20 Phylogeny

Overview: Investigating the Evolutionary History of Life Legless lizards and snakes evolved from different lineages of lizards with legs Legless lizards have evolved independently in several different groups through adaptation to similar environments 2

Figure 20.1 Figure 20.1 What kind of organism is this? 3

No limbs Eastern glass lizard Monitor lizard Iguanas ANCESTRAL Snakes Figure 20.2 No limbs Eastern glass lizard Monitor lizard Iguanas ANCESTRAL LIZARD (with limbs) Snakes Figure 20.2 Convergent evolution of limbless bodies No limbs Geckos 4

Phylogeny is the evolutionary history of a species or group of related species The discipline of systematics classifies organisms and determines their evolutionary relationships 5

Concept 20.1: Phylogenies show evolutionary relationships Taxonomy is the ordered division and naming of organisms 6

Binomial Nomenclature 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 7

The two-part scientific name of a species is called a binomial 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) 8

Hierarchical Classification Linnaeus introduced a system for grouping species in increasingly broad categories The taxonomic groups from narrow to broad are species, genus, family, order, class, phylum, kingdom, and domain 9

Kingdom: Animalia Domain: Bacteria Domain: Archaea Domain: Eukarya Figure 20.3 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 10

A taxonomic unit at any level of hierarchy is called a taxon The broader taxa are not comparable between lineages For example, an order of snails has less genetic diversity than an order of mammals 11

Linking Classification and Phylogeny Systematists depict evolutionary relationships in branching phylogenetic trees 12

Order Family Genus Species Felidae Panthera pardus (leopard) Panthera Figure 20.4 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) 13

Linnaean classification and phylogeny can differ from each other Systematists have proposed that classification be based entirely on evolutionary relationships 14

Sister taxa are groups that share an immediate common ancestor A phylogenetic tree represents a hypothesis about evolutionary relationships Each branch point represents the divergence of two taxa from a common ancestor Sister taxa are groups that share an immediate common ancestor 15

A polytomy is a branch from which more than two groups emerge A rooted tree includes a branch to represent the most recent common ancestor of all taxa in the tree A basal taxon diverges early in the history of a group and originates near the common ancestor of the group A polytomy is a branch from which more than two groups emerge 16

where lineages diverge Taxon A Figure 20.5 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. 17

What We Can and Cannot Learn from Phylogenetic Trees Phylogenetic trees show patterns of descent, not phenotypic similarity Phylogenetic trees do not generally indicate when a species evolved or how much change occurred in a lineage It should not be assumed that a taxon evolved from the taxon next to it 18

Applying Phylogenies Phylogeny provides important information about similar characteristics in closely related species Phylogenetic trees based on DNA sequences can be used to infer species identities For example: A phylogeny was used to identify the species of whale from which “whale meat” originated 19

(Southern Hemisphere) Figure 20.6 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 20

Concept 20.2: Phylogenies are inferred from morphological and molecular data To infer phylogeny, systematists gather information about morphologies, genes, and biochemistry of living organisms The similarities used to infer phylogenies must result from shared ancestry 21

Morphological and Molecular Homologies Phenotypic and genetic similarities due to shared ancestry are called homologies Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences 22

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 23

Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages 24

Figure 20.7 Figure 20.7 Convergent evolution of analogous burrowing characteristics 25

Bat and bird wings are homologous as forelimbs, but analogous as functional wings Analogous structures or molecular sequences that evolved independently are also called homoplasies 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 26

Evaluating Molecular Homologies Molecular homologies are determined based on the degree of similarity in nucleotide sequence between taxa Systematists use computer programs when analyzing comparable DNA segments from different organisms 27

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 Figure 20.8-1 Figure 20.8-1 Aligning segments of DNA (step 1) 28

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 Figure 20.8-2 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 C A G A G T C C 2 C C A T C A G A G T C C G T A Insertion Figure 20.8-2 Aligning segments of DNA (step 2) 29

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 Figure 20.8-3 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 C A G A G T C C 2 C C A T C A G A G T C C G T A Insertion 1 C C A T C A A G T C C Figure 20.8-3 Aligning segments of DNA (step 3) 2 G T A C C A T C A A G T C C G 30

