Adapted with permission from Gendron, R. P. (2000). The Classification & Evolution of Caminalcules. The American Biology Teacher, 62(8), 570-576. University of California Press.
Introduction:
Figure 1: Taxonomic groups are hierarchical, lower groups are nested within higher groups
Recall from the previous lab that taxonomy is the branch of biology that describes, names, and classifies species and groups of species. A species is typically defined as a group of organisms in which genetic exchange through reproduction is possible. Humans, for example, are a separate species from chimpanzees, because although humans can reproduce with each other (and thereby exchange genetic information), they cannot reproduce with chimps. Because of this genetic isolation, different species typically don’t pass on heritable traits to each other, and are, therefore, thought to be independent evolutionary units.
Also, recall that taxonomists use the Linnaean system of classification, in which each species is given a scientific name composed of two parts: the genus and species (e.g. Homo sapiens or Escherichia coli). The Linnaean taxonomic system is hierarchical in that it groups species and genera into more inclusive categories: species, genus, family, order, class, phylum, kingdom, domain (Fig. 1). A named taxonomic group at any level of the hierarchical system is called a taxon (plural = taxa). Modern taxonomists strive to incorporate evolutionary history into taxonomic classification schemes and vice versa. Ultimately, taxonomy should reflect the true evolutionary history of an organism (its phylogeny), and vice versa.
In an attempt to reconstruct the evolutionary history of life, biologists analyze patterns of change in the heritable features of organisms. These features could be morphological traits, physiological traits, behaviors, or genetic sequences. The resulting evolutionary relationships among taxa can be represented as branching phylogenetic trees (Fig. 2). Each branch point on a phylogenetic tree represents the divergence of two taxa from a common ancestor (Fig. 2). Phylogenetic trees typically proceed chronologically from the past to the present (Fig. 3). Those taxa that share a more recent common ancestor are more closely related. Those that share a more ancient common ancestor are less related (Fig. 3).
Because phylogenetic trees are hypotheses, they are always subject to further scientific analysis and revision in light of new data. New data may include newly discovered morphological characteristics, fossils, types of analyses, or molecular data such as DNA sequences. All of these pieces of evidence can be used to test phylogenetic hypotheses and refine taxonomic classification to better reflect the true evolutionary history of a group of organisms.
In this lab exercise, you will work with morphological characters and DNA sequences to generate hypotheses about the evolutionary relationships between hypothetical organisms called caminalcules. Caminalcules are imaginary organisms, first created by Joseph H Camin (Sokal, 1983). Camin first started with a primitive ancestral form of caminalcule, and then gradually modified the forms (Sokal, 1983). Because caminalcules are artificial organisms, you have no preconceived ideas about how they should be classified or how they are related. Therefore, caminalcules can be useful to explore taxonomy, phylogeny, and the connection between classification of living species and their evolutionary relationships.
Part A: Taxonomy of Living Caminalcules
You have been provided with an envelope containing drawings of 14 living species of caminalcules (Figure 4). Your first task is to organize these living species into a hierarchical (taxonomic) classification, based on morphological characters. Work in pairs for this portion of the lab.
Figure 4. Living caminalcules. A number is used to identify each species, in lieu of a name. Adapted with permission from Gendron, R. P. (2000). The Classification & Evolution of Caminalcules. The American Biology Teacher, 62(8), 570-576. University of California Press.
University of California Press.
First, use morphological characteristics of each species to combine species into genera, using the criteria that members of a genus should resemble each other more than they resemble members of another genus. Note that it is possible for a genus to have only one species but, for this activity, no genus should have more than 3 species.
Keep members of each genus together as you combine similar genera into families. Be sure to create at least 3 families. Note that a family might have only one genus.
Now decide which families to combine into orders. Be sure to create at least 2 orders. Note that an order might have only one family.
Once you are confident in your organizational scheme, place the species numbers into the Species row in Table 1, so that species in a common genus are listed next to one another, genera you decided were in the same family are next to one another, and families you decided were in the same order are next to one other.
To indicate the separation between different genera, draw vertical lines in the Genus row of Table 1. To determine the separation between families, draw vertical lines in the Family row. To determine the separation between Orders, draw vertical lines in the order row. In the end, only the bottom row will have species numbers.
As you learned last week in the Phylogeny lab, modern taxonomists strive to create classification systems that reflect the evolutionary history of a group of organisms, as depicted in a phylogenetic tree. Working in pairs, follow the directions below to develop a phylogenetic tree based on your taxonomy (Part A) for the living caminalcules. Draw your tree on scratch paper first and check it with your instructor. Then draw the tree in the space on the next page. Work in pairs for this portion of the lab.
All the existing species of caminalcules will be on the tips of the branches, while hypothetical ancestral taxa will be at the nodes. At the tips of the tree all species in the same genera must be side by side and must share a common ancestor not shared by other genera. When you have three or more species in a genus, you must look at the morphology of the three species to decide which of the two species are most closely related and create a branching pattern similar to Figure 6.
Branches containing genera in the same family must be adjacent on the cladogram and must share a common ancestor not shared by the other families. As you did with species above, if there are three or more genera in the same family, you must decide which genera look more similar to one another (are more closely related) and draw the tree so they share a more recent common ancestor (similar to Figure 6 except each genus may branch again into species).
Branches containing families in the same taxonomic order must be adjacent and must share a common ancestor not shared by the other order. As you did for other levels of classification above, if there are three or more families in the same order, your branching pattern must reflect which two appear to be more related.
Draw your hypothesized phylogenetic tree for living caminalcules below. Compare your phylogeny to that of other groups. Are they the same? Different?
Part C: Develop a Phylogenetic Tree Based on the Fossil Record for Caminalcules
Your taxonomy and phylogenetic tree from the previous exercise represents an evolutionary hypothesis based on morphology of living species. This hypothesis can be tested. How? By using the morphological data and dating of fossils. In the following laboratory exercise, you will use the caminalcule fossil record to test the validity of your proposed tree for living caminalcules. Work in groups of 4 (your table) for the rest of this lab.
Obtain a white board labeled with a time scale in millions of years before present, and an envelope containing 57 fossil caminalcules. Each caminalcule is labeled with a species number. In addition, the number in parentheses on each fossil is the age of each fossil in millions of years.
Take all living species used previously and place them on the “Present” (top) dateline on the whiteboard. The order left to right on the top line does not matter at this point.
Sort the fossil caminalcules onto the whiteboard according to age in millions of year ago (MYA). Again, the order left to right on each MYA line does not matter at this point.
Starting with the oldest fossils, develop a cladogram for the fossil caminalcules, ending with the living caminalcules you studied in Parts A and B. Begin with the fossil that is 19 million years old. This is the common ancestor for all caminalcules. Use the morphology of the fossils and the IMPORTANT HINTS provided in Figures 7, 8 and 9 below to determine how to connect the fossil species!
First, connect the fossils that are 18 million years old to the 19 million year old fossil. How many separate lineages now exist? _______
Next, continue with the next time period. Three fossils are 17 million years old. Consider how they are related to the 18 million year old fossils.
Continue working up the fossil record ADDING FOSSILS FROM ONE ROW AT A TIME, until you get to living caminalcules.
Once your cladogram is complete, please check with your instructor. You must refer to this tree in order to answer Follow up questions 1-2 at the end of the lab so keep it assembled!
What trait in caminalcule number 41 defines the lineage that evolved from it? _______
Compare part of your fossil tree to the one you drew previously based on just living species (Part B):
Look at the fossil tree and choose two modern species that share a more recent common ancestor (closest modern relatives) with each other than they do with any other species.
Look for these two species on the phylogeny of living taxa you drew in part B. Are the two species also each other’s closest relatives on this tree?
If they are, the fossil (Part C) and living tree (Part B) support the same phylogeny for those species compared.
If they are not, how could you reconcile this difference?
Repeat this comparison process on two different, but closely related species, including answering the same questions asked above.
Using just these two points of comparison, does your initial phylogeny of living species from Part B match the phylogeny you developed using fossil evidence? _____________ Is the addition of more data usually helpful in building the best hypothesized phylogeny? __________________
Hints for building your fossil cladogram:
The fossil record is incomplete so you should not expect to have one fossil from each lineage every million years (Figure 7 depicts a gap). When determining which species to connect a younger fossil to, you may need to look back to a species two or more million years older.
