Chapter 25

1. Chapter 25 Phylogeny and Systematics

2. 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. 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. These organisms have analogous structures from Living in similar environments, but do not share a Recent common ancestor

5. 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. 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. Binomial Nomenclature • Genus species • G. species

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

9. LE 25-9 Panthera pardus (leopard) Mephitis mephitis (striped skunk) Lutra lutra (European otter) Canis familiaris (domestic dog) Canis lupus (wolf) Species Genus Panthera Mephitis Lutra Canis Family Felidae Mustelidae Canidae Each branch point represents the divergence of two species Systematists depict evolutionary relationships in branching phylogenetic trees Carnivora Order

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

11. 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. Cladistics • Clades can be nested in larger clades, but not all groupings or organisms qualify as clades

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

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

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

16. 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. 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. 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 TAXA Lancelet (outgroup) Salamander Lamprey Leopard Turtle Tuna Hair Amniotic (shelled) egg CHARACTERS Four walking legs Hinged jaws Vertebral column (backbone) Character table Leopard Turtle Hair Salamander Amniotic egg Tuna Four walking legs Lamprey Hinged jaws Lancelet (outgroup) Vertebral column Cladogram

20. Phylogenetic Trees and Timing • Phylogenetic trees depict RELATIVE TIMING – • Four walking legs appeared after vertebral columns but before hair

21. Drosophila Fish Lancelet Amphibian Rat Bird Human Mouse LE 25-12 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. 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 Mushroom Tulip Human 0 30% 40% Mushroom 0 40% Tulip 0 Percentage differences between sequences Tree 2 – Mushrooms must have slowed DNA mutation rates and plants sped up 25% 15% 15% 20% 15% 10% 5% 5% Tree 1: More likely Tree 2: Less likely Comparison of possible trees

24. 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 Lizard Bird Mammal You cannot just use one characteristic as a basis for phylogeny Four-chambered heart Mammal-bird clade Lizard Bird Mammal Four-chambered heart Four-chambered heart Lizard-bird clade

26. 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. 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 b hemoglobin genes

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

30. 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. 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. 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. 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. 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. 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