Benjamin Peter

This is a really cool study and I'm glad to see it come out!

My summary of the new papers about Neanderthal interbreeding

The first paper is a systematic survey of Neandertal ancestry through time; a joint effort with @moorjani_priya ’s lab at UC Berkeley, co-led by @IasiLeonardo and @M_Chintalapati. Leo has a great summary of our main findings here:

Today is a very big day for our research group, with two of my students, @arevsumer and @IasiLeonardo publishing papers on the same day! science.org/doi/10.1126/sc… nature.com/articles/s4158… #Neanderthals #Geneflow

9) We searched for candidates of adaptive selection using an outlier approach. We found that many previously published candidate regions related to skin pigmentation, metabolism, and immunity were immediately selected, with some regions becoming adaptive at a later stages.

8) We examined the distribution of Neandertal ancestry over time and found that the ancestry landscape, including the Neandertal deserts, were formed quickly after the gene flow supporting theoretical predictions. We infer the initial Neandertal gene flow may have been >5%.

7) Our data supports a single extended pulse of Neandertal gene flow that took place around 47,000 years ago, with a duration of around 6,000 years.

6) Digging deeper, we infer the timing of Neandertal gene flow per individual by studying the ancestry covariance across the genome.

5) The Early out of Africa individuals including Oase1, Ust’ Ishim and the Bacho Kiros have the highest unique Neandertal ancestry and significantly different matching profile to sequenced Neandertals than later modern humans- a possible indication of diversified gene flow.

4) By exploring the colocalization of Neandertal ancestry segments and contrasting it to genome-wide allele sharing, we uncovered that most (>90%) Neandertal ancestry is shared among individuals and follows the overall population structure.

3) We inferred Neandertal segments in the individuals using admixfrog (github.com/BenjaminPeter/…), and used the ancestry covariance for dating (github.com/MoorjaniLab/Pr…).

2) We use genomic data from 59 ancient modern human individuals ranging between 45,000–2,200 yBP with 275 diverse present-day individuals from worldwide populations forming 16 clusters for our analysis.

1) Previous studies characterized the Neandertal ancestry segments in present-day populations and found a non-homogeneous distribution. But how did this distribution look like in the past?

In a collaboration between @M_Chintalapati ,@SkovLaurits , Alba Bosoms Mesa, @MatejaHajdi , @benmpeter and @moorjani_priya , we've journeyed into our shared history with Neandertals by analyzing over 300 genomes spanning 50,000 years. A thread 🧵🧬 biorxiv.org/content/10.110…

Come join us at @MPI_EVA_Leipzig! The Dept of Primate Behavior & Evolution is looking for a lab manager/coordinator to integrate our molecular genetic, cell culture, and field-based labwork. Details here: tinyurl.com/2p83xj4p

Newly published paper by myself and @LoganCorina, @DieterLukas, and @popgenchen on the range expansion of the great-tailed grackle, and range stability of the boat-tailed grackle! peercommunityjournal.org/articles/10.24… #TheGrackleProject @PeerComJournal

Open again: postdoc position (18 months) for great apes and viruses! Apply here: univis.univie.ac.at/ausschreibungs…

Ever wondered how accurate genetic genealogy is? @rvrohlfs and I have a NIJ funded PhD position to investigate this! Please reach out with any questions

Complete genomes of almost all individuals of the critically endangered kākāpō 🇳🇿🦜🧬 biorxiv.org/content/10.110…

An exciting new preprint !!! Can wait to have a closer look 🤓