Dmitri Petrov is a Michelle and Kevin Douglas Professor of Biology and the Director of the Program for Conservation Genomics. 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, was promoted to Associate Professor in 2005, Professor in 2009, and Michelle and Kevin Douglas Chair in the School of Humanities and Sciences in 2011. Petrov Lab does theoretical, computational and experimental work to address questions in molecular evolution and molecular population genomics. The primary focus at the moment is on the process of rapid evolution. Our experimental systems include seasonal adaptation in Drosophila (in collaboration with Prof. Paul Schmidt), experimental evolution in yeast, and the mouse model of lung cancer (in collaboration with Prof. Monte Winslow). For papers from the Petrov Lab please visit the Publications page. Petrov CV is here and Petrov Biosketch is here. Google Scholar Page is here. E-mail: dpetrov@stanford.edu.

Susan Mello is the Petrov Lab Administrator (2015-now). Susan is originally from Boston and joined Stanford most recently from Atlanta, where she worked as an admin in an accounting firm. She has more than 12 years of experience supporting high-level partners, executives, and managers in the public and private sector. Susan's family recently relocated to the Bay Area in September. Here is what Susan says about herself: "I am very excited and extremely lucky to be a part of the Stanford community. I look forward to a long-term career at Stanford, especially with the Biology department." For questions about the lab, please email somello@stanford.edu

Elena Yujuico is the Petrov Lab Administrator (2013-2014). 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

Jane Park is a graduate student at UC Davis. She was a Research Assistant in the Petrov Lab (2011-2014). 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.

Susanne Tilk is a graduate student in the Petrov and Curtis Labs where she is working on the role of purifying selection and deleterious passenger mutations on the evolution of cancer. She was a research assistant in the Petrov Lab (2014-2017) and worked on a number of projects primarily related to our effort to understand pattersn of seasonal adaptation in Drosophila. Susanne received her B.S. in Cell and Developmental Biology from UCSB, where she worked with Tom Turner studying the genetics basis of different behavioral preferences within Drosophila. She is primarily focused on cancer biiology and how non-recombining somatic tumorlineages manage to survive the constant barrage of deleterious mutations.

Tuya Yokoyama is a research assistant in the Petrov Lab (2017-now). Tuya received her B.S. from Stony Brook University, where she studied cell heterogeneity in isogenic yeast populations in different metabolic environments in Josh Rest's lab. She is interested in evolutionary medicine, which applies evolutionary perspective to medicine in order to find "why" we get sick, rather than "how".

James Cai is an Associate Professor (with tenure) 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. His current research focuses on understanding the genetic basis of phenotypic variability in humans. Members of James’ lab (www. genomezoo.net) all work at the interface of human genetics, computational statistics, and data science. They use a high-performance scientific computing language Matlab to develop computational tools, and use these tools to assess the impact of common and rare genetic variant and chromatin dynamics on gene expression variability in humans.

Josefa Gonzalez is a CSIC Tenured Scientist 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. She has received a highly prestigious ERC Consolidator Grant to investigate the role of transposable elements in adaptive evolution. She is the co-organizer, together with Thomas Flatt and Martin Kapun, of the European Drosophila Population Genomics Consortium (DrosEU) that brings together 40 laboratories from 18 countries. Since her return to Spain, she has been actively involved in several science outreach projects including a citizen science project that involves high-school students from rural areas in collecting, classifying, and analyzing Drosophila melanogaster in nature. More information on this project can be found here (link: melanogaster.eu). 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.

Ruth Hershberg is an Associate Professor (with tenure)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.

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.

Philipp Messer is an Associate Professor (with tenure) in the Department of Biological Statistics at Cornell. He was a Research Associate in the Petrov Lab (2008-2014). 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.

Jamie Blundell is a Group Leader in the Department of Oncology, University of Cambridge, and in the CRUK Cambridge Center Early Detection Program. His work aims to understand and quantify the evolutionary dynamics going on inside our tissues as we age. Focusing predominantly on blood, his group uses novel genetic lineagetracking tools, deep sequencing of longitudinal samples and mathematical models to identify mutant clones which are under strong positive selection. He received his Ph. D. from the University of Cambridge in theoretical physics, studying the statistical physics of biological polymers and their networks. While at Stanford he worked closely with the Petrov lab (was a postdoc here 2011-2013), Daniel Fisher (with whom he was also a postdoc), 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. Check out these two papers if you are interested in the topic: Levy&Blundell et al, Nature, 2015 and Venkataram&Dunn et al, Cell 2016. He also collaborated with Zoe Assaf on understanding staggered sweeps. More details of can be found at blundelllab.com.

