1. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Evolutionary biology is about both process and history. The processes of evolution are natural selection and other mechanisms that change the genetic composition of populations and can lead to the evolution of new species. A major goal of evolutionary biology is to reconstruct the history of life on earth.

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

3. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 Molecular systematics, which uses comparisons of nucleotide sequences in DNA and RNA to help identify evolutionary relationships between individual genes or even entire genomes.

4. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 Fossils are the preserved remnants or impressions left by organisms that lived in the past. In essence, they are the historical documents of biology.

5. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Sedimentary rocks form from layers of sand and silt that are carried by rivers to seas and swamps, where the minerals settle to the bottom along with the remains of organisms. As deposits pile up, they compress older sediments below them into layers called strata. The fossil record is the ordered array in which fossils appear within sedimentary rock strata. These rocks record the passing of geological time.

6. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Fossils can be used to construct phylogenies only if we can determine their ages. The majority of living things were not captured as fossils upon their death. Of those that formed fossils, later geological processes destroyed many. Only a fraction of existing fossils have been discovered.

7. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Morphological and Molecular Homologies Similarities due to shared ancestry are called 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

8. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

9. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages Similar analogous adaptations may evolve in such organisms. Analogies are not due to shared ancestry.

10. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Distinguishing homology from analogy is critical in the reconstruction of phylogeny. For example, both birds and bats have adaptations that allow them to fly. However, a close examination of a bat’s wing shows a greater similarity to a cat’s forelimb that to a bird’s wing.

11. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Fossil evidence also documents that bat and bird wings arose independently from walking forelimbs of different ancestors. Thus a bat’s wing is homologous to other mammalian forelimbs but is analogous in function to a bird’s wing. Analogous structures or molecular sequences that evolved independently are also called homoplasies.

12. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings In general, the more points of resemblance that two complex structures have, the less likely it is that they evolved independently. For example, the skulls of a human and a chimpanzee are formed by the fusion of many bones. The two skulls match almost perfectly, bone for bone. It is highly unlikely that such complex structures have separate origins. More likely, the genes involved in the development of both skulls were inherited from a common ancestor.

13. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Systematists compare long stretches of DNA and even entire genomes to assess relationships between species. If genes in two organisms have closely similar nucleotide sequences, it is highly likely that the genes are homologous.

14. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Evaluating Molecular Homologies Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms Deletions or insertions may shift the remaining sequences, making it difficult to recognize closely matching nucleotide sequences.

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

16. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

17. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Binomial Nomenclature The two-part scientific name of a species is called a binomial nomenclature 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)

18. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Hierarchical Classification Linnaeus introduced a system for grouping species in increasingly broad categories Linneaus’s classification was not based on evolutionary relationships but simply on resemblances between organisms. Each taxonomic level is more comprehensive than the previous one. As an example, all species of cats are mammals, but not all mammals are cats.

19. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The named taxonomic unit at any level is called a taxon. Example: Panthera is a taxon at the genus level, and Mammalia is a taxon at the class level that includes all of the many orders of mammals.

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

21. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Linking Classification and Phylogeny Systematists depict evolutionary relationships in branching phylogenetic trees The branching of the tree reflects the hierarchical classification of groups nested within more inclusive groups. Methods for tracing phylogeny began with Darwin, who realized the evolutionary implications of Linnaean hierarchy.

22. 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

23. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Each branch point represents the divergence of two species “Deeper” branch points represent progressively greater amounts of divergence

24. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 25.3: Phylogenetic systematics informs the construction of phylogenetic trees based on shared characteristics If shared characteristics are homologous and, thus, explained by common ancestry, then the cladogram forms the basis of a phylogenetic tree. 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

25. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings A shared derived character is an evolutionary novelty unique to a particular clade The presence of a backbone can qualify as a shared derived character, but at a deeper branch point that distinguishes all vertebrates from other mammals. Among vertebrates, the backbone is a shared primitive character because it evolved in the ancestor common to all vertebrates.

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

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

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

29. 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

30. 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

31. 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

32. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Phylogenetic Trees and Timing Any chronology represented by the branching of a phylogenetic tree is relative rather than absolute in representing timing of divergences 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

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

34. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

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

36. 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

37. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

38. 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

39. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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)

40. LE 25-15ab Sites in DNA sequence I Species 1 Base-change event Bases at site 1 for each species 234567 II III IV IIIIIIIV

41. 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

42. LE 25-16 LizardBirdMammal Four-chambered heart Mammal-bird clade LizardBirdMammal Four-chambered heart Four-chambered heart Lizard-bird clade

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

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

45. 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

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

47. 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

48. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes

49. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 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

50. 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

51. 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

52. 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

53. 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