Investigating the Tree of Life: Tracing Phylogeny and Systematics

1. Chapter 25 Phylogeny and Systematics

2. Overview: Investigating the Tree of Life • This chapter describes how biologists trace phylogeny • The evolutionary history of a species or group of related species

3. Biologists draw on the fossil record • Which provides information about ancient organisms Figure 25.1

4. Biologists also use systematics • As an analytical approach to understanding the diversity and relationships of organisms, both present-day and extinct

5. Currently, systematists use • Morphological, biochemical, and molecular comparisons to infer evolutionary relationships Figure 25.2

6. Concept 25.1: Phylogenies are based on common ancestries inferred from fossil, morphological, and molecular evidence

7. 1 Rivers carry sediment to the ocean. Sedimentary rock layers containing fossils form on the ocean floor. 2 Over time, new strata are deposited, containing fossils from each time period. 3 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 The Fossil Record • Sedimentary rocks • Are the richest source of fossils • Are deposited into layers called strata Figure 25.3

8. 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

9. (c) Leaf fossil, about 40 million years old (b) Petrified tree in Arizona, about 190 million years old (a) Dinosaur bones being excavated from sandstone (d) Casts of ammonites, about 375 million years old (f) Insects preserved whole in amber (e) Boy standing in a 150-million-year-old dinosaur track in Colorado (g) Tusks of a 23,000-year-old mammoth, frozen whole in Siberian ice Figure 25.4a–g • Though sedimentary fossils are the most common • Paleontologists study a wide variety of fossils

10. Morphological and Molecular Homologies • In addition to fossil organisms • Phylogenetic history can be inferred from certain morphological and molecular similarities among living organisms • In general, organisms that share very similar morphologies or similar DNA sequences • Are likely to be more closely related than organisms with vastly different structures or sequences

11. Sorting Homology from Analogy • A potential misconception in constructing a phylogeny • Is similarity due to convergent evolution, called analogy, rather than shared ancestry

12. Convergent evolution occurs when similar environmental pressures and natural selection • Produce similar (analogous) adaptations in organisms from different evolutionary lineages Figure 25.5

13. Analogous structures or molecular sequences that evolved independently • Are also called homoplasies

14. 1 Ancestral homologous DNA segments are identical as species 1 and species 2 begin to diverge from their common ancestor. C C A T C A G A G T C C 1 C C A T C A G A G T C C 2 A C G G A T A G T C C A C T A G G C A C T A T C A C C G A C A G G T C T T T G A C T A G Deletion 2 Deletion and insertion mutations shift what had been matching sequences in the two species. 1 C C A T C A G A G T C C Figure 25.7 C C A T C A G A G T C C 2 Insertion G T A 3 Homologous regions (yellow) do not all align because of these mutations. C C A T C A A G T C C 1 C C A T G T A C A G A G T C C 2 4 Homologous regions realign after a computer program adds gaps in sequence 1. C C A T C A A G T C C 1 Figure 25.6 C C A T G T A C A G A G T C C 2 Evaluating Molecular Homologies • Systematists use computer programs and mathematical tools • When analyzing comparable DNA segments from different organisms

15. Concept 25.2: Phylogenetic systematics connects classification with evolutionary history • Taxonomy • Is the ordered division of organisms into categories based on a set of characteristics used to assess similarities and differences

16. Binomial Nomenclature • Binomial nomenclature • Is the two-part format of the scientific name of an organism • Was developed by Carolus Linnaeus

17. The binomial name of an organism or scientific epithet • Is latinized • Is the genus and species

18. Panthera pardus Species Panthera Genus Felidae Family Carnivora Order Mammalia Class Chordata Phylum Animalia Kingdom Eukarya Domain Hierarchical Classification • Linnaeus also introduced a system • For grouping species in increasingly broad categories Figure 25.8

19. Panthera pardus(leopard) Mephitis mephitis (striped skunk) Canis familiaris (domestic dog) Canislupus (wolf) Lutra lutra (European otter) Species Genus Panthera Lutra Canis Mephitis Family Felidae Mustelidae Canidae Carnivora Order Linking Classification and Phylogeny • Systematists depict evolutionary relationships • In branching phylogenetic trees Figure 25.9

20. Leopard Domestic cat Common ancestor • Each branch point • Represents the divergence of two species

21. Wolf Leopard Domestic cat Common ancestor • “Deeper” branch points • Represent progressively greater amounts of divergence

22. Concept 25.3: Phylogenetic systematics informs the construction of phylogenetic trees based on shared characteristics • A cladogram • Is a depiction of patterns of shared characteristics among taxa • A clade within a cladogram • Is defined as a group of species that includes an ancestral species and all its descendants • Cladistics • Is the study of resemblances among clades

23. Cladistics • Clades • Can be nested within larger clades, but not all groupings or organisms qualify as clades

24. Grouping 1 E J K D H G F C I B A (a)Monophyletic. In this tree, grouping 1, consisting of the seven species B–H, is a monophyletic group, or clade. A mono-phyletic group is made up of an ancestral species (species B in this case) and all of its descendant species. Only monophyletic groups qualify as legitimate taxa derived from cladistics. • A valid clade is monophyletic • Signifying that it consists of the ancestor species and all its descendants Figure 25.10a

25. Grouping 2 G J K H E D C I F B A (b)Paraphyletic. Grouping 2 does not meet the cladistic criterion: It is paraphyletic, which means that it consists of an ancestor (A in this case) and some, but not all, of that ancestor’s descendants. (Grouping 2 includes the descendants I, J, and K, but excludes B–H, which also descended from A.) • A paraphyletic clade • Is a grouping that consists of an ancestral species and some, but not all, of the descendants Figure 25.10b

26. D E J G H K I F C B A (c)Polyphyletic. Grouping 3 also fails the cladistic test. It is polyphyletic, which means that it lacks the common ancestor of (A) the species in the group. Further-more, a valid taxon that includes the extant species G, H, J, and K would necessarily also contain D and E, which are also descended from A. • A polyphyletic grouping • Includes numerous types of organisms that lack a common ancestor Grouping 3 Figure 25.10c

27. Shared Primitive and Shared Derived Characteristics • In cladistic analysis • Clades are defined by their evolutionary novelties

28. A shared primitive character • Is a homologous structure that predates the branching of a particular clade from other members of that clade • Is shared beyond the taxon we are trying to define

29. A shared derived character • Is an evolutionary novelty unique to a particular clade

30. Outgroups • Systematists use a method called outgroup comparison • To differentiate between shared derived and shared primitive characteristics

31. As a basis of comparison we need to designate an outgroup • which is a species or group of species that is closely related to the ingroup, the various species we are studying • Outgroup comparison • Is based on the assumption that homologies present in both the outgroup and ingroup must be primitive characters that predate the divergence of both groups from a common ancestor

32. TAXA Lancelet(outgroup) Salamander Leopard Lamprey Turtle Tuna 0 0 0 Hair 0 0 1 CHARACTERS 0 0 0 0 1 1 Amniotic (shelled) egg 0 0 0 1 1 1 Four walking legs 0 0 1 1 1 1 Hinged jaws (a) Character table. A 0 indicates that a character is absent; a 1 indicates that a character is present. 0 1 1 1 1 1 Vertebral column (backbone) Leopard Turtle Hair Salamander Amniotic egg Tuna Four walking legs Lamprey Hinged jaws Lancelet (outgroup) (b) Cladogram. Analyzing the distribution of these derived characters can provide insight into vertebrate phylogeny. Vertebral column • The outgroup comparison • Enables us to focus on just those characters that were derived at the various branch points in the evolution of a clade Figure 25.11a, b

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

34. Drosophila Fish Amphibian Lancelet Human Mouse Rat Bird 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 Figure 25.12

35. Amphibian Drosophila Human Lancelet Mouse Fish Bird Rat Cenozoic 65.5 Mesozoic 251 Paleozoic 542 Proterozoic Millions of years ago Ultrametric Trees • In an ultrametric tree • The branching pattern is the same as in a phylogram, but all the branches that can be traced from the common ancestor to the present are of equal length Figure 25.13

36. Maximum Parsimony and Maximum Likelihood • Systematists • Can never be sure of finding the single best tree in a large data set • Narrow the possibilities by applying the principles of maximum parsimony and maximum likelihood

37. Among phylogenetic hypotheses • The most parsimonious tree is the one that requires the fewest evolutionary events to have occurred in the form of shared derived characters

38. Mushroom Tulip Human Human 30% 0 40% Mushroom 40% 0 0 Tulip (a) Percentage differences between sequences • Applying parsimony to a problem in molecular systematics Figure 25.14

