Chapter 10 - Classification and Phylogeny

Notes for Chapter 10:
Classification and Phylogeny of Animals

Click link to return to Lecture Schedule
back to Previous Chapter
or ahead to Chapter 6

Ch. 10: 196-207; RQ10: 2-7, 9
see here for help on RQ10:7

Introduction: Order in diversity
     Featured Animal: Cone shell,
          Conus sp.
(these are cool snails with deadly toxins - see one nail and devour a passing fish with its harpoon-like radular tooth by downloading the movie at link 8)
          Links: 1 - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 9

I. Linnaeus and the Development of Classification

Key Terms: hierarchical system, taxa (taxon), taxonomic ranks, binomial nomenclature, genus, species

A. Discovering pattern and classifying

1. Systematists have three goals:

a. discover all species
b. reconstruct phylogeny (genealogical relationships)
c. classify according to phylogeny

2. Taxonomy: system for naming and classifying
3. Systematics: includes taxonomy but also phylogenetic and evolutionary studies

B. Linnaeus and the Linnaen System

1. Classifying dates at least back to Aristotle in ancient Greece
2. John Ray (English) refined classification and notions of species
3. Current binomial classification system introduced by Linnaeus

a. Linnaeus was Swedish botanist whose specialty was flowering plants
b. His more ambitious Systema Naturae classified animals and plants

4. Linnaeus introduced concept of taxomic hierarchy (Table 10-1)

a. He had 7 major ranks: kingdom, phylum, class, order, family, genus, species.
b. Taxa (singular: taxon) are names at any rank (e.g., Animalia)
c. Today taxa are usually subdivided (e.g., superclass, suborder, etc.)
d. Some groups are divided into many levels (30 for insects)

5. Linnaeus introduced binomial nomenclature

a. Each animal name has two words (binomial) as in Turdus migratorius.
b. Genus is capitalized; species is lower case
c. By convention, always italics (Turdus migratorius) or underlined
d. Never use species name alone; always include genus
e. For animals, genus names must be unique
f. Higher-level taxa not italicized but capitalized (e.g. Reptilia).
g. Trinomial names sometimes used to indicate geographic subspecies

II. Taxonomic Characters and Phylogenetic Reconstruction

Key Terms: phylogeny, characters, homology, homoplasy

A. Using Character Variation to Reconstruct Phylogeny

Key Terms: ancestral vs. derived character states, polarity (the ancestral state is generally the one that is also present in the outgroup, by outgroup comparison), clade (ancestor plus all its descendents), synapomorphy (derived novelty that helps us recognize a clade, e.g., feathers in birds), plesiomorphy (ancestral or "primitive" state, not necessarily the most "simple" state), nested hierarchy, symplesiomorphic (shared "primitive" similarities - these do NOT help us recognize clades, e.g., lack of backbone in a fly and a snail), cladogram vs. phylogenetic tree (similar, but the "y-axis" of a cladogram means nothing, whereas it might in a phylogenetic tree, e.g., geological time) - Note: Don't worry, these terms are difficult at first and we will be reinforcing them over the entire semester -- See Cladogram Exercise 1.

1. Estimating a phylogeny depends on characters (traits)

a. only characters that vary are interesting
b. the different forms of the charater are termed states

2. One observes similarities that could be homologous

a. a homology is a similarity due to common ancestry
b. this means the common ancestor had the same state
c. a homologous similarity only has to evolve once

3. Alternatively, similarities might have evolved separately (convergently)
4. Any similarity not due to homology is termed a homoplasy (includes convergence)
5. The parsimony criterion is used to choose some trees as better than others

a. The most parsimonious tree explains as much as possible by homology
b. A tree is more parsimonious than another when it requires fewer changes
c. The most parsimonious tree is the one with the least homoplasy
d. This is because homoplasies require extra changes; homologies do not

B. Study of Character Variation Can Reveal Ancestral Conditions

1. Given a phylogeny, one can determine which character state is ancestral
2. The ancestral state of a character is the state found in the ancestor
3. Character states arising later are termed derived states
4. In practice, we cannot normally observe the common ancestor

a. Instead we use a closely related taxon as an outgroup to estimate ancestral state
b. We can also use multiple outgroups
c. Example: we observe no teeth in birds and teeth in lizards; which is primitive?

