To get the most out of this course/workshop you should...

• Know some basic command-line and R skills. By Day 2 (or before), you should be able to write a Bash script to automate components of your bioinformatics analyses.
• Read/skim the 1-3 papers listed as "Recommended Readings" under each lecture below. You can find them on the UM Box website, that URL will be emailed to you by one of the ConGen organizers.
• Download the worksheets and PowerPoint slides for hands-on exercises by instructors will be available on the UM Box site under each instructor's name.
• Watch the pre-recorded lectures under each instructor's name in Box. For example, the DNA sequence statistics and "the coalescent" lecture on Day 2 by Mike Miller will be under the "Mike Miller" folder on Box. To maximize your learning, please watch the first 1-2 hours (Part I, some of Part II) if possible BEFORE Tuesday Sept 8th when Mike discusses DNA sequence data, statistics, and the Coalescent. Why? Coalescent modeling is as important for modern population genomics as Hardy-Weinberg is to classical population genetics.

All times listed in the schedule below are in Mountain daylight savings time (MDT). MDT is 7 hours behind Coordinated Universal Time (UTC; England, Spain, Morocco). 9 AM MDT (Mountain (Montana) daylight saving time is 5 PM CEST (Central Europe Summer Time; France, Sweden, Egypt), and 2 PM in Sydney Australia). 1 PM MDS is 9 PM CEST and 6 AM in Sydney (9 AM in Perth). New Zealand (NZST) is 18 hour ahead of Montana. Sydney Australia is 17 hours ahead of MDT. Bejing is 14 hours ahead.

Starting ~2 weeks before the course, open help sessions will also available to do computer checks with Brian Hand and Ted Cosart. Feel free to email them at ted.cosart@flbs.umt.edu and brian.hand@flbs.umt.edu to set up a time. You DO NOT need to run Linux or R studio on your computer as it is available on the cloud.

Most instructors will be available for 1-on-1 meetings (or small group meetings) via Zoom. Most instructors will be available by appointment from 8-9 AM and/or 4-5 PM the 2 days following their lecture. There are no other ConGen lectures scheduled during those times. Most meetings will be less than 15 minutes to allow many students to have time with the instructors, so be efficient when asking your questions! You also can send written questions to instructors via their Slack Channel.

We will use Slack, the free communication platform, to facilitate communication, interaction, and your ability to find information before, during, and after ConGen. When joining Slack, please use your full name so we can identify you as a student or instructor. Users who do not use their real name and cannot be identified as a student or instructor will be removed. Please send an introduction of yourself on Slack as soon as possible. You can run Slack through your browser or download their desktop application for free on their website. Check your email for an invitation to the ConGen channel.

A recording of each lecture, Q & A session (after each lecture), and hands-on sessions (after each lecture) be added to a UM Box folder for you.

9:00-9:30 AM – Welcome, Course Business, and Introduction

• Instructor: Gordon Luikart, University of Montana
• Recommended Reading: Hendricks et al. 2018 (Evol Apps)

9:30-10:30 AM – Introduction & Overview of Conservation Genetics/Omics and Data Analysis

• Keynote Lecturer: Craig Primmer, University of Helsinki, Finland
• Lecture: Conservations Genomics: Why?
• Recommended Readings:
  • Shafer, et al (2015). Genomics and the challenging translation into conservation practice. Trends in Ecology & Evolution, 30(2), 78-87. doi: 10.1016/j.tree.2014.11.009
  • Garner, et al. (2016). Genomics in conservation: case studies and bridging the gap between data and application. Trends in Ecology & Evolution, xx(2), 1-3. doi: 10.1016/j.tree.2015.10.009
  • Shafer, et al. (2016). Reply to Garner et al. Trends in Ecology and Evolution, 31(2).
  • Aykanat, T., Lindqvist, M., Pritchard, V. L., Primmer, C. R., Lindqvist, M., & Primmer, C. R. (2016). From population genomics to conservation and management: ... . Journal of Fish Biology, 89(6), 2658-2679. doi: 10.1111/jfb.13149

10:30-11:30 AM – Elevator Speeches (Live or Recorded)

Each student-participant has 45-60 seconds and one PowerPoint slide with no animations. Please email leif.howard@umontana.edu by Sept 4th if you'd like to participate. 

