BIOL4585 J-term

Evolutionary Genomics (J-term 2021-2022)

In this course, we will use cutting edge genomic techniques to understand how studying whole genomes can shed light into the fundamental processes which allow natural populations to survive, and thrive in the context of complex ecological interactions. This is an advanced course and will provide a full two-week immersion program into the world of genomics.
Programming in R and Unix is preferable but not required, as there will be resources to learn these computer languages. As part of this course, we will engage in analyses of real and simulated genomic data. Each meeting will be divided in three portions. First a lecture, second a student-lead discussion on a selected paper, lastly a practicum on genomics data.

Frequently Asked Questions:

When is the course being offered?

This is a J-term course offered January 2022. The course will meet Jan 3 - Jan14, 2022. The class meets for 4 hours, from 10 am to 3 pm. This includes a lunch break at noon.

What is the intended audience for this course?

This class is aimed at biologists as well as individuals who are very interested in evolutionary genomics. The course will have a strong emphasis on reading primary literature about how the fundamental evolutionary forces: natural selection, mutation, recombination, and demography, shape species genomes and phenotypes. We will also explore data via practicums on our UVA supercomputer (Rivanna).

I am an advanced coder, is this class relevant for me?

This class is focused on the biology of genomes, thus, even if you are an advanced coder, there may still be value in joining us to explore the wonderful world of evolutionary genomics

What items do I need for this class?

You need a computer able to connect to the internet. PC or Mac, both work. If you don't have a personal computer you may get a loaner from UVA for the term. The course will have audio visual materials to go over during class and at home so headphones can be useful too.

How can I find the course in SIS?

This course is listed in SIS as  BIOL 4585 offered in the 2022 January term. Section 001-SEM (10072). Topic: Evolutionary Genomics. The course is considered a seminar with 3 credits

Do I need to know coding to do well in the class?

No, you don't need to be an advanced coder to do well on the class. As part of this course we will learn the basis of doing biology in supercomputers. These skills will be covered from scratch. There will be a project portion of the class that includes coding but I will provide you with the tools to complete it.

I am a graduate student. Can I take the class?

This class is geared towards undergraduates. But, graduate students may join on a lecture-to-lecture basis, e.g., to discuss a paper of great interest. This is contingent on instructor permission, i.e., grad students should come talk to me first!

What are the prerequisite courses?

To take this course you should have completed the introductory biology series. e.g., BIOL2200, and BIOL3020 Evolution and Ecology.

 
 

What a class session looks like:

10 am - 11 am

A lecture discussing  theory and applications of the day's topic

11 am -12 pm

A paper discussion led by a student or group of students

1 pm - 2 pm

Practicum on bioinformatic skills using UVA's supercomputer Rivanna

2 pm - 3 pm

Practicums may continue or may break into small group discussions

Supercomputer Tutorials

 

Topics:

Jan 3

Lecture: Fundamentals of Evolutionary thinking: history and trajectory of the field

Hands on: A Primer on Bioinformatics and Rivanna [click here to go to the practicum]

Jan 4

Lecture: Fundamentals of DNA technology: how do we sample genomes?

Paper: DNA sequencing at 40: past, present, and future. Shendure et al. [find it here: link]

Hands on: Working with Sequencing data: how to assemble a genome from pieces to whole

Jan 5

Lecture: Genomes evolving in phylogenetic "trees" (i.e., the tree of life)

Paper: The hidden biology of sponges and ctenophores. Dunn et al. [find it here: link]

Hands on: Characterizing the genome: discovering and annotating genes

Jan 6

Lecture: Genome-wide Mutation rates and the fundamentals of molecular evolution

Paper: The Causes and Consequences of HIV Evolution. Rambaut et al. [find it here: link]

Hands on: How to discover mutations in populations: Mapping DNA onto genomes

Jan 7

Lecture: Experimental design for genomic studies: Reverse Ecology

Hands on: Basics of Git for version control

Hands on: Open Workshop for group projects I

Jan 10

Lecture: Genomic consequences of evolution in finite populations: mating systems and genetic drift

Paper: Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction. Robinson et al. [find it here: link]

Hands on: Measuring genetic diversity in whole genomes

Jan 11

Lecture: Genomes as records of populations moving in space: Migration and biogeography

Paper: Genes mirror geography within Europe. Novembre et al. [find it here: link]

Hands on: Measuring population structure in genomic data

Jan 12

Lecture: What is, and what isn’t an adaptation? – A genomic perspective

Paper: The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Gould and Lewontin. [find it here: link]

Hands on: Discovering footprints of natural selection in populations I

Jan 13

Lecture: A needle in a haystack: Finding evidence of natural selection in whole genomes

Paper: Footprints of natural selection at the mannose-6-phosphate isomerase locus in barnacles. Nunez et al. [find it here: link]

Hands on: Discovering footprints of natural selection in populations II  +

Hands on: Open Workshop for group projects II

Jan 14

Final Presentations

 

Assignments

Class participation (500 pts)

Students will be given points for actively participating in class (up to 50 pts per class x 10 sessions). Participation will be assessed based on a predetermined rubric.

Class discussion leader (700 pts)

Students will obtain points based on their performance when leading the week’s discussion. This will be assessed based on a predetermined rubric.

Reading summaries (700 pts)

Every day, students will turn-in a short (1/2 page long) reading summary of the daily assigned reading. This will be assessed based on a predetermined rubric. 100 pts per paper (x 7 papers).

Final presentation (800 pts)

For the final project, students will analyze a mystery dataset and will use their new skills to discover what processes are at play in the dataset. This dataset will be given on the Friday of week one (giving a whole week for students to play with the data). Prior to final submission, the students will have the opportunity to obtain feedback from the instructor via an online platform and class dialogue. This assignment will be assessed based on a predetermined rubric.

Coding homework (200 pts)

I will give a small coding quiz at the end of each practicum to test newly acquired coding skills. Each mini-quiz is worth 25 pts. These are low-stakes quizzes  meant to help solidify new concepts. These quizzes are intended for students who are brand new to coding.