Taxonomy: Hierarchical Organization: Domain Kingdom Phylum Class Order Family Genus species Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Figure 26.3 Hierarchical classification Phylum: Chordata Kingdom: Animalia Domain: Eukarya Bacteria Archaea

Evolutionary Relationships Order Family Genus Species Felidae Panthera Pantherapardus Taxidea Taxidea taxus Carnivora Mustelidae Lutra lutra Lutra Figure 26.4 The connection between classification and phylogeny Canis latrans Canidae Canis Canis lupus Phylogenetic Trees Evolutionary Relationships

Polytomy is a branch from which more than two groups emerge A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree: Branch point (node) Taxon A Taxon B Sister taxa Taxon C ANCESTRAL LINEAGE Taxon D Taxon E Figure 26.5 How to read a phylogenetic tree Taxon F Common ancestor of taxa A–F Polytomy is a branch from which more than two groups emerge

Possible Phylogenetic Trees: Provide important information about similar characteristics in closely related species. A B D B D C C C B D A A (a) (b) (c)

Cladistics - Groups Organisms using Evolutionary Relationships B Group I B B C C C D D D E E Group II E Group III F F F G G G Figure 26.10 Monophyletic, paraphyletic, and polyphyletic groups Monophyletic group / clade Paraphyletic group Polyphyletic group

Inferring Phylogeny from Shared Characters TAXA Lancelet (outgroup) (outgroup) Lancelet Salamander Lamprey Leopard Lamprey Tuna Turtle Vertebral column (backbone) Tuna 1 1 1 1 1 Vertebral column Hinged jaws 1 1 1 1 Salamander Hinged jaws CHARACTERS Four walking legs 1 1 1 Turtle Four walking legs Amniotic (shelled) egg 1 1 Figure 26.11 Constructing a phylogenetic tree Amniotic egg Leopard Hair 1 Hair (a) Character table (b) Phylogenetic tree

Maximum Parsimony Human Mushroom Tulip Human 30% 40% Mushroom 40% 30% 40% Mushroom 40% Tulip (a) Percentage differences between sequences 15% 5% 5% Figure 26.14 Trees with different likelihoods 15% 15% 10% 20% 25% Tree 1: More likely Tree 2: Less likely (b) Comparison of possible trees

Phylogenetic bracketing - predicts features of an ancestor from features of its descendents: Lizards and snakes Crocodilians Ornithischian dinosaurs Common ancestor of crocodilians, dinosaurs, and birds Saurischian dinosaurs lFigure 26.16 A phylogenetic tree of birds and their close relatives Birds

(a) Fossil remains of Oviraptor and eggs Front limb Hind limb Eggs (a) Fossil remains of Oviraptor and eggs Figure 26.17 Fossils support a phylogenetic prediction: Dinosaurs built nests and brooded their eggs (b) Artist’s reconstruction of the dinosaur’s posture

Orthologous genes Paralogous genes Orthologous genes Paralogous genes Ancestral gene Ancestral species Speciation with divergence of gene Orthologous genes Species A Species B Species A Figure 26.18 How two types of homologous genes originate Gene duplication and divergence Paralogous genes Species A after many generations Paralogous genes

Divergence time (millions of years) Molecular Clocks 90 60 Number of mutations 30 Figure 26.19 A molecular clock for mammals 30 60 90 120 Divergence time (millions of years)

HIV Virus 0.20 0.15 Computer model of HIV Index of base changes between HIV sequences 0.10 Range Figure 26.20 Dating the origin of HIV-1 M with a molecular clock 0.05 1900 1920 1940 1960 1980 2000 Year

Three Domain System EUKARYA BACTERIA ARCHAEA Land plants Dinoflagellates Green algae Forams Ciliates Diatoms Red algae Amoebas Cellular slime molds Euglena Trypanosomes Animals Leishmania Fungi Sulfolobus Green nonsulfur bacteria Thermophiles (Mitochondrion) Figure 26.21 The three domains of life Spirochetes Halophiles Chlamydia COMMON ANCESTOR OF ALL LIFE Green sulfur bacteria BACTERIA Methanobacterium Cyanobacteria ARCHAEA (Plastids, including chloroplasts)

Review 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

Clades - Characters

You should now be able to: Explain the justification for taxonomy based on a PhyloCode. Explain the importance of distinguishing between homology and analogy. Distinguish between the following terms: monophyletic, paraphyletic, and polyphyletic groups; shared ancestral and shared derived characters; orthologous and paralogous genes. Define horizontal gene transfer and explain how it complicates phylogenetic trees. 5. Explain molecular clocks and discuss their limitations.