Chapter 26 Phylogeny and the Tree of Life

Chapter 26 Phylogeny and the Tree of Life Power. Point® Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fig. 26 -1

Overview: Investigating the Tree of Life • Phylogeny is the evolutionary history of a species or group of related species • The discipline of systematics classifies organisms and determines their evolutionary relationships • Systematists use fossil, molecular, and genetic data to infer evolutionary relationships Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fig. 26 -2

Concept 26. 1: Phylogenies show evolutionary relationships • Taxonomy is the ordered division and naming of organisms Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Binomial Nomenclature • In the 18 th 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 Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

• 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) Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Hierarchical Classification • Linnaeus introduced a system for grouping species in increasingly broad categories • The taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species • A taxonomic unit at any level of hierarchy is called a taxon Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

Linking Classification and Phylogeny • Systematists depict evolutionary relationships in branching phylogenetic trees Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

• Linnaean classification and phylogeny can differ from each other • Systematists have proposed the Phylo. Code, which recognizes only groups that include a common ancestor and all its descendents Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

• A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree • A polytomy is a branch from which more than two groups emerge Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

• A phylogenetic tree represents a hypothesis about evolutionary relationships • Each branch point, or node, represents the divergence of two or more species • A node behind another node indicates a common ancestor that lived prior. • Sister taxa are groups that share an immediate common ancestor Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

What We Can and Cannot Learn from Phylogenetic Trees • * Phylogenetic trees may not indicate when a species evolved or how much genetic change occurred in a lineage. Old divisions were arbitrarily chosen by taxonomists using general homological evidence from studying morphology and fossils. • * It shouldn’t be assumed that a taxon evolved from the taxon behind it, as we continually update by placing new species, finding extinct species, and in general examining current evidence. Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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 Sister taxa

Applying Phylogenies • Ex: We know the closest living relatives of corn based on DNA data. They are two species of wild grasses we can use as “reserve” organisms of beneficial genes! • Ex: A phylogeny was used to identify the species of whale from which “whale meat” originated. This proved illegal harvesting of endangered species was taking place. • Ex: Phylogenies of anthrax bacteria helped researchers identify the source of a particular strain of anthrax Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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)

Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

Concept 26. 2: Phylogenies are inferred from morphological and molecular data • To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Morphological and Molecular Homologies • Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Sorting Homology from Analogy • When constructing a phylogeny, we need to distinguish whether a similarity is the result of homology or analogy! • Homology is similarity due to shared ancestry, from DIVERGENT evolution. • Analogy is similarity due to CONVERGENT evolution. Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

• CONVERGENT evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages. Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Which creatures/structures show convergency/analogy and which show divergency/homology? Last common ancestor-320 mya Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fig. 26 -7 Australian marsupial (a mole-like mammal) North American MOLE (a eutherian) Last known common ancestor-140 mya

• 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 Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Evaluating Molecular Homologies • Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fig. 26 -8 1 Deletion 2 Insertion 3 4

Fig. 26 -8 a 1 Deletion 2 Insertion

Fig. 26 -8 b 3 4

• It is also important to distinguish homology from analogy in molecular similarities • Mathematical tools help to identify molecular homoplasies, or coincidences • Molecular systematics uses DNA and other molecular data to determine evolutionary relationships Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fig. 26 -9

Concept 26. 3: Shared characters are used to construct phylogenetic trees • Once homologous characteristics have been identified, they can be used to determine phylogeny (evolutionary history). • Several species placed into a group that centers around a specific homologous characteristic is known as a CLADE. Clades include ancestral species and all of it’s descendants that share the ancestor’s specific characteristic identified. • The study of clades is known as CLADISTICS. Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Cladistics • Clades can be nested in larger clades, but not all groupings of organisms qualify as clades • A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

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 Provide 1 example of a monophyletic clade using your previously drawn Carnivora tree.

