Laboratory 1 – Taxonomic keys and phylogenetic trees

Laboratory 1: Taxonomic Keys and Phylogenetic Trees

Learning Objectives
 Understand how to operate and care for a standard dissecting microscope
 Record useful and concise observations
 Place organisms into hierarchical classifications
 Understand how to use a taxonomic/dichotomous key to identify an organism
 Be able to identify an organism’s unique characteristics using proper terminology
 Create a dichotomous key that allows the correct identification of various skulls

Prior to Attending Lab

 Read all of the Laboratory 1 handout and the Laboratory Safety Policies handout on the
lab eClass site.
 Review the two BIOL 1000 videos on microscope use:
o https://vimeo.com/107172869/5afca45790 (~ 8 mins)
o https://vimeo.com/110134001/c6fbc195e5 (~ 12 mins)
 Complete the Lab 1 pre-lab quiz (on the lab eClass site). This quiz addresses material
from the readings and videos listed above. This quiz must be completed before your
scheduled lab. Failing to do so will render a grade of zero.

What to bring to your lab session

 This handout, either as a hard copy or in an electronic form that you can access during
the lab.
o Pages 1-4 are to be completed before the lab and shown to your TA at the
beginning of the lab.
o Pages 8-9 and 15-17 are to be completed and shown during the lab. If you won’t
be bringing a hard copy, bring 4-5 sheets of blank paper to use for these
exercises.
 Laboratory coat and safety goggles.
 Pencil and eraser
 Extra pages of scrap paper for rough work.

** In addition to the pre-lab quiz there is also a post-lab quiz associated with this lab. The
post-lab quiz can be found on eClass and is due within one week of completing the lab.
It covers material addressed in Lab 1 **
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Introduction and Pre-Lab
In science, the results obtained from scientific investigation often lead to the formation of new
questions. Quite often, experiments yield unexpected or conflicting results. All good scientists
therefore keep detailed notes on their procedures and record observations as they work.
Researchers often draw the objects/organisms that they observe. These drawings are typically
not artist quality. What purpose do these drawings serve? (1 mark)

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Taxonomy:

Please see below in the Lab section (after the Pre-lab section!) as well!!

Body shapes are identified and compared in order to classify animals and plants. Lower
organisms (like microbes) are mainly classified by similarities in DNA sequence (as are animals
and plants but body comparisons are still used). As such, there are a few basic terms and
concepts to note. Some of these terms and examples of such, are in the pictures below (from
https://www.researchgate.net/publication/264936044_Nose_to_tail_roots_to_shoots_Spatia
l_descriptors_for_phenotypic_diversity_in_the_Biological_Spatial_Ontology). Check out the
website and your text for more information!! Science baby!

Figure 1: Comparison of animal body axes.

Figure 2: Body Planes

(Full article -
https://www.researchgate.net/publication/264936044_Nose_to_tail_roots_to_shoots_Spatial_
descriptors_for_phenotypic_diversity_in_the_Biological_Spatial_Ontology#fullTextFileContent

What do you think Bilateral symmetry means?

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We have a bilateral symmetry (each side is a mirror of the other) but many organisms do not
have this type of symmetry. Also, even in bilaterally symmetric organisms, the inner tissues and
organs may not be symmetric. In your body think of a heart or a liver versus eyes, hands, and
feet. The latter body parts are on either side of your body whereas a heart and liver are on one
side or the other. Thus when we are making or using dichotomous keys, we need to understand
the symmetry – both in and out – of the organisms we are identifying.

To make accurate observations you need to use the correct descriptors. Specific terminology is
used when referring to the location and orientation of a characteristic on an organism. Below
are 8 common “anatomical” directions for you to define. (1 mark)

 Anterior

 Posterior

 Dorsal

 Ventral

 Lateral

 Medial

 Proximal

 Distal

Have a look at this article (and the videos in it) to gain an understanding of Phylogeneic Trees
and then answer the following questions. Also use your textbook and the information below in
the Lab section!

https://bioprinciples.biosci.gatech.edu/module-1-evolution/phylogenetic-trees/

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 What is a Phylogenetic Tree? How is one created? (1 mark)

So now you see what a Phylogenetic Tree is – all based on comparisons. In order to use a tree to
help identify an organism, we can use a Dichotomous key. What is that? Well here is a great
little source from the University of Guelph Arboretum that simply discusses this very topic!

