ConGen-January 2028, Quito, Ecuador: Agenda
Pre-Course Preparation Lectures:
Students are encouraged to join us for a series of pre-workshop Zoom lectures to be held during Nov-Dec, 2027. These lectures are designed to maximize the student's learning potential during the workshop. The hands-on activities are designed teach novice users the commandline basics and serve as a refresher for seasoned coders
Basic R Studio & Linux
Keynote lecturer: Will Hemstrom.
Consider doing the “DataCamp” at https://www.datacamp.com/courses/introduction-to-bash-scripting, Also: see “Learning the Shell” at LinuxCommand.org: Learning the shell.. The data camp is free and lasts up to 3-4 hours.
Genomic Data, The fastq Format & Basic Quality Control
Keynote lecturers: Will Hemstrom.
Hands-on: Using your laptop, we’ll conduct a brief activity to ensure everyone has a foundational understanding of using BASH to be more prepared for the course.
Basic-to-Advanced Bioinformatics Strategies for NextGen Data Analyses.
KeyNote: Rena Schweitzer
Careers & Advice for Success in Conservation Genetics
KeyNote: Helen Taylor or TBD
Probability, Bayesian Stats, MCMC, Genotype Likelihoods.
Keynote lecturer: Eric Anderson
Hands-on: Using R on your laptop: Visualizing and understanding genotype likelihoods, propagating uncertainty. Required software: R (tidyverse, viridis, vcfR packages).
The Coalescent.
Keynote lecturer: Arun Sethuraman
Hands-on: Using your laptop: Coalescent simulations, and the Site Freq Spectrum
Conservation/Pop genomics: Concepts & Tools to Answer Eco-Evo Questions
Keynote lecturer: Paul Hohenlohe
Role of Genetics in South American/Ecuadorian Conservation: Needs & Success Stories
Keynote lecturer: Jaime Chaves
Workshop Schedule:
Day 1 (Monday, Jan 4) – Arrival, move-in, computer testing, welcome & overview
Introduction & overview of conservation genetics/omics
Keynote address: “What is the role of genomics in conservation?”, Marty Kardos
Recommended reading: Kardos et al. 2021 - PNAS; May et al. (2025, Mol Ecol,
Student-attendee BRIEF elevator speech introductions. 1 minute per student. One slide maximum showing your ONE main research question and main study species. No slide animations please!
Day 2 (Tuesday) – Topics: Markers, data filtering, genotype calling w/ next gen data
Genetics markers in conservation: microsats-to-WG-seq
Keynote lecturer: Paul Hohenlohe
Hands-on: Raw reads to genotype calls with and without a reference, PCR dups, MAF, etc.
Keynote lecturer: TBA
Software/Scripts: STACKS, GATK, samtools
Hands-on: Raw reads to genotypes continued
The F-word: Filtering best-practices, effects of F choices - on PCAs, etc.
Keynote lecturer: Will Hemstrom (with Laura Bertola)
Hands-on: Post-genotyping filtering effects on PCAs and genetic diversity statistics.
Keynote lecturer: Will Hemstrom (with Laura Bertola)
Software/Scripts: snpR
Q & A with instructors
Attend a group session on genotyping with (or without) a reference; or book a time slot with an instructor or to ask questions about your research, data, hands-on exercises, etc.
Day 3 – (Wednesday) Filtering, HW, GTseq, inbreeding & runs of homozygosity
Hardy-Weinberg: The null model for population genetics
Keynote lecturer: Will Hemstrom
Hands-on: Detecting & interpreting patterns and causes of HWE deviations
Keynote lecturer: Will Hemstrom
Snakemake pipelines
Keynote Lecturer: Eric Anderson
PID, Match probability, forensics applications
Keynote Lecturer: Eric Anderson (or TBD)
Hands-on: Calculating probability of identity and designing marker sets
Keynote Lecturer: TBD
Software/Scripts: GenAlEx
GTseq panels for genetic monitoring, ESU identification
Keynote Lecturer: Lisette Waits
Inbreeding, runs of homozygosity, LD distributions, & identification of deleterious alleles
Keynote lecturer: Marty Kardos
Hands-on: Inbreeding estimation and RoH data analysis with R
Day 4 (Thursday) – Structure & Cons Units, Ne inference
Effective population size: what it is and how to estimate it
Keynote lecturer: Robin Waples
Hands-on: 1) Exploring genetic drift in R; 2) Estimating Ne in butterflies or in simulated data (e.g. with vs w/o substructure, immigration, etc.)
Inferring population structure & conservation units using genetics & omics
Keynote lecturer: Chris Funk, Brenna Forester
Hands-on with background information: Delineating conservation units
Time with Instructors: ask questions about your data, etc.
Popgen pipeline platform, hybridization, and role of AI in genomic data analyses
Keynote lecturer: Arun Sethuraman
Hands-on: Hybridization
Day 5 (Friday) – Ne indices, Assignment Tests, Landscape Genomics & Adaptation
Population assignment tests for forensics, conservation, and ecology
Keynote lecturers: Will Hemstrom
Hands-on: Discrete assignment (Rubias); Continuous Assignment (OriGen)
Detecting local adaptation using genotype-environment associations
Keynote lecturer: Brenna Forester
Hands-on: Genotype-environment association analysis using RDA and LFMM
Discussion – with everyone, all instructors + regional managers?
What are the main barriers to immediately improving the use of genetics for conservation (and how can we overcome them)? How to spark grant collaborations (SA-USA-etc.)? How to promote resource sharing (markers & data production, databases, bioinformatics, teaching, etc.). Can we genotype samples (cheaper) regionally and internationally? Best marker system for low cost, flexibility in # of loci (needed for many questions), and multi-species (cross-species transfer)? Recommended reading: Chap 24 in Allendorf et al. 2022 book; Helen Taylor’s Video-Lecture
Day 6 - 7 (Saturday - Sunday) Field Trip
Optional field trip to the Amazon Field Station. More info HERE.
Day 8 (Monday) – Genome assembly; Phylogenomics; eDNA & metabarcoding (multispecies analyses)
Genome sequencing & assembly: Conceptual and practical aspects
Keynote lecturer: Ellie Armstrong
Hands-on with background information: Assembling the Jocoto? (or Hornbill?) genome
Keynote lecturers: Ellie Armstrong (with Natalie Molea)
Phylogenomics for research and conservation
Keynote lecturer: Jaime Chaves
Hands-on: Interpreting program outputs
Final Discussion: Future research & teaching directions, questions, advice, and publishing a ConGen Review.
eDNA Metabarcoding for conservation & biodiversity research (concepts & examples)
Keynote lecturers: Steve Spear, Leif Howard
Hands-on: Estimating species diversity with two stringencies
Metabarcoding Hands-On
Final dinner (please sign up!); some leave/fly out
Day 9-13 Field Trip
Optional Field trip to Galapagos Research Station. More info HERE