1. Reconstructing and Using Phylogenies

2. Phylogeny: the evolutionary history of a species
Systematics: the study of biological diversity in an evolutionary context
Taxonomy, a subdivision of systematics, is the theory and practice of classifying organisms.
The fossil record: the ordered array of fossils, within layers, or strata, of sedimentary rock
Paleontologists: scientists who study fossils

3. The fossil record
Sedimentary rock: rock formed from sand and mud that once settled on the bottom of seas, lakes, and marshes
Dating:
1- Relative~ geologic time scale; sequence of species
2- Absolute~ radiometric dating; age using half-lives of radioactive isotopes

4. Pangaea-250 mya √ Permian extinction
Biogeography: the study of the past and present distribution of species
Pangaea-250 mya √ Permian extinction
Geographic isolation-180 mya
√ African/South American reptile fossil similarities
√ Australian marsupials

5. Mass extinction
Permian extinction (250 million years ago): 90% of marine animals; Pangea merge
Cretaceous extinction (65 million years ago): death of dinosaurs, 50% of marine species; low angle comet

7. Phylogenetics
The tracing of evolutionary relationships (phylogenetic tree)
Linnaeus
Binomial nomenclature
Genus, specific epithet
Homo sapiens
Taxon (taxa)

8. Phylogenetic Trees
Cladistic Analysis: taxonomic approach that classifies organisms according to the order in time at which branches arise along a phylogenetic tree (cladogram)
Clade: each evolutionary branch in a cladogram
Types:
1- Monophyletic single ancestor that gives rise to all species in that taxon and to no species in any other taxon; legitimate cladogram
2- Polyphyletic members of a taxa are derived from 2 or more ancestral forms not common to all members; does not meet cladistic criterion
3- Paraphyletic lacks the common ancestor that would unite the species; does not meet cladistic criterion

9. Phylogenetic Trees
A phylogeny is a hypothesis proposed by a systematist that describes the history of descent of a group of organisms from their common ancestor.
A phylogenetic tree represents that history.
A lineage is represented as a branching tree, in which each split or node represents a speciation event.
Systematists reconstruct phylogenetic trees by analyzing evolutionary changes in the traits of organisms.

10. Phylogenetic Trees
Systematists expect traits inherited from an ancestor in the distant past to be shared by a large number of species.
Traits that first appeared in a more recent ancestor should be shared by fewer species.
These shared traits, inherited from a common ancestor, are called ancestral traits.

11. A Cladogram

12. Phylogenetic Trees
Any features (DNA sequences, behavior, or anatomical feature) shared by two or more species that descended from a common ancestor are said to be homologous.
For example, the vertebral column is homologous in all vertebrates.
A trait that differs from its ancestral form is called a derived trait.

13. Phylogenetic Trees
To identify how traits have changed during evolution, systematists must infer the state of the trait in an ancestor and then determine how it has been modified in the descendants.
Two processes make this difficult:
Convergent evolution occurs when independently evolved features subjected to similar selective pressures become superficially similar.
Evolutionary reversal occurs when a character reverts from a derived state back to an ancestral state.

14. Figure 25.2 The Bones Are Homologous, but the Wings Are Not

15. Phylogenetic Trees
Convergent evolution and evolutionary reversal generate homoplastic traits, or homoplasies: Traits that are similar for some reason other than inheritance from a common ancestor.

16. Phylogenetic Trees
Distinguishing derived traits from ancestral traits may be difficult because traits often become very dissimilar.
An outgroup is a lineage that is closely related to an ingroup (the lineage of interest) but has branched off from the ingroup below its base on the evolutionary tree.
Ancestral traits should be found not only in the ingroup, but also in outgroups. Derived traits would be found only in the ingroup.

17. Steps in Reconstructing Phylogenies
Molecular traits are also useful for constructing phylogenies.
The molecular traits most often used in the construction of phylogenies are the structures of nucleic acids (DNA and RNA) and proteins.

18. Steps in Reconstructing Phylogenies
Comparing the primary structure of proteins:
Homologous proteins are obtained and the number of amino acids that have changed since the lineages diverged from a common ancestor are determined.
DNA base sequences:
Chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) have been used extensively to study evolutionary relationships.

19. Steps in Reconstructing Phylogenies
Relationships between apes and humans were investigated by sequencing a hemoglobin pseudogene (a nonfunctional DNA sequence derived early in primate evolution by duplication of a hemoglobin gene).
The analysis indicated that chimpanzees and humans share a more recent common ancestor with each other than they do with gorillas.

20. Reconstructing a Simple Phylogeny
A simple phylogeny can be constructed using eight vertebrates species: lamprey, perch, pigeon, chimpanzee, salamander, lizard, mouse, and crocodile.
The example assumes initially that a derived trait evolved only once during the evolution of the animals and that no derived traits were lost from any of the descendant groups.
Traits that are either present (+) or absent (–) are used in the phylogeny.

21. Table 25.1 Eight Vertebrates Ordered According to Unique Shared Derived Traits (Part 1)

22. Table 25.1 Eight Vertebrates Ordered According to Unique Shared Derived Traits (Part 2)

23. Reconstructing a Simple Phylogeny
Examining the table reveals that the chimpanzee and mouse share two traits: mammary glands and fur.
Since mammary glands and fur are absent in the other animals, the traits can be attributed to a common ancestor of the mouse and chimpanzee.
Using similar reasoning, the remaining traits are assigned to common ancestors of the other animals until the phylogenetic tree is complete.
Note that the group that does not have any derived traits (the lamprey) is designated as an outgroup.

24. Figure 25.5 A Probable Phylogeny of Eight Vertebrates

25. Reconstructing a Simple Phylogeny
The example phylogeny was simplified by the assumption that derived traits appear only once in a lineage and were never lost after they appeared.
If a snake were included in the group of animals used in the phylogeny, the assumption that traits are never lost would be violated.
Lizards, which have limbs and claws, are the ancestors of snakes, but these structures have been lost in the snake.

26. Reconstructing a Simple Phylogeny
Systematists use several methods to sort out the complexities of phylogenetic relationships.
The most widely used method is the parsimony principle.
This principle states that one should prefer the simplest hypothesis that explains the observed data.
In reconstruction of phylogenies, this means minimizing the number of evolutionary changes that need to be assumed over all characters in all groups in the tree.
In other words, the best hypothesis is one that requires fewest homoplasies.

27. Reconstructing a Simple Phylogeny
The maximum likelihood method is used primarily for phylogenies based on molecular data and requires complex computer programs.
Determining the most likely phylogeny for a given group can be difficult. For example, there are 34,459,425 possible phylogenetic trees for a lineage of only 11 species.
A consensus tree is the outcome of merging multiple likely phylogenetic trees of approximately equal length. In a consensus tree, groups whose relationships differ among the trees form nodes with more than two branches.

28. Figure 25.8 Phylogeny and Classification (Part 1)

29. Figure 25.8 Phylogeny and Classification (Part 2)

30. Biological Classification and Evolutionary Relationships
The traditional class Reptilia is paraphyletic because it does not include all descendants of its common ancestor; birds are excluded.
This emphasizes that birds have evolved unique derived traits since they separated from reptiles, and are thus a distinct grade.
The current tendency is to change classifications to eliminate paraphyletic groups; however, some of the familiar taxonomic categories (such as reptiles) are paraphyletic and will probably remain in use.