Course Description

Course Description

Couse Description.

Goals: To train students, postdocs, faculty, and agency researchers to understand and use population genetics principles and DNA data to improve biodiversity conservation, population management, and eco-evolutionary research. The course teaches participants to understand, analyze, and interpret genetics datasets including microsatellites, SNPs, and genome-scale sequencing datasets (RADseq, amplicon-seq, targeted capture, WGseq). We will teach how to take raw sequencing reads through to genotyping (with & w/o a reference genome), along with genome assembly. This course often feels like a workshop because multiple instructors ask questions and provide helpful comments during another instructor’s lecture to help advance learning of basic and advanced concepts and approaches. The course will help bridge the gap between researchers and managers to improve conservation. This course is urgently needed given the biodiversity crisis and the recent Kunming-Montreal Global Biodiversity Framework in which 196 parties “committed to reporting the status of genetic diversity for all species"– wild and domestic (Mastretta-Yates et al. 2024; Hoben et al. 2024).

Target audiences: 

  • Advanced undergrads and technicians
  • Master's and Ph.D. students
  • Postdocs, faculty, government researchers or PIs
  • Conservation and wildlife managers (especially the overview & introductory lectures)

Recommended knowledge and background:

  1. Understanding of DNA markers (Microsatellites, SNPs, RADseq, WGseq), population genetic diversity metrics (H, allelic richness, haplotype diversity) and mechanisms of evolutionary change: genetic drift, gene flow, selection, & mutation. See Chap 4 in Allendorf et al. (2022) book. Ask for a free copy .pdf.
  2. Understanding of pop gen concepts and testing: effective population size, inbreeding depression, testing for HW and linkage disequilibrium, etc.). You’ll learn and conduct HW testing during the course.  See Chapters 5-9 in Allendorf et al. (2022) book. Ask instructors to send you Chapter 5 and the Appendix.
  3. Experience using R and Linux. You will learn basic R skills and Linux during our introductory lectures early in/before course. RStudio is used (on a cloud server) most weeks.
  4. Participants should understand English (written and spoken).

Workshop content:

ConGen teaches fundamental statistical and computational approaches that help prepare students and professionals to use population genetic and genomic data in their work. Microsatellites and SNP datasets will be discussed and analyzed – with forensics and other applications (individual ID and match probabilities). Emphasis will be on next-generation sequence (NGS) data analysis (RADs and genome sequencing/resequencing) and interpretation of output from fundamental and novel statistical approaches and software programs (including R and Linux command line). The course promotes interactions among early-career researchers e.g., grad students & postdocs), mid-career faculty and agency researchers, and leaders in population genomics to help develop our "next generation" of conservation and evolutionary geneticists. We will identify and discuss developments needed to improve data analysis approaches to advance the field. This course often feels like a workshop because multiple instructors ask questions and provide helpful comments during another instructor’s lecture to help advance learning of basic and advanced concepts and approaches.

This course will cover concepts and methods including the coalescent, Bayesian, and likelihood-based approaches. Special lecture sessions and hands-on exercises will be conducted on assessing population structure, testing for HW proportions, detecting selection, genetic monitoring (of Ne, FST, Nm, etc.), inbreeding detection (RoH), population assignment (with microsatellites then lcWGseq data), whole-genome sequencing & assembly, phylogeny construction & phylogenomics, and more.

We will use popular programs like Structure, NeEstimator, and packages in Rstudio. We’ll analyze datasets (hands-on) using key software packages including GenePop, Structure, Bottleneck programs, GeneClass, Rubias, WGSassign, etc.). We’ll discuss approaches for detecting illegal trafficking and quantifying dispersal of individuals using assignment tests. Finally, participants will learn to assess Ne without (and with) genetic data to help countries address the recent Kunming-Montreal Biodiversity Framework adopted by the UN Convention on Biodiversity (CBD) (see Mastretta-Yanes et al. 2024; Hoban et al. 2024).

You will learn about the latest/new services and technologies from companies like PacBio, Element, Oxford NanoPore, and Diplomics who also contribute training and sponsorship.

Video Recordings, Non-synchronous participation, TIME ZONE,

All lectures & hands-on sessions are recorded (on Zoom) and uploaded to Google Drive (immediately) for viewing or re-viewing later, after the lecture. This facilitates participation by attendees from other countries and time zones. Remote or non-synchronous participants can email questions to ConGen organizers or lectures. We typically have participants from overseas and from over 10 countries.

All lecture times listed in the schedule below are in Mountain Daylight Time (MDT).

Course Publications:

This course/workshop has led to publications describing the main topics, course outcomes, and recent advances in the field that facilitate data analysis for population geneticists worldwide. We hope to publish together a meeting review or mini-review after each ConGen. Email organizers to request participation in co-authoring a review paper.  For example, see 4 pubs and recommended reading list below: