hands on human evolution: a laboratory based … on human evolution: a laboratory based approach ......

Hands on Human Evolution: A Laboratory Based Approach

Margarita Hernandez

Summer Science Institute: Exploring the Tree of Life

July 15, 2015

What organisms evolve?

Misconceptions about Human Evolution

We came from monkeys!

Misconceptions about Human Evolution

We are no longer evolving!

All in the Family (or should I say genus?)

What you’ll be doing today…

• Familiarizing yourself with species closely related to Homo sapiens

• Exploring morphological features of several hominids and hominins

• Determining what trends are evident from these casts

• Looking at relatedness of extant species using both morphological and genetic data

Part 1: Lab Station Rotations

• Small groups (4-5 people)

• 7-8 minutes per station

• Packets to guide you through the stations

• Human evolution tree hand out

• Work together! Think and collaborate!

• We will be working with: – Chromosomes

– Amino acid sequences

– Base pair sequences

• Continue working in your groups

Part 2: Genetic Data Activities

Station 1: Cranial Capacity in the genus Homo

At this station, the following casts are present: H. habilis, H. erectus, H. neanderthalensis and H.

sapiens (your species name). All of these species are within the genus Homo, which is the same

genus we are part of. Using the beans and measuring apparatus, determine which species has

the largest brain capacity, which has the middle brain capacity and which has the smallest.

Directions for measuring brain capacity:

1. Place skull upside-down on the cushion provided for you. This will aid in the stability

and protection of the skull during this activity.

2. Place the funnel inside of the foramen magnum (hole at the bottom on the skull where

the spinal cord would be).

3. Using your small cup, scoop out beans and begin funneling them into the skull.

4. Make sure to move the beans around in the skull in order to ensure that all places

inside the cranium are filled with beans.

5. Once the skull is full, carefully dump the beans from the skull into a large beaker by

simply turning the skull right side up into the glassware. Make sure to have a good grip

on the skull as it can get heavy due to the added weight of the beans.

6. Make sure all the beans are transferred from the skull into the beaker. This may take a

bit of shaking of the skull.

7. Measure the amount of beans you have in mL. In the metric system, mL = cm3, which is

a standard measurement for volume. Use cm3 to record skull volume.

H. habilis: ____________

H. erectus: ____________

H. neanderthalensis: ______________

Based on the phylogeny given to you, what brain capacity would you expect modern day

humans, H. sapiens, to have and why?

Using the H. sapiens skull as your reference, what differences do you see between anatomically

modern humans and e other three species in front of you?

Using your phylogeny, line the skulls up from the oldest to the youngest in terms of existence

on Earth. What general trends do you see going from the oldest to the youngest species?

Station 2: Bipedalism

Shown here are the hip bones of various species of hominids. Chimpanzees walk on all four

limbs (quadrupedal) and have a very distinct hip morphology. Their hip bones are orientated

along their backs and are very slender and narrow. Modern day humans have a drastically

different hip morphology due to the fact that we walk on two legs (bipedal). Human hips are

oriented beneath the body and are wider and more “bowl” shaped.

Based on the above descriptions, circle the form of locomotion you think the species below

had. Use their hip morphology as an indicator.

Australopithecus afarensis

Quadrupedal Bipedal

Ardipithecus ramidus

Quadrupedal Bipedal

What does this tell us about the appearance of bipedalism during the course of human

evolution?

Station 3: Apes and Humans

At this station, small scale casts are present for modern day humans, gorillas and chimpanzees.

List the physical similarities between gorillas and chimps.

List the physical differences between the group of apes and humans.

What similarities do you see in all three species?

Based on all the characteristics listed above, draw a small level phylogeny for the three species,

denoting which two you think are more closely related to each other, with the exclusion of the

third.

Station 4: Cranial Capacity in the Australopithecines

At this station are members of the genus Australopithecus. The following casts are present: A.

africanus and A. afarensis. Using the beans and measuring apparatus, determine which species

has the largest brain capacity and which has the smallest.


1. Place skull upside-down on the cushion provided for you. This will aid in the stability and

protection of the skull during this activity.




4. Make sure to move the beans around in the skull in order to ensure that all places inside

the cranium are filled with beans.








A. africanus: ______________

A. afarensis: ______________

What major similarities and differences do you see between these two species?

Station 5: Investigating differences between Homo and Australopithecus

At this station, small scale casts are present from two species within the genus Homo and two

species within the genus Australopithecus. Without looking at their tags, what two do you think

belong in each respective genus and why? Use the numbers in front of each species in order to

discuss them below.

What are the major differences between the two groups?

Using your phylogeny and the names of the species on their tags, order the species from the

oldest to youngest. What features do you see change over the course of the millions of years

between these species?

Station 6: Ardipithecus ramidus

In the station are images of the skeletons of A. ramidus (Ardi), Gorilla gorilla (Gorilla), and

Homo sapiens.

Provided for you is a triple Venn diagram for you to compare and contrast each species to each

other.

Which species does Ardi appear to be more similar to? Remember, many of these fossils show a

mosaic of traits that are particular to both species. This is important to keep in mind, as the

ancestors of certain lineages will also have a mosaic of traits for the species they gave rise to.

Station 7: How do you teach evolution?

At this station you will notice large poster papers and markers for your use. Write your

methodology for teaching human evolution in the classroom or if you do not teach this topic. If

a previous group wrote a methodology you use, draw a large red dot next to it. If a previous

group wrote a methodology you would like to use, draw a green star. We will discuss these

approaches after the activity.

Station 1: Cranial Capacity in the genus Homo

At this station, the following casts are present: H. habilis, H. erectus, H. neanderthalensis and H.

sapiens (your species name). All of these species are within the genus Homo, which is the same

genus we are part of. Using the beans and measuring apparatus, determine which species has

the largest brain capacity, which has the middle brain capacity and which has the smallest.


1. Place skull upside-down on the cushion provided for you. This will aid in the stability and

protection of the skull during this activity.




4. Make sure to move the beans around in the skull in order to ensure that all places inside

the cranium are filled with beans.








H. habilis: __smallest_____(~620 cm3)

H. erectus: __middle_____(~880 cm3)

H. neanderthalensis: _largest___(~1400 cm3)

Based on the phylogeny given to you, what brain capacity would you expect modern day

humans, H. sapiens, to have and why?

H. sapiens would be expected to have a larger brain capacity than any of the species mentioned

above. This would be because one of the trends within human evolution is that later species

have larger brains.

Using the H. sapiens skull as your reference, what differences do you see between anatomically

modern humans and the other three species in front of you?

H. habilis has a broader gave, smaller brain case, and more robust features.

H. erectus has a sagittal keel present, very prominent brow ridges and a more protruding facial

region.

H. neanderthalensis also has prominent brow ridges, but more gracile than H. erectus. The

features of this skull are overall more gracile and has a more protruding facial region.

Using your phylogeny, line the skulls up from the oldest to the youngest in terms of existence

on Earth. What general trends do you see going from the oldest to the youngest species?

More robust to less robust.

Brow ridges present to no brow ridges.

Mid facial region becomes less protruding as you get younger.

Station 2: Bipedalism

Shown here are the hip bones of various species of hominids. Chimpanzees walk on all four

limbs and have a very distinct hip morphology. Their hip bones are orientated along their backs

and are very slender and narrow. Modern day humans have a drastically different hip

morphology due to our bipedal form of locomotion. Human hips are oriented beneath the body

and are wider and more “bowl” shaped.

Based on the above descriptions, circle the form of locomotion you think the species below

had. Use their hip morphology as an indicator.

Australopithecus afarensis

Quadrupedal Bipedal

Ardipithecus ramidus

Quadrupedal Bipedal

What does this tell us about the appearance of bipedalism during the course of human

evolution?

Bipedalism appeared very early in human evolution. The ability to walk on two legs within our

evolution history must have evolved over 4 million years ago. This differs from the time we see

increased brain capacity in Homo, as the genus must have evolved just over 2 million years ago.

What we see here is that characteristics that make us strictly “human” were acquired at

different times over our evolutionary history.

Station 3: Apes and Humans

At this station, small scale casts are present for modern day humans, gorillas and chimpanzees.

List the physical similarities between gorillas and chimps.

Presence of sagittal crest. Robusticity of skull. Large canines. Strong brow ridges. Protruding

lower face etc.

List the physical differences between the group of apes and humans.

Humans more gracile. Humans have smaller canines. They have a more gracile skull etc.

What similarities do you see in all three species?

Same number and types of teeth. Post orbital closure etc.

Based on all the characteristics listed above, draw a small level phylogeny for the three species,

denoting which two you think are more closely related to each other, with the exclusion of the

third.

Humans and chimps are more closely related to each other, with gorillas falling outside that

clade. The students may say that chimps and gorillas are more closely related. We will further

explore why morphological features may not always hold the key to phylogenetic relationships.

Station 4: Cranial Capacity in the Australopithecines

At this station are members of the genus Australopithecus. The following casts are present: A.

africanus and A. afarensis. Using the beans and measuring apparatus, determine which species

has the largest brain capacity and which has the smallest.


1. Place skull upside-down on the cushion provided for you. This will aid in the stability

and protection of the skull during this activity.




4. Make sure to move the beans around in the skull in order to ensure that all places

inside the cranium are filled with beans.








A. africanus: _____largest_ (~320 cm3)___

A. afarensis: ____smallest_(~250 cm3)____

What major similarities and differences do you see between these two species?

Presence of brow ridges. Small brain cases. Protrusion of the lower face.

Station 5: Investigating differences between Homo and Australopithecus

At this station, small scale casts are present from two species within the genus Homo and two

species within the genus Australopithecus. Without looking at their tags, what two do you think

belong in each respective genus and why? Use the numbers in front of each species in order to

discuss them below.

What are the major differences between the two groups?

The australopithecines have a smaller brain case than the members of the genus Homo. Their

skulls are overall more robust and they have more protrusion of the lower face. The nuccal area

of the australopithecines is also larger and more robust.

Using your phylogeny and the names of the species on their tags, order the species from the

oldest to youngest. What features do you see change over the course of the millions of years

between these species?

Getting more gracile from oldest to youngest. Larger brain case from oldest to youngest.

Station 6: Ardipithecus ramidus

In the station are images of the skeletons of A. ramidus (Ardi), Gorilla gorilla (Gorilla), and

Homo sapiens.

Provided for you is a triple Venn diagram for you to compare and contrast each species to each

other.

Which species does Ardi appear to be more similar to? Remember, many of these fossils show a

mosaic of traits that are particular to both species. This is important to keep in mind, as the

ancestors of certain lineages will also have a mosaic of traits for the species they gave rise to.

Ardi is a bipedal ape. It shares many similarities between both species and clearly shows

transitions from an ape like ancestor for chimps and humans to a more human like appearance.

Station 7: How do you teach evolution?

At this station you will notice large poster papers and markers for your use. Write your

methodology for teaching human evolution in the classroom or if you do not teach this topic. If

a previous group wrote a methodology you use, draw a large red dot next to it. If a previous

group wrote a methodology you would like to use, draw a green star. We will discuss these

approaches after the activity.

Answers will vary.

Gorilla Ardi

Human

Thick bones

Large canines

Tall and narrow hips Divergent toe

Wide rib cage

Presence of brow ridge

Robust cranial features

Gracile facial features

Toe is not divergent

Narrow rib cage

Large brain case

Thinner bones

Small canines

All primate

features

1

3

2

4

5

7

6

Article

Teaching the Process of Molecular Phylogenyand Systematics: A Multi-Part Inquiry-Based Exercise

Nathan H. Lents, Oscar E. Cifuentes, and Anthony Carpi

Department of Sciences, John Jay College, The City University of New York, New York, NY 10019

Submitted October 13, 2009; Revised February 16, 2010; Accepted April 12, 2010Monitoring Editor: John Jungck

Three approaches to molecular phylogenetics are demonstrated to biology students as theyexplore molecular data from Homo sapiens and four related primates. By analyzing DNA se-quences, protein sequences, and chromosomal maps, students are repeatedly challenged todevelop hypotheses regarding the ancestry of the five species. Although these exercises weredesigned to supplement and enhance classroom instruction on phylogeny, cladistics, and sys-tematics in the context of a postsecondary majors-level introductory biology course, the activitiesthemselves require very little prior student exposure to these topics. Thus, they are well suitedfor students in a wide range of educational levels, including a biology class at the secondarylevel. In implementing this exercise, we have observed measurable gains, both in studentcomprehension of molecular phylogeny and in their acceptance of modern evolutionary theory.By engaging students in modern phylogenetic activities, these students better understood howbiologists are currently using molecular data to develop a more complete picture of the sharedancestry of all living things.

INTRODUCTION

Teaching fundamental mechanisms of evolution by naturalselection is more important than ever, both to biology stu-dents and the general student population, and fresh peda-gogical approaches to accomplish this are needed at alllevels (Dagher and BouJaoude, 1997; Robbins and Roy, 2007;Labov and Kline Pope, 2008). Perhaps more than any othersubdiscipline of biological sciences, the study of systematicstangibly and powerfully invokes the biological results ofevolution and selection. Thus, its inclusion throughout alllevels of the biology curriculum has long been stronglyrecommended. However, as powerfully argued by Rudolphand Stewart (1998), misunderstandings about evolution are

largely philosophical, rooted in a poor understanding of thescientific method and how it applies to the study of naturalhistory. Indeed, even advanced biology students can harborstriking misconceptions regarding the fundamental basis ofevolutionary history (O’Hara, 1997; Robbins and Roy, 2007).

This lack of fundamental understanding by students iscompounded by the seemingly subtle differences amongdifferent systematic approaches. Phenetics seeks to classifyorganisms based on observable differences regardless ofevolutionary history, while cladistics, which also examinesobservable characteristics, has the explicit goal of inferringshared ancestry and constructing a hierarchical classifica-tion. Molecular phylogenetics is similar to cladistics, butinstead of relying on primitive and derived morphologicalcharacteristics, it uses molecular sequence data and otherquantifiable measures to establish data matrices to inferlikely evolutionary relationships. Further, there exists a va-riety of possible forms for expressing the results of system-atic analyses: phylogenetic trees, cladograms, phylograms,dendograms, ultrametric trees, etc. Thus, it is not surprisingthat students sometimes fail to grasp the larger conceptualframework amid this disciplinary complexity.

DOI: 10.1187/cbe.09–10–0076Address correspondence to: Nathan H. Lents ([email protected]).

© 2010 N. H. Lents et al. CBE—Life Sciences Education © 2010 The AmericanSociety for Cell Biology. This article is distributed by The American Societyfor Cell Biology under license from the author(s). It is available to thepublic under an Attribution–Noncommercial–Share Alike 3.0 UnportedCreative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

CBE—Life Sciences EducationVol. 9, 513–523, Winter 2010

513

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Explicitly teaching the process and nature of scientificresearch results in considerable learning gains, amongscience majors and nonmajors alike (Lederman, 1992,1999; Lombrozo et al., 2008). The National Academy ofScience (NAS) and the National Science Foundation (NSF)have explicitly called for the teaching of the practice ofscience within the existing science curricula, especially inrelation to evolutionary theory (Alberts and Labov, 2004;Miller et al., 2006; Ayala, 2008). However, this pedagogicalapproach is not trivial to implement. First, there are atleast two distinct conceptual frameworks to consider: thephilosophical nature of the scientific pursuit, and the true-to-life realities of the modern scientific practice, which aremarkedly different among disciplines (Matthews, 1994;Rudolph and Stewart, 1998; Staver, 1998; Schwartz andLederman, 2002). Second, using real datasets that chal-lenge students to apply scientific concepts and analysis iskey to learning scientific thinking (Wise and Okey, 1983;Soloway et al., 1999). These active-learning methods areoften met with student confusion and resistance, espe-cially if they have not learned this way before (Gosser,2003; Shetlar, 2005). Considerably more effort and thoughtis required of students, compared with traditional passivelearning approaches involving didactic lectures and pro-tocol-driven laboratory exercises in which students sim-ply follow clear experimental procedures and interpretdata as instructed (Hofstein and Lunetta, 2004; Hanauer etal., 2006).

Several new educational resources have emerged that spe-cifically give attention to the methods and practice of the mod-ern field of systematics (Clough, 1994; Alles, 2001; Perry et al.,2008). Because the majority of biology students don’t properlygrasp discrete information conveyed by a simple phylogenetictree, groups including the “tree-thinking group” (http://tree-thinking.org) have resolved to develop resources and supportfor biology teachers at all levels (O’Hara, 1997; Baum et al.,2005). Other tools include the Understanding Evolution re-source (http://evolution.berkeley.edu) from the University ofCalifornia Museum of Paleontology in Berkeley, CA, resourcesfrom the NAS (www.nationalacademies.org/evolution/index.html), the Public Broadcasting Station (www.pbs.org/wgbh/evolution), and Visionlearning (visionlearning.com), which is funded by the NSF and the U.S. Departmentof Education.

In designing the educational method described herein,we aimed to develop another teaching tool for demon-strating the modern practice of molecular phylogeneticsby using actual datasets and challenging students to in-terpret those data using their own skills in deductivereasoning. We do this by providing DNA sequences, pro-tein sequences, and chromosomal electron density mapsof five closely related species, and then asking students tomake simple hypotheses regarding the phylogeny of thesespecies. There are several unique features of this ap-proach. First, by having students participate in the scien-tific process of hypothesis-making, they gain familiaritywith “what scientists do” with experimental data. Second,by engaging several types of data addressing the sameunderlying question, we demonstrate to students howscientists use multiple lines of evidence to support orrefute hypotheses. Third, by exposing students to rawdata that can be used to elucidate the common evolution-

ary origins of related species, we may break throughresistance that some students have to evolution in general(Clough, 1994; Lombrozo et al., 2008; Perry et al., 2008). Inour chosen method of implementation, unbeknownst tothe students, the raw data they will be handling aretaken from Homo sapiens and four closely related primates,thus shedding light on the biological origin of humanity.Fourth, the method that students will use, comparativegenomics, is currently used by evolutionary biologistsin exactly this context (Zhu et al., 2007), thus accurately“mimicking” a relevant and cutting-edge scientificpractice.

EXPERIMENTAL METHODS

Student Assessment GroupsAssessment took place in spring of 2009 in the course

Biology 104 (Bio104), Principles of Modern Biology II, thesecond semester of the majors-track introductory biologycourse at John Jay College, a large, urban, minority-serv-ing institution, and part of the City University of NewYork (CUNY) university system. All three activities wereconducted in one 2.5-h laboratory session, with studentsworking in their normal laboratory group (pairs). Thelaboratory took place after the second week of the course,immediately after the course lecture on phylogeny andsystematics, which follows lectures on natural selection,micro- and macroevolution, speciation, and Hardy–Wein-berg equilibrium. Two laboratory sections (28 studentseach) meet jointly for course lectures. For the assessment,both lab sections met with the same course instructor atthe same time, thus providing for a case-controlledexperimental design. One lab section completed the tra-ditional laboratory exercise [chapters 20 and 21 of theHelms biology laboratory manual (Helms et al., 1998)]and is referred to as the control section, while theexperimental section completed the exercises describedherein.

Performance on Exam QuestionsThe three phylogeny-related exam questions referred to in

the Assessment of the Activity section were as follows:

Q1. If two modern organisms are distantly related in anevolutionary sense, then one should expect that…

A1. they should share fewer homologous structures thantwo more closely related organisms.

Q2. In evolutionary terms, the more closely related twodifferent organisms are, the…

A2. more recently they shared a common ancestor.Q3. The theory of evolution is most accurately

described as…A3. an overarching explanation, supported by much

evidence, for how populations change over time.

These questions were given in multiple-choice format(other answer choices are available upon request), and theresults shown in the Assessment of the Activity sectionrepresent the percentage in each group that selected thecorrect answer.

N. H. Lents et al.

CBE—Life Sciences Education514



Surveys Regarding Perceptions of EvolutionThe surveys used in this study (results shown Assessment

of the Activity section) were devised and twice validated byadministration to similar student sections in previous se-mesters and were deemed exempt from full panel review bythe John Jay College Institutional Review Board (IRB). Sev-eral “control statements” were included regarding the ac-ceptance of the scientific validity of current understand-ings of geologic time, which had shown in previousvalidations of this survey to be relatively stable in groupresponses before and after learning about evolution indetail. Next, we included a series of overlapping state-ments about 1) evolution, 2) natural selection, and 3) howthose processes contributed to the emergence of Homosapiens, which, in previous validations, had generatedresponses that were subject to change as students studiedthe mechanisms of evolution.

