Title: A capstone research experience in evolutionary genomics
Christopher H. Chandler1*
Affiliations:
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Department of Biological Sciences, SUNY Oswego, Oswego, NY 13126
*Correspondence to: Christopher Chandler, christopher.chandler@oswego.edu, SUNY Oswego
address....
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Abstract Page
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that sets the teaching challenge that you address in this manuscript, provide background
information specific to this Lesson, briefly description the Lesson, and end with a concluding
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Course
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Lesson Length
o Portion of one class period
o One class period
o Multiple class periods
o One term (semester or quarter)
o One year
o Other
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Key Scientific Process Skills
o Reading research papers
o Reviewing prior research
o Asking a question
o Formulating hypotheses
o Designing/conducting experiments
o Predicting outcomes
o Gathering data/making
observations
o Analyzing data
o Interpreting results/data
o Displaying/modeling results/data
o Communicating results
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Pedagogical Approaches
o Think-Pair-Share
o Brainstorming
o Case Study
o Clicker Question
o Collaborative Work
o One Minute Paper
o Reflective Writing
o Concept Maps
o Strip Sequence
o Computer Model
o Physical Model
o Interactive Lecture
o Pre/Post Questions
o Other
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Bloom’s Cognitive Level (based on
learning objectives & assessments)
o Foundational: factual knowledge &
comprehension
o Application & Analysis
o Synthesis/Evaluation/Creation
Biochemistry
Cell Biology
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Genetics
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Molecular Biology
Introductory Biology
Course Level
o Introductory
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Class Type
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Audience
o Life Sciences Major
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o Non-Traditional Student
o 2-year College
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Class Size
o 1 – 50
o 51 – 100
o 101+
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Principles of how people learn
o Motivates student to learn material
o Focuses student on the material to
be learned
o Develops supportive community of
learners
o Leverages differences among
learners
o Reveals prior knowledge
o Requires student to do the bulk of
the work
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Vision and Change Core Concepts
o Evolution
o Structure and Function
o Information flow, exchange and
storage
o Pathways and transformations of
energy and matter
o Systems
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Vision and Change Core Competencies
o Ability to apply the process of
science
o Ability to use quantitative
reasoning
o Ability to use modeling and
simulation
o Ability to tap into the
interdisciplinary nature of science
o Ability to communicate and
collaborate with other disciplines
o Ability to understand the
relationship between science and
society
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Key Words: List 3 – 10 key words that are
relevant for the Lesson (e.g. mitosis;
meiosis; reproduction; egg; etc.)
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Scientific Teaching Context Page
Learning Goal(s):
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Students will understand the utility of next-generation DNA sequencing, especially
applications for studying evolution and non-model organisms.
Students will be able to formulate a scientific question and hypothesis relating to
evolutionary genomics, design and carry out a test of this hypothesis (either a novel
experiment or with existing data), and analyze and interpret data.
Students will be able to communicate their results with others.
Students will be able to analyze and evaluate scientific literature.
Learning Objective(s):
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Write a project proposal clearly describing a novel research question and its significance
and the methods (utilizing next-gen sequence data) that will be used to address it.
Write a clear, complete final paper formatted like a journal article that provides the
rationale behind the study and the specific question or hypothesis it addresses, the
methods used, the results, and the interpretation and significance of those results.
Write a detailed, constructive, formal peer review of another student's paper.
Give a clear 12-15 minute presentation on the project that includes an appropriate amount
of detail.
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Main Text
1. Introduction:
Rough outline:
—Rationale: Next gen sequencing is revolutionizing the way biological research is conducted.
Interdisciplinary skills (especially computational and quantitative skills) are increasingly
important for success in a variety of biological careers. Understanding of the scientific method
and the ability to communicate effectively is also essential for a scientifically literate society.
—Intended audience: This is a 3-credit capstone research experience (BIO 492 at SUNY Oswego). The
students are senior biology and zoology majors who have taken genetics, at least one biological
statistics course, and a variety of electives in the biological sciences. There are twelve students
per section.
—Pre-requisite student knowledge: Students are expected to understand basic principles of inheritance
and molecular genetics as well as essential evolutionary concepts (e.g., mutation, genetic drift,
and selection).
—Learning time: 14-week course (+1 final meeting during exam week for presentations); the course
meets for a single 3-hour block each week. Students are also expected to commit substantial time
outside of class to work on their projects independently.
2. Scientific Teaching Themes:
—Active learning: The course will utilize in-class lab exercises giving students an opportunity to learn
and apply bioinformatic skills, with instructor and peer support. Group discussions of primary
literature on problems in genomics will reinforce key concepts. Students (working in pairs) will
develop their own research questions within a single research framework that can be answered
using existing datasets. They will continue analyses on their own outside of class time, and a
portion of class time will be used similar to a lab meeting, in which students will share their
progress and challenges they are facing, and provide suggestions to help other groups. Students
will also provide peer reviews of rough drafts of papers and on final presentations.
—Assessment: Smaller assessments will be given throughout the semester to test students' understanding
of key concepts (e.g., importance of quality control for NGS data). After students complete these
assessments individually or in small groups, their responses will be discussed as a class. There
will also be multiple large assignments: a final paper in the form of a scientific manuscript
describing the students' research project; a formal peer review of another students' final paper
rough draft (written as though the draft was being reviewed for publication in a journal); and a
12-15 minute presentation, similar to a conference talk.
