Tree Thinking %28WorkbookCh4%29

Tree Thinking %28WorkbookCh4%29 - \m “Va-KM? Teruko and...

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Unformatted text preview: \m “Va-KM? Teruko and herfriend Sear; Were gagging érQUnd a {rack after work {’50, Teruk'oghgw Was your - brother’s wedding in 33pm??? Sear-1: asked. _ _ I ' {fit was amating} '3 {Du-Sdr‘i‘t believe at! the cére— _ was'thékurrai" 1. . ._ .. = :- “Wat's k¢.Jir.a?’-f Sear asked. *' cg'stoms agent;rock-itat{he'a'rzrgébrtg'f - ' Q'Ja'p'anir'fflr ' swims-out that you Carri bring irr én‘grprodircé that is fm'adga from marinemarrrmals becay'se st? many ' many," Teruko said. “E‘he reception had Some un— '. 'Lrsual food prepared byspeCi-aighéfs; My fcfivqréte _- 'if’it’s- Whaie meat," Terng 'lrepiiiédQ Wheh Sear; _'j:- I - mac-38 rage, Yer-ukaiciontirrued "ii know it Spqnds I: ' -_aw'§ur, buféfigfied SQ got-3am rapt; myriad even :_ _ f Iitriéd Id -bri_rrg._som_e:ahrrediwhale rri'ear_bé<:k,_gbut -. Q I-seiar} agked'21‘isn’r.wha]ih_g Sort 'C'u3rdrhé;_i§t ' " _: spécée's are endah‘g-ered,”f Tamika; _e>§_;j_¥a'§rréd. ; Z 1 Treerhmkmg [7-05, ihatrhékes sense, ” Sear: said. “So, did .- ' "-3310:er dad 'g'et into trouble at the airport?" '_-".‘-No, my just took the cans may," "femko "sighed.”.'j_-.._ . . __ ' - .II "i‘zré :héarfi there‘s a the black market-for -' " '._- Where martin Asia, and SOmé peopieipéy the " ' ' -:_.-eggiv_ale_nt_0f $40'Ggéjpiotirrd," Sean added". " . "_'_:"_Yes_,'_érzd ihéyexreg'j hav'eibioie'chtefis new tr.) ' I réllzifrhé rhea-airsreafiyifromIWha'lésL’t _ ' ' " ' _ can they téll What :ypé Cfrfieatfi in't'hé '_ '- I gar)?”- gééan'askedr ' ' ' u I' I I ' _' ' -__’"We'il_','they éXZra'cfr EDNA-from the sampie and '_ -- icm'pé-reérs?séqté'ehéé Mrs—om BNAIwhaie' .se—I - j - .' -quénces;_Iidraggj'rqgensicbrig tesiihg'of were . _' '- insiméiaffrbm Ask-mi markéis'jhas rumba; up diaibhi'h; H .; l_;ha_rrg,-anfiMen-mg meat.“ j_' j ' -' '. _- _. C’THrn'QMéfrbéIhey sthEd-mnéhésa'me festsoh W Z fthe-rhgarwehad' ét'lrrrjcri yesterday’fiean __ .- .. laugh-ed;mowitwasTe'fQRO’sjum'tcirnakeé'facégf. _ CHAPTER 4: Tree Thinking Q 45 CASE ANALYSES 1. Recognize potential issues and major topics in the case. What is this case about? Underline terms or phrases that seem to be. important to understanding this case. Then list three or four biology—related topics or issues in the case. 2. What specific questions do you have about these topics? By yourself, or better yet, in a group, list what you already know about this case in the “What Do I. Know?” column. List questions you would like to learn more about in the “What Do I Need to Know?” column What Do I Know? What 90 I Need to Know? 3. Put a check mark by one to three questions or issues from the “What Do i Need to Know?” list that you think are most important to explore. 4. What kinds of references or resources would help you answer or explore these ques— tions? Identify two different resources and explain what information. each resource is likely to give that will help you answer the question(s). Choose specific resources. 46 D BIOLOGICAL INQUJRY: A Workbook of investigative Cases Core Investigations I. Critical Reading To complete this investigation, you should have aiready read Chapter 26: Phylogeny and Systematics. A. Morphological Observations: identifying Characters in the Dendrogrammaceae. In this exercise, you will observe and record morphological characters and investigate the construction of a ciadogram based on five characters. Begin by reviewing Figure 4.2 and Table 4.1. Then record the presence or absence of the five characters that are examined in Table 4.1. A “0” indicates that a taxon does not exhibit the par- ticular character. Enter a "1" if the taxon does exhibit a particular character. For exampie, taxa B, C, and D have narrow leaves, so a "1 ” has been entered in the table. Figure 42.2 The Dendrogrammaceae, an imaginary family of flowering piants (Wagner, W. H, Jr., 200?). CHAPTER 4: Tree Thinking <3 47 Table 4.1 Observation and Identification of Morphoiogica! Characters (Refer to your text for definitions of unknown terms.) 1 2 3 4 m7" 5 Seiected Taxa Leaves United Tubeiike Eiongateci Flower with Silateraf, Narrow Petais, Not Petals Sepals Not Radial, Symmetry Separate “.1”... 