Lab 1 -- Homology and Analogy

homology -- Similarity in characteristics resulting from shared ancestry.

homologous structures -- Structures in different species that are similar because of common ancestry.

analogy -- The similarity of structure between two species that are not closely related; attributable to convergent evolution.

-- from the Glossary, Biology, N. Campbell

The distinction between homology and analogy turns around the two most fundamental principles of evolutionary biology, descent with modification from common ancestors and adaptation. Long before Darwin’s publication of his theory of how evolution occurred, naturalists had noted the exquisite adaptations of organisms to their environments, and in fact used them to support their belief that all species had been created by a supernatural process in their current form. Darwin’s Origin of Species is a landmark in biology not only because it provided a natural mechanism for adaptation, but because it constituted an argument for descent of all organisms from common ancestors that was backed up by an almost withering amount of evidence. The ability to distinguish between homologous and analogous structures forms the basis of this evidence.

Darwin’s evidence for evolutionary change via "descent with modification" can be divided into three broad categories: two predictions about the relationship between organismal structure and function, and a logical argument:

Prediction 1: If species have diverged while adapting to different environmental conditions, they should do so only in certain features, retaining ancestral traits unmodified by this adaptive process. The result should be that species resemble each other in many traits, leaving clues to their history of ancestry in the fine structure of their adaptations (e.g., "Man still bears in his bodily frame the indelible stamp of his lowly origin." from Darwin’s The Descent of Man and Selection in Relation to Sex). The term homology was used by earlier biologists such as Agassiz and Cuvier to mean "similarity due to shared developmental pathways." Homology can thus be recognized when structures evolve from the same precursor cells in embryos. Darwin argued that the most logical explanation for this sharing of pathways among different organisms was (1) that organisms had diverged from common ancestors, and (2) that early developmental stages had changed relatively less than later stages during evolution. In this lab exercise, you will see that evidence of homology between structures of rather different outward appearance and function is often found by comparing their fine anatomical details and tracing their developmental origins.

Prediction 2: If different lineages of organisms encounter the same environmental conditions, they may converge in structures that provide the same functional advantage in these environmental. Essentially, they evolve the same adaptations. Such similarity is NOT evidence for recent common ancestry, however, but rather a testimony to the power of natural selection. How can such analogous similarity be distinguished from homology? Darwin argued, and you will discover, that evidence that structures are analogous rather than homologous is often found in differences in their anatomical structure or developmental origins.

Logical argument: What do we do when comparing the fine structure or developmental origins of features does not clearly indicate whether features are homologous or analogous? Evolutionary change can erase evidence of homology sufficiently that we may have to rely on other criteria to distinguish homology from analogy. For example, suppose you discovered that humans and earthworms share an identical biochemical feature encoded by an identical gene, but that no other organisms share this feature. Should you conclude that this similarity at the molecular level is an analogy, or should this single shared feature lead you to conclude that worms and humans are close relatives, and that all the other morphological and molecular similarities shared by all primates and humans (and earthworms and other annelids) evolved convergently? The preference for the simpler explanation, that which requires the fewest assumptions of convergent evolution, is known as the principle of parsimony. Darwin used this principle to argue, for example, that cave insects in North America and Europe must have adapted independently to cave life, since in most features each group was most similar to surface insects of the same continent, and the similarities were confined to features involved adaptation to cave life. You shall see that the principle of parsimony is used when evidence of developmental origins is not available and forces us to consider and balance evidence for common ancestry from a wide variety of sources.

Evolutionary biology has been revitalized by the integration of new sources of data from molecular, cellular, structural and behavioral biology that are helping us refine, and sometime revise, our hypotheses of the history of life. The study of the structure and function of organisms is a fundamental part of understanding their evolutionary history, even when done by scientists who use molecular sources of information to reconstruct the relationships among organisms (just ask Prof. Brown!).


Prelab reading: Before you come to lab, review the following pages in Campbell: Chapter 26 537-541; Chapter 27 (547-56; 564-569), Chapter 29 (589-594), and Chapter 30 (628-632). Bring along your textbook to lab, as you may find it a useful reference.

In lab: The activities of this lab are divided into three clusters that correspond to the three broad categories of argument used to distinguish homology and analogy (Common origins, Different origins and Parsimony). Each cluster has three study stations that focus on a particular set of similarities among organisms and pose questions as to the evidence for their homology or analogy. The lab time will be divided into four periods, followed by a final study period to answer the general questions at the end of this lab.

Learning groups: You will be divided into groups of three students whose task it will be (by the end of the first period) to understand and be able to explain the answers to questions posed at the three stations in one cluster.