Pleuni Pennings is an Associate Professor in the Biology Department at the University of San Francisco. She was a Research Associate in the Petrov Lab (2012-2014). 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/).

Alan Bergland is an Assistant Professor at the Department of Biology at UVA (2016-now). As a Postdoctoral Fellow in the Petrov Lab (2010-2015) Alan worked on various projects aimed at the integration of 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. Specifically he investigated the evolution of D. melanogaster and D. simulans in temperate environments and discovered that hundreds of loci fluctuate in frequency by as much as 20% between the Fall and the Spring in temperate populations of D. melanogaster. The paper describing this key study was published in PLoS Genetics. The link to his website with more details is here. The majority of Alan's work in the Petrov lab was part of a long-standing collaboration between the Petrov and Schmidt labs on the nature of seasonal evolution in Drosophila in space and time. 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.

Meike Wittmann is a Junior Professor (similar to Assistant Professor in the US) in Theoretical Biology at Bielefeld University in Germany. While at Stanford, Meike was a CEGH Postdoctoral Fellow in the groups of Dmitri Petrov and Tadashi Fukami (2014-2015). She primarily worked on mathematical models for strong seasonally fluctuating selection at a large number of loci and on investigating how local adaptation and priority effects influence the maintenance of species diversity in a metacommunity. Meike is interested in theoretical ecology and evolution, especially in developing mathematical models for the interaction of ecological and evolutionary processes. She received her PhD on stochastic models for the ecology and population genetics of introduced species under the supervision of Dirk Metzler and Wilfried Gabriel at the University of Munich (LMU) in Germany in 2014.

Dave Yuan is a Scientist at Zymergen. As a Postdoctoral Fellow in the Petrov lab (2014-2017), he worked on building and characterizing a large collection of adaptive mutations in yeast in order to gain a more quantitative understanding of adaptation. Using experimental evolution and lineage-tracking molecular barcodes, Dave, in collaboration with the Sherlock and Fisher labs at Stanford and the Desai lab at Harvard, obtained and precisely measured the fitness of adaptive mutations that arose in different physical and genetic (ploidy) environments, with the goal of answering questions on overdominance and pleiotropy. 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 yeast in order to understand how the mutational process shapes variation in gene expression and 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.

David Enard is an Assistant Professor in the Ecology and Evolution Department at the University of Arizona. His lab focuses on unfderstanding of the selective impact that pathogens have on the evolution of their hosts. As a Postdoctoral Fellow in the Petrov Lab (2011-now) David published a number of beautiful papers, including one that showed that adaptation did in fact leave strong signatures in the human genome (Genome Research, 2014), that viruses are a dominant driver of protein evolution in their hosts (Elife, 2016), and that two species of humans, Neandertha;s and us, exchanged both viruses and defenses sagainst the viruses during the periods of contact and interbreeding (Cell, 2018). Overall, David's work established that viruses and other pathogens are a truly powerful source of selective pressures not just on the specialized immune proteins but on the whole proteome (and like on the whole genome) and that it is possible to learn much about past epidemics from the signatures left by natural selection in the hist genomes. 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.

Ryan W. Taylor is currently the CEO of End2End Genomics but continues to collaborate with the Petrov Lab. He was a postdoctoral scholar in the Petrov Lab (2013-2017) and also served as the Associate Director of the Program for Conservation Genomics. His works focused on the development of genomics technology for the study of terrestrial animals in the field. 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.

