D5: Phylogeny & Systematics 5 hours

D.5.1Outline the value of classifying organisms. This refers to natural classification: How organisms truly grouped together in nature Identifying unknown organisms, using ID keyIdentifying unknown organisms, using ID key How organisms related evolutionarily (DNA evidence for current species; anatomical for fossils b/c no DNA)How organisms related evolutionarily (DNA evidence for current species; anatomical for fossils b/c no DNA) Predicting characteristics similar to those found in related organismsPredicting characteristics similar to those found in related organisms

D.5.2Explain the biochemical evidence provided by the universality of DNA and protein structures for the common ancestry of living organisms. Supports Mendels, Darwins ideasSupports Mendels, Darwins ideas Universality…genetic engineeringUniversality…genetic engineering –Not possible unless have a common ancestor! All proteins in all living organisms use same 20 amino acidsAll proteins in all living organisms use same 20 amino acids –Can engineer organism to synthesize a new protein never made before –All are left-handed…no right-handed ones! TOK: The universality of DNA and the genetic code had a profound effect on Marshall Nirenberg and other pioneering biochemists, as it showed that humans were part of the overall tree of life and were not set apart genetically. This must affect the way in which we view ourselves and the rest of the living world.

D.5.3 Explain how variations in specific molecules can indicate phylogeny. Phylogeny: study of evolutionary past of a speciesPhylogeny: study of evolutionary past of a species Most similar = most closely relatedMost similar = most closely related Molecular evidenceMolecular evidence –Polypeptides Hemoglobin, cytochrome C (mitochondrial), chlorophyllHemoglobin, cytochrome C (mitochondrial), chlorophyll DNA sequencing (nuclear, mitochondrial)DNA sequencing (nuclear, mitochondrial) Compare!Compare! TOK: Variations are partly due to mutations, which are unpredictable and chance events, so there must be caution in interpreting them.

D.5.4 Discuss how biochemical variations can be used as an evolutionary clock. Mutations occur each generationMutations occur each generation Differences accumulate steadily, graduallyDifferences accumulate steadily, gradually Estimate time 2 related species splitEstimate time 2 related species split Count # differences in molecules (base pairs)Count # differences in molecules (base pairs) –More diff = longer since split –Use mathematical model to infer time periods Example in bookp. 451Example in bookp. 451 ESTIMATE! Compare to morphological data, etc.ESTIMATE! Compare to morphological data, etc. TOK: We must be careful not to suggest that this clock moves on at a constant and invariable rate, so interpretation of data here must be very carefully done, with the uncertainties made clear.

D.5.5 Define clade & cladistics. Cladistics: grouping taxa according to recently evolved characteristicsCladistics: grouping taxa according to recently evolved characteristics Primitive traits (plesiomorphic)Primitive traits (plesiomorphic) –Same structure & function, evolved early & derived traits (apomorphic)& derived traits (apomorphic) –Same structure and function, but evolved more recently as modification of previous trait shared by organismsshared by organisms more recent vs more distant splits more recent vs more distant splits

D.5.5 Define clade & cladistics. Clade:Clade: –Group with certain derived traits, different from the group it splits with –(2 groups are 2 separate clades) Monophyletic:Monophyletic: –Most recent ancestor & all descendants

D.5.6 Distinguish, with examples, between analogous characteristics & homologous characteristics. AnalogousAnalogous –Same function but not necessarily same structure –Not derived from common ancestor –Wings: pterosaurs, birds, insects, bats –Not in same clade of flight; must consider many other differences –Fins: dolphin, shark (mammal vs fish) HomologousHomologous –From same part of Common ancestor –Pentadactyl limb (human, bat, whale)same general format –Eyes (molluscs to birds)

D.5.7 Outline the methods used to construct cladograms and the conclusions that can be drawn from them. Cladogram: visual diagram to show evolutionary relationshipsCladogram: visual diagram to show evolutionary relationships List organisms to be includedList organisms to be included List characteristics of eachList characteristics of each –Morphological, biochemical, etc. Search for commonalities and differences, make a table (-, +)Search for commonalities and differences, make a table (-, +) –Derived traits Place accordinglyPlace accordingly Node (split) = new species/cladeNode (split) = new species/clade Ancestral trait = common to all (primitive characteristic)Ancestral trait = common to all (primitive characteristic) Fewest derived traits = bottom of cladogramFewest derived traits = bottom of cladogram –Oldest in evolutionary terms Most topMost top –Most recent to evolve

D.5.8 Construct a simple cladogram. Morphological or biochemical data can be used. Example –p. 455

D.5.9 Analyse cladograms in terms of phylogenetic relationships. Example from class AncestorAncestor Primitive characteristicPrimitive characteristic Timeline of sortsTimeline of sorts Close on cladogram branches = closely related vs farther apartClose on cladogram branches = closely related vs farther apart Lines on cladogram = derived characteristicsLines on cladogram = derived characteristics –All organisms above it share the char.

D.5.10 Discuss the relationship between cladograms and the classification of living organisms. Derived nodes can be used to interpolate the classification of a group –Hair mammals Oddities...birds. Feathers are unique, but share MANY other char. w/dinosaurs –Linnaean groups not clearly defined (phylum = ???) –Clades are more clear-cut; more likely that birds evolved from dinosaurs instead of another common ancestor