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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, geographical distribution, behavior, and life history to infer evolutionary relationships Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Concept 26.1: Phylogenies show evolutionary relationships • Taxonomy is the ordered division and naming of organisms • 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 • The two-part scientific name of a species is called a binomial nomenclature • 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 Fig. 26-3 Species: Panthera pardus • 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 Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Kingdom: Animalia Bacteria Domain: Eukarya Archaea Linking Classification and Phylogeny • Systematists depict evolutionary relationships in branching phylogenetic trees • 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 • 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 Fig. 26-4 Order Family Genus Species Taxidea 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 Redraw this tree, rotating the branches around branch points “2” & “4”. Does your new version tell a different story about the evolutionary relationships? Sister taxa 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., publishing as Pearson Benjamin Cummings 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 • 13 samples of “whale meat” from Japanese fish markets where sequenced. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 26-6 RESULTS Minke (Antarctica) Minke (Australia) Unknown #1a, 2, 3, 4, 5, 6, 7, 8 Minke (North Atlantic) Unknown #9 This analysis indicated that DNA sequences of six of the unknown samples (in red) were most closely related to DNA sequences of whales that are not legal to harvest. Humpback (North Atlantic) Humpback (North Pacific) Unknown #1b Gray Blue (North Atlantic) Blue (North Pacific) Unknown #10, 11, 12 Unknown #13 Fin (Mediterranean) Fin (Iceland) Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 26-UN1 (a) A B D B D C C C B D A A (b) (c) Which of the trees shown below depicts a different evolutionary history for taxa A – D than the other two tress? Explain Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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 • Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages • Bat and bird wings are homologous as forelimbs, but analogous as functional wings • 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 Fig. 26-7 Convergent evolution of analogous burrowing characteristics Evaluating Molecular Homologies • Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms 1 Ancestral homologous DNA segments are identical as species 1 and species 2 begin to diverge from their common ancestor. Deletion 2 Insertion Of the three homologous 3 regions, two (shaded orange) do not align because of these mutations. Homologous regions realign 4 after a computer program adds gaps in sequence 1. Deletion and insertion mutations shift what had been matching sequences in the two species. Concept 26.3: Shared characters are used to construct phylogenetic trees • Cladistics groups organisms by common descent • A clade is a group of species that includes an ancestral species and all its descendants Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 26-10 • A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants 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) • A clade is monophyletic, signifying that it consists of the ancestor species and all its descendants Group II (b) Paraphyletic group E Group III (c) Polyphyletic group • A polyphyletic grouping consists of various species that lack a common ancestor Shared Ancestral and Shared Derived Characters • In comparison with its ancestor, an organism has both shared and different characteristics • 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 • 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. 26-11a Tuna (a) Character table - A 0 indicates that a character is absent, a 1 indicates that a character is present Leopard TAXA Vertebral column (backbone) 0 1 1 1 1 1 Hinged jaws 0 0 1 1 1 1 Four walking legs 0 0 0 1 1 1 Amniotic (shelled) egg 0 0 0 0 1 1 Hair 0 0 0 0 0 1 (b) Phylogenetic tree – Analyzing the distribution of these derived characters can provide insight into vertebrate phylogeny Lancelet (outgroup) Lamprey Tuna Vertebral column Salamander Hinged jaws Turtle Four walking legs Amniotic egg Leopard Hair Fig. 26-15-1 Species I Species III Species II Three phylogenetic hypotheses: I I III II III II III 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 I 1/C II I III III II 1/C II III 1/C I 1/C Tabulate the molecular data for the species. The data represent a DNA sequence Consisting of just four nucleotide bases. Now focus on site 1 in the DNA sequence. In the tree on the left, a single base Change event, represented by the purple hatchmark on the branch leading to Species I and II is sufficient to account for the site 1 data. In the other two trees, Two base-change events are necessary 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 I 1/C II I III III II 1/C II III I 1/C 3/A 2/T I 2/T 3/A 3/A 4/C II II 2/T 4/C III 2/T 4/C III 3/A 4/C I III II 4/C 1/C I 2/T 3/A Continuing the comparison of bases at sites 2, 3, and 4 reveals that each of the three trees requires a total of five additional base change events. 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 I 1/C II I III III II 1/C II III I 1/C 3/A 2/T I 2/T 3/A 3/A 4/C 6 events 3/A 4/C III II 2/T 4/C II III To identify the most parsimonious tree (simplest), we total all of the base change events. Conclusion is the first tree is the most parsimonious. I III II 4/C 1/C I 2/T 3/A 2/T 4/C I I III II III II III II I 7 events 7 events 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 • When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared • Molecular clocks are calibrated against branches whose dates are known from the fossil record Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Use the clock to estimate the divergence time for a mammal with a total of 30 mutations in the seven proteins. 90 60 30 0 0 30 60 90 Divergence time (millions of years) 120 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, Inc., publishing as Pearson Benjamin Cummings Fig. 26-20 0.20 0.15 0.10 Computer model of HIV Range 0.05 0 1900 1920 1940 1960 Year The points in the corner are based on DNA sequences for a specific HIV gene collected from patients at different know times. If we project the rate at which changes occurred back in time, we intersect 1980 2000 the x-axis in the 1930’s 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. The domain taxonomic level contains a single ancestor for all its members, the five kingdom system does not. • 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, 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) • 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 1 – Most recent common ancestor of all living things 2 – Gene transfer between mitochondrial ancestor and ancestor of eukaryotes 3 – Gene transfer between chloroplast ancestor and ancestor of green algae Bacteria 2 3 1 Eukarya Archaea 4 3 2 Billions of years ago 1 0 Fig. 26-23 Eukarya Bacteria Archaea • 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 Fig. 26-UN9 Fig. 26-UN10 Fig. 26-UN10a Fig. 26-UN10b You should now be able to: 1. Explain the importance of distinguishing between homology and analogy 2. Distinguish between the following terms: monophyletic, paraphyletic, and polyphyletic groups; shared ancestral and shared derived characters 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