1. Phylogenetic Trees
Systematics, the scientific study of the diversity of organisms, reveals the evolutionary relationships between organisms.
Taxonomy, a subdivision of systematics, is the theory and practice of classifying organisms.

2. Phylogenetic Trees
A phylogeny is a hypothesis which 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.

3. Figure 25.1 How to Read a Phylogenetic Tree

4. 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.

5. 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.

6. Phylogenetic Trees
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.

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

8. Steps in Reconstructing Phylogenies
Systematists use many characters to reconstruct phylogenies, including physiological, behavioral, molecular, and structural characters of both living and fossil organisms.
The more traits that are measured, the more inferred phylogenies should converge on one another and on the actual evolutionary pattern.

9. Steps in Reconstructing Phylogenies
An important source of information for systematists is morphology, which describes the sizes and shapes of body parts.
Early developmental stages of many organisms reveal similarities to other organisms, but these similarities may be lost in adulthood.
Human gill slits during development.

10. 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.

11. 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.

12. Steps in Reconstructing Phylogenies
Relationships between apes and humans were investigated by sequencing a hemoglobin pseudogene.
Chimpanzees and humans share a more recent common ancestor with each other than they do with gorillas.

13. Reconstructing a Simple Phylogeny
A simple phylogeny can be constructed using eight vertebrates species: lamprey, perch, pigeon, chimpanzee, salamander, lizard, mouse, and crocodile.
Traits that are either present (+) or absent (–) are used in the phylogeny.

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

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

16. Figure 25.5 A Probable Phylogeny of Eight Vertebrates

17. Biological Classification and Evolutionary Relationships
The system of biological classification used today was developed by Carolus Linnaeus in 1758.
His two-name system is referred to as binomial nomenclature.
The first name identifies the genus; the other name identifies the species.

18. Biological Classification and Evolutionary Relationships
Homo sapiens is the name of the modern human species.
The generic name is always capitalized, whereas the specific name is not, and both names are italicized.

20. Phylogenetic Trees Have Many Uses
Biologists determined that the hundreds of diverse cichlids could not have evolved in such a short time.
A new phylogeny of the cichlids of Lake Victoria and other lakes in the region was developed using 300 mtDNA sequences.
This phylogeny suggested that the ancestors of the Lake Victoria cichlids came from the much older lake Kivu.
The phylogeny also indicated that some of the cichlid lineages found only in Lake Victoria split at least 100,000 years ago, suggesting that the lake did not completely dry up about 15,000 years ago.