evolutionary biology 2000 - system a tics, character, homology

8/2/2019 Evolutionary Biology 2000 - System a Tics, Character, Homology

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2/1/00 Chapter 4: Characters page 1

Note: Some of this material is redundant with that in Chapter 3, and will beedited out when we make some decisions about Chap 3.

Characters are the stuff of systematics. At a general level, characters areused to quantify geographic variation, to investigate changes in organismal shapeduring both ontogeny and phylogeny, to describe variation in genotypes, and toelucidate the functioning of organisms from physiological to biomechanical toethological levels of organization. Characters are also used to distinguish taxa,without regard to relationships among the taxa.

But importantly, characters are evidence of descent with modification, andthey are the data by which we perform a phylogeneticanalysis, that is, the estimateof phylogenetic relationships among a series of organisms or taxa. Although aphylogeny exists whether or not we can recover it, we cannot recover it withoutcharacters.

Phylogenetic analysis proceeds by assembling data on characters that varyamong a group of organisms for which we want to infer relationships. This isusually done by assembling a character-by-taxon (or organism) data matrix. Thischapter is concerned with the theory, assumptions, and some practical aspects oforganizing characters for phylogenetic analysis.

The set of possible states of a character is called a transformationseries.Characters with only two defined states are called binary; those with more than twoare multistate. For multistate characters, a transformation series may be ordered orunordered. The distinction between ordered and unordered does not apply tobinary characters. For unordered states, any state may transform directly into any

other state (Figure 1). In contrast, ordered states have a determinate sequence oftransformation (Figure 1). Fully ordered states are arrayed in a linear series, andpartially ordered states can be visualized as a character-state tree (Figure 1).

In defining character states we assume that one state changes into another,both within a population and through evolutionary time. The state that existedearlier in time is said to be ancestral, primitivei or plesiomorphic relative to thederived or apomorphic state (nouns, plesiomorphy and apomorphy) into which itchanges. This directionality is the polarity. The ordering of a transformation seriesmust be carefully distinguished from the polarity of the series.

Ancestral and derived are relative according to the context of thetransformation. If state 0 changes to 1, then 1 is derived and 0 is ancestral. If state 1then changes to 2, then 1 is still derived with respect to 0, but it is ancestral withrespect to 2.

In conducting a phylogenetic analysis, we usually make an a priori hypothesisof character polarity, either explicitly or implicitly. There are several techniques fordetermining the polarity of a transformation series, such as outgroup comparison


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and the ontogenetic criterion. These are discussed in Chapter 5 under RootingMethods.

Assumptions About Characters

A primary assumption about characters in phylogenetic analysis is that theyare heritable; that is, they have a genetic basis and are passed on from ancestor todescendant. Some organismal characters are induced by the environment and arenot heritable. Many plants assume characteristic morphologies when grown undercertain environmental conditions. Common-garden experiments can be used to

Chap 4, Fig 1

Characters and Character-states

Transformation series

Ordered:

Unordered:

Partiallyordered:

0 1 2 3

A B C

0 1

2

A G

T C

0 1 23

4

Binary characters

Phragmoplast

0: Present1: Absent

Supralabial scales

A: 6 scalesB: 7 scales

Multistate characters

LDH-1 locusA: allele aB: allele bC: allele c

Eusociality

0: short-term monogyny1: long-term monogyny2: long-term polygyny

Site 215 of 16S rRNA geneA: adenineG: guanineC: cytosineT: thymine

Polarity

0 1 2

0

1

2

2

1

0

1

2 0

Unpolarized

Plesiomorphy

Apomorphy

Polarized


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distinguish between characters with a genetic basis and those induced by theenvironment.

A second assumption is that the states of a transformation series arehomologous. For the moment, let us consider homology to be similarity or identity

due to common ancestry. In the context of character states, this means that thefeatures examined among taxa are comparable in that all observed states of a specificcharacter were derived from a state in the last common ancestor of the taxa understudy. Homology is discussed below.

A third assumption is that the characters are independent of each other.Almost all systematists agree that characters should be independent, but twoworkers might substantially disagree on the interpretation of independence of twogiven characters. One possible definition of characterindependence is that theprobability of a character changing is not dependent on change in any othercharacter. That is, the characters are have independent genetic bases for their

expression. Character independence means that each contributes distinctinformation about phylogeny. Demonstrating independence or nonindependenceis not always straightforward. Nonindependence can be thought of as an intrinsicrelation between characters, without reference to a phylogeny. Becausenonindependence exaggerates the amount of phylogenetic information, we cancorrect for nonindependence by downweighting those characters. Some causes ofnonindependence are genetic correlations due to linkage, developmental/functional constraints, such that one character cannot change without effectingchange in a second character. For example, the secondary structure of certain rRNAmolecules can produce nonindependence among nucleotides in the stem regionsbecause of hydrogen bonding between segments of the stem. A mutation in one

nucleotide forces a change in its partner in order to maintain Watson-Crick pairing.Another cause of nonindependence lies in the definition of the characters. Ifcharacter A is the presence/absence of a tail in a species of bird, and character B is thecolor of the tail if present (red or blue). It is clear that the color of the tail is notindependent of its presence. However, this type of nonindependence is trivial inthat it is easily fixed by redefining the character or weighting the two charactersappropriately.

The concept of character independence is easily and often confused with orcharactercorrelation or covariance, which is best thought of as an a posterioristatistical phenomenon, given a particular phylogeny. For example, selection may

cause two independent characters to covary significantly. Several unrelated lineagesof lizards are fossorial and share two features: reduction of limbs and an increase innumber of vertebrae. A priori there is no developmental or functional reason toexpect a relationship of limb reduction and trunk elongation. However, given thatknowledge of the phylogeny informs us that these two characters have appearedtogether several times, the appropriate statistical analysis (e.g., W. Maddisons [1990]correlated-changes test; see Chapter 7) that takes phylogeny into account wouldindicate that these two characters are significantly correlated. However, if these


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various lineages were in fact a single clade, the association of limb reduction andincrease in vertebral number would not be significant.

Homology

Homology, like many other concepts, has been so variously employed that itsmeaning is unclear when used out of context. Sir Richard Owen (1843) first used theword homolog as the same organ under every variety of form and function. Thisis the classical use of the concept of homologyan essential similarity in structure,position, and development.

In a phylogenetic context, homology can be defined as identity, similarity orcomparability due to common ancestry. Two features in different taxa arehomologous (noun, homologs) if their similarity (comparability) derives from therelationship of common ancestry. Homology is both the concept and an instance ofthe concept. When one posits a homology between two features, one is said to

homologize the states.The term "identity" does not need explanation, but we should examine what

we mean by similarity or comparability. Let us posit that the similarity of the eyesof a squid and the eyes of a bony fish is homologous. We can test this hypothesis byexamining the distribution of this character on a phylogeny (assuming we have awell-supported tree of the relevant groups). Doing so indicates that the commonancestor of a squid and bony fish did not have eyes, and therefore eyes are nothomologous in these two groups. In this case similarity was not indicative ofcommon ancestry. Likewise, we can score a particular allelomorph observed in twotaxa as b based on the similarity in their mobility on a starch gel; this hypothesis ofhomology can be similarly testedii. If allele b is inferred to be continuously presentback to the common ancestor of the two taxa, then the allele is homologous in thosetwo taxa.

Homology can also exist between two apparently dissimilar features that arein fact comparable (the same in some sense) at a more general level, because they aremodified forms of a feature found in the common ancestor. For example, the stapes(middle ear bone) of a turtle and the hyomandibula (cartilage that supports the jaws)of a shark are not very similar, but they are homologous at a more general level,because both are modified forms of the first branchial skeletal arch present in theircommon ancestor. A related example in molecular systematics concerns thealignment of two nucleotide sequences. Given these two aligned sequences:

ACCTTTCGCA Taxon 1

ACCTATCGCA Taxon 2

There is certainly no similarity between the A and T at position 5.Nonetheless, these two states are comparable and homologous in that they are states


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of the character position 5 and one or both of them evolved from an ancestralstate at position 5.

One could argue that the notion of comparability is simply similarity at amore general level. We agree, but we include the notion of comparability because

the similarity of two homologous states is not always apparent, whereas the notionof sameness is.

