TABLE OF CONTENTS          

I. The Methods of Molecular Phylogenetics

• Molecular phylogenetics refers to any method of inferring evolutionary relationships from similarities or differences in molecular structure.
• Molecular characters suffer from problems that also afflict morphological characters. For example, neither molecules nor morphology may be able to resolve the phylogeny of evolution that was both ancient and rapid, as in the Cambrian Explosion.
• Another problem shared by molecular and morphological characters is homoplasy (nonhomologous characters appearing to be similar in different taxa).
• Other problems shared by molecular and morphological phylogenetics arise from polymorphism (homologous characters appearing differently in the same species). Because of polymorphism, the time of divergence may appear to be earlier than it was.
• Polymorphism can also result in the incorrect phylogenetic sequence.
• Similar problems result from different copies of duplicated genes.
• Another problem with molecular phylogenetics is long-branch attraction: the tendency of fast-evolving molecules to appear more closely related than they actually are.
• Molecular phylogenetics has gained wide acceptance in spite of these and other problems because it provides a large amount of evidence that is independent of morphology, as well as other advantages.
• Several kinds of experiments support the validity of molecular phylogenetics.
• Molecular characters can be of two types: discrete (qualitative) differences in molecular sequence and continuous (quantitative) distance between molecules.
• The first step in molecular phylogenetics is to select a suitable molecule that is homologous in all the taxa to be included in the phylogeny.
• Many molecular characters are much less susceptible to homoplasy and long-branch attraction than are nucleic-acid sequences. These characters include amino-acid sequences, the positions of short and long interspersed elements, and Hox genes.
• Elongation factors, actin, and tubulins are among the widely used proteins.
• The positions of short and long interspersed elements (SINEs and LINEs) are another increasingly common source of discrete characters.
• Hox genes have also been used to infer phylogenetic relationships.
• The most commonly used molecular data for higher taxonomic levels are base sequences from genes that encode ribosomal RNA, especially 18S rDNA.
• Nucleic-acid sequences must be aligned before they can be compared.
• Assumptions may be needed about the probabilities of different molecular changes.
• Molecular relationships are represented as trees constructed of branches with nodes at both ends of each branch.
• Inferring (reconstructing) a phylogeny consists of creating or selecting one tree out of perhaps millions of possible ones.
• The neighbor-joining method (NJ) is an algorithm that generates one tree with the shortest total branch length.
• The maximum parsimony method (MP) selects the cladogram with the minimum number of changes in character state.
• The maximum likelihood method (ML) begins with an explicit model of evolution and possible trees, then it attempts to find the tree that is most likely with the given data.
• With more than a few taxa, any method requires a computer.
• To show the temporal sequence of divergence, trees have to be rooted. The root represents the most recent common ancestor of the study group.
• For convenience in printing large trees, branches are often represented as horizontal lines joined by vertical lines representing internal nodes. Branches may be unscaled, or they may be scaled according to a distance measure.
• Phylogenies reconstructed by different methods are generally similar to each other.
• Confidence in an internal branch can be tested by bootstrapping.
• A branch with low bootstrap support may be collapsed. A consensus tree can be created by collapsing branches that are not supported in all trees created by different methods of analysis.
• A consensus tree can also be produced by comparing molecular and morphological trees.
• Molecular and morphological data can be combined to create a "total-evidence tree."
• Because of long-branch attraction, differences in sequence alignment, limitations in the size of study groups, and different methods of tree reconstruction, conflicting molecular phylogenies have been proposed. As techniques have improved and more molecules from more species have been sequenced, many of the past conflicts have been resolved.

