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The Life System and Environmental & Evolutionary Biology II

EESC V2300y / ENVB W2002y

Laboratory 2 (01/28/04)

Systematics and Taxonomy

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SYNOPSISIn this lab we will give an overview of the methodology of biological systematics and taxonomyby using real techniques on a series of non-biological taxa – nails and screws.We do this so we don’t get bogged down in getting the “right answer” for real taxa or complexmorphological nomenclature. We will:

1) look at the “evolutionary relationships” with cladistic techniques.2) develop a taxonomic classification based on this method.3) examine a key in a field guide.

INTRODUCTION

Systematics and taxonomy are venerable names for the human penchant to classify thingsinto groups. Biological systematics is the study of order in biological diversity and its evolution.Taxonomy, a subdivision of systematics, is the science of biological classification andidentification.

The profound order that becomes apparent when different organisms are compared givesspecial meaning to biological systematics. The study of systematics long predates Darwin or anyevolutionary theory, but ever since Darwin there has been an emphasis on systematics thatfocuses on the evolutionary relationships of organisms. In other words systematics has becomethe mechanism for unraveling evolutionary history, otherwise known as phylogenies, or familyhistories.

It may come as a surprise to learn that fossils really do not in general provide a series offorms that indicate ancestor-descendent relationships. Instead, evolutionary transmutation isinferred largely from extant organisms. Darwin was an apologist for the fossil record, because atthe time, systematic theory predicted a series of intermediate forms between major groups oforganisms, say birds and reptiles, or humans and apes, that simply were not known. Darwin feltthat this was a result of a very incomplete fossil record. However the combination of pre-evolutionary systematics and Darwinian evolution predicted quite clearly what intermediateforms should look like and which groups they would unite. In other words the groups whichwould have intermediates is highly non-random. One of the most strikingly beautiful thingsabout systematics is in fact that by now so many spectacular and utterly convincing intermediateforms have been found, vindicating evolutionary predictions (despite the wishful thinking ofcreationsists). Systematic techniques have now matured to the point where evolutionary groupsranging in scale from the species level to kingdoms and domains can be understood inconsiderable detail.

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Taxonomic classifications are produced for specific purposes. A classification thatdistinguishesedible from inedible organisms will tend to be very different from one whichproports to reflect evolutionary relationships. Since Darwin, increasing importance has beenplaced on “natural classifications,” and this has come to mean classifications that reflect theevolutionary history of the organsisms that are classified. There are, however, exceptions, mostnotably in bacterial relationships, where this concept is by no means universally.

A key is a device for linking unknown organisms to some taxonomic level (e.g., species,genus, family, etc.). Keys assume that all the taxa in an area of interest (biologically orgeographically) are known. The most common type of key is the dichotomous key, which isconstructed of a series of couplets, each consisting of two statements describing characteristics ofa particular organism or group of organisms. A choice between the two statements is made thatbest fits the organism in question that leads to yet another pair of choices. The statementstypically begin with broad characteristics and become narrower as one proceeds down thesequence of choices. Keys have no necessary logical connection with either a classification (untilnames are identified) nor do they have a necessary basis in evolutionary relationships. They arevery useful, however, in identifying taxa you have never seen before.

I. DEVELOP HYPOTHESES OF EVOLUTIONARY RELATIONSHIPS

Introduction

As you might imagine, all inferences of evolutionary relationships, and hencephylogenies, are based on similarity, of which there are two kinds: general similarity and specialsimilarity. Cladistics uses a specific kind of special similarity. Before discussing cladistics,however, we need to have a few bits of terminology defined.

character: a feature, thing, or measurement we wish to “quantatize” (as opposed toquantify) for our analysis. Characters can be represented by a description, a name, apicture, or a number.

homologous character: a character shared by two taxa by their descent from a commonancestor. The main bones of the fore limbs (e.g. humerus) of birds, bats, and pterosaurs(extinct flying relative of dinosaurs) are homologous characters. In other words, theancestor of birds, bats, and pterosaurs had these bones.

analogous characters: a character shared by two taxa because of independent convergentevolution in separate lineages. The wing of birds, bats, and pterosaurs are analogouscharacters because the common ancestor of birds, bats, and pterosaurs did not have awing, instead each group developed wings independently.

Cladistics

In cladistics, only homologous characters are considered to have information indicativeof evolutionary relationships (i.e., special similarity). Characters inherited without change from

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ancestors are considered to have no information of value to relationships. In cladistics themeaning of characters and the hypothesis of relationship are iteratively interdependent. In otherwords, whether or not a character is homologous is defined by the specific hypothesis ofrelationship between taxa. Each analogous character that is a consequence of the specifichypothesis of relationship is cause for an ad hoc explanation. The principle of parsimonydictates that the hyothesis with the least number of ad hoc explanations is the best – it is anotherversion of Occam’s razor. A cladogram is kind of branching diagram that depicts the sequencein which various characters were acquired though time among a group of related organisms.Cladistics can be done using morphological, behavioral, or molecular data on living or fossiltaxa. Cladistics is also termed Phylogenetic Systematics or Phylogenetic Taxonomy.

How we do Cladistics

We will use the cladistic method in this lab since it allows us to build and testrelationships based on the distribution of the states of the characters and to build groups byrecognizing their shared derived characters, i.e. homologous characters. Cladistics consistsbasically of a search for shared derived characters with which to recognize monophyletic groups(groups descended from a common ancestor).

In this lab we will use nails and screws as proxy organisms firs with diagrams ofhypothetical examples, then with real ones. This avoids the potential snags of a complexanatomical nomenclature, as well as thesearch for the “right” set of phylogenetic relationshipsamong real organisms.

The mechanics of the process consists of a set of hypotheses and tests.

1. Construct a hypothesis of relationship for the “organisms” in question. This hypothesiscan come from anywhere, but a good way to begin is to look for a logical set oftransformations by lining then up in a row.

2. Choose one of the taxa as an “outgroup,” it should look like it might be the most“primitive” form.

3. Define characters that allow you to define groups.4. Look for the distribution of primitive characters that stand in contrast to the derived

characters.5. Look for unique derived characters that define each of the organisms.6. Construct a cladogram and hang the distribution of the characters on it. OK-- - now we

have groups defined by shared derived characters and we have our cladogram with ourcharacters.

7. It is now time to test the hypothesis by looking at the characters that could definegroups other than the hypothesis in question. These characters are in conflict and mustbe explained by some ad hoc argument other than simple descent from a commonancestor. If you need more ad hoc arguments to justify your cladogram than you haveshared derived characters supporting your cladogram, your cladogram must bediscarded.

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8. If your cladogram survives this test, the next step is to look for more characters andhang them on your cladogram and see how they fit.

9. If they do not and there are a lot of them, again your hypothesis fails10. If your hypothesis fails, you must look for a new and better one.11. Try moving one or more taxa around on your cladogram. See if you get a better result.12. Your hypothesis may suggest modifications in the characters or additional “better”

characters – use them!13. Once you get a highly corroborated cladogram, identify the monophyletic groups and

the shared derived characters that define them.

Remember, the cladogram is not an evolutionary tree of ancestor-descendentrelationships. Instead of symbolizing the splitting of a lineage, the branching points reflect thesequence in which characters were acquired.

Example

Here is a very simplified cladogram of some vertebrates. All of the characters listed areaccounted for in this cladogram and all define monophyletic groups with no conflicts.

Here are the taxa:

CICHLID [modern bony fish, examples include many aquarium fish (Jack Dempsey) as well as acommon farm-raised food fish (Tilapia)]

has backbone, paired appendages (fins), dorsal nerve cord and aorta which are shared derivedcharacters uniting the cichlid with frogs, turtles, kangaroos, mice, and humans.

FROG

has all those plus legs.

TURTLE

has all those plus a hard shelled egg called an amniotic egg.

KANGAROO -

all those plus hair, warm blood, and egg develops inside.

MOUSE -

all those plus placental development

HUMAN -

all those plus very large brain and loss of hair

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This cladogram is a hypothesis of the order in which the characters were acquired. It predicts thatother characters should be consistent with this postulated set of relationships. It also predictswhat kind of forms might be found in the fossil record and the order in tine in which they shouldoccur. For example one would expect to find fossil forms with characters intermediate betweenfins and legs, and these taxa would lack an amniotic egg, hair, placenta, and a large brain. Itshould look like a fish with sort-of legs. The fossil record confirms that such creature existed andthat it is earlier in time than all other tetrapods. Put its overall structure could be inferred fromthe cladogram without any fossil record at all. The fossil record thus provides a test of thecladogram, not by finding ancestors per se, but rather by providing taxa that have combinationsof characters that must fit comfortably within the cladogram. If they don’t there is a problem.

Each shared derived character defines a monophyletic group: The presence of a backbonedefines the Vertebrata that includes (in this cladogram) cichlids, frogs, turtles, kangaroos, miceand humans. The common ancestor of all vertebrates possessed a backbone. The presence of legsdefines the Tetrapoda that contains frogs, turtles, kangaroos, mice and humans. The presence ofan amniotic egg defines the Amniota that includes turtles, kangaroos, mice and humans. Thepresence of hair defines the Mammalia that includes kangaroos, mice and humans. The presenceof a placenta defines the placental mammals that includes mice and humans. The presence of avery large brain defines the humans (genus Homo).

It is very important to note how the shared primitive characters do not define any groupsat all within cladistics. Many groups of organisms, in common parlance, are groups defined bythe presence of primitive characters, however. An excellent example is the group we call fish.Fish are the vertebrates that lack limbs! But of course a jellyfish also lack limbs, and one fishspecies was also the ancestor of all tetrapods. Groups defined by primitive characters tend to tellus very little about evolutionary relationships although they can be useful in separating “us fromthem”!

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Note that in the above example there are no characters that define any of the taxathemselves except for humans. These unique derived characters actually define the taxa a distinctfrom the other taxa identifying them as monophyletic groups.

In this cladogram, we have placed the unique derived characters for these taxa. They are, withthe primitive state in parentheses: 1, symmetrical tail fin (asymmetrical fin); 2, tadpole withmetamorphosis (direct development with no distinct larval change); 3, shell covering body (noshell); 4, thick heavy tail (thin tail); 5, ever-growing incisors (incisors that are replaced onceduring life); 6, very large brain (smaller brain).

As many characters as possible should be placed on the cladogram. Eventually, if the researcherhas made an honest attempt to analyze the characters, some will be found that require additionalassumptions other than, “it was inherited from the common ancestor of the group.” Thesecharacters will require additional ad hoc explanations for their existence, requiring for example”that the same shape would evolve independently twice. These characters are analogous orhomoplastic characters and if there are more of them than characters needing only the primaryassumption, the principle of parsimony is violated and the hypothesis must be discarded. Fossilsare used exactly the same way. They provide additional taxa with combinations of characters thattest the cladogram. Conversely, the cladogram provides a clue for what age strata should besearched for such fossil taxa that can provide key tests of the cladogram.

Problem: Constructing and testing a cladogram.

One of the problems often faced by students when first learning phylogeneticsystematics, is that they end to be intimidated by the anatomical nomenclature and by desire toget the “right answer”. For this reason we have selected a neutral set of “taxa” – screws and nails(below). With these taxa, we want you to produce a hypothesis of relationship among the taxa.Produce a cladogram of the taxa and then define a series of characters that you will “hang” on

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the cladogram. Note that you should define both the primitive state of that character and aderived state (which also defines the character polarity) and unique derived characters (and theirprimitive states) as well as shared derived characters. Also, search for homoplastic charcters andplace them on the cladogram, identifying them as such.

The “outgroup” is a taxon selected from outside the big group hypothesized to hold allthe other taxa. In this case we have selected one for you. The outgroup helps defines the polarityof the characters.

After producing your cladogram, identify and define the various monophyletic groupsyou have made.

Then, amongst these taxa, select a different outgroup and come up with a completelydifferent cladogram. Which has fewer homoplastic characters?

OTHER METHODOLOGIES FOR ASSESSING EVOLUTIONARY RELATIONSHIPS

Phenetics

In phenetics all characters are more or less equal. Relationships are inferred by the degreeof general similarity, which is generally determined numerically and with an algorithm. Today, itis common for molecular data to be analyzed phenetically. A branching diagram called aphenogram is often used to depict the phenetic relationships, in which the lengths of thebranches denote the distance between taxa. Hypotheses of relationship are generated by apreponderance of similarity among taxa as estimated from the characters via the specificalgorithm. Different algorithms can give different results for the same data. Phenetics can bedone using morphological, behavioral, or molecular data on living or fossil taxa. Phenetics isalso called Numerical Taxonomy. While this method may seem more “objective”, in fact the

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results are strongly biased by primitive characters, and while the clusters so produced may bequite stable, they generally tell little about evolutionary relationships unless the data are asignificant part of the organisms’ genome.

Evolutionary Systematics

In Evolutionary Systematics a hypothesis of relationship is primarily based on ancestor-descendant relationships. These relationships are generally (but not necessarily) determined bygeneral similarity, among temporally closely spaced fossils assumed to comprise a lineage.Relationships are expressed by an evolutionary tree (a phylogeny) in which all branches areconsidered to be lineages of ancestors and descendants. Neither cladograms or phenograms areevolutionary trees. Evolutionary Systematics can only be done with fossil or real-life data or withthe assumption that some living taxa are representative of ancient ones (i.e., that a living taxoncould be ancestral to another living taxon).

II. CONSTRUCT A TAXONOMIC CLASSIFICATION

Using the two cladograms from the above exercise, produce a classification (inclusive hierarchy)for one of the taxa in each. Give the taxa names.

III. Examination of a field guide key.

Look over and analyze the attached key. Imagine keying out a species of mushroom using it.

The following and the key are extracted from: Lange, M. and Hora, F. B., 1963, A Guide toMushrooms and Toadstools, E. P. Dalton & Co., 257 p. While this guide is intended for laypersons, the methodology employed is exactly the same in technical identification keys.

Questions:

1. What are some of the problems with using this kind of key?

2. What are the principle advantages of using this key?

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USE OF THE KEY

The Key should present no difficulties to those familiar with the usual dichotomous(paired, contrasted characters) type. First the fungi are divided into six main divisions on thebasis of fruit-body shape, and then, within each division, subsequent dichotomies lead for mostdivisions to a genus. The species is then determined with the help of the illustrations anddescriptions.

After a little experience, the main divisions can be spotted on sight. In the Agaric division(Key A), it is also necessary to know the colour of spores in the mass, i.e. from a thick sporeprint on white paper.

For those unfamiliar with the dichotomous type of key, it may be pointed out that at eachstage, two sets of contrasted characters are given and the appropriate one followed on; or,sometimes, one set of characters only is given. The alternative being "not so" or "otherwise”. Forexample:

13. Red, densely scaly, 1413. Otherwise, 15

If the fungus under consideration is both red and densely scaly, one would proceed to thenext set of characters under 14; if the fungus was red and smooth or brown and densely scaly,one would then go to 15. Where two sets of contrasted characters are given, only that set ischosen which is wholly applicable. Thus:

15. Brown, flesh thick, on wood, 1615. Brown or reddish violet, on soil, 17

If the fungus is brown and thick-fleshed but grows on soil, one would take the second setof characters because "Brown or reddish violet, on soil" is wholly applicable. If neither of thealternatives apply, it is possible that one may have slipped up at an earlier point in the Key, orthe specimen under consideration may be abnormal or it may be an excluded species of unusualcharacters notcovered by the Key.