Synapomorphy

The special similarity that is due to common ancestry is calledsynapomorphy. Consider Figure 2b. A and B share state 1, which is inherited fromtheir common ancestor. Therefore, the similarity of A and B is homologous.However, state 0 is present in C and in the ancestor of A, B, and C. State 1 is derivedrelative to state 0, and state 1 unites the monophyletic group A, B, and theirancestoriii to the exclusion of other taxa. Therefore, we say that state 1 is asynapomorphy (a shared, derived character state) of A + B. A and B are said to besister-groups: two terminals that share an ancestor that is not shared by any otherdescendant. We say that synapomorphies diagnose monophyletic groups, and thetopology of a cladogram, then, can be inferred by nested sets of synapomorphies.

Autapomorphy

Although a synapomorphy is evidence of the monophyly of a group, it givesno evidence of the relationship of that group to others. If the monophyly of thegroup is not at issue, the synapomorphy is termed an autapomorphy. To be precise,we should say that the presence of seeds is a synapomorphy of angiosperms andgymnosperms, but an autapomorphy of the Spermatophyta. In practice, we often

speak of seeds as a synapomorphy of Spermatophyta, when what we mean is thatthe presence of seeds unites angiosperms and gymnosperms into a monophyleticgroup. Species are usually considered to have an autapomorphy rather than asynapomorphy of the individual organisms. The important point is that anautapomorphy gives no information about the relationship of its taxon to othertaxa.

Fig. 2 here

Symples iomorphy

In Figure 2c, A and B share state 1 of a second character, but so does C. Thetransformation from 0 to 1 occurred at a lower level of the tree, and the presence of 1in A and B does not diagnose that group to the exclusion of C; in other words, state 1says nothing special about the phylogenetic relationship of A and B. Rather, itmakes a statement of relationships at a broader level: A, B, and C are more closelyrelated to each other than to any other taxon. Within the clade A, B, and C, 1 is a


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Chap 4, Fig 2

A B C

X

Y

(a) (b)

1 0

1

0

1 0

0

D

Z

(c)

1 1

1

1

1 0

0

A B C D

State 1 ofcharacter 1

State 1 ofcharacter 2

(d)

Character 1

Character 2

Synapomorphy

Synapomorphy

Symplesiomorphy

(e)

1 2

1

1

1 0

0

Character 2

Synapomorphy

Symplesiomorphy

plesiomorphic state shared by A and B, and is thus called a symplesiomorphy of Aand B (as well as of A + C or B + C). The designation of state 1 as a synapomorphy orsymplesiomorphy depends on which hierarchical level of the tree is considered.Symplesiomorphy is a relation of homology, because the similarity derives fromcommon ancestry.

A synapomorphy at a particular node of a tree is always a symplesiomorphy ata more restricted (higher) level; thus synapomorphy encompasses the notion ofsymplesiomorphy. For example, the presence of tracheids is a synapomorphy of thetaxon Tracheophyta (gymnosperms and angiosperms), but a symplesiomorphy ofAngiospermae, which is a clade within Tracheophyta. The question is not so muchwhether a character is synapomorphy or symplesiomorphy, but rather at what levelin the tree is this character a synapomorphy.

Consider the case in which state 1 further transforms to state 2 (Figure 2e).Although state 1 remains a synapomorphy of A, B, and C, it is only apparent in A

and B; C possesses the more derived state 2. The similarity of A and B is due tosymplesiomorphy, and givesno special evidence of therelationships of A and B. Inother words, one cannotconclude that A and B aresister-groups solely on the basisof having character 1.However, the similarity of state1 in A and B is homologousbecause it was present in the

ancestor of the two taxa, but itis plesiomorphic similarity.

Homology, then,encompasses both the conceptsof symplesiomorphy andsynapomorphy. As Eldredgeand Cracraft (1980:37) statedSynapomorphies are sharedsimilarities (homologies)inherited from an immediate

common ancestor;symplesiomorphies are sharedsimilarities (homologies)inherited from ancestors moreremote than the immediatecommon ancestor. However,some cladists (Nelson, 1989;Patterson, 1982, 1988) use


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Chap 4, Fig 3

A B C

X

Y

(a) (b)

0 0

0

0

1 1

0

D

Z

(c)

Convergence Convergence

1 1

1

1

0 1

1

Reversal

0

0

E

0

0

homology as an exact equivalent of synapomorphy, and exclude the concept ofsymplesiomorphy from homology.

