Chapter 26 - Phylogenetic Trees

Chapter 26 - Phylogenetic Trees
Phylogeny and the Tree of Life Lecture Presentation by Nicole Tunbridge and Kathleen Fitzpatrick Unit6: Evolutionary Biology

Concept 26.1: Phylogenies show evolutionary relationships
Chapter 26 - Phylogenetic Trees Concept 26.1: Phylogenies show evolutionary relationships Phylogeny is the evolutionary history of a species or group of related species For example, a phylogeny shows that legless lizards and snakes evolved from different lineages of legged lizards The discipline of systematics classifies organisms and determines their evolutionary relationships Taxonomy is the scientific discipline concerned with classifying and naming organisms Unit6: Evolutionary Biology

Legless lizards have evolved independently in several different groups
Chapter 26 - Phylogenetic Trees Legless lizards have evolved independently in several different groups Geckos ANCESTRAL LIZARD (with limbs) No limbs Snakes Iguanas Monitor lizard Figure 26.2 Convergent evolution of limbless bodies Eastern glass lizard No limbs Unit6: Evolutionary Biology

Binomial Nomenclature
Chapter 26 - Phylogenetic Trees Binomial Nomenclature C. Linnaeus: Taxonomy based on resemblances Binomial: 2-part scientific names for species Genus (1st Letter Capitalized) Specific epithet: Unique for each species w/in genus BOTH parts name the species Binomial is italicized Hierarchical classification Unit6: Evolutionary Biology

Animation: Classification Schemes

Hierarchical Classification
Chapter 26 - Phylogenetic Trees Hierarchical Classification System for grouping species in increasingly inclusive categories Taxonomic groups from broad to narrow: Domain, kingdom, phylum, class, order, family, genus, & species Taxon: Taxonomic unit at any level of hierarchy Broader taxa are not comparable between lineages Example: Order of snails has less genetic diversity than an order of mammals Phylogenetic Tree Evolutionary history of a group of organisms Represented in a branching diagram Unit6: Evolutionary Biology

Figure 26.3 Cell division error Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Figure 26.3 Linnaean classification Phylum: Chordata Kingdom: Animalia Domain: Bacteria Domain: Archaea Domain: Eukarya Unit6: Evolutionary Biology

Figure 26.4 Chapter 26 - Phylogenetic Trees Order Family Genus Species Felidae Panthera pardus (leopard) Panthera Taxidea taxus (American badger) Taxidea Carnivora Mustelidae Lutra lutra (European otter) Lutra 1 Figure 26.4 The connection between classification and phylogeny Canis latrans (coyote) Canidae Canis 2 Canis lupus (gray wolf) Unit6: Evolutionary Biology

A Phylogenetic Tree Represents a Hypothesis About Evolutionary Relationships Classification system recognizes groups that include a common ancestor and its descendants Branch Point: Divergence of two species (#1,2,3) Branches can be rotated around a branch point Sister Taxa: Share immediate common ancestor (#4) Rooted Tree: Branch to represent last common ancestor of all taxa in the tree (#2) Basal Taxon: Diverges early in the history of group Originates near common ancestor of the group (#1G) Polytomy: Branch from which >2 groups emerge (#5) Unit6: Evolutionary Biology

Figure 26.5 Chapter 26 - Phylogenetic Trees Branch point: where lineages diverge Taxon A 3 Taxon B Sister taxa 4 Taxon C 2 Taxon D Taxon E 5 ANCESTRAL LINEAGE 1 Taxon F Basal taxon Figure 26.5 How to read a phylogenetic tree Taxon G This branch point represents the common ancestor of taxa A–G. This branch point forms a polytomy: an unresolved pattern of divergence. Unit6: Evolutionary Biology

Phylogenetic Trees Show Patterns of Descent
Chapter 26 - Phylogenetic Trees Phylogenetic Trees Show Patterns of Descent Provide information about similar characteristics in closely related species Phylogenetic Trees do NOT show phenotypic similarity Do not indicate when species evolved or how much change occurred in a lineage A taxon did not necessarily evolve from adjacent taxon A phylogeny was used to identify the species of whale from which “whale meat” originated. Unit6: Evolutionary Biology

Figure 26.6 Results Minke (Southern Hemisphere) Unknowns #1a, 2, 3, 4, 5, 6, 7, 8 Minke (North Atlantic) Unknown #9 Humpback Unknown #1b Blue Figure 26.6 Inquiry: What is the species identity of food being sold as whale meat? Unknowns #10, 11, 12, 13 Fin Unit6: Evolutionary Biology

