1 Taxonomy, Phylogeny, and Cladograms - 1120 PDF

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Lab Assignment 1...

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TAXONOMY, PHYLOGENY, AND CLADOGRAMS Objectives:    

Become acquainted with the relationship between evolution the taxonomy Become familiar with the taxonomic categories Acquire a basic understanding of phylogeny Determine how cladograms can be used to evaluate the relationships between organisms

Introduction Humans have an insatiable need to categorize objects, whether they are living or otherwise. Taxonomy is the branch of biology that is concerned with identifying, naming, and classifying living organisms. EXERCISE 1 Understanding Taxonomy

All living organisms can be placed into three broad categories or domains. They are the Domain Eukarya, Domain Bacteria and Domain Archaea. Bacteria and Archaea are examples of prokaryotes and have a unique cell structure compared to other living organisms. All living organisms in Domain Eukarya are eukaryotes. The difference between eukaryotes and prokaryotes centers on the fact that prokaryotes do not have a nucleus but eukaryotes do. Below is an example of the categories used in the standard taxonomic system. 1. 2. 3. 4. 5. 6. 7. 8.

Domain all inclusive category Kingdom Phylum Class Order Family Genus Species very restricted category

As previously mentioned, most of the above categories can be subdivided. For example, class may be subdivided into super class, class, and subclass or there may be an addition of a super family or subfamily.

Created by Dr. Jennifer Knapp and Revised by Dr. Kevin Ragland

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There are six kingdoms to which all organisms can be classified. The kingdoms that make up the living world include, but aren’t limited to, Animalia, Plantae, and Fungi. On the surface, the members of the Domains and Kingdoms appear to be extremely diverse in shape, size, color and function but, in fact, they share many common characteristics. These characteristics include cellular organization, biochemistry, and molecular biology. These common characteristics are what unify the living world. The most restrictive categories, genus and species, are used for identifying an organism. For example, Homo sapiens identifies human beings. The genus and species names are also referred to as an organism's scientific name. An organism’s scientific name is two words or a binomial, the genus and species. The names are either Greek or Latin. The genus and species are written in italics. The genus is always capitalized and the species is always written with the genus. The genus may be abbreviated (for example H. sapiens for humans) if it is written out completely the first time it is used. Who names an organism? The first person to describe it gets to name it. How and what they name it is totally up to them. By rule, if two individuals happen to discover and name the same species, whichever name was used first has priority and the second one will be discarded. Answer the following questions by writing the answers in the blanks provided.

1. What are eukaryotic cells? Cells that contain a nucleus and organelles, and are enclosed by a plasma membrane. 2. Which taxon level is considered to be the most inclusive? Domain has the most individuals in a group. 3. Which taxon level is the most restricted? Species.

EXERCISE 2 Understanding Evolution

Phylogeny is the origin and evolution of a set of organisms. Phylogenetic taxonomy is a way to classify groups of organisms by their evolutionary relatedness.

This exercise utilizes the Understanding Evolution Tutorial from University of California Berkeley. This tutorial can be accessed from the following link: Link for Evolution Activity Actual link (http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_toc_01 ) Complete each of the tutorials in the following categories:  

An introduction to evolution The history of life: looking at the patterns

While completing the tutorials, answer the following questions by writing the answers in the blanks provided.

Introduction to Evolution Tutorial 1. What is microevolution or small-scale evolution?

Microevolution is evolution on a small scale and happens within a single population 2. What is macroevolution or large-scale evolution?

It is large scale evolution and happens above the species level. Family Tree tutorial 1. What is the term that refers to the origin and evolution of a group of organisms? This is often referred to as a “family tree”. Phylogeny

2. What is the name given to a single common ancestor and all of the descendants of that ancestor? Clade

3. What are the three major clades in which all of life can be organized? These are often referred to as domains. Archaea, Bacteria, and Eukaryotes

Understanding Phylogenies 4. What does the root of the phylogeny represent?

The ancestral lineage 5. What do the tips of the branches of a phylogeny represent?

It represents the evolutionary relationships among a set of organisms or group of organisms.

6. How many species are included in a clade? 4

7. What is the relationship between humans and chimpanzees? Did humans evolve from chimpanzees?

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

Building the Tree 8. What are characters and what value do they have in constructing phylogenetic trees? 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, genetic sequences, and behavioral traits. 9. What is the difference between a shared character and a derived character? Shared character is one that 2 linages have in common, and derived character is one that evolved in the lineage leading up to a clade and that sets members pf that clade apart from individuals.

Homologies and analogies 10.What are homologous characters and what value do they have in constructing phylogenetic trees?

Homologous characters are characters in different organisms that are similar because they were inherited from a common ancestor that also had that character. 11.What are analogous characters?

