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

4. 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

6. 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

7. The Fossil Record • Sedimentary rocks are the richest source of fossils • Sedimentary rocks are deposited into layers called strata Video: Grand Canyon

8. LE 25-3 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

9. The fossil record is based on the sequence in which fossils have accumulated in such strata • Fossils reveal ancestral characteristics that may have been lost over time

10. Though sedimentary fossils are the most common, paleontologists study a wide variety of fossils Animation: The Geologic Record

11. 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

12. 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

13. 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

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

16. Analogous structures or molecular sequences that evolved independently are also called homoplasies

17. Evaluating Molecular Homologies • Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms

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

20. 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

21. 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)

22. Hierarchical Classification • Linnaeus introduced a system for grouping species in increasingly broad categories Animation: Classification Schemes

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

24. Linking Classification and Phylogeny • Systematists depict evolutionary relationships in branching phylogenetic trees

25. 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 Carnivora Order

26. Each branch point represents the divergence of two species

27. LE 25-UN497 Leopard Domestic cat Common ancestor Wolf Leopard Domestic cat Common ancestor

28. “Deeper” branch points represent progressively greater amounts of divergence

29. 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

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

31. A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants

32. LE 25-10a Grouping 1 Monophyletic

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

34. LE 25-10b Grouping 2 Paraphyletic

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

36. LE 25-10c Grouping 3 Polyphyletic

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

38. 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

39. 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

40. 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

41. 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

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

43. 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

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

45. 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

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

47. 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

48. 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

49. 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

50. 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)