April 30th: Ben Wilson: Soft selective sweeps in complex demographic scenarios

Ben Wilson

Ben Wilson

Ben Wilson is a Graduate Student in Petrov Lab (2010-now). He received his B.S. from the University of Arizona where he worked with Joanna Mazel. Ben is interested in the theoretical population genetics of adaptation, particularly in populations that fluctuate in size over various time-scales. He is also interested in how complex adaptive landscapes contribute to the evolutionary trajectories we see in adaptation. Ben uses a combination of theoretical approaches with experimental evolution and genomic inference to test theoretical predictions.

Talk: Soft selective sweeps in complex demographic scenarios

Frequent mutation can cause multiple copies of a beneficial allele to arise in the population before the allele has swept to fixation,
producing a so-called ‘soft’ selective sweep. While this process is well understood in the case of populations that are constant in size through time, it is not currently known how soft selective sweeps behave in populations that fluctuate in size. We describe some of the important phenomenological behavior of soft selective sweeps in fluctuating populations and provide a generalized framework for calculating the probability of observing a soft sweep in populations under complex demographic scenarios. In particular we find that soft sweeps can be ‘hardened’ by strong, recurrent population bottlenecks and that strong selection is more likely to produce soft sweeps than weak selection when population fluctuations are common.

Seminar details

Wednesday April 30th, 2014
1:15 PM Seminar (no lunch, sorry!)
Location: Clark Auditorium

April 23rd, Joachim Hermisson: The genetic basis of phenotypic adaptation: Adaptation to a moving optimum

Joachim Hermisson will speak on the 23rd of april about  adaptation to a moving optimum.

Joachim Hermisson will speak on the 23rd of april about adaptation to a moving optimum.

Joachim studied Physics and Philosophy and did a PhD on Quantum Phase Transitions before he switched to model Real Life. He worked with Günter Wagner at Yale and started his own junior research group in Munich in 2002. In October 2007, he started his position as a Professor of Mathematics and Biosciences at the University of Vienna. Joachim’s work is on theoretical population genetics where he combines molecular and phenotypic approaches. His most recent work focusses on the conditions for adaptation in variable environments and on models of speciation with gene flow. Joachim’s website.

Talk: The genetic basis of phenotypic adaptation:
Adaptation to a moving optimum

Does adaptive evolution proceed in many small steps or in fewer, but larger steps? The distribution of adaptive step sizes has been a
contentious issue in evolutionary research since it early days. On the theoretical side, models by Fisher, Gillespie, and Orr have shaped our intuition has to what we should be expect for a single adaptive bout. However, all these models assume that adaptation responds to a single, sudden shift in the environment. In my talk, I’ll consider the opposite case, where a phenotypic trait follows a gradually moving optimum. I’ll summarize some older and very recent results and discuss how our intuition about adaptive step sizes under these conditions should differ.

[Joint work with Michael Kopp and Sebastian Matuszewski]

Seminar details

Wednesday April 23rd, 2014
1:15 PM Seminar (no lunch)
Location: Clark Auditorium

April 16th, Caitlin Pepperell: Evolution of Mycobacterium tuberculosis

Caitlin Pepperell, University of Wisconsin-Madison

Caitlin Pepperell, University of Wisconsin-Madison

Caitlin Pepperell is an evolutionary biologist who focuses on pathogenic microbes. She is curious about a range of topics, including pathogen emergence, the evolutionary influences shaping extant pathogen populations, the impact of pathogenic microbes on human evolution, and the role of human genetic variation in determining the outcome of infections. Work in the Pepperell lab centers on analysis of genomic and other data from natural populations of microbes and hosts. Pepperell is also a practicing infectious diseases physician, who has worked on the front lines of several epidemics.

Pepperell received her B.A. in English Literature from McGill University in Montreal, and her M.D. from Queen’s University, in Kingston, Ontario. She completed specialty training in internal medicine at the University of Toronto, and subspecialty training in infectious diseases at the University of Toronto and Stanford. Her post-doctoral research training was also at Stanford, where she was mentored by Marc Feldman and studied evolution of M. tuberculosis in Canadian First Nations. She left Stanford in 2011 to start her own lab at the University of Wisconsin-Madison, where she is an assistant professor in the departments of Medicine and Medical Microbiology and Immunology.

Talk: Evolution of Mycobacterium tuberculosis

Mycobacterium tuberculosis is an obligate human pathogen and major threat to global public health. Evolution of this bacterium is shaped by the hostile, dynamic environment within individual hosts, the complex ecology of tuberculosis, and broad scale changes in host biology and connectivity.  I will discuss the state of the M.tb evolution field, with an emphasis on open questions and controversies. These questions are important in their own right; I also argue for a role of evolutionary population genomic approaches to tackling the global TB crisis.

Seminar details

Wednesday April 16th, 2014
1:00 PM Lunch outside the Clark Auditorium, food cannot be taken inside (sign up below)
1:15 PM Seminar
Location: Clark Auditorium

April 9th, Adi Stern: Costs and benefits of mutational robustness

Adi Stern

Adi Stern

Adi is a post-doc working with Raul Andino in UCSF and Rasmus Berkeley in UC Berkeley. Her interests lie in understanding the “arms-race” evolution of viruses and their hosts. Adi received a B.Sc. in Biology and Psychology, and an additional B.Sc. in Math, from Tel-Aviv University. In her PhD research with Tal Pupko, she developed phylogenetic models of evolution, and used them to study adaptationin different HIV strains. Next, during a postdoc in the Weizmann institute with Rotem Sorek, she studied the evolution of the CRISPR antiviral system, and documented diversity of phages and CRISPRs in the human gut microbiome. Currently, Adi combines population genetics theory with experimental evolution to study the constraints governing the evolution of “mutant-clouds” of RNA viruses. In Oct. 2014 Adi is starting a research group in Tel Aviv University, where she plans to continue combining theory with experimental evolution to study how viruses of all types and forms adapt to continuously changing environments. For more information, have a look at her website.

Talk: Costs and benefits of mutational robustness

Hidden genetic variability, in the form of neutral mutations, is thought to facilitate evolution by providing a reservoir of potentially adaptive alleles. Mutational robustness, which is the ability of a population to buffer deleterious mutations, determines the neutral variability in a population. Here we focus on a particular type of robustness, namely multiple viruses replicating in the same cell. During high multiplicity of infection (MOI), complementation between virus variants can buffer the effect of detrimental mutations. We examine this prediction by comparing populations of RNA viruses grown at high or low MOI.  Comparison of the minor allele composition of these populations demonstrated that indeed high MOI buffers detrimental mutations. Next, guided by these experimental results, we developed a theoretical framework to compare the evolutionary behavior of robust viral populations and non-robust, i.e. brittle, populations as they adapt to the challenges of an environmental change. We find that robust populations adapt more rapidly but purge novel deleterious mutations more slowly. Brittle populations are better prepared to adapt if neutral alleles in a given environment become predominantly deleterious in a new environment. Whether mutational robustness facilitates or hinders adaptation to a new condition depends on the ratio of beneficial to detrimental mutations hidden within the “neutral” genetic variability in the starting population. We illustrate different types of environmental changes where mutational robustness, or lack there of, plays a role in viral adaptation. Thus, under certain conditions, diversity may actually be an impediment for viral adaptation.

Seminar details

Wednesday April 9th, 2014
1:00 PM Lunch (sign up below)
1:15 PM Seminar
Location: Clark Center S360
If you would like to speak with Adi, contact Pleuni Pennings (pleuni@stanford.edu)