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).

Lab News: Summer 2014

We’ve been having lots of fun lately in the lab.  Some recent highlights are (in a rough reverse chronological order):

  • We hosted the first Midwest Popgen Group meeting with the help of the great staff and students/postdocs here at U of C and organizing committee with Sebastian Zollner (U Michigan), Don Conrad (Wash-U), and Bret Payseur (U Wisc-Madison). We had approximately 80 attendees, from 20 different off-campus labs and 17 on-campus labs. Attendees drove in from Illinois, Michigan, Indiana, Missouri, Wisconsin, and Minnesota. There were 11 talks total, with 7 by grad-students/postdocs and 4 by assistant professors, and 15 posters.  We had a great set of talks and then a fun BBQ at the Point.  Mo Siddiq is preparing a website with photos from the event.  (7/19)
  • We have released a new teaching/research tool.  The Geography of Genetic Variants browser.  This is the hard work of our “programmer-at-large” Joe Marcus.  It’s also a pilot project for a grant we submitted earlier this summer to work on challenges that arise visualizing population structure in genomic-scale variation data.  (7/15)
  • Huffington Post article quotes me raising doubts about a recent PNAS paper on how genetics influence friend pairings (7/14)
  • Joel Smith and Hussein Al-asadi successfully defended their thesis proposals!
  • Genetics recently published an invited short perspective piece on the new fastSTRUCTURE paper in which I give an overview of work on the model behind STRUCTURE and its subsequent variants.  (7/1)
  • We have enjoyed some great summer conferences including the SMBE meeting in Puerto Rico back in June and a meeting with our SardiNIA project collaborators in Ann Arbor, Michigan earlier in July.
  • Darren Kessner and Eunjung Han submitted their final chapters for publication and successfully defended their PhDs!  Darren is off to a fantastic job at the elite Marlborough School in Los Angeles where he will be teaching math and expanding the computer science curriculum.   Eunjung (a.k.a. Christine) is now joining the excellent team at AncestryDNA developing tools for interfacing genealogical and genetic data. We had a big party in LA to celebrate their achievement and are wishing them the best as they move onwards in their new adventures!

Lab News: Trips and Visitors

I returned from a wonderful trip to India last week where I helped teach a population genetics workshop at the International Center for Theoretical Sciences at the Tata Institute in Bangalore.  Organizers Deepa Agashe and Kavita Jain did a fantastic job putting together the workshop and attached discussion conference.  I was able to meet lots of great students and researchers (a highlight was Kumarasamy Thangaraj who has done lots of great work on the population genetics of India).  Moreover, getting to spend time with the other instructors (Brian and Debra Charlesworth, Mike Whitlock, and Michael Desai) was a treat.  Afterwards, Richard Gomulkeiwicz and I stayed an extra day and gave talks at the National Center for Biological Sciences, and while there I caught up with Uma Ramakrishnan, a colleague of many years.  The NCBS has fantastic facilities and it’s clear there is a cadre of young faculty in Bangalore, like Deepa, Kavita, Uma, and Krushnamegh Kunte (and I’m sure others I didn’t meet) that are  making it an interactive and exciting place to do science.

In other lab news, I’m excited to announce Enrique Lessa has just arrived to my lab as a sabbatical visitor.  Enrique hails from the Evolution faculty at the Universidad de la Republica in Montevideo, Uruguay. He is a population geneticist who has worked extensively on the mammals of South America, particularly the fauna of Patagonia and Tierra del Fuego, and closer to Uruguay, the diverse and curious genus of tuco-tucos.  Enrique has long been interested in methodological issues in population genetics – from methods to survey DNA polymorphism to data analysis/interpretation problems (one of his most cited papers is on interpretation of multiple dimensional scaling of geographical data – a topic close to home for us here).  I first met Enrique in Berkeley (where he was once a postdoc with the legendary Jim Patton) – and then got to know him better in my visits to Uruguay.  It’s going to be a real pleasure to have his company here over the upcoming months.

Dog/wolf data


We’ve long hoped the data we generated for our recent PLoS Genetics paper would be a resource for studies in canid genomics.  We’ve had several requests for the data, and we now have an sftp site set up for accessing the data (vcf, bams, and fastq).  If you’d like access, please contact me or Adam Freedman.


More on dogs and wolves…

The good news:  Our recent paper on dog domestication has been recommended by F1000. Thanks to F1000 member Norman Johnson for taking note of our work!

The bad news:  Our paper was misinterpreted and misused by Ham during the Nye/Ham debate regarding creationism and evolution.  There are many angles on which one could respond, but I want to quickly reinforce:  We clearly see dogs are a close relative of wolves on the basis of DNA sequence similarity.  Everything we observe is consistent with a history of descent with modification and the very same figure he cited shows how dogs fit into an evolutionary tree with related lineages of wolves and a golden jackal.

More generally speaking as a geneticist: Numerous subtle predictions of evolutionary theory are borne out in DNA sequence data. As genome-scale sequences have finally become available to us, it’s been amazing to see how a single theoretical framework can predict so many patterns seen in these massive datasets.  It would be impossible to make sense of our observations without it.  In more practical terms, numerous advances in the understanding and treatment of heritable and infectious diseases, as well as in conservation biology, would not have been possible without an evolutionary framework for analysis and interpretation of data.

To read more, writer Stephanie Pappas has an article summarizing immediate scientific responses to the debate.  Find it here.

Wolf/dog genomes paper out


This last week we had our work on using wolf and dog genomes to understand dog domestication go to press!

Here’s a set of the relevant links to read more in depth:

  1. The main paper in PLoS Genetics.
  2. A nice paired perspective piece “How much is that in dog years” in PLoS Genetics from Greger Larson and Dan Brady.
  3. A great post from Ilan Gronau on how the multiple methods we used helped illuminate an overall picture of dog domestication.

And a big thanks to all the great researchers who contributed to this project, especially my former postdoc Adam Freedman who was first author on the project and colleague Robert Wayne who was the co-senior author with me.


Updated software and resources

A few maintenance items:

  • I have just moved the ENCprime software over to github and updated the link on the software/resources page.  This small piece of software computes a measure of codon usage bias for FASTA formatted sequences.
  • I also added to the software/resources a link to a github repository with several files that help reproduce the main figure of the Novembre et al (2008) paper as from time to time I get requests for some help along those lines.

And in lab news, there have been some nice developments: