1. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Chapter 25 Phylogeny and Systematics

2. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.1 A dragonfly fossil from Brazil, more than 100 million years old

3. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.2 An unexpected family tree

4. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.3 Formation of sedimentary strata containing fossils 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

5. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.4 A gallery of fossil types (a) Dinosaur bones being excavated from sandstone (g) Tusks of a 23,000-year-old mammoth, frozen whole in Siberian ice (e) Boy standing in a 150-million-year-old dinosaur track in Colorado (d) Casts of ammonites, about 375 million years old (f) Insects preserved whole in amber (b) Petrified tree in Arizona, about 190 million years old (c) Leaf fossil, about 40 million years old

6. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.5 Convergent evolution of analogous burrowing characteristics

7. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.6 Aligning segments of DNA 1 C C A T C A G A G T C C 2 C C A T C A G A G T C C G T A Deletion Insertion 1 C C A T C A A G T C C 2 C C A T G T A C A G A G T C C 1 C C A T C A A G T C C 2 C C A T G T A C A G A G T C C 1Ancestral homologous DNA segments are identical as species 1 and species 2 begin to diverge from their common ancestor. 2Deletion and insertion mutations shift what had been matching sequences in the two species. 3Homologous regions (yellow) do not all align because of these mutations. 4Homologous regions realign after a computer program adds gaps in sequence 1.

8. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.7 A molecular homoplasy 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

9. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.8 Hierarchical classification Panthera pardus Panthera Felidae Carnivora Mammalia Chordata Animalia Eukarya Domain Kingdom Phylum Class Order Family Genus Species

10. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.9 The connection between classification and phylogeny Panthera pardus (leopard) Mephitis mephitis (striped skunk) Lutra lutra (European otter) Canis familiaris (domestic dog) Canis lupus (wolf) Panthera Mephitis Lutra Canis FelidaeMustelidaeCanidae Carnivora Order Family Genus Species

11. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Unnumbered Figure p.497 Leopard Domestic cat Common ancestor

12. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Unnumbered Figure p.497 Leopard Domestic cat Common ancestor Wolf

13. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.10 Monophyletic, paraphyletic, and polyphyletic groupings (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.) (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. DE C GH F JK I DE C GH F JK I DE C GH F JK I B A B A B A Grouping 2 Grouping 3 Grouping 1 (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.

14. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.11 Constructing a cladogram Salamander TAXA Turtle Leopard Tuna Lamprey Lancelet (outgroup) 000 00 1 000 01 1 000 11 1 001 11 1 011 11 1 Hair Amniotic (shelled) egg Four walking legs Hinged jaws Vertebral column (backbone) Leopard Hair Amniotic egg Four walking legs Hinged jaws Vertebral column Turtle Salamander Tuna Lamprey Lancelet (outgroup) (a)Character table. A 0 indicates that a character is absent; a 1 indicates that a character is present. (b)Cladogram. Analyzing the distribution of these derived characters can provide insight into vertebrate phylogeny. CHARACTERS

15. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.12 Phylogram Drosophila Lancelet Amphibian Fish Bird Human Rat Mouse

16. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.13 Ultrametric tree Drosophila Lancelet Amphibian Fish Bird Human Rat Mouse Cenozoic Mesozoic Paleozoic Proterozoic 542 251 65.5 Millions of years ago

17. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.14 Trees with different likelihoods Human Tree 1: More likely Mushroom Tulip 40% 0 30% 0 0Human Mushroom Tulip (a) Percentage differences between sequences (b) Comparison of possible trees Tree 2: Less likely 15% 5% 15%20% 5% 10% 15% 25%

18. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.15 Applying Parsimony to a Problem in Molecular Systematics 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. Species I Species II Species III Species IV IIIIIIIVIIIIIIIV I IIIII Sites in DNA sequence Three possible phylogenetic hypothese 1 2 3 4 5 6 7 A G G G G G T G G G A G G G G A G G A A T G G A G A A G I II III IV I IIIIIIV AGGG G G G Bases at site 1 for each species Base-change event 1 First, draw the possible phylogenies for the species (only 3 of the 15 possible trees relating these four species are shown here). 2 Tabulate the molecular data for the species (in this simplified example, the data represent a DNA sequence consisting of just seven nucleotide bases). 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. Species

19. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings IIIIIIIV IIIIIIIV I IIIII IIIIIIIV IIIIIIIV I IIIII IIIIIIIV IIIIIIIV I IIIII IIIIIIIV IIIIIIIV I IIIII GG AA GG AA GG AAGGAA GG AAGGAA GG TGTG T T T TTGG T G T TGGT T T T 10 events 9 events 8 events 4Continuing 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). 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.) Two base changes

20. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.16 Parsimony and the analogy-versus- homology pitfall Lizard Four-chambered heart Bird Mammal Lizard Four-chambered heart Bird Mammal Four-chambered heart (a) Mammal-bird clade (b) Lizard-bird clade

21. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.17 Two types of homologous genes Ancestral gene Speciation Orthologous genes Ancestral gene Gene duplication Paralogous genes (a) (b)

22. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 25.18 The universal tree of life BacteriaEukaryaArchaea 4Symbiosis of chloroplast ancestor with ancestor of green plants 3Symbiosis of mitochondrial ancestor with ancestor of eukaryotes 2Possible fusion of bacterium and archaean, yielding ancestor of eukaryotic cells 1Last common ancestor of all living things 4 3 2 1 1 2 3 4 0 Billion years ago Origin of life