Phylogeny The evolutionary history of a species or

Fossil Record – Provides information about ancient organisms Figure 25. 1 Copyright © 2005

Systematics – As an analytical approach to understanding the diversity and relationships of organisms,

• Currently, systematists use – Morphological, biochemical, and molecular comparisons to infer evolutionary

The Fossil Record • Sedimentary rocks – Are the richest source of fossils –

• Though sedimentary fossils are the most common – Paleontologists study a wide

• Convergent evolution occurs when similar environmental pressures and natural selection – Produce

Hierarchical Classification • Linnaeus also introduced a system – For grouping species in increasingly

Linking Classification and Phylogeny • Systematists depict evolutionary relationships Species Panthera Order Family Panthera

• Each branch point – Represents the divergence of two species Leopard Domestic

• “Deeper” branch points – Represent progressively greater amounts of divergence Wolf Leopard

• The outgroup comparison – Enables us to focus on just those characters

Phylogenetic Trees as Hypotheses • The best hypotheses for phylogenetic trees – Are those

• Sometimes there is compelling evidence – That the best hypothesis is not

• Much of an organism’s evolutionary history is documented in its genome •

Gene Duplications and Gene Families • Gene duplication – Is one of the most

• Orthologous genes – Are genes found in a single copy in the

• Paralogous genes – Result from gene duplication, so they are found in

Molecular Clocks • The molecular clock – Is a yardstick for measuring the absolute

Applying a Molecular Clock: The Origin of HIV • Phylogenetic analysis shows that HIV

The Universal Tree of Life • The tree of life – Is divided into

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Systematics – As an analytical approach to understanding the diversity and relationships of organisms, both present-day and extinct Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Currently, systematists use – Morphological, biochemical, and molecular comparisons to infer evolutionary relationships Figure 25. 2 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The Fossil Record • Sedimentary rocks – Are the richest source of fossils – Are deposited into layers called strata 1 Rivers carry sediment to the ocean. Sedimentary rock layers containing fossils form on the ocean floor. 2 Over time, new strata are deposited, containing fossils from each time period. 3 As sea levels change and the seafloor is pushed upward, sedimentary rocks are exposed. Erosion reveals strata and fossils. Younger stratum ��with more recent fossils Figure 25. 3 Older stratum with older fossils Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Though sedimentary fossils are the most common – Paleontologists study a wide variety of fossils (c) Leaf fossil, about 40 million years old (b) Petrified tree in Arizona, about 190 million years old (a) Dinosaur bones being excavated from sandstone (d) Casts of ammonites, about 375 million years old (f) Insects preserved whole in amber Figure 25. 4 a–g (g) Tusks of a 23, 000 -year-old mammoth, frozen whole in Siberian ice Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings (e) Boy standing in a 150 -million-year-old dinosaur track in Colorado

• Convergent evolution occurs when similar environmental pressures and natural selection – Produce similar (analogous) adaptations in organisms from different evolutionary lineages Figure 25. 5 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Hierarchical Classification • Linnaeus also introduced a system – For grouping species in increasingly broad categories Panthera Species pardus Panthera Genus Felidae Family Carnivora Order Class Phylum Kingdom Figure 25. 8 Domain Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Mammalia Chordata Animalia Eukarya

Linking Classification and Phylogeny • Systematists depict evolutionary relationships Species Panthera Order Family Panthera Mephitis Canis Lutra lutra pardus mephitis familiaris lupus (European (leopard) (striped skunk) otter) (domestic dog) (wolf) Genus – In branching phylogenetic trees Mephitis Felidae Lutra Mustelidae Carnivora Figure 25. 9 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Canidae

• The outgroup comparison – Enables us to focus on just those characters that were derived at the various branch points in the evolution of a clade Lamprey Tuna Salamander Turtle Leopard Hair 0 0 0 1 Amniotic (shelled) egg 0 0 1 1 Four walking legs 0 0 0 1 1 1 Hinged jaws 0 0 1 1 Vertebral column (backbone) 0 1 1 1 CHARACTERS Lancelet (outgroup) TAXA Turtle Salamander Tuna Lamprey Lancelet (outgroup) Figure 25. 11 a, b (a) Character table. A 0 indicates that a character is absent; a 1 indicates that a character is present. Leopard Hair Amniotic egg Four walking legs Hinged jaws Vertebral column Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings (b) Cladogram. Analyzing the distribution of these derived characters can provide insight into vertebrate phylogeny.

Phylogenetic Trees as Hypotheses • The best hypotheses for phylogenetic trees – Are those that fit the most data: morphological, molecular, and fossil Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Sometimes there is compelling evidence – That the best hypothesis is not the most parsimonious Bird Lizard Mammal Four-chambered heart (a) Mammal-bird clade Bird Lizard Mammal Four-chambered heart Figure 25. 16 a, b (b) Lizard-bird clade Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Much of an organism’s evolutionary history is documented in its genome • Comparing nucleic acids or other molecules to infer relatedness – Is a valuable tool for tracing organisms’ evolutionary history Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Gene Duplications and Gene Families • Gene duplication – Is one of the most important types of mutation in evolution because it increases the number of genes in the genome, providing further opportunities for evolutionary changes Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Orthologous genes – Are genes found in a single copy in the genome – Can diverge only once speciation has taken place Ancestral gene Speciation (a) Figure 25. 17 a Orthologous genes Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Paralogous genes – Result from gene duplication, so they are found in more than one copy in the genome – Can diverge within the clade that carries them, often adding new functions Ancestral gene Gene duplication Figure 25. 17 b (b) Paralogous genes Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Molecular Clocks • The molecular clock – Is a yardstick for measuring the absolute time of evolutionary change based on the observation that some regions of genomes appear to evolve at relatively constant rates Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Applying a Molecular Clock: The Origin of HIV • Phylogenetic analysis shows that HIV – Is descended from viruses that infect chimpanzees and other primates • A comparison of HIV samples from throughout the epidemic – Has shown that the virus has evolved in a remarkably clocklike fashion Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The Universal Tree of Life • The tree of life – Is divided into three great clades called domains: Bacteria, Archaea, and Eukarya • The early history of these domains is not yet clear Billion years ago Bacteria Eukarya Archaea 0 4 Symbiosis of chloroplast ancestor with ancestor of green plants 1 3 Symbiosis of mitochondrial ancestor with ancestor of eukaryotes 2 Possible fusion of bacterium and archaean, yielding ancestor of eukaryotic cells 1 Last common ancestor of all living things 4 2 3 1 Figure 25. 18 4 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Origin of life