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Classification and Phylogenetic Systematics




Please help me, I'm going out of my mind! Attached please find a file that has my problem. I need to know the full answer to procedure 3 which starts on page 5 goes to page 6 with the animals listed on page 9. The assignment for this procedure is listed on page 6 under the list of 11 things. I need the whole assignment (for procedure 3). I know this looks like a lot and I need it tonight if at all possible. This is for a class for biology majors.;Attachment Preview;bio3aclassificationlab.pdf Download Attachment;Bio 3A Lab: Classification and Phylogenetic Systematics;Objectives;1. Understand the difference between a system of classification and a phylogeny, and how;they are related.;2. Understand the basic method used in cladistic analysis.;3. Generate simple phylogenies based upon this method.;4. Compare traditional and cladistic classifications.;Systems of Classification;Classification of "things" seems to come naturally to the human species. You do it on a;regular basis. Enter any kitchen and you'll find the pots and pans grouped together, the;spices in a single cabinet, the dinnerware stacked neatly by type. Within a certain category;there are sub-categories. Open the silverware drawer. The overall category: Eating Utensils.;Within this category we find sub-categories, such as spoons, forks, knives, and chopsticks.;Look closer and each of the sub-categories are further subdivided. Within spoons there are;soupspoons, teaspoons, sugar spoons, serving spoons. This type of classification system is;called a hierarchy. You may have used a similar method to organize your thoughts before;writing a paper (the outline), or, if you are familiar with organizational structure of your;computer, think of the root directory. In the culinary example above, we could organize our;objects in the following way;Major Category: Kitchen Items;1st Sub-category: Silverware;2nd Sub-category: Spoons;Final Sub-category: Soupspoons (or any of the others);A natural outcome of this kind of thinking was the sorting of plants and animals into;hierarchical groups. You should know that this kind of sorting was originally begun before the;concept of evolution was elaborated. Carl von Linne' (a.k.a. Carolus Linneaus) was one of;the first to put forth a coherent method for organizing organisms. He was, in fact, a botanist;and his original work dealt with plants. Later, he worked on animals. In Linne's time there;was a real need to organize the plants and animals in some coherent way. People were;traveling extensively and bringing back or reporting hundreds (and soon thousands) of new;organisms. Museums began to fill up, and you had to handle all of this new material. Linne;and those who followed, gave us a framework for sorting out the potential mess.;Thus, the first plant and animal classification systems were created primarily for;convenience. In other words, for the convenience of the user, just like your kitchen;classification system. In using such a system, we usually work from the "top down." For;11/19/2006;Classification Lab, Page 1 of 9;instance, you purchase a new type of soupspoon. In finding the proper place for it, you will a);enter the kitchen, b) go to the silverware drawer, c) look at the spoon area, d) place the new;soup spoons into the soup spoon sub-category. Another example is found in the library. To;find a reference to the moons of Jupiter, you might have to drop through several hierarchical;categories such as science, astronomy, solar system, planets, Jupiter, and moons. In fact;learning to use the library means learning the librarian's classification system. Creating;systems and classifying organisms is called taxonomy (the process of grouping, a taxon is a;group). The idea as you can see is probably as old as the human brain.;Following the growth of evolutionary theory, it became clear that a classification system;could do much more. It could indicate the evolutionary relationships between organisms.;Classifying organisms based upon relatedness is called systematics, and on the surface it;may appear rather straightforward, even simple. In some cases, it may be, for instance, you;probably have no trouble grouping birds together as a single related taxon. However, when;the first specimens of the platypus were sent to the British museum, taxonomists were unsure;whether they were birds or mammals. Today, heated debates rage on concerning the;relationships of various groups of organisms. Moreover, there is considerable controversy;over how we should go about quantifying our measurements of similarity. When I show you a;bird, you look at it, and create a quick mental "scorecard" of characteristics. The first;character that you note is probably the presence of feathers. Next, you might look at the;characters of the feet or beak, or color patterns on the body. When you have assessed the;suite of characters, you do a quick mental calculation, and decide that it is a cardinal.;At this time, there are a few competing methods used in systematics. The major;competitor is called cladistic analysis. In a nutshell, cladistic analyses attempt to group taxa;based upon recently evolved (derived), shared characteristics. The attempt is to determine;the common ancestry of the groups. The method is, by far, the most rigorous and objective of;the systematic methods.;Cladograms;As we postulate relatedness, we can begin to illustrate in