BIOL 112 1st Edition Lecture 9Outline of Last Lecture I. Observed SpeciationII. QuestionsIII. Shift in Host AvailabilityIV.Divergence of Fly PopulationsV. Speciation in Action?VI.Classification and DiversityVII. Naming OrganismsVIII. Carl von LinnéIX.Systema NaturaeX. Binominal System of NomenclatureXI.Genus NameXII. Specific Epithet (Descriptor)XIII. Proper Use of BinominalXIV. What is a Species?XV. Ways of DefiningXVI. Larger Linnaean CategoriesOutline of Current LectureXVII. Goal of SystematicsXVIII. Systematics ApproachesXIX. CladisticsXX. Phylogenetic TreesThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.XXI. Problems with TechniquesXXII. Hypothesis FormationXXIII. How many Kingdoms?XXIV. DomainsCurrent LectureI. Goal of SystematicsDevelop a scheme of organization which reflects the phylogeny (evo-lutionary "family tree") of organismsValue judgments: similarities and differences among organisms as ba-sis of systematic schemes•Birds and Mosquitos: both fly... should they be in the same cate-gory?•No -- Traits being compared for such a scheme should reflect a shared common ancestry. Birds and mosquitos do not.Traits important to categories should be homologous: common originConsequences of Goal:•Create monophyletic categories:All organisms in category (taxon) have immediate common evo-lutionary ancestry, including ancestors•Avoid polyphyletic or paraphyletic taxaParaphyletic: leave creatures out of the taxa that make the data invalidPolyphyletic: include other taxa that isn't homologous with the data, has a different lineageII. Systematics ApproachesClassical Evolutionary Systematics:Combines fossil records and fundamental homologies, tried to cre-ate a "balanced" scheme of evolution and obvious characters of liv-ing groups (not widely used these days because it's obsolete).Phenetics:Ignored (or missing) fossil record. Analysis based upon characteris-tics of living organisms. Didn't attempt to sort out homologies or analogies. Scored hundreds or thousands of characters. Used com-puters to develop categories based on numbers of common charac-ters between organisms. Closer-related organisms will share more traits and analogies were regarded as "random noise" that would cancel itself out in the analyses. Pioneered computer use in system-atics. Obsolete.Cladistics (major modern systematics approach)Concentrates upon evolutionary developments. Evolutionary inno-vations are critical to develop nested sets of categories (clades)III. CladisticsObjective approach to evaluating data in the construction of degrees ofrelatednessProduct is a diagram called a cladogram (discussed in labs a lot): a se-ries of branch points that represent evolutionary divergence of two species from a common ancestor, and nested categories called cladesClade contains ancestral species and all its descendantsThe lower the branch on the cladogram, the more ancient the diver-gence, so the structure of a cladogram can represent a historical evolu-tionary sequence.Criteria:•Identify similar characteristics that would have taxonomic value•Separate homologous characteristics; discard analogous characters•Identify shared primitive characters (plesiomorphies -- every organ-ism in the group has these, so they have no value in our analysis)•Identify shared derived characters (apomorphves -- evolutionary novelties that allow us to distinguish history of emergence of cladesin the group)Go to http://evolution.berkeley.edu/evolibrary/article/phylogenetics_01 for a demonstration on developing and using cladograms.Molecular CladisticsCompares sequences for particular selected genes of evolutionary significance•16S rRNA sequences, for example•Or some genes common to all creatures in group being ana-lyzedComputer programs set to construct clades and cladograms based on reconstruction of sequence changes necessary to produce the range of sequences in the group being studied.IV.Phylogenetic TreesProduct of cladistics (cladogram) is not necessarily a phylogenetic tree (a reconstruction of evolutionary history of group)Need evolutionary history data: fossils and/or DNA sequence change informationCladogram can be a hypothesis of evolutionary sequence, but exten-sive data needed to give historical information to reconstruct evolu-tion in phylogenetic treeV. Problems with TechniquesSimplest cladistic trees can produce erroneous relationships in clado-gramsGroups formed might not correspond to known evolutionary relation-shipsRequires careful application of cladistic methods to avoid these er-rors: principle of maximum likelihoodVI.Hypothesis FormationCladograms and phylogenetic trees can be the basis for development of testable evolutionary hypothesesVII. How many Kingdoms?Oldest scheme (Linnaeus), Two Kingdoms: Plantae and AnimalIntuitive categories, but fitting organisms in was difficult by mid-19th CenturyWhittaker-Margulis scheme, Five Kingdoms: Monera, Protista, Plantae, Animalia, FungiNew schemes based on emerging molecular information, 9 to 16 ormore kingdoms (now up to 100)VIII. DomainsRecent work using molecular data has indicated the need for a taxon larger than Kingdom and for a radical reorganization of the larger cat-egoriesDomains reflect major structural, biochemical and molecular (DNA se-quences) categories of life:•D. Bacteria -- Prokaryotic, familiar biochemistry•D. Archaea -- Prokaryotic, less familiar biochemistry•D. Eukarya -- Eukaryotic formsArchaeans closer in many features to eukaryans than than they are to bacteriaLUCA = "last universal common