1. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings PowerPoint Lectures for Biology, Seventh Edition Neil Campbell and Jane Reece Lectures by Chris Romero Chapter 25 Phylogeny and Systematics

2. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Overview: Investigating the Tree of Life Phylogeny is the evolutionary history of a species or group of related species Biologists draw on the fossil record, which provides information about ancient organisms Systematics is an analytical approach to understanding the diversity and relationships of organisms, both present-day and extinct Systematists use morphological, biochemical, and molecular comparisons to infer evolutionary relationships

3. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 25.1: Phylogenies are based on common ancestries inferred from fossil, morphological, and molecular evidence To infer phylogenies, systematists gather information about morphologies, development, and biochemistry of living organisms They also examine fossils to help establish relationships between living organisms

4. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Morphological and Molecular Homologies In addition to fossils, phylogenetic history can be inferred from morphological and molecular similarities in living organisms Organisms with very similar morphologies or similar DNA sequences are likely to be more closely related than organisms with vastly different structures or sequences

5. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Sorting Homology from Analogy In constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy Homology is similarity due to shared ancestry Analogy is similarity due to convergent evolution Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages Analogous structures or molecular sequences that evolved independently are also called homoplasies

6. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 25.2: Phylogenetic systematics connects classification with evolutionary history Taxonomy is the ordered division of organisms into categories based on characteristics used to assess similarities and differences In 1748, Carolus Linnaeus published a system of taxonomy based on resemblances. Two key features of his system remain useful today: two-part names for species and hierarchical classification

7. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Binomial Nomenclature The two-part scientific name of a species is called a binomial The first part of the name is the genus The second part, called the specific epithet, is unique for each species within the genus The first letter of the genus is capitalized, and the entire species name is latinized Both parts together name the species (not the specific epithet alone)

8. LE 25-8 Species Panthera pardus Panthera Genus Family Felidae Carnivora Order Mammalia Class Phylum Chordata Kingdom Animalia Eukarya Domain

9. LE 25-9 Carnivora Panthera pardus (leopard) Mephitis mephitis (striped skunk) Lutra lutra (European otter) Canis familiaris (domestic dog) Canis lupus (wolf) Species Genus Family Order FelidaeMustelidaeCanidae PantheraMephitisLutraCanis

10. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 25.3: Phylogenetic systematics informs the construction of phylogenetic trees based on shared characteristics A cladogram depicts patterns of shared characteristics among taxa A clade is a group of species that includes an ancestral species and all its descendants Cladistics studies resemblances among clades

11. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Cladistics Clades can be nested in larger clades, but not all groupings or organisms qualify as clades

12. LE 25-10a Grouping 1 Monophyletic A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants

13. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants

14. LE 25-10b Paraphyletic Grouping 2

15. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings A polyphyletic grouping consists of various species that lack a common ancestor

16. LE 25-10c Polyphyletic Grouping 3

17. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings A shared primitive character is a character that is shared beyond the taxon we are trying to define A shared derived character is an evolutionary novelty unique to a particular clade

18. LE 25-11 Hair Amniotic (shelled) egg Four walking legs Hinged jaws Vertebral column (backbone) Character table CHARACTERS TAXA Lancelet (outgroup) LampreyTunaSalamander TurtleLeopard Turtle Leopard Hair Amniotic egg Four walking legs Hinged jaws Vertebral column Salamander Tuna Lamprey Lancelet (outgroup) Cladogram

19. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Phylogenetic Trees and Timing Any chronology represented by the branching of a phylogenetic tree is relative rather than absolute in representing timing of divergences

20. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Phylograms In a phylogram, the length of a branch in a cladogram reflects the number of genetic changes that have taken place in a particular DNA or RNA sequence in that lineage

21. LE 25-12 Drosophila Lancelet Fish Amphibian Bird Human Rat Mouse

22. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Ultrametric Trees Branching in an ultrametric tree is the same as in a phylogram, but all branches traceable from the common ancestor to the present are equal length

23. LE 25-13 Drosophila Lancelet Fish Amphibian Bird Human Rat Mouse Cenozoic Mesozoic Paleozoic 65.5 251 542 Neoproterozoic Millions of years ago

24. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings In considering possible phylogenies for a group of species, systematists compare molecular data for the species. The most efficient way to study hypotheses is to consider the most parsimonious hypothesis, the one requiring the fewest evolutionary events (molecular changes)

25. LE 25-15ab Sites in DNA sequence I Species 1 Base-change event Bases at site 1 for each species 234567 II III IV IIIIIIIV

26. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 25.4: 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

27. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Neutral Theory Neutral theory states that much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection It states that the rate of molecular change in these genes and proteins should be regular like a clock

28. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Difficulties with Molecular Clocks The molecular clock does not run as smoothly as neutral theory predicts Irregularities result from natural selection in which some DNA changes are favored over others Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty

29. 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 Comparison of HIV samples throughout the epidemic shows that the virus evolved in a very clocklike way

30. 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