How a Dichotomous Key works:

A scientific key is a tool that allows you to identify different things in the natural world, including plants
and animals. A dichotomous key is a specific type of scientific key. The word “dichotomous” (pronounced
“die-cot-o-mus”) means “divided into two parts” and a “key” refers to a series of questions that help you
to identify something. So, a dichotomous key gives you two choices at each step to describe something.
By answering these questions, the key leads you to the correct name of the thing you are trying to
identify. Let’s give a dichotomous key a try. Suppose you wanted to be able to tell apart these nine
backyard birds. The next page shows you a dichotomous key with a series of yes or no questions that
separates the birds until you get to each species. You only need to read the questions that give you the
correct answer. For example, to identify the blue bird, you would only have to answer two questions.
First, does the bird have a crest? Yes. Then, is the bird blue? Yes. Then the answer is Blue Jay. You didn’t
have to ask the other questions in the key because they didn’t relate to the path of questions that you
were on. Now pick one of the other birds shown here and use the dichotomous key to figure out the
bird’s common name. Did it work? Try it with a few of the birds to get familiar with using one of these
keys.

(from:
https://arboretum.uoguelph.ca/system/files/Dichotomous%20Key%20Activities.pdf Check out
the site for a little more information!

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What is a Taxonomic / Dichotomous Key? How is one created? (1 mark)

What is in a Name?
Many of the organisms you have come into contact with have both a common and a scientific
name. While the common names of rose, monkey and fish are sufficient for the majority of the
population to describe some organisms, these names are often misleading and/or vague. For
example, is a jellyfish really a fish? Find out.
As biologists, we often rely on the scientific names of organisms when communicating to ensure
that the organism of interest is clearly identified. Each species’ scientific name has a Latin (or
sometimes Greek) binomial designation - binomial nomenclature. For example, a giraffe is
Giraffa camelopardalis. Notice that the first letter of the first word (genus) in a scientific name is
capitalized, the second word (specific/species name or specific epithet) is not, and both parts of
the name are italicized. Since it is difficult to write in italics, when writing scientific names by
hand it is appropriate to underline the entire name.
 Identify the genus (circle) and specific name (underline) in the following.
Elephas maximus Carduelis tristis

Based on your understanding of binomial nomenclature, hierarchical classification, and

taxonomy, organize the organisms below into groups of relatedness (organisms that are most
related to one another). Write out the groupings in the space provided. (2 marks)
Canis lupus
Panthera onca
Elephas recki
Canis latrans
Megaptera novaeangliae
Canis mesomelas
Panthera tigris
Canis adustus
Elephas maximus
Panthera leo
Canis simensis
Panthera atrox

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 When used in a document, the first mention of the name includes both the genus and specific
name. In all subsequent uses only the first initial of the genus is included and the full specific
name. For example: first occurrence would be Giraffa camelopardalis. The next entry in the
report would be G. camelopardalis.
Write out how the following animal names would be presented after the first occurrence in a
report. (1 mark)
Orcinus orca
Procyon lotor

--------------------------------------------------End of Pre-Lab----------------------------------------------
The Compound Microscope - Reminder from BIOL 1000
You may have learned about and used the compound microscope in BIOL 1000. The compound
microscope is used to look at objects (such as cells) that are smaller than the limit of resolution
of our unaided eyes. It is called a compound microscope because it has more than one glass
element in the lens.
Following is an explanation of the function of each part of the microscope, starting from the
light source and ending at where your eye receives the magnified image.
Remember to setup Köhler Illumination before using the microscope (described in the second
BIOL 1000 lab video above).

 Light Source: A lamp is located in the base of the microscope. Light intensity is adjusted by
the intensity control knob on the side of the microscope.
 Field Diaphragm: The field diaphragm controls the amount of light from the lamp that enters
the condenser. It helps remove stray light that can interfere with the image. The
diaphragm can be opened and closed by turning the field diaphragm ring.
 Condenser: The condenser contains a lens system that captures light from the lamp,
concentrates it and focuses it onto the specimen. It can be raised or lowered with the
condenser focus knob. It can be aligned with the light source and objective lens by using
the condenser centering screws. It also has a diaphragm (the condenser diaphragm),
that controls how much light leaves the condenser and enters the objective lens. It is
opened and closed by a lever on the condenser.
 Stage: The stage supports and moves the specimen, which is normally mounted on a glass
slide. Your microscope has a mechanical stage which allows you to move the specimen
with precision control. There is also a clip that secures the slide on the stage. Stage
motion knobs move the slide on the stage. The opening in the centre of the stage allows
light to pass through your specimen and into the objective lens.
 Objective: The objective contains several lenses that capture the light from the specimen and
create a magnified image of it. There are four objectives on your microscope: the 4X
objective is primarily for scanning, the 10X objective is the low power objective and the
40X objective is the high power objective. The 100X objective is an even higher-powered
objective but it requires oil and will not be used.