Chris McFarland is an Assistant Professor of Genetics & Genome Sciences at Case Western Reserve University. As a graduate student under the guidance of Prof. Leonid Mirny, Chris argued that tumors harbor many ‘deleterious passenger’ mutations that are harmful to cancer cells, yet nevertheless accumulate and alter progression. These mutations may be exploitable by both future and existing therapies. Chris joined the Petrov lab as a postdoc (2014-2019), and worked with folks in Monte Winslow’s lab to develop a high-throughput technology that combined DNA barcoding with CRISPR-based genome engineering to study combinatorial tumor suppressor losses in mice. This approach discovered a rugged fitness landscape of context dependencies between drivers and formed the basis of an approach to study pharmacogenomic interactions in cancer. In collaboration with a graduate student in the lab, Susanne Tilk, Chris confirmed his predictions from graduate school that deleterious mutations are indeed accumulating in cancer and that the lack of signal of purifying selection in cancer genomes is due to the inability of selection to weed damaging mutations out rather than due to the fact that these mutations are not damaging to begin with. He was a CEGH fellow from 2014-2015 and Cancer Systems Biology Fellow (2015-2017), and received an NIH (NCI) K99/R00 award to carry out his work.

Kerry Geiler-Samerotte is an Assistant Professor in the Biodesign Institute, in the Mechanisms of Evolution Research Center. As a Postdoctoral Fellow in the Petrov Lab (2014 - 2018) her research aimed to elucidate mechanisms that regulate the amount of phenotypic variation within clonal populations as well as across genotypes. Such mechanisms are not well understood, yet have important consequences. For example, the breakdown of mechanisms that buffer phenotypic variation may allow adaptation to novel environments, as well as contribute to complex genetic disease. Kerry became interested in protein-folding chaperones as possible regulators of phenotypic variation while quantifying the fitness cost of protein misfolding during her graduate work at Harvard University in the laboratories of Dan Hartl and Allan Drummond. Her recent research as a postdoctoral fellow in Mark Siegal's lab at New York University focuses on a particular protein-folding chaperone, HSP90. This work demonstrates that HSP90 suppresses non-genetic phenotypic heterogeneity, but interacts epistatically with genetic perturbations (rather than strictly as a suppressor).

Sharon Greenblum is a Computational Biologist at the Joint Genome Institute. She was a Postdoctoral Fellow in the Petrov Lab (2015-2019). Sharon comes from an engineering, systems biology, and bioinformatics background, and is interested in using computational tools to understand evolutionary processes. She completed her PhD in Genome Sciences at the University of Washington in Elhanan Borenstein’s lab, where she studied the human gut microbiome. She worked on designing network models showing how the thousands of microbial species in the gut work together, and how cooperation and co-evolution between species creates an interconnected metabolic system that is shaped by the gut environment. In the Petrov lab she investigated rapid adaptation to a changing environment by studying allele frequency shifts in Drosophila populations.

Stefan Prost was a Postdoctoral Fellow in the Petrov lab (2016-2018). His research focusses on evolutionary genomics, genome architecture changes and genome assembly. More precisely, he studies how the genome changes in response to adaption to new environments and living conditions in a variety of taxa. Beside modern DNA, he also works in paleogenomics, studying the genomics of extinct species such as the Haast's eagle or the Wooly rhino. He is currently setting up a large scale Drosophila comparative genomics project with Dmitri Petrov and other colleagues. Beside evolutionary genomics, he is also interested genome assembly methods, and works with 2nd and 3rd generation sequencing technologies.

David Gokhman is a Postdoctoral Fellow in the Petrov and Fraser labs (2018-now). During his PhD at the Hebrew University of Jerusalem, David studied the evolution of gene regulation along the lineages of modern and archaic humans. He developed a method to reconstruct DNA methylation maps from ancient genomes, providing a first glimpse into the epigenetics of extinct species. His grounbreaking Science paper is here. Through comparative analyses of the methylation maps of the Neanderthal, the Denisovan and modern humans, David showed that the regulation of facial and vocal anatomy have gone through particularly rapid evolution, which is unique to modern humans. David received Human Frontiers, Rothschild, Fulbright (declined), and Zuckerman (declined) fellowships to come to Stanford. In the Petrov lab, David is interested in studying the evolutionary dynamics of gene regulation in humans and other great apes, and elucidating the forces that propel regulatory divergence. David's papers can be found here.

Chuan Li is a Postdoctoral Fellow in the Petrov lab (2017-now). Her research interests include epistasis and speciation. She received her Ph.D. in Ecology and Evolutionary Biology with a dual degree in Statistics from the University of Michigan in 2017. During her Ph.D. at Dr. Jianzhi Zhang’s lab, she worked in quantifying intergenic and intragenic epistasis at a large scale with both experimental and computational approaches using yeast as the model system. She published already a highly influential paper on the empirical determination of the fitness landscape of the tRNA gene. In the Petrov lab, she studies the interaction between protein interfaces and antagonistic pleiotropy. She uses a high throughput Bar-seq methodology to systematically quantify intergenic epistasis between two interacting partners, GAL3 and GAL80, in a well-studied gene regulatory pathway metabolizing galactose in yeast, which will allow estimation of the ruggedness of fitness landscape and provide ample and in-depth information on these interaction interfaces. Chuan just won a prestigious CEHG postdoctoral fellowship that will provide funding for her first year at Stanford!

