CLASSIFICATION
LAB 08
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The purpose of this week’s lab is to:
· review classification of organisms
· construct and map the relationship of members of the Kingdom Animalia
I. Systematics
Systematics is the study and classification of organisms with the goal of reconstructing their evolutionary history. Taxonomy is more general than systematics and can be defined as the science of identifying, naming and classifying organisms into groups. Taxonomists may or may not use evolutionary principles in developing classification schemes. Most taxonomists use a hierarchical system to classify species into increasingly broad groups based on extent of similarities in morphology and other characteristics. Linnaeus, a Swedish physician/botanist in the 1700s, helped develop the two part, or binomial naming system that we use today to classify organisms. The first word of the name is the genus to which the species belongs. The second name is the specific epithet of the species. For example, the scientific name for the domestic cat is Felis silvestri (underlined or italicized). The cat belongs to a larger group (taxon), the family Felidae. The classification process continues hierarchically. The next higher group is the order Carnivora, which is followed by the class Mammalia, subphylum Vertebrata, phylum Chordata, and kingdom Animalia (Table. I). (Note: For plant, the term “Division” is used in place of “Phylum”)
Table I. Classification of the Domestic Cat
Category
/ Domestic CatKingdom
/Animalia
Phylum
/ ChordataSubphylum
/ VertebrataClass / Mammalia
Order / Carnivora
Family
/ FelidaeGenus
/ FelisSpecies / silvestri
The classification scheme we will use is a six-kingdom system that divides prokaryotes into two kingdoms (Eubacteria and Archaebacteria), the Eukaryotes into the Kingdom Protista, Plantae, Fungi, and Animalia. There are other classification schemes such as a three domain system that separates organisms into the superkingdoms of Eubacteria, Archaebacteria, and Eukarya; and an eight kingdom system that divides prokaryotes into two kingdoms (Eubacteria and Archeabacteria) and divides protists into three kingdoms (Archaezoa, Chromista, and Protista). These different schemes of classification also illustrate two extremes among taxonomists -- lumpers and splitters. Taxonomists who are lumpers prefer to classify things in only a few, broad groups while splitters favor naming many groups, so there are fewer taxa in each group.
What are some more creative ways we can classify organisms? List as many as you can think.
Exercise 1: The Nuts and Bolts of Classification
Divide into four research teams. You will be handed a bag containing various fasteners (nails, staple, screws, etc.). As renowned taxonomists, you are to develop a classification scheme that meets the established rules of the Linnean system. Be prepared to defend your classification scheme orally and answer questions regarding your classification choice—what roles did form vs. function play in your classification scheme? How did you delineate each of your hierarchical groupings?
Specific Tasks:
1. Make a classification tree of your objects using the poster paper, tape, and objects. Include all of the categories from phylum to species. What rationale(s) did you use for each category and what criteria did you use to differentiate among categories? Did you rely more on "form" or "function?" Did heavily weigh shared traits in making your groupings, or did you consider differences among objects more important in making your categories? Provide descriptive names for each category from phylum, class, order, family, genus and species to the furthest level you can. Apply names that best describe each object and their hierarchical location in your classification scheme. Based on your scheme, would you consider yourself more of a lumper or a splitter?
2. What are some of the difficulties and differences between classifying inanimate objects and living organisms? Is it easier or more difficult to classify living or inanimate objects? Why? If you knew nothing about each object's function, how would your classification scheme be different?
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II. The Fate of the Coelacanth
Fig. 1. Coelacanth.
The coelacanth, once thought to have gone extinct 80 million years ago, was found in 1938 off the coast of the Comoro Islands. It is regarded as a living fossil and is a clue to the evolutionary transition of bony fish to terrestrial amphibians. The coelacanth possesses a fat filled lung, fleshy lobed-fins, circulatory system, inner ear, and tooth enamel, as well as other characteristics, closely related to tetrapods.
Fig. 2. Anatomical comparison between sarcopterygian, amphibian, and reptile.
