Joe Lachance

Joseph Lachance, Ph.D.

NIH Kirschstein postdoctoral fellow

Department of Genetics
Perelman School of Medicine
University of Pennsylvania
422 Clinical Research Building
415 Curie Boulevard
Philadelphia, PA 19104-6145

lachance.joseph@gmail.com
           

Research

My long-term research focus is in the field of population genetics. This includes studying the genomics of human adaptation and developing theoretical models to determine how molecular and evolutionary processes influence the risk of hereditary disease. Outstanding problems in population genetics include understanding the extent that genomes have been shaped by natural selection and determining how well genetic data from one population can be used to predict disease risks in other populations. By bridging the gap between evolutionary genomics and genetic epidemiology, I will be able to make progress towards answering these and other questions.

As an undergraduate with Chung-I Wu at the University of Chicago, I studied genetic interactions underlying the incipient speciation of Zimbabwe populations of D. melanogaster. As a Ph.D. student at Stony Brook University, I was a member of the Department of Ecology and Evolution and the Graduate Program in Genetics. During my doctoral training with John True, my research focused on the genetic interactions in D. melanogaster. In addition, I used mathematical theory and computer simulations to model how genetic interactions and natural selection shape population genetic variation.

During the early stages of postdoctoral training at the University of Pennsylvania, my research has shifted towards human population genetics and the evolutionary genomics of diverse African populations. Since joining the Tishkoff lab in December 2010, I have studied high-coverage whole genome sequences of African hunter-gatherers. This led to a first-author paper in Cell and the discovery of multiple genetic signatures of local adaptation. My human genomics work has also included detecting admixture between ancient hominins, quantifying the effects of SNP ascertainment bias, and examining the public health implications of GC-biased gene conversion.

Education

Ph.D.

Genetics, Stony Brook University, 2010
Advisor: John True
Dissertation: “Life after beanbag genetics: theoretical and empirical studies on epistasis and penetrance”

 

Graduate-level studies in genetics, Duke University, 1996-1997

A.B.

Biology, University of Chicago, 1996
Advisor: Chung-I Wu
Dissertation: “Epistatic interactions underlie incipient speciation in Zimbabwe Drosophila melanogaster

Current position

NIH Kirschstein postdoctoral fellow in Sarah Tishkoff’s lab at the University of Pennsylvania

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Publications

RESEARCH PUBLICATIONS

  • Lachance J and Tishkoff (SA2013) Population genomics of human adaptation. Annual Review of Ecology, Evolution, and Systematics doi:10.1146/annurev-ecolsys-110512-135833.
  • Wang S, Lachance J, Tishkoff SA, Hey J, and Xing J (2013) Apparent variation in Neanderthal admixture among African populations is consistent with gene flow from non-African populations. Genome Biology and Evolution (in press)
  • Lachance J, Jung L, and True JR (2013) Genetic background and GxE interactions modulate the penetrance of a naturally occurring wing defect in Drosophila melanogaster. G3: Genes|Genomes|Genetics doi:10.1534/g3.113.007831.
  • Lachance J and Tishkoff SA (2013) SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it. BioEssays 35:780-786.
  • Johnson NA and Lachance J (2012) The genetics of sex chromosomes: evolution and implications for hybrid incompatibility. Annals of the New York Academy of Natural Sciences: The Year in Evolutionary Biology 1256: E1-E22.
  • Lachance J, Vernot B, Elbers CC, Ferwerda B, Froment A, Bodo JM, Lema G, Fu W, Nyambo TB, Rebbeck TR, Zhang K, Akey JM, and Tishkoff SA (2012) Evolutionary history and adaptation from high coverage whole-genome sequences of diverse African hunter-gatherers. Cell 150:457-469.*
    *Cover article (media coverage: NY Times, Washington Post, Science, Nature, Nature Genetics, Scientific American, Chronicle of Higher Education, ScienceNews, io9, GenomeWeb, and others)
  • Pickrell J, Patterson N, Carbieri C, Berthold F, Gerlach L, Güldemann T, Kure B, Mpolaka SW, Nakagawa H, Nauman C, Lipson M, Loh PR, Lachance J, Mountain J, Bustamante C, Berger B, Tishkoff SA, Henn B, Stoneking M, Reich D, and Pakendorf B (2012) The genetic prehistory of southern Africa. Nature Communications doi:10.1038/ncomms2140.
  • Lachance J, Johnson N, and True JR (2011) The population genetics of X-autosome synthetic lethals and steriles. Genetics 189:1011-1027.
  • Lachance J (2010) Genome-wide association studies reveal that disease associated alleles are enriched for derived low frequency alleles relative to HapMap and neutral expectations. BMC Medical Genomics 3:57.
  • Lachance J and True JR (2010) X-autosome incompatibilities in Drosophila melanogaster: tests of Haldane’s rule and geographic patterns within species. Evolution 64:3035-3046.
  • Lachance J (2009) Inbreeding, pedigree size, and the most recent common ancestor of humanity. Journal of Theoretical Biology 261:238-247.
  • Lachance J (2009) Detecting selection-induced departures from Hardy-Weinberg proportions. Genetics Selection Evolution 41:15.
  • Lachance J (2008) A fundamental relationship between genotype frequencies and fitnesses. Genetics 180:1087-93.
  • Yukilevich R, Lachance J, F. Aoki F, and True JR (2008) Long-term adaptation of epistatic genetic networks. Evolution 62:2215-2235.