• Recommended Reading: Elevator Pitch article on Wikipedia

11:30 AM-12:30 PM – Lunch/Brain-Break

12:30-3:00 PM – Linux Command Line Instruction

• Keynote Lecturer: Amanda Stahlke, Idaho, USA
• Lecture: Review of Linux, line commands, and scripting
• Recommended Readings:
  • Linux Command Line dot Org article
  • See also Mike Miller’s lecture (from ConGen 2019)

9:00-12:00 PM – The Coalescent and NGS Data Analysis

• Keynote Lecturer: Mike Miller, UC Davis, California
• Lecture: Coalescent and population genetics
• Recommended Videos: Part I & Part II from Mike Miller's folder in "Instructor videos" on UMBox

12:00-1:00 PM – Lunch/Brain-Break

1:00-2:00 PM – Continued: The Coalescent and NGS Data Analysis

2:15-4:30 PM – Bayesian Statistics, MCMC, Probability, Genotyping Errors

• Keynote Lecturer: Eric Anderson, National Marine Fisheries Service, Santa Cruz, California
• Lecture: Bayesian data analysis, MCMC. Example: estimating GBS genotyping error rates.
• Recommended Readings:
  • Shoemaker et al. 1999
  • MC Lecture notes 1999
• Hands-on: Detecting genotyping errors in your NGS data set using new software and a model-based approach.

9:00-10:00 AM – Conservation/Population Genomics: Tools to Answer Eco-Evolutionary Questions

• Keynote Lecturer: Paul Hohenlohe, University of Idaho
• Lecture: Population Genomics and Concepts for Conservation & Molecular Ecology
• Recommended Readings:
  • Andrews et al. 2016
  • Hohenlohe et al. 2018

10:15 AM-12:00 PM – Discussion/Lecture

• Instructor: Amanda Stahlke, University of Idaho
• Hands-on: From raw RADseq reads to genotyping de novo and effects of parameter choices on F_ST
• Recommended Readings:
  • Paris et al. 2017.
  • Rochette et al. 2019. Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Mol Ecol.; 28: 4737-54.
• Note: Participants may need help getting through initial FASTQ quality control and de-multiplexing, etc. Amanda can provide one-on-one (or small group) consultation on Day 3 and 4 by appointment.

12:00-1:00 PM – Lunch/Brain-Break

1:00-2:00 PM – Continued: From Raw RADseq Reads to Genotyping

2:15-4:30 PM – Discussion/Lecture

• Instructor: Rena Schweizer, University of Montana
• Hands-on: Reference-based Genotyping with the GATK pipeline & best practices
• Recommended Reading

9:00-9:45 AM – DNA Capture and Loci Under Selection

• Keynote Lecturer: Rena Schweizer, University of Montana
• Lecture: Conceptual and Practical Aspects of Gene-Targeted Capture with Empirical Examples
• Recommended Readings:
  • Schweizer et al. 2016
  • Jones and Good 2016
  • Hendricks and Schweizer et al. 2018 (Heredity)

10:00 AM-12:00 PM – Hands-on: Targeted Capture: Filtering variants and predicting functional effects of coding region variants

12:00-1:00 PM – Lunch/Brain-Break

1:00-1:45 PM – Genome Sequencing & Assembly

• Keynote Lecturer: Gregg Thomas, University of Montana
• Lecture: Conceptual and Practical Aspects of Genome Sequencing & Assembly
• Recommended Readings:
  • Heather and Chain 2016
  • Rice and Green 2019
  • Gopalakrishnan et al. 2017

2:00-4:00 PM – Hands-on: Assembly Activity/Lesson

Instructor: Ellie Armstrong, Stanford University

9:00-9:45 AM – Assembly and Quality

• Keynote Lecturer: Robert Waterhouse, University of Lausanne, Switzerland
• Lecture: BUSCO Assessments, Phylogenomics, and Gene Family Evolution
• Recommended Readings:
  • Waterhouse et al. 2019
  • Waterhouse et al. 2017
  • Simao et al. 2015
  • Waterhouse et al. 2013
  • Waterhouse 2015

10:00 AM-12:00 PM – Hands-on: BUSCO and How to Estimate & Improve BUSCO Scores

12:00-1:00 PM – Lunch/Brain-Break

1:00-1:45 PM – PacBio: Long-read Technology and Advantages

• Keynote Lecturers:
  • Kristin Mars, Sequencing Applications Specialist, PacBio
  • Sarah Kingan, Senior Staff Bioinformatics Scientist, PacBio
• Lecture: Genome Assembly with PacBio HiFi Data: What is High Quality and How Do You Get There?

2:00-2:45 PM – Dovetail Genomics

• Keynote Lecturer: Mark Daly, Dovetail's Director of Business Development
• Lecture: Building the Best de novo Genome Assemblies, Hi-C, the Future

9:00-9:45 AM – Haplotyping

• Keynote Lecturer: Eric Anderson, National Marine Fisheries Service, Santa Cruz, California
• Lecture: Principles and Practical Aspects of Calling Haplotypes from Short Read Data
• Recommended Reading: Baetscher et al. 2017 (Mol Ecol Res)

10:00 AM-12:00 PM – Hands-on: Using Microhaplot Software for Genotyping (using SE reads)

12:00-2:00 PM – Lunch/Brain-Break

2:00-2:45 PM – Structural Variants

• Keynote Lecturer: Maren Wellenreuther, University of Auckland, New Zealand
• Lecture: Structural Variants and Fitness
• Recommended Reading: Wellenreuther et al. 2019 TREE

