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What You'll Study
  • Tutorials that emphasize hands-on training in computational tools used in conservation genomic analyses
  • Study design considerations for conservation genomic projects
  • Data collection via whole genome sequencing
  • Genome assembly and annotation
  • Read data processing and mapping
  • Variant calling and genotyping
  • Analysis of genetic structure and admixture
  • Analysis of genome-wide diversity
  • Inbreeding detection
  • Detection and inference of deleterious variants
  • Inference of demographic history
  • Phylogenomic/comparative genomic analysis
  • Use of Unix command line to access Smithsonian high-performance computing resources and pre-compiled software

 

Participants should have completed basic genetics and evolutionary biology coursework or have previous experience with genetics, genomics, or evolutionary biology.

Program Details
Dates

October 9-18, 2024

Available Formats

Graduate (CONS 697, 3 credits)
Professional Training (SMSC 530, 6.75 CEUs)

Total Cost

Graduate: See Mason’s graduate tuition rates

Professional Training: $2,213.00*

*Professionals from certain countries are eligible for a reduced rate of $1,713.00 which will automatically be reflected during the registration process.

Scholarships & financial aid

Deadlines

Apply by September 2, 2024

Payment Deadline: September 13, 2024

Meet the Faculty

Klaus Koepfli
Senior Research Scientist
Smithsonian-Mason School of Conservation
Dr. Koepfli is a Senior Research Scientist in the Smithsonian-Mason School of Conservation at George Mason University specializing in genomics and its application to the conservation of biodiversity. He and his students and collaborators generate and analyze whole genome sequencing data to assess genetic diversity relative to demographic history, dissect the underlying causes of inbreeding depression, and inform conservation management strategies of species at risk for extinction.
Carlos Francisco Arias Mejia
Data Scientist and Bioinformatics Manager
Smithsonian Tropical Research Institute
Dr. Carlos F. Arias Mejia is a Research Data Scientist in the Data Science Lab at the Smithsonian Office of the Chief Information Officer and the Smithsonian Tropical Research Institute (STRI) in Panamá. His research focuses on the evolutionary processes and mechanisms driving and constraining the origin of new species in nature. Carlos uses population genomics and bioinformatic approaches to characterize patterns of genome-wide divergence at both local and regional spatial scales within neotropical taxa.
Alex White
Data Scientist
Smithsonian Institution Data Science Lab, Office of the Chief Information Officer
Alex White’s areas of scholarly expertise include statistical modeling in biogeography, quantitative ecology, ornithology, and community phylogenetics. Dr. White’s research focuses on how ecological and evolutionary forces (e.g., dispersal, range expansion, competition, and speciation) interact…
Taylor Hains
PhD Candidate
Committee on Evolutionary Biology, University of Chicago
Taylor Hains is a PhD candidate at the University of Chicago and the Field Museum in the Committee on Evolutionary Biology. He is conducting his dissertation research with Dr. John Bates and Dr. Shannon Hackett…
Lauren Hennelly
NSF Postdoctoral Research Fellow
Globe Institute, University of Copenhagen, Denmark
Lauren Hennelly is a NSF Postdoctoral Research Fellow at the University of Copenhagen and a Research Associate at the Smithsonian’s National Zoo and Conservation Biology Institute. She uses genomic tools to study how divergence, adaptation,…

Curriculum

This course provides an in-depth survey of the concepts, methods, and software used in conservation genomics research. Participants will learn how to: 1) design conservation genomics projects, 2) handle complex genomic data, 3) use common population genomics software packages and tools, 4) interpret, visualize, and publish results, and 5) practice collaborative research. For this course, participants will be working with a novel dataset from a threatened species for which a genome assembly and whole genome sequencing data of additional individuals will already have been generated. Participants will collaborate with each other and the instructors to analyze these data and then prepare a genome report manuscript for submission to a peer-reviewed journal (e.g., G3, Genome Biology and Evolution, Journal of Heredity, or Molecular Ecology Resources). THIS is an example of the type of publication participants will work toward. Participants that actively work on the analysis and writing process will be included as coauthors on the resulting manuscript. Please note that analyses and manuscript preparation may extend beyond the 10-day course. A Slack channel for the course will be set up to foster communication among participants and instructors where messages, papers, and programs can be shared. This experience will provide participants the opportunity to conduct sophisticated genomic analyses as applied to conservation using a real dataset and learn best practices for collaborations. Finally, there will be evening lectures by several invited speakers that will discuss and share their research in conservation genomics.

Target Audience

This course is designed for graduate students, postdoctoral researchers, and early-career scientists interested in designing conservation genomics projects or already generating genome data to acquire the skills necessary to: assemble and annotate a genome or transcriptome, estimate genetic diversity and structure, calculate inbreeding levels, detect deleterious variants, infer demographic history, and compare data and results to existing genomic resources. The hands-on tutorials in this workshop will be performed on a High-Performance Computing Cluster via the Unix command line. Although some review of Unix will be included in the course, all participants should be familiar with basic Unix commands. We recommend this short tutorial: (https://swcarpentry.github.io/shell-novice/).

What’s Included

The total cost for professional training includes our Housing ($588.50) and Dining ($374.66) Packages and covers:

  • Instruction, course manual, and other course materials
  • Airport pick-up and drop-off shuttle service at Dulles International Airport (IAD) at pre-arranged times. We do not provide ground transportation shuttle service to or from any other airports in the Washington, DC, region
  • Transportation for course activities
  • Daily full-service buffet at the SMSC Dining Commons.
  • Housing at the SMSC Residential Facility, including a shared room with bathroom (single rooms available at twice the cost of shared housing)

 Acceptance does not guarantee you a seat in the course. Seats are allocated as registration payments are received, and early registration is strongly encouraged to ensure you get a spot.

Venue

The course will take place in the Volgenau Academic Center at the Smithsonian-Mason School of Conservation, located on the campus of the Smithsonian’s National Zoo and Conservation Biology Institute in Front Royal, Virginia, USA. SMSC is located approximately 72 miles west of Washington, D.C. and the north entrance of Shenandoah National Park is only a 10-minute drive away.

Interested in Commuting?

Participants with a documented, permanent address local to campus may elect to commute with permission from SMSC. Commuters are required to purchase a reduced meal plan ($130) which includes lunch and snack breaks for each day of instruction. Additional dining options are available and may be selected during registration.  Email SCBItraining@si.edu for additional information.

“This course was incredibly informative about the methods and field of conservation genomics. I couldn’t believe how much knowledge was packed into one room and shared with us. Ten days to soak in my field – I couldn’t have asked for anything more informative for my research. Thank you!”

Heather W. 2023 Course Participant

“This course was fast-paced and challenging, yet everything was provided for each participant to be successful. I learned a tremendous amount in just a short time, and while I’m not an expert on any of the subjects covered after the course, I feel confident in my knowledge and abilities now to become much more proficient in each area.”

Tyler B. 2023 Course Participant
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