Lab 6 pre-lab.

To create phylogenies and research the relatedness and evolutionary trajectory of various species and life on Earth, taxa must be described, classified, and identified. Therefore, taxonomy plays a vital role in our understanding of evolution. Your task in Lab 6 will be to learn how to make and use taxonomic keys, common tools for ecologists and evolutionary biologists. You will work together to make a key of your classmates, use ID cards of various isopods species to create and test your own dichotomous key, and use an existing key to identify cichlids in our class tank. This lab will connect us to our next unit on ecology and the following lab on biodiversity.

• Introduction
• Do you know enough?
• What we will do in lab?
• LABridge

<

>

What is taxonomy?

Taxonomy is the practice of describing, classifying, and naming species. At first glance this may seem like an easy endeavor, but labeling taxa that have evolved and are still evolving organically, is very difficult. Nature just is. It was not specially produced to fashion unique items or sets of species. Consequently, the job of a taxonomist can be challenging and quite complex. It also means their task is never complete; as we learn new things about groups of organisms, their taxonomy inevitably needs to change as well.

Taxonomists have created a nested hierarchical system to identify, label, and categorize life. These are referred to as levels of taxonomy and include (from largest to smallest):  Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species. You can use this mnemonic sentence to remember the order: “Dear King Philip Came Over For Good Spaghetti." We recognize Carl Linnaeus as the father of taxonomy. He developed the system of binomial nomenclature, the Latin-based, scientific names we ascribe to species as: genus species. This universal system allows for collaboration to proceed smoothly, without the confusion of highly variable and local common names. It also includes the genera to which a species belongs, signifying the larger group within which it is nested. 

A primary complicating factor in taxonomy is there is no agreed-upon definition of what even defines a species. The three most common species concepts (biological, morpho, and phylogenetic) are described below along the advantages and disadvantages of each. Most biologists are comfortable using the biological species concept for most taxa, but others require the more refined phylogenetic concept. We will discuss this concept more next week when we explore systematics. But for now, understand that depending on the concept applied, species are somewhat fluid as is their classification within various genera or families. As we learn more and discover new species, a taxa can be demoted (become sub-species) or promoted (to a genera), they can be merge into larger taxonomic groups, and even disappear as a classification altogether.  As we have moved from using mostly morphological traits to categorize organisms, to highly specific phylogenetic analysis, entire phyla and even kingdoms (more on this later), are being revised. 

From your lecture text (ch 24, Pearson). Click to enlarge.

You should know what taxonomy is, who "founded" it, and the levels of taxonomy in order.

Make sure you are comfortable with all the bold faced terms on this page.

You need to understand what a species concept is and be able to define the biological species concept.

Levels of taxonomy.

This crayfish is potentially a new species. It was first discover 10 years ago in KY, but taxonomists have yet to agree if it is a new species or new variant of an existing species.

DO you know enough about dichotomous keys?

The most robust way ascertain the identity of a species, be it bacteria or a primate, is through genetic analysis. However, ecological and evolutionary research is often conducted in the field, away from sophisticated lab equipment. So, how do scientists in the field determine the identity, or taxonomy, of species in question? They use dichotomous keys.
A dichotomous key is a tool that allows the user to determine the identity of species in the natural world. Keys consist of a series of choices that lead the user to the correct name of a given item (e.g., like a chose-your-own adventure book or Minecraft "story mode"). "Dichotomous" means "divided into two parts. By using paired, mutually- exclusive choices, called couplets, a scientist can narrow-down the identity of an unknown species.
General Rules for Designing a Good Key

1. Couplets offer characteristics that can be observed by scientists.
2. They must be mutually exclusive, meaning an organism meet one requirement or the other. They cannot meet both and they cannot fall in-between. 
   