Homoplasy

If similarity inherited from a common ancestor is homology, then similaritynot inherited from a common ancestor is homoplasy. In Figure 3, A and D share astate 1, but state 1 is not present in the common ancestor. Thus, we say that state 1 isa homoplasy, or is homoplastic. Homoplasies are of two types; the independentevolution of similar states that are not present in the common ancestor is calledconvergence or parallelismiv.

A second type of homoplasyis the reversal of a derived state toone that is apparently, but notreally, plesiomorphic, as in Figure

3c. Taxon E has the primitive state0, and B, C, and D have the derivedstate 1, but in A, 1 has reversed to0. The homoplastic similarity of Aand E is due to reversal. State 0 isplesiomorphic in A, butapomorphic in E. In cases ofreversal, the nonhomologoussimilarity was acquired only in onelineage (taxon E in this example),whereas in convergence, the

similarity was acquired in two ormore lineages.

In a comparison analogous to that of symplesiomorphy and synapomorphy,we can see that a feature that is convergent at one level is synapomorphic at eachmore restricted level at which it appeared. Conversely, a synapomorphy may be (butis not necessarily) a convergence at a more general level. When comparing birds toother tetrapods, the wing (defined as a forelimb modified for flight) is asynapomorphy of Aves (birds); Similarly, the wing is a synapomorphy forChiroptera (bats). When comparing the presence/absence of wings in birds, bats,and other amniotes, wings are convergent in birds and bats.

The three types of similarity correspond, not coincidently, to the three classesof taxa discussed earlier. A monophyletic taxon is diagnosed by synapomorphies. Aparaphyletic group is usually formed on the basis of symplesiomorphy; the taxa aregrouped because they share primitive states, but these states give no special evidenceof relationship. In both paraphyletic and monophyletic taxa, the similarity shared bythe members is homologous. A polyphyletic group is united by a state that wasinitially believed to be homologous (i. e., a synapomorphy), but which upon further


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study proved to be homoplastic, usually due to convergence. Thus, polyphyletictaxa are a mistake; no systematist sets out to erect polyphyletic taxa. AlthoughHennig (1966) made the conceptual link between the three types of similarity andthree classes of taxa, it was later demonstrated (Farris, 1975) that the termsmonophyly, paraphyly, and polyphyly are better defined by reference to taxa rather

than to defining characters. Paraphyletic and polyphyletic taxa are closely associatedwith the evolutionary idea of grades and adaptivezones. That is, the justificationfor the nonmonophyletic taxon was that it conformed to some level of evolutionaryorganization, such as overall similarity.

Tests of Homology

At this point, it might seem that homology is a circular concept; that is, we saythat states of a transformation series are homologous, but the very act of definingthe states as part of the same series implies that we believe them to be homologous.

The initial test of homology is almost intuitive: we hypothesize features to behomologous if they share a similarity or correspondence of some sort. If they lackthis basic similarity, the features are rejected as worthy of further consideration. Wemight ask Are the eye of cat and the ear of a dog homologous? The answer wouldbe a perfunctory no. We also might ask Is the shark hyomandibula homologouswith the stapes of a mammal? A no in this case would be wrong.

Several criteria have been used to posit homology on the basis of similarity(Remane, 1956; Wiley, 1981); these have the same common theme of similarity ofposition or relation to other characters. Structures that are in the same topographicposition and/or bear the same relation to other body parts can be hypothesized to behomologous. Although the classic criteria of homology were formulated foranatomical structures, they apply equally to other types of data. For example, in theabsence of other information, the amino acids or nucleotides at position 20(compared among taxa) would be hypothesized to be homologous. Likewise, thebands on an allozyme gel that have migrated 5.2 cm from the origin would be scoredas allele a , and therefore, hypothesized as homologous.

It is possible that true homologs may fail the test of similarity, if the level ofsimilarity is not readily apparent. For example, the level of similarity may be at amore general ontogenetic level than the observer recognizes. Based on thedissimilarity of adult structure, one might reject the homology of the hyomandibulacartilage (part of the upper jaw) of a shark and the stapes (ear bone) of a turtle. But ifone dissects their embryos and observes that the element that articulates with thepalatoquadrate cartilage develops into the hyomandibula in the shark and the stapesin the turtle, then the test of similarity is passed, and a hypothesis of homology canbe made.