II. Testing the Validity of Traditional Morphological Characters by Seeing Whether They Are Consistent With Molecular Trees

• To be consistent with a given phylogenetic tree, a character must map onto the tree with few changes in character state.
• For example, bilateral symmetry is consistent with the traditional morphology-based cladogram for the Big Nine phyla (those with more than 5,000 named species), since it requires only one change in character state.
• Segmentation, however, is less consistent with traditional morphology based phylogenetic trees, because it requires at least two changes in character state: one for annelids and arthropods and one for chordates.
• Lack of consistency implies that either the character is not synapomorphic (homologous), or the phylogenetic tree is incorrect.
• A character that is consistent with both a morphological and a molecular phylogeny is more likely to be phylogenetically informative.
• Morphological characters have not led to a consensus phylogeny.
• The following morphological characters traditionally used in phylogenetics are also consistent with the widely accepted molecular phylogenetic tree of the Big Nine Phyla: bilateral symmetry and triploblasty, deuterostomy, and spiral cleavage pattern.
• Bilateral symmetry and triploblasty are also consistent with a molecular phylogenetic tree that includes all animal phyla.
• Deuterostomy in Echinodermata, Hemichordata, and Chordata is also consistent in a molecular phylogenetic tree of all animal phyla.
• The spiral-cleavage pattern is somewhat consistent with a molecular phylogenetic tree that in-cludes all animal phyla.
• The lophophore by itself is not consistent with a molecular phylogenetic tree, and it may not be a homology.
• The occurrence and type of body cavity (whether the animal is acoelomate, pseudocoelomate, or coelomate) is not consistent with the molecular phylogenetic tree and is not homologous.

III. Molecular Phylogenetic Trees as Alternative Hypotheses

• Protozoa are not monophyletic.
• Metazoans are monophyletic, and choanoflagellates may be their sister group.
• Myxozoans appear to be metazoans rather than protozoans.
• Mesozoans may be flatworms.
• Anthozoa appear to be basal within Cnidaria.
• Protostomates appear to be divided into two major clades: Ecdysozoa and Lophotrochozoa. Annelida and Arthropoda belong to Lophotrochozoa and Ecdysozoa, respectively, and are therefore not closely related.
• Ecdysozoa, the major protostomate clade that includes Arthropoda, also includes Nematoda and other groups with a cuticle that molts all at once.
• Arthropoda is monophyletic; Uniramia is not valid.
• Pentastomids are crustaceans.
• Lophotrochozoa, the major protostomate clade that includes Mollusca and Annelida, also includes other animals with trochophore larvae, the lophophorates, and all descendants from their most recent common ancestor. Lophotrochozoa includes spiralians.
• Flatworms appear to be lophotrochozoans rather than basal to other Bilateria.
• Acoela may or may not be basal to other Bilateria.
• Nemertea may be closer to "coelomates" than to flatworms.
• Gastrotrichs are not closely related to nematodes.
• Acanthocephalans are closely related to rotifers.
• Cycliophora appear to be related to rotifers.
• Echiura and Pogonophora may be polychaete annelids.
• Chaetognatha may not be closely related to other deuterostomates.
• Molecular evidence supports the conventional phylogeny of echinoderm classes.
• Concentricycloids may be asteroids.
• Hemichordata may be closer to Echinodermata than to Chordata.
• Vertebrates apparently did not evolve from an echinoderm.
• Cephalochordata, rather than Urochordata, may be the sister group of Vertebrata.
• Turtles may be the sister group of Crocodilia + Aves rather than basal Reptilia.
• Placental mammals may be divided into four superordinal clades.

IV. Incorporating Molecular Phylogenies Into Teaching

• The most important conclusions from animal molecular phylogenetics are that Bilateria (triploblasts) and Deuterostomia are each monophyletic, and protostomes comprise the two clades Lophotrochozoa and Ecdysozoa.
• The traditional approach of proceeding from the simplest animals to the more complex is pedagogically sound.
• The practice of treating the "acoelomates" and the "pseudocoelomates" together as clades outside of coelomates should be abandoned.
• More natural groupings would be Lophotrochozoa and Ecdysozoa.
• The following proposed sequence of topics is consistent with molecular phylogenetics without departing too radically from the traditional zoology syllabus.

GLOSSARY

REFERENCES

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