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UUnniitt PPllaann TTeemmppllaattee Note: Type in the gray areas. Click on any descriptive text, then type your own.

Unit Authors

First and Last Names Yi Kong; Arzu Saka

Authors’ E-mail Addresses ykong@purdue.edu; arzus123@gmail.com

Target Course Basic Biology Course

Student characteristics Biology student teachers first level

School(s) Name(s) Karadeniz Technical University

• Stage 1 Unit Overview: Identify desired outcomes and results.

Students will know… (understand)

Unit

Plan

Title

Tools for studying evolution: Phylogenetic Trees

Curriculum-Framing Questions

Essent

ial

Quest

ion

https://wiki.bio.purdue.edu/K12Evolution/index.php/Tools_for_stu

dying_evolution:_Phylogenetic_Trees

Essential Questions:

1.What is the Phylogenetic Trees?

2.How Phylogenetic Trees help us studying evolution theory?

3.How does Phylogenetic Tree show the relationship among

different organisms?

4.What is the common misconceptions of Phylogenetic Trees?

Unit

Quest

ions

https://wiki.bio.purdue.edu/K12Evolution/index.php/4.What_is_the_common_misconceptions_of_Phylogenetic_Trees%3F What is the common misconceptions of Phylogenetic Trees?

Unit Summary

Many students, teachers, and even some scientists struggle to make sense of phylogenetic trees, which are commonly used in both textbooks and classroom instruction. We list some common misconceptions of Phylogenetic Trees, to help students understand the Phylogenetic Trees accurately.

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Subject Area(s) (List all subjects that apply)

Misconceptions; Phylogenetic Trees

Grade Level [Click box(es) of all grade level(s) that your Unit targets]

K-2

6-8

ESL

Gifted and Talented

3-5

9-12

Resource

Other: Biology student teachers

Targeted State Frameworks/Content Standards/Benchmarks

National Science Standard:

Biological classifications are based on how organisms are related. Organisms are

classified into a hierarchy of groups and subgroups based on similarities which reflect

their evolutionary relationships. Species is the most fundamental unit of classification.

State Standard:

1. Discriminates relationships when using a classification model to group living

things.

2. Uses terms and processes employed in scientific research.

Stage 2: Determine what constitutes acceptable evidence of competency in the

outcomes and results (assessment). List Student Objectives/Learning

Outcomes:

Students will be able to:

1. understand phylogenetic tree

2. interpret a phylogenetic tree

3. notice their misconceptions

4. avoid their misconceptions

• Stage 3: Plan instructional strategies and learning experiences that will bring

students to these competency levels. What sequence of teaching and

learning experiences will equip students to develop and demonstrate the

desired understanding? List the Procedures:

1. Where are we going? Why, What is expected?

Many students, teachers, and even some scientists struggle to make sense of

phylogenetic trees (Baum et al., 2005), which are commonly used in both textbooks and

classroom instruction (Halverson, 2010).

College students struggle with abstract reasoning and problem solving skills, especially

in biological sciences (where visual representations have not been well studied). In order to be

efficient problem solvers in systematics and evolutionary biology, students must develop

expertise in phylogenetic tree thinking (Halverson, Pires & Abell 2008).

Representations affect multiple aspects of learning including: reasoning through

problems and phenomena, developing deeper understandings of the relationships among

phenomena. In science, visual representations are used to display data, organize complex

information, and promote a shared understanding of scientific phenomena. These

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representations are often used to present multiple relationships and processes that are difficult to

describe (Halverson, 2009).

Meir et al (2007) were identified four common misconceptions about students‘ interpretations

of phylogenetic trees. These are listed below:

1.Incorrect mapping of time: Many students were confused about spatial representation

of the flow of time on an evolutionary tree. While reading vertically-oriented trees, in which

time flows from bottom to top, students often thought that the horizontal order in which extant

species were drawn across the top was significant, and assumed that the older species were on

the left and the younger species on the right. Students also frequently thought that the tree was

anchored at the upper left species, and assumed that this species was the common ancestor of

the others on the tree.

2.Tip proximity indicates relationship: Students often thought that species drawn closer

together at the tips of tree were more closely related to each other than those drawn farther

apart.

3.Node counting: Some students thought that the number of nodes crossed in tracing a

path between two species on a tree indicated how closely related they were.

4. Straight line equals no change: Many students interpret that the species at the tip of

the straight line is the ancestor of the others that branch off of the line.

