Autumn
2012

FISH/BIOL 340 - Genetics and Molecular Ecology

Course Description

Rationale

In the past few decades, molecular genetics has become one of the fastest growing fields in the life sciences. The application of molecular methods has spread to virtually all fields of modern biology, including ecology, conservation, breeding and natural resource management, leading to the establishment of a new discipline, Molecular Ecology. With the expansion of the application of molecular tools, it has become crucial that all biologists have a basic understanding of genetics and molecular biology, and the application of molecular tools to the detection of kin, the identification of populations, the reconstruction of phylogenetic relationships, and more recently, to the understanding of local adaptation and evolution. Rather than providing an overview of classical genetics, the aim of the course is to provide an understanding of the genetic principles underpinning these applications, thus allowing an assessment of the potential and limitations of molecular approaches to specific questions in ecology, evolution and resource management.

The course will be important to students for the following main reasons:

Basic understanding: The current ubiquity of molecular genetic studies in virtually all fields of biology requires some basic understanding of the genetic principles underpinning molecular methods. Continuing developments in molecular technology, statistical analyses and computer power will further widen potential applications. Thus, even if students do not envisage using genetics in their own research, some genetic knowledge will be necessary in almost any career track.
Practical application: If molecular genetic methods are to be applied effectively in ecology, evolution and general biology, they have to be carefully chosen according to the ecological and biological circumstances, assumptions of the methods and desired outcomes. Furthermore, an understanding of the evolutionary dynamics of molecular markers in the context of the biological question of the research is a crucial prerequisite for the interpretation of genetic data. It is thus necessary that students have a good overview of available methods, their appropriate application and potential shortcomings.
Communication: Many of the current problems in the application of genetic data are founded in conceptual misunderstandings between scientists applying genetic methods and the end users of their research (fisheries managers, breeders, forest managers, conservationists). It is therefore important that students are aware of these misunderstandings and are able to understand and explain genetic research.

Aim

To provide students with a fundamental understanding of genetic principles underlying the application of molecular genetic techniques.

Specific Objectives

Students will be able:

To understand basic principles of molecular genetics
To apply such principles to ecological, environmental and conservation research
To interpret genetic data in an applied context
To communicate and disseminate the results of their research

Basic Approach

We will achieve the above aim and objectives by the following means

Lectures: lectures will be the basic means of teaching in this class. Powerpoint files will be uploaded on the syllabus page on the day of the previous lecture. These lectures will be much more useful if you interrupt me and ask questions if anything at all is unclear. Despite the large class size, I am aiming for a dialogue rather than a monologue. At the beginning of class we will consider some questions from the previous lectures, and we will also work through some questions from the exams of previous years. This year, we will use clickers to broaden audience participation.
Textbook: there is no required textbook for this class, but some are highly recommended (see Readings page). On the last slide of each lecture, I will provide a study guide with reference to specific sections in the textbook. These sections will be material that may be on the exam.
Primary literature: There are links to primary literature in the field on the Readings page. All these papers are fairly brief and easy. Don't worry too much about details of the methods, but consider the problem, the approach the authors took, their general results and their interpretation of the results. You should read these papers - although they won't be on the exam per se, they may be used as examples in exam questions aiming at lecture material. Furthermore, they will help you deciding on style and detail needed for your project report.
Laboratories: computer labs and molecular labs will be used to improve and deepen your understanding of concepts and procedures from lecture and textbook. (see also the Labs page). In the computer laboratories we will use simulation programs to learn about genetic processes and analysis programs to analyze sample data sets. The molecular laboratories demonstrate some commonly used methods, and will be used for a lab project on the species identification of endangered seahorses.
Project Report: In the molecular laboratories, we will conduct a study identifying the species and possibly the origin of seahorses seized by the US Fish and Wildlife Service at SeaTac airport and other entry points (see lab project). Students will submit a 2500 word (about 8-10 double spaced pages) project report, which aims at integrating lecture material, laboratory experiments and literature and also will help to improve communication skills. We will write sections for this report for specific labs as the quarter progresses, using an online peer review system called SWORD.