Figure 20.1 What kind of organism is this?

No limbs Eastern glass lizard Monitor lizard Iguanas ANCESTRAL Snakes (with limbs) Snakes Figure 20.2 Convergent evolution of limbless bodies No limbs Geckos

Kingdom: Animalia Domain: Bacteria Domain: Archaea Domain: Eukarya Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Figure 20.3 Linnaean classification Phylum: Chordata Kingdom: Animalia Domain: Bacteria Domain: Archaea Domain: Eukarya

Order Family Genus Species Felidae Panthera pardus (leopard) Panthera Taxidea taxus (American badger) Taxidea Carnivora Mustelidae Lutra lutra (European otter) Lutra 1 Figure 20.4 The connection between classification and phylogeny Canis latrans (coyote) Canidae Canis 2 Canis lupus (gray wolf) 4

where lineages diverge Taxon A Branch point: where lineages diverge Taxon A 3 Taxon B Sister taxa 4 Taxon C 2 Taxon D 5 Taxon E ANCESTRAL LINEAGE 1 Taxon F Figure 20.5 How to read a phylogenetic tree Basal taxon Taxon G This branch point represents the common ancestor of taxa A−G. This branch point forms a polytomy: an unresolved pattern of divergence. 5

(Southern Hemisphere) Results Minke (Southern Hemisphere) Unknowns 1a, 2, 3, 4, 5, 6, 7, 8 Minke (North Atlantic) Unknown 9 Humpback Unknown 1b Blue Figure 20.6 Inquiry: What is the species identity of food being sold as whale meat? Unknowns 10, 11, 12, 13 Fin 6

Figure 20.7 Convergent evolution of analogous burrowing characteristics

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 Deletion 1 C C A T G T A Insertion 1 C C A T C A A G T C C Figure 20.8-4 Aligning segments of DNA (step 4) 2 G T A C C A T C A A G T C C G 1 C C A T C A A G T C C 2 G T A G C C A T C A A G T C C 8

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 Figure 20.9 A molecular homoplasy 9

(a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group A A A 1 1 B Group I B B Group III C C C D D D E E Group II E 2 2 Figure 20.10 Monophyletic, paraphyletic, and polyphyletic groups F F F G G G 10

TAXA Lancelet (outgroup) (outgroup) Lancelet Lamprey Leopard Bass Frog Turtle Vertebral column (backbone) 1 1 1 1 1 Bass Vertebral column Hinged jaws 1 1 1 1 Frog Four walking legs Hinged jaws CHARACTERS 1 1 1 Turtle Four walking legs Amnion 1 1 Figure 20.11 Constructing a phylogenetic tree Amnion Hair 1 Leopard Hair (a) Character table (b) Phylogenetic tree 11

Drosophila Lancelet Zebrafish Frog Chicken Human Mouse Figure 20.12 Branch lengths can represent genetic change Mouse 12

Drosophila Lancelet Zebrafish Frog Chicken Human Mouse 542 251 Figure 20.13 Branch lengths can indicate time Mouse PALEOZOIC MESOZOIC CENOZOIC 542 251 65.5 Present Millions of years ago 13

Three phylogenetic hypotheses: Technique 1/C I I III 1/C II III II 1/C III II I 1/C 1/C Species I Species II Species III 3/A 2/T 3/A Three phylogenetic hypotheses: I I III 2/T 3/A 4/C I I III II III II II III II 4/C 4/C 2/T III II I 3/A 4/C 2/T 4/C 2/T 3/A III II I Site Figure 20.14 Research method: applying parsimony to a problem in molecular systematics 1 2 3 4 Results Species I C T A T I I III Species II C T T C II III II Species III A G A C III II I Ancestral sequence A G T T 6 events 7 events 7 events 14

Lizards and snakes Crocodilians Ornithischian dinosaurs Common ancestor of crocodilians, dinosaurs, and birds Saurischian dinosaurs Figure 20.15 A phylogenetic tree of birds and their close relatives Birds 15

Figure 20.16 A crocodile guards its nest.

(b) Artist’s reconstruction of the dinosaur’s posture based on Front limb Hind limb Eggs Figure 20.17 Fossil support for a phylogenetic prediction (b) Artist’s reconstruction of the dinosaur’s posture based on the fossil findings (a) Fossil remains of Oviraptor and eggs 17

Divergence time (millions of years) 90 60 Number of mutations 30 Figure 20.18 A molecular clock for mammals 30 60 90 120 Divergence time (millions of years) 18

Index of base changes between 0.15 HIV Index of base changes between HIV gene sequences 0.10 Range Adjusted best-fit line (accounts for uncertain dates of HIV sequences 0.05 Figure 20.19 Dating the origin of HIV-1 1900 1920 1940 1960 1980 2000 Year 19

Euglenozoans Forams Diatoms Ciliates Domain Eukarya Red algae Green algae Land plants Amoebas Fungi Animals Nanoarchaeotes Archaea Domain Methanogens COMMON ANCESTOR OF ALL LIFE Thermophiles Figure 20.20 The three domains of life Proteobacteria (Mitochondria)* Chlamydias Spirochetes Domain Bacteria Gram-positive bacteria Cyanobacteria (Chloroplasts)* 20

Domain Eukarya Archaea Domain Domain Bacteria Fungi Plantae Chloroplasts Methanogens Archaea Domain Ancestral cell populations Mitochondria Thermophiles Figure 20.21 A tangled web of life Cyanobacteria Proteobacteria Domain Bacteria 21