Fig 26 1 Fig 26 2 Fig 26

Fig. 26 -1

Fig. 26 -2

Fig. 26 -3 Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Kingdom: Animalia Bacteria Domain: Eukarya Archaea

Fig. 26 -3 a Class: Mammalia Phylum: Chordata Kingdom: Animalia Bacteria Domain: Eukarya Archaea

Fig. 26 -3 b Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora

Fig. 26 -4 Order Family Genus Species Taxidea taxus Lutra Mustelidae Panthera Felidae Carnivora Panthera pardus Lutra lutra Canis Canidae Canis latrans Canis lupus

Fig. 26 -5 Branch point (node) Taxon A Taxon B Taxon C ANCESTRAL LINEAGE Taxon D Taxon E Taxon F Common ancestor of taxa A–F Polytomy Sister taxa

Fig. 26 -6 RESULTS Minke (Antarctica) Minke (Australia) Unknown #1 a, 2, 3, 4, 5, 6, 7, 8 Minke (North Atlantic) Unknown #9 Humpback (North Atlantic) Humpback (North Pacific) Unknown #1 b Gray Blue (North Atlantic) Blue (North Pacific) Unknown #10, 11, 12 Unknown #13 Fin (Mediterranean) Fin (Iceland)

Fig. 26 -6 a RESULTS Minke (Antarctica) Minke (Australia) Unknown #1 a, 2, 3, 4, 5, 6, 7, 8 Minke (North Atlantic) Unknown #9

Fig. 26 -6 b Humpback (North Atlantic) Humpback (North Pacific) Unknown #1 b Gray Blue (North Atlantic) Blue (North Pacific)

Fig. 26 -6 c Unknown #10, 11, 12 Unknown #13 Fin (Mediterranean) Fin (Iceland)

Fig. 26 -UN 1 (a) A B D C C C B D A A (b) (c)

Fig. 26 -7

Fig. 26 -8 1 Deletion 2 Insertion 3 4

Fig. 26 -8 a 1 Deletion 2 Insertion

Fig. 26 -8 b 3 4

Fig. 26 -9

Fig. 26 -10 A A A B B C C C D D D E E F F F G G G B Group I (a) Monophyletic group (clade) Group II (b) Paraphyletic group E Group III (c) Polyphyletic group

Fig. 26 -10 a A B Group I C D E F G (a) Monophyletic group (clade)

Fig. 26 -10 b A B C D E Group II F G (b) Paraphyletic group

Fig. 26 -10 c A B C D E Group III F G (c) Polyphyletic group

Fig. 26 -11 Lamprey Tuna Salamander Turtle Leopard Lancelet (outgroup) CHARACTERS TAXA Vertebral column (backbone) 0 1 1 1 Hinged jaws 0 0 1 1 Lamprey Tuna Vertebral column Salamander Hinged jaws Four walking legs 0 0 0 1 1 1 Amniotic (shelled) egg 0 0 1 1 Hair 0 0 0 1 (a) Character table Turtle Four walking legs Amniotic egg Leopard Hair (b) Phylogenetic tree

Lamprey Tuna Salamander Turtle Leopard TAXA Lancelet (outgroup) CHARACTERS Fig. 26 -11 a Vertebral column (backbone) 0 1 1 1 Hinged jaws 0 0 1 1 Four walking legs 0 0 0 1 1 1 Amniotic (shelled) egg 0 0 1 1 Hair 0 0 0 1 (a) Character table

Fig. 26 -11 b Lancelet (outgroup) Lamprey Tuna Vertebral column Salamander Hinged jaws Turtle Four walking legs Amniotic egg Leopard Hair (b) Phylogenetic tree

Fig. 26 -12 Drosophila Lancelet Zebrafish Frog Chicken Human Mouse

Fig. 26 -13 Drosophila Lancelet Zebrafish Frog Chicken Human Mouse PALEOZOIC 542 MESOZOIC 251 Millions of years ago CENOZOIC 65. 5 Present

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

Fig. 26 -14 a Human Mushroom Tulip 0 30% 40% 0 40% Tulip (a) Percentage differences between sequences 0

Fig. 26 -14 b 15% 5% 5% 15% 10% 25% 20% Tree 1: More likely Tree 2: Less likely (b) Comparison of possible trees

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

Fig. 26 -15 -2 Site 1 2 3 4 Species I C T A T Species II C T T C Species III A G A C Ancestral sequence A G T T 1/C II I III II 1/C II III 1/C

Fig. 26 -15 -3 Site 1 2 3 4 Species I C T A T Species II C T T C Species III A G A C Ancestral sequence A G T T 1/C II I III II 1/C II I 1/C 3/A 2/T I 2/T 3/A 4/C II II 2/T 4/C III 3/A 4/C I II 4/C 1/C I 2/T 3/A

Fig. 26 -15 -4 Site 1 2 3 4 Species I C T A T Species II C T T C Species III A G A C Ancestral sequence A G T T 1/C II I III II 1/C II I 1/C 3/A 2/T I 2/T 3/A 4/C III II 2/T 4/C II III 6 events I II 4/C 1/C I 2/T 3/A 2/T 4/C I I III II II I 7 events

Fig. 26 -16 Lizards and snakes Crocodilians Common ancestor of crocodilians, dinosaurs, and birds Ornithischian dinosaurs Saurischian dinosaurs Birds

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

Fig. 26 -17 a Front limb Hind limb Eggs (a) Fossil remains of Oviraptor and eggs

Fig. 26 -17 b (b) Artist’s reconstruction of the dinosaur’s posture

Fig. 26 -18 Ancestral gene Ancestral species Speciation with divergence of gene Species A Orthologous genes Species B (a) Orthologous genes Species A Gene duplication and divergence Paralogous genes Species A after many generations (b) Paralogous genes

Fig. 26 -18 a Ancestral gene Ancestral species Speciation with divergence of gene Species A Orthologous genes (a) Orthologous genes Species B

Fig. 26 -18 b Species A Gene duplication and divergence Paralogous genes Species A after many generations (b) Paralogous genes

Number of mutations Fig. 26 -19 90 60 30 0 0 30 60 90 Divergence time (millions of years) 120

Index of base changes between HIV sequences Fig. 26 -20 0. 15 0. 10 Computer model of HIV Range 0. 05 0 1900 1920 1940 1960 Year 1980 2000

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

Fig. 26 -21 a Green nonsulfur bacteria (Mitochondrion) Spirochetes COMMON ANCESTOR OF ALL LIFE Chlamydia Green sulfur bacteria BACTERIA Cyanobacteria (Plastids, including chloroplasts)

Fig. 26 -21 b Sulfolobus Thermophiles Halophiles Methanobacterium ARCHAEA

Fig. 26 -21 c EUKARYA Land plants Green algae Cellular slime molds Dinoflagellates Forams Ciliates Red algae Diatoms Amoebas Animals Fungi Euglena Trypanosomes Leishmania

Fig. 26 -22 Bacteria Eukarya Archaea 4 3 2 Billions of years ago 1 0

Fig. 26 -23 Eukarya Bacteria Archaea

Fig. 26 -UN 2 Node Taxon A Taxon B Taxon C Taxon D Taxon E Most recent common ancestor Polytomy Taxon F Sister taxa

Fig. 26 -UN 3 Monophyletic group A A A B B B C C C D D D E E E F F F G G G Paraphyletic group Polyphyletic group

Fig. 26 -UN 4 Salamander Lizard Goat Human

Fig. 26 -UN 5

Fig. 26 -UN 6

Fig. 26 -UN 7

Fig. 26 -UN 8

Fig. 26 -UN 9

Fig. 26 -UN 10

Fig. 26 -UN 10 a

Fig. 26 -UN 10 b