48 1. b BIOLOGICAL INQUIRY: A Workbook of investigative Cases Which trait in Table 4.1 is shared by at least four taxa? Which taxa are they? . All five characters are present in which taxon? . Are any of these characters shared by all five taxa? . One methodology that has proven useful in developing cladograms is to include a taxon that is less related to the other taxa. This “outgroup” is assumed to have ancestral forms of the characters found in these taxa. Characters that are not shared with this “outgroup” taxon are considered derived. Which taxon is the outgroup in this plant family exampie? . Examining a Cladogram. By constructing a cladogram using the morphologicai characters recorded in Table 4.1, you can infer relatedness among the taxa. Ciadograms can be helpful depictions of patterns in leveis of relatedness for shared characters among taxa. Taxa are sorted by presence or absence of characters. However, branch distances in a cladograrrt do not tmeiy chronology. (Phylogenetic trees present hypotheses about the evolution of taxa and imply chromi— ogy in diverging branch points.) Using the characters in Table 4.1, the following cladogram indicates the reiationships among the five taxa selected from the Dendrogrammaceae. Notice that there are branches in Figure 4.3 asso- ciated with each taxon. Each node is caiied a clade. Branches C and D are nested within the iarger clade that includes B. Figure 4.3 The characters are pierced below the diagonal. The taxa A, B, C, D, and E are positioned in branches along the diagonal to indicate which characters they share. . Which character in Figure 4.3 is exclusiveiy shared by taxa C and D? . Consider character 1 in the cladogram. Which taxa lack this character? . Can you estimate how much time passed between the development of character 2 and character 4? Explain. CHAPTER 4: Tree thinking Q 49 4. Compare the table of characters to the cladogram. Do cladograms contain the same infor~ mation as the table? Are cladogranis more useful? Explain. C. identifying Primitive Versus Derived Characters. Simple observation helps differentiate morphological characteristics of these plant taxa, but what characters can help us understand the evolutionary relationships between taxa? To be useful for cladistics, characters must be homologous (reflect shared ancestry). Among the homologous characters, we need to identity the following: a Shared primitive characters: homologous traits that are common to larger taxonomic groups; for example, flowers are found in all angiosperms. a Shared derived characters: homologous traits that are limited to particular taxa; for example, flowers with united petals are found in only some angiosperms. Depending on the taxa included in a cladogram, the same character could be considered primitive in one cladogram and derived in another. For example, consider milk production of mammals. When the taxa are all mammals, then milk production is a primitive character. However, when the taxa include reptiles, birds, and mammals, then milk production is a derived character. 1. Look at the complete group of taxa in Figure 4.2. Select a taxon with a morphological. character (other than those you used in Table 4.1) that you think is a shared derived character. What makes it likely to be derived? D. Revising a Cladogram. Systematlsts use existing data or gather new data to consider carefully which characters to use in constructing a cladogram. Determination of the branch points is based on these characters. As new data are discovered, a cladogram may be reconstructed to incorpo- rate the new information. Figure 4.4 Sketch based on a new fossil of extinct Dendrogrammaceae, taxon F. 50 l} BIOLOGICAL ENQUIRY: A Workbook of Investigative Cases 1. See Figure 4.4 to observe characteristics of a new fossil, taxon E Enter your observations of [axon F in Table 4.2.. Note: These are the same five characters used in Table 4.1. Table 4.2 Character Table for Taxon F 1 2 3 4 5 Selected Taxa Leaves United Tubelike Elongated Flower with Bilateral, Narrow Petals, Not Petais Sepals Not Radial, Symmetry Separate 2. Use the character information from [axon F to redraw the Cladogram (Figure 4.3). ll. "Whale Meat Forensics" A. Using Biotechnology and Systematics. in this investigation you wiil be working with DNA sequence anaiysis. You should be familiar with the DNA analysis methods covered in Chapter 20. Peopie in many regions of the world rely on animals harvested from the sea as a significant source of protein. Several cultures enjoy traditional dishes made from whale meat (Figure 4.5). With declining populations of cetaceans (the mammalian order to which whales and their close relatives belong), however, this practice has come under international scrutiny. Figure 4.5 Several dishes made from different cuts of whale meat. CHAPTER 4; Tree Thinking <1 51 From 1993 to 1999, researchers from New Zealand (Baker et al., 2000) analyzed genetic varia- tions in a defined region of cetacean DNA. One of their goals was to identify food products con- taining meat from protected or endangered cetacean species or noncetacean sources. investiga- tors began by taking tissue samples from beached and harvested cetaceans. Specles identifications of the animals were done onsite by experts in cetacean systematics using multiple morphological characters. DNA from the identified cetacean tissue samples was extracted and the targeted DNA was sequenced. The researchers then sequenced the DNA of