Concept 26.2: Phylogenies are inferred from morphological and molecular data Phylogeny Development: Morphologies, genes, and biochemistry of living organisms Morphological and Molecular Homologies Homologies: Phenotypic and genetic similarities due to shared ancestry Similar morphologies or DNA sequences: Organisms more closely related than organisms with different structures or sequences Evaluating Molecular Homologies Analyze comparable DNA segments from different organisms Distinguish homology from analogy in molecular similarities Homoplasies: Molecular coincidences Unit6: Evolutionary Biology

Sorting Homology from Analogy
Chapter 26 - Phylogenetic Trees Sorting Homology from Analogy Analogy: Similarity due to convergent evolution Example: Bat & bird wings Homologous as forelimbs Analogous as functional wings Homoplasies: Analogous structures or molecular sequences that evolved independently Homology: Similarity due to shared ancestry Distinguished from analogy by comparing fossil evidence and degree of complexity More similar elements in 2 complex structures  More likely homologous Unit6: Evolutionary Biology

Figure 26.7 Australian marsupial “mole” Figure 26.7 Convergent evolution in burrowers North American eutherian mole Unit6: Evolutionary Biology

Figure Chapter 26 - Phylogenetic Trees Cell division error 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 Aligning segments of DNA (step 4) 2 C C A T G T A C A G A G T C C 1 C C A T C A A G T C C 2 C C A T G T A C A G A G T C C Unit6: Evolutionary Biology

A molecular Momoplasy 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 26.9 A molecular homoplasy Unit6: Evolutionary Biology

Concept 26.3: Shared characters are used to construct phylogenetic trees Homologous characters used organize a phylogeny Cladistics: Groups organisms by common descent Clade: Group of species that includes an ancestral species and all its descendants Clades can be nested in larger clades Not all groupings of organisms qualify as clades Unit6: Evolutionary Biology

Figure 26.10 Chapter 26 - Phylogenetic Trees (a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group A A A 1 B Group I B B Group III C C C D D 3 D E E Group II E F 2 F F Figure Monophyletic, paraphyletic, and polyphyletic groups G G G Unit6: Evolutionary Biology

Types of Clades Monophyletic: Consists of the ancestor species and all its descendants Paraphyletic: Grouping consists of ancestral species and some, but not all, of the descendants Polyphyletic: Grouping includes distantly related species Does not include most recent common ancestor Biologists avoid defining polyphyletic groups Reclassify organisms if evidence suggests they are polyphyletic Unit6: Evolutionary Biology

Figure 26.11 Paraphyletic group Common ancestor of even-toed ungulates Other even-toed ungulates Hippopotamuses Cetaceans Seals Figure Examples of a paraphyletic and a polyphyletic group Bears Other carnivores Polyphyletic group Unit6: Evolutionary Biology

Shared Ancestral and Derived Characters
Chapter 26 - Phylogenetic Trees Shared Ancestral and Derived Characters An organism has both shared and different characteristics compared to its ancestor Shared Ancestral Character: Originated in an ancestor of the taxon Shared Derived Character: Evolutionary novelty unique to a particular clade Character can be BOTH ancestral and derived Determining Evolutionary Relationships Useful to know in which clade a shared derived character first appeared Unit6: Evolutionary Biology

Figure 26.12 Chapter 26 - Phylogenetic Trees TAXA Lancelet (outgroup) (outgroup) Lancelet Lamprey Leopard Lamprey Bass Frog Turtle Vertebral column (backbone) 1 1 1 1 1 Bass Vertebral column Hinged jaws 1 1 1 1 Frog Hinged jaws Four walking legs CHARACTERS 1 1 1 Turtle Four walking legs Amnion 1 1 Figure Constructing a phylogenetic tree Amnion Hair 1 Leopard Hair (a) Character table (b) Phylogenetic tree Unit6: Evolutionary Biology

Figure 26.UN06 (outgroup) Lancelet Salamander Lamprey Leopard Dolphin Tuna Turtle Character (1) Backbone 1 1 1 1 1 1 (2) Hinged jaw 1 1 1 1 1 (3) Four limbs 1 1 1 1* (4) Amnion 1 1 1 (5) Milk Figure 26.UN06 Test your understanding, question 9 (characters) 1 1 (6) Dorsal fin 1 1 *Although adult dolphins have only two obvious limbs (their flippers), as embryos they have two hind-limb buds, for a total of four limbs. Unit6: Evolutionary Biology

