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 Chapter 26 Phylogeny and the Tree of Life

2. Fig. 26-1

3. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Overview: Investigating the Tree of Life Phylogeny is the evolutionary history of a species or group of related species The discipline of systematics classifies organisms and determines their evolutionary relationships Systematists use fossil, molecular, and genetic data, geographical distribution, behavior, and life history to infer evolutionary relationships

4. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Concept 26.1: Phylogenies show evolutionary relationships Taxonomy is the ordered division and naming of organisms In the 18th century, 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 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 italicized Both parts together name the species (not the specific epithet alone)

5. Fig. 26-3 Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Kingdom: Animalia ArchaeaDomain: Eukarya Bacteria Linnaeus introduced a system for grouping species in increasingly broad categories The taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species A taxonomic unit at any level of hierarchy is called a taxon

6. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Linking Classification and Phylogeny Systematists depict evolutionary relationships in branching phylogenetic trees A phylogenetic tree represents a hypothesis about evolutionary relationships Each branch point represents the divergence of two species Sister taxa are groups that share an immediate common ancestor A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree A polytomy is a branch from which more than two groups emerge

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

8. 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 Redraw this tree, rotating the branches around branch points “2” & “4”. Does your new version tell a different story about the evolutionary relationships?

9. 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

10. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Applying Phylogenies Phylogeny provides important information about similar characteristics in closely related species A phylogeny was used to identify the species of whale from which “whale meat” originated 13 samples of “whale meat” from Japanese fish markets where sequenced.

11. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 26-6 Fin (Mediterranean) Fin (Iceland) RESULTS Unknown #10, 11, 12 Unknown #13 Blue (North Pacific) Blue (North Atlantic) Gray Unknown #1b Humpback (North Atlantic) Humpback (North Pacific) Unknown #9 Minke (North Atlantic) Minke (Antarctica) Minke (Australia) Unknown #1a, 2, 3, 4, 5, 6, 7, 8 This analysis indicated that DNA sequences of six of the unknown samples (in red) were most closely related to DNA sequences of whales that are not legal to harvest.

12. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 26-UN1 A B A A B B C CC D D D (a) (b) (c) Which of the trees shown below depicts a different evolutionary history for taxa A – D than the other two tress? Explain

13. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Sorting Homology from Analogy When 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 Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages 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

14. Fig. 26-7 Convergent evolution of analogous burrowing characteristics

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

16. Deletion Insertion 1 2 3 4 Ancestral homologous DNA segments are identical as species 1 and species 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.

17. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Concept 26.3: Shared characters are used to construct phylogenetic trees Cladistics groups organisms by common descent A clade is a group of species that includes an ancestral species and all its descendants

18. Fig. 26-10 A A A BBB CCC D D D EEE FF F G GG Group III Group II Group I (a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group A clade is monophyletic, signifying that it consists of the ancestor species and all its descendants A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants A polyphyletic grouping consists of various species that lack a common ancestor

19. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Shared Ancestral and Shared Derived Characters In comparison with its ancestor, an organism has both shared and different characteristics A shared ancestral character is a character that originated in an ancestor of the taxon A shared derived character is an evolutionary novelty unique to a particular clade A character can be both ancestral and derived, depending on the context When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared

20. Fig. 26-11a TAXA Lancelet (outgroup) Lamprey Salamander Leopard Turtle Tuna Vertebral column (backbone) Hinged jaws Four walking legs Amniotic (shelled) egg CHARACTERS Hair (a) Character table - A 0 indicates that a character is absent, a 1 indicates that a character is present 0 00 0 0 0 0 0 0 0 00 0 00 1 1 1 1 11 1 11 1 1 11 1 1

21. Hair Hinged jaws Vertebral column Four walking legs Amniotic egg (b) Phylogenetic tree – Analyzing the distribution of these derived characters can provide insight into vertebrate phylogeny Salamander Leopard Turtle Lamprey Tuna Lancelet (outgroup)

22. Fig. 26-15-1 Species I Three phylogenetic hypotheses: Species II Species III I II III I I II III

23. Fig. 26-15-2 Species I Site Species II Species III I II III I I II III Ancestral sequence 1/C 4 321 C C C C T T T T T TA AA A G G Tabulate the molecular data for the species. The data represent a DNA sequence Consisting of just four nucleotide bases. Now focus on site 1 in the DNA sequence. In the tree on the left, a single base Change event, represented by the purple hatchmark on the branch leading to Species I and II is sufficient to account for the site 1 data. In the other two trees, Two base-change events are necessary

24. Fig. 26-15-3 Species I Site Species II Species III I II III I I II III Ancestral sequence 1/C 4 321 C C C C T T T T T TA AA A G G I I I II III 3/A 2/T 4/C Continuing the comparison of bases at sites 2, 3, and 4 reveals that each of the three trees requires a total of five additional base change events.

25. Fig. 26-15-4 Species I Site Species II Species III I II III I I II III Ancestral sequence 1/C 4 321 C C C C T T T T T TA AA A G G I I I II III 3/A 2/T 4/C I I I II III 7 events 6 events To identify the most parsimonious tree (simplest), we total all of the base change events. Conclusion is the first tree is the most parsimonious.

26. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Concept 26.5: 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 When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared Molecular clocks are calibrated against branches whose dates are known from the fossil record

27. Use the clock to estimate the divergence time for a mammal with a total of 30 mutations in the seven proteins. Divergence time (millions of years) Number of mutations 120 90 60 30 0 0

28. Copyright © 2008 Pearson Education, Inc., publishing as Pearson 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 Application of a molecular clock to one strain of HIV suggests that that strain spread to humans during the 1930s

29. Fig. 26-20 Year Index of base changes between HIV sequences 1960 0.20 194019201900 0 19802000 0.15 0.10 0.05 Range Computer model of HIV The points in the corner are based on DNA sequences for a specific HIV gene collected from patients at different know times. If we project the rate at which changes occurred back in time, we intersect the x-axis in the 1930’s

30. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings From Two Kingdoms to Three Domains 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. The domain taxonomic level contains a single ancestor for all its members, the five kingdom system does not. The tree of life suggests that eukaryotes and archaea are more closely related to each other than to bacteria The tree of life is based largely on rRNA genes, as these have evolved slowly

31. 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

32. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings There have been substantial interchanges of genes between organisms in different domains Horizontal gene transfer is the movement of genes from one genome to another Horizontal gene transfer complicates efforts to build a tree of life

33. 3 Archaea Bacteria Eukarya Billions of years ago 4 21 0 1 – Most recent common ancestor of all living things 2 – Gene transfer between mitochondrial ancestor and ancestor of eukaryotes 3 – Gene transfer between chloroplast ancestor and ancestor of green algae 1 2 3

34. Fig. 26-23 Archaea Bacteria Eukarya Some researchers suggest that eukaryotes arose as an endosymbiosis between a bacterium and archaean If so, early evolutionary relationships might be better depicted by a ring of life instead of a tree of life

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37. Fig. 26-UN10a

38. Fig. 26-UN10b

39. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings You should now be able to: 1.Explain the importance of distinguishing between homology and analogy 2.Distinguish between the following terms: monophyletic, paraphyletic, and polyphyletic groups; shared ancestral and shared derived characters 4.Define horizontal gene transfer and explain how it complicates phylogenetic trees 5.Explain molecular clocks and discuss their limitations