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 Figure 20.8-4 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 C A G A G T C C 2 C C A T C A G A G T C C 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 31

Shared bases in nucleotide sequences that are otherwise very dissimilar are called molecular homoplasies 32

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 Figure 20.9 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 33

Concept 20.3: Shared characters are used to construct phylogenetic trees Once homologous characters have been identified, they can be used to infer a phylogeny 34

Cladistics Cladistics classifies organisms by common descent A clade is a group of species that includes an ancestral species and all its descendants Clades can be nested in larger clades, but not all groupings of organisms qualify as clades 35

A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants 36

(a) Monophyletic group (clade) (b) Paraphyletic group Figure 20.10 (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 37

(a) Monophyletic group (clade) Figure 20.10a (a) Monophyletic group (clade) A 1 B Group I C D Figure 20.10a Monophyletic, paraphyletic, and polyphyletic groups (part 1: monophyletic) E F G 38

A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants 39

(b) Paraphyletic group Figure 20.10b (b) Paraphyletic group A B C D Figure 20.10b Monophyletic, paraphyletic, and polyphyletic groups (part 2: paraphyletic) E Group II 2 F G 40

A polyphyletic grouping consists of various taxa with different ancestors 41

(c) Polyphyletic group Figure 20.10c (c) Polyphyletic group A 1 B Group III C D Figure 20.10c Monophyletic, paraphyletic, and polyphyletic groups (part 3: polyphyletic) E 2 F G 42

Shared Ancestral and Shared Derived Characters In comparison with its ancestor, an organism has both shared and different characteristics 43

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 44

Inferring Phylogenies Using Derived Characters When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared 45

TAXA Lancelet (outgroup) (outgroup) Lancelet Lamprey Leopard Bass Frog Figure 20.11 TAXA Lancelet (outgroup) (outgroup) Lancelet Lamprey Leopard Bass Frog Turtle Lamprey 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 46

TAXA (outgroup) Lancelet Lamprey Leopard Bass Turtle Frog Vertebral Figure 20.11a TAXA (outgroup) Lancelet Lamprey Leopard Bass Turtle Frog Vertebral column (backbone) 1 1 1 1 1 Hinged jaws 1 1 1 1 Four walking legs CHARACTERS 1 1 1 Figure 20.11a Constructing a phylogenetic tree (part 1: character table) Amnion 1 1 Hair 1 (a) Character table 47

Lancelet (outgroup) Lamprey Bass Vertebral column Frog Hinged jaws Figure 20.11b Lancelet (outgroup) Lamprey Bass Vertebral column Frog Hinged jaws Turtle Four walking legs Figure 20.11b Constructing a phylogenetic tree (part 2: phylogenetic tree) Amnion Leopard Hair (b) Phylogenetic tree 48

The outgroup is a group that has diverged before the ingroup An outgroup is a species or group of species that is closely related to the ingroup, the various species being studied The outgroup is a group that has diverged before the ingroup Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics 49

Characters shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups from a common ancestor 50

Phylogenetic Trees with Proportional Branch Lengths In some trees, the length of a branch can reflect the number of genetic changes that have taken place in a particular DNA sequence in that lineage 51

Drosophila Lancelet Zebrafish Frog Chicken Human Mouse Figure 20.12 Figure 20.12 Branch lengths can represent genetic change Mouse 52

In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record 53

Drosophila Lancelet Zebrafish Frog Chicken Human Mouse 542 251 Figure 20.13 Drosophila Lancelet Zebrafish Frog Chicken Human Figure 20.13 Branch lengths can indicate time Mouse PALEOZOIC MESOZOIC CENOZOIC 542 251 65.5 Present Millions of years ago 54

Maximum Parsimony Systematists can never be sure of finding the best tree in a large data set They narrow possibilities by applying the principle of maximum parsimony 55

Computer programs are used to search for trees that are parsimonious Maximum parsimony assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely Computer programs are used to search for trees that are parsimonious 56

Three phylogenetic hypotheses: Figure 20.14 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 57

I I III II III II III II I Species I Species II Species III Figure 20.14a Technique Species I Species II Species III Three phylogenetic hypotheses: Figure 20.14a Research method: applying parsimony to a problem in molecular systematics (part 1: hypothesis) I I III II III II III II I 58

Technique Site 1 2 3 4 Species I C T A T Species II C T T C Figure 20.14b Technique Site 1 2 3 4 Species I C T A T Species II C T T C Species III A G A C Figure 20.14b Research method: applying parsimony to a problem in molecular systematics (part 2: table) Ancestral sequence A G T T 59

Technique 1/C I I III 1/C II III II 1/C III II I 1/C 1/C 3/A 2/T 3/A I Figure 20.14c Technique 1/C I I III 1/C II III II 1/C III II I 1/C 1/C 3/A 2/T 3/A I I III 2/T Figure 20.14c Research method: applying parsimony to a problem in molecular systematics (part 3: comparison) 3/A 4/C II III II 4/C 4/C 2/T III II I 3/A 4/C 2/T 4/C 2/T 3/A 60

Results I I III II III II III II I 6 events 7 events 7 events Figure 20.14d Results I I III II III II III II I Figure 20.14d Research method: applying parsimony to a problem in molecular systematics (part 4: results) 6 events 7 events 7 events 61

Phylogenetic Trees as Hypotheses The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil Phylogenetic hypotheses are modified when new evidence arises 62

Phylogenetic bracketing allows us to predict features of ancestors and their extinct descendants based on the features of closely related living descendants For example, phylogenetic bracketing allows us to infer characteristics of dinosaurs based on shared characters in modern birds and crocodiles 63

Lizards and snakes Crocodilians Ornithischian dinosaurs Common Figure 20.15 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 64

The fossil record supports nest building and brooding in dinosaurs Birds and crocodiles share several features: four-chambered hearts, song, nest building, and brooding These characteristics likely evolved in a common ancestor and were shared by all of its descendants, including dinosaurs The fossil record supports nest building and brooding in dinosaurs 65

Figure 20.16 Figure 20.16 A crocodile guards its nest. 66

(b) Artist’s reconstruction of the dinosaur’s posture based on Figure 20.17 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 67

(a) Fossil remains of Oviraptor and eggs Figure 20.17a Front limb Hind limb Figure 20.17a Fossil support for a phylogenetic prediction (part 1: fossil) Eggs (a) Fossil remains of Oviraptor and eggs 68

(b) Artist’s reconstruction of the dinosaur’s posture based on Figure 20.17b Figure 20.17b Fossil support for a phylogenetic prediction (part 2: artist’s reconstruction) (b) Artist’s reconstruction of the dinosaur’s posture based on the fossil findings 69

Concept 20.4: Molecular clocks help track evolutionary time To extend molecular phylogenies beyond the fossil record, we must make an assumption about how molecular change occurs over time 70

Molecular Clocks A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change The number of nucleotide substitutions in related genes is assumed to be proportional to the time since they last shared a common ancestor 71

Individual genes vary in how clocklike they are Molecular clocks are calibrated by plotting the number of genetic changes against the dates of branch points known from the fossil record Individual genes vary in how clocklike they are 72

Divergence time (millions of years) Figure 20.18 90 60 Number of mutations 30 Figure 20.18 A molecular clock for mammals 30 60 90 120 Divergence time (millions of years) 73

Differences in Clock Speed Some mutations are selectively neutral and have little or no effect on fitness Neutral mutations should be regular like a clock The neutral mutation rate is dependant on how critical a gene’s amino acid sequence is to survival 74

Potential Problems with Molecular Clocks Molecular clocks do not run as smoothly as expected if mutations were selectively neutral Irregularities result from natural selection in which some DNA changes are favored over others Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty The use of multiple genes may improve estimates 75

Applying a Molecular Clock: Dating the Origin of HIV Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates HIV spread to humans more than once Comparison of HIV samples 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 76

Animation: Class Schemes Right click slide / Select play

Index of base changes between Figure 20.19 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 78

Concept 20.5: New information continues to revise our understanding of evolutionary history Recently, systematists have gained insight into the very deepest branches of the tree of life through analysis of DNA sequence data 79