Teaching groups: You will then be assigned to a new group of three, in which each member will have been in a learning group studying a different cluster of stations. During each of the next three periods, the ‘experienced’ member of the group will help the others in the group understand the problems posed and possible answers at the three stations in her/his cluster.


Cluster 1 -- Common origins of divergent structures


Station 1 -- Early developmental events and the relationships of animal phyla

Pages 590-594 in Campbell briefly review the similarities and differences in overall body plans of animals.

Q1. Explain the difference between radial and bilateral symmetry. What are some groups of animals that share these features of the body plan? How might you (in principle) tell whether each of these similarities was homologous or analogous?









Review the process of gastrulation outlined in Fig. 29.3 and illustrated in the slides on display. Gastrulation leads to the development of different germ layers in the embryo. Review figure 29.4 and the text to understand the structure and function of a coelom and observe the x-sections of acoelomate, pseudocoelomate and coelomate animals on display.

Q2. Is the presence of a coelom in the members of phyla Chordata and Echinodermata a homology or an analogy? Explain carefully the evidence for your answer. Would the similarity in body cavity between Annelids and Arthropods be considered a homology? Why or why not?












Note the other developmental differences between protostome and deuterostome phyla described in figure 29.5.

Q3. Describe the evidence for homology between an annelid worm’s mouth and a rat’s anus.








Station 2 -- Developmental homologies in chordates

Vertebrate animals belong to the phylum Chordata, which also contains two groups of invertebrate animals (see pages 628-632). Examine the specimens on display and the figures in your book to answer the following questions:

Q4. What features of invertebrate chordates (subphyla Urochordata and Cephalochordata) are shared with vertebrates? What evidence suggests that they are homologous?










Q5. Like many other sessile invertebrates, tunicates (subphylum Urochordata) are filter feeders. Describe features of vertebrates that are homologous with the filter-feeding structure of the tunicate (see figure 30.2).











Q6. Why are tunicates considered to be chordates, when adults only have one of the four vertebrate characteristics? What does this suggest about the role of developmental changes in evolution?










Station 3 -- Organs of flowering plants

Examine the clasping tendrils of Passiflora and the spines of Bouganvillea. These plants are not very closely related. Try to identify the anatomical point of origin of each structure and its relationships to other parts of the plant.

Q7. Can you develop a hypothesis for each structure’s function? Describe your ideas here.










Q8. Do you think the spines of Bouganvillea are homologous or analogous to those of Cereus? Explain.








Cluster 2 -- Different origins of functionally equivalent structures

Station 4 -- Shells

Consider the specimens and drawings of mollusks, brachiopods and barnacles. Note that each of these specimens have hard, calcareous (CaCO3-containing) shells protecting their bodies. (N.B.: not all brachiopod shells contain calcium carbonate).


Q9. What common function might these structures perform? What evidence could you obtain to support the contention that these structures are adaptations for this function?








Q10. Using the available reference, describe evidence that these are analogous features.











Station 5 -- Eyes

Some cephalopods (octopi and squid) have remarkably similar eyes to vertebrates. Compare the figures illustrating mollusk eyes and the illustration of the human eye. Eyes function by focusing light onto a surface covered by photosensitive cells. The pigments undergo a chemical change which causes a signal to be sent via intermediary cells to ganglia, which then pass the signals via nerve fibers to the brain (see Fig. 45.11). Compare the orientation of pigment and sensory cells in the human and mollusk eyes, and trace the pathways by which the nerve fibers connect to the brain.


Q11. What evidence is there that the similarity in eye structure is an analogy in these two groups?








Q12. What selection pressures could have lead to convergent evolution of eyes? Describe what evidence you could gather to support your answer.


Station 6 -- Pollinator attraction

Many flowering plants are pollinated by animals, meaning that animals forage for food (usually pollen and/or nectar) in flowers and carry the plants' gametes (strictly speaking, their male gametophytes) into position for fertilization. Usually, it is the petals that attract the animals to flowers, but in many groups of plants, other floral structures (or even modifications of non-floral organs) serve this role.

Review the examples. Identify what anatomical features function as pollinator attractants in each one. Is it always petals or sepals?

Q13. What features do the pollinator attracting structures share (regardless of what kinds of organs possess these features)? Why is there convergent evolution of these features?









Q14. What clues did you use to identify the anatomical origin of the pollinator attractants (i.e., what evidence indicates that they are analogous structures)?











Cluster 3 -- Parsimony

Station 9 -- Homology of DNA

As you probably know, genetic instructions are encoded in DNA, which consists of a linear chain of small molecules called nucleotides. At each position in a DNA strand, there can be one of 4 nucleotides, which for the moment we will represent by the letters A, G, C and T. Variation in the information encoded in the DNA is generated by variability in the sequence of bases in the strand (for example, AAGCCTGGA means something different than CAGCCTGGA) With improvements in DNA technology, we now have available lots of information on the similarities between different taxa in their DNA sequences for many genes. But how can we tell if a similarity in a gene sequence is a homology or analogy (after all, we can’t look at it’s developmental origin!)?