Outgroups and Ingroups
Chapter 26 - Phylogenetic Trees Outgroups and Ingroups Outgroup: Species, or group of species, closely related to ingroup that has diverged before the ingroup Ingroup: Various species being studied Compare Ingroup Species with Outgroup Differentiate between shared derived and ancestral characteristics Characters shared by outgroup and ingroup: Ancestral characters that predate the divergence of both groups from a common ancestor Unit6: Evolutionary Biology

Phylogenetic Trees with Proportional Branch Lengths
Chapter 26 - Phylogenetic Trees Phylogenetic Trees with Proportional Branch Lengths Length of Branch # genetic changes taken place in a particular DNA sequence in that lineage Chronological time Branching points determined using fossil records Drosophila Lancelet Zebrafish Frog Chicken Human Mouse Unit6: Evolutionary Biology

Branch Lengths Can Indicate Time
Chapter 26 - Phylogenetic Trees Branch Lengths Can Indicate Time Drosophila Lancelet Zebrafish Frog Chicken Human Mouse Figure Branch lengths can indicate time PALEOZOIC MESOZOIC CENO- ZOIC 542 251 65.5 Present Millions of years ago Unit6: Evolutionary Biology

Maximum Parsimony and Maximum Likelihood
Chapter 26 - Phylogenetic Trees Maximum Parsimony and Maximum Likelihood Maximum Parsimony Assumes tree that requires fewest appearances of shared derived characters is the most likely Principle of Maximum Likelihood Rules about how DNA changes over time  Tree can be found that reflects the most likely sequence of evolutionary events Computer programs used to search for trees that are parsimonious and likely Unit6: Evolutionary Biology

Figure 26.15 Technique 1/C 3 1/C I I III II III II 1/C III II I 1/C 1/C Species I Species II Species III Three phylogenetic hypotheses: 3/A 2/T 3/A 1 4 I I III I I III 2/T 3/A 4/C II III II II III II 4/C 4/C 2/T III II I III II I 3/A 4/C 2/T 4/C 2/T 3/A Site 2 1 2 3 4 Results I I III Species I Figure Research method: applying parsimony to a problem in molecular systematics C T A T II III II Species II C T T C Species III III II I A G A C 6 events 7 events 7 events Ancestral sequence A G T T Unit6: Evolutionary Biology

Phylogenetic Trees as Hypotheses
Chapter 26 - Phylogenetic Trees Phylogenetic Trees as Hypotheses Best phylogenetic trees fit the most data: Morphological, molecular, and fossil Phylogenetic Bracketing: Allows feature predictions of an ancestor using features of descendants Example: Infer characteristics of dinosaurs Unit6: Evolutionary Biology

Birds & Crocodiles Have Many Shared Features
Four-chambered hearts Song Nest building Brooding Likely evolved in a common ancestor Shared by all descendants Including dinosaurs! Fossil record supports nest building and brooding in dinosaurs

Figure 26.16 Chapter 26 - Phylogenetic Trees Lizards and snakes Crocodilians Ornithischian dinosaurs Common ancestor of crocodilians, dinosaurs, and birds Saurischian dinosaurs Figure A phylogenetic tree of birds and their close relatives Birds Unit6: Evolutionary Biology

Fossil support for a phylogenetic prediction: Dinosaurs built nests and brooded their eggs! Front limb Hind limb Eggs Figure Fossil support for a phylogenetic prediction: Dinosaurs built nests and brooded their eggs. (a) Fossil remains of Oviraptor and eggs (b) Artist’s reconstruction of the dinosaur’s posture based on the fossil findings Unit6: Evolutionary Biology

Concept 26.4: An organism’s evolutionary history is documented in its genome Determine relatedness by compare nucleic acids, or other molecules  Trace organisms’ evolution DNA coding for rRNA changes slowly Investigate branching points mya mtDNA evolves rapidly Explore recent evolutionary events Unit6: Evolutionary Biology

Gene Duplications and Gene Families
Chapter 26 - Phylogenetic Trees Gene Duplications and Gene Families Gene duplication increases # genes  Evolutionary changes Repeated gene duplications result in gene families Duplicated genes can be traced to a common ancestor Orthologous Genes: Single copy in genome Homologous between species Can diverge only after speciation occurs Paralogous Genes: Gene duplication >1 copy in the genome Can diverge within the clade that carries them Often evolve new functions Unit6: Evolutionary Biology

