People in the Petrov Lab

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Principal Investigator

Dmitri Petrov is a Michelle and Kevin Douglas Professor of Humanities and Sciences in the Biology Department at Stanford. He received his Ph.D. in 1997 from Harvard University under the guidance of Daniel Hartl and Richard Lewontin. He was a Junior Fellow at the Harvard Society of Fellows and a Research Fellow in the Genetics Department at Harvard Medical School under the guidance of Chao-Ting Wu. Dmitri came to Stanford in 2000 as an Assistant Professor. Petrov Lab does theoretical, computational and experimental work to address questions in molecular evolution and molecular population genetics. The primary focus at the moment is on (i) population genetics and molecular mechanisms of adaptation and (ii) genome evolution. For projects and papers in the Petrov Lab please visit the Research and Publications pages. Petrov CV is here. E-mail: dpetrov@stanford.edu.

Administrative Assistant

Elena Yujuico is the Petrov Lab Administrator (2013-now). Elena has extensive experience working in higher education administration, at both Stanford University and at the University of Texas. Elena provides expert administrative support for the lab's research and education activities. For questions about the lab, please email elenay@stanford.edu

Amanda Sargent was the Petrov Lab Administrator (2011-2013). Amanda has extensive experience in higher education including working at the University of Utah, Sacramento State, and Stanford. She makes sure everything is running smoothly. If you have questions about our lab please email her at sargent4@stanford.edu

Research Assistants

Jane Park is a Research Assistant in the Petrov Lab (2011-now).  Jane received her undergraduate degree in biology from Wellesley College, where she worked with Heather Mattila and Martina Koniger. She is interested in learning about the intersection of molecular, theoretical, and environmental components of evolutionary biology, and is now working with Drosophila to enter this field.

Postdoctoral Fellows

Josefa Gonzalez is a Ramon y Cajal Researcher (akin to an Asistant Professor) at the Institute of Evolutionary Biology (IBE) in Barcelona. IBE is a joint institute between the CSIC (Spanish National Research Council) and the UPF (Pompeu Fabra University) and is part of the PRBB (Barcelona Biomedical Research Park). Josefa is primarily interested in genome evolution with a focus on structural variation induced by transposable elements. During her time as a Postdoctoral Fellow in the Petrov Lab (2005-2011) Josefa focused on the understanding of the adaptive role that transposable elements (TEs) play in Drosophila. She spearheaded the first genome-wide screen for recent TE-induced adaptations in D. melanogaster. Using several independent criteria she identified a set of 13 adaptive TEs and estimated that ~25-50 TEs have played adaptive roles since the migration of D. melanogaster out of Africa. This paper was published in Plos Biology in 2008 (here is a blog article about this paper). Josefa is continuing to collaborate with our lab on the project to discover all of the adaptive TEs and uncover general patterns of TE-driven adaptation. Josefa also collaborated with Anna Fiston-Lavier on the methods of identification of TEs from next-generation sequencing data (the package is called T-lex and the paper can be found here). She also coauthored two papers in MBE in 2008 and 2009 on ways to distinguish adaptive TE insertion from neutral ones, a more in-depth analysis of one adaptive TE inserted near several conserved developmental genes, and coauthored a major study that convincingly showed that ectopic recombination between TEs is the source of purifying selection acting against TEs. Josefa's website can be accessed here. She is curently looking for postdoctoral and predoctoral students. Please send her an email if you are interested.

James Cai is an Assistant Professor in the Department of Veterinary Integrative Biosciences at Texas A&M University. James is interested in the elucidation of genotype-phenotype relationships using computational genomics approaches. His lab seeks evolutionary interpretation of causal and associated variants underlying genetic disorders and complex traits of different organisms. During his time as Postdotoral Fellow in the Petrov Lab (2006-2010) James discovered the first clear signatures of recurrent adaptation in the patterns of human genetic variation, worked on understanding of patterns of evolution of genes of different evolutionary age, and peculiar network and evolutionary properties of genes that can underlie human disease. James develops various statistical tests and computational tools to understand the processes shaping genome variability patterns within and between species and maintains three Matlab toolboxes for population genetics, molecular evolution, and systems biology. The website of his lab at Texas A&M can be accessed here. The lab news story about James can be found here.

