Monthly Archives: January 2015

Lab News: 2015

As we start the New Year, I’m happy to share several updates from the lab:

  • We have had the addition of two new outstanding postdoctoral fellows:
    • Mark Reppell, a PhD graduate of the Department of Biostatistics at the University of Michigan under Sebastian Zollner and Mike Boehnke.  Mark brings to the lab substantial expertise on coalescent models of rapidly growing populations.
    • Ben Peter, a PhD graduate of the Department of Integrative Biology at the University of California-Berkeley under Monty Slatkin and Rasmus Nielsen.  Ben has been working extensively on spatial expansion models and will continue to work on spatial population genetic problems here.
  • PhD students Evan Koch, Hussein Al-asadi, and Joel Smith are now all past their qualifying exams.  This impressive trio also each has their own NSF Graduate Research Fellowship. Congratulations to them on all accounts!  We’re excited for what lies ahead now that they move into the full research phase of their PhD training.
  • As a group we all attended the ASHG meeting in San Diego and enjoyed the meeting immensely.  Beyond the science, we shared an airBnB house and took an afternoon to go surfing and both proved to be a lot of fun.  We have wrapped up our thoughts on the meeting in a small invited meeting summary that will appear in Genome Biology.
  • Our sabbatical visitor Enrique Lessa left us in the late summer, and he is greatly missed.  Thanks are due to Enrique for all the great company and wisdom he provided during his stay.  We hope he learned much during his visit, but I think the benefits were mainly ours.
  • Congratulations are due to recent PhD graduate Eunjung Han, who has had the final chapter of her PhD published: Fast and accurate site frequency spectrum estimation from low coverage sequence data and it describes algorithms that we are contributing to the Nielsen Lab’s angsd software for carrying out population genetic analyses on next-generation sequence.  She is now working as a Computational Biologist for ancestryDNA in San Francisco.
  • We have 3 posted new preprints on BioRxiv/arXiv:
    • The first is with lead author Darren Kessner and represents the culminating chapter of his PhD dissertation.  In the paper, he uses the forqs software he developed earlier to assess the power of artificial selection experiments for mapping the genetic basis of quantitative traits.  Thanks to the efficient simulation techniques we are able to evaluate how these methods would perform while explicitly modeling selection on multiple loci underlying quantitative traits.
    • The second is with lead author Desislava Petkova and senior author Matthew Stephens. Matthew and I began on this problem of identifying barriers in isolation-by-distance settings as part of the original intention of my postdoc with him back in 2006.  I got distracted by the POPRES data and understanding PCA, and it wasn’t until Desi stepped in later that this project really got fleshed out and evolved into something quite beautiful.  It was the major work of her PhD dissertation at the University of Chicago.  We’re excited for the methodology and possible applications of the software.
    • The third is from lead author Charleston Chiang, a postdoctoral fellow in the group with collaborator Peter Ralph.  It treats the challenges of interpreting the lengths of inferred IBD tracts, as they are sometimes made up of two or more shorter IBD tracts that are confused for a single contiguous one (conflated in our terms).  This has real consequences for approaches that try to build inferences by converting lengths into times to common ancestry and the paper stresses the need to apply appropriate filters or modeling steps to avoid being misled.
  • Finally, a collaborative paper with Wen-Yun Yang, Eleazar Eskin, Bogdan Pasanuic, and members of my group (Alex Platt and Charleston Chiang) on spatial localization of recent ancestors of admixed individuals has been published in G3.  This paper extends the SPA framework we previously developed to have a local ancestry HMM (akin to Falush et al 2003 model but with ancestry described using continuous locales in place of discrete source populations).