Figure 26.18 Chapter 26 - Phylogenetic Trees (a) Formation of orthologous genes: a product of speciation (b) Formation of paralogous genes: within a species Ancestral gene Ancestral gene Ancestral species Species C Speciation with divergence of gene Gene duplication and divergence Figure Two types of homologous genes Orthologous genes Paralogous genes Species C after many generations Species A Species B Unit6: Evolutionary Biology

Genome Evolution Orthologous genes are widespread Extend across many widely varied species Example: Humans and mice diverged ~65 mya 99% of our genes are orthologous Gene number and complexity of an organism not strongly linked Humans: 4x # genes as single-celled yeast Genes in complex organisms very versatile Each gene can encode multiple proteins  Perform many different functions Unit6: Evolutionary Biology

Concept 26.5: Molecular clocks help track evolutionary time
Chapter 26 - Phylogenetic Trees Concept 26.5: Molecular clocks help track evolutionary time Molecular Clock: Estimates absolute time of evolutionary change using constant rates of evolution in some genes Calibrated against branches with known dates Individual genes vary in how clocklike they are Orthologous Genes Nucleotide substitutions proportional to time since they last shared a common ancestor Paralogous Genes Nucleotide substitutions proportional to time since the genes became duplicated Unit6: Evolutionary Biology

Figure 26.19 90 60 Number of mutations 30 Figure A molecular clock for mammals 30 60 90 120 Divergence time (millions of years) Unit6: Evolutionary Biology

Differences in Clock Speed
Chapter 26 - Phylogenetic Trees Differences in Clock Speed If evolutionary change in genes and proteins has no effect on fitness  Rate of molecular change should be regular like a clock Differences in clock rate for different genes indicate: Function of the importance of the gene How critical the specific amino acid is to protein function Unit6: Evolutionary Biology

Potential Problems with Molecular Clocks
Chapter 26 - Phylogenetic Trees Potential Problems with Molecular Clocks Molecular clock does not run as smoothly as expected if mutations were 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 Use of multiple genes or genes that evolved in different taxa may improve estimates Unit6: Evolutionary Biology

Applying a Molecular Clock: Dating the Origin of HIV
Chapter 26 - Phylogenetic Trees Applying a Molecular Clock: Dating the Origin of HIV Phylogenetic analysis shows 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 A more advanced molecular clock approach estimated the first spread to humans around 1910 Unit6: Evolutionary Biology

Figure 26.20 Cell division error 0.20 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 Dating the origin of HIV-1 M 1900 1920 1940 1960 1980 2000 Year Unit6: Evolutionary Biology

Concept 26.6: Our understanding of the tree of life continues to change based on new data Important Role of Horizontal Gene Transfer Tree of life suggests eukaryotes and archaea are more closely related to each other and less closely to bacteria Based largely on rRNA genes Some other genes reveal different relationships Unit6: Evolutionary Biology

Figure 26.21 Chapter 26 - Phylogenetic Trees Cell division error Euglenozoans Forams Diatoms Ciliates Red algae Domain Eukarya Green algae Land plants Amoebas Fungi Animals Nanoarchaeotes Methanogens Domain Archaea COMMON ANCESTOR OF ALL LIFE Thermophiles Proteobacteria Figure The three domains of life (Mitochondria)* Chlamydias Spirochetes Domain Bacteria Gram-positive bacteria Cyanobacteria (Chloroplasts)* Unit6: Evolutionary Biology

Horizontal Gene Transfer
Chapter 26 - Phylogenetic Trees Horizontal Gene Transfer Many interchanges of genes between organisms in different domains has occurred. Horizontal Gene Transfer: Movement of genes from one genome to another Occurs by exchange of transposable elements and plasmids, viral infection, and fusion of organisms Explains disparities between gene trees Key role in the evolution of both prokaryotes and eukaryotes Horizontal gene transfer may have been so common that early history should be represented as a tangled network of connected branches Unit6: Evolutionary Biology

Mediterranean House Gecko: Recipient of Transferred Genes
Chapter 26 - Phylogenetic Trees Mediterranean House Gecko: Recipient of Transferred Genes Figure A recipient of transferred genes: the Mediterranean house gecko (Hemidactylus turcicus) Unit6: Evolutionary Biology

West Indian Manatee Figure 26.UN07 Test your understanding, question 11 (West Indian manatee) Unit6: Evolutionary Biology

Chapter 26 - Phylogenetic Trees

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