Ruth Hershberg is a Senior Lecturer (akin to an Associate Professor) in the Ruth & Bruce Rappaport Faculty of Medicine at the Technion (Israel Institute of Technology), Haifa, Israel. During her time as a postdoc in the Petrov Lab (2006-2011), Ruth studied the ways in which purifying selection changes within and between different organisms. She has demonstrated that the strength of selection changes between different strains of E. coli and Shigella and causes significant differences in the rate of gene loss; that M. tuberculosis evolve under extremely reduced purifying selection, leading to a large proportion of differences among M. tuberculosis strains having functional consequences; that mutation is universally biased towards AT and that the genomic GC content variation in bacteria is most likely driven by selection; and that the choice of optimal codons across organisms is driven by selection at the level of the genomic GC content. She received her Ph.D. from Hebrew University (summa cum laude) under the guidance of Hannah Margalit. The website of her lab in Technion can be accessed here. The lab news story about Ruth can be found here.

Philipp Messer is a Research Associate in the Petrov Lab (2008-now). He joined the lab in 2008 as a Postdoc after obtaining his PhD at the Max-Planck Institute for Molecular Genetics in Berlin with Peter Arndt. The focus of Philipp's research lies in understanding the role of adaptation in molecular evolution, which he addresses through theory and the analysis of population genomic data. His studies have provided diverse lines of evidence that adaptation is at times pervasive, often rapid, and frequently involves mutations of large selective effects. Philipp has shown that in many species adaptation should in fact not be limited by the availability of individual mutations, explaining why phenotypic adaptation such as the evolution of pesticide resistance can occur on surprisingly short ecological time-scales. He has also shown that rapid adaptation often proceeds in complex modes, such as soft selective sweeps or balancing selection. More information about Philipp's research can be found on his personal website.

Anna-Sophie Fiston-Lavier is an Assistant Professor at the Institute of Science of Evolution in Montpellier (ISEM). Anna's research is focused on the impact of structural variation and repetitive elements on genome function and evolutionary adaptation. While in the Petrov Lab (2008-2013) Anna developed the T-lex package for TE discovery, annotation, and population analysis using NGS data and worked on a number of projects focused on TE function and evolution. She received her Ph.D. from the Pierre and Marie Curie University in Paris under the guidance of Hadi Quesneville in 2008. She investigated the evolutionary dynamics of Transposable Elements (TEs) and their impact on genome structure and evolution combining comparative genomic and phylogenomic approaches. She showed that the gene density is the main force that shapes the TE sequence evolution in Arabidopsis thaliana. Her analysis of segmental duplications in Drosophila melanogaster contributed to propose a mechanistic model of segmental duplication formation based on non-allelic homologous recombination. She provided evidences of TE role in the duplication formation (Fiston-Lavier et al Genome Research 2007). Infering the evolutionary events that have led to the formation of a new operon-like cluster from A. thaliana, she also showed the role of TEs in the formation and the maintenance of duplications (Field, Fiston-Lavier et al PNAS 2011). Anna's research project is to investigate the contribution of TEs on genome adaptive evolution developing accurate and powerful computational tools for TE dynamic analysis. She started designing an interactive tool to estimate the recombination rate along the D. melanogaster genome sequences (Fiston-Lavier et al Gene 2010). Using this tools, she were able to investigate the TE evolutionary dynamics in Drosophila (Petrov, Fiston-Lavier et al MBE 2011 ). She then developped a computational pipeline for TE annotation in population using next-gen sequencing data (Fiston-Lavier et al NAR 2010).

Fabian Staubach is an Assistant Professor at the University of Freiburg in Germany's beautiful black forest. The Biology department at the University of Freiburg is supported by the German “Excellence Initiative”, a program that supports only the best Universities in the country. While in the Petrov Lab (2010-2013) Fabian studied the bacterial flora associated with Drosophila in the wild and in the lab. During his PhD at the Max Planck Institute for Evolutionary Biology Fabian studied the evolution of gene expression in house mice and discovered a new gene, which emerged from noncoding sequence in the house mouse lineage. In the Petrov Lab Fabian studies the bacterial flora associated with Drosophila and its contribution to adaptive evolution of the host.

Alan Bergland is a Postdoctoral Fellow in the Petrov Lab (2010-now). His research aims to integrate the role of environmental variation with long- and short-term evolutionary processes through an understanding of the genetics, physiology, and morphology that regulate life histories. During his graduate work at Brown University under the guidance or Marc Tatar, Alan focused on the relationship between larval nutrition and adult fecundity in Drosophila melanogaster. This research used a combination of evolutionary demography, ecology, molecular and quantitative genetics, and physiology to investigate how life history plasticity evolves in natural populations. As a post-doc, he is investigating the evolution of D. melanogaster and D. simulans in temperate environments. One aspect of this project focuses on exploring the demographic consequences of seasonal population booms and busts. The other aspect focuses on identifying the location, function and evolutionary history of alleles underlying adaptations to temperate environments. The link to his website with more details is here.