José Aguilar-Rodríguez is a Postdoctoral Fellow in the Petrov and Jarosz labs (2018-now). His research aims to elucidate how genotypes map onto phenotypes in diverse biological systems—and endeavor with important consequences for evolution, development, and disease. During his PhD in the lab of Andreas Wagner at the University of Zurich he studied empirical adaptive landscapes and genotype-phenotype maps, the role of molecular chaperones in protein evolution, and the metabolic determinants of enzyme evolution. José received a postdoctoral fellowship from the Swiss National Science Foundation to work at Stanford. In collaboration with the Fraser lab, José studies how the fitness effects of mutations in important biological modules of a cell change with the environment and the genetic background. To do so, he combines computational approaches with cutting-edge techniques for genome editing and high-resolution lineage tracking, which are revolutionizing the experimental study of evolution. His list of publications can be found here.

Monica Sanchez is Postdoc Research Associate in the Biosecurity and Public Health Group at the Los Alamos National Laboratory. She was a Postdoctoral Fellow in the Petrov lab (2017-2020) where she worked understanding of the concepot of long-term fitness and overdominance . She received her Ph.D in Molecular and Cellular Biology at the University of Washington. She completed her graduate work in Maitreya Dunham’s lab in the department of Genome Sciences studying how divergent species of yeast adapt to nutrient limited environments using comparative genomics and experimental evolution. Specifically, she identified changes in non-coding regions that shape multiple different evolutionary outcomes across the Saccharomyces clade. This work was published in PLoS Genetics in 2017. She is interested in studying the effect of genetic background differences on general mechanisms of evolvability and aims to understand how genetic and environmental interactions affect adaptation and complex traits.

Bernard Kim is a Postdoctoral Fellow in the Petrov lab (2018-now). He is broadly interested in understanding how population genetic processes shape genetic diversity at the macroevolutionary timescale. During his PhD with Kirk Lohmueller at UCLA, he studied the distribution of fitness effects in humans (see his 2017 Genetics paper here) and showed how segregating deleterious variation plays an important role in shaping patterns of introgression between hybridizing species (the paper is on biorxiv). In the Petrov Lab, Bernard is leading the effort to build a large scale, comparative polymorphism dataset of many species of Drosophila, with colleagues from the Drosophila community. He hopes to learn how the landscape of adaptation and constraint changes at this time scale, and what the importance of gene flow is in shaping these processes.

Carly Weiss is a Postdoctoral Fellow in the Petrov Lab (2019-now) who is interested in applying the power of computational biology to evolutionary questions. She has worked on a variety of systems in microbiology, genomics and evolutionary biology. During her PhD at UC Berkeleyin Rachel Brem's lab she developed a new method to map interspecific trait variation in yeast, where she applied reciprocal hemizygosity analysis to uncover basic housekeeping genes underlying thermotolerance differences between wild yeast species (published in Nature Genetics). In the Petrov lab, she is transferring her genomics knowledge to the evolving field of ancient human genetics and deciphering the roles of genetic changes specific to modern humans. She is hoping to learn more about the quantitative side of evolution and adaptation in the process.

Katie Solari is a Postdoctoral Scholar in the Petrov Lab (2019-now) and the Associate Director of the Program for Conservation Genomics (PCG). Katie’s PhD work in the Hadly Lab at Stanford University focused on investigating what mechanisms pika species (small mammals related to rabbits) are using to afford them hypoxia-tolerance at high elevations. Her results show that different pika species have genetic adaptations specializing them to the general elevational range of the species, but that on a local and even individual scale, changes in gene expression may offer a mechanism by which pikas can rapidly acclimate to hypoxic conditions. Check out this paper that describes some of this work. As part of the Petrov Lab and PCG, Katie will be working to develop pipelines, tools, and collaborations to help bring genomics into the field of conservation management. To read more about Katie and her work check out her personal website.