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Having passed this initial test of similarity, the next test is that ofconjunction. If two supposed homologs are found in the same organism, then theyare not homologous. Were we to dissect a turtle (or a shark) and find ahyomandibula and an stapes, we would reject the homology of the two elements.Likewise the wings of angels can be rejected as homologous with the forelimbs of

tetrapods because angels possess both.

The third, and most crucial, of these tests is that of congruence. To reject themonophyly of a clade, one must demonstrate that another postulated clade isincongruent with it (two taxa are congruent if one is a subset of the other, or if the

taxa are the same). Because synapomorphies are the primary evidence ofmonophyly, it follows that the test of a synapomorphy must be othersynapomorphies. Therefore, the test of congruence is this: if the distribution of aputative synapomorphy diagnoses a taxon that is congruent with othersynapomorphies (and their taxa), then that synapomorphy is corroborated. If thetaxon specified by the putative homolog is not congruent with other taxa, then thatfeature is rejected as a synapomorphy at that level .

If a presumed homology passes all three tests, then we conclude that it is atrue homology or synapomorphy. But what if one of these tests is failed?

Failure of the test of similarity is often trivial; if two features are different,then one likely is comparing two features that ought not to be compared, such as thewing of a housefly and the wing of a sparrow. The similarity of these structures issuperficial and the convergence easily detected after a brief study of the organisms.The relation is this termed two homologies or convergence. In other cases inwhich the similarity is not immediately evident (such as the example of the shark

Tests of Homology

Similarity

Yes

Yes

No Two homologies"Convergence"

Type of Relation

Morphological Molecular

Two orthologies

Begin

Chap 4, Fig. 4

Conjunction No Homonymy Paralogy

Congruence No Homoplasy Xenology

Yes

Homology Orthology


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hyomandibula and turtle stapes), failure would cause one to reject the hypothesis ofhomology when it was true. If one is predisposed to look for differences rather thansimilarity, the possibility of wrongly rejecting the hypothesis of homology is high.

Failure of the test of conjunction yields a relation known as homonymy in

morphology (or paralogy in molecular biology; see below). This is the repetition ofmany copies of the homolog in a single individual, anatomical plurals vs.anatomical singulars (Riedl, 1979) as in the case of hair or blood cells in a mammal,or leaves on an oak tree. Homonymy owing to metamerism or segmentation of theorganism is called serialhomology.

Serial Homology

The term is useful to describe the relation of metameric anatomical parts thatare dissimilar, such as antenna, mandible, maxilla, maxilliped, cheliped, andswimmeret of Crustacea; these are all serial homologs. This usage of the wordhomology has no phylogenetic connotation; a maxilliped in an individualcrayfish is serially homologous with the mandible, maxilla, etc., in the sameindividual, not with those in other individuals. However, the first maxilliped ishomologous (presumably) with the first maxilliped in other taxa of crustaceans.Homology as used to describe homologous chromosomes is also serial homology.

Serial homology is the rule rather than the exception in plants, which areinherently modular organisms. Whereas animals generally have a single, complexpattern of cell morphogenetic movements, the processes of cell division anddifferentiation are repeated over and over in the multiple units that comprise anindividual plant (Mishler, 1988). This may render the conjunction test less usefulin plants than in animals.

Failure of the test of congruence is a decisive rejection of an hypothesis ofhomology; i. e. that the feature is not synapomorphic at the level tested . If thehomology proves to be synapomorphic of a larger, more inclusive group, then it is asymplesiomorphy at the level originally tested. If the putative homology wasshown to be synapomorphic of a more restricted set(s) of taxa, then it is homoplastic(convergent).

Homology in a molecular context

The terms used to express of similarity of molecular sequence data have been

particularly troublesome. Homology was originally used in molecular biology toindicate overall similarity in sequences of amino acids or nucleotides, regardless ofancestry, and it was common to speak of two proteins sharing 30% homology. Tobring the terminology more into line with evolutionary thinking, Fitch (1970)introduced the term orthology to indicate sequence similarity due to commonancestry of taxa. Two orthologous sequences can be considered homologous in thatthey are corresponding sets of homologous characters. A molecular sequence is astring of characters that can be treated as a larger character, just as a group of


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topographically related morphological characters can be considered as a single, largercharacter (as in the case of the phalanges, carpals, radius, ulna, and humerus makingup the tetrapod forelimb). By extension, the alpha hemoglobin genes in two speciesare homologous, as are the linkage groups and the chromosomes.