David Enard is a Postdoctoral Fellow in the Petrov Lab (2011-now). He is broadly interested in finding new methods to characterize the prevalence of positive selection. During his PhD in Hugues Roest Crollius's lab at the École normale supérieure in Paris he developed a comparative population genomics approach that allowed him to demonstrate that vertebrates as distant as human and pufferfish often adapt with the same genes. In the Petrov Lab, David focuses on detecting positive selection in the human genome as well as on new approaches to detect selection from frequency changes over very few generations.

Jamie Blundell is a Postdoctoral Fellow in the Daniel Fisher Labs (2013-now). He received his Ph. D. from the University of Cambridge in theoretical physics, studying the statistical physics of biological polymers and their networks. His research now focuses on evolutionary dynamics, using both theoretical and experimental approaches. At Stanford he worked colsely with the Petrov lab (was a postdoc here 2012-2013), Sasha Levy and Gavin Sherlock on lineage tracking in barcoded yeast populations, where one can infer to a high degree of accuracy the distribution of fitness effects over time. He also collaborated with Zoe Assaf on understanding staggered sweeps.

Pleuni Pennings is a Research Associate in the Petrov Lab (2012-now). She studies the evolution of drug resistance in HIV using genetic and epidemiological data and population genetic theory. She has analyzed the role of standing genetic variation for drug resistance in HIV (Pennings, 2012) and currently works on selective sweeps and mutation-selection balance in HIV. Before joining the Petrov lab, she worked with John Wakeley at Harvard University and with Susanne Foitzik at the University of Munich (LMU). Her graduate work with Joachim Hermisson let to a series of seminal papers on the genetics of adaptation. With these papers they coined the term "soft sweep" (Hermisson and Pennings, 2005; Pennings and Hermisson 2006a and 2006b). Pleuni also makes videos about science. A video about her recent HIV paper can be found here (https://vimeo.com/43346265), one about recent work on slavemaking ants is here (http://www.youtube.com/watch?v=zTzX-P14zxI) and an old favorite about experimental evolution is here (http://www.youtube.com/watch?v=OjI5ZglXJLE). The link to her website is here (http://pleunipennings.wordpress.com/).

Ryan W. Taylor is a Postdoctoral Scholar in the Petrov Lab (2013-now). During his PhD at Michigan State University he studied animal personality in a wild population of red squirrels that experience a temporally flucutating environment. This research used a combination of quantitative genetic, selection and mate-choice analyses (with a lot of field work!) to investigate the importance of personality to red squirrel fitness and possible mechanisms that might maintain genetic variation in personality. In the Petrov lab Ryan is lerning molecular evolutionary techniques while studying Drosophila melanogaster populations sampled temporally within and across years. He will also sequence the red squirrel genome (Tamiasciurus hudsonicus) in order to bring population genomic techniques to the model Kluane red squirrel system. More information about Ryan's research can be found on his website.

Dave Yuan is a Postdoctoral Fellow in the Petrov lab (2014-now). He is broadly interested in the role mutation plays in evolution. In his PhD work with Trisha Wittkopp at the University of Michigan, he investigated the effects of novel mutations and polymorphisms on expression of a glycolytic gene in Saccharomyces cerevisiae in order to understand how the mutational process shapes variation in gene expression and, ultimately, phenotypic evolution. Specifically, he compared the effect sizes of cis- and trans-regulatory mutations, tested for evidence of selection among natural cis-regulatory variation using a mutation spectrum built from the novel mutations, and characterized the impact of genotype-by-environment interaction and epistasis on mutational effect. In the Petrov lab, Dave is shifting focus to the dynamics of the mutational process in terms of fitness—the ultimate phenotype in evolution—on a genome-wide scale using lineage tracking with molecular barcodes in yeast. Using this system, he is planning to address questions regarding 1) overdominance in the effects of adaptive mutations on fitness and 2) how interactions between and among genetic backgrounds and the environment affect short- and long-term evolutionary trajectories of adaptive mutations.

Graduate Students

Jerel Davis is a Principal at a venture capital firm, Versant Ventures, in Menlo Park. He was a graduate student in the Petrov Lab from 2000-2005 where he pursued both computational and wet lab projects, studying molecular evolution at the genome scale and focusing much of his time on gene duplication. Prior to Stanford, Jerel was a researcher at Amgen and did his undergraduate degree at Pepperdine University where he majored in Biology and Mathematics. From Stanford, Jerel joined McKinsey and Company where he served as a Junior Partner advising healthcare corporations in pharmaceuticals, biotechnology, medical device, and molecular diagnostic fields. During his 6 years at McKinsey, he worked in a number of geographies including the US, Europe, China, Russia, and India. In 2011, Jerel joined Versant Ventures where he specializes in venture capital biotechnology investing.

Nadia Singh is an Assistant Professor in the Department of Genetics at North Carolina State University. She was a graduate student in the Petrov Lab from 2001-2006. Nadia did her undergraduate work at the University of Chicago and Harvard. Prior to joining the lab, she was working as a research technician in the Program for Population Genetics at the Harvard School of Public Health. Nadia's research in the Petrov lab focused on molecular evolutionary genomics in Drosophila. In particular, Nadia investigated variation in single nucleotide substitutional patterns both within and between species, and the implications of this variation for genome evolution. After receiving her Ph.D. from Stanford, Nadia did a postdoc with Andy Clark and Chip Aquadro at Cornell University in the Department of Molecular Biology and Genetics. Nadia joined the faculty of the Department of Genetics at North Carolina State University in 2010 as an Assistant Professor. Her research continues to focus on the joint and individual roles of non-selective evolutionary forces to genome evolution in Drosophila, with a particular interest on recombination rate variation. You can learn more about Nadia's current research here.

David Lawrie is a Postdoctoral Fellow in the lab of Sergey Nuzhdin at USC. While in the Petrov lab David was a Graduate Student in Petrov Lab (2007-2013) working primarily on the inference of functionality from genomics data. One of his most exciting discoveries was the finding that a fifth of all synonymous sites in Drosophila appear to be suject to very strong selection constraint. This paper was published in PLoS Genetics. In addition, David showed that weak selection and mutational biases can produce unexpected results with, for example, unconstrained sequences evolving slower than constrained ones in the absence of adaptation. The news report about this work can be found here. David did his undergraduate work in computational biology at Cornell with Andy Clark and Adam Siepel and came to Stanford Genetics Department as a graduate student in 2007.

Diamantis Sellis is a Graduate Student in Petrov Lab (2007-now). Diamantis focuses on the effects that diploidy has on the process of adaptive evolution using both modelling and experimental evolution in yeast. He showed that adaptation in diplods might lead to a high prevalence of transient balancing selection and maintenance of much greater amounts of consequential genetic variation than would be expected in haploids. This work was published in PNAS in 2011 and the news report about it can be found here. The experimental evolution work is in progress.

Yuan Zhu is a Graduate Student in Petrov Lab (2008-now). Yuan Zhu did her undergraduate work at Duke with Susan Alberts and came to Stanford Genetics Department as a graduate student in 2008. In the Petrov Lab she focused on the application of next-generation sequencing of whole pooled populations for asking a broad range of questions in genomic evolution, including areas such as genotype phenotype interaction, evolution of complex traits, and population genetics. She showed that pooled resequecing is a remarkably efficient and precise tool for the estimation of allele frequencies and is using this technique now to (i) identify deleterious mutations in mutation-accumulation lines of yeast, (ii) assess genetic variation across S. cerevisiae, and (iii) estimate patterns of mutation using both natural polymorphism and mutation-accumulation data.

Nandita Garud is a Graduate Student in Petrov Lab (2009-now). Nandita did her undergraduate work in computational biology at Cornell with Andy Clark and came to Stanford Genetics Department as a graduate student in 2009. She is interested in understanding how genetic diversity is maintained in a population. Currently, Nandita is studying “soft sweeps” in Drosophila in which whereby multiple copies of a beneficial allele rise in frequency in a population simultaneously. She is also working on a project to characterize the prevalence of balancing selection in the butterfly species, E. gillettii. In her work in the recent past Nandita worked on identifying RNA editing sites in humans and on the demographic inference of rice. She also concurrently completed an M.S. in Statistics at Stanford. The link to her website with more details is here.

Heather Machado is a Graduate Student in Petrov Lab (2010-now). She received both her B.S. and M.S. from Portland State University where she worked with Mitch Cruzan and then worked as a Research associate in Suzy Renn's lab at Reed. Heather joined the Stanford Biology Department as a graduate student in 2010. In the Petrov Lab she is planning to work on understanding adaptation particularly in the context of recent radiations or environmental shifts.