OTHER PUBLICATIONS

  • Lachance J (2013) Book Review: Human Evolutionary Genetics, 2nd ed. by Jobling, Hollox, Hurles, Kivisild, and Tyler-Smith. Quarterly Review of Biology (in press).
  • Lachance J (2013) Book Review: An Introduction to Population Genetics: Theory and Applications by Nielsen and Slatkin. Quarterly Review of Biology (in press).
  • Lachance J (2012) The genomics of African hunter-gatherers: what cutting-edge technology can tell us about human history. Huffington Post (invited guest blog)
  • Lachance J (2011) Book Review: How Many Friends Does One Person Need? By Robin Dunbar. Quarterly Review of Biology 86:104.
  • Lachance J and Bourdeau P (2010) Evolution by Doug Futuyma: online supplements, 2nd ed. Sinauer Associates, Sunderland MA.
  • Lachance J (2009) Book Review: Evolving Pathways edited by Alessandro Minelli and Giuseppe Fusco. Quarterly Review of Biology 84:102-103.
  • Lachance J (2008) Subject to Change. Nature 454:916.
  • Lachance J (2008) Forgotten Ancestors. University of Chicago Magazine 100:6.
  • Lachance J (2008) Book Review: Modelling for Field Biologists and Other Interesting People by Hanna Kokko. Quarterly Review of Biology 83:296.
  • Lachance J (2007) Book Review: Compositional Evolution by Richard A. Watson. Quarterly Review of Biology 82:148-149

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Grants and Awards

2011-2014


NIH F32 Kirschstein National Research Service Award: Population genomics of geographically and ethnically diverse Africans (NHGRI, F32HG006648)

2012
Selected to give a platform talk at the 2012 meeting of the American Society of Human Genetics in San Francisco, CA

2012
Chosen to receive additional pedagogical training through the PENN-PORT program at the University of Pennsylvania (competitive enrollment)

2010

Selected to give a university-wide lecture as part of the Provost’s Graduate Student Lecture Series at Stony Brook University

2009

Summer Institute in Statistical Genetics fellowship recipient at the University of Washington (comparative genomics and molecular evolution, coalescent theory)
Cedar Brook Award for best student talk at the Ecology and Evolution departmental retreat at Stony Brook University

“Subject to Change” featured as an exceptional Nature Futures story by Concatenation (www.concatenation.org)

2008

Stony Brook graduate student organization Research Access Program funding

2007

King-Miller travel award to attend the Evolution 2007 conference in Christchurch, NZ

2005 – 2007

NIH T32 Predoctoral training grant fellowship, Stony Brook University

1996 – 1997

NIH T32 Predoctoral training grant fellowship, Duke University

1995

Howard Hughes summer undergraduate fellowship

1992 – 1996

National Merit Scholar, University of Chicago

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Teaching experience

2006 – present


Mentor: Stony Brook University and the University of Pennsylvania

Helped guide the research of five high school students, six undergraduates, and three Ph.D. students (work presented at URECA, LISEF, Intel, and Siemens science fair competitions)

2013

Instructor: University of Pennsylvania
Taught the human population genetics block of a Ph.D.-level course in genetics

2012

Instructor: University of Pennsylvania

Co-taught a seminar course for undergraduates on human evolutionary genomics

2011

Guest Instructor: University of Pennsylvania (Perelman School of Medicine)

Led population genetics discussions for medical students

2007-2009

Guest Instructor: Stony Brook University


Assisted in field laboratory components of a molecular diversity class for undergraduate and graduate students.

2009
Guest Instructor: Stony Brook University (CESAME)

Introduced high school students to a range of genetics research projects

2008


Lecturer: Stony Brook University



Taught the population genetics and evolutionary developmental biology block of a Ph.D.-level course in genetics

1996

Teaching Assistant: University of Chicago

Assisted in teaching a genetics course for non-majors

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