However, controversy exists concerning its relationship to the lungfish and the lungfishes relationship to the tetrapods. Several tests have been conducted to determine the coelacanth’s ancestry. A mtDNA test has concluded that the mtDNA of lungfish is closer to the mtDNA of land animals such as frogs than the coelacanths (Roush, 1997). In another study, Zardoya and Myer (1996) analyzed 3,500 base pairs of the 28S ribosomal RNA gene. The results indicated that the lungfishes and coelacanths form a monophyletic group and are equally closely related to terrestrial vertebrates. Bogart, Balon, and Bruton (1994) found that the karyotype of the coelacanth is very similar to the 46-chromosome karyotype of one ancient frog, Ascaphus truei, but is unlike the karyotype found in lungfish. Blood hemoglobin of the coelacanth was found to be similar to tadpoles, but not to adult frogs (Forey, 1991; Gorr, Kleinschmidt, & Fricke, 1991).
A fourth form or organization of an immunoglobin gene (VH) was found in the coelacanth; the other three forms are found in mammalian, avian, and elasmobranches (Amemiya, et al., 1993). The VH gene of the coelacanth was shown to share more similarities with tetrapods (vertebrae possessing two pairs of limbs such as amphibians, reptiles, birds, and mammals) than elasmobranches (sharks, skates, and rays).
Physiological characteristics such as the spiral valve intestine, giving birth to live young, osmoregulatory strategy, and the possession of a long cartilaginous tube instead of a backbone is a trait it shares with the sharks. However, it possesses a bony head, teeth and scales similar to bony fish. In addition, it is the only vertebrate with an intracranial joint, a feature once found in ancient frogs.
The coelacanth’s phylogenetic classification remains inconclusive.
Fig. 3. Alternative hypotheses of sister group relationship between Sarcopterygii and tetrapods.
Fig. 4. A general evolutionary view of the radiation of lobed-fin fishes into present-day lungfishes and coelacanths (Latimeria).
III. Taxonomy
Philosophically speaking, which view of the world is more accurate?
1. There is order in the world if we can discover it.
2. There is chaos in the world; we can apply an artificial order system to it.
Some taxonomists have the first view while others have the second. No wonder there is much contention over the best way to classify things.
Regardless of their worldview, taxonomists all have two main objectives:
1. Sort out closely related organisms, assign them species names, and describe diagnostic characteristics that distinguish the species from one another.
2. Classification of species- arrange species in broader taxonomic categories
Several terms are important in understanding evolution-based classification schemes of organisms.
Homology refers to a similarity in a trait or traits of two organisms resulting from a common origin. For example, a whale flipper and human hand share similar morphological characteristics that are derived from a common ancestor and have been modified over evolutionary time.
Human Arm Whale Flipper
Fig. 5. Anatomical comparison of human arm and whale flipper. An example of homology.
Analogy refers to a similarity in a trait or traits that have independent evolutionary origins. This can be attributed to convergent evolution. For example, in a bird and fly, the wings developed independently as adaptations for flight.
Phylogeny (cladistics)- evolutionary history of a set of taxa, usually portrayed as a branching tree with individual taxa at the branch tips. Elucidates putative evolutionary relationships of organisms.
IV. School of Systematics
Today we have three main schools of systematics:
Classical evolutionary systematics—classification is based on observed similarities and differences among groups of organisms. Classification must be based on genealogy (evolutionary history), which coincides with Darwin’s views; however, genealogy alone is not enough to determine classification. In other words, this classical approach considers primarily traits that are thought to be related to evolutionary history, but other traits such as ecological roles, and patterns of distribution of the organisms may also be considered if they are particularly outstanding. For example, while classical systematists acknowledge that DNA evidence shows that crocodiles share a more recent common ancestor with birds than with lizards, they combine lizards and crocodiles in a taxon that excludes birds. This is because the ability to fly was an evolutionary breakthrough that placed birds in a major new adaptive zone. Ecologically, crocodiles and lizards seem a lot more alike than crocodiles and birds. Evolutionary systematics places birds into their own class (Aves). A phylogram is used to represent an organism’s lineage, which shows genetic distance (Fig. 8).
Figure 6. Phylogram of bird and reptile phylogeny.
Criticisms of the approach:
It is subjective -- when are differences in ecological traits different enough to warrant placement of the taxa in a new group even though it is inconsistent with evolution (e.g. the case of birds)?
Phenetics—argues that classification should be based exclusively on phenetic characters (phenotype), and that similarities between organisms should be measured objectively and explicitly. The general procedure is as follows:
1. Numerous characters are evaluated/measured.
2. All characters have equal weight.
3. Each character is measured numerically.
4. Measures of similarity and clustering of species and taxonomic distances are calculated via statistical algorithms, usually involving computer programs because of the many traits and measurements that must be analyzed together.
