Lab news: 2017

Here’s a running log of some of the major lab events of 2017 thus far:

  • PhD student Arjun Biddanda successfully defended his PhD proposal (5/17)
  • PhD student Evan Koch is participating in the NSF GROW program by spending a few months in Uppsala, Sweden where he is working in the lab of Hans Ellegren (5/17-7/17)
  • John gave a keynote at the Great Lakes Bioinformatics Meeting here in Chicago (5/17)
  • John served as an external examiner for the PhD of Jose Victor Moreno Mayar, a student of Eske Willerslev and Anna Sapfo Malaspinas in the GeoGenetics Institute in Copenhagen (5/17)
  • The SardiNIA/Progenia project had a paper led by Mauro Pala and Stephen Montgomery’s team published in Nature Genetics and the long awaited BAFF paper led by Maristella Steri and Francesco Cucca’s team was published in the New England Journal of Medicine! (5/17)
  • The search for a population geneticist in the Ecology and Evolution department is complete and we’re excited that Matthias Steinrucken will be coming this September to join our faculty! (5/17)
  • long interview article published by Quanta magazine featured John (4/17)
  • The lab enjoyed a visit from Erik Lundgreen, a PhD student with Peter Ralph, working on non-stationary isolation-by-distance problems (4/17)
  • We welcomed a new postdoctoral fellow Daniel Rice, who is part of the prestigious Chicago Fellows program! (3/17)
  • Evan and John’s paper on the impact of demography and selection on deleterious variation is out in G3. (3/17)
  • Joe Marcus and John travelled to the Gordon Conference for Quantitative Genetics where John gave plenary on their collaborative work (2/17)

Lab news: 2016 and part II 2015

Here’s a running log of some of the major lab news events of 2016 and 2015:

  • The lab enjoyed a week-long hackathon on the geographic distribution of genetic variants (12/16)
  • A new version of our “Geography of Genetics Variants” server has been posted that allow simple url-based query of a variant.  (12/16)
  • Our pre-print on demographic history and population structure of Sardinia is now on the bioRxiv.  (12/16)
  • Ben and John contributed to a large collaborative paper led by Tomas Marques on chimpanzee and bonobo genetics that is now published in Science. (11/16)
  • John spoke at the NAS/Kavli Frontiers of Science Symposium in Irvine.  (11/16)
  • Joe and John’s paper on the “Geography of Genetic Variants” server went online at Bioinformatics.  (10/16)
  • The whole lab travelled to Vancouver to attend and present at the annual ASHG convention. (10/16)
  • Hussein attended and presented at the Probabilistic Genomes meeting at Oxford. (10/16)
  • Ben and John’s review on fine-scale population structure in humans goes online at Current Opinions Genetics and Development as part of an excellent special issue edited by Anna Di Rienzo and Josh Akey. (9/16)
  • Arjun Biddanda and Joe Marcus officially joined the lab as our newest PhD students!  (9/16)
  • We hosted the 3rd annual Midwest PopGen meeting here at UChicago – it was once again a great amount of fun. (8/16)
  • Summer travel: Arjun, Joe, and John travelled to Sardinia to teach in the summer school short course on Complex Disease Mapping and had some excellent side adventuring.  Arjun, Joe, Hussein, and John all attended the Computational Genomics Summer Institute at UCLA.  Evan attended SSE in Austin and presented a poster. Joel did an internship on science policy in Brasilia, Brazil. (6/16-8/16)
  • PhD student Diego Ortega del Vecchyo crossed the threshold and defended his PhD – he’ll be greatly missed and is now onto a postdoctoral fellowship at UC-Berkeley. (6/16)
  • Charleston’s paper on the challenges of interpreting IBD tract lengths is published in G3. (5/16)
  • John, David Witonsky and Anna Di Rienzo submitted their report to the Army Corps of Engineers reanalyzing the aDNA data with regards to the origins of the Kennewick Man Sample (4/16).
  • Adam’s paper on the inferring regions of selection in early dog domestication is published in PLoS Genetics. (3/16)
  • Our paper with Desi Petkova and Matthew Stephens on visualizing migration surfaces (the EEMS method) was published in Nature Genetics. (1/16)
  • November issue of Nature Genetics highlights Sardinia genetics and includes two papers we contributed to! (11/15)
  • Ask-Me-Anything series on Reddit put John to the test. (11/15)
  • John was awarded a MacArthur fellowship!   Check out the video biography they did, with background cameos from various members of the lab.  (10/15)
  • Summer conference travel: Much of the lab attended SMBE in Austria where talks were given by Diego Ortega, Ben Peter, and myself and a poster was presented by Evan Koch.  Many of us also attended the second edition of the Midwest Population Genetics meeting, this time held at the University of Michigan.  Joel Smith attended SSE in Brazil where he gave a talk, and Ben Peter gave a talk at the ESEB meeting in Laussane (7/15, 8/15)
  • Lab programmer Joe Marcus spent three months of the summer in the lab of our collaborator Francesco Cucca in Cagliari, Sardinia as part of our work in the SardiNIA/Progenia project  (6/15)
  • The lab was awarded one of a new BD2K targeted software development awards based on our research proposal “Tools for Visualization of Geographic Structure in Population Genomic Data” (6/15)
  • John authored a News and Views article “Human evolution: ancient DNA steps into the language debate” (6/15)
  • The lab enjoyed a great 1-day retreat at the University’s Warren Woods research station. (6/15)
  • Former postdoctoral fellow Charleston Chiang did a tour in China and Taiwan giving talks, finished his fellowship, and transitioned to a new position at UCLA with Nelson Freimer (6/15).
  • Anna di Rienzo and John organized and hosted the Department of Human Genetics Mitchell Symposium with a focus this year on ancient DNA.  We enjoyed great talks from David Reich, Matthias Meyer, Tina Warriner, and Alan Cooper.  The event brought together a diverse audience on campus and was held in the University of Chicago’s home for archaeology, the Oriental Institute.  (5/15)
  • Johannes Krause visited for a Human Genetics seminar, and with Johannes we took a joy trip to see the Cahokia Mounds outside of “Mound City” (a.k.a. St. Louis).
  • Former PhD student Eunjung Han and Darren Kessner both had their final chapters put into press:

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.