These misconceptions are fundamental barriers to understanding how evolution operates

and phylogenetic reasoning is central to much contemporary research on evolution.

Meir et al (2007) identified as being important in thinking correctly about evolutionary

trees. One of these skill is ―reconstructing trees‖. Being able to accurately read and interpret

phylogenetic tree has important implications for student ability to really understand biological

models. If students don‘t have the skills to drawing the phylogenetic tree it means they don‘t

understand, use, and draw diagrams.

Rather than ignore student struggles, it is time to address the challenge of ―tree thinking‖

by developing ways to help students learn how to read these diagrams.

Referances:

Baum, D.A. Smith, S.D. & Donovan S.S (2005). The Tree Thinking Challenge. Science, 310,

979-980.

Halverson, Kristy L., Sandra K. Abell, Patricia M. Friedrichsen, and J. Chris Pires (2009).

Testing a model of representational competence applied to phylogenetic tree thinking NARST

2009

Halverson, K.L. (2010). Using Pipe Cleaners to Bring the Tree of Life to Life. The American

Biology Teacher, Vol. 72, No: 4, p. 223-224

E. Meir, J. Perry, J.C. Herron & J. Kingsolver, (2007). College Students‘ Misconceptions About

Evolutionary Trees, The American Biology Teacher, 69(7): e71-e76.

Kristy L. Halverson, J. Chris Pires, and Sandra K. Abell (2008) Undergraduates‘ Abilities to

use Representations in Biology: Interpreting Phylogenetic Tree Thinking NARST 2008

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E. Mayr (2004). What Makes Biology Unique: Considerations on the Autonomy of a Scientific

Discipline, Cambridge University Press.

2. How will we hook and hold student interest?

Halverson created a manipulative model that pushes students to explore phylogenetic trees and

think more deeply about evolutionary relationships. This simple, inexpensive pipe-cleaner

model gives students a 3D experience of what is typically represented in two dimensions.

Students manipulate the tree to rotate branches, compare topologies, map complete lineages,

identify informative phylogenetic features, and examine the effects of superficial structural

changes. For example, when this model was used in a college biology course, one student said

that ―the pipe cleaners allow us to see how manipulating the tree by twisting and straightening

does nothing to the tree‘s meaning, just its appearance.‖ Another student had struggled with

how two rotated trees could illustrate the same relationships. She stated, ―I had trouble

imagining the ‗rotation‘ of the branches in my head, and this provided a physical rotation that I

could see.‖

Halverson K.L.(2010).Using Pipe Cleaners to Bring the Tree of Life to Life, The American

Biology Teacher, 72(4), 223–224.

3.How will we equip students for expected performances?

We can explain some details about “Understanding Phylogenies”.

Understanding Phylogenies

Understanding a phylogeny is a lot like reading a family tree. The root of the tree represents the

ancestral lineage, and the tips of the branches represent the descendents of that ancestor. As you

move from the root to the tips, you are moving forward in time.

When a lineage splits (speciation), it is represented as branching on a phylogeny. When a

speciation event occurs, a single ancestral lineage gives rise to two or more daughter lineages.

Phylogenies trace patterns of shared ancestry between lineages. Each lineage has a part of its

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history that is unique to it alone and parts that are shared with other lineages.

Similarly, each lineage has ancestors that are unique to that lineage and ancestors that are

shared with other lineages—common ancestors.

A clade is a grouping that includes a common ancestor and all the descendents (living and

extinct) of that ancestor. Using a phylogeny, it is easy to tell if a group of lineages forms a

clade. Imagine clipping a single branch off the phylogeny—all of the organisms on that pruned

branch make up a clade.

Clades are nested within one another—they form a nested hierarchy. A clade may include many

thousands of species or just a few. Some examples of clades at different levels are marked on

the phylogenies below. Notice how clades are nested within larger clades.

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So far, we‘ve said that the tips of a phylogeny represent descendent lineages. Depending on

how many branches of the tree you are including however, the descendents at the tips might be

different populations of a species, different species, or different clades, each composed of many

species.

Several times in the past, biologists have committed themselves to the erroneous idea that life can be organized on a ladder of lower to higher organisms. This idea lies at the heart of Aristotle’s Great Chain of Being (see right).

Similarly, it’s easy to misinterpret phylogenies as implying that some organisms are more “advanced” than others; however, phylogenies don’t imply this at all.