• A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

• A polyphyletic grouping consists of various species that lack a common ancestor Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

Shared Ancestral and Shared Derived Characters • In comparison with its ancestor, an organism has both shared and different characteristics Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

• 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 Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Inferring Phylogenies Using Derived Characters • When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

Fig. 26 -11 a Tuna Salamander Turtle Leopard 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 CHARACTERS Lancelet Lamprey TAXA (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 -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

• An outgroup is a species or group of species that is closely related to the ingroup, the various species being studied • Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

• Homologies shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups from a common ancestor Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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 Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

• In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

Maximum Parsimony and Maximum Likelihood • Systematists can never be sure of finding the best tree in a large data set • They narrow possibilities by applying the principles of maximum parsimony and maximum likelihood Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

• Maximum parsimony assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely • The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

• Computer programs are used to search for trees that are parsimonious and likely Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

Phylogenetic Trees as Hypotheses • The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil • Phylogenetic bracketing allows us to predict features of an ancestor from features of its descendents Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

• This has been applied to infer features of dinosaurs from their descendents: birds and crocodiles Animation: The Geologic Record Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

Concept 26. 4: An organism’s evolutionary history is documented in its genome • Comparing nucleic acids or other molecules to infer relatedness is a valuable tool for tracing organisms’ evolutionary history • DNA that codes for r. RNA changes relatively slowly and is useful for investigating branching points hundreds of millions of years ago • mt. DNA evolves rapidly and can be used to explore recent evolutionary events Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Gene Duplications and Gene Families • Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes • Like homologous genes, duplicated genes can be traced to a common ancestor Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

• Orthologous genes are found in a single copy in the genome and are homologous between species • They can diverge only after speciation occurs Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

• Paralogous genes result from gene duplication, so are found in more than one copy in the genome • They can diverge within the clade that carries them and often evolve new functions Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

Genome Evolution • Orthologous genes are widespread and extend across many widely varied species • Gene number and the complexity of an organism are not strongly linked • Genes in complex organisms appear to be very versatile and each gene can perform many functions Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Concept 26. 5: Molecular clocks help track evolutionary time • To extend molecular phylogenies beyond the fossil record, we must make an assumption about how change occurs over time Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Molecular Clocks • A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change • In orthologous genes, nucleotide substitutions are proportional to the time since they last shared a common ancestor • In paralogous genes, nucleotide substitutions are proportional to the time since the genes became duplicated Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

• Molecular clocks are calibrated against branches whose dates are known from the fossil record Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

Neutral Theory • Neutral theory states that much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection • It states that the rate of molecular change in these genes and proteins should be regular like a clock Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Difficulties with Molecular Clocks • The molecular clock does not run as smoothly as neutral theory predicts • 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 Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Applying a Molecular Clock: The Origin of HIV • Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates • Comparison of HIV samples throughout the epidemic shows that the virus evolved in a very clocklike way • Application of a molecular clock to one strain of HIV suggests that strain spread to humans during the 1930 s Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

Concept 26. 6: New information continues to revise our understanding of the tree of life • Recently, we have gained insight into the very deepest branches of the tree of life through molecular systematics Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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 Animation: Classification Schemes Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

A Simple Tree of All Life • 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 r. RNA genes, as these have evolved slowly Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

• 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 complicates efforts to build a tree of life Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

What might this indicate about the influence of bacteria in our gut? Bacteria Eukarya Archaea 4 3 2 Billions of years ago 1 0

Is the Tree of Life Really a Ring? • Some researchers suggest that eukaryotes arose as an endosymbiosis between a bacterium and archaean • If so, early evolutionary relationships might be better depicted by a ring of life instead of a tree of life Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

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Fig. 26 -UN 10 a

Fig. 26 -UN 10 b

You should now be able to: 1. Explain the justification for taxonomy based on a Phylo. Code 2. Explain the importance of distinguishing between homology and analogy 3. Distinguish between the following terms: monophyletic, paraphyletic, and polyphyletic groups; shared ancestral and shared derived characters; orthologous and paralogous genes Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

4. Define horizontal gene transfer and explain how it complicates phylogenetic trees 5. Explain molecular clocks and discuss their limitations Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings