Cladistics [MT Dorak]

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CLADISTICS

M.Tevfik Dorak, M.D., Ph.D.

Definitions

clade: A group of organisms evolved from a common ancestor (from Greek klados meaning branch). An ancestor and all its descendants are called a clade. Clade is synonym of monophyletic group.

cladistics: A method of classification of animals and plants on the basis of those shared derived characteristics that were not present in their distant ancestors (synapomorphies) which are assumed to indicate common ancestry. It uses strict monophyly as the only criterion for grouping related species. In cladistic taxonomy, evolution is seen as a process of progressive bifurcations of lineages. Every species, therefore, has a sister species whether recognizable or not, and this pair derived from an ancestral species. Two taxa are more closely related to each other (sister groups) if they share a more recent common ancestor relative to a third. Anagenetic component of evolutionary change is ignored in cladistics. Cladistics is accepted as the best method available for phylogenetic analysis because it recognizes and employs evolutionary theory.

cladogram: The output as a branching diagram from a (cladistic) phylogenetic analysis postulating relationship of different taxa. All cladograms are hypothetical and none can be proved correct for sure. Among the alternative cladograms the one which is best supported by the character/sequence data is the most representative one.

cladogenesis: The evolutionary division (bifurcation) of lineages causing a proliferation of species.

anagenesis: Descent with modification within any given single lineage (change without speciation). Anagenetic changes create grade groupings (as opposed to clade groupings).

grades: A grouping of taxa which show similar modifications with respect to their ancestors. Grade taxa may be polyphyletic, paraphyletic or monophyletic. A paraphyletic taxon is the lowest grade in a phylogenetic tree (see below).

phylogeny: Evolutionary relationship that can be studied in three ways:

1. Phenetics (Mayr): Method of classification in which taxa are grouped together with other taxa that they most closely resemble phenotypically. It is based on overall similarity. It accepts all monophyletic, paraphyletic and polyphyletic groups. An important issue in the phenetic method is the question of measuring phenetic similarity (it is not objective). If molecular sequence data is used in phenetic analysis, stochastically constant rates of molecular evolution (the molecular clock theory) must be assumed if the phenogram is to be equated with a phylogeny. Pheneticists usually make no assumptions to distinguish sources of resemblance. Any similarity, whether symplesiomorphy or synapomorphy, is taken into account.

2. Evolutionary Systematics (an eclectic approach, Simpson). This is a synthesis of phenetics and cladistic principles. There is no single underlying method of analysis. It defines groups by homologies (although without distinguishing between primitive and derived homologies) and ignores analogies. (This method uses both paraphyletic and monophyletic groups but excludes polyphyletic groups.)

3. Cladistics (Hennig): Inferred recency of common ancestry. The members of a group in a cladistic classification share a more recent common ancestor with one another than with the members of any other group. Only monophyletic groups are used in this analysis. Cladists attempt to distinguish between symplesiomorphic and synapomorphic similarity and to identify clades on the basis of synapomorphs only. A cladogram shows only the hierarchical arrangement of increasingly inclusive synapomorphies observed in a set of compared taxa. A cladogram is not precisely equivalent to a phylogeny, because none of the compared taxa is recognized as an ancestor. The nodes can be treated as representing unknown ancestors.

plesiomorphy: A primitive (ancestral) character state (the original state of the characteristic). This character is present in the ancestor or in the outgroup.

Criteria suggesting primitiveness of a character:

1. Presence in fossils (paleontological antiquity),

2. Commonness in an array of taxa,

3. Early appearance in ontogeny,

4. Presence in an outgroup.

apomorphy: A derived or newly evolved (specialized, advanced) character state (the changed state of the characteristics). For example, presence of hair is a primitive character state for all mammals, whereas the hairlessness of whales is a unique derived state (autapomorphy) for one subclade within the Mammalia. The opposite of apomorphy is plesiomorphy (primitive character).

symplesiomorphy: A primitive character state shared by two or more taxa. The opposite of symplesiomorphy is synapomorphy.

synapomorphy: A derived character state shared by two or more taxa and held to reflect their common ancestry. This is the key in inferring relationships to common ancestry. It is not just the presence of shared characteristics that is important (as in phenetics) but also the presence of shared derived characteristics. Synapomorphies can be identified by the study of developmental patterns (ontogeny) or outgroup comparison.

autapomorphy: A derived character state unique to one taxon. A species with an autapomorphy is unlikely to be the ancestor of the other species in the clade on the grounds of parsimony. It is more parsimonious if it is the further evolved species (rather than the ancestor). The absence of autapomorphies allows the possibility of a species being directly ancestral to another.

monophyletic group: A set of taxa containing a common ancestor and all of its common descendants.

paraphyletic group: A paraphyletic group can be recognized from a cladogram as a group representing a primitive grade grouping and including some but not all of the descendants of a common ancestor. A paraphyletic taxon is united by common possession of shared primitive characters (symplesiomorphy) but not the derived (specialized) characters (synapomorphy), thus, those included in the paraphyletic group have changed little from their ancestor. In other words, a paraphyletic group lacks the derived character states of the other descendants. The taxa included in a paraphyletic group are those that have continued to resemble the ancestor; the excluded taxa have evolved rapidly and no longer resemble their ancestor. Among the lizards, crocodiles and birds, the reptiles (lizard+crocodile) are paraphyletic to birds. In determination of the evolutionary relationships, paraphyletic groups are best avoided as they convey no information. Paraphyletic grouping implies a closer relationship among the taxa within the group, but the descendants left out may be more closely related to a taxon in the paraphyletic group.