Sean Schneider was a Postdoctoral Fellow in the Petrov lab (2019-2019). He received his Ph.D in Genome Sciences at the University of Washington where he studied the evolutionary consequences of viruses integrating their genomes into the DNA of their host organisms. During his thesis work, he proposed an evolutionary model in which a vertebrate gene family, C2H2 zinc fingers, coevolve with endogenous retroelements invading vertebrate genomes. This study was published in Genome Research. His work demonstrating that certain parasitoid wasps can use specialized viruses to permanently transfer their genetic material into the genomes of their prey species was featured in The Atlantic. In the Petrov lab, he hopes to learn more about how environmental perturbations leave genomic signatures in resident organisms. His research primarily examines how populations of Drosophila can evolve between seasons to adapt to their changing environment. This work is in collaboration with Paul Schmidt and his lab.

Gabor Boross is a Postdoctoral Fellow in the Petrov lab (2019-now). He completed his PhD in the lab of Balazs Papp in Hungary, where he worked on a number of different projects in the intersection of molecular evolution and systems biology, including compensatory evolution, the emergence of dominance and the evolution of gene expression noise in yeast, antibiotic resistance in bacteria, adaptation of antigen presenting proteins in the human immune system in response to pathogen pressure and metabolome evolution in mammals. In the Petrov lab, Gabor is planning to shed light on how passenger mutations are spreading in cancerous tumors and what might be the therapeutical implications of this process.

Katherine Xue is a Postdoctoral Fellow in the Petrov and Relman labs (2019-now). She is interested in understanding ecological and evolutionary dynamics in microbial communities. During her PhD work with Jesse Bloom and Josh Akey at the University of Washington, she studied the evolutionary dynamics of influenza. She showed that viruses can cooperate with one another in cell culture and that influenza can evolve within patient infections in ways that mirror global evolutionary dynamics. She has won many awards in her graduate career including the Crow Award at PEQG, the Weintraub award, and Hertz Fellowship, and others.

Mark Bitter is a Postdoctoral Fellow in the Petrov lab, working jointly with Paul Schmidt’s group at the University of Pennsylvania (2020-now). His research aims to explore the dynamics of rapid adaptive processes– their ubiquity across systems, their generality through time, and the predominant selective forces altering the variation in natural populations. During his PhD at the University of Chicago with Cathy Pfister, Mark demonstrated the extent to which the standing variation present in natural populations of the Mediterranean mussel could facilitate rapid adaptation to the declines in seawater pH expected as a result of global climate change (read the publication here). In collaboration with the Schmidt Lab, Mark is resolving how quickly populations of Drosophila melanogaster adapt to seasonally fluctuating selection pressures, as well as the interplay between the biotic and abiotic factors underpinning this process.

Marianna (Marianthi) Karageorgi is a Postdoctoral Scholar in the Petrov lab (2020-now). Her research is focused on understanding how novel adaptive traits emerge and evolve in nature. She did her undergraduate studies in the University of Crete and the University of Heidelberg. During her PhD in the lab of Dr. Benjamin Prud’homme in Marseille, supported by a Marie Curie Fellowship, she studied how the agricultural pest Drosophila suzukii evolved its novel egg-laying behavior (Karageorgi et al., Current Biology, 2017). In her postdoctoral research in the lab of Prof. Noah Whiteman at Berkeley, she studied how monarch butterflies and other specialist insects have evolved resistance to cardiac glycoside toxins produced by their host plants (Karageorgi et al., Nature, 2019). In the Petrov lab, Marianna is studying how resistance to cardiac glycosides toxins and pesticides emerge in wild Drosophila populations. To read more about Marianna’s check out her personal website.

Clare Abreu is a postdoctoral fellow in the Petrov lab (2020-now). After studying microbial ecology with model laboratory systems in her graduate studies in the Gore Lab, she has become interested in microbial evolution. Her previous work showed that small communities of soil bacteria responded in universal ways to environmental changes including increasing mortality and temperature. She is now interested in how environmental disturbances affect long-term eco-evolutionary dynamics in both model systems and natural communities. She is working with a community of yeast strains, subject to fluctuations in a spatially and temporally heterogenous environment, to determine how fitness is affected by the abiotic environment and biotic interactions.