In this highly simplified phylogeny, a speciation event occurred resulting in two lineages. One led to the mosses of today; the other led to the fern, pine, and rose. Since that speciation event, both lineages have had an equal amount of time to evolve. So, although mosses branch off early on the tree of life and share many features with the ancestor of all land plants, living moss species are not ancestral to other land plants. Nor are they more primitive. Mosses are the cousins of other land plants.

So when reading a phylogeny, it is important to keep three things in mind:

1. Evolution produces a pattern of relationships A B C D among lineages that is tree-like, not ladder-like.

2. Just because we tend to read phylogenies from left to right, there is no correlation with level of “ advancement.”

3. For any speciation event on a phylogeny, the choice of which lineage goes to the right and which goes to the left is arbitrary. The following phylogenies are equivalent:

Aristotle’s vision of a Great Chain of Being, above. We now know that this idea is

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Biologists often put the clade they are most interested in (whether that is bats, bedbugs, or bacteria) on the right side of the phylogeny.

Misconceptions about humans The points described above cause the most problems when it comes to human evolution. The phylogeny of living species most closely related to us looks like this:

It is important to remember that:

1. Humans did not evolve from chimpanzees. Humans and chimpanzees are evolutionary cousins and share a recent common ancestor that was neither chimpanzee nor human.

2. Humans are not “higher” or “more evolved” than other living lineages. Since our lineages split, humans and chimpanzees have each evolved traits unique to their own lineages.

Building the Tree

Like family trees, phylogenetic trees represent patterns of ancestry. However, while families

have the opportunity to record their own history as it happens, evolutionary lineages do not—

species in nature do not come with pieces of paper showing their family histories. Instead,

biologists must reconstruct those histories by collecting and analyzing evidence, which they use

to form a hypothesis about how the organisms are related—a phylogeny.

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To build a phylogenetic tree such as the one to the right,

biologists collect data about the characters of each

organism they are interested in. Characters are heritable

traits that can be compared across organisms, such as

physical characteristics (morphology), genetic

sequences, and behavioral traits.

In order to construct the vertebrate phylogeny, we begin

by examining representatives of each lineage to learn

about their basic morphology, whether or not the

lineage has vertebrae, a bony skeleton, four limbs, an

amniotic egg, etc.

Using shared derived characters

Our goal is to find evidence that will help us group organisms into less and less inclusive clades.

Specifically, we are interested in shared derived characters. A shared character is one that two

lineages have in common, and a derived character is one that evolved in the lineage leading up

to a clade and that sets members of that clade apart from other individuals.

Shared derived characters can be used to group organisms into clades. For example, amphibians,

turtles, lizards, snakes, crocodiles, birds and mammals all have, or historically had, four limbs.

If you look at a modern snake you might not see obvious limbs, but fossils show that ancient

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snakes did have limbs, and some modern snakes actually do retain rudimentary limbs. Four

limbs is a shared derived character inherited from a common ancestor that helps set apart this

particular clade of vertebrates.

However, the presence of four limbs is not useful for determining relationships within the clade

in green above, since all lineages in the clade have that character. To determine the relationships

in that clade, we would need to examine other characters that vary across the lineages in the

clade.

Ref: http://evolution.berkeley.edu/evosite/evo101/IIC1Homologies.shtml

5. How will be help students rethink and revise?

We can apply this activity:

You will need five pipe cleaners of different colors for each tree. Here, I use pink, purple,

green, blue, and orange to represent each element of a single tree or lineage. There are four

steps to building the model.

(1) Gather the five pipe cleaners together so that they are flush at each end.

(2) Twist them together at one end, using about 2 inches of the bundle.

(3) Take the other end of the pink pipe cleaner and wrap it around the others once. Then twist

the remaining pipe cleaners together for another 1.5 to 2 inches. Repeat this step with the

remaining pipe cleaners until they have all been isolated in the following order: pink, purple,

green, blue, orange.

(4) Bend the pipe cleaners 90° at each point of intersection and another 90° at each halfway

point (see Figure 1).

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This model works well in addressing the challenge of tree thinking because

(1) it uses color to help identify complete lineages;

(2) it is bendable, so that it can be transformed into multiple styles of trees;

(3) to alter relationships, students must deconstruct and rebuild the model – much like a real

tree;

(4) students can use additional pipe cleaners to incorporate additional species and information;

and

(5) the model can be modified easily by using a hole punch

to add taxa to the tips to provide a more concrete learning tool. This model has been used at

high school and postsecondary levels to help students read trees, build them, and understand

what they represent.

