Investigating the Tree of Life: Phylogeny and Systematics Overview

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 • Biologists draw on the fossil record, which provides information about ancient organisms

3. 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

4. The Fossil Record • Sedimentary rocks are the richest source of fossils • Sedimentary rocks are deposited into layers called strata Rivers carry sediment to the ocean. Sedimentary rock layers containing fossils form on the ocean floor. Over time, new strata are deposited, containing fossils from each time period. 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 Older stratum with older fossils Video: Grand Canyon

5. LE 25-4 Leaf fossil, about 40 million years ago Petrified trees in Arizona, about 190 million years old Insects preserved whole in amber Dinosaur bones being excavated from sandstone Casts of ammonites, about 375 million years old Boy standing in a 150-million-year-old dinosaur track in Colorado Tusks of a 23,000-year-old mammoth, frozen whole in Siberian ice

6. Morphological and Molecular Homologies • Organisms with very similar morphologies or similar DNA sequences are likely to be more closely related than organisms with vastly different structures or sequences

7. 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

8. Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages

9. LE 25-6 1 2 Deletion 1 2 Insertion 1 2 1 2

10. 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

11. 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)

12. LE 25-8 Panthera pardus Species Linnaeus introduced a system for grouping species in increasingly broad categories Panthera Genus Felidae Family Carnivora Order Mammalia Class Chordata Phylum Animalia Kingdom Eukarya Domain

13. Linking Classification and Phylogeny • Systematists depict evolutionary relationships in branching phylogenetic trees Lutra lutra (European otter) Panthera pardus (leopard) Mephitis mephitis (striped skunk) Canis familiaris (domestic dog) Canis lupus (wolf) Species Genus Panthera Mephitis Lutra Canis Family Felidae Mustelidae Canidae Carnivora Order

14. Each branch point represents the divergence of two species Leopard Domestic cat Common ancestor Wolf Leopard Domestic cat Common ancestor

15. 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

16. Cladistics • Clades can be nested in larger clades, but not all groupings or organisms qualify as clades • A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants

17. LE 25-10a Grouping 1 Monophyletic

18. A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants

19. LE 25-10b Grouping 2 Paraphyletic

20. A polyphyletic grouping consists of various species that lack a common ancestor

21. LE 25-10c Grouping 3 Polyphyletic

22. Shared Primitive and Shared Derived Characteristics • In cladistic analysis, clades are defined by their evolutionary novelties

23. 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

24. 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

25. 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

26. 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

27. Phylogenetic Trees and Timing • Any chronology represented by the branching of a phylogenetic tree is relative rather than absolute in representing timing of divergences

28. 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

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

30. 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

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

32. 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

33. The most parsimonious tree requires the fewest evolutionary events to have occurred in the form of shared derived characters • The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events

34. LE 25-14 Human Mushroom Tulip Human 0 30% 40% Mushroom 0 40% Tulip 0 Percentage differences between sequences 25% 15% 15% 20% 15% 10% 5% 5% Tree 1: More likely Tree 2: Less likely Comparison of possible trees

35. 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)

36. LE 25-15ab Sites in DNA sequence 1 2 3 4 5 6 7 I II Species III IV I II III IV Bases at site 1 for each species Base-change event

37. 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

38. LE 25-16 Lizard Bird Mammal Four-chambered heart Mammal-bird clade Lizard Bird Mammal Four-chambered heart Four-chambered heart Lizard-bird clade

39. 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

40. Gene Duplications and Gene Families • Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes

41. Orthologous genes are genes found in a single copy in the genome • They can diverge only after speciation occurs

42. LE 25-17a Ancestral gene Speciation Orthologous genes

43. 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

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

45. Genome Evolution • Orthologous genes are widespread and extend across many widely varied species • 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

46. Concept 25.5: Molecular clocks help track evolutionary time • To extend molecular phylogenies beyond the fossil record, we must make an assumption about how change occurs over time

47. 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

48. 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

49. 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

50. 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