New species do not always evolve from branching of an ancestral common ancestor into two new species. If two species are similar but have evolved to be somewhat different in morphology, they may need to be connected directly with no branching (Figure 8).
Some species don’t evolve into new species even over millions of years. If you see two fossils with the same species number in different years, simply connect them when building your tree (Figure 9).
Part D: DNA barcodes
Phylogenetic trees are hypotheses about evolutionary relationships among organisms. Scientists who make phylogenetic trees can use many different types of evidence, such as morphological characteristics of living or fossil specimens or molecular data to test the validity of their trees. The best trees often use multiple lines of evidence to confirm their validity.
In this portion of the exercise, you will use molecular evidence to construct a phylogenetic tree for a subset of caminalcules. For some fossil caminalcules, soft tissues were preserved in amber, allowing viable DNA to be isolated (like the mosquitos in Jurassic Park). DNA sequences (“barcodes”) were obtained from the same location in the genome of these fossils and three modern caminalcules. The sequences consist of one letter abbreviations for the four nucleotides that polymerize to form DNA (A = adenine, T= thymine, G= guanine and C= cytosine).
Sometimes when DNA replicates (makes copies of itself) individual nucleotides in the DNA sequence can change by accident. This is called a mutation. Mutations tend to be very rare, but occasionally a mutation can become “fixed”, meaning that it is a permanent, heritable mutation in the DNA sequence that is passed on from generation to generation. In other words, it is a heritable trait. Over millions of years and generations, fixed mutations can accumulate. These mutations can accumulate in different patterns for different lineages of organisms. Over time a DNA sequence that was similar in a shared common ancestor can become very different in two distantly related species. This change in DNA sequences over time is called sequence divergence. Understanding what DNA sequence divergence is and how it can be used to assess evolutionary relationships of organisms will be vital for you to understand DNA barcoding and how it works. This exercise will help you to understand these concepts.
You’ve been provided with an envelope with 13 DNA barcodes from both living and fossil caminalcules with their species number. First, sort the caminalcules according to age in millions of years on a second white board or the large piece of paper provided. You should not consult the fossil tree while building the molecular taxonomy. You will be asked to compare the fossil and molecular trees when you are done.
Starting at the bottom with the DNA barcodes from the oldest organism (species 73, 19 MY), construct a phylogenetic tree up through the most recent species. Nucleotides that mutate (change) over time are colored and remain colored in more recent species. The hints provided in Part C (Figures 7, 8, 9) are still useful here. Draw the tree in the space provided below by placing the species numbers on branches.
Compare your molecular-based phylogenetic tree to the tree based on the fossil record. To do so, start at the bottom of the fossil tree at the 19 MY old fossil species 73. Put the molecular sequence for species 73 on top of the fossil caminalcule 73. Continue to move up the tree transferring molecular sequences onto the fossil phylogeny to see if the branching patterns of the 2 phylogenies are identical. What does it mean if they are not and what should you do next?
QUESTION: You find a new species of living caminalcule that has the following DNA sequence: GCAGCGGGAGGTGAG. According to this DNA barcode, with which species of caminalcule is this newly discovered species most likely to be most closely related? Why?
QUESTION: Which genetic sequence(s) is/are the most divergent from the initial 19 MY old sequence?
QUESTION: Which genetic sequence(s) is/are the least divergent from the initial 19 MY old sequence?
Follow up Questions 1-2 must be answered while still in the lab since you will need to be able to consult the fossil and molecular trees and the actual fossil species to answer some of these questions:
What is the most recent common ancestor of fossil caminalcule species 66 and species 51? Check your answer with your instructor while still in class so they can evaluate your answer relative to your fossil tree since all trees may not be the same.
Using the tree you developed using the fossil evidence and the actual species so you can study their morphology, describe an example of convergent evolution in caminalcules.
Adapted with permission from Gendron, R. P. (2000). The Classification & Evolution of Caminalcules. The American Biology Teacher, 62(8), 570-576. University of California Press.
