Phylogeny And The Tree Of Life - Psd202

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Chapter 26Phylogeny and the Tree of LifePowerPoint Lecture Presentations forBiologyEighth EditionNeil Campbell and Jane ReeceLectures by Chris Romero, updated by Erin Barley with contributions from Joan SharpCopyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Overview: Investigating the Tree of Life Phylogeny is the evolutionary history of a species orgroup of related species. The discipline of systematics classifies organismsand determines their evolutionary relationships. Systematists use fossil, molecular, and genetic data toinfer evolutionary relationships. Taxonomy is the ordered division and naming oforganisms.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Binomial Nomenclature In the 18th century, Carolus Linnaeuspublished a system of taxonomy based onresemblances. The two-part scientific name: Genus species. The first letter of the genus is capitalized, andthe entire species name is italicized Both parts together name the species. This isthe species specific epithet.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

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

ation:Genus: eciesFamily: FelidaeOrder: CarnivoraClass: MammaliaPhylum: ChordataKingdom: AnimaliaBacteriaDomain: EukaryaArchaea

Linking Classification and PhylogenyEvolutionary Relationships Systematists depict evolutionary relationships inbranching phylogenetic trees. Their PhyloCode recognizes only groups that includea common ancestor and all its descendents. A phylogenetic tree represents a hypothesis aboutevolutionary relationships. Each branch point represents the divergence of twospecies. Sister taxa are groups that share an immediatecommon ancestor.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

OrderFamily daeLutra lutraCanisCanidaeEvolutionary RelationshipsPantheraFelidaeCarnivoraPhylogenetic TreesSpeciesCanislatransCanislupus

A rooted tree includes a branch to represent the last common ancestor of alltaxa in the tree:Branch point(node)Taxon ATaxon BTaxon CANCESTRALLINEAGETaxon DTaxon ETaxon FCommon ancestor oftaxa A–FPolytomy is abranch from which morethan two groups emergeSistertaxa

What We Can and Cannot Learn fromPhylogenetic Trees Phylogenetic trees do show patterns of descent. Phylogenetic trees do not indicate when speciesevolved or how much genetic change occurred in alineage. It shouldn’t be assumed that a taxon evolved from thetaxon next to it. Phylogeny provides important information aboutsimilar characteristics in closely related species.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Possible Phylogenetic Trees:Provide important information about similar characteristics inclosely related species.(a)ABDBDCCCBDAA(b)(c)

Concept 26.2: Phylogenies are inferred frommorphological and molecular data Organisms with similar morphologies or DNAsequences are likely to be more closely related thanorganisms with different structures or sequences. When constructing a phylogeny, systematists need todistinguish whether a similarity is the result ofhomology or analogy. Homology is similarity due to shared ancestry. Analogy is similarity due to convergent evolution.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Convergent Evolution - Similar EnvironmentalSelecting Agents Convergent evolution occurs when similarenvironmental pressures and natural selectionproduce similar /analogous adaptations inorganisms from different evolutionary lineages. Bat and bird wings are homologous asforelimbs, but analogous as functional wings. Analogous structures or molecular sequencesthat evolved independently are also calledhomoplasies.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Homology can be distinguished from analogy bycomparing fossil evidence and the degree ofcomplexity. The more complex two similar structuresare, the more likely it is that they are homologous. Molecular systematics uses DNA and othermolecular data to determine evolutionaryrelationships. Once homologous characters have been identified,they can be used to infer a phylogeny.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Cladistics groups organisms by common descent A clade is a group of species that includes anancestral species and all its descendants. Clades can be nested in larger clades, but not allgroupings of organisms qualify as clades. A valid clade is monophyletic, signifying that itconsists of the ancestor species and all itsdescendants. A paraphyletic grouping consists of an ancestralspecies and some of the descendants. A polyphyletic grouping consists of various speciesthat lack a common ancestor.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Cladistics - Groups Organisms using EvolutionaryARelationshipsAABBCCCDDDEEFFFGGGBGroup IMonophyletic group / cladeGroup IIParaphyletic groupEGroup IIIPolyphyletic group

Shared Ancestral and Shared Derived Characters In comparison with its ancestor, an organismhas both shared and different characteristics. A shared ancestral character is a characterthat originated in an ancestor of the taxon. A shared derived character is an evolutionarynovelty 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 Phylogeny from Shared al column(backbone)011111Hinged ed jawsFour walking legs000111TurtleFour walking legsAmniotic (shelled) egg000011Hair000001Amniotic egg(a) Character tableLeopardHair(b) Phylogenetic tree

