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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 🤓

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

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

Newly published paper by myself and Corinⓐ Logan (she/her), Dieter Lukas, and Nancy Chen 陳嵐欣 on the range expansion of the great-tailed grackle, and range stability of the boat-tailed grackle! peercommunityjournal.org/articles/10.24… #TheGrackleProject Peer Community Journal

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

In a collaboration between ManjushaChintalapati ,@SkovLaurits , Alba Bosoms Mesa, Mateja Hajdinjak , Benjamin Peter 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…

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?

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.

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

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.

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.

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

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.

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%.

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.

My summary of the new papers about Neanderthal interbreeding

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

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 Leonardo N. M. Iasi and ManjushaChintalapati. Leo has a great summary of our main findings here:

@moorjani_priya Benjamin Peter Leonardo N. M. Iasi ManjushaChintalapati @SkovLaurits Mateja Hajdinjak @arevsumer This is a really cool study and I'm glad to see it come out!