polyphyletic group: A set of taxa descended from different ancestors. The ultimate common ancestor of all taxa in the group is not a member of the group. A polyphyletic taxon assembles species with independently evolved similarities derived from separate ancestors. Birds and bats evolved to have wings but are not descendants of a common ancestor, thus, they form a polyphyletic group. Such taxa are rejected from modern systems of classification except phenetics.

sister species: taxa stemming from the same node in a phylogeny. They may be morphologically identical but will be genetically divergent.

homology: Similarity by common ancestry; a character shared by a set of species which was present in their common ancestor (a similarity in a character or sequence between two species may be due to homology 'evolutionary relationship' or analogy 'convergent evolution'). For a homology to become established, characters must also occur in the same topographical position within an organism and also agree with other characters (congruence) about relationship of taxa. If the structure has been modified through descent in one lineage (anagenesis), it may be difficult to establish homology. Homologies are divided into two groups: derived homologies are those unique to a particular group of species and their ancestors; ancestral homologies are found in the ancestor of a group of species and some, but not all, of its descendants. Recognition of homology becomes increasingly difficult with increased time since divergence.

analogy: Characters showing similarity due to convergence (as opposed to shared ancestry). Endothermy in birds and mammals is believed to be analogous.

homoplasy: The component of overall similarity due to convergence from unrelated ancestors. Repeated events in the evolution of a taxon that result in possession by two or more species of a similar or identical trait that has not derived from a common ancestor; A homoplastic character may arise from convergence, parallel evolution, or evolutionary reversal. Homoplasies create noise in cladistic analysis unless overcome by a large number of informative synapomorphies.

parallel evolution: The evolution of similar or identical features independently in related lineages, thought to be based on similar modifications of the same developmental pathways.

outgroup: A related taxon retaining many primitive characters and is believed to have a common ancestor more distantly in the past than the taxa being classified. Baboon or macaque are an outgroup to humans, chimpanzees and gorillas because they split off from the common ancestor of humans, chimpanzees and gorillas earlier. (A taxon that diverged from a group of other taxa before they diverged from each other.) The outgroup taxon is the least related one to the others in a group of taxa. Outgroup comparison of homologous sequences in cladistic analysis of molecular data is used to determine the primitive-derived polarity of alternative bases at a given position. A prominent danger in outgroup comparison of molecular data arises from the probability that some mutations (e.g., base substitutions) may be repeated and others reversed. This may brought about the appearance of plesiomorphy in lineages which in fact is doubly apomorphic. Presence in an outgroup is the best indicator for a character to be primitive.

coalescent (coalesce=unite into one whole): The approximated ancestral allele/ haplotype/ sequence in a cladogram from which all other alleles in the sample may have descended (the ancestral sequence). If a population remains intact, the average coalescence time is the substitution time for neutral alleles.

Principles of Cladistics

There are three basic assumptions in cladistics:

1. Any group of organisms are related by descent from a common ancestor,

2. There is a bifurcating pattern of cladogenesis,

3. Change in characteristics occurs in lineages over time. This is the most important and the least controversial assumption.

Hierarchic order in nature is manifested in the distribution of characters shared among organisms. Common ancestry is worked out from the number of synapomorphies among taxa. For any three taxa, two taxa are more closely related to each other if they share a more recent common ancestor relative to a third.

In a phylogenetic tree, it is assumed that all branches are dichotomous (not polytomic). A single ancestral lineage split to give rise to two descendants. It is also assumed that lineages split but never rejoin lineages (reticulation). These are unrealistic assumptions of cladistics which are violated in real life.

Methods in phylogenetic analysis

1. Analysis of character states: synapomorphies are the basis for cladistics. (A supposed synapomorphy should not be the result of independent evolutionary development!) The hypothesis of a fossil species being a direct ancestor may be rejected if it possesses autapomorphies.

2. Outgroup comparisons

3. Embryology: ontogeny recapitulates phylogeny, development proceeds from general to particular (systematic hierarchy).

4. Molecular sequence data: For a group of closely related organisms, one needs a rapidly evolving molecule that varies sufficiently within the group. Mitochondrial DNA (mtDNA) is a good example. It is abundant in the cell, therefore, easier to get hold of from some fossils; its inheritance is strictly maternal, its total sequence is known and short; and it does not cross-over (Y chromosomes do not cross-over either). For a more distantly related group, a slowly evolving molecule such as rRNA would be better. The more similar the sequence, the more recent we infer that the duplication event has occurred. The selection of unambiguously aligned DNA segment is essential to ensure homology in sequence comparisons. Chance matching in non-homologous alignments would confuse the cladistic analysis.

5. Area cladograms

Methods to construct an evolutionary tree (phylogenetic inference)

1. Maximum parsimony: The selection of the simplest phylogenetic tree requiring the least number of substitutions from among all possible phylogenetic trees as the most likely to be the true phylogenetic tree.

2. Maximum likelihood: For this method, protein sequences are much more reliable than the DNA sequences.

3. Neighbour-joining: A simplified version of the minimal evolution method. An evolutionary distance is computed for all pairs of sequences, and a phylogenetic tree is constructed from pairwise distances by using the smallest distances by inferring a bifurcating tree.

How to construct cladograms

1. Choose the taxa which are evolutionarily related,

2. Determine the characters,

3. Determine the polarity of characters (original or derived) by:

i. outgroup comparisons (primitive character),

ii. presence in fossils (primitive character),

iii. early appearance in ontogeny (primitive character),

iv. commonness in an array of taxa (primitive character).

4. Group taxa by synapomorphies not symplesiomorphies,

5. Work out conflicts that arise by some clearly stated method like parsimony (minimizing the number of conflicts),

6. Build the cladogram following these rules:

i. all taxa go to the endpoints of the cladogram, not at nodes (splitting