25th Summer Institute in Statistical Genetics (SISG)

Module 4: Endangered Populations & Non-model Organisms

Mon, July 13 to Wed, July 15

Module dates/times: Live sessions will start no earlier than 8 a.m. Pacific and end no later than 2:30 p.m. Pacific, except for Wednesdays. For modules that end on Wednesday, live sessions will end by 11 a.m. Pacific. For modules that start on Wednesday, live sessions will begin no earlier than 11:30 a.m.

This module provides training in conceptual foundations and practical aspects of genetics and genomics tools relevant for natural populations, threatened populations, and non-model organisms. Many of the motivating examples are relevant to issues in conservation of species. Students will learn foundational models in population and evolutionary genetics, as well as core methods used in genetics and genomics. Topics covered include genetic variation, dynamics of small populations, effective population size, population fragmentation and gene flow, phylogeography, inbreeding and inbreeding depression, and natural selection. It also covers methods for developing genomic resources for non-model organisms, with an emphasis on next generation sequence data generation and analysis (RAD-seq, whole genome sequencing, transcriptome sequencing). As it introduces many of the principles and applications of populations genetics, it serves as an excellent precursor to Population Genetics (SISG Module 7). Topics covered are easily applied to model organisms.

This module has been developed using the framework of Scientific Teaching (1). Specifically, we implement backwards design, student-centered learning, and assessment. The course highlights diversity on every axis, including the students, instructors, mode of teaching, and course content. The instructors also intentionally cultivate inclusivity in the classroom using techniques from Tanner (2) which include wait time, think-pair-share, whip around, and multiple hands multiple voices. Student-centered learning activities for this specific course include bookending with discussion (3) and group brainstorming/crowdsourcing (4). In addition, computer-based learning (4) will be implemented using R (in R Markdown) to illustrate fundamental concepts such as sampling, Hardy-Weinberg Equilibrium, and Random Genetic Drift.

After completing this module, students will be able to:

  1. Articulate various uses of DNA polymorphism data with some emphasis on endangered and non-model species.
  2. Recognize some of the inherent challenges in defining species and subspecies divisions, both with respect to genetic information and public policy.
  3. Understand connections between random genetic drift, small population sizes, inbreeding coefficients, and inbreeding depression; and, articulate the consequences of these factors for real populations.
  4. Describe the concept of heritability on a theoretical level and an intuitive level, and explain how estimates of heritability are relevant to assessing a population's potential to survive in the face of a changing environment.
  5. Provide examples of how phylogenetics methods can be used to inform conservation practices

Nadia Singh is an Associate Professor of Biology and a member of the Institute for Ecology and Evolution at the University of Oregon. Her research focused on the causes and consequences of variation in fundamental genetic processes for evolution. She is particularly interested in phenotypic plasticity in recombination and the molecular mechanisms underlying this phenomenon. She recently published “Wolbachia Infection Associated with Increased Recombination in Drosophila” G3: Genes, Genomes, Genetics, 9(1) 229-237, 2018. She is a recent graduate of the University of Oregon Mobile Summer Institute on Scientific Teaching, and recently completed Science Communication Training associated with the Alan Alda Center for Communicating Science. At the University of Oregon she is the chair of the Diversity, Equity and Inclusion committee for the Biology Department and the founder and chair of the Natural Sciences Diversity Leadership Committee. She is also currently serving on the Diversity, Equity and Inclusion committee for the Genetics Society of America.

Dahlia Nielsen is an Associate Professor of Biological Sciences and a resident member of the Bioinformatics Research Center at North Carolina State University. Her research focuses on methods development and applications in identifying genes underlying complex traits, including gene expression responses and molecular signaling between hosts and pathogens. She has been engaged in various projects to develop genomic resources for non-model species. She recently published “Networks Underpinning Symbiosis Revealed Through Cross-Species eQTL Mapping.” Genetics 206(4): 2175-2184, 2017. She has attended workshops in teaching STEM, including a multi-day workshop in Active Learning taught by Rebecca Brent and Richard Felder. Drs. Brent and Felder are pioneers in learner-centered approaches to teaching.

  1. Handelsman, J., et al. Scientific Teaching. New York: W.H. Freeman and Company. 2007.
  2. Tanner, K. D. 2013. Structure Matters: Twenty-One Teaching Strategies to Promote Student Engagement and Cultivate Classroom Equity. Cell Biology Education 4(4) pp 262-268.
  3. Allen, D. and K. Tanner. 2017. Infusing Active Learning into the Large-enrollment Biology Class: Seven Strategies, from the Simple to Complex.  
  4. Handelsman, J. et al. 2004. Scientific Teaching. Science 304(5670) pp 521-522.