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 Ocular Lens (also called eyepiece): The eyepiece captures the image produced by the
objective and enlarges it further, producing the image your eyes see. Your microscopes
are binocular (have two oculars). Usually one ocular can be focused separately to adjust
for differences between your two eyes. The ocular magnifying power is 10X.

 Focus Adjustment Knobs: These knobs move the stage up and down to focus the specimen.
The Coarse Focus Adjustment allows the stage to move large distances for quick basic
focusing. The Fine Focus Adjustment Knob moves the stage very small distances and
brings the specimen into sharp focus.

Binocular eyepiece

Diopter ring Stage slide

clamp

Revolving nosepiece

Objective
On/Off switch
Stage

Light
Condenser
intensity
centering
dial
screws

Coarse
Condenser
focus knob

Stage motion
knobs

Fine focus
knob
Field diaphragm

Condenser
focus knob
Light source
Condenser
diaphragm
lever
The Compound
Microscope

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The Dissecting Microscope

The dissecting microscope is used to look at objects that are too large to view with a compound
microscope but are small enough that magnification is warranted. A dissecting microscope
allows images to be magnified in three dimensions because each ocular is independent of the
other. Specimens are commonly dissected with the aid of a dissecting microscope. Again, it is
important that you understand how the microscope works to get the maximum value from
using it. Many of the components of the dissecting microscope are similar to the compound
microscope.

 Illuminator Lamp: An illuminator can take many different forms. It can be mounted in the
arm of the microscope or may come from an external lamp that shines onto the stage or
is reflected from underneath the stage. Our current dissecting microscopes have an
illuminator stand with two light sources: reflected and transmitted.

Stage: This is where your specimen is placed for viewing. It is often placed inside of a shallow
container, such as half of a Petri plate.

Objective: Unlike the compound microscope, the objective lens on the dissecting microscope
is stationary. Magnification is controlled by changing the magnification adjustment knob.
Various dissecting microscopes have different magnifications available.

Focus Adjustment Knob: These knobs move the entire microscope body up and down to
allow for the specimen to come into focus. Some models have both a coarse and a fine
adjustment, while others will only have a coarse adjustment.

 Eyepiece (Ocular): This is the lens that captures the image produced by the objective and
enlarges it further, producing the image your eyes see. Your microscopes are binocular
(in other words, there are two oculars). Some dissecting microscopes have a diopter
adjustment to compensate for differences between your right and left eyes.

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Instructions for using a Dissecting Microscope

1. Position the illuminator so that the stage area of your microscope will be illuminated.
Turn on the light source but do not use more light than needed or it will negatively affect
the image observed.
2. Adjust the magnification to the lowest power. Adjust the ocular lenses to fit to your
eyes so that one image is observed.
3. Position your specimen on the stage in a shallow container.
4. Lower the microscope body with the focus knob to the lowest position.
5. Use the focus knob to raise the microscope body up until the image comes into focus.
Adjust the diopter ring on each ocular until the image is in focus. If you change the
magnification, you will likely need to refocus.
Proper Care and Handling of the Microscope
The microscopes in this lab are shared by all of the students in the course so it is very important
to treat them well.
 Use both hands when moving the microscope – handle the base and back support. Be
sure to keep it in an upright position.
 Use only the provided lens paper for cleaning lenses. Paper towels or facial tissues will
scratch them. Avoid damaging fingerprints.
 Never force adjustments. If the microscope is not operating smoothly, ask your TA.
 Check your microscope before each laboratory session and contact your TA if there are
missing parts.
 Before leaving the lab: make sure the lowest magnification or objective is selected, the
light switch is off, and the microscope is unplugged. The cord must never be wrapped
around the microscope since this can damage the components. Fold the cord neatly and
store it behind the microscope as demonstrated by your TA. Cover the microscope only
if your TA instructs you to do so.

Making Detailed Observations

In the fume hood you will find various specimens that you will view using a microscope. To
begin this exercise, choose the most appropriate microscope for each specimen. You will focus
on and observe each specimen individually. Use your keen observational skills and make
detailed notes and drawings of each specimen (use pages 8-9, or blank sheets of paper). You
will use your notes to help identify the specimen later. This is the only time you’ll have access
to the specimens.

Caution: do not remove the lid of the container holding each specimen sample. Focus through
the clear portion of the bottle.