3. The observable characteristics must be objective, not subjective. For example, one should never use wording like "bigger" or "smaller" but "greater than 15cm" or "less than or equal to 15cm instead.
4. When using a measurement, you must be precise about what exactly is being measured (e.g., length, width, etc.).
5. You most account for growth; from juvenile to adult. Your key should work all the time, for every individual of the species.
6. Although color is often used in couplets as diagnostic tool, do so with caution. What if someone used "green" as a diagnostic tool in a dichotomous key? Would that include teal, turquoise, and lime? It is best to use color differences only if they are dramatic and far from each other on the color wheel. You could use red vs. blue, but using green vs. blue would not be recommended. 
7. When building a dichotomous key, it is important to check that your key has one less couplet then the number of species to identify. For example, if you are trying to build a key to distinguish between 10 tree species in a forest, your dichotomous key should have 9 couplets.
8. Your key should also reflect the evolutionary relationships of the species involved. They should be grouped by close evolutionary relationships.

Common keys.

Click the image to explore the online dichotomous key of trees.

Let us practice with these four taxa.

Example 1

1a. Has hair or fur on the body...go to 2
1b. Is hairless...go to 3

2a. Has 2 pairs of legs... Canis lupus (grey wolf)
2b. Has 4 pairs of legs... Latrodectus variolus (n. black-widow spider)
​
3a. Has wings... Haliaeetus leucocephalus (bald eagle)
3b. Does not have wings... Copris fricator (dung beetle)

Example 2

1a. Body measures greater than 5cm in length -- go to 2
1b. Body measures less than 5cm in length -- go to 3

2a. Body covered in hair... Canis lupus (grey wolf)
2b. Body covered in feathers... Haliaeetus leucocephalus (bald eagle)
​
3a. Has 3 pairs of legs... Copris fricator (dung beetle)
3b. Has 4 pairs of legs... Latrodectus variolus (n. black-widow spider)

Notice that these four species were identified using three couplets, one less than the number of animals involved, in both example keys. However, example 1 does not reflect the correct evolutionary relationships between the taxa in question; mammals and birds are more closely related and so are insects and spiders. Also, example 1 incorrectly identifies beetles as "wingless" simply because the wings are not visible from the outside. A closer examination would show that many beetles do, in fact, have wings. They are tucked under protective covers called elytra, so they are hidden. The dichotomous key in example 2 represents the same four species of animals but does so in the correct evolutionary context and using proper diagnostic characteristics.

You should know what a dichotomous key is, what a couplet is, and how keys work.

Click on the Arbor Day Foundation's online Tree Key. Explore it and get and understanding of keys are used.

Be sure you know the general rules for making a good dichotomous key.

Review the two example keys and make sure you understand the primary difference between the two.

What will we do in lab & how will we do iT?

Lab 6 contains three exercises

1. ​Practice making a key: You will work together to make a key of your classmates.
2. Construct & test a key: You will use ID cards of various isopods species to create a usable dichotomous key. You will then test your key using isopods from our colony.
3. Use a key: You will use several methods to try and identify cichlids in our class tank.

Important to know...Why cichilds?

Cichlids are an amazing group of freshwater fish, found in the South America, Africa, and southern Asia. They are well known for their bright colors and are sometimes referred to as "freshwater coral fish," making them a favorite in the pet trade. Most are yellow and blue (directly across from each on the color wheel), but cichlids that live deeper in the water column will have more red and silver, as the available light spectrum differs. Cichlids also have many interesting natural history traits. For example, some species use a lek matting system, wherein many males construct nests, or bowers, near each other, and wait for females to make their preferred mate-choice based on the quality of their bower. Their mating rituals also involve dance routines and mouth brooding, where the female carries the eggs, and sometimes fry (baby fish), in their mouth for protection (see the image in the sidebar).
The cichlid family (Cichlidae) are a textbook example of the phenomenon of adaptive radiation, wherein a single species evolves into many distinct species to fill various, available, ecological niches. Darwin's famous finches are another example. Most cichlids are from Africa, whose large, freshwater lakes, like Lake Malawi, Lake Tanganyika, and Lake Victoria, hold more than 1,600 species, with hundreds of unique and endemic (i.e., found only in that area) species in each. For example, Lake Victoria houses over 500 species of cichlid, all having evolved in the last 10 to 15,000 years. This type of of rapid speciation, the formation of new species, is exceedingly rare in the animal kingdom. In fact, no other vertebrate group has as many species with as much variation (in color, body shape, behavior and natural history) as the cichlids.
Even more astounding, and as evidence for natural selection, many similar adaptions and species-types can be found in lakes that have never been connected. These fish evolved in similar niches and therefore look and act nearly identical, while sharing no recent evolutionary history. This is an example of convergent evolution, which we will discuss in later labs (see images in the sidebar). 
The taxonomy of groups as large, diverse, and morphologically similar as the Cichlidae family is constantly in flux. The construction and use of quality taxonomic keys is paramount for experts in the field. ​

You should know the basic facts about cichlids from this page.

