Chapter 26

Phylogeny and the Tree of Life

PowerPoint® 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

26-2 .Fig.

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

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.Binomial Nomenclature • In the 18th century. publishing as Pearson Benjamin Cummings .

. Inc. called the specific epithet. publishing as Pearson Benjamin Cummings . is unique for each species within the genus • The first letter of the genus is capitalized.• The two-part scientific name of a species is called a binomial • The first part of the name is the genus • The second part. and the entire species name is italicized • Both parts together name the species (not the specific epithet alone) Copyright © 2008 Pearson Education.

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

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

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

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

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

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

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

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

. 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.

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

Inc. publishing as Pearson Benjamin Cummings ..What We Can and Cannot Learn from Phylogenetic Trees • Phylogenetic trees do show patterns of descent • Phylogenetic trees do not indicate when species evolved or how much genetic change occurred in a lineage • It shouldn’t be assumed that a taxon evolved from the taxon next to it Copyright © 2008 Pearson Education.

. Inc.Applying Phylogenies • Phylogeny provides important information about similar characteristics in closely related species • A phylogeny was used to identify the species of whale from which “whale meat” originated Copyright © 2008 Pearson Education. publishing as Pearson Benjamin Cummings .

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

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

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

Fig. 26-6c

Unknown #10, 11, 12 Unknown #13 Fin (Mediterranean) Fin (Iceland)

• 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-UN1

A B C D (a) (b)

B D C A (c)

D C B A

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

Inc.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.. publishing as Pearson Benjamin Cummings .

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 Copyright © 2008 Pearson Education..Sorting Homology from Analogy • When constructing a phylogeny. Inc. publishing as Pearson Benjamin Cummings .

26-7 .Fig.

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.• Bat and bird wings are homologous as forelimbs. publishing as Pearson Benjamin Cummings . the more likely it is that they are homologous Copyright © 2008 Pearson Education. 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.

. 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.

Fig. 26-8 1 Deletion 2 Insertion 3 4 .

26-8a 1 Deletion 2 Insertion .Fig.

26-8b 3 4 .Fig.

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

26-9 .Fig.

Inc.Concept 26. publishing as Pearson Benjamin Cummings ..3: Shared characters are used to construct phylogenetic trees • Once homologous characters have been identified. they can be used to infer a phylogeny Copyright © 2008 Pearson Education.

Cladistics • Cladistics groups 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. Inc.. publishing as Pearson Benjamin Cummings . but not all groupings of organisms qualify as clades Copyright © 2008 Pearson Education.

publishing as Pearson Benjamin Cummings . signifying that it consists of the ancestor species and all its descendants Copyright © 2008 Pearson Education. Inc..• A valid clade is monophyletic.

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

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

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

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

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

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

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

Inc..• 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. publishing as Pearson Benjamin Cummings .

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.

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

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

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

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 .• An outgroup is a species or group of species that is closely related to the ingroup.

• 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. publishing as Pearson Benjamin Cummings .. Inc.

Inc. publishing as Pearson Benjamin Cummings .. 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.Phylogenetic Trees with Proportional Branch Lengths • In some trees.

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

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

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

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. publishing as Pearson Benjamin Cummings .. Inc.

.• 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 Human Mushroom Tulip 0 Mushroom 30% 0 Tulip 40% 40% 0 (a) Percentage differences between sequences 15% 5% 15% 5% 15% 10% 20% 25% Tree 1: More likely Tree 2: Less likely (b) Comparison of possible trees .

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

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

• 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 I Species II Species III Three phylogenetic hypotheses: I I II III III II III II I .

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

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

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

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

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

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

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

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

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

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 rRNA changes relatively slowly and is useful for investigating branching points hundreds of millions of years ago • mtDNA evolves rapidly and can be used to explore recent evolutionary events Copyright © 2008 Pearson Education.Concept 26.. publishing as Pearson Benjamin Cummings . Inc.

Gene Duplications and Gene Families • Gene duplication increases the number of genes in the genome. publishing as Pearson Benjamin Cummings . 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 .. Inc.• 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.

• 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. 26-18a

Ancestral gene

Ancestral species Speciation with divergence of gene

Species A

Orthologous genes

Species B

(a) Orthologous genes

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

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

publishing as Pearson Benjamin Cummings . nucleotide substitutions are proportional to the time since they last shared a common ancestor • In paralogous genes..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 the genes became duplicated Copyright © 2008 Pearson Education. Inc.

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

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

publishing as Pearson Benjamin Cummings .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.

.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 .

Inc.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 that strain spread to humans during the 1930s Copyright © 2008 Pearson Education.. publishing as Pearson Benjamin Cummings .

05 0 1900 1920 1940 1960 Year 1980 2000 .15 0. 26-20 Index of base changes between HIV sequences 0.Fig.20 0.10 Computer model of HIV Range 0.

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

Archaea. five kingdoms were recognized: Monera (prokaryotes).. Protista. Inc.From Two Kingdoms to Three Domains • Early taxonomists classified all species as either plants or animals • Later. and Animalia • More recently. Plantae. the three-domain system has been adopted: Bacteria. publishing as Pearson Benjamin Cummings . and Eukarya • The three-domain system is supported by data from many sequenced genomes Animation: Classification Schemes Copyright © 2008 Pearson Education. Fungi.

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

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

26-21b Sulfolobus Thermophiles Halophiles Methanobacterium ARCHAEA .Fig.

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

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 rRNA genes. as these have evolved slowly Copyright © 2008 Pearson Education. publishing as Pearson Benjamin Cummings .. Inc.

Inc.• 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.. publishing as Pearson Benjamin Cummings .

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

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

26-23 Eukarya Bacteria Archaea .Fig.

26-UN2 Node Taxon A Taxon B Taxon C Taxon D Taxon E Sister taxa Most recent common ancestor Polytomy Taxon F .Fig.

Fig. 26-UN3 Monophyletic group A B C D E F G A B C D E F G Paraphyletic group A B C D E F G Polyphyletic group .

Fig. 26-UN4 Salamander Lizard Goat Human .

Fig. 26-UN5 .

Fig. 26-UN6 .

Fig. 26-UN7 .

26-UN8 .Fig.

26-UN9 .Fig.

26-UN10 .Fig.

26-UN10a .Fig.

26-UN10b .Fig.

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

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

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