Fitch (1970) also introduced the term paralogy to indicate similar sequencesthat have arisen via gene duplication; it is the relation between genes of the samegene family. Paralogy is roughly the molecular equivalent of homonymy, exceptthat homonymy arises by duplication of structures in ontogeny, and paralogyderives from gene duplication in phylogeny (Patterson, 1988). Like homonymy,paralogy passes the test of similarity but fails the test of conjunction; one canobserve, for example, a and b hemoglobin genes in the same organism. Geneduplication events represent the origin of new taxa of genes, and the phylogeny ofa gene can be reconstructed from characters taken from paralogous sequences.However, to reconstruct the phylogeny of taxa, orthologous sequences must be used.

Are paralogous genes homologous; i.e., do they indicate common ancestry?Because homology is about common ancestry, the term is applicable to many typesof individuals (in addition to taxa) that undergo descent with modification---genes,chromosomes, mitochondria, chloroplasts. Paralogous genes owe their similarity toan ancestral gene, not an ancestral taxon. The a hemoglobin sequence of taxon Amay be very similar to the b hemoglobin sequence of taxon B, but the similarity isnot due to taxic but rather gene homology; the phylogeny of genes is not necessarilyconcordant with the phylogeny of taxa. Therefore, similarity of paralogous genes ishomology in if one is concerned with the phylogeny of the genes. However,paralogous genes are not homologous when one is interested in the relationships oftaxa.

The term isology (Wegnez, 1987) has been used to indicate overall similarityof sequences, regardless of whether the similarity is based in common ancestry.Both paralogous and homologous sequences are isologous.

Xenology is a term introduced by Gray and Fitch (1983) to reflect similarity insequences due to the acquisition of foreign genes (lateral gene transfer throughretroviruses; symbiosis, endoparasitism). Although the similarity of the sequencesderives from common ancestry (homology), a phylogeny of taxa based on sequenceswill be incongruent with phylogeny based on other sources of data, and theincongruence will be reflected as homoplasy.

The word homologous is used in other senses in molecular biology. Amolecular probe is homologous if it is used in the same species from which it wasderived, and heterologous if used to probe the truly homologous sequence inanother taxon. The chromosomes of a pair of chromosomes in a diploid organismare called homologs, while the truly homologous pair in another taxon are calledhomoeologs.


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Coding Characters for Phylogenetic Analysis

Optimality Criterion

Phylogenetic analysis amounts to estimating evolutionary relationships, in

the form of a tree or a set of trees, by using a data set, in most cases a data set fromcharacters. Given that there are many possible trees for a set of terminals, it is usefulto have an optimalitycriterion by which we can select one tree over others. Becauseoptimal tree is only meaningful in the context of particular set of data, we must beexplicit about how an optimal tree is selected. That is, we must have explicitassumptions or models about how characters change, even if those assumptions areminimal.

If we knew exactly how characters evolve, and if we had enough data, wecould theoretically estimate the phylogeny without error. But this is seldom thecase. Fortunately, the methods of analysis are often robust to slight violations of the

model.In anticipation of the next chapter, in which methods of phylogenetic analysis

are treated, we will here discuss ways of preparing character data for phylogeneticanalysis under a relatively simple optimality criterion, that of maximumparsimony. Under this criterion, the most-parsimonious tree (shortest) is one thatminimizes the number of evolutionary steps (changes from one character state toanother) in the entire data set. (For the moment, we will ignore the issue of howone finds the most-parsimonious tree out of all the possible trees).

Models of Character Change

Quantifying the number of evolutionary steps directly depends on a model ofcharacter evolution or character-state change. Perhaps the simplest situation is thatof a binary character, say with states A and B. We can write this more formallyusing a step matrix or cost matrix.

To: A BFrom: A -- 1

B 1 --

The matrix is read as: From (a state in the vertical array) to (a state in the horizontalarray). This particular matrix says that a change from A to B counts as 1 step, andthe reverse change is true as well. In other words, the distance between states A and

B is 1.

Unordered characters

Now, consider a slightly more complicated case of the four possiblenucleotides (A, C, G, T) at a particular site, in which we assume that any nucleotidecan change or reverse to any other, with equal probability. This is written as:


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A C G TA -- 1 1 1C 1 -- 1 1G 1 1 -- 1

T 1 1 1 --

This step matrix defines an unordered character. It also defines a particular modelof character change called Fitch parsimony, after Walter M. Fitch, molecularevolutionist.

Ordered characters

Another commonly used model of character evolution is that of an orderedcharacter, in which the states are arrayed in a linear series, and change from onestate to another requires passing through any intermediate states. The model iscalled Wagner Parsimony, after the noted fern systematist, Herb Wagner. Let usimagine that there are three discrete conditions of the eyes in a group of cavecrayfishes: 0: Eyes present, of normal size; 1: Eyes present, but reduced in size; 2: Eyesabsent.

Say we assume that before a crayfish can lose its eyes, it must reduce them, inan evolutionary sense. So, loss must occur in the sequence 0 --> 1 --> 2. Further, wealso assume (perhaps naively), that the reverse sequence is also required to go fromstate 2 to 0: 2 --> 1 --> 0. The change matrix that reflects these assumptions is:

0 1 20 1 21 1 12 2 1

Irreversible characters

Suppose in the crayfish eye example, we have new evidence fromdevelopmental research that reduced eyes cannot be re-evolved from no eyes, andthat normal eyes cannot be re-evolved from reduced eyes. We can incorporate theseassumptions as follows.

0 1 20 1 21 12

The symbol means that the change in the indicated direction is not possible.This general model of change is called irreversible.


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Dollo characters

In another scenario, we assume eyes are either present (1) or absent (0), andthat the absence of eyes is plesiomorphic. We further assume that the complexity ofthe eye makes it very unlikely that eyes evolved more than once. This character

model is called the Dollo character model:

0 10 1 W1 1

Here, W is a large weight or cost that is applied to the change from eyes absent toeyes present. The magnitude of W makes it unlikely that the gain of eyes will occurmore than once, but the loss of eyes (several) is much more likely. It is important tokeep in mind that these step matrices are essentially hypotheses of how characterschange, and that one can discover that a particular model does not reflect whatreally happens.

Triangle Inequality

Whatever the model of change used in the step matrix, it is important thatthe distances obey the triangleinequality. This property derives from Euclideangeometry, in which the length of one side of any triangle must be less than the sumof the lengths of the remaining sides. Here, distance between any two statesrepresents the length of one side of the triangle. In order for the step matrix to obeythe triangle inequality, a distance between two states cannot be greater than the sumof the distances from those two states to a third state. The matrix below violates thisproperty because 5 is greater than 2 + 1.

0 1 20 5 21 5 12 2 1

Ordering Character-states

The idea of ordered states can be extended so that states are defined as a

character-state tree. This tree specifies the path along which states can evolve. Acost for the change from one state to another can be specified, so that character-statetrees are readily convertible to step matrices and vice-versa.


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A B C D E FA 1 1 2 3 4B

C 1 2 1 2 3D 4 5 3 1 2E 5 6 4 1 3F 5 6 4 1 2

Because the information in ordered characters and character-state trees ishierarchical, they can be decomposed into binary characters. This is only possiblewhen there are no cycles (complete loops) in the character-state tree. An example ofthis is shown below. This may be useful in cases where data matrices must be in abinary format.

Some have argued that all multistate characters should be coded as unorderedin order to minimize assumptions about the evolutionary process. In other words,acceptance of parsimony as a scientific methodology leads one to invoke only thosead hoc hypotheses of change that are absolutely necessary.

Unordered and ordered characters behave differently in phylogenetic analysis.Suppose that a tree has four terminals, each with a different state: 0, 1, 2, and 3. Ifthe states are ordered 0, 1, 2, 3, then one of the three unrooted trees is the best fit,with three steps, but the other two trees require four steps. However, if the states areunordered, then all three possible trees of equal length, 3 steps. A simple extensionof this example will demonstrate that when each terminal has a different state,ordering the states will yield 2n-3 equally most-parsimonious trees, and treating thestates unordered will yield as many equally parsimonious trees as possible trees!What this extreme example indicates is that unordered states have minimal powerto distinguish among possible trees.

A number of criteria for ordered states have been proposed.

1. Definition of the states. Perhaps the best reason for ordering states is thatthe definition of the states logically requires it. Consider the character eyes in

A

B

C D

E

F1

1

13

21

1 1

1

Chapter 4, Fig. 5


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which the states are A: eyes red, B: eyes orange, C: eyes absent. Treating these statesas unordered means that a possible transformation is that C gives rise to A and Bindependently, meaning that eyes arose at least twice in the group, and therefore arenot homologous.