Sandeep Venkataram is a Graduate Student in Petrov Lab (2010-now). He received his B.S. from the Washington University in St.Louis where he worked with Justin Fay. In the Petrov Lab Sandeep is using artificial evolution in yeast to shed light on the patterns of compensatory evolution.

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.

Zoe Assaf is a Graduate Student in Petrov Lab (2010-now). Zoe did her undergraduate work in molecular and developmental biology at Berkeley and then stayed a year working as a Research Technician in Zac Cande's lab. Zoe came to Stanford Genetics Department as graduate student in 2010. Zoe is interested in studying the theoretical, computational, and experimental aspects of evolutionary biology. Shew is combiningmodelling and experimental evolution in Drosophila to study adaptation from standing variation.

Jacqueline Ou was a Graduate Student in Petrov and Sherlock Labs (2010-2011). Jackie did her undergraduate work in mathematics at Duke and then spent several years working for a number of companies (Foundation Medicine / Third Rock Ventures, Bain & Company, HIV/AIDS Initiative in Southern & Eastern Africa at Clinton Foundation). Jackie came to Stanford to pursue her graduate work at Stanford Genetics Department in 2010. Jackie is interested in the potential repeatability and predictability of evolution, using both theoretical and directed evolution approaches. Recent literature has theoretically suggested that evolutionary paths to drug resistance are constrained by their fitness landscapes in various settings. Working in both the Petrov and Sherlock laboratories, she is interested in experimentally exploring whether these theoretical models are accurate and in further developing theoretical approaches to predict evolution in constrained fitness landscapes. Jackie is currently on leave.

Rajiv McCoy is a Graduate Student in the Boggs and Petrov Labs (2010-now). He received his B.S. in Biology and Ecosystem Science & Policy from the University of Miami where he worked in Barbara Whitlock's lab. Rajiv is interested in evolution of small populations, working at the intersection of evolutionary and ecological genomics. His current project in the Petrov lab investigates the prevalence of balancing selection in an introduced population of the checkerspot butterfly Euphydryas gillettii.

Alison Feder is a Graduate Student in the Petrov Lab. She did her undergraduate work in mathematics at the University of Pennsylvania with Joshua Plotkin and spent a year at Oxford studying statistical genetics in the group of Gilean McVean. Alison is interested in understanding how selection acts on quantitative trait loci in different environments and the role epistasis plays in shaping fitness landscapes.

Yuping Li is a Rotation Graduate Student in the Petrov Lab. She did her undergraduate study in Bioinformatics at Huazhong University of Science and Technology, China. Then she spent two years working as a research assistant in Dr. Hong Zhang's lab. Yuping is interested in understanding the dynamics of adaptive evolution by using barcoded yeast populations.

Undergraduate Students

Talia Karasov is a Graduate Student at the University of Chicago in the laboratory of Joy Bergelson. Talia did her undergraduate work at Stanford, and joined the Petrov lab during her Sophomore year in 2006. She also worked as a research assistant in the lab on a joint project with Gretchen Daily. Her research in the lab focused primarily on the evolution of insecticide resistance in Drosophila. The work culminated in a paper published in PLoS Genetics that challenged the conventional wisdom and suggested that adaptation in Drosophila is not mutation limited and that Drosophila populations are more than 100-fold larger in their effective size than was previously thought. The news story about this work can be found here. In 2009 she moved to Chicago to start her PhD. She is currently investigating the evolution of host-pathogen interactions in Arabidopsis.

Philip Bulterys is currently a second-year MD/PhD student in the UCLA/Caltech Medical Scientist Training Program (MSTP). He received his B.S. in Biology from Stanford University in 2010, and worked on an HIV evolution project in the Petrov lab from 2008 to 2010. He is interested in the ecology and evolution of infectious diseases and firmly committed to public health. Philip is a recepient of the Paul & Daisy Soros Fellowship for New Americans.The lab news story about Philip can be found here.

Felicia King Felicia King is an Undergraduate Student in Petrov Lab (2010-now).  Felicia is currently studying adaptation of Drosophila to local climate change in Northern California populations under the guidance of Postodoctoral Fellow Alan Bergland. To test for local adaptation, Felicia is collecting flies along an elevational gradient from the Central Valley to the Sierra Nevadas and assays them for genetic markers and traits known to be winter-adaptive.