Know the bold-face terms regarding cichlid traits and evolution.

Download the cichlid ID app FishVerify app in the sidebar.

A mouth brooding cichlid.

Cichlid convergent evolution in two separate lakes. Click to link to the article.

Two very similar looking species from two different lakes.

Download FishVerify app

If you feel confident with this material, click the bridge icon below and navigate to Blackboard to take the LABridge for this week. Be ready to tested on this material before you go to the quiz, and make sure you have your Lab Notebook Guide ready to submit as well.

Click here to get to WKU's blackboard to take your LABridge for this week.

Lab 6 Protocol

Following this lab you should be able to...

• Understand taxonomy and dichotomous keys
• Build a dichotomous key for identification
• Use a dichotomous key for identification​
• Associate taxonomy with key evolutionary concepts like speciation and adaptive radiation.

Overview. In today's lab you will practice making and using dichotomous keys.

1. ​Exercise I. Practice Making a Taxonomic Key as a Class
2. Exercise II. Create and Test a Taxonomic Key for Terrestrial Isopods
3. Exercise III. Use a Taxonomic Key to Identify Cichlids

• Exercise I
• Exercise II
• Exercise III

<

>

Exercise I. Practice Making a dichotomous key

We are going to make a taxonomic key for everyone in class, on the board. Here are a few things to keep in mind:

• Trait selection: Objective vs. subjective and use of color.​
• Make big divisions first.
• Top of couplet (1 or 1a) gets a name (id) or # (go to 4).
• Bottom of couplet (1’ or 1b) gets an id OR leave blank and come back.
• Finish “naming” all of one section before starting on the next.​
• Sections will funnel from large to small.
• Once a section is complete start the next one according to the closest couplet (from the bottom).
• Total couplets = 1 less than number of students.

Creating a key with humans requires a few addtional considerations:

• ​Do not use sensitive or inappropriate traits (e.g., weight, gender, waist size, etc.).
• Genus = last name & species = first name, underline or italicize these scientific names.
• ​Assume you are all frozen in time, for the purposes of this activity.
• Good trait ideas: height, presence or absence of items (e.g., glasses, hats, etc.), visible tattoos/piercings, length of sleeves or pants, hoods/no hoods, length of hair...& many more.

Procedure.​

1. Follow along with your TA as you construct the key together.
2. Volunteer to write on the board.
3. You should write your copy of the class key down in a notebook.

Click to download.

Exercise II. Create and test a dichotomous key 

Now it's time to for you to try this on your own.

Materials: You will be provided with unknown isopods to test your key and should use your phones to take photos and help with identification.

Test chambers.

Species ID cards.

Pillbug/Sowbug colony.

Dissecting microscope.

To move isopods..

For measurement.

Procedure.

1. Review the stack of ispod ID cards at your stations. An example is in the sidebar. 
2. Each one of these is a unique species and their scientific name is listed on each card.
3. Use the rules we developed to construct a dichotomous key for these isopods.
4. Use the diagrams below to refer to various parts of each specimen (e.g., thorax, abdomen, uropod).
5. Once you are finished with your key, alert your TA. They will do a quick check.
6. Next, they will bring you a few live, unknow isopods from our colony.
7. Get familar with the dissecting microscope at your station. 
8. Take notes in your Lab Notebook Guide.
9. Use your key to try to identify the specimen you were provided. 
10. To match measurements from the cards use this scale: 7.5cm (card) = 1cm (actual isopod).
11. Check your ID with your TA.

Remember these guidelines.

