Applied to humans, we identify e.g. a human lineage expanding ~50kya outside & within Africa and a much deeper event between two hominin groups impacting Neanderthals & ancestral modern humans; remarkably the two predominant PRDM9 alleles in humans today evolved separately in each of these groups!
Individuals are modelled as mixtures of (ghost) ancestors and we simultaneously infer their local ancestry contributions. Additionally, we propose looking at "types of mutations" in each of the ancestry segments, which is not used in GhostBuster, to provide independent evidence for these events.
Very honoured and I owe a lot to all my mentors and colleagues, thank you!
New preprint led by Hrushikesh Loya, me, and Simon Myers where we introduce GhostBuster! www.biorxiv.org/content/10.6...
The idea is to find all the different ways a target individual relates to reference groups in genealogies, to "bust the ghosts" in our ancestry.
Postdoc position in my group in Tokyo!
Please get in touch if you are interested.
And happy to discuss projects - these would range from developing new methods to analysis of new genomes that we are now sequencing in the lab.
Job Ad: www.riken.jp/en/careers/r...
Lab page: speidellab.github.io
New ad for an independent postdoc in mathematics/statistics/machine learning for Biology in my institute at RIKEN (not my lab), ranging from 3 to 7 years. Our institute is entirely English-run, and a good mix of expertise on maths/physics/stats/bio! www.riken.jp/en/careers/r...
1/ New paper out in Nature Communications!
We studied the salivary amylase gene, AMY1, in Indigenous Andean populations and found evidence that high AMY1 copy number rapidly increased in frequency, likely through recent positive selection.
doi.org/10.1038/s414...
Postdoctoral job announcement: come to Cambridge and work on population genetic modelling with environmental and ancient DNA, jointly with @gamzeandgursoy.bsky.social and me. Details at www.jobs.cam.ac.uk/job/55580/ - applications by June 16th.
šŗš§ŖPreprint of 1039(!) whole ancient human genomes from Britain, mainly dating to 1st Millennium CE, representing the best part of 7 years of my life. Herculean effort by @marinasdsilva.bsky.social to get this over the line. 'Migration Period' is more migrationy than we could have possibly imagined.
Our preprint is now out, looking at genomic history and selection in Britain, with a focus on the Roman and early medieval periods. Comments welcome!
www.biorxiv.org/content/10.6...
@boothicus.bsky.social @leospeidel.bsky.social @pontus-skoglund.bsky.social
The salivary amylase gene exhibits copy-number variation linked to dietary shifts. Here, the authors describe an adaptive expansion of the amylase gene in Indigenous Andean populations coinciding with...
Research Associate in Population Genetics Modelling and Environmental DNA (Fixed Term) in the Department of Applied Mathematics and Theoretical Physics at the University of Cambridge.