Another example is in continuous characters.2. Similarity (morphocline analysis). States are ordered such that the amount

of change among the states (usually morphological) is minimized. Such orderingassumes that change is gradual, by small steps, so that one must pass through anintermediate state to reach another state. Ordering according to a morphocline isproblematic if there is no explicit algorithm for minimizing the amount of inferredchange. Many morphoclines might be equally reasonable. [The fossil record is oftenused as evidence for the existence of morphoclines.]

3. Ontogeny. Say that one observes the following states in the adults ofvarious species: The use of ontogeny assumes that ontogeny reflects phylogeny insome way. One must implicitly accept Haeckelian or von Baerian recapitulation(see Wiley p. 155).

4. Polymorphism. Suppose a terminal is polymorphic for two character-states, as when some species are fixed for allele a (state 0), others are fixed for allele b(state 2), and others species have both alleles a and b (state 1). Therefore, one canorder the states 0 --> 1 --> 2.

5. Correlation with trends in other characters. Patterns in digit loss, body sizereduction. This assumes a priori there is uniformity in the pattern.

6. Stratigraphic distribution.The stratigraphy to order character states meansthat one accepts the stratigraphic record as an extrinsic source of information aboutevolutionary change (Develop this further).

7. Transformation series analysis. This is an iterative procedure that seeks thecharacter-state tree that best fits a cladogram. If the character-state tree does not fitthe cladogram, then the initial character-state is replaced by the one that does.


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Literature Cited

Eldredge, N., and J. Cracraft. 1980. Phylogenetic patterns and the evolutionaryprocess. Columbia Univ. Press, New York. pp.

Farris, J. S. 1975[1974]. Formal definitions of paraphyly and polyphyly. Syst. Zool.23:548-554.

Fitch, W. M. 1970. Distinguishing homologous from analogous proteins. Syst.Zool. 19:99-113.

Gray, G. S. and W. M. Fitch. 1983. Evolution of antibiotic resistance genes: TheDNA sequence of a kanamycin resistance gene from Staphylococcus aureus .Mol. Biol. Evol. 1:57-66.

Hennig, W. 1966. Phylogenetic Systematics. Univ. Illinois Press, Urbana, Illinois.

pp.

Maddison, W. P. 1990. A method for testing the correlated evolution of two binarycharacters: are gains or losses concentrated on certain branches of aphylogenetic tree? Evolution 44:539-557.

Mickevich, M. F., and S. J. Weller. 1990. Evolutionary character analysis: tracingcharacter change on a cladogram. Cladistics 6:137-170.

Mishler, B. D. 1988. Relationships between ontogeny and phylogeny, with referenceto bryophytes. Pages 117-136 i n Ontogeny and Systematics (C. J. Humphries,

ed.).

Owen, R. 1843. Lectures on comparative anatomy and physiology of theinvertebrate animals, delivered at the Royal College of Surgeons in 1843.Longman, Brown, Green, and Longman, London.

Panchen, A. L. 1994. Richard Owen and the concept of homology. Pages 21-62 i nHomology: The hierarchical basis of comparative biology (B. K. Hall, ed.).Academic Press, New York.

Patterson, C. 1982. Morphological characters and homology. Pages 21-74 i nProblems of phylogenetic reconstruction (K. A. Joysey and A. E. Friday, eds.).Academic Press, London.

Patterson, C. 1988. Homology in classical and molecular biology. Mol. Biol. Evol.5:603-625.

Remane, A. 1956. Die Grundlagen des naturlichen systems der vergleichendenAnatomie und Phylogenetik. Geest und Portig K. G., Leipzig. pp. [check thisone]


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Riedl, 1979

Wegnez, M. 1987. Letter to the editor. Cell 51:516.

i Primitive has the unfortunate connotation of inferiority or less desirable.

ii How one does this is discussed in detail later.

iii It is implicit here and elsewhere in the book that a synapomorphy of a monophyletic group ofterminals also applies to the ancestors. When only the terminals of a monophyletic group arementioned, it is implied that the ancestors are included.

iv Some workers distinguish these two, but for our purposes they are the same.

evolutionary biology 2000 - system a tics, character, homology

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