samples from whale products ("unknowns") sold at retail markets in Japan and the Republic of (South) Korea. By comparing the genetic sequences of the unknowns with the known sequences, the researchers could infer the similarity and species identification of the meat in the “whale” products. Analysis of 655 products revealed meat from baleen whales (eight species or subspecies), sperm whaies, pygmy sperm whales, peaked whales (two species}, porpoises, killer whaies, dolphins (numerous species), and sharks, as well as from domestic sheep and horses (Baker et at, 2000). ,. What types of biotechnology techniques were used to investigate products sold as whale meat? . The researchers combined systematics with the use of biotechnology to do their forensic work. Define systematics. . Why was it important for a systematist to identify the “known” cetacean species from which DNA was extracted and sequenced? . Based on your reading in the case, why do you think vendors would substitute horse meat for whale meat in some of the Asian markets? . How Is the Analysis of Whale Products Done? This next investigation introduces forensic tools that were used to study whale products, as well as some of the reasoning processes used by systematists to deveiop hypotheses about reiatlonships. In our whale meat example, the task of species identification began with isolating DNA from the unknown meat and then looking for a tiny portion of the genomic DNA. A mitochondrial DNA (mtDNA) control region (shaded, Figure 4.6) consisting of only 500 base pairs (bp) was targeted. 52 i} BiOLOGICAL INQUIRY: A Workbook of investigative Cases Although much of this region is highly conserved (retained with few differences among species), known differences within a hypervariabie subsection of the region were used to distinguish among cetacean species. {Dip 1.5 Dip 10 MD” “DB-v w I Hypervanabie region . . . in oetaoeene 3319 4 DID 5 Dip 8G l 249 bp i 301 bp 500 bp 800 bp Figure 4.6 A schematic map of the mtDNA control region as weii as the binding sites and orientation of the primers used in isolating cetacean DNA. The shaded region represents the portion of the control region covered by most sequences in the reference data sets. Researchers used ?C8 to ampiify the target mtDNA sequence in the unknown meats. The tatget mtDNA was then sequenced and aligned with the data set of known cetacean sequences for this segment of QNA. A computer ptogram first connpared the target sequence of the sampie to known cetacean sequences. Then the program generated a modei based on the overall sirniiarities between the target sequence and known cetaCean sequences (Figure 4.7). bowhead bowhead pygmy right whaie pygmy right whaEe Antarctic minke whaie North Pacific minke where North Atlantic minke whale dwarf minke whaie gray whaie gray whaie sei whale - sei Whaie Bryde’s whaie Bryde‘s whale blue whale bEue whaée humpback whale humpback where fin whale iin whale Figure 4.7 Resuiting genetic similarity tree showing reiative position of unknown samples. Note that the genetic simiEai’ity within species is shown by muEtipie sampies in known species, for exampie, blue whale sampies. CHAPTER 4: Tree Thinking <3 53 .1. Which cetacean does the unknown sample most closely match? The Convention on lnternational Trade in Endangered Species (CiTES) works to conserve endan— gered species by regulating and, where necessary, banning international trade. International trade is banned for those species threatened with extinction. international trade in species that are less endangered or that may become so is permitted when properly regulated. (Note: The cetacean identified in your answer to question i is found in the second group.) 2. Phylogenetic trees are hypotheses that show a pattern of evolutionary relationships, based on analyses of multiple characters, for multiple taxa. A phylogenetic tree implies a chrono- logical sequence of divergence (branching). Expiain why Figure 4.7 is not a phylogenetic tree . 3. Divergence of cetacean species occurred within the last 50 Lo 65 million years (O’Leary and Geisler, 1999). Explain the difference between the use of a fragment of hypervariable mitochondrial DNA as a molecular marker and the use of a gene such as the one that encodes for hemoglobin. How might you use each of these to compare DNA sequences between cetaceans and other organisms? (Hint: See the information in Chapter 26 on molecular clocks.) 4. An attorney defending a whale meat supplier accused of improperly labeling rneat would most likely claim that the inlerences drawn from the prosecution’s evidence were question— able. “Provide a potential argument that specifically describes a weakness in the methodol- ogy used to infer species identity of the whale meat in this investigation. 5. How might the prosecuting attorney answer this argument? (Note: Defend the methodology that was criticized above.) (.1. Going Further: Testing Unknowns with "Witness for the Whaies." At the website “Witness for the Whales,“ users can submit unknown rntDNA sequences to be compared against known 54 b BIOLOGICAL INQUIRY: A Workbook of investigative Cases cetacean sequences. Genetic similarity analyses can be performed. Resuits are returned in tree and table format, summarizing the genetic distances between the unknown and reference sequences. {60 to the Case 800k website for access to and instructions for "Witness for the Whales”) Ill. Which Mammals Are Related Most Closely to Whales? A. The Ungulates. Most scientists agree that whales are members of the ungulates, or booted mammals. Some evidence suggests that whales share a common ancestor that gave rise to other living ungolates such as deer, rhinoceroses, horses, camels, pigs, and hippopotamuses. The relationship between whales and other ongulate taxa is still under investigation (O’Leary and Geisler, 1999). The ungulates are divided into two orders. Horses, zebras, tapirs, and rhinoceroses are odd-toed hoofed mammals, stiil known as the 9erissodactyla. Even-teed ungulates such as deer, sheep, pigs, and cows are known as the Artiodactyla. Until recently, systematists considered Artiodactyla and Cetacea as two distinct mammaiian orders. However, severai sources of scientific data sup» port the idea that whales are closely related to the members of Artiodactyia. Artiodactyls and cetaceans are now placed in the same ordeeretartiodactyla. The idea of whales sharing an ancestor with these ungulates would seem unlikely if we compared anatomy in living species only. . List three characters that you could observe in living whales that white-tailed deer or other even»toed ungniates do not seem to share. . Molecular data can also be used to examine relationships between organisms, but the inac- cessibility of comparative DNA samptes for extinct taxa limits the usefulness of these data. Evidence for shared. characters between whales and ungulates based on protein or nucleic acid sequences involves sampling of extant taxa only. However, whale skeletal data incorporate extensive paleontological data from fossils as well as data from extant species. Scientists use fossil data to help reconstruct the hypothetical relationships among whales and other even-teed ungulate taxa. This is a valuable source of data, because like many other taxa, most of the even-teed ungulates that have existed are now extinct. Name a character you would expect to find in fossils of early whales that would provide evidence that whales share a common ancestor with other even-med ungulates. . Explore Whale Evolution with the Whippo Problem Space. A good place to begin exploring the relationship between whales and other mammals is the Whippo Problem Space at the BEDROCK bioinformatics education site (see the Case Book website for access information). This Whippo site organizes diverse resources including data and tools to support inquiry. Consider Figure 4.8. Examine the two trees carefully. Each represents different hypotheses about the evoiationary reiationships among the whaies and various ungoiates. Note that althoogh there are differences in branching patterns (tree shape), both trees include the same outgroup. CHAPTER 4: "free Thinking (l 55 ruminants % oameis whaies Perissodaotyls i1» odd-toad unguiates 3 o l l l p l "E j (5. 6. m o O U) serelnfiuo poor—mews SWOEDOEW E 3. 3 u) E’, (D seiegnfiun peeinueAe smioepouiv Petissodaotyis oddetoed unguiates Figure 4.8 Phylogenetic tree representing different hypotheses about the relationships between artiodactyis, the even—toed ungulates. Note the position of whales in each. . What is the hypothesized outgroup for both trees? . Which tree shows Whales and hippos sharing the closest relationship? . Tree thinking is a term biologists use to describe the process of approaching biological probw lern solving by considering the role of descent with modification based on phyiogenetic evidence This can result in controversies such as that surrounding the evolution of birds. Did the clade that includes birds diverge from a particular group of dinosaurs? Or did it diverge from a line of reptiles that did not include dinosaurs? These types of questions have fueled much debate and extensive research efforts for decades. Because multiple sources of data exist, both the conclusions reached and the trees drawn by independent researchers may not agree. Not only the selection but also the interpretation. of characters 56 i} BIOLOGICAL INQUERY: A Workbook of investigative Cases can support different phylogenies. Biologists try to resolve these questions by carefully weighing evidence from multiple sources. Look closely at the tree shape in Figure 4.9. When you investigate the reasonableness of a tree, you should examine all the hypotheses it contains (Donovan and Hornack, 2004). Each branch point in the tree represents a hypothesis about the relationships among memw bers of the ungulates. The order in which groups diverged is also an explicit hypothesis. Hypothesis A: Hippos and whales shared a common ancestor more recently with each other than with other unguiates. The two groups have since diverged. Each possesses derived characters not found in the other groups. Hypothesis B: The group containing deer and giraffes diverged from the group containing hippos and Whales These two groups also shared a common ancestor but iess recentéy than the one shared by hippos and whaies. Figure 4.9 Hypotheses in tree 8 (Figure 4.8) represented by the letters A, B, C, and D. After you have reviewed the descriptions of hypothesis A and hypothesis B, describe hypothesis D. 4. What does hypothesis D tell us about the retationship between penissodaetyls and artiodactyls? CHAPTER 4: Tree Thinking <3 57 k-casein Figure 4.10 Different phylogenetic trees based on select genetic sequences for different molecuies. (Note: You can read more about tree interpretation on the Whippo site.) 5. Which of the trees based. on molecular sequence data shown in Figure 4.10 supports hypothesis A in tree B? Explain. 6. Does either tree in. Figure 4.10 support hypothesis B in tree B? Explain. 7. Do you think molecular sequence data are helpful characters to use to infer phylogenetic relationships? What concerns might you have if a tree were based on a single molecule? Additional investigation “I. Position Paper on Whaling Explore the management of whaitog in the modern world. Explain the role of biotechnology and sys— tematics in increasing the global potential for biologically sustainable management of Whale populations. Introduce two or more historical, cultural, economic, political, or ethical issues that should be addressed by poticies governing whaling practices. énciude reiiabie resources of data on whale population biology. 58 l) BIOLOGICAL INQUIRY: A Workbook of Investigative Cases Reason from information and data to prepare a three- to five-page position paper that specifically addresses your findings about modern Whaling policy, Examples of issues that your paper might address include: a How are vvhale populations sampled? a How much might they be harvested? e What ethical issues are raised by the use 0 Are cetacean sanctuaries feasible? 0f blOieChm'Ogy t0 DOIlCe the Whale o is the 0.3. ban on all marine mammal market? products reasonable? ’ ShOUId 503/009 be allowed to Whale? a What are relevant cultural issues that Why or Why not? might need to be considered? - Which cetaceans should or could be harvested? Resources and links to‘some websites can be found on the Case Book website. V. OpenwEnded Investigations A. Four new species of additional Dendrograrnmaceae have been discovered. How might this change your phylograrn? Evolution can include both acquisition and loss of traits, so more than one cladogram may be possible without further information. B. Consider using Biology Workbench (http://worl<bench.sdsu.edu) to explore the relation— ships between. cetaceans and taxa other than artiodactyles using genes from the same mito— chondrial control region. References Baker, C. 8., G. M. Lento, F. Cipriano, and S, R. Palurnbi. Predicted decline of protected whales based on molecular genetic monitoring of japanese and Korean markets. Proceedings of the Royal Society of London B, 267(l449):1191w199, 2000. Baker, C. S., M. L Dalebout, G. M. Lento, and N. Funahashi. Gray Whale products sold in 00111111613— cial markets along the Pacific Coast ofjapan. Marine Mammal Science, 18:295—300, 2002. Donovan, S., and D. lz-iornack. Losing the forest for the trees: Learning to compare trees and assess support for phylogenetic hypotheses. Poster. NABT National Conference, 2004. O’ieary, M. A, and G. H. Geisler. The position of Ceiacea within Marrnnalia: Phylogenetic analysis of morphological data from extinct and extant taxa. Systematic Biology, 48(3):455—490, 1999. Ross, H. A, G. M. Lento, M. L. Dalebout, M. Goode, G. Ewing, P. McLaren, A. G. Rodrigo, S. Lavery, and C. S. Baker. DNA surveillance: Web~based molecular identification of whales, dolphins and porpoises. journal of Heredity, 94:111wll4, 2003. Wagner, W. Ii, jr. Dendrogrannnaceae. in E. D. Stanley, “Visual Data Sets,” BioQUEST Library VI. San Diego: Academic Press, 2001. Witness for the Whales. http://wwwcebl.auclilandac.nz:9000/page/Whales/title {accessed October 10, 2007). ...
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This note was uploaded on 05/31/2011 for the course BIO 2108 taught by Professor Ammons during the Spring '11 term at Georgia Southern University .

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Tree Thinking %28WorkbookCh4%29 - \m “Va-KM? Teruko and...

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