Characters that have separate evolutionary origins. 12.What is convergent evolution? Process in which two distinct linear evolution a similar characteristic independently of one another.

Using the tree for classification

13.What is a useful mnemonic for remembering the standard Linnaean system of classification? King Philip Came Over For Good Soup. 16.

What do each of the beginning letters in the mnemonic represent? (i.e. Name the 7 groups used in the classification system.)

k-kingdom p-phylum c-class o=order f=family g-genus sspecies. 17.

How is the Linnaean system of classification different from the phylogenetic system of classification? The Linnaean system assigns every organisms to a kingdom, phylum, class, order, family, genus, and species while the phylogenetic system names only the clades groups that are all descended from a common ancestor .

How we know what happened when 18.

What are three methods or types of evidence used by scientists to determine when things happened?

Radiometric dating, Stratigraphy, and molecular clocks

EXERCISE 3 Using Cladograms

A clade is an organism and all the descendants of that organism. For example, birds and reptiles are members of the same clade, because they descended from the same ancestor. A diagram in the form of a tree can be created which shows the organisms and their descendants. This diagram is called a cladogram. This exercise utilizes the virtual web activity, What Did T. Rex Taste Like, from University of California Berkeley. The tutorial uses cladograms to evaluate how life is related. This tutorial can be accessed from the following link: Link for Cladogram Activity Actual link (http://www.ucmp.berkeley.edu/education/explorations/tours/Trex/navigation1b.ht ml)

Complete the virtual activity. While completing the tutorials, answer the following questions by writing the answers in the blanks provided. Each of the questions correspond to questions or information that you will find in the virtual activity. 1. Which is the best definition for lineage? a.) A single line showing age b.) A continuous line of descent c.) A set of parallel lines 2. Within the folder you compared the history of a single family to the history of all life. What are some things they have in common? a.) Both have a point of common ancestry b.) In both, descendants inherit features from previous ancestors c.) In both, descendants more closely resemble their recent ancestors than more distant ancestors d.) All of the above e.) None of the above

3. Draw a dot in the area that represents the most recent common ancestor for A and C.

4. Draw a dot in the area that represents the most recent common ancestor for B and C.

5. Circle the part of the diagram that represents the shared history of A, B, and C. The entire C line

6. Circle the part of the diagram that represents the unique history of B. Between B and C

7. Which is more closely related to caimans – hares or parrots? Why?

Parrots they share a common ancestor 8. Circle the part of the diagram that represents the common ancestor of hares, caimans, and parrots?

9. How are sharks different from the rest of the vertebrates pictured in the cladogram? Sharks don’t have a bony skeleton

10.What trait is shared by frogs, humans, hares, caimans, and parrots?

all have 4 limbs

11.Which feature do humans, hares, caimans, and parrots share that the other lineages did not inherit? a.) bony skeleton b.) hair c.) amniotic egg 12.Which of the tetrapods have an opening in the skull in addition to those openings for the eye, nose, and mouth? a.) hare and crocodile b.) frog and hare c.) bird and crocodile 13.Use the cladogram in the online activity to complete the following chart. If the species possesses the trait, place a + in the appropriate box. If the species does not possess the character, place a 0 in the box. If we cannot determine whether the species possesses the trait or not, place a ? in the box.

CHARACTER

SHARK TUNA FROG HUMAN HARE + + + + +

+

CAIMAN +

PARROT +

T.REX

0

+

+

+

+

+

+

+

0

0

+

+

+

+

+

+

0

0

0

+

+

+

+

a

0

0

0

+

+

0

0

a

Opening in 0 front of eye

0

0

0

0

+

+

+

Vertebrae Bony Skeleton

Four limbs Amniotic Egg

Hair

14.Use the cladogram and the information you obtain from the online activity to complete the following chart. If the species possesses the trait, place a + in the appropriate box. If the species does not possess the character, place a 0 in the box. If we cannot determine whether the species possesses the trait or not, place a ? in the box.

CHARACTER

CAIMAN PARROT T.REX + 0 0

Heel 0

+

+

0

+

+

Bipedal

4th and 5th finger lost

15. What did T. rex taste like?

chicken 16. With the cladogram and data tables that you have, try to answer the following questions about T. rex. If there is not enough information to determine, simply write not enough information. If you can answer the question, please indicate how you know as well. a.) Did T. rex have an amniotic egg?

Yes b.) Was T. rex warm-blooded or cold-blooded?

c.) Could T. rex have had feathers? yes

d.) Did T. rex have color vision? yes

e.) How many chambers were there in T. rex’s

heart? 4 chambers

f.) Did T. rex sing to its offspring? yes...