• Trait selection: Real World vs. Best Case (Objectives vs. Subjective)​
• Make big divisions first
• Top of couplet (1 or 1a) gets a name (id) or # (go to 4)
• Bottom of couplet (1’ or 1b) gets an id OR leave blank and come back
• Finish “naming” all of one section before starting on the next​
• Sections will funnel from large to small
• Once a section is complete start the next one according to the closest couplet (from the bottom)
• Total couplets = 1 less than number of students

Parts diagram for our dissecting microscopes.

Generic isopod anatomy. Click to enlarge.

General parts of a pillbug-like isopod. Click to enlarge.

More detailed diagram. Click to enlarge.

Exercise iii. use a taxonomic key to identify cichlids

There are three major groups of African Cichlids, the "mbunas," "haps," and "peacocks." These are not scientific classifications, but common names for these various groups.Our tank houses mbuna from Lake Malawi. 

• Mbunas. The term "mbuna" mean "rockfish" in the Chitumbuka language spoken in northern Malawi. These fish hide and establish territories among the rockpiles close to shore. 
• Haps. This group is actually a tribe called the Haplochromini tribe. It's a group within the sub–family Pseudocrenilabrinae, and includes the genus Haplochromis, plus a number of closely related genera such as Aulonocara, Astatotilapia, and Chilotilapia, which were originally all considered to be a single genus. 
• Peacocks. All the fish in this group are from the genus Aulonocara. As their name implies they are best known for their striking colors. 

Our tank has substrate comprising round rocks, similar to to those in Lake Malawi. You might also notice our tank appears crowded. Cichlids are generally very territorial and fairly aggressive fish. Crowding them in an all-male tank, like ours, prevents individual fish from staking out their own territories and becoming overly aggressive. It also allows for a beautiful viewing experience and a lot of diversity.
There are two species of fish in our tank that are not cichlids but serve as detrivores. These are the Ancistrus cirrhosus (bristlenose pleco) and Synodontis multipunctatus (cukoo catfish).
​*Fun fact: The cuckoo catfish is a brood parasite of cichlids; they lay their eggs in the cichlid nest and are then protected by the females during mouth brooding. 

Recent Discovery!

Cichlid taxonomy.

Lake Malawi (from the UMW Report).

---

Special thanks to Dr. McElroy and Dr. Huskey  for their knowledge on cichlids and fish husbandry.

Materials. The cichlid tank is located on the back lab bench as well as copies of the key.

Cichlid tank

Cichlid Species List

Reference book

PictureFish App

ID Cards

​Procedure.

1. Go back to our cichlid tank and spend 5 minutes (timed) recording observations in your manual.
2. Try to identify 5 species using the cichlid key. You will record these in your Lab Notebook Guide.
3. You have several methods to attempt to make a correct ID.
   1. Use this dichotomous key (reference chapter 5, page 85)
   2. Use the PictureFish app (free for iphones and androids).
   3. Use these species ID cards.
4. Get your TA to check your identifications.
5. Complete your Lab Notebook Guide.
6. Complete the form included on this page.
7. Clean up your station and check-out.

Excellent article on the adaptive radiation of mbuna cichlids. Click for pdf.

Faculty Spotlight: Doug McElroy

Dr. McElroy began his research career specializing in the genetics and speciation in African cichlid fishes, and the statistical analysis of population genetic data. He has also addressed questions related to wildlife molecular forensics, morphometrics, and conservation. Currently, his research focuses on applying evolutionary principles and multivariate statistical methods to examine processes of curricular change and assessment in higher education. He also does a lot of work with our Pre-Med program and collaborates  regularly with physicians at the Medical Center Bowling Green on several projects examining the impact of risk factors and treatment interventions on cardiovascular outcomes. If you are interested in participating in his clinical research course, Med Center internship, or current research, please contact him: [email protected]. 
​
Sexual selection, reproductive behavior, and speciation in the Mbuna species flock of Lake Malawi (Pisces: Cichlidae)...
Coloration in African Cichlids: Diversity and Constraints in Lake Malawi Endemicsc Arctic Lake...