolution #aDNA 🧪⚱️🧬🖥️
If you are in Paris before December 16th and are interested in the #Neolithic and #Paleogenomics, you can visit the exhibition Eva-Maria Geigl and myself organized: AGRIPOP 1/10
culture.u-paris.fr/actualites/a...
If you are in Paris before December 16th and are interested in the #Neolithic and #Paleogenomics, you can visit the exhibition Eva-Maria Geigl and myself organized: AGRIPOP 1/10
culture.u-paris.fr/actualites/a...
Université Paris Cité| Culture | AGRIPOP
AGRIPOP | De l'Anatolie à la vallée de l’Aisne, les migrations néolithiques ont amené ce mode de vie sédentaire de producteurs-agriculteurs qui est toujours le nôtre.
culture.u-paris.fr
November 28, 2024 at 5:55 PM
Some of the icons did not allow my post to reach the places I targeted 🏺🧪 and #aDNA
#Evolution #aDNA 🧪⚱️🧬🖥️
If you are in Paris before December 16th and are interested in the #Neolithic and #Paleogenomics, you can visit the exhibition Eva-Maria Geigl and myself organized: AGRIPOP 1/10
culture.u-paris.fr/actualites/a...
If you are in Paris before December 16th and are interested in the #Neolithic and #Paleogenomics, you can visit the exhibition Eva-Maria Geigl and myself organized: AGRIPOP 1/10
culture.u-paris.fr/actualites/a...
Université Paris Cité| Culture | AGRIPOP
AGRIPOP | De l'Anatolie à la vallée de l’Aisne, les migrations néolithiques ont amené ce mode de vie sédentaire de producteurs-agriculteurs qui est toujours le nôtre.
culture.u-paris.fr
November 28, 2024 at 5:52 PM
#Evolution #aDNA 🧪⚱️🧬🖥️
If you are in Paris before December 16th and are interested in the #Neolithic and #Paleogenomics, you can visit the exhibition Eva-Maria Geigl and myself organized: AGRIPOP 1/10
culture.u-paris.fr/actualites/a...
If you are in Paris before December 16th and are interested in the #Neolithic and #Paleogenomics, you can visit the exhibition Eva-Maria Geigl and myself organized: AGRIPOP 1/10
culture.u-paris.fr/actualites/a...
This interesting post missed the #aDNA tag to appear in the paleogenetic group.
Excited to share our review article on Denisovans, now published in Nature Genetics 🥳 I am very grateful to
Emilia Huerta-Sanchez for making this possible! Check it out 🔎🧬
www.nature.com/articles/s41...
🔎Here's the free link:
rdcu.be/dY9G1
Emilia Huerta-Sanchez for making this possible! Check it out 🔎🧬
www.nature.com/articles/s41...
🔎Here's the free link:
rdcu.be/dY9G1
A history of multiple Denisovan introgression events in modern humans - Nature Genetics
This review describes evidence of multiple Denisovan populations, each with varying relatedness to Altai Denisovans, that introgressed into modern humans and highlights how introgression influenced hu...
www.nature.com
November 28, 2024 at 7:14 AM
This interesting post missed the #aDNA tag to appear in the paleogenetic group.
An interesting piece of evidence about the beginning of sheep domestication and its spread into Europe thanks to our collaboration with the Metu group, where we brought a perspective from Neolithic France. academic.oup.com/mbe/article/...
🧪 ⚒️ #Paleobio 🖥️🧬🏺
🧪 ⚒️ #Paleobio 🖥️🧬🏺
The Population History of Domestic Sheep Revealed by Paleogenomes
Abstract. Sheep was one of the first domesticated animals in Neolithic West Eurasia. The zooarchaeological record suggests that domestication first took pl
academic.oup.com
October 24, 2024 at 7:17 PM
An interesting piece of evidence about the beginning of sheep domestication and its spread into Europe thanks to our collaboration with the Metu group, where we brought a perspective from Neolithic France. academic.oup.com/mbe/article/...
🧪 ⚒️ #Paleobio 🖥️🧬🏺
🧪 ⚒️ #Paleobio 🖥️🧬🏺
Oui, c'est clair que si le PR qui décide quels sont les axes de recherche à soutenir, il y a 100% de chances que tout arrive trop tard. On est en train de focaliser le pays sur le créneau de la destination touristique.
#ESR Perso, l'état stratège qui décide en Science ce qui est prioritaire de ce qui ne l'est pas, je suis loin d'être fan.
La liberté académique, la sérendipité & la recherche curieuse et désintéressée sont à l'origine des plus grandes découvertes.
Macron vient d'achever la recherche fondamentale
La liberté académique, la sérendipité & la recherche curieuse et désintéressée sont à l'origine des plus grandes découvertes.
Macron vient d'achever la recherche fondamentale
December 9, 2023 at 9:21 AM
Oui, c'est clair que si le PR qui décide quels sont les axes de recherche à soutenir, il y a 100% de chances que tout arrive trop tard. On est en train de focaliser le pays sur le créneau de la destination touristique.
Nice work, I like the second benchmark
🧪 🏺
Two new pre-print is online from our lab!
1) We benchmark the accuracy of widely kinship methods in low-coverage #ancientdna data.
www.biorxiv.org/content/10.1...
2) We explore the effect of preprocessing steps in aDNA studies and we release bamRefine.
www.biorxiv.org/content/10.1...