5. Organisms are place into groupings based on the statistical similarity of their traits.
6. The diagram of relationships that emerges is called a phenogram (Fig. 7). The phenogram does not necessarily portray evolutionary relationships.
Features
Pear orange grapefruit apple plum greengage
hard + + + + - -
round - + + + - +
stone - - - - + +
thin skin + - - + + +
smooth + - - + + +
sweet + + - + + +
stalk + - - + + +
segments - + + - - -
Similarities
pear
orange 3
grapefruit 2 7
apple 7 4 3
plum 6 1 0 4
greengage 5 2 1 6 7
pear orange grapefruit apple plum
Figure 7. A phenogram of fruits
Criticisms of the approach:
All traits are weighed equally. Aren't some more important than others?
Does not consider genealogy (evolutionary relatedness) among the taxa. Convergent evolution can sometimes lead to distantly related species being grouped together.
Cladistics (phylogenetic systematics)— This school was founded by Willi Hennig (1950). The name cladistics is derived from the Greek word “Clados” meaning branch or twig. The basic principle is that classification of biological organisms must reflect ONLY their evolutionary history (genealogy). Other criteria should never be considered. Furthermore, all characters are NOT considered equal, as in phenetics. Instead, classification is based exclusively on characters that are shared within a group, but absent in other groups. Such characters are called "shared, derived characters" (synapomorphies). The trait is "shared" because occurs in more than one taxon, and "derived" it does NOT occur in taxa outside the group being defined by the trait. Traits that are shared by all taxa in the world are not useful for making groupings. Cladists use shared, derived traits to build a phylogenetic tree (cladogram- see Fig. 8), illustrating the evolutionary relationships among organisms. The cladogram contains the names of the taxa at the branch tips, and neighboring branch tips are called "sister groups" because they are most closely related. Each fork in the branch is called a "node" and each node is defined by a shared, derived character. In otherwords, all sister groups share a shared, derived character defined by their node, and no other groups may possess this character.
Figure 8. Cladogram
This branched diagram shows the relationship of a group of species based on the fewest number of shared changes that have occurred from generation to generation. The cladists argue that the only way speciation can take place is by a dichotomous split, so a phylogenetic tree is always a dichotomous tree (each node involves exactly 2 branches).
Exercise 2: Animal Classification
The purpose of this lab is to illustrate the principles of classification and some of the processes of evolution (e.g. convergent evolution). In this lab you will develop a taxonomic classification and phylogenetic tree for organisms in the Kingdom Animalia. Examine these animals and note the variety of appendages, skeletal features, color pattern, etc. In your notebook, write down their characteristics (traits). Then on a large piece of paper create a hierarchical classification of these species, using the format in Figure 8.
The first step in this exercise is to decide which species belongs in the same Phylum. Depending on how you organize the species, you may only get up to the level of order or class
Part 2. The Phylogenetic Analysis
Construct a phylogenetic tree (cladogram) based only on your examination of the sample species. You may use your taxonomic classification as a starting point for building your phylogenetic tree, but recall that the positions of species on a phylogenetic tree are based only on shared, derived traits. At each node (intersection of two branches) of your tree, list the shared, derived trait possessed by the species at the corresponding branch tips. For example, let us say you have put species A and G and you think they evolved from a common ancestor based on A and G sharing a particular trait (x) that no other species have. Then species A and G, when mapped on your phylogenetic tree, would look like the diagram below (Fig. 9).
Figure 9
Figure 10 illustration a phylogenetic tree with 3 species. Figure 10 indicates that species E and K are more closely related to each other than either is to C. We hypothesize that E and K have a common ancestor based on a shared, derived trait (y) that is not shared by C. Trait z is shared by all three species.
Figure 10
Below is a character matrix and two different cladograms based upon it.
mouse bat bird fish
lungs + + + -
4 bony limbs + + + -
milk glands + + - -
hair + + - -
wings - + + -
feathers - - + -
jaws + + + +
Figure 11. “A” is based on share traits; “B” is based on ancestry
Hints, Suggestions and Warnings
a. Draw lines faintly in pencil to indicate the path of evolution. Only after your instructor has checked your tree should you glue the figures in place and darken the lines.
b. Branching should involve only two lines at a time:
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