1. Reconstructing and Using Phylogenies 16

2. Concept 16.1 All of Life Is Connected through Its Evolutionary History All of life is related through a common ancestor: Phylogeny—the evolutionary history of these relationships Phylogenetic tree—a diagrammatic reconstruction of that history

4. Concept 16.1 All of Life Is Connected through Its Evolutionary History A phylogenetic tree may portray the evolutionary history of: All life forms Major evolutionary groups Small groups of closely related species Individuals Populations Genes

5. Concept 16.1 All of Life Is Connected through Its Evolutionary History The common ancestor of all the organisms in the tree forms the root of the tree.

6. Concept 16.1 All of Life Is Connected through Its Evolutionary History Evolutionary relationships among species form the basis for biological classification. As new species are discovered, phylogenetic analyses are reviewed and revised. The tree of life’s evolutionary framework allows us to make predictions about the behavior, ecology, physiology, genetics, and morphology of species.

7. Concept 16.1 All of Life Is Connected through Its Evolutionary History Homologous features: Shared by two or more species Inherited from a common ancestor They can be any heritable traits, including DNA sequences, protein structures, anatomical structures, and behavior patterns.

10. Concept 16.1 All of Life Is Connected through Its Evolutionary History Similar traits can develop in unrelated groups: Convergent evolution—when superficially similar traits may evolve independently in different lineages

12. Figure 16.2 The Bones Are Homologous, the Wings Are Not

15. Concept 16.2 Phylogeny Can Be Reconstructed from Traits of Organisms Molecular data: DNA sequences have become the most widely used data for constructing phylogenetic trees. Nuclear, chloroplast, and mitochondrial DNA sequences are used. Information on gene products (such as amino acid sequences of proteins) are also used.

17. Concept 16.3 Phylogeny Makes Biology Comparative and Predictive Molecular clocks: The molecular clock hypothesis states that rates of molecular change are constant enough to predict the timing of lineage splits. A molecular clock uses the average rate at which a given gene or protein accumulates changes to gauge the time of divergence. They must be calibrated using independent data—the fossil record, known times of divergence, or biogeographic dates.

18. Figure 16.9 A Molecular Clock of the Protein Hemoglobin

19. Concept 16.3 Phylogeny Makes Biology Comparative and Predictive A molecular clock was used to estimate the time when HIV-1 first entered human populations from chimpanzees. The clock was calibrated using the samples from the 1980s and 1990s, then tested using the samples from the 1950s. The common ancestor of this group of HIV-1 viruses can also be determined, with an estimated date of origin of about 1930.

20. Concept 16.4 Phylogeny Is the Basis of Biological Classification The biological classification system was started by Swedish biologist Carolus Linnaeus in the 1700s. Binomial nomenclature gives every species a unique name consisting of two parts: the genus to which it belongs, and the species name. Example: Homo sapiens Linnaeus (Linnaeus is the person who first proposed the name)

21. Gorilla gorilla gorilla

22. Concept 16.4 Phylogeny Is the Basis of Biological Classification Species and genera are further grouped into a hierarchical system of higher categories such as family—the taxon above genus. Examples: The family Hominidae contains humans, plus our recent fossil relatives, plus our closest living relatives, the chimpanzees and gorillas. Rosaceae is the family that includes the genus Rosa (roses) and its relatives.

23. Concept 16.4 Phylogeny Is the Basis of Biological Classification Families are grouped into orders Orders into classes Classes into phyla (singular phylum) Phyla into kingdoms The ranking of taxa within the Linnaean classification is subjective.

24. Concept 16.4 Phylogeny Is the Basis of Biological Classification Linnaeus recognized the hierarchy of life, but he developed his system before evolutionary thought had become widespread. Today, biological classifications express the evolutionary relationships of organisms.