PhylogeniesReconstructing the Past

The field of systematicsStudiesthe mechanisms of evolutionevolutionary agentsthe process of evolutionspeciation eventsthe products of evolutiondiscovery, nomenclature, classification, tools for identification of extant organisms

Phylogenetic AnalysisPhylogenychronicle of the descent of a group of organisms from a common ancestorillustrated as a branching, tree-like diagramanagenesis operating along branchescladogenesis producing new branchesshows the origins of different groups from an ancestral group

Phylogenetic Reconstructiona phylogenetic tree (cladogram) is a hypothesis of events in the evolution of a groupbased on the analysis of characters of extant organismsidentifies the speciation events (branch points) in the evolution of the groupestimation of time spans or identification of ancestral organisms is extraneous

Phylogenetic Reconstructionan ideal data setthe complete morphological and genetic description of each member of the lineagebetter than nothingthe complete fossilized remains of each member of a lineageOne approach thats always feasibleinference from extant members

Phylogenetic Reconstructionclues to the phylogenetic history of a grouphomologiestwo features descended from a common ancestral feature are homologousmay or may not resemble each othermay or may not perform the same functions

tetrapod limbs -

homologs

Figure 1.2Figure 25.2

bat, bird, insect wings -

not homologsFigure 25.2

leaf homologs in flowering plantsFigure 25.3

Phylogenetic Reconstructionclues to the phylogenetic history of a groupcommon ancestry is inferred from the presence of homologous traitstraits inherited from a distant ancestor are shared by many taxatraits inherited from a recent ancestor are shared by few taxa

Homoplasiestraits that are similar due to something other than inheritance from a common ancestorconvergent evolutionparallel evolutionevolutionary reversal

Homoplasiestraits that are similar due to something other than inheritance from a common ancestorconvergent evolutionEuphrobiaceaeCactaceaeAsclepiadaceaeFigure: three plants that all look like cactus but come from Three distinct families -

Homoplasiestraits that are similar due to something other than inheritance from a common ancestorconvergent evolutionparallel evolutionFigure: butterfly/moth wings with similar patterns

Homoplasiestraits that are similar due to something other than inheritance from a common ancestorconvergent evolutionparallel evolutionevolutionary reversalFigure:Magnolia & grass

Phylogenetic Reconstructionsteps in the reconstruction of a phylogenyidentification of members of the groupkey homologous traitse.g. a vertebral columnselection of characterscharacters with traits that differ in the groupancestral vs. derived(plesiomorphies vs. apomorphies)

Phylogenetic Reconstruction=>during the history of a lineage, some traits change from the ancestral conditionancestral => derived=>taxa that change pass on the changes

=>closely related taxa share traits from a recent ancestor and a distant ancestor

=>distantly related taxa share traits from a distant ancestor only

Phylogenetic Reconstructionsteps in the reconstruction of a phylogenyidentification of ancestral and derived character statesselect an outgrouptraits shared with the outgroup are ancestraldistinguish between homologies and homoplasiesassume similar traits are homologousother characters will test the assumption

Table 25.1

phylogeny of selected vertebratesFigure 25.5

dealing with the real worldunrecognized homoplasies happenmultiple trait changes, reversals, convergence, parallelseach analysis produces multiple possible treessome trees explain the evolution of the group by assuming many speciation eventssome trees explain the evolution of the group by assuming few speciation eventshow to select the right tree?

dealing with the real worldselecting the right treecant be done (with certainty)Principle of Parsimonythe best hypothetical tree is the one that requires the fewest unverified assumptions (events)the best tree is the shortest tree, for nownew data, new insights, may provide evidence supporting a different tree

dealing with the real worldselecting the right treeMaximum Likelihoodanalyzes trees using additional informationcertain possible events are more likely than others and are given greater weighte.g. transitions are more likely than tranversions

dealing with the real worldfinal trees are often inconclusive, soconsensus trees combine results from several best-scoring treesunresolved nodes support multiple branches

dealing with the real worldcladistic analysis is a highly documented hypothetical processassumptions are explicittaxon selection criteria are explicitcharacter/trait selection criteria are explicithomoplasy identification is explicitsoftware choices are explicittree reconciliation is explicit

shared developmental features may demonstrate links between taxa with little adult similarityFigure 25.4

Useful Characters for Phylogeniesheritable, quantifiable charactersmorphological charactersanatomical charactersdevelopmental biologymolecular traitsproteinsnucleic acids

Dendroica fusca hierarchyFigure 25.6

Classification of OrganismsBiological Classification uses a hierarchical systema taxon is identified by diagnostic characteristicslower taxa belong to higher taxa along with sister taxa

Rosa gallica hierarchyFigure 25.6

Classification of OrganismsBiological Classification uses a hierarchical systemthe taxonomic hierarchy is information richdiagnostic characters are reliable as predictors

Classification of OrganismsBiological Classification applies a unique name to each speciesA binomial is applied to each speciesevery known species possesses a binomialeach binomial is applied to only one speciesbinomial nomenclature is accepted universally among scientists

Mertensia sp.BoraginaceaeCampanula sp.CampanulaceaeEndymion sp.LiliaceaeThree different species, all calledBluebells

Classification of OrganismsBiological Classification applies a unique binomial to each speciescommon names are insufficientunregulatedincomplete

Arabidopsis thalianathe primary flowering plant molecular model systema.k.a.

Arabidopsis thaliana

Classification of OrganismsBiological Classification applies a unique binomial to each speciesbinomials consist of two partsGenus name: e.g. Echinocactusspecific epithet: E. enneacanthus

Classification of OrganismsBiological Classification applies a unique binomial to each speciesbinomials replaced polynomial phrase namesLinnaeus is credited with development of binomial nomenclature, ~1750