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 80

Euglenozoans Forams Diatoms Ciliates Domain Eukarya Red algae Figure 20.20 Euglenozoans Forams Diatoms Ciliates Red algae Domain Eukarya 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)* 81

Euglenozoans Forams Diatoms Ciliates Domain Eukarya Red algae Figure 20.20a Euglenozoans Forams Diatoms Ciliates Red algae Domain Eukarya Green algae Land plants Figure 20.20a The three domains of life (part 1: eukarya) Amoebas Fungi Animals 82

Nanoarchaeotes Archaea Domain Methanogens Thermophiles Figure 20.20b Figure 20.20b The three domains of life (part 2: archaea) 83

Proteobacteria (Mitochondria)* Chlamydias Domain Bacteria Spirochetes Figure 20.20c Proteobacteria (Mitochondria)* Chlamydias Spirochetes Domain Bacteria Gram-positive bacteria Figure 20.20c The three domains of life (part 3: bacteria) Cyanobacteria (Chloroplasts)* 84

Domains Bacteria and Archaea are single-celled prokaryotes The three-domain system highlights the importance of single-celled organisms in the history of life Domains Bacteria and Archaea are single-celled prokaryotes Only three lineages in the domain Eukarya are dominated by multicellular organisms, kingdoms Plantae, Fungi, and Animalia 85

The Important Role of Horizontal Gene Transfer 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, which have evolved slowly, allowing detection of homologies between distantly related organisms Other genes indicate different evolutionary relationships 86

Horizontal gene transfer complicates efforts to build a tree of life 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 occurs by exchange of transposable elements and plasmids, viral infection, and fusion of organisms Horizontal gene transfer complicates efforts to build a tree of life 87

Horizontal gene transfer may have been common enough that the early history of life is better depicted by a tangled web than a branching tree 88

Domain Eukarya Archaea Domain Domain Bacteria Fungi Plantae Figure 20.21 Fungi Domain Eukarya Plantae Chloroplasts Methanogens Archaea Domain Ancestral cell populations Mitochondria Thermophiles Figure 20.21 A tangled web of life Cyanobacteria Proteobacteria Domain Bacteria 89

Domain Eukarya Fungi Plantae Ancestral cell populations Figure 20.21a Figure 20.21a A tangled web of life (part 1: eukarya) 90

Archaea Domain Domain Bacteria Methanogens Thermophiles Ancestral cell Figure 20.21b Methanogens Archaea Domain Thermophiles Ancestral cell populations Cyanobacteria Proteobacteria Domain Bacteria Figure 20.21b A tangled web of life (part 2: archaea and bacteria) 91

(a) (b) (c) A B A B D C C C B D A A Figure 20.UN01 Figure 20.UN01 Concept check 20.1, p. 385 (a) (b) (c) 92

Reptiles (including birds) OTHER TETRAPODS Dimetrodon Cynodonts Figure 20.UN02 Reptiles (including birds) OTHER TETRAPODS Dimetrodon Cynodonts Figure 20.UN02 Concept check 20.3, p. 392 Mammals 93

Brown bear Polar bear American black bear Asian black bear Sun bear Figure 20.UN03 Brown bear 7 Polar bear 4 American black bear 6 Asian black bear 5 3 Sun bear 2 Figure 20.UN03 Skills exercise: interpreting data in a phylogenetic tree Sloth bear 1 Spectacled bear Giant panda 94

Branch point Taxon A Most recent Taxon B common ancestor Sister taxa Figure 20.UN04 Branch point Taxon A Most recent common ancestor Taxon B Sister taxa Taxon C Taxon D Taxon E Figure 20.UN04 Summary of key concepts: evolutionary relationships Polytomy Taxon F Taxon G Basal taxon 95

A A A B B B C C C D D D E E E F F F G G G Monophyletic group Figure 20.UN05 Monophyletic group Polyphyletic group A A A B B B C C C D D D E E E Figure 20.UN05 Summary of key concepts: shared characters F F F G G G Paraphyletic group 96

Salamander Lizard Goat Human Figure 20.UN06 Figure 20.UN06 Test your understanding, question 5 Human 97

Figure 20.UN07 Figure 20.UN07 Test your understanding, question 8 98