39. 25% 15% 20% 15% 15% 10% 5% 5% Tree 1: More likely Tree 2: Less likely (b) Comparison of possible trees • Applying parsimony to a problem in molecular systematics Figure 25.14

40. APPLICATION In considering possible phylogenies for a group of species, systematists compare molecular data for the species. The most efficient way to study the various phylogenetic hypotheses is to begin by first considering the most parsimonious—that is, which hypothesis requires the fewest total evolutionary events (molecular changes) to have occurred. TECHNIQUE Follow the numbered steps as we apply the principle of parsimony to a hypothetical phylogenetic problem involving four closely related bird species. 1 First, draw the possible phylogenies for the species (only 3 of the 15 possible trees relating these four species are shown here). SpeciesIV SpeciesIII SpeciesI SpeciesII I II II I IV III II III IV III I IV Three possible phylogenetic hypothese Sites in DNA sequence 1 4 2 5 3 6 7 2 Tabulate the molecular data for the species (in this simplified example, the data represent a DNA sequence consisting of just seven nucleotide bases). I A G T G G G G A G G G G G G II Species G III A G G T A A IV G G A G A G A I II III IV A G G G Bases at site 1 for each species G G 3 Now focus on site 1 in the DNA sequence. A single base-change event, marked by the crossbar in the branch leading to species I, is sufficient to account for the site 1 data. Base-changeevent G • The principle of maximum likelihood • States that, given certain rules about how DNA changes over time, a tree can be foundthat reflects the most likely sequence of evolutionary events Figure 25.15a

41. I II III IV I III II IV I IV II III I II III IV I III II IV I IV II III GG GG AA AA GG AA GG AA GG AA GG AA AA GG GG GG GG GG GG GG GG I II III IV I III II IV I IV II III T G T G T T G G T G G T T G T T T T T T T I II III IV I III II IV I IV II III 8 events 9 events 10 events 4 Continuing the comparison of bases at sites 2, 3, and 4 reveals that each of these possible trees requires a total of four base-change events (marked again by crossbars). Thus, the first four sites in this DNA sequence do not help us identify the most parsimonious tree. 5 After analyzing sites 5 and 6, we find that the first tree requires fewer evolutionary events than the other two trees (two base changes versus four). Note that in these diagrams, we assume that the common ancestor had GG at sites 5 and 6. But even if we started with an AA ancestor, the first tree still would require only two changes, while four changes would be required to make the other hypotheses work. Keep in mind that parsimony only considers the total number of events, not the particular nature of the events (how likely the particular base changes are to occur). Two base changes 6 At site 7, the three trees also differ in the number of evolutionary events required to explain the DNA data. RESULTS To identify the most parsimonious tree, we total all the base-change events noted in steps 3–6 (don’t forget to include the changes for site 1, on the facing page). We conclude that the first tree is the most parsimonious of these three possible phylogenies. (But now we must complete our search by investigating the 12 other possible trees.) Figure 25.15b

42. Phylogenetic Trees as Hypotheses • The best hypotheses for phylogenetic trees • Are those that fit the most data: morphological, molecular, and fossil

43. Bird Lizard Mammal Four-chamberedheart (a) Mammal-bird clade Bird Lizard Mammal Four-chamberedheart Four-chamberedheart (b) Lizard-bird clade • Sometimes there is compelling evidence • That the best hypothesis is not the most parsimonious Figure 25.16a, b

44. 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

45. Gene Duplications and Gene Families • Gene duplication • Is one of the most important types of mutation in evolution because it increases the number of genes in the genome, providing further opportunities for evolutionary changes

46. Ancestral gene Speciation (a) Orthologous genes • Orthologous genes • Are genes found in a single copy in the genome • Can diverge only once speciation has taken place Figure 25.17a

47. Ancestral gene Gene duplication Paralogous genes • Paralogous genes • Result from gene duplication, so they are found in more than one copy in the genome • Can diverge within the clade that carries them, often adding new functions Figure 25.17b (b)

48. Genome Evolution • Orthologous genes are widespread • And extend across many widely varied species • The widespread consistency in total gene number in organisms of varying complexity • Indicates that genes in complex organisms are extremely versatile and that each gene can perform many functions

49. Concept 25.5: Molecular clocks help track evolutionary time

50. Molecular Clocks • The molecular clock • Is a yardstick for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates