Mailund on the Internet

The paper has been available as “advanced access” for a while, but now it is out in its finished form: Ancestral population genomics: The coalescent hidden Markov model approach.

A short description, from the issue highlights:

Ancestral population genomics: The coalescent hidden Markov model approach, pp. 259–274

Julien Y. Dutheil, Ganesh Ganapathy, Asger Hobolth, Thomas Mailund, Marcy K. Uyenoyama and Marcy K. Schierup

The genealogy varies along the genome of species with close speciation times and large ancestral population sizes. Information on population genetics processes and the speciation process itself can therefore be extracted from genomic alignments, particularly when there is incomplete lineage sorting, i.e., part of the genome has a different tree than the species tree. These authors develop a framework for inferring ancestral population genetics parameters from an alignment of four species, using a hidden Markov model and coalescent arguments. They investigate the properties of the model by extensive simulations and apply it to human-chimp-gorilla-orangutan alignments.

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I’m off to Leipzig to visit Svante Pääbo’s group at the Max-Planck Institute there, to try to get in on future Neanderthal analysis.

The first Neanderthal paper should be out soon(ish) so of course it is too late to get in on that, but we hope to be able to use our CoalHMM methodology on future data.

I don’t know how much I will be able to blog while away, so you might not hear from me for a few days… we will see.

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