For this survey, students were asked to report their accep-tance of the statements on a five-point scale: strongly agree,agree, neither agree nor disagree, disagree, strongly dis-agree. Importantly, similar concepts were repeated in sev-eral variations, because studies have shown that studentsmay key in to certain “trigger words” including theory,Darwin, evolution, scientists, and descent; and differentwordings can lead to different survey results, even with thesame students (Evans, 2001; Scott and Branch, 2009). Formost statements, a response of “strongly agree” was scoredas a “1” and indicated the strongest acceptance of currentscientific theory, while a response of “strongly disagree”was scored as a “5” and indicated the strongest opposition tocurrent scientific theory. However, three statements wereexpressed as “inverts,” such that agreement would indicatea rejection of currently accepted scientific theory. The nu-merical scoring of these questions was inverted to maintainthe pattern that the lowest score indicates the strongestacceptance of scientific theory. The survey questions were asfollows:

Control QuestionsC1. I agree with the scientific evidence that dates the

earth to more than 4 billion years of age.**C2. Although some scientists claim otherwise, the

earth is not more than 10,000 years old.C3. I agree with the theory that, over the course of

time, the positions of the great land masses(continents) have undergone many dramaticchanges.

Probative Questions**Q1. I believe that, with only a few exceptions, the life

forms that exist on the planet today are, more orless, the same that have always been here sincelife first began on earth.

Q2. I believe that, over many generations, naturalselection has contributed to the gradual evolutionof animals and plants into their present forms.

**Q3. I believe that evolution by natural selection is justone theory about how life on earth came to itspresent form and I personally don’t support it.

Q4. I feel that a large body of evidence supports theDarwinian theory of evolution by naturalselection.

Q5. I support the theory that the biological species,Homo sapiens (Human beings) evolved from anearlier species of primates.

Q6. I agree with Charles Darwin, who first suggestedthat the current form of human beings wasinfluenced through the process of evolution bynatural selection.

Q7. Because human beings are mammals, I believethat they have a shared ancestry with all othermammals.

Q8. I believe that human beings descended to theirpresent form through natural processes, includingnatural selection.

**�inverted statements; scoring is reversed.

Survey responses were tabulated, scores for invert state-ments were reversed, and group patterns were analyzed.First, responses to the control questions were analyzed toensure that the two groups were comparable. To assesschanges in perception, we scrutinized pre- and posttreat-ment responses to identical questions and performed thefollowing calculation on the “average group scores”(arithmetic mean) to individual questions: 100% � (pre �post)/pre. By placing the pretest values in the denomina-tor, this formula normalizes for beginning differences inthe two student groups and expresses change relative tothe initial condition. Error bars were added to indicaterelative variance in survey responses, as calculated by thefollowing formula: (SD)/(average response) multiplied bythe “percent change” score for that question for properscaling.

DESCRIPTION OF THE ACTIVITIES

This activity, suitable for laboratory, discussion, or any othergroup work setting, is broken into three parts. Although com-mon connections are drawn at the conclusion, each individualpart could be done at different times or stand entirely on itsown. Further, each part could be simplified, further extendedto include a quantitative parsimony analysis, or otherwisemodified, as explained within each description. Thus, theseexercises are flexible and can accommodate many teachingenvironments. The driving theme is to provide actual scientificdata to students and challenge them to draw conclusions aboutthe data in ways that lead them to propose a hypotheticalphylogram describing the evolutionary relatedness of the spe-cies involved. Although it may be best if these activities followa lecture on systematics that covers the differences betweencladistics and phylogenetics, as we have done, this may not bestrictly essential and a short primer on systematics (see www.ncbi.nlm.nih.gov/About/primer/phylo.html) might suffice,depending on the academic background of the students. Thecomplete student handout for this exercise is provided asSupplemental Material 1, while the complete instructorguide is provided as Supplemental Material 2.

Teaching Molecular Phylogeny

Vol. 9, Winter 2010 515



Activity One: Molecular Phylogenetics Using aPseudogeneIn the first activity, students are given four short DNAsequences (Ohta and Nishikimi, 1999), shown in Figure 1A,with a brief description.

• Below are four gene sequences. These are taken from fouranimals that are believed to have “recent shared ancestry”(are closely related).

• The gene sequences are from a so-called “broken gene” orpseudogene, the evolutionary remnant of a gene, which isnow nonfunctional, in a given species or group of relatedspecies. In this case, the gene is called GULO (L-gulonolac-tone oxidase), which codes for the enzyme which catalyzes akey step in the synthesis of ascorbic acid (vitamin C). Alongthe way, some animals have lost the function of this gene (byrandom mutation) and must consume vitamin C in theirdiet.

Procedure

1. Examine the four gene sequences below and mark anydifferences among the sequences that you can find.

2. Discuss the following questions with your lab partner: Doyou notice any specific pattern? What could this patternmean regarding the ancestry/relatedness of the four species?

3. Together with your lab partner, make a hypothesis aboutthe ancestry of these four species in the form of a phyloge-netic tree. Draw this tree on a separate sheet of paper andmake a few notes explaining why you drew it this way.

In an effort to reduce intellectual resistance to the topic, weelect not to reveal the identity of the species until all activ-ities are complete (Lombrozo et al., 2008). Studies have

shown that many self-identified Christians in the UnitedStates have brokered a psychological compromise betweenscience and faith by accepting the validity of geologic timeand evolutionary change but maintaining that these pro-cesses had little to do with the divinely instituted emergenceof Homo sapiens (Smith, 1994; Meadows et al., 2000; Miller etal., 2006). The DNA sequences are derived from a pseudo-gene, which opens up an interesting discussion in itself(Nishikimi and Yagi, 1991; Eyre-Walker and Keightley,1999). As students begin to examine the DNA sequences,they have little trouble identifying the differences betweenthe species, highlighted in Figure 1B. However, if studentsare then unsure what to do next, we let them wanderthrough the initial confusion and discuss how to approachthe problem with their lab partner and other classmates,reinforcing the collaborative nature of scientific research.Eventually, students focus on the differences marked withasterisk in Figure 1B, and nearly all student pairs draw aphylogram similar to that shown in Figure 1C. A quantita-tive analysis of parsimony might enrich this activity signif-icantly for more advanced students. Based upon such aquantitative parsimony analysis, the phylogram shown inFigure 1C is indeed the most parsimonious relationshipbased on these DNA sequences (data not shown).

Activity Two: Amino Acid Sequences of FunctionalHomologous ProteinsIn this activity, we present students with sequences fromrelated species and challenge them to deduce a phylogram.However, this exercise is more complicated because thereare sequences provided from five species, and students areprovided with the amino acid sequences of a functionalprotein, chromosome-encoded SCML1 protein that func-

Figure 1. (A) Aligned genomic DNA sequences from the GULO pseudogene taken from the short arm of chromosome #8 (8p21 inhumans) of the following species: #1 � Pan troglodytes, #2 � Pongo pygmaeus, #3 � Homo sapiens, and #4 � Macaca mulatta. (B)The discrete nucleotide differences among the four DNA sequences have been highlighted. The asterisks indicate key positions thathelp reveal ancestry. (C) The most likely phylogram indicating the ancestry and divergence of the species based on these DNAsequences.

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tions in male embryonic development and male fertility (vande Vosse et al., 1998; Wu and Su, 2008). Because mutationand evolutionary change are more “constrained” in a pro-tein sequence (Nachman and Crowell, 2000), these se-quences utilize the “…/…” symbol to denote long stretchesof protein sequence with no differences in amino acids. Thisopens a discussion of different silent mutations that mightbe present in these species, both of the wobble and intronicvariety. The five sequences provided to students are shownin Figure 2A (Wu and Su, 2008).

The differences between the homologous sequences, high-lighted in black in Figure 2B, are more numerous in thisactivity, but because of the practice they had in activity one,students are more prepared to “see through the noise” andignore instances in which one species has a unique aminoacid at a certain position. Another new challenge faced bystudents in this activity is the inclusion of data from fivespecies, instead of just four, which will require a morecomplicated phylogram. Although most of the studentgroups will notice the early divergence of the ancestor of #1and #2, from the ancestor of #4 and #5, these same groups

are often split evenly regarding which side of the branchpoint includes the most recent unique ancestor of species #3.Thus, most students begin by constructing their phylogramsaccording to one of the options shown in Figure 2C, evenlysplit between the two possibilities.

The fact that two hypothetical phylograms are nearlyequally likely provides a good teaching moment as thisintroduces the nature of scientific controversy and debate.We encourage students to present data for their position,and we have observed that some lab groups argue stronglythat, using the positions marked with an asterisk in Figure2B, there are three examples of species #3 being similar to #1and #2, and only two examples when #3 is similar to #4 and#5. Because three is more than two, this does argue, albeitweakly, that the convergence of species #3 from #1 and #2was more recent than its divergence from #4 and #5. Thisopens a discussion of “weight of evidence” and the need formuch larger sets of sequence data, from many genes, tobuild stronger hypotheses. Further still, this provides a nicesegue to the next activity, which is a wholly differentmethod of analysis, and how scientific research relies on

Figure 2. (A) Aligned amino acid sequences from the SCML1 gene product of the following species: #1 � Homo sapiens, #2 � Pan troglodytes,#3 � Gorilla gorilla, #4 � Pongo pygmaeus, and #5 � Macaca mulatta. The symbol …/… indicates a long stretch of amino acids with nodifferences among the species. (B) The discrete amino acid differences among the five protein sequences have been highlighted. The asterisksindicate key positions that help reveal ancestry. (C) The two most likely phylograms indicating the first (most distant) divergence of thespecies based on these protein sequences. (D) The two most likely complete phylograms indicating the ancestry of the species based on theseprotein sequences.


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multiple lines of evidence from different methodologies,resulting in an inherently self-correcting march toward amore detailed understanding of the natural world.

Activity Three: Electron Density Maps ofChromosomesIn the final activity, students are given chromosomal maps(cytogenetic ideograms) of a few of the larger chromosomesfrom four different species (Murphy et al., 2005). This opensup a short discussion about euchromatin versus heterochro-matin, and how and why some DNA is kept “silent” (Yunisand Prakash, 1982). The maps are shown in Figure 3A andare provided to students with the chromosomes clearly ar-ranged by species. Students are instructed to cut each chro-mosome out and compare them to each other in a search forhomologous chromosomes shared by all four species. After

some time, most student groups identify the three sets ofhomologues shared by all species (Figure 3B).

Concentrating only on the three sets of homologues, stu-dents are challenged to make qualitative comparisons aboutthe similarities and shared features of the homologues, andin so doing, infer the relatedness of the four species.Through a process of hypothesis testing, the students workthrough the three sets of four homologous chromosomesand most come to recognize that species #1 and #4 aremarkedly more similar to each other than to the others, andthe same is true for species #2 and #3. Thus, most studentsbegin their phylogram as shown in Figure 3C. However,before the students simply further branch the two sides intosymmetrical final branches, a new challenge is given. Stu-dents are asked to make a hypothesis regarding which di-vergence occurred more recently. In other words, studentswere asked to return to the sets of homologues and makequalitative judgments regarding which pair shows more

Figure 3. (A) Chromosomal maps (cytogenetic ideograms) for assorted chromosomes from the following species: #1 � Pan troglodytes, #2 �Pongo pygmaeus, #3 � Gorilla gorilla, and #4 � Homo sapiens. (B) The same chromosomes, but arranged by homologues that are shared by allfour species. (C) The two most likely phylograms indicating the first (most distant) divergence of the species based on the degree of similarityamong the chromosomal maps of the homologues. (D) The two most likely complete phylograms indicating the ancestry of the species basedon the chromosomal maps. (E) A cladogram showing the ancestry expressed in 3D. (F) The arrangement of chromosomes showing howspecies #4 has one unique chromosome with two long arms, each of which shares substantial similarity with other chromosomes from theother species. This is evidence that this long chromosome in species #4 is actually the result of a chromosomal fusion of two smaller ancestralchromosomes.

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similarity in their chromosome heat maps: #1 with #4 or #2with #3. Such patterns of similarity can provide one line ofevidence regarding the relative relatedness of the species interms of evolutionary time (Nachman and Crowell, 2000;Murphy et al., 2005).

Importantly, each student group will attack this problemwith a slightly different approach and this diversity of meth-odology is encouraged—there is no “right way” to solve theproblem and no “answer key” that will verify the correctanswer. This reflects how science really works: We speak in“weight of the evidence” and theories that are supported by“multiple lines of reasoning,” not in the absolutes of “correctanswers” and foregone conclusions. Additionally, thechallenge of deducing relative age of the branch points(Figure 3D) in this exercise provides a nice opportunity toconnect with another common way of representing evo-lutionary relationships: the cladogram. Although cla-dograms are usually constructed based on shared andderived characteristics, they share with phylograms thefundamental basis of evolution and shared ancestry.Thus, students gain important understanding by learninghow to interpret both. Figure 3E shows a cladogram thatexpresses the conclusion that the divergence between spe-cies #2 and #3 occurred earlier than the divergence be-tween species #1 and #4.

Following the construction of the phylograms, but beforewe move to the final discussion, we “resurrect” the outlierchromosomes previously set aside because they did notform part of a homologue set shared by all species. It isobvious that the real outlier is the very long chromosomefrom species #4. We ask students to set this chromosome infront of them and compare to the other outlier chromo-somes, especially those from the species that is most related,which they now know is species #1. The realization beingsought is that the lone outlier chromosome from species #4,which has no homologue in the other species, has regions ofvery substantial similarity with two of the other outlier chro-mosomes from the other species, as shown in Figure 3F.Ayala and Coluzzi (2005) inferred that an ancestor of species#4 possibly suffered a mitotic catastrophe that was repairederroneously through the fusion of two different chromo-somes together. This opens a discussion of chromosomalbreakage and repair phenomena such as fusions, transloca-tions, etc.

Because the activities are now finished and the session isabout to proceed to the postlab discussion, this is a perfectopportunity to “break the code” and tell the students that“species #4” in activity three is actually Homo sapiens. Hu-mans indeed have one fewer pair of chromosomes (23) thanall other living primates (Zhu et al., 2007). From these anal-yses, scientists have concluded that the second longest hu-man chromosome is actually the result of a fusion betweentwo smaller chromosomes (#12 and #13 in chimps and greatapes), which occurred in a primate ancestor of humanswithin the last 3 million years (Ijdo et al., 1991). This conclu-sion is strongly supported by extensive DNA evidence, suchas the presence of two telomere-like stretches arranged end-to-end within chromosome #2 and the remnants of an addi-tional centromere (Wienberg et al., 1994; Navarro and Bar-ton, 2003; Zhang et al., 2004). All of these concepts, especiallyif they have previously been covered in lecture, provide an

excellent discussion with the students to connect this exer-cise to other material covered in introductory biology.

The Postactivity DiscussionThe discussion at the end of the activity is crucial for “driv-ing home” the main points of this pedagogical method.Several points should be explicitly stressed during this dis-cussion (see Supplemental Material 2). First, the sequencesshown in Figure 1, A and B were selected for this exerciseessentially at random. There is no reason to think that thesegenes are somehow exceptional and that selecting othergenes would paint a significantly different picture. In fact, ifan Internet connection is available, these sequences canactually be used to break the code of which species iswhich, using the BLAST bioinformatics search tool at theNational Library of Medicine’s website (http://blast.ncbi.nlm.nih.gov/Blast.cgi). This means that the hypotheticalphylograms built in activity one can now be redrawn withthe species names shown in Figure 4A.

The second activity involves five species, and once againthe protein sequences shown in Figure 2 are real, and theidentity of these can be revealed through a protein BLASTsearch. At this point in the discussion, we point out that theSCML1 protein sequences and the GULO pseudogene se-quences both led students to conclude that humans andchimpanzees are more related to each other than to macaqueand orangutan and vice versa. This reinforces the concept of“multiple lines of evidence.” However, because gorilla wasnot included, the activity one phylograms cannot help re-

Figure 4. (A) The phylograms derived from the three exerciseswith the species identities revealed. (B) A representative cladogramexpressing the current scientific consensus regarding the sharedancestry of the five genera examined in this exercise.


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solve the unanswered question of how gorilla best fits intothe evolutionary scheme. For evidence on this question, wemove on to activity three.

For activity three, one cannot easily do a bioinformaticssearch with the chromosome maps. However, an Internetsearch with the terms “chromosome map [species name]”will show similar examples of these maps so that studentscan see that these are indeed real maps from these fourspecies. Further, with the addition of the third phylogram,students can now address the question left unresolved fromactivity two—where gorillas fit into the evolutionary schemeof the apes. The annotated phylogram shown in Figure 4Aargues that gorilla and orangutan share a more recent com-mon ancestor than gorilla does with humans and chimps.Thus, the students can return to the sequence data fromactivity two and observe that, although there were threeincidents of gorilla sequence matching humans and chimpsand only two where the gorilla sequenced matched with theorangutan and macaque sequence, the chromosome densitymaps argue that the gorilla is more closely related to oran-gutans than to humans or chimps. This demonstrates theneed for more and longer sequences for comparisons andhow evolutionary relationships are explored through manyoverlapping methods in order to reach a more solidlyfounded conclusion.

At this point in the discussion, it is often powerful todemonstrate how the phylograms constructed by the stu-dents compare with phylograms drawn by experts in theevolutionary biology of apes and humans (Zhu et al., 2007).If an Internet connection is present, simple Internet searchesfor “phylogram [species names]” will produce hits that linkto different phylograms. Importantly, many different phy-lograms will be found, with different groupings based onwhich species and taxonomic groups are included. Thishelps to underscore the concept that phylograms are drawnto express relationships between species of interest: they arenot meant to be all-inclusive. Figure 4B shows the currentscientific consensus regarding the evolutionary history ofthe five genera involved in this activity.

ASSESSMENT OF THE ACTIVITY

As this activity was designed, implemented, and refined, wetook efforts to assess the degree to which it accomplishes theoriginal goal of gains in student learning through explicitlyengaging the scientific process. Toward that end, we moni-tored several aspects of the student experience. First, eachterm we collected student work and assessed how successfulthey were at completing each activity as expected. Thisresulted in substantial revisions of the activity worksheetsand refinement of the activity itself. These revisions to theexercise improved the students’ ability to understand andcomplete the challenges such that, in the present form, thesuccess rate is �80%, �70%, and �60%, respectively, for thethree activities (data not shown). The lower rate of successindicates progressively challenging activities, but we ob-serve that even students who are unable to reach the ex-pected conclusions on their own are able to comprehend themethodologies during the postactivity discussions. We havewondered whether guided inquiry or a problem-based re-search approach assist the students with these challenges.

A second form of assessment that we analyzed was theperformance on lecture exam questions related to this topic.For this comparison, we arranged a case-control experimen-tal design and two different sections of Bio104 were selected.Both groups had 28 students and the same instructor for thelecture part of the course, in which all course topics aretaught. The control group completed a traditional laboratoryexercise on evolution, phylogeny, and classification: chap-ters 20 and 21 of Biology in the Laboratory (Helms et al., 1998),while the experimental group completed the exercise de-scribed here. Then, we compared performance on the courseexam, which is common among all sections and is relativelyunchanged year to year.

As Figure 5A shows, the two groups’ general exam scoresindicate that the control group was composed of measurablyhigher-performing students than the experimental group.However, because this difference is �10% and within the95% confidence interval for each group, we considered thegroups comparable for the purposes of this assessment. Weidentified three questions on exam one that specifically ad-dress the issue of phylogenetics and the deduction of evo-lutionary relationships (described in Experimental Methods).Importantly, both groups were taught this material by thesame instructor, and both groups worked from the sametextbook, from which these three questions derived (Biology,7th ed. (Campbell and Reece, 2005). Figure 5A shows that,despite scoring lower on the exam overall, the experimentalsection slightly outperformed the control group on all threeof these select exam questions. Although these differencesare not dramatic, they are consistent, especially when con-sidering that phylogeny was just one concept on an examcovering four weeks’ worth of material.

Finally, we performed a third mode of assessment aimed atinferring student perceptions regarding evolution. As part ofan ongoing assessment project regarding teaching the processand nature of science, we utilized pre- and postsurveys toscrutinize student perceptions regarding the scientific theory ofevolution by natural selection, how those perceptions are af-fected by learning more about the theory in a formal biologycourse, and what role, if any, this activity plays in the alterationof those perceptions. For this inquiry, we used the same controland experimental groups described above. At the beginning ofthe semester, both groups were given a survey instrumentpreviously validated to reveal student perceptions regardingevolution and natural selection. Then, both groups weresurveyed again 2 wk after the first examination, whichwas thus 1 mo after the execution of this experimentallaboratory activity. More detail regarding the compositionand scoring of the survey instrument is included in theExperimental Methods section. Briefly, all survey responseswere scaled 1–5 and calculations were performed to yielda “percent change” value for each question, with a posi-tive value indicating an increase in acceptance of thescientific theory of evolution by natural selection.

As seen in Figure 5B, a noticeable difference between thetwo groups was observed. In the control group, dependingon the particular question, group responses sometimes re-flected slightly increased acceptance of evolution and some-times indicated slightly decreased acceptance of evolution.The experimental group, however, responded to instructionabout evolution in a dramatically more consistent manner.Regardless of the question, the average scores on all ques-

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tions concerning the acceptance of evolution showed anupward deflection, indicating that, as a whole, the groupmore consistently came to accept the scientific validity ofmodern evolutionary theory. This provides support for abreakthrough study (Lombrozo et al., 2008) that found thatstudent perceptions and acceptance of the theory of evolu-tion are directly impacted by their understanding of thenature and process of science and research.

CONCLUSIONS

The inquiry-based student activity described herein is anovel approach toward the instruction of the practice ofmolecular phylogeny and systematics. Such approaches arestrongly mandated, both because of recent threats to properbiology education in our country due to poor understandingof evolutionary theory (Miller et al., 2006; Ayala, 2008) andbecause this approach has been shown to be more effectivethan traditional approaches to teaching (O’Hara, 1997; Rob-bins and Roy, 2007; Lombrozo et al., 2008). Although theskills that are required and reinforced by this group exerciseare part and parcel of most any introductory biology curric-ulum, these activities may also be applicable to students inbiology courses at the nonmajor and even secondary educa-tion levels. No advanced quantitative skills are necessary,nor is a high-level understanding of molecular biology or

evolutionary theory. In fact, these exercises are designed tohelp enlighten these very concepts to students.

Educators who use educational innovations involving stu-dent-centered learning modalities have often encounteredstudent resistance (Giroux, 2001). This has been specificallynoted in various inquiry-based methods in science educa-tion (Anderson, 2002; Hofstein and Lunetta, 2004) and inefforts to explicitly teach the process and nature of science(McComas et al., 2006). Indeed, in our implementation ofthese activities, we encountered some initial resistanceamong our students. This is not surprising, given that intro-ductory science students are often accustomed to beinggiven precise experimental protocols and being told exactlyhow to proceed in their laboratory courses. Thus, the resis-tance and confusion we observed was generally limited tothe first initiation of the activity as students are instructed toexamine the DNA sequences in activity one. During thisperiod, we consider it crucial that the instructor not give inand simply walk them through the activity. One of they keyfeatures of our educational approach is that students mustactively consider the data, contrive different possible meth-ods of analysis, and decide on the strategy they think is best.That there may be a multitude of approaches used by agiven class of students is a strength of inquiry-based learn-ing, helping students learn to think for themselves regardingthe interpretation of data (Hanauer et al., 2006).

Figure 5. (A) Performance of the control and experi-mental sections of students on all course exams, the firstexam, both with error bars indicating the 95% confi-dence interval, together with three specific exam ques-tions that explicitly test comprehension of phylogenyand natural selection. (B) Percent change of averagestudent responses to eight questions on a pre- andposttest survey measuring acceptance of the moderntheory of evolution by natural selection. Positive valuesindicate an overall group change toward more accep-tance of modern evolutionary theory, while negativevalues indicate change toward less acceptance. The textof the survey questions and a description of the calcu-lations are found in the Experimental Methods.


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By completing these exercises, students will mimic thescientific process engaged by contemporary biologists. Firstof all, the technique of comparative genomics is at the fore-front of evolutionary biology, anthropology, structural andmolecular biology, and even medical genetics. The first ac-tivity provides students with a familiarity of concepts andtechniques that they are likely to read or hear about inreports of scientific discoveries in scientific journals and thepopular press. Second, students also execute several distinctcomparisons, with completely different sources of data, inan effort to explore a single concept: the descent of human-kind from primate ancestors. This underscores the scientificpractice of pursuing multiple lines of evidence when ap-proaching unresolved scientific questions. Third, the collab-orative, cooperative nature of science is illustrated becausestudents are encouraged to work in small groups but alsocollaborate with other groups. Fourth and perhaps mostimportant, in these exercises, students are not working to-ward a preconceived conclusion, using a predeterminedseries of steps, only to reveal something that they probablyalready learned about as a “known fact.” Instead, studentsare encouraged to use their prior scientific knowledge, de-sign their own approaches, draw their own unique conclu-sions, and identify the data that support those conclusions.Such pedagogical approaches have been shown in a varietyof contexts to facilitate significant gains not just in contentlearning but in the understanding and internalization ofbroad concepts.

In addition, by withholding the identities of the species inquestion, students who may have been resistant to the con-cept of human evolution from primate ancestors are encour-aged to let their guard down and work freely on the projectat hand. While this aspect of the exercise is by no meansrequired, it is our hypothesis that this could help breakthrough the psychological resistance that some studentshave to the biological understanding of human origins. Weare bolstered in that belief by our survey results, whichreveal that, on average, students who explore the concept ofphylogeny in this manner are more likely to make gains intheir acceptance of modern evolutionary theory than thosewho complete a more traditional laboratory exercise. Wehope that this laboratory exercise will inspire further suchapproaches and that the arsenal of process-oriented inquiry-based tools for teaching evolutionary theory will continue togrow. In so doing, we can help reverse some of the disturb-ing trends regarding public acceptance of evolutionary the-ory, as well as help to educate more budding young scien-tists about the true nature, process, and practice of science.

ACKNOWLEDGMENTSFor this work, N.H.L. was supported by the CCRAA-HSI programof the U.S. Department of Education (grant P031C080210) and A.C.was supported by the FIPSE program of the U.S. Department ofEducation (grant P116B060183).

The authors thank Daniel Cocris and Ron Pilette for their crucialhelp in launching, assessing, and refining these activities.

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a p

seu

do

ge

ne

•

Be

low

are

fo

ur

ge

ne

se

qu

en

ces.

T

he

se a

re t

ake

n f

rom

fo

ur

an

ima

ls t

ha

t a

re b

eli

eve

d t

o h

ave

“re

cen

t sh

are

d a

nce

stry

” (a

re c

lose

ly

rela

ted

).

•

Th

e

ge

ne

se

qu

en

ces

are

fr

om

a

so

-ca

lle

d

“bro

ke

n

ge

ne

” o

r p

seu

do

ge

ne

, th

e

evo

luti

on

ary

re

mn

an

t o

f a

g

en

e,

wh

ich

is

n

ow

no

nfu

nct

ion

al,

in

a g

ive

n s

pe

cie

s o

r g

rou

p o

f re

late

d s

pe

cie

s.

In t

his

ca

se,

the

ge

ne

is

call

ed

GU

LO (

L-g

ulo

no

lact

on

e o

xid

ase

), w

hic

h

cod

es

for

the

en

zym

e w

hic

h c

ata

lyze

s a

ke

y s

tep

in

th

e s

yn

the

sis

of

asc

orb

ic a

cid

(vit

am

in C

).

Alo

ng

th

e w

ay,

som

e a

nim

als

ha

ve

lo

st

the

fu

nct

ion

of

this

ge

ne

(b

y r

an

do

m m

uta

tio

n)

an

d m

ust

co

nsu

me

vit

am

in C

in

th

eir

die

t.

Pro

ced

ure

:

1.

Exa

min

e t

he

fo

ur

ge

ne

se

qu

en

ces

be

low

an

d m

ark

an

y d

iffe

ren

ces

am

on

g t

he

se

qu

en

ces

tha

t yo

u c

an

fin

d.

_

#1 GGAGCTGAAGGCCATGCTGGAGGCCCACCCCGAGGTGGTGTCCCACTACCTGGTGGGGCTACGCTTCACCTGGAGG

#2 GGAGCTGAAGGCCATGCTGGAGGCCCACCCTGAGGTGGTGTCCCACTACCCGGTGGGGGTGCGCTTCACCCAGAGG

#3 GGAGCTGAAGGCCGTGCTGGAGGCCCACCCTGAGGTGGTGTCCCACTACCTGGTGGGGGTACGCTTCACCTGGAGG

#4 GGAGATGAAGGCCATGCTGGAGGCCCACCCTGAGGTGGTGTCCCACTAACCGGTGGGGGTGCGCTTCACCCAAGGG

-

2.

Dis

cuss

th

e f

oll

ow

ing

qu

est

ion

s w

ith

yo

ur

lab

pa

rtn

er:

D

o y

ou

no

tice

an

y s

pe

cifi

c p

att

ern

?

Wh

at

cou

ld t

his

pa

tte

rn m

ea

n r

eg

ard

ing

the

an

cest

ry/r

ela

ted

ne

ss o

f th

e f

ou

r sp

eci

es?

3.

To

ge

the

r w

ith

yo

ur

lab

pa

rtn

er,

ma

ke

an

hyp

oth

esi

s a

bo

ut

the

an

cest

ry o

f th

ese

fo

ur

spe

cie

s in

th

e f

orm

of

a p

hylo

ge

ne

tic

tre

e.

Dra

w t

his

tre

e o

n a

se

pa

rate

sh

ee

t o

f p

ap

er

an

d m

ake

a f

ew

no

tes

exp

lain

ing

wh

y y

ou

dre

w i

t th

is w

ay.



Page 2

Act

ivit

y #

2 –

Mo

lecu

lar

ph

ylo

ge

ne

tics

usi

ng

a c

od

ing

se

qu

en

ce (

pro

tein

)

•

Wh

ile

no

nco

din

g D

NA

se

qu

en

ces

are

ext

rem

ely

use

ful

in a

na

lyzi

ng

th

e s

ha

red

an

cest

ry o

f d

iffe

ren

t sp

eci

es,

pro

tein

-co

din

g D

NA

seq

ue

nce

s a

re a

lso

use

ful.

•

Ho

we

ve

r, t

he

mu

tati

on

an

d e

vo

luti

on

of

pro

tein

-co

din

g s

eq

ue

nce

s o

f D

NA

is

mo

re “

con

stra

ine

d.”

Wh

y m

igh

t th

is b

e?

•

Be

low

is

the

am

ino

aci

d s

eq

ue

nce

fo

r a

pro

tein

ca

lle

d S

CM

L1,

an

en

zym

e n

ece

ssa

ry f

or

ma

le e

mb

ryo

nic

de

ve

lop

me

nt

an

d m

ale

fe

rtil

ity

in m

am

ma

ls.

It

is e

nco

de

d b

y a

ge

ne

on

th

e X

-ch

rom

oso

me

.

•

Th

e a

min

o a

cid

se

qu

en

ce i

s o

nly

sli

gh

tly d

iffe

ren

t a

mo

ng

st f

ive

ma

mm

als

, a

s sh

ow

n b

elo

w:

( “

…/…

” re

pre

sen

ts a

str

etc

h o

f id

en

tica

l

am

ino

aci

ds,

an

d i

s th

is o

mit

ted

.)

_

#1 MSNS…/…VIKT…/…DDNTI…/…EQLKTVDD…/…DALQN…/…RFHARSLWTNHKRYG…/…KKHSYRLVL…/…YETF…

#2 MSDS…/…VVKT…/…DDNTI…/…EQLRTVND…/…DALQN…/…RFYARSLWTNRKRSG…/…KKHSYRPVL…/…YETF…

#3 MSNS…/…VVKT…/…DDDTI…/…EQLKTVND…/…DAMQN…/…RFHARFLWANRKRYG…/…KKHSYRLVL…/…YETF…

#4 MSNS…/…VVKT…/…DDDTI…/…EQLKTVND…/…DAMQN…/…RFHARSLWTNRKRYG…/…KKYSYRLVA…/…YESF…

#5 MSSS…/…VVKT…/…DDDTI…/…EQQKTVND…/…DAMQN…/…RFRARSLWTNRKRYG…/…KKYSYRLVA…/…YESF…

-

Pro

ced

ure

:

1.

Exa

min

e t

he

fiv

e a

min

o a

cid

se

qu

en

ces

ab

ove

an

d m

ark

an

y d

iffe

ren

ces

am

on

g t

he

se

qu

en

ces

tha

t yo

u c

an

fin

d.

2.

As

in a

ctiv

ity #

1,

use

th

e d

iffe

ren

ces

in a

min

o a

cid

se

qu

en

ce t

o r

etr

ace

th

e a

nce

stry

of

the

se f

ive

ma

mm

als

. M

ake

an

hyp

oth

esi

s in

the

fo

rm o

f a

ph

ylo

ge

ne

tic

tre

e.

Dra

w t

his

tre

e o

n a

se

pa

rate

pie

ce o

f p

ap

er,

alo

ng

wit

h y

ou

r n

ote

s e

xpla

inin

g it.



Page 3

Act

ivit

y #

3 –

Ev

olu

tio

n o

f G

ross

Ch

rom

oso

ma

l S

tru

ctu

re

•

No

t a

ll g

en

eti

c ch

an

ge

s a

re a

s su

btl

e a

s si

ng

le b

ase

-pa

ir c

ha

ng

es

in D

NA

. S

om

eti

me

s, l

arg

e c

hro

mo

som

al

rea

rra

ng

em

en

ts o

ccu

r.

•

Th

ese

la

rge

re

arr

an

ge

me

nts

occ

ur

as

err

ors

in

me

iosi

s, o

fte

n i

n t

he

fo

rm o

f ch

rom

oso

ma

l b

rea

ka

ge

, fo

llo

we

d b

y i

mp

erf

ect

re

pa

ir.

•

Imp

erf

ect

re

pa

ir i

ntr

od

uce

s a

ma

jor

stru

ctu

ral

cha

ng

e t

o t

he

ch

rom

oso

me

. S

om

e e

xam

ple

s in

clu

de

: •

Tra

nsl

oca

tio

n –

wh

en

pa

rt o

f o

ne

ch

rom

oso

me

s b

rea

ks

loo

se,

an

d i

s in

ad

ve

rte

ntl

y g

lue

d b

ack

on

to

th

e e

nd

of

a d

iffe

ren

t

chro

mo

som

e.

•

Inv

ers

ion

– w

he

n p

art

of

a c

hro

mo

som

e b

rea

ks

loo

se a

nd

is

glu

ed

ba

ck i

n p

lace

, b

ut

in t

he

ba

ckw

ard

s o

rie

nta

tio

n.

•

Du

pli

cati

on

– W

he

n e

rro

rs i

n D

NA

re

pli

cati

on

ca

use

a c

ert

ain

re

gio

n o

f a

ch

rom

oso

me

to

be

in

ad

ve

rte

ntl

y r

ep

ea

ted

. •

De

leti

on

– W

he

n e

rro

rs in

DN

A r

ep

lica

tio

n (

or

me

iosi

s) c

au

se t

he

pe

rma

ne

nt

loss

of

pa

rt o

f a

ch

rom

oso

me

. •

It m

ay s

ee

m d

iffi

cult

to

im

ag

ine

ho

w s

uch

a d

rast

ic c

ha

ng

e i

n c

hro

mo

som

al

stru

ctu

re,

resu

ltin

g i

n l

arg

e a

lte

rati

on

s to

ge

ne

s a

nd

ge

ne

tic

ma

teri

al,

co

uld

po

ssib

ly t

ole

rate

d.

Ho

we

ve

r, s

uch

ch

an

ge

s w

ou

ld n

ot

alw

ays

be

le

tha

l fo

r th

e c

ell

or

ind

ivid

ua

l in

wh

ich

th

is

err

or

occ

urs

. •

Co

nsi

de

r a

sim

ple

hyp

oth

eti

cal e

xam

ple

: o

Su

pp

ose

a s

ma

ll r

eg

ion

of

chro

mo

som

e #

14

in

a c

ert

ain

an

ima

l b

rea

ks

off

du

rin

g t

he

fo

rma

tio

n o

f g

am

ete

s (m

eio

sis)

. o

Th

is s

ma

ll r

eg

ion

co

nta

ins

ma

ny c

ruci

al g

en

es.

o

Th

e e

xact

po

int

of

chro

mo

som

al

bre

aka

ge

is

just

up

stre

am

of

a c

ert

ain

ge

ne

in

vo

lve

d w

ith

ce

llu

lar

me

tab

olism

an

d e

ne

rgy

con

sum

pti

on

. L

et’

s ca

ll t

his

ge

ne

ME

TA

B1

. T

he

co

din

g r

eg

ion

of

ME

TA

B1

is

inta

ct,

bu

t it

is

no

w s

ep

ara

ted

fro

m m

ost

of

its

“re

gu

lato

ry s

eq

ue

nce

s” (

pro

mo

ters

, e

nh

an

cers

, e

tc.)

. o

Th

e c

ell

de

tect

s th

is e

rro

r a

nd

act

s to

fix

th

e e

rro

r b

y “

glu

ing

” th

e s

ma

ll c

hro

mo

som

e p

iece

ba

ck i

n p

lace

. H

ow

eve

r, i

t co

mm

its

an

err

or

an

d g

lue

s th

e p

iece

ba

ck o

nto

a d

iffe

ren

t ch

rom

oso

me

. o

Th

e c

hu

nk o

f D

NA

is

resc

ue

d a

nd

in

tact

, b

ut

no

w i

n a

ne

w l

oca

tio

n.

Wit

h t

he

exc

ep

tio

n o

f M

ET

AB

1,

all

ge

ne

s o

n t

he

sm

all

“bre

aka

wa

y”

pie

ce o

f ch

rom

oso

me

are

sti

ll s

urr

ou

nd

ed

by

th

eir

no

rma

l re

gu

lato

ry s

eq

ue

nce

s a

nd

eve

ryth

ing

wo

uld

wo

rk n

orm

all

y

wit

h t

he

se g

en

es.

o

Th

e c

od

ing

re

gio

n o

f M

ET

AB

1,

ho

we

ve

r, i

s n

ow

fo

un

d i

n a

ne

w g

en

om

ic “

ne

igh

bo

rho

od

” w

ith

dif

fere

nt

DN

A s

eq

ue

nce

up

stre

am

,

me

an

ing

a d

iffe

ren

t p

rom

ote

r a

nd

re

gu

lato

ry s

eq

ue

nce

s.

o

Pe

rha

ps

the

ne

w u

pst

rea

m s

eq

ue

nce

s o

f M

ET

AB

1 c

au

se t

his

ge

ne

to

be

exp

ress

ed

at

twic

e t

he

le

ve

l a

s b

efo

re.

o

In a

ll c

ell

s o

f th

is o

rga

nis

m,

the

re w

ou

ld n

ow

be

tw

ice

th

e a

mo

un

t o

f th

e p

rod

uct

of

the

ME

TA

B1

ge

ne

. o

Wit

h t

wic

e t

he

exp

ress

ion

of

ME

TA

B1

, p

erh

ap

s o

rga

nis

ms

wit

h t

his

ch

rom

oso

ma

l re

arr

an

ge

me

nt

are

ab

le t

o r

un

fa

ste

r fo

r a

lo

ng

er

len

gth

of

tim

e,

ge

ne

rate

mo

re b

od

y h

ea

t d

uri

ng

co

ld w

inte

rs,

or

oth

er

be

ne

fici

al

eff

ect

s o

f a

fa

ste

r m

eta

bo

lism

.

(Th

is h

yp

oth

eti

cal

exa

mp

le a

ssu

me

s th

at

the

an

ima

ls h

ave

ple

nti

ful a

cce

ss t

o f

oo

d,

wh

ich

wo

uld

be

re

qu

ire

d b

y a

fa

ste

r m

eta

bo

lism

.)

o

In t

his

ca

se,

na

tura

l se

lect

ion

wo

uld

fa

vo

r th

ose

in

div

idu

als

wit

h t

he

ne

w c

hro

mo

som

al

arr

an

ge

me

nt

an

d o

ve

r ti

me

, th

e s

pe

cie

s

wo

uld

evo

lve

as

this

ne

w c

hro

mo

som

al

arr

an

ge

me

nt

too

k o

ve

r in

th

e p

op

ula

tio

n.



Page 4

•

On

th

e a

tta

che

d s

he

et

are

dra

win

gs

of

the

gro

ss c

hro

mo

som

al

stru

ctu

re o

f so

me

ch

rom

oso

me

s o

f fo

ur

rela

ted

an

ima

ls.

Th

ese

are

call

ed

cy

tog

en

eti

c id

eo

gra

ms

an

d t

he

pa

tte

rns

of

ba

nd

s o

n t

he

ch

rom

oso

me

re

pre

sen

t a

lte

rna

tin

g d

eg

ree

s o

f e

lect

ron

de

nsi

ty.

Ina

ctiv

e r

eg

ion

s o

f a

ch

rom

oso

me

(h

ete

roch

rom

ati

n)

are

pa

cke

d m

ore

de

nse

ly t

ha

n a

ctiv

e a

rea

s (e

uch

rom

ati

n),

giv

ing

th

e b

an

din

g

pa

tte

rn s

ho

wn

. P

roce

du

re:

1.