Focus on a specimen and make as many observations as you can about it. Observations about
the anatomy of the specimen are best. An observation about size is not always useful as this can
vary between members of the same species. For example:
 How many appendages?
 Anterior and/or posterior projections present/absent?
 Number of eyes (black dots)?
 General shape?
 Range of lengths (based on multiple samples of same species)?

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 NAME:
Registered Lab Section: (e.g. M.08)__________________
Record your observations (text and drawings) and submit these completed pages to your
TA at the end of class.

Specimen #1 (bacterial slide) (2 marks)

Specimen #2(2 marks)

Colour of the sticker sample:

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 Laboratory 1 – Taxonomic keys and phylogenetic trees

NAME:
Registered Lab Section: (e.g. Lab 08)__________________

Specimen #3 (2 marks)
Colour of the sticker sample:

Specimen #4 (2 marks)
Colour of the sticker sample:

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 Laboratory 1 – Taxonomic keys and phylogenetic trees

Identification Guides (Taxonomic or Dichotomous Key)

Identification skills are essential in all areas of biology: from use by medical personnel
attempting to diagnose a particular illness to ecologists trying to determine whether a particular
organism might be a new invasive species.

With considerable experience, it is possible for scientists to identify some diseases or organisms
“at a glance”. However, in most situations an identification guide (taxonomic/dichotomous key)
is necessary. These may be as simple as lists of illustrations, as in many identification guides for
birds or flowers. However, identification through illustrations will only work if all species are
comparatively invariant in structure and/or colour and there are few species to be identified. In
most cases more complex identification guides are required.

Relationships between organisms (e.g. physical characteristics) are determined and can be used
to construct a phylogenetic tree. Most of us are familiar with the concept of phylogenetic trees
as they are similar to family trees. When looking at a variety of species, it is a great visual tool
for mapping relationships.

Using the characteristics that are unique to an organism, we can organize and display this
information in a classification tool called a taxonomic/dichotomous key. The
taxonomic/dichotomous key is used to identify organisms based on the principle that an
organism either has or does not have an observed physical characteristic. It is called
dichotomous because each couplet (pair of contrasting statements) in the key leads to two
choices. These choices may lead you to additional couplets or to successful identification of the
organism. Eventually all organisms can be identified unless you have one that has not previously
been seen or described. As keys are usually (but not always) restricted in use to particular
geographic areas (for example, the bumble bees of eastern Canada), a newly invasive species is
unlikely to be easily identified. The key must then be updated in order to contain the new
organism.

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Identify the Following Organism

Figure 1.1

1 a) Number of antennal segments equal to or greater than 12; abdomen separated from thorax
by a narrow constriction or “waist”……………...……..........................go to couplet 2
1 b) Number of antennal segments fewer than 7; abdomen broadly attached to thorax, no
narrow waist is present...................................................................go to couplet 3
2 a) Head bright orange, contrasting with black rest of body; hind legs covered in short
spines…………………………………………………………........................Mumbo jumbo
2 b) Head and body black or dark brown; hind legs covered in long hairs
…………………………………………………………………...........................Mumbo bushano
3 a) Eyes large, wider than the distance that separates them; antennae with only 3
segments……………………………………………………….........................Enigma brevicornis
3 b) Eyes small and narrow, distance separating them at least 1.5 times their maximum width;
antennae with between 4 and 6 segments………...…………................go to couplet 4
4 a) Head and thorax metallic blue………………………………….......... Enigma metallica
4 b) Head and thorax dull brown…………………………………........…Enigma mediocrita

What is the organism?

Closer Look at the Key

Notice that when different features of the organism are referred to in a key they are separated
by semicolons. If a feature is unique, it might serve to separate the organisms (or groups of
organisms), as in the last couplet above (4a, b). However, if there is more than one feature that
can easily be used to separate the organisms then they can all be used. When describing the
organism, a wide variety of different types of characteristics can be used such as colouration,
relative sizes or shapes of structures, different numbers of segments etc.

An important feature of any key is that the characteristics used should NOT vary within a
species. For example, size is not a good characteristic for organisms that continue growth
through their adult lives, such as lobsters; colour might not be a good characteristic for
organisms that change colour, such as chameleons.

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Identify your specimens

 You may work with a Lab Partner
 Obtain a taxonomic key from your TA.
 Based on your observational notes and drawings of Specimen 2, 3 and 4 (pages 8-9)
identify each of the unknown specimens (each are a type of zooplankton).