—Inclusive teaching: Given the student makeup at SUNY Oswego and that taking a BIO492 is required,
students with a variety of backgrounds are expected to enroll. Within the framework of the
course, students will have freedom to develop their own specific research question/hypothesis,
facilitating the exchange of ideas and viewpoints.
3. Lesson Plan:
Week
1
Topic
Introduction: present students with the broad research framework to be addressed in the
course (bring a few specimens of the study organism to class), and the datasets that are
available to them. Students will brainstorm some specific research questions and have
a discussion about how those questions might be answered.
Afterwards, to expose students to some potential applications of NGS, pairs of students
will be assigned journal articles to read in which genomic data were used to answer an
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evolutionary question. Students will prepare short presentations on their assigned
papers for the following week.
Brief student presentations on applications of NGS data
Overview of sequencing technologies and how they work
Introduction to UNIX—directories and files
Assignment: log in and run some basic commands (e.g., cd, pwd, cp, mv, rm, mkdir)
Sequence QC (trimming/filtering)
Sequence assembly and measures of assembly quality (e.g., N50)
Assignment: perform small sequence assembly and explore how varying k affects
assembly quality
Transcriptomes and brief introduction to annotation
Assignment: perform a local BLAST search of a transcriptome to identify homologs of a
specific protein
ddRADseq and potential applications—identifying SNPs and sex-specific/sex-linked
markers
Assignment: 1-paragraph project idea utilizing datasets available to students
Share and discuss preliminary project ideas
Comparative genomics
Assignment: Revise project ideas
Discuss revised project ideas
Introduction to R (using variables)
Assignment: R exercise, begin analyses to address research questions
R continued (if statements, loops)
Analyses—group "lab meeting"
Assignment: R exercise, continue analyses
R continued (data frames and plotting)
Analyses—group "lab meeting"
Assignment: R exercise, continue analyses
Analyses—group "lab meeting" (by this point, analyses should be nearly complete)
Assignment: tie up loose ends in analyses; draft Introduction
Due: Introductions
In class: Exchange Introduction sections, provide informal peer feedback, discuss writing
& revising strategies
Assignment: Draft Methods & Results, including a figure
In class: Exchange Methods & Results sections, provide informal peer feedback, discuss
writing
Assignment: A complete rough draft of final paper
In class: Discuss peer review process and look at examples of actual peer reviews
Assignment: Peer reviews
In class: Return and discuss peer reviews; discuss presentations and begin working on
presentations
Finals week; due: presentations & revised final paper
In the pilot version of the course at SUNY Oswego, student projects will center on the evolutionary
genetics of a local species of terrestrial isopod (Trachelipus rathkei). They will have access to at
least two datasets: a transcriptome dataset (raw Illumina reads from mRNA extracted from
head/antenna, leg, ventral muscle/nerve, and gonads, from one male and one female); and a
ddRAD-seq dataset (gDNA from 13 males and 13 females).
Potential student projects could include:
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—Identifying homologs of specific genes in the transcript data (e.g., look for homologs of doublesex),
and comparing predicted protein sequences to those of other crustaceans or more distant
arthropods (e.g., which regions are highly conserved or divergent?)
—Demographic inferences based on allele frequencies from ddRAD-seq (e.g., inbreeding, polymorphism
in coding vs. non-coding regions)
—Exploring how varying parameter values affects assembly outcomes with these datasets
4. Teaching Discussion:
Potential modifications/add-ons:
—The open "lab meeting" weeks provide a buffer in case earlier activities take longer than expected.
—While budget constraints will likely preclude generating new NGS datasets during the course, there
may be some money for smaller follow-up work in the molecular lab. Thus, during weeks 7-11, if
students finish NGS analyses early, they may be able to perform some follow-up experiments
(e.g., use qRT-PCR to test for sex-specific or sex-biased expression of candidate genes)
(Further detail to be added after course is taught)
 Subheadings: can be included within the sections above to increase readability and clarity.
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Acknowledgments
Begin the Acknowledgements on a new page. The acknowledgements can be multiple
paragraphs.
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References
Begin the References on a new page.
* Cite references in the text using superscript Arabic numbers. Use commas to separate multiple
citation numbers. Superscript numbers are placed outside periods and commas and inside colons and
semicolons.
1. Begin the reference list on a new page. The reference list is comprehensive and spans the text, figure
captions and materials.
2. Number references in the order in which they appear in the text. Follow ASM style and abbreviate
names of journals according to the journals list in NCBI. List all authors and/or editors up to 6; if
more than 6, list the first 3 followed by “et al.” Note: Journal references should include the issue
number in parentheses after the volume number.
Examples of reference style:
1. Knight JK, Wood WB. 2005. Teaching more by lecturing less. Cell Biol Educ. 4(4):298-310.
2. Samford University. How to get the most out of studying: A video series.
www.samford.edu/how-to-study/. Accessed August 20, 2013.
3. Handelsman J, Miller S, Pfund C. 2006. Scientific Teaching. New York, NY:W.H. Freeman.
3. Please add notes to the end of the reference list; do not mix in references with explanatory notes.
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