D5: Phylogeny & Systematics 5 hours. D.5.1Outline the value of classifying organisms. This refers to natural classification: How organisms truly grouped.

D5: Phylogeny & SystematicsD5: Phylogeny & Systematics

5 hours5