Identity of Species 2:

Check with your TA if this is an accurate identification. If not, that is ok. Check that you are
using the taxonomic key correctly and try again. No marks are lost for multiple attempts.
Key is that you understand how to use the key by the end of this exercise. The post-lab
quiz will require you to use a taxonomic key.

Identity of Species 3:

Identity of Species 4:

Include the species name at the top of the associated observational notes

***Return the taxonomic key to your TA***

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Relationship of Taxonomic Keys and Scientific Names

As you have just experienced (with the zooplankton key), these identification guides are based
on the idea that each species has both similar and different characteristics from other species.
This is the basis of taxonomy. This system of organizing organisms into a hierarchical
classification was popularized in the 18th century by a man named Carolus (“Carl”) Linnaeus. All
species are placed into a series of groups; domain is the largest and genus is one of the smallest
(Figure 1.2). Binomial nomenclature, using genus and species to scientifically name organisms,
is based on this organization. For example Canis familiaris is the domestic dog. Canis is the
genus and Canis familiaris is the species (see pre-lab page 3). Scientific names are always either
italicized or underlined (if hand written) and are the form included in scientific reports.

Figure 1.2: The simplified structure of hierarchical classification.

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Skull Exercise
 Although you will be working with a lab partner for this portion of the lab, the following
(#1 to 3) will be submitted by each student individually at the end of lab.

Lab Partner’s Name:

1. Working in pairs, you will first observe the animal skulls mounted on a plaque. Do NOT
attempt to remove the skulls from the plaque. Do NOT write on the skulls. Handle
gently.
 Each of the skulls being examined is of a different species. Some of the species
are closely related, others are not. All are from the class Mammalia.
 Closely examine the skulls mounted on the plaque. Use the diagrams of skulls
(and the associated glossary) available at your work station to assist in
recognizing the main components of a skull.
 On page 15 (or a blank sheet of paper), make detailed observations of the skulls
using proper scientific terminology (i.e. anatomical direction, names of
structures)
o What are the common characteristics, if any?
o What are the notable differences?
 Submit these notes at the end of class. (2 marks)
2. Work in pairs.
 Organize the skulls into groups based on those similarities and differences noted.
Use page 15. (2 marks)
 Illustrate your classification/groupings of the skulls as a phylogenetic tree. Use
page 16. Remember a phylogenetic tree demonstrates your hypothesized
relationship between these specimens. (2 marks)
 This tree will serve as a template for the construction of your
dichotomous/taxonomic key.
3. Work in pairs.
 Construct a dichotomous/taxonomic key using proper anatomical terminology
when describing the skulls. Use page 17. (2 marks)
 This key must permit others to identify the skulls if they were not labeled.
 When finished your taxonomic/dichotomous key, exchange it with another
group. Use their key to attempt skull identification. Critique the key. Provide
feedback on what you felt worked well and what needs further work.
 Modify your key based on the provided feedback.
 Submit the final draft of your taxonomic/dichotomous key (page 17) to your TA
at the end of class.

Remember that although you worked with a lab partner, #1 to 3 above is to be submitted by
each student individually at the end of lab.

Please include your name, student number and registered lab section on each page.

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NAME: Registered Lab Section: (e.g. Lab 08)

#1 Skull Observations (2 marks)

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NAME: Registered Lab Section: (e.g. Lab 08)

#2 Skull Observations (Groupings) based on similarities and differences (2 marks)

Phylogenetic Tree (2 marks)

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NAME: Registered Lab Section: (e.g. Lab 08)

#3 Taxonomic Key (2 marks)

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Grading
This lab is worth 5% of your final course grade.
Percent contribution of each Lab 1 component to the final Lab 1 grade is shown below. Mark
breakdown of each of these components is also indicated.

Pre-Lab Quiz (completed on Lab eClass site) 10%

Pre-Lab Exercise 10%

 Page 1 to 4 7 marks

In-Lab 60%
 Bacteria and zooplankton observations (page 8 to 9) 8 marks

Submitted at the end of class

 Skull observations and notes (page 15) 2 marks
 Skull organization/groupings (page 16) 2 marks
 Phylogenetic Tree (page 16) 2 marks
 Taxonomic Key (page 17) 2 marks

Post-Lab Quiz 20%

 Complete within one week of the end of your lab.
o E.g. if your lab finished at 5:30 p.m. on Tuesday May 28th, you must
complete the post-lab quiz by 5:30 p.m. on Tuesday June 4th.
Overdue quizzes will receive a grade of 0.
 The quiz addresses material covered in this lab (Lab 1)

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