1. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings PowerPoint ® Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp BIG IDEA I The process of evolution drives the diversity and unity of life. Enduring Understanding 1.B Organisms are linked by lines of descent from common ancestry. Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today.

2. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Essential Knowledge 1.B.1: Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Learning Objectives: – (1.14) The student is able to pose scientific questions that correctly identify essential properties of shared, core life processes that provide insights into the history of life on Earth. – (1.15) The student is able to describe specific examples of conserved core biological processes and features shared by all domains or within one domain of life, and how these shared, conserved core processes and features support the concept of common ancestry for all organisms. – (1.16) The student is able to justify the scientific claim that organisms share many conserved core processes and features that evolved and are widely distributed among organisms today.

3. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings New Information Continues to Revise our Understanding of the Tree of Life Recently, we have gained insight into the very deepest branches of the tree of life through molecular systematics. Early taxonomists classified all species as either plants or animals. Later, five kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia. More recently, the three-domain system has been adopted: Bacteria, Archaea, and Eukarya. The three-domain system is supported by data from many sequenced genomes.

4. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 26-21 Fungi EUKARYA Trypanosomes Green algae Land plants Red algae Forams Ciliates Dinoflagellates Diatoms Animals Amoebas Cellular slime molds Leishmania Euglena Green nonsulfur bacteria Thermophiles Halophiles Methanobacterium Sulfolobus ARCHAEA COMMON ANCESTOR OF ALL LIFE BACTERIA (Plastids, including chloroplasts) Green sulfur bacteria (Mitochondrion) Cyanobacteria Chlamydia Spirochetes

5. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings The Three Domain System Describes classification as: – Not all prokaryotes are closely related (not monophyletic) – Prokaryotes split early in the history of living things (not all in one lineage) – Archaea are more closely related to Eukarya than to Bacteria – Eukarya are not directly related to Bacteria – There was a common ancestor for all extant organisms (monophyletic) – Eukaryotes are more closely related to each other (than prokaryotes are to each other)

6. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 26-UN9

7. Classification of Living Things Go to Section:

8. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Structural and functional evidence supports the relatedness of all domains. Illustrative examples include: 1.DNA and RNA are carriers of genetic information through transcription, translation and replication. 2.Major features of the genetic code are shared by all modern living systems (Central Dogma). 3.Metabolic pathways are conserved across all currently recognized domains.

9. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Structural evidence supports the relatedness of all eukaryotes. Illustrative examples include: 1.Cytoskeleton 2.Membrane-bound Organelles 3.Endomembrane Systems 4.Linear Chromosomes

10. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings PowerPoint ® Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp BIG IDEA I The process of evolution drives the diversity and unity of life. Enduring Understanding 1.B Organisms are linked by lines of descent from common ancestry. Essential Knowledge 1.B.2 Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested.

11. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Essential Knowledge 1.B.2: Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested. Learning Objectives: – (1.17) The student is able to pose scientific questions about a group of organisms whose relatedness is described by a phylogenetic tree or cladogram in order to (1) identify shared characteristics, (2) make inferences about the evolutionary history of the group, and (3) identify character data that could extend or improve the phylogenetic tree. – (1.18) The student is able to evaluate evidence provided by a data set in conjunction with a phylogenetic tree or a simple cladogram to determine evolutionary history and speciation. – (1.19) The student is able to create a phylogenetic tree or simple cladogram that correctly represents evolutionary history and speciation from a provided data set.

12. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Phylogenies show evolutionary relationships. Phylogeny is the evolutionary history of a species or group of related species. It is constructed by using evidence from systematics, a discipline that focuses on classifying organisms and their evolutionary relationships. Its tools include fossils, morphology, genes, and molecular evidence. Taxonomy is an ordered division of organisms into categories based on a set of characteristics used to assess similarities and differences.

13. Fig. 26-4 Species Canis lupus Panthera pardus Taxidea taxus Lutra lutra Canis latrans OrderFamilyGenus Carnivora Felidae Mustelidae Canidae Canis Lutra Taxidea Panthera

14. Fig. 26-2

15. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 26-5 Sister taxa ANCESTRAL LINEAGE Taxon A Polytomy Common ancestor of taxa A–F Branch point (node) Taxon B Taxon C Taxon D Taxon E Taxon F

16. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Phylogenetic trees and cladograms can represent traits that are either derived or lost due to evolution. These are graphical representations (models) of evolutionary history that can be tested.

17. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Derived / Lost Traits – Illustrative Examples Using phylogenetic trees and cladograms, we can represent traits that are either derived (newly evolved) or lost due to evolution. Illustrative examples include: – Number of heart chambers in animals – Absence of legs in some sea mammals

18. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Derived Traits – Illustrative Example A powerful four-chambered heart was an essential adaptation of the endothermic way of life characteristic of mammals and birds. The separation of the systemic and pulmonary circuits, each independently powered, allows organisms to deliver much more fuel and O 2 to tissues – because endotherms use about 10 times as much energy as ectotherms.

19. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Lost Traits – Illustrative Example

20. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings What We Can and Cannot Learn from Phylogenetic Trees Phylogenetic trees do show patterns of descent Phylogenetic trees do not indicate when species evolved or how much genetic change occurred in a lineage It shouldn’t be assumed that a taxon evolved from the taxon next to it Phylogeny provides important information about similar characteristics in closely related species

21. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Phylogenies are inferred from morphological and molecular data. To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences

22. Fig. 26-7

23. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Bat and bird wings are homologous as forelimbs, but analogous as functional wings. Homology can be distinguished from analogy by comparing fossil evidence and the degree of complexity. The more complex two similar structures are, the more likely it is that they are homologous. Molecular systematics uses DNA and other molecular data to determine evolutionary relationships. The more alike the DNA sequences of two organisms, the more closely related they are evolutionarily. Sorting Homology from Analogy

24. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

25. Fig. 26-8 1 Ancestral homologous DNA segments are identical as species 1 and 2 begin to diverge from their common ancestor. Deletion and insertion mutations shift what had been matching sequences in the two species. Of the three homologous regions, two (shaded orange) do not align because of these mutations. Homologous regions realign after a computer program adds gaps in sequence 1.

26. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Ancestral and Derived Characters In comparison with its ancestor, an organism has both shared and different characteristics: – An ancestral character is a character that originated in an ancestor of the taxon. – A derived character is an evolutionary novelty unique to a particular clade. – Derived characters are used to construct phylogenetic trees because they infer evolutionary change!

27. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 26-11 TAXA Lancelet (outgroup) Lamprey Salamander Leopard Turtle Tuna Vertebral column (backbone) Hinged jaws Four walking legs Amniotic (shelled) egg CHARACTERS Hair (a) Character table Hair Hinged jaws Vertebral column Four walking legs Amniotic egg (b) Phylogenetic tree Salamander Leopard Turtle Lamprey Tuna Lancelet (outgroup) 0 00 0 0 0 00 0 0 00 000 1 11 1 1 1 1 11 1 1 11 11 Performing Outgroup Comparisons

28. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 26-UN5 Practicing Outgroup Comparisons

29. Copyright © 2008 Pearson Education, Inc., publishing as Pearson 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 two important phylogenetic principles: – the principle of maximum parsimony; – and the principle of maximum likelihood

30. Fig. 26-14 Human 15% Tree 1: More likelyTree 2: Less likely (b) Comparison of possible trees 15% 5% 10% 25% 20% 40% 30%0 0 0 (a) Percentage differences between sequences Human Mushroom Tulip

31. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Phylogenetic Trees as Hypotheses The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil record evidence. Phylogenetic bracketing allows us to predict features of an ancestor from features of its descendants. This has been applied to infer features of dinosaurs from their descendants: birds and crocodiles.

32. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 26-16 Common ancestor of crocodilians, dinosaurs, and birds Birds Lizards and snakes Crocodilians Ornithischian dinosaurs Saurischian dinosaurs

33. Fig. 26-17 Eggs Front limb Hind limb (a) Fossil remains of Oviraptor and eggs (b) Artist’s reconstruction of the dinosaur’s posture

34. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings New information continues to revise our understanding of the tree of life. Taxonomy is flux and constantly changing in the light of new data. The most recently adopted classification for our tree of life is the three domain system, which includes Bacteria, Archaea, and Eukarya. This system arose from the finding that there are two distinct lineages of prokaryotes. As we gain more tools for analysis, earlier ideas about evolutionary relatedness are changed, and so taxonomy, too, continues to evolve. CharacteristicBacteriaArchaeaEukarya Nuclear EnvelopeNo Yes Membrane- enclosed Organelles No Yes IntronsNoYes Histone ProteinsNoYes Circular Chromosomes Yes No

35. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Revisiting the Central Ideas Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested. Phylogenetic trees and cladograms can represent traits that are either derived or lost due to evolution. Phylogenetic trees and cladograms illustrate speciation that has occurred, in that relatedness of any two groups on the tree is shown by how recently two groups had a common ancestor. Phylogenetic trees and cladograms can be constructed from morphological similarities of living or fossil species, and from DNA and protein sequence similarities – by employing computer programs that have sophisticated ways of measuring and representing relatedness among organisms. Phylogenetic trees and cladograms are dynamic – constantly being revised based on current and emerging knowledge.