Course Description
Biological diversity and how ecological questions are addressed through patterns of genetic diversity. The focus is on how genetic data can reflect demographic processes. An integrative overview of how field and genetic studies complement each other for describing the distribution and abundance of organisms.
Additional Requirements for Graduate Students:
Writing assignments for graduate students will be expected to
synthesize results across studies in a more formal meta-analysis
or model-based form. All students will be presented with reading
and lecture-based material and opportunities for in-class data
exploration or analysis. Graduate students will, in addition,
work through a series of training exercises to be able to
manipulate and analyze population genetic data using R and
simulation software. Graduate students will also be required to
generate syntheses of data or results, as well as gain
analytical expertise. Writing will be assessed with a common
rubric but with higher standards for the number or breadth of
resources included in the graduate reports.
Athena Title
Molecular Ecology
Prerequisite
GENE 3000-3000D or GENE 3000H or GENE 3000E or (ECOL 3500 and ECOL 3500L) or ECOL 3505H-3505L or PBIO 3650-3650L or (FANR 3200W and FANR 3200L) or permission of department
Semester Course Offered
Offered spring
Grading System
A - F (Traditional)
Course Objectives
Students successfully completing this course will learn how to evaluate coalescent hypotheses, set up basic simulations and analyses, and will understand how genetic data can, and cannot, be used to describe the demographic history of populations. The application of such analyses to conservation, biogeography, and ecology will be discussed. The successful student will also learn to explore multilocus or genomic data sets for outliers from the prevailing demographic history to identify genes that may be adaptive. Students will read papers from the primary scientific literature and be prepared to present the methods and conclusions of those papers orally to the class.
Topical Outline
1. Diversity within samples (alpha diversity) Molecular markers Modes of inheritance Measures of genetic diversity Molecular models of evolution Hardy Weinberg Wahlund effects Coalescent theory Random genetic drift Mutational diversity within populations Temporal changes in diversity Measures of effective population size Neutrality tests Unit 2 – Diversity among samples (beta diversity) Population “structure” Gene flow Differentiation statistics and AMOVA Population/spatial models Outlier distributions Phylogeography Net divergence Dating Reciprocal monophyly STRUCTURE Diagnosis of movement/dispersal/gene flow Outlier data Candidate loci Whole genome data Unit 3 – Diversity, interactions, and responses to environmental change How environmental stress is mirrored in molecular changes in individuals or populations Range of responses – physiology, acclimation, changes in expression, transgenerational plasticity Longer term adaptation and strong selection How molecular markers describe immediate and long-term responses to shift in environment Microbiome/holobiome Predictions of organismal response to change Persistence Plasticity