Upper Division

EBIO 3080: Evolutionary Biology

Anonymous — Fri, 09 Jun 2017 21:12:37 +0000

EBIO 3080: Evolutionary Biology Anonymous (not verified) Fri, 06/09/2017 - 15:12

Evolutionary biology is a subject that unifies biology because it addresses questions about why the natural world is the way it is. This course focuses on the study of the principles of evolution and covers such topics as the origin of variation, how evolution happens, and the history of biological diversity on the planet from the origin of life to the present.

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Curriculum

The curriculum for Evolutionary Biology EBIO 3080 was developed by professors Nancy Emery, Nolan Kane and Andrew Martin in a manner that uses research-supported best practices in higher education. The readings are provided free to students and students are encouraged to engage in critical and creative work in a respectful, inclusive, and supportive learning environment.

Teaching and Learning Strategies

We use research-supported best practices that have been shown to produce significant learning gains. Our approaches include the following: (click on each one for examples)

Illustrate the methods

Visual representations of biology have been widely used by scientists to understand and explain phenomena, from the representational anatomical works of Leonardo da Vinci to the theoretical phylogenetic work of Charles Darwin. We encourage students to create drawings (illustrations) as a means of better understanding details of experimental design, where data comes from, and as a means of activating the brain in ways that advance creative and critical thinking. For more information, see Quillin and Thomas.

Examples of student illustrations of experimental design used for testing the predictions of evolutionary hypotheses:

Top. Experimental design of guppy predation. Bottom. Experimental design for estimating survival of asexual and sexual snails to test the predictions of theory

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Draw or re-draw graphs to effectively convey information

Annotate tables, graphs, and text-based information

Annotation is an important tool for students to "own" the information in tables, graphs, or text based descriptions of the world. Students write directly on graphs with the goal of making the relevant information evident in a manner that facilitates making evidence-based claims and teaching each other.

An example of student annotations that illustrates an emphasis on gaining relevant information from visualizations of data.

Construct concept maps

Concept maps are explicit descriptions of knowledge and the inter-connections among key concepts. Concept maps "...provide a unique window into the way learners structure their knowledge, offering an opportunity to assess both the propositional validity and the structural complexity of the knowledge base." (Pearsall et al. 1993: 198).

Develop and evaluate a model

Students set up and evaluate analytical models to explore evolution. For example, students derive a simple two phenotype model (e.g. for two asexual and sexual reproduction) and explore the conditions that promote change in the characteristics of the population over time. The derived analytical model, ∆p = pqs/W, indicates that evolution is directly proportion to the amount of variation (pq) and the strength of natural selection (s) and inversely proportional to average fitness (W).

Students construct R scripts to simulate evolution or investigate the dependence of evolution on the magnitude of selection. Here is an example of a student's R script to simulation 10 generations of evolution assuming a two-fold cost of sex

#simulating evolution using a simple two phenotype model

#make a vector to store values of p
p <- rep(NA, 10)

#initialize the vector with the observed frequency of asexuals
p[1] <- 0.05

#simulate evolution
for (i in 1:9){
W <- p[i] + (1-p[i])*0.5
p[i + 1] <- p[i]/W
}

#plot the data
quartz()
plot(1:6, p, xlab="Generations", ylab="Frequency of asexuals", type="l", cex=2, ylim=c(0,1), xlim=c(1,10), xaxt="n")
points(1:10, p, pch=19)
axis(1, seq(1,10), seq(0,5))

Construct a hypothesis and design an experiment that tests the prediction(s) of the hypothesis

Students design and illustrate experiments to test hypotheses: in this case, the hypothesis is that tail length causes the variation in reproductive success of males. The hypothesis was based on an observation of a correlation in nature.

Make and evaluate evidence-based claims

Collaborate with your peers

Collaboration involves people working together to solve problems and in the process individuals develop key skills including the ability to effectively communicate, listening for understanding, and sharing knowledge and skills that enable greater productivity than can be achieved by individuals acting alone. Importantly, collaboration builds communities.

Evidence of collaboration and community-building in EBIO:

Development of a social network in evolutionary biology during a semester (see Buchenroth-Martin 2016):

Each point is a student and lines indicate interactions that connect students.

Student Outcomes

Students often engage in an in depth study of a topic of interest and present the results of their work in a public symposium. Student products are often posters, but there are examples of videos, written case studies, and presentations. The pictures below are examples of student work. You can learn more about a particular project by clicking on the images below.

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Innovative Courses: Insect Biology (EBIO 4660/5660)

Anonymous — Tue, 08 Dec 2015 20:47:27 +0000

Innovative Courses: Insect Biology (EBIO 4660/5660) Anonymous (not verified) Tue, 12/08/2015 - 13:47

Students from Insect Biology (EBIO 4660/5660, taught by Deane Bowers and Tim Szewczyk) lab dyeing silk (produced by caterpillars of the silk moth, Bombyxmori) with a dye made from cochineal insects (a small white scale insect that feeds on prickly pear cactus). The dark pink is from the insects alone, and the orange is from the insect extract plus lime juice; changing the pH with acidic lime juice changes the color. After a short time in the dye bath, the scarves turn these gorgeous colors! The students used tie-dyeing techniques to decorate their scarves and then got to take them home. The cochineal insect also occurs here in ŷ��ڱ��Ƶ on our local prickly pear cactus.

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Innovative Courses: Genomics EBIO 4460/5460

Anonymous — Mon, 15 Jun 2015 19:58:05 +0000

Innovative Courses: Genomics EBIO 4460/5460 Anonymous (not verified) Mon, 06/15/2015 - 13:58

The chloroplast, where all photosynthesis occurs in plants, is derived from ancient, free-living algae. Over the past 900 million years, however, it has lived inside of plant cells and their green algal ancestors, evolving to be an integral part of these organisms. However, each chloroplast still has it's own separate DNA, encoding many of the key proteins required for all life today. Students taking EBIO 4460/5460 – Genomics study the chloroplast genomes, to understand the important organelle in plant cells, but also to learn how genomes are put together. The highest quality genomes, after careful checking, are published on NCBI (the National Center for Biotechnology Information - Genbank). All of the flowering plant chloroplast genomes to date are published on NCBI's Chloroplast database.

Graduate and advanced undergraduate students contribute substantially to expand the understanding of these sub-cellular engines that ultimately power nearly all carbon-based life. Each student starts the semester with a large file consisting of millions of small DNA sequences (reads); over the course of the semester, students learn to process that information – to identify the informative sequences, assemble the reads into larger sequences (contigs), determine the proper arrangement of the contigs, and ultimately construct the entire chloroplast genome of their organism. The chloroplast genome is typically 140,000-160,000 bases of DNA, in a long circle, placing millions of small pieces of DNA together in the correct order to complete a giant circular sequence is quite a challenge!

However, this is only the beginning, as a long DNA sequence is hard to understand on its own. Students identify the locations of all of the genes that encode many necessary functions: 1) make proteins, tRNAs, and rRNAs; 2) regulate the expression of these products; and 3) replicate the DNA to make new chloroplasts as needed. Once all of this information is known and has been verified, students submit their sequences to NCBI, making the new sequence freely available to scientists around the world. The genome sequences produced in this course will help us better understand this important component of life on earth. So far, students have put together dozens of high quality genomes, a substantial portion of the five hundred that have been assembled for all flowering plants. Browse the gallery below to see visualizations and links to the genbank page for each of these genomes.

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