On display is a matrix of DNA sequences from a group of insects studied by Prof. Brown. Each line is a DNA sequence (from the same gene) found in a different species of moth from the genus Greya, plus a sequence from another species in a closely related genus. Find positions in the sequence where all taxa share the same nucleotide, and where taxa vary in nucleotides. How could we tell whether these are homologous or analogous similarities?

Go to the computer and open the file on the desktop called "Greya." There should appear an evolutionary tree of these taxa based on the data you have just looked at. This tree is (currently) our best-supported hypothesis of the evolutionary relationships among these taxa, because it is the one that MINIMIZES that numbers of changes in nucleotides over the tree -- that is, it is the most parsimonious tree. The box at the bottom of the screen should tell you how many changes this tree requires -- write down that number.

Painted in color on the branches of this trees is the inferred evolutionary history of one nucleotide position -- where the branch changes color, one nucleotide has been substituted for another in the sequence, i.e., that nucleotide position in the DNA strand has evolved! In the lower right corner of the screen is a box that shows how colors match with nucleotides and how many steps (or substitutions) have occurred at this position over the tree. Using the arrows at the bottom of this box, find a variable position from the data matrix you were just examining.

Q15. How can you tell whether shared DNA characters are homologies or analogies? Make sure you find a examples of both types of shared characters.





Ah, but you say, what if this is not the TRUE evolutionary tree? What evidence do we really have that a similarity at any one position is analogous if this isn’t the true tree? Choose two taxa that share the same nucleotide but do so (according to this tree) analogously, i.e. due to convergent evolution. Using the mouse and arrow, drag one branch to another branch and let go of the mouse button. What has changed?

Q16. Can you now explain how we have used parsimony as evidence for the analogy of nucleotide similarities in DNA? Do you think it is good evidence? Why or why not?







Close the "GREYA" file and upon the second file on the desktop, called "Lysozyme". The tree shown is the most parsimonious tree based on the amino acid sequence of lysozyme, a protein involved in digestion. [Note that proteins, like DNA, are linear strings of variable building blocks, which in this case are amino acids instead of nucleotides. Each position in an amino acid sequence can have one of 20 amino acids (compared to 4 nucleotides in DNA).

Notice that this tree based on the lysozyme sequence proposes that Hanuman langurs (a species of Asian monkey) are more closely related to cows than they are to humans.

Q17. What does this result suggest about molecular similarities among organisms?







Q18. What evidence would you use to argue that similarities between the langurs and the cow in this gene are analogous rather than homologous? Propose a hypothesis for why this gene shows analogous similarities.









Station 10 -- Plant life cycles

Plant life cycles exhibit alternation of generations (e.g., Figs. 27.2, p. 548; 27.15, p. 559), in which multicellular haploid and multicellular diploid bodies occur in different parts of the cycle. Plants share this feature with several groups of algae (e.g., Fig. 26.25, p. 541), including many familiar "seaweeds" (see the blanched specimen of Fucus, a brown alga, in Phylum Phaeophyta). Living charophytes, however, do not exhibit alternation of generations.

Q . Is alternation of generations in plants and algae homologous or analogous? Describe the evidence for your hypothesis.








Station 11 -- Locomotion

Flight and swimming are two modes of locomotion in vertebrates. Compare the wings of birds and bats and the flippers of the dolphin with the pectoral fins of a fish.

Q13. Are bird and bat wings are analogous or homologous? Describe the two lines of evidence that support your answer.







Q14. What evidence is there that locomotory structures of the dolphin and fish are analogous?








Q15. What evidence suggests that the marine mammal’s ancestors were terrestrial?








Discuss possible answers to these questions in groups. Writing out answers to them would be an excellent way to review the ideas in this lab in preparation for the first exam.


1. What is the logic behind Darwin’s argument that the sharing of developmental pathways indicates descent from common ancestors? What does it presume about how developmental pathways evolve?



2. Darwin often used the presence of vestigial structures as evidence for evolution via descent from common ancestors. Describe the logic of Darwin’s approach using the ideas of homology and/or analogy developed in this lab. Provide an example in your answer.



3. Molecular biologists who compare DNA sequences from the same or different organisms often refer to the percentage of all positions in the sequence that have the SAME nucleotide as "% homology." Discuss whether this is an appropriate use of the term homology.

On to Lab 2 - Sources of Phenotypic Variation

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