Maximum parsimony assumes that the tree thatrequires the fewest evolutionary events (appearancesof 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 likelysequence of evolutionary events. The best hypotheses for phylogenetic trees fit themost data: morphological, molecular, and fossil. Phylogenetic bracketing predicts features of anancestor from features of its descendents.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Mushroom0Tulip(a) Percentage differences between sequences15%5%5%15%15%10%20%25%Tree 1: More likelyTree 2: Less likely(b) Comparison of possible trees

Phylogenetic bracketing - predicts features of an ancestorfrom features of its descendents:Lizardsand snakesCrocodiliansCommonancestor ofcrocodilians,dinosaurs,and ds

Front limbHind limbEggs(a) Fossil remains of Oviraptorand eggs(b) Artist’s reconstruction of the dinosaur’s posture

Concept 26.4: An organism’s evolutionary historyis documented in its genome Comparing nucleic acids or other molecules to inferrelatedness is a valuable tool for tracing organisms’evolutionary history. DNA that codes for rRNA changes relatively slowlyand is useful for investigating branching pointshundreds of millions of years ago. mtDNA evolves rapidly and can be used to explorerecent evolutionary events. Gene duplication increases the number of genes inthe genome, providing more opportunities forevolutionary changes.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Like homologous genes, duplicated genes can betraced to a common ancestor. Orthologous genes are found in a single copy in thegenome and are homologous between species. They can diverge only after speciation occurs. Paralogous genes result from gene duplication, soare found in more than one copy in the genome. They can diverge within the clade that carries themand often evolve new functions.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Orthologous genesAncestral geneAncestral speciesSpeciation withdivergence of geneSpecies AOrthologous genesSpecies BSpecies AGene duplication and divergenceParalogous genesParalogous genesSpecies A after many generations

Molecular Clocks A molecular clock uses constant rates of evolution insome genes to estimate the absolute time ofevolutionary change. Molecular clocks are calibrated against brancheswhose dates are known from the fossil record. Neutral theory states that much evolutionary changein genes and proteins has no effect on fitness andtherefore is not influenced by Darwinian selection. It states that the rate of molecular change in thesegenes and proteins should be regular like a clock.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Molecular Clocks90603000306090Divergence time (millions of years)120

Difficulties with Molecular Clocks Irregularities result from natural selection inwhich some DNA changes are favored overothers. Estimates of evolutionary divergences older thanthe fossil record have a high degree ofuncertainty. The use of multiple genes may improveestimates.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Applying a Molecular Clock: The Origin of HIV Phylogenetic analysis shows that HIV isdescended from viruses that infectchimpanzees and other primates. Comparison of HIV samples throughout theepidemic shows that the virus evolved in a veryclocklike way. Application of a molecular clock to one strain ofHIV suggests that that strain spread to humansduring the 1930s.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

HIV Virus0.200.150.10Computer modelof HIVRange0.0501900192019401960Year1980 2000

Three Domain SystemEUKARYADinoflagellatesForamsCiliates DiatomsRed algaeLand plantsGreen algaeCellular slime ngiSulfolobusGreen nonsulfur NANCESTOROF lfur bacteriaBACTERIACyanobacteriaARCHAEA(Plastids, includingchloroplasts)

There have been substantial interchanges ofgenes between organisms in different domains. Horizontal gene transfer is the movement ofgenes from one genome to another. Horizontal gene transfer complicates efforts tobuild a tree of life. Some researchers suggest that eukaryotesarose as an endosymbiosis between abacterium and archaean.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

ReviewMonophyletic groupAAABBBCCCDDDEEEFFFGGGParaphyletic groupPolyphyletic group

Clades - Characters

You should now be able to:1. Explain the justification for taxonomy based on aPhyloCode.2. Explain the importance of distinguishing betweenhomology and analogy.3. Distinguish between the following terms: monophyletic,paraphyletic, and polyphyletic groups; shared ancestraland shared derived characters; orthologous andparalogous genes.4. Define horizontal gene transfer and explain how itcomplicates phylogenetic trees.5. Explain molecular clocks and discuss theirlimitations.Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Like homologous genes, duplicated genes can be traced to a common ancestor. Orthologous genes are found in a single copy in the genome and are homologous between species. They can diverge only after speciation occurs. Paralogous genes result from gene dupli

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