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 Associate Professor (with tenure) in the Department of Biology at the University of Oregon. 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, and was promoted to an Associate Professor of Biological Sciences with tenure in 2016. She joined the faculty at the University of Oregon in 2017 as an Associate 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.

Penka Markova-Raina was a Graduate Student in the Petrov Lab from 2005-2011 where she pursued computational projects studying molecular evolution at the whole genome scale. Her research focused on molecular evolutionary genomics in Drosophila, primarily inference of selection, methods for selection inference in the presence of flawed genomics data, and evolution in disordered protein regions. Her main paper was published in Genome Research and caused quite a stir. Prior to her PhD work, Penka completed Masters degrees in Computer Science and Electrical Engineering at Stanford University and a Computer Science undergraduate degree at Purdue University.

David Lawrie is a Postdoctoral Scholar in the lab of Kevin Thornton at UC Irvine. 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 Postdoctoral Fellow in the Laurent Duret Laboratory at the University of Lyon. As a Graduate Student in Petrov Lab (2007-2014), Diamantis focused 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 confirmed that the first, and the largest-effect mutations, in diploid evolution of yeast in a chemostat involves mutations overdominant in fitness. Diamantis also worked on modelling of evolution in pathways and published a really nice paper together with a fellow graduate student Mark Longo.

Yuan Zhu is a Research Fellow (equivalent of a Postdoctoral Fellow) in the lab of Swaine Chen at the Genome Institute of Singapore. She is applying population genetics and genomic methods to pathogenic bacterial populations, such as pathogenic E. Coli strains responsible for human UTIs (urinary tract infections). While in the Petrov lab (2008-2013) Yuan focused on the application of next-generation sequencing to answering a broad range of questions in genomic evolution, population structure, and population evolution. She showed that pooled re-sequencing is a remarkably efficient and precise tool for the estimation of allele frequencies in a population (PLOS One 2012). She also characterized the genome-wide mutation spectrum of lab yeast with ~1000 mutations from a large scale mutation accumulation experiment, noting that mutations are AT biased and context dependent, with evidence suggesting possible methylation in yeast (PNAS 2014). She was also studying the population structure of clinical yeast strains, as well as the possibility of extracting young mutations and the mutation spectrum from deep population sequencing data. Yuan did her undergraduate work at Duke with Susan Alberts, looking at father-daughter behavioral patterns in baboons.

Nandita Garud is an Assistant Professor in the Ecology and Evolutionary Biology department at UCLA. As a graduate student, Nandita worked on characterizing signatures of rapid adaptation in natural populations of Drosophila. Specificially, she developed haplotype statistics for detection and differentiation of hard and soft sweeps from population genomic data and discovered that soft sweeps dominate the strong adaptation in D. melanogaster. Nandita continues to study adaptation in natural populations and lately has been focused on bacteria in the gut microbiome. Nandita completed her postdoctoral work with Katie Pollard at Gladstone UCSF and undergraduate work with Andy Clark at Cornell. A link to her website with more details is here.

Heather Machado is a Postdoctoral Fellow in the lab of Peter Campbell at the Wellcome Trust Sanger Institute (2017-now). She is studying the evolution of hematopoietic lineages and how that relates to age-related changes in immune function (in humans!). She was a Graduate Student in Petrov Lab (2010-2017) where she conducted work on understanding of adaptation particularly in the context of recent radiations or environmental shifts. 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. More information can be found at https://machadoheather.wordpress.com/

Sandeep Venkataram is a post-doc with Sergey Kryazhimskiy at UCSD (2016-now). He was a graduate student in the Petrov lab (2010-2016), where he used DNA barcode technology to track the dynamics of experimentally evolving yeast populations, isolate single adaptive events, and characterize their genotype-fitness map. He received his B.S. from the Washington University in St. Louis where he worked with Justin Fay.

Ben Wilson is a Population Geneticists at AncestryDNA. He received his B.S. from the University of Arizona where he worked with Joanna Mazel. As a Graduate Student in Petrov Lab 2010-2015), Ben was interested in the theoretical population genetics of adaptation, particularly in populations that fluctuate in size over various time-scales. He was also interested in how complex adaptive landscapes contribute to the evolutionary trajectories we see in adaptation.

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 postdoctoral fellow in the lab of Josh Akey in the Department of Genome Sciences at the University of Washington, where he is using genomic approaches to study human evolutionary history. Specific projects are focused on identifying segments of modern human genomes inherited from archaic hominins, including Neanderthals and Denisovans, as well as understanding the functional characteristics of these introgressed regions.