Two new pre-print is online from our lab!
1) We benchmark the accuracy of widely kinship methods in low-coverage #ancientdna data.
www.biorxiv.org/content/10.1...
2) We explore the effect of preprocessing steps in aDNA studies and we release bamRefine.
www.biorxiv.org/content/10.1...
Pre-processing of paleogenomes: Mitigating reference bias and postmortem damage in ancient genome da...
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
November 13, 2023 at 10:19 PM
Nice work, I like the second benchmark
Reposted by Thierry Grange
The Orange Puffer, also known as the Bottom-feeding Liar Fish. It is avoided by all marine creatures since it poisons the waters around itself.
November 11, 2023 at 6:36 PM
The Orange Puffer, also known as the Bottom-feeding Liar Fish. It is avoided by all marine creatures since it poisons the waters around itself.
Yes, great stuff and ideas were already formalized a while ago. We often have the technologies now to address with more precision these ideas, but the ideas were there sitting for a long time. Ideas now are often finding the way to apply the technology to tackle these old fundamental ideas.
From time to time (usually when writing intros), I come back to Holliday & Pugh (1975) Science , and im re-amazed by it. They basically laid out the future of developmental epigenetics research before we even know what genes to mutate science.org/doi/abs/10.1...
October 23, 2023 at 8:46 PM
Yes, great stuff and ideas were already formalized a while ago. We often have the technologies now to address with more precision these ideas, but the ideas were there sitting for a long time. Ideas now are often finding the way to apply the technology to tackle these old fundamental ideas.
Finally, for French-speaking readers, we summarized our finding in this article from @FR_Conversation . 14/14
theconversation.com/homo-sapiens...
theconversation.com/homo-sapiens...
October 23, 2023 at 8:13 PM
Finally, for French-speaking readers, we summarized our finding in this article from @FR_Conversation . 14/14
theconversation.com/homo-sapiens...
theconversation.com/homo-sapiens...
None of this would have been possible without an amazing collaboration with Andy Bennett, Oguzhan Parasayan and Eva-Maria Geigl and the Ukrainian-French archeologists team. Eva-Maria has contributed a behind the story blog about it. 13/14
ecoevocommunity.nature.com/posts/crimea...
ecoevocommunity.nature.com/posts/crimea...
October 23, 2023 at 8:13 PM
None of this would have been possible without an amazing collaboration with Andy Bennett, Oguzhan Parasayan and Eva-Maria Geigl and the Ukrainian-French archeologists team. Eva-Maria has contributed a behind the story blog about it. 13/14
ecoevocommunity.nature.com/posts/crimea...
ecoevocommunity.nature.com/posts/crimea...
Finally, the Buran Kaya III individuals are more closely related to present-day individuals from Europe. 12/14
October 23, 2023 at 8:12 PM
Finally, the Buran Kaya III individuals are more closely related to present-day individuals from Europe. 12/14
The Gravettian culture has produced stunning female sculptures like the various Venuses of Vestonice and Willendorf and the head of the Dame de Brassempouy. The genetic relationships support the initial assumption of a. Yanevich that Buran Kaya III represented an early Gravettian stage. 11/14
October 23, 2023 at 8:11 PM
The Gravettian culture has produced stunning female sculptures like the various Venuses of Vestonice and Willendorf and the head of the Dame de Brassempouy. The genetic relationships support the initial assumption of a. Yanevich that Buran Kaya III represented an early Gravettian stage. 11/14
The Buran Kaya III individuals were most closely related to later individuals from Western Europe associated with the Gravettian culture, in particular those of the Fournol cluster. 10/14
October 23, 2023 at 8:09 PM
The Buran Kaya III individuals were most closely related to later individuals from Western Europe associated with the Gravettian culture, in particular those of the Fournol cluster. 10/14
They shared also ancestry with individuals from the Caucasus suggesting that this Out of Africa wave used this route to Eurasia. 9/14
October 23, 2023 at 8:07 PM
They shared also ancestry with individuals from the Caucasus suggesting that this Out of Africa wave used this route to Eurasia. 9/14
In contrast to what was previously assumed, our analyses revealed that the Homo sapiens arriving after the Campanian-Ignimbrite eruption encountered survivors of the previous migration events and admixed with individuals related to the Zlaty Kun woman. 8/14
October 23, 2023 at 8:06 PM
In contrast to what was previously assumed, our analyses revealed that the Homo sapiens arriving after the Campanian-Ignimbrite eruption encountered survivors of the previous migration events and admixed with individuals related to the Zlaty Kun woman. 8/14
Even though the bones contained only traces of ancient DNA, using our improved aDNA lab procedures and thanks to the aseptic excavations, we could obtain enough genomic information to study 740 000 SNPs for comparison with previously obtained more recent and more ancient genomes. 7/14
October 23, 2023 at 8:04 PM
Even though the bones contained only traces of ancient DNA, using our improved aDNA lab procedures and thanks to the aseptic excavations, we could obtain enough genomic information to study 740 000 SNPs for comparison with previously obtained more recent and more ancient genomes. 7/14
We studied partial genomes of two tiny pieces of skulls that were collected aseptically in 2009 by Laurent Crépin. 6/14
October 23, 2023 at 8:03 PM
We studied partial genomes of two tiny pieces of skulls that were collected aseptically in 2009 by Laurent Crépin. 6/14