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 Systematics is an analytical approach to understanding the diversity and relationships of organisms, both present-day and extinct Uses morphological Biochemical and molecular comparisons to infer evolutionary relationships

3. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Sorting Homology from 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

4. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings These organisms have analogous structures from Living in similar environments, but do not share a Recent common ancestor

5. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Evaluating Molecular Homologies Not as simple as you would think Systematists use computer software to find and realign similar sequence in DNA between two species

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-part names for species (binomial nomenclature) – hierarchical classification

7. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Binomial Nomenclature Genus species G. species

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 Systematists depict evolutionary relationships in branching phylogenetic trees Each branch point represents the divergence of two species

10. LE 25-UN497 LeopardDomestic cat Common ancestor LeopardDomestic catWolf Common ancestor “Deeper” branch points represent progressively greater amounts of divergence

11. 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

12. 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

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

14. LE 25-10b Paraphyletic Grouping 2 A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants

15. LE 25-10c Polyphyletic Grouping 3 A polyphyletic grouping consists of various species that lack a common ancestor

16. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Shared Primitive and Shared Derived Characteristics In cladistic analysis, clades are defined by their evolutionary novelties 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

17. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Outgroups An outgroup is a species or group of species that is closely related to the ingroup, the various species being studied Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared primitive characteristics

18. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Outgroup comparison assumes that homologies shared by the outgroup and ingroup must be primitive characters that predate the divergence of both groups from a common ancestor It enables us to focus on characters derived at various branch points in the evolution of a clade

19. 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

20. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Phylogenetic Trees and Timing Phylogenetic trees depict RELATIVE TIMING – – Four walking legs appeared after vertebral columns but before hair

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

22. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Maximum Parsimony and Maximum Likelihood Systematists can never be sure of finding the best tree in a large data set They narrow possibilities by applying the principles of maximum parsimony and maximum likelihood The simplest explanation is the best explanation and therefore most likely

23. LE 25-14 Human 0 Mushroom 30% 0 Tulip 40% Human Mushroom 0Tulip Percentage differences between sequences Comparison of possible trees 15% 20% 5% 10% 15% 25% Tree 1: More likelyTree 2: Less likely Tree 2 – Mushrooms must have slowed DNA mutation rates and plants sped up

24. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Phylogenetic Trees as Hypotheses The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil Sometimes the best hypothesis is not the most parsimonious

25. LE 25-16 LizardBirdMammal Four-chambered heart Mammal-bird clade LizardBirdMammal Four-chambered heart Four-chambered heart Lizard-bird clade You cannot just use one characteristic as a basis for phylogeny

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 Really useful for organisms that have diverged a long time – like humans and monerans “Seven Daughters of Eve” uses mDNA

27. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Gene Duplications and Gene Families Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes Orthologous genes are genes found in a single copy in the genome They can diverge only after speciation occurs Paralogous genes result from gene duplication, so are found in more than one copy in the genome They can diverge within the clade that carries them, often adding new functions

28. LE 25-17a Ancestral gene Speciation Orthologous genes Genes are found in separate gene pools - Human & mice  hemoglobin genes

29. LE 25-17b Ancestral gene Gene duplication Paralogous genes

30. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Genome Evolution The widespread consistency in total gene number in organisms indicates genes in complex organisms are very versatile and that each gene can perform many functions Humans have five times as many genes as yeast – so our genes must be more versatile

31. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Molecular Clocks The molecular clock is a yardstick for measuring absolute time of evolutionary change based on the observation that some genes and other regions of genomes seem to evolve at constant rates

32. 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

33. 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

34. 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

35. 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