5.How will students self evaluate and reflect on their learning? Ask students to

rethink and reflect

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If you were to add a trout to the phylogeny shown above, where would its lineage attach to the

rest of the tree?

Answer: ‗c‘ is the correct answer. This depends on only the knowledge that a salmon and a

trout are very closely related. Therefore they must share a more recent common ancestor with

each other than with any other included species. Position ‗c‘ is the only place such an ancestor

could be.

6) Which of trees below is false given the larger phylogeny above?

Answer: ‗d‘ is the correct answer. ‗d‘ shows yeast being more closely related to plants than it is

to animals. The true phylogeny (right) shows that yeast is more closely related to human than to

any of the plants (green algae, lily, and fern).

6. How will we tailor learning to varied needs, interests, styles? Students self-

evaluate and reflect on their learning

We can use Baum‘s Tree-Thinking Quizzes I and II questions.

Baum, D.A. Smith, S.D. & Donovan S.S (2005). The Tree Thinking Challenge. Science, 310,

979-980.

7. How will we organize and sequence the learning?

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1. Explaining and preparing activity

2. Explaining understanding pyhilogenies

3. Doing hand on activity

4. Give examples about interpret phylogenetic tree

5. Assessment

Approximate Time Needed

Eight 50-minute class periods, eight weeks in two month

Prerequisite Skills

Command the basic skills of using internet web browser.

Materials and Resources

Technology – Hardware (Click boxes of all equipment needed)

Camera

Computer(s)

Digital Camera

DVD Player

Internet Connection

Laser Disk

Printer

Projection System

Scanner

Television

VCR

Video Camera

Video Conferencing Equip.

Other:

Technology – Software (Click boxes of all software needed.)

Database/Spreadsheet

Desktop Publishing

E-mail Software

Encyclopedia on CD-ROM

Image Processing

Internet Web Browser

Multimedia

Web Page Development

Word Processing

Other:

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Printed

Material

s

1. Textbook: Evolution The Triumph of an idea. Zimmer (2006)

2. Meir, E., Perry, J., Herron, J. C., Kingsolver, J. (2007). College students’ misconceptions about evolutionary trees. American Biology Teacher, 7, 71-76 3. Baum, D.A., Smith, S.D., Donovan S.S.(2005). Thr Tree-Thinking Challenge. Science 310, 979. 4. Halverson, K.L., Pires, C.J. & Abell S.K. (2011).Exploring the Complexity of Tree Thinking Expertise in an Undergraduate Systematics Course. Science Education, 1-30. 5. Halverson, K. L. (2010). Using pipe cleaners to bring the tree of life to life.American Biology Teacher, 74, 223-224. 6. Halverson, K. L., Pires, C.J. & Abell, S. K. (2008). Undergraduates abilities to use representations in biology: Interpreting phylogenetic tree thinking.Paper presented at the 2008 annual meeting of the National Association for Research in Science Teaching. Baltimore, MD. 7. Halverson K.L, Abell S.K,Friedrichsen P.M & Pires C.J.(2009). Testing a model of representational competence applied to phylogenetic tree thinking. Paper presented at the 2009 annual meeting of the National Association for Research in Science Teaching. 8. Halverson, K.L. (2010). Exploring the link between mental rotation and college student learning with phylogenetic trees. Paper presented at the annual meeting of the National Association for Research in Science Teaching, Philadelphia, PA.

Supplies

Internet

Resourc

es

http://bilbo.bio.purdue.edu/~npelaez/evolution/

https://wiki.bio.purdue.edu/K12Evolution/index.php/Tools_for_studying_evolution:_Phylogenetic_Trees

https://purdue.qualtrics.com/SE/?SID=SV_3C7BTnaZ3SopWfy

Others

Accommodations for Differentiated Instruction

Non-Native English

Speaker

The reading is suitable even for elementary school students. It has been translated to Turkish and Chinese.

Gifted Student It is interesting for gifted students. The questions are challenge and interesting even for gifted students.

Other (explain) the reading level is suitable even for students with below

average language.

Student Assessment (Refer back to Stage 2, above)

Using https://purdue.qualtrics.com/SE/?SID=SV_3C7BTnaZ3SopWfy

to assess students in the below objections:

1) understand phylogenetic tree

2) interpret a phylogenetic tree

3) notice their misconceptions

4) avoid their misconceptions