1) We note that outgroups (e.g., mammals, salamanders and fish) all have teeth
2) Thus, the common ancestor of birds and lizards probably had teeth
3) Thus, the presence of teeth in lizards is a primitive state
4) Thus, the lack of teeth in birds is a derived state

5. A clade is a natural taxon of organisms bound in space and time

a. A clade is defined as a common ancestor and all of its descendants
b. In practice, we recognize a clade by its derived similarities
c. Example: clade - birds includes ancestor of birds and all its descendants
d. Feathers is a derived similarity found only in birds (no living outgroup has feathers)
e. It is most parsimonious to suppose that the common ancestor of birds was feathered
f. Because lizards lack feathers, feathers probably arose after lizards and birds diverged
g. In other words, the last common ancestor of lizards and birds lacked feathers

6. Technically, a derived character state is termed an apomorphy
7. A shared derived character state is termed a synapomorphy
8. Synapomorphies are typically nested hierarchically

a. Example: All placental mammals have a placenta; placenta is a synapomorphy
b. All marsupial mammals have a marsupial pouch and lack a placenta
c. Both placentals and marsupials have hair and mammory glands (as do all mammals)
d. mammals and lizards both have an amnion around their eggs (as do all amniotes)
e. amniotes and salamanders both have four limbs (as do all tetrapods)
f. tetrapods and sharks both have jaws (as do all gnathostomes)

9. An ancestral (not derived) state is termed a plesiomorphy
10. A shared ancestral state is termed symplesiomorphy.

C. Sources of Phylogenetic Information

Key Terms: comparative morphology, biochemistry, and cytology

1. Morphology: includes shape, size, and development

a. Examples: Skull or limb bones, scales, hairs, feathers
b. Can be observed in fossils as well as living specimens

2. Biochemical comparison (now the most common evidence used)

a. Examples: Protein or DNA sequence comparison
b. Occasionally fossils have remnants of DNA preserved, but not easy to recover

3. Cytological comparison

a. Examples: examines variation in number, shape and size of chromosomes
b. Only used for living organisms

4. Dating a fossil is possible (with radioactive dating methods)
5. Estimating when lineages diverged is also possible with sequence comparisons

III. Theories of Taxonomy

Key Terms: monophyly, paraphyly, polyphyly

1. Three types of groupings are recognized

a. Monophyletic: includes common ancestor and all its descendants
b. Paraphyletic: includes common ancestor and only some of its descendants
c. Polyphyletic: does not include the most recent common ancestor of its members

2. Evolutionary and cladistic systematists only disagree about the case of paraphyletic groups

a. Both agree monophyletic groupings should be recognized
b. Both agree polyphyletic groupings should be rejected
c. Only evolutionary systematists allow paraphyletic groups
d. In contrast, cladists only formally name groups thought to be monophyletic
e. The cladistic principle is known as the "rule of monophyly"
f. Many taxa in widespread use are paraphyletic

Note: The following section of the text, which contrasts evolutionary and cladistic approaches, is understandably sympathetic to the former. First, evolutionary taxonomy is pervasive throughout the text, and would require a major rewriting effort by the authors to eliminate. Second, the authors understandably do not want to alienate those instructors who are not yet ready to conform strictly to the rule of monophyly as would be required by an entirely cladistic approach. They want to sell as many textbooks as they can. However, such an approach is possible and would be wonderful to see, in my opinion. This is because cladistic classifications have essentially taken over the field of animal classification. Any doubters need only browse GenBank's Taxonomy Browser to see a working system of classification that includes all organisms and strictly conforms to the rule of monophyly. It works and is much simpler than the older evolutionary taxonomies it replaces. Moreover, emphasis of paraphyletic groups has a well documented tendency to confound phylogenetic understanding, often in subtle and insidious manner. The following notes under the "Key Terms" sections should suffice to characterize the distinctions between these schools, which need to be studied primarily to appreciate how to recognize the distinction between the older evolutionary taxonomy approach (still wildly popular thanks to the common use of paraphyletic group names in common usage and by the unwillingness of textbook authors to rock the boat) and the current cladistic approach as employed by most practicing systematists.

Also see here for help with the related RQ 10:7.

A. Traditional Evolutionary Taxonomy

Key Terms: evolutionary taxonomy (i.e., older approaches that are common in this text but are not emphasized in this class, you will be expected to recognize when a grade is not necessarily a clade), adaptive zone (old-fashioned approach where a group of animals is "elevated" to a higher rank in a classification because it has diversified into a new ecological realm, e.g., birds, humans), phenetic taxonomy (grouping by overall similarity, both synapomorphies and symplesiomorphies - this approach has been mostly abandoned - current systematists agree that only synapomorphies can provide evidence of monophyly of a group)

B. Phylogenetic Systematics/Cladistics

Key Terms: sister group, cladistics (this is the approach most commonly emphasized today and the one that will be used in this class, but note that there is relatively little controversy about how to find the best phylogenetic tree for a group, but much more controversy about how to turn this tree into a classification, e.g., whether or not to allow known paraphyletic taxa to have formal taxon names -- in this class we say NO, only monophyletic groups should have formal names -- this is the "Rule of Monophyly")

C. Current State of Animal Taxonomy

IV. Species (Please read - this should be review from Biol. 131)

V. Major Divisions of Life (skip - tree has major flaws)

VI. Major Subdivisions of the Animal Kingdom (skip - very old-fashioned)

Click link to return to Lecture Schedule
back to Previous Chapter
or ahead to Chapter 6