Exa

min

e t

he

ch

rom

oso

me

s o

n t

he

att

ach

ed

ha

nd

ou

t. K

ee

p in

min

d t

ha

t yo

u a

re l

oo

kin

g o

nly

at

a f

ew

of

the

la

rge

r ch

rom

oso

me

s

for

the

fo

ur

spe

cie

s, a

nd

alt

ho

ug

h a

ll o

f th

ese

sp

eci

es

are

dip

loid

, w

e a

re o

nly

lo

okin

g a

t o

ne

ch

rom

oso

me

of

ea

ch p

air

.

2.

Usi

ng

sci

sso

rs,

cut

ou

t a

ll o

f th

e c

hro

mo

som

es,

bu

t b

e s

ure

to

la

be

l e

ach

on

e a

s to

wh

ich

sp

eci

es

it c

om

es

fro

m.

3.

No

w,

ma

tch

up

th

e c

hro

mo

som

es

tha

t ve

ry o

bvio

usl

y a

re “

ho

mo

log

ou

s.”

On

ce y

ou

ha

ve

th

e h

om

olo

gu

e f

rom

all f

ou

r o

f th

e

spe

cie

s, p

lace

th

ose

ho

mo

log

ou

s ch

rom

oso

me

s in

se

pa

rate

pil

es.

4.

So

me

ch

rom

oso

me

s m

ay

be

le

fto

ve

r, m

ea

nin

g y

ou

ca

nn

ot

ide

nti

fy a

cle

ar

ho

mo

log

ue

fo

r a

ll f

ou

r sp

eci

es.

S

et

the

se a

sid

e in

a

sep

ara

te p

ile

, a

nd

yo

ur

inst

ruct

or

wil

l d

iscu

ss t

ho

se l

ate

r.

5.

Fo

r th

ose

ch

rom

oso

me

s th

at

ha

ve a

n o

bvio

us

ho

mo

log

ue

in

all

fo

ur

spe

cie

s, a

s in

th

e p

revio

us

exe

rcis

es,

use

th

e d

iffe

ren

ces

yo

u

see

in

th

e c

hro

mo

som

al st

ruct

ure

to

re

tra

ce t

he

an

cest

ry o

f th

ese

fo

ur

an

ima

ls.

6.

Th

e b

est

str

ate

gy i

s to

fir

st c

on

sid

er

ea

ch c

hro

mo

som

e s

ep

ara

tely

. L

oo

kin

g o

nly

at

the

fir

st c

hro

mo

som

e,

wh

ich

tw

o o

r th

ree

spe

cie

s lo

ok t

he

mo

st s

imil

ar,

etc

.?

Th

en

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if y

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Page 5



Page 6

II.

Po

st-l

ab

dis

cuss

ion

of

the

Ph

ylo

ge

ne

tic

Tre

es

Dis

cuss

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me

wo

rk q

ue

stio

ns:

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) W

hy a

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sue

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s a

nd

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no

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NA

se

qu

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term

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ile

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eth

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s yo

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? R

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if

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cess

ary

.



Instructor Guide – Page 1

Instructor Guide and Heuristics: Molecular Phylogenetics

Before the Exercise Begins:

• If the students have already had lectures on systematics, cladistics, and phylogeny, you can keep your introduction very

brief. But even if so, be sure to review how a phylogram is drawn and what it m

eans. The practice of cladistics builds

hierarchical classification based on observable shared and derived characteristics, while phylogenetics explores

evolutionary relationships based on m

olecular data. Both have the goal of revealing shared ancestry. It’s very important

that the m

ultiple approaches to evolutionary biology not result in confusion for the students. The m

ultiple approaches

complement each other and scientists in different fields learn from one another.

Activity #1:

• Before setting the students loose on the activity, lead a small discussion of what a “pseudogene” is and how a gene could

become “broken” through random mutations. Here are some good questions to pose to students, either as pre-lab

homework, or to ponder right now.

Q: If the GULO gene is needed for the synthesis of Vitamin C, and Vitamin C is so important to life, how would the m

utation

destroying this gene have been tolerated? In other words, why w

ould it not have been quickly elim

inated from the

population by natural selection?

A: If the m

utation occurred in an individual or population that already had an abundance of citrus fruit in their diet (say, in

Africa, or other tropical regions), there would be no real disadvantage of a “broken allele” for the “vitamin C gene.” With

no selection against this allele, the DNA would persist in the population as a pseudogene.

Q: Can you name a species with a functional GULO gene and some with a nonfunctional version? How can you tell?

A: Species that require Vitamin C in their diet might have a broken G

ULO gene. Humans are an example – Vitamin C is

called “essential” because we m

ust get it from our diet. Dogs and cats, however, do not need fruit or any other vitamin C

supplement in their diet. This is because their GULO gene works and they produce their own Vitamin C in their cells.

Q: Why are pseudogenes so useful to biologists in examining ancestry of closely related species?

A: A DNA sequence that is not expressed can suffer changes over time, often without any negative effects. Thus,

pseudogenes have much higher mutation rates in a species over time. (More on this at the end.)




• As the students begin the activity, here are the differences that the students are going to find:

1 GGAGCTGAAGGCCATGCTGGAGGCCCACCCCGAGGTGGTGTCCCACTACCTGGTGGGGCTACGCTTCACCTGGAGG

2 GGAGCTGAAGGCCATGCTGGAGGCCCACCCTGAGGTGGTGTCCCACTACCCGGTGGGGGTGCGCTTCACCCAGAGG

3 GGAGCTGAAGGCCGTGCTGGAGGCCCACCCTGAGGTGGTGTCCCACTACCTGGTGGGGGTACGCTTCACCTGGAGG

4 GGAGATGAAGGCCATGCTGGAGGCCCACCCTGAGGTGGTGTCCCACTAACCGGTGGGGGTGCGCTTCACCCAAGGG

▲ ▲ ▲ ▲

• They will like start doing “counts” of the differences between species. Although there is an easier way, let them do this,

because it can be helpful. The counts of difference between two species are as follows:

1:2= 6

1:3= 3

1:4= 10

2:3= 5

2:4= 4

3:4= 9

• But what does this m

ean? It m

ay not jump out at students, but the point is that, the fewer the difference between two

species, the more closely related they likely are. This, #2 and #4 are and #1 and #3 are the most closely related pairs.

• In addition to the laborious m

ath above, you m

ight also point out there are three examples (or four bases) where #1 and #3

have one thing, but #2 and #4 have something else ( shown as “ ▲ ” above).

• Thus, if they were to build a phylogentic tree, the rule of parsimony (without doing the full calculations) would dictate that the

divergence between the ancestor of #1 and #3 and the ancestor of #2 and #4 occurred before the further divergence of

these species. And the hypothetical tree that they draw should reflect that.

• Another way to simply this activity for them – tell them to ignore all mutations that exist in just one species. This is because

this one obviously occurred after it diverged from the others are not helpful for retracing shared ancestry with other species.

However, this is an opportunity to discuss the “molecular clock;” the number of mutations being useful for determ

ining the

time that has passed since the divergence of two species.

• I could not find the gorilla G

ULO pseudogene (perhaps it isn’t sequenced to date), but that’s okay. They will build other

trees that include G

orilla, and they will assemble a final tree that combines the results of all three activities. This m

imics

how the science of systematics actually works, so point this out to them. Also, at the end, after the species identities are




#3

#1

#2

#4

#3

#1

#2

#4

revealed, you can tell them why G

orilla wasn’t included in activity #1: the sequence hasn’t been reported yet. You could

then also challenge the students to use the trees to predict what the Gorilla GULO gene might look like.

• Thus, the phylogenetic tree that they draw should look like this:

• BEFORE M

OVING O

N TO Activity #2 - have them hand in the tree that they draw, with whatever essential math or

explanation is necessary to defend why they drew it that way.

• The m

ajor point to discuss here is that this is just a short stretch of DNA, less than 100bp, and still, the relatedness of the

four species can be deduced. M

olecular evolutionary biologists generally analyze millions of basepairs of DNA sequence to

help them retrace ancestry.

• It m

ight even be worth telling them (and this is no lie or exaggeration) that this particular stretch of sequence was picked

pretty m

uch at random. The gene was chosen on purpose (a pseudogene), but the person who designed this activity (Prof.

Lents) did not try out a bunch of sequences and then choose the stretch that “worked best” for this activity. This stretch was

the first one he selected and although perhaps others m

ight work even better and show the ancestry in an even m

ore

obvious way, he decided to keep this “first attempt,” as a demonstration that the m

olecular evidence for shared ancestry is

not hard to find!

• Code: But do not break this until the very end!!!!

#1 = Pan troglodytes (chimpanzee)

#2 = Pongo pygmaeus (orangutan)

#3 = Homo sapiens (humans)

#4 = Macaca mulatta (macaque or Rhesus monkey)




• One idea for the final wrap-up discussion, if there is time, is to do a BLAST search, or genome browser search for the

human sequence and show how the human genome sequence is now fully available and searchable online. Just a short

demo of bioinform

atics can really “wow” them.

Activity #2:

• Before setting the students loose on the activity, lead a small discussion of how using a protein sequence is different from

using a DNA sequence. Protein is the expressed product of a gene. There could be lots of silent mutations lurking in this

gene, which do not result in a change to the protein. Here are some possible discussion questions.

Q: Why is a protein sequence more evolutionarily “constrained?”

A: All mutations are random and thus, most mutations in a functioning gene would diminish or disrupt the function of the

gene product. In most cases, a gene product with diminished function would reduce the viability or health of the

organism. Thus, most of these m

utations w

ould be quickly removed from the population through the death of the

organism. However, silent or conservative mutations would be tolerated.

Q: Can mutations ever actually improve the function of the gene and help the organism survive?

A: Yes! W

hile this is rare, occasional advantageous m

utations are the basis of adaptation! Such are often called “gain of

function” mutations because they enhance the function of a gene, or even give a new function or property to a gene.

Q: So wait, if m

any m

utations are silent or neutral, how do they result in a perm

anent change in all members of a certain

species? How do neutral alleles take over an entire population?

A: Remember that, during speciation, the “founders” of a new species are generally a very small group of individuals. In a

phenomenon called “genetic drift,” these individuals m

ight have combinations of “neutral” alleles that are not necessarily

reflective of the larger population. Thus, some neutral alleles, even rare ones, could become fixed in the new population

only because it happened to be present in the founders, not because they give any adaptive advantage to the

population.

• Below the differences that they are going to find are highlighted:




_

#1 MSNS…/…VIKT…/…DDNTI…/…EQLKTVDD…/…DALQN…/…RFHARSLWTNHKRYG…/…KKHSYRLVL…/…YETF…

#2 MSDS…/…VVKT…/…DDNTI…/…EQLRTVND…/…DALQN…/…RFYARSLWTNRKRSG…/…KKHSYRPVL…/…YETF…

#3 MSNS…/…VVKT…/…DDDTI…/…EQLKTVND…/…DAMQN…/…RFHARFLWANRKRYG…/…KKHSYRLVL…/…YETF…

#4 MSNS…/…VVKT…/…DDDTI…/…EQLKTVND…/…DAMQN…/…RFHARSLWTNRKRYG…/…KKYSYRLVA…/…YESF…

#5 MSSS…/…VVKT…/…DDDTI…/…EQQKTVND…/…DAMQN…/…RFRARSLWTNRKRYG…/…KKYSYRLVA…/…YESF…

- * * * * * *

• Once again, the goal is to get them to see how certain pairs are closer than other pairs. C

ounting up all the individual

differences will be very laborious (but still get them to the right answer). This one is a bit harder for them to see, but let

them search for it for a while.

• Again, the trick to m

ake it easier is to ignore all of the cases where there is a change only in O

NE species, since it likely

occurred after it diverged from all the others (and is thus, recent, and not helpful in tracing backward.) The trick is to look for

patterns, which is m

uch faster than detailed numerical calculations. (Although in reality, a subjective analysis is never a

complete substitute for quantitative analysis.)

• The ones that are the most helpful are marked with “*” but only give them this hint if it looks like no one is getting anywhere.

• The pattern that they should hopefully discover is that species #1-#2 and #4-#5 are the m

ost similar pairs to each other.

This should be relatively easy for them to see.

o The problem will be – where to put #3? Likely some will put it with #1-#2, others will put it with #4-#5.

• There are three instances w

here #3 is similar to #1-#2 and only two instances w

here #3 is similar to #4-#5, so there is

slightly m

ore evidence that #3 is m

ore closely related to #1-#2 than with #4-#5. However, students will likely be divided on

the issue. This is totally okay – do not try to correct this – the students can debate this!

o Putting all these together, the students will get one of the phylogenies below:




• Once again, remind them that this is just a short stretch of protein sequence, but biologists would analyze the sequence of

hundreds of proteins, as m

ore data becomes available.

• Once again, you can tell them that this protein was picked pretty m

uch at random, as one whose protein sequence was

easy to find online for all these species. W

e did not try out a bunch of proteins and then choose the one that “worked best”

or gave us the result we wanted for this activity.

• Code: But do not break this until the very end – when you are doing the final wrap-up!

#1 = Homo sapiens (humans)

#2 = Pan troglodytes (chimpanzee)

#3 = Gorilla gorilla (Gorilla)

#4 = Pongo pygmaeus (orangutan)

#5 = Macaca mulatta (macaque or Rhesus monkey)

• Again, you could do a protein BLAST search with one of the stretches that is long enough, to show them the databases.

You could even use one of the nonhuman sequences and search against the human proteome. The search result will be

the “best hit” (human SCLM1) but it will m

ark the differences, that should match up with what is seen here.

#1 #2 #3 #4 #5

1,2,3 4,5

1,2,3 4,5

1,2 3,4,5

1,2 3,4,5

#1 #2 #3 #4 #5

OR OR




Activity #3:

• In this activity, much m

ore “content” in the form

of background inform

ation is included in the handout. However, if preferred,

this could be deleted from the student handout and the inform

ation could be given as a lecture or a student-driven

discussion.

• This activity is m

uch m

ore subjective, and it’s m

ore likely that they will have a hard time m

aking the big separations and

instead see the changes as more of a gradual transition from one to the other. Students will need more guidance.

• When searching for the homologous chromosomes (share by all four), there will be a common tendency to m

atch up, then

stick with, regions of only partial homology. You will have to constantly remind students that for chromosomes to be

considered true homologues, they m

ust share significant homology throughout the length of the chromosome, and for this

exercise, we are only interested in homologues shared by all four species.

• Students will also notice that one species has one fewer chromosome, to which we respond that a) this is not important for

building the phylograms, and b) it is true that species #4 indeed has one fewer chromosome than the other three species

(although all four have many more chromosomes than are shown here).

• Once the students have found the three homologous chromosomes shared by all four species, they can proceed with the

attempt to dissect the ancestry of the four species. This will not be a trivial task for them – remind them to consider the

entire length of the chromosomes. But if they take each chromosome set one at a time, they point to the same relationship:

#1 and #4 are considerably closer to each other than either is to #2 and #3.

• However, before simply branching the two sides into symmetrical final branches, give a new challenge:

o Which of the two pairs is m

ore similar, which are more different? How could this be communicated in the phylogram?

o The conclusion of this is that #2 and #3 have been evolving separately from each other for a longer period of time

than #1 and #4. Thus, they should get something like this for their phylogenetic tree:

2,3 1,4

2,3 1,4

#1

#4

#3

#2

#1

#4

#1

#4

#3

#2

#3

#2

2,3 1,4

2,3 1,4




•

This process w

ill be m

ore laborious than the others, but the real trick to see this is to look at one set of chromosomal

homologues at a time, make an hypothesis, then look at another set and refine the hypothesis continually.

•

There will almost certainly be some in the class that will notice what is going with the “leftover chromosomes.” The second-

to-largest chromosome in species #4 (humans!) has no true homologue in the other species.

•

However, if you take the smallest two chromosomes of the other three species (this works best with #1, chimps, but you can

see it with any of them), and fuse them together (one upside down compared to the other), the resulting fused

chromosome… viola!! It looks almost identical to that lone second chromosome #2 of species #4.

o I would only reveal the following points if some student has already heard about this and begins to speak openly

about it… (otherwise, do it at the end)

o The reality here is that humans have 23 pairs of chromosomes, while all other great apes have 24. W

here did this

missing chromosome go in the Homo sapiens lineage? Nowhere! O

ur chromosome #2 is the result of the fusion

between two other chromosomes in a human ancestor some time after the divergence from our most recent common

ancestor with chimpanzees, our closest relatives.

� Explain that this theory is strongly supported by extensive DNA evidence, such as the presence of two telomere-

like stretches arranged end-to-end within chromosome #2 and the remnants of an additional centromere.

� Interestingly, some anthropologists propose that this chromosomal fusion event contributed to the reproductive

isolation of the human ancestor population from the ancestor population of the m

odern chimpanzee, solidifying

the unique genetic divergence of our ancestors

o If this discussion happens now, rather than after the end, go ahead and break the code for activity #3:

� #1 = Chimpanzees;

#2 = Orangutan;

#3 = Gorilla;

#4 = Humans;

Final Discussion

•

You should have collected the students’ phylograms and notes for each exercise as they go. Hand the papers back to the

students, but tell them NOT to correct or change anything (they need not be graded on getting them “correct.”). Now you

can “break the code” and have the students re-write the three phylograms on these sheets, but instead of the unnamed

species numbers, have them write the actual species names on the three phylograms from the three exercises. Now they

can compare the results from the three exercises to see if they agree.




•

This m

imics the m

ulti-disciplinary nature of biology. S

ome scientists w

ork w

ith D

NA sequences and build phylograms.

Others study anatomical structures and build cladograms. Scientists all over the w

orld study the biochemistry, nutrition,

lifestyle, behavior, and physiology of all the biodiversity on the planet, past and present. These “multiple lines of evidence”

all cooperate to help scientists retrace the ancestry of species.

•

Students’ phylograms will look something like this:

•

One neat thing to point out to them – the results of exercise #3 help to clarify the dispute in exercise #2. Even though there

was, perhaps, slightly m

ore data supporting gorillas being closer to humans and chimps, the chromosomal maps argue the

opposite. This is scientific controversy! Conflicting results tell a slightly different story, but the m

ore data that is gathered, a

clearer picture emerges and the scientific community incremental advances toward a more complete and correct

understanding of the natural world.

More Discussion Points:

•

The exercises above involve REAL data, real DNA sequence, etc. Nothing was fabricated or exagerated. These

examples were chosen largely at random, NOT because they happen to uphold current scientific dogma.

macaque

orangutan

chimp

human

macaque

orangutan

chimp

human

gorilla

human

chimp

orangutan

macaque

gorilla

human

chimp

orangutan

Exercise 3

Exercise 2

Exercise 1

gorilla

human

chimp

orangutanmacaque

Or




Hominoidea

(apes)

Cercopithecidae

(old world monkeys)

Primates

Ponginae

Homininae

Gorillini

Pongo

Gorilla

Pan

Homo

Hominini

Macaca

Hominoidea

(apes)

Cercopithecidae

(old world monkeys)

Primates

Ponginae

Homininae

Gorillini

Pongo

Gorilla

Pan

Homo

Hominini

Macaca

•

You can use B

LAST searching or one of the genome browser to demonstrate a) the validity of the data, and b) the

bioinform

atics tools available to scientists.

•

The sequence comparisons of this exercise involved only a short stretch of data. E

volutionary scientists use tens of

thousands or hundreds of thousands of DNA base-pairs, or even whole genomes to conduct their research, which can take

years. In general, the more data one considers, the more likely they are to “get it right” and capture the true ancestry.

•

There is no one complete and correct phylogenetic tree. They are m

ade to convey relationships between a few species,

even m

any species.

•

As m

ore fossilized remains and DNA sequences become available, our knowledge about the evolutionary history of life on

earth becomes m

ore complete. Although phylogenies are considered “hypotheses,” some are supported by so m

uch data

from a whole variety of disciplines that scientists have a great deal of confidence that they are correct. On the other hand,

occasionally, existing phylogenetic trees have to be refined in light of new data. Even m

ore rarely, new data challenges a

currently dominant hypothetical phylogeny. In this way, the collaborative, skeptical, and self-correcting nature of scientific

research continually advances our knowledge.

•

Shown here is the currently accepted phylogenetic tree that

shows the relationships among the five genera considered

today. It is worthwhile to put this on the board, to show

them how their results helped to uphold the current theory of

human origins.

•

Further, the diagram here supports the conclusion drawn in

activity #3 that Gorillas are m

ore closely related to humans

and chimps than they are to O

rangutans, but only slightly.

This is why this issue was somewhat difficult to resolve by

only looking at short stretches of DNA and protein.

•

Anthropologists examine D

NA and protein sequences and

chromosomal maps, but they also consider skeletal shapes

and features, anatomy of organs and tissues, physiology,

diet and nutrition, and even behavioral patterns and social structures. Thus, the cladogram shown here, while technically a

“hypothesis,” is anything but a wild guess. It is based on mountains of data from countless sources and disciplines.

hands on human evolution: a laboratory based … on human evolution: a laboratory based approach ......

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