While in the Petrov lab (2010-2015), Rajiv worked on a range of projects applying novel genomic technologies to address basic evolutionary, ecological, and clinical questions. Rajiv's initial graduate work demonstrated that inference approaches using population genomic data were capable of accurately estimating the timing of known events in the demographic history of an introduced butterfly population (Molecular Ecology 2014). In a second thesis project, Rajiv and other members of the Petrov lab evaluated the utility of Illumina synthetic long-read technology (Moleculo) for de novo genome assembly, finding that the synthetic long-read approach is superior at resolving genomic repeats compared to approaches that use short read data alone (PLOS ONE 2014). Rajiv was co-advised by Dmitri and Carol Boggs while at Stanford.

His most recent work, in collaboration with the genetic testing company Natera, investigated the causes and consequences of extra or missing chromosomes in human embryos and the impacts on fertility. This phenomenon, termed aneuploidy, affects approximately three-quarters of preimplantation embryos and is the leading cause of pregnancy loss. Rajiv and collaborators at Stanford and Natera demonstrated that a maternal genetic variant influences the rate of aneuploidy and that the associated genomic region displays signatures of a selective sweep in ancient humans (Science 2015). More information about Rajiv's research can be found on his website (http://rajivmccoy.wordpress.com).

Alison Feder is a Miller Fellow in the labs of Oskar Hallatschek and Monty Slatkin at UC Berkeley. As a graduate student in the Petrov lab, Alison studied the evolutionary dynamics of rapidly adapting intra-patient pathogen populations through time and space. She did her undergraduate work in mathematics at the University of Pennsylvania with Joshua Plotkin and earned her MSc at Oxford studying statistical genetics in the group of Gil McVean. 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 the evolutionary dynamics of rapid adaptation over time and across space, and in particular how these processes play out in pathogen populations evolving drug resistance within their hosts. Her personal website is here.

Yuping Li is a Graduate Student in the Sherlock and 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.

Emily Ebel was a Graduate Student in the Petrov Lab (2014-2019). She is interested in how malaria, as a persistent pathogen over evolutionary time, may have driven adaptation in humans and many other mammals. Emily completed an M.A. in 2014 with Sean Mullen at Boston University, where she used genomic markers in tropical butterflies to evaluate species relationships, diversification rates, and their connections to phenotypic evolution. She has also previously worked on the evolution of sexual conflict, sex-specific inbreeding depression, and sex ratio in the Patrick Phillips lab at the University of Oregon.

Anisa Noorassa was a Graduate Student in the Petrov Lab (2015-2017) and worked on issues related to long-term evolution in yeast. Anisa completed her B.S. in Cellular, Molecular, and Developmental Biology at the University of Washington in Seattle. She worked in Jennifer Nemhauser’s lab studying auxin signal transduction in Arabidopsis using a synthetic yeast system. After graduating from UW, she worked as a lab technician in Nicholas Ingolia’s lab at UC Berkeley for a year before coming to Stanford. She is interested in working on experimental evolution in yeast.

Yiwen Chen was a Rotation Graduate Student in the Petrov Lab. She did her undergraduate work in Chemical Engineering at Purdue University and then came to Stanford to get her master’s degree. Fascinated about the beauty of biology and how elegantly the Mother Nature has engineered the complex systems of life, Yiwen subsequently joined the Department of Chemical and Systems Biology. She is interested in understanding how epigenetic changes may contribute to rapid adaptations under fluctuating environments.

Grant Kinsler is a Graduate Student in the Petrov Lab (2016-now). He is using a combination of mathematical models and experimental evolution to uncover the mechanisms of adaptation to new environments, and how these mechanisms influence fitness in other environments. Grant did his undergraduate work in applied mathematics at Harvard University. There, he worked with Martin Nowak on mathematical models of evolutionary dynamics, particularly those involving prelife and the origin of life. You can reach Grant's website here

Ellie Armstrong is a graduate student in the Petrov and Hadly Labs (2016-now). She received her B.S. from UC Berkeley and her M.S. from the University of Hawaii, Hilo, where she studied genome evolution in picture-wing Drosophila in the Price Lab. Ellie is interested in studying genome adaptation and evolution in natural systems which have undergone rapid adaptation in response to ecological pressures.