3:00-4:00 PM – Discussion on Data Interpretation and Detecting Inversions

• Keynote Lecturer: Maren Wellenreuther, University of Auckland, New Zealand

9:00-9:45 AM – Effective Population Size, Genomics, and the Value of Simulations

• Keynote Lecturer: Robin Waples, NOAA, National Marine Fisheries Service, Seattle
• Lecture: N_e, N_b, Genomics, and Age Structured Populations
• Recommended Readings:
  • Waples et al. 2013
  • Hollenbeck et al. 2016

10:00 AM-12:00 PM – Hands-on: What is the value of simulations? N_e simulations to understand N_e

• Recommended Readings:
  • Waples and Do 2010
  • Balloux 2001 (EasyPop note)

12:00-1:00 PM – Lunch/Brain-Break

1:00-1:45 PM – Whole Genome Sequences, Chromosomal Tracts, Runs of Homozygosity, and Inbreeding

• Keynote Lecturer: Marty Kardos, NOAA, National Marine Fisheries Service (NMFS)
• Lecture: Genomics, Inbreeding, and Runs of Homozygosity
• Recommended Readings:
  • Kardos et al. 2016 (Evol. Apps.)
  • Kardos et al. 2018 (Nature Ecol. & Evol.)

2:00-4:00 PM – Hands-on & Discussion: Inbreeding Estimation and RoH Data Analysis with R

9:00-9:45 AM – Landscape Genomics

• Keynote Lecturer: Brenna Forester, Colorado State University, Ft. Collins
• Lecture: Detecting Local Adaptation with Genomic and Environmental Data
• Recommended Reading: Rellstab et al. 2015

10:00 AM-12:00 PM – Hands-on: Genotype-Environment Association Analysis Using RDA and LFMM

12:00-1:00 PM – Lunch/Brain-Break

1:00-1:45 PM – Genome-Wide Association Analysis

• Keynote Lecturer: Marty Kardos, NOAA, National Marine Fisheries Service (NMFS)
• Lecture: GWAS Overview, Recent Examples, and Power Analysis

2:00-4:00 PM – Hands-on: Genome-Wide Association Analysis

• Recommended Readings:
  • Husby et al. 2015
  • Kardos et al. 2016 (Mol Ecol Res)
  • Schielzeth & Husby 2014

9:00-9:45 AM – Gene Expression, Transcriptomics, GWAS, Selection and Adaptive Evolution

• Keynote Lecturer: Joanna Kelley, Washington State University
• Lecture: RNA Sequencing, Gene Expression Analysis, and Adaptation
• Recommended Readings:
  • Ozsolak and Milos 2011 (NRG)
  • Kelley et al. 2012 (BMC)

10:00 AM-12:00 PM – Hands-on: Read Mapping, Exact Tests for Differential Expression

12:00-1:00 PM – Lunch/Brain-Break

1:00-3:00 PM – Zoom with Instructors for Advice/Feedback on Data Analysis

• Instructors:
  • Joanna Kelley, Washington State University
  • Marty Kardos, NOAA, National Marine Fisheries Service (NMFS)
  • Brenna Forester, Colorado State University, Ft. Collins
  • Robin Waples, NOAA, National Marine Fisheries Service, Seattle
  • And others... Contact them for an appointment.

3:00-4:00 PM – N_e Student Reports from Group Projects: Simulations & Evaluating N_e Estimators

• Instructor: Robin Waples, NOAA, National Marine Fisheries Service, Seattle

9:00-9:45 AM – Connectivity & Assignment Tests

• Keynote Lecturer: Steven Mussmann, US Fish & Wildlife Service
• Lecture: Estimating Contemporary Gene Flow/Connectivity & MU Identification
• Recommended Readings:
  • Lowe Allendorf 2010
  • Meirmans 2014
  • Faubet et al. 2007

10:00 AM-12:00 PM – Hands-on: Inferring Connectivity Using BayesAss & BA3-SNPs

12:00-1:00 PM – Lunch/Brain-Break

1:00-2:00 PM – Conservation Genetics, Population Structure and the Delimitation of CUs

• Keynote Lecturer: Chris Funk, Colorado State University, Ft. Collins
• Lecture: Inferring Population Structure and Conservation Units Using Genomics, and "Putting the Conservation in ConGen"
• Recommended Reading: Funk WC, McKay JK, Hohenlohe PA, Allendorf FW (2012)

2:00-3:00 PM – Hands-on: Inferring Population Structure Using SNP Data

• Instructor: Brenna Forester, Colorado State University, Ft. Collins

3:00-4:00 PM – Course Review, Take-Home Messages, Wrap Up

• Lecturers/Leaders: Gordon Luikart, Joanna Kelley, Marty Kardos, Brenna Forester, Robin Waples, Chris Funk, Amanda Stahlke, Eric Anderson et al.

4:30-4:45 PM – Course Evaluations

• Check your email to receive a link to answer a few questions to help improve ConGen for future students.