a diagram. In this case, the;diagram is called a cladogram.;C;B;A;Figure 1. Sample cladogram with three operational taxonomic units, A, B, and C;In Figure One, group A has more derived characters in common with group B than with;group C. A and B are more closely related to each other, than to group C.;As you might guess, you could draw cladograms for all sorts of things, and the single most;important part of the analysis would be the selection of characters. In the "real systematic;world" this is touchy business. The characters chosen must be homologous, that is they;must represent common evolutionary origins. For instance, looking at the characteristics of;the humerus in three species of higher primates would be perfectly acceptable, as the;humerus is homologous in this group. However, characters of the wings of bats and flies is;clearly disallowed, since those structures are clearly not related (they are analogous, similar;11/19/2006;Classification Lab, Page 2 of 9;function, different origins). Next, the character must be evolutionarily new to the group (or;groups). So far we have called such characters "derived", but cladists have their own;nomenclature. They call such evolutionary novelties apomorphies. Primitive characters are;called plesiomorphies. You will recall that the method of grouping was based upon shared;derived characters (shared apomorphies). There is a word that covers that, as well;synapomorphies: shared derived characters. And, of course, there's a word for shared;primitive characters: symplesiomorphies.;Okay, let's try to put some of this to use. One problem that systematists face is;determining the direction of the evolutionary transformation. Another way of saying this, we;need to know whether the particular character is present in the common ancestor do decide;whether it is primitive or derived. This direction is referred to as polarity. This determination;may be very difficult. The usual method for this determination is to compare the group of;interest to a taxon that is known to be primitive. This is called outgroup comparison. If we;wanted to determine the affinities of lizards, horses and humans, we could use amphibians as;a logical outgroup. Lizards, humans and horses share a very important derived character, the;amniotic egg. Amphibians have a generally more primitive egg type. At this time we can;construct an initial cladogram like the one seen in Figure Two.;Figure 2. Initial cladogram showing relationships among the groups horses, lizards, amphibians and humans;Humans, horses and lizards are all arising from the same node, since we only know at this;time that they form a group separate from the amphibia. We need to "resolve" the node, and;determine the affinities within our sample group. In the above cladogram the horizontal line;marked "am" indicates that groups above that point possess an amniotic egg. Now let's;consider another character, the presence of hair. A score sheet for this character is shown in;Table One.;Group;amphibians;lizards;horses;humans;Hair;+;+;Table 1. Score sheet for the characteristic "hair;Using these data we can clarify the cladogram, and represent those affinities based upon;our character analysis, as shown in Figure Three.;11/19/2006;Classification Lab, Page 3 of 9;Figure 3. Cladogram for OTU's shown in Figure two using two character states;There could be an alternative interpretation of this diagram. What if some hypothetical;ancestor of lizards (the "x" on the diagram) had hair? Then hair in horses and humans would;be primitive, and the loss would be derived in lizards. However, the cladistic method always;assumes that evolutionary novelties probably occur in the fewest number of steps (unless the;data clearly indicate otherwise). For instance, the appearance of hair in horses and human;lineage requires only one step. But the alternate hypothesis requires that hair be evolved in;lizards, horses and humans, and then lost in lizards (two events). Thus we should accept the;first hypothesis. This reliance on the "path of least resistance" is called the rule of;parsimony, or Occam's Razor1.;Procedure 1: Classification of inanimate objects.;Let's try a bit of cladistic analysis with some hardware store items. You will be give four;different type of screws. The object of this exercise is to determine the relationships;(phylogeny) among these three of them (one will be the outgroup).;The screws are labeled A B C and D. We are interested in the relationships between A B;and C, with D as the out group. You must derive sets of character states for each of your;species. Enter your data on the sheets provided in lab.;1. Choose five character states to analyze. Try to avoid easily modified characters like;color. Use characters such as heads shape, thread counts, etc...;2. Determine the presence or absence of the characters among each of your species;3. Use the outgroup method to determine polarity. Circle those characters that you have;determined are derived.;4. Determine the number of shared derived characters between all possible pair-wise;combinations of your species, i.e. group A and B, group B and C, etc... Enter these numbers;in the spaces provided.;5. Construct a cladogram using the rule that species with the greatest number of shared;characters are most closely related. Remember to minimize the number of steps.;6. Construct a classification from your cladogram. Call the group containing the three;related species a family. Within the family, the two species most closely related should form a;single genus, the other species should form a second genus. On your cladogram circle the;family, genera and species. Before you go on to procedure 2, compare your cladograms with;11/19/2006;Classification Lab, Page 4 of 9;others in the class. If there are differences, how can you account for them?;Monophyly and Cladistics;Classification based upon the cladistic analyses is quite different from the type of simplistic;organizational classification" we discussed at the beginning of this lab. The fact that;organisms are grouped together by shared derived characteristics implies a common origin;for the group. Groups which share a common origin (i.e. have more derived characters in;common with each other than with other such groups) are said to be monophyletic (along a;single lineage). In the cladogram shown in Figure Four, several different, monophyletic;groups are circled. Two things should be obvious from this illustration. First, any number of;lineages that can be rooted back to a single branch qualify as monophyletic. Second, the;groupings form nested sets within each other. These nested sets are the basis for;hierarchical classification.;Figure 4. Sample cladogram showing nested sets and monophyletic groups;Procedure 2: Vertebrate Classification and Diversity;The Traditional Vertebrate Classification;In the lab you will find an array of vertebrates and their parts. Alfred Sherwood Romer;was one of the most famous vertebrate biologists of the twentieth century. He used a system;of classification similar to that described early in this lab. In lab you will be provided with;Romers Synoptic Classification of the Vertebrates. Using the Romers characteristics;classify the vertebrate specimens in the lab to class. Pay particular attention to the;descriptions Romer uses for each group.;Procedure 3: A Nested Sets Approach (classification by monophyletic groups);In the answer section of the lab you will find the names of several taxa listed in a diagram.;The names are similar to those used in our Romerian classification system (the traditional;approach). In the following exercise we'll group these taxa by synapomorphies. On the;11/19/2006;Classification Lab, Page 5 of 9;diagram, you should draw a circle around the group whose members display the listed;character(s). This should give you 11 circles, with no lines crossing (i.e. nested sets).;Synapomorphic characteristics of vertebrates for use in nested sets analysis;1;2;3;4;5;6;7;8;9;10;11;hair and mammary glands present;feathers present;amniotic membrane present;pectoral and pelvic appendages present: limbs and girdles;paired fins (or limbs) with a base of muscle and bone;lung present (or swim bladder);pelvic claspers present in males;jaws and paired appendages present;skeleton of cartilage or bone, brain and pharyngeal muscles;notochord (at some developmental stage);distinct head region incorporating anterior end of notochord;When you're done compare this nested set system with the traditional one presented by;Romer. You should find agreement in some areas, disagreement in others. Illustrate the;relationships in a phylogenetic tree based upon the traditional grouping and a cladogram;based upon the nested sets grouping. Discuss the differences between these in a few;paragraphs.;1;William of Occam (1284-1347) was an English philosopher and theologian. His work on knowledge, logic and;scientific inquiry played a major role in the transition from medieval to modern thought. He based scientific;knowledge on experience and self-evident truths, and on logical propositions resulting from those two sources. In;his writings, Occam stressed the Aristotelian principle that entities must not be multiplied beyond what is;necessary. This principle became known as Occam's Razor, a problem should be stated in its basic and simplest;terms. In science, the simplest theory that fits the facts of a problem is the one that should be selected.;(;11/19/2006;Classification Lab, Page 6 of 9;Name;Section;Procedure 1: Cladogram for Inanimate Objects;Operational Taxonomic Units;Character States;a.;RED;BLUE;GREEN YELLOW;b.;c.;d.;e.;f.;g.;h.;Pair-wise comparisons of synapomorphies;Pair;RED;BLUE;GREEN;YELLOW;RED;BLUE;GREEN;YELLOW;Complete your cladogram here, include the character states;11/19/2006;Classification Lab, Page 7 of 9;On your cladogram circle a proposed family in red, the proposed e genera in blue and the;species in green.;Procedure 2. Traditional (Romerian) Grouping of the Vertebrates;List species and characteristics (as shown in Romer) in this table;Urochordates (outgroup);Subphylum Vertebrata;Class Agnatha;Class Chondrichthyes;Class Osteichthyes;Class Amphibia;Class Reptilia;Class Aves;Class Mammalia;11/19/2006;Classification Lab, Page 8 of 9;Procedure 3. Nested Sets approach;Draw circles around the groups displaying the characteristics (label circles);Traditional Romerian Classification;Urochordates;Urochordates;Hagfishes;Agnatha;Lampreys;Chondrichthyes;Chondrichthyes;Non-amniotes;Ray-finned fishes;Osteichthyes;Lobe-finned fishes;Amphibians;Amphibia;Reptiles;Reptilia;Birds;Mammals;Aves;Amniotes;Mammalia;Now, illustrate the proposed evolutionary relationships in a phylogenetic tree based upon the;traditional grouping and a cladogram based upon the nested sets grouping. Discuss the;differences between these in a few paragraphs.;11/19/2006;Classification Lab, Page 9 of 9


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