Nicole Nova is a graduate student in the Petrov and Mordecai Labs (2016-now). She received her undergraduate training in dental surgery and M.Sc. at Karolinska Institutet, Sweden. She also studied electrical engineering for a year at the Royal Institute of Technology, Sweden. She then spent a year at Dana-Farber/Harvard Cancer Center working on mathematical modeling of cancer evolution in the Michor Lab. Then, she worked on eco-evolutionary dynamics of infectious disease (i.e., within-host modeling of HIV and antibody co-evolution) in the Koelle Research Group at Duke. Nicole is interested in population genetics, disease ecology, and rapid adaptation of pathogens and mammals in wildlife. Her research focuses on large carnivores and their conservation. More information can be found here.

Susanne Tilk is a graduate student in the Petrov and Curtis Labs where she is working on the role of purifying selection and deleterious passenger mutations on the evolution of cancer. She was a research assistant in the Petrov Lab (2014-2017) and worked on a number of projects primarily related to our effort to understand pattersn of seasonal adaptation in Drosophila. Susanne received her B.S. in Cell and Developmental Biology from UCSB, where she worked with Tom Turner studying the genetics basis of different behavioral preferences within Drosophila. She is interested in learning about molecular, genetic, and developmental biology from an evolutionary perspective.

Emily Shuldiner is a graduate student in the Petrov lab (2018-present). Emily is broadly interested in somatic evolution of cancer and is currently working with collaborators in the Winslow lab to understand how mutations interact to drive tumor growth. Prior to the Petrov lab, Emily was a postbaccalaureate fellow in Michael Ombrello’s lab at the NIH, where she studied the genetics of childhood autoinflammatory disease. Emily did her undergraduate work in Ecology & Evolutionary Biology at Princeton University, where she worked on canine behavioral genetics in Bridgett vonHoldt’s lab.

Roshni Patel is a rotation student in the Petrov Lab. She graduated from U.C. Berkeley in 2018, where she worked on machine learning approaches to variant interpretation in Mendelian diseases. More recently, she has become interested in evolutionary dynamics within microbial communities, including (but not limited to) the human microbiome. She is excited to work on rapid evolution in diploid yeast populations during her rotation.

Talia Karasov is a Postdoctoral Fellow in the laboratory of Detlef Weigel at the Max Planck Institute for Developmental Biology in Tuebingen Germany. Her research in the Weigel lab focuses on microbial population genomics and is funded by two, count them two, very prestigious fellowships: the EMBO long-term research fellowship as well as a Human Frontiers in Science Program Post-doctoral fellowship. Talia completed her Ph.D. at the University of Chicago in the laboratory of Joy Bergelson. Her thesis research was awarded the best dissertation award from the Committee on Genetics Genomics and Systems Biology at UChicago. 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.

Philip Bulterys is an 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. 

Grace Lam is a research intern in the Petrov lab (2016-now). She is currently a senior at Palo Alto High School. She is interested in discovering how machine learning and informatics can be used to model features in evolutionary biology. She is passionate about Biology and Computer Science, and wants to pursue research that is cross-disciplinary and borders both fields. She is interested in studying how adaptive mutations affect the gene expression and organism-level phenotypes of organisms from a bioinformatics standpoint. She is being mentored by the postdoctoral fellow in the lab, Kerry Geiler-Samerotte.

Alycia Cary is a research intern at the Petrov Lab (2017-now), and is a senior at The Harker School. She is passionate about learning more about molecular biology and genetics, and hopes to merge her enthusiasm for biology with her enjoyment of computer science. Under the mentorship of postdoctoral fellow Kerry Geiler-Samerotte, she is studying the effect of Hsp90 inhibition on population dynamics in yeast, and developing higher-throughput ways to both quantify the role of Hsp90 on adaptive evolution in yeast, as well as identify mutational pathways through which this adaptive evolution can occur.

Esther Cao is currently a senior at Palo Alto High School. She is a research intern in the Petrov lab (Summer 2017-now) and is studying the mechanisms that underlie adaptation, and how protein-folding chaperones influence evolutionary dynamics. In the future, she also hopes to explore how machine learning/artificial intelligence can be applied to biology to help analyze data. She is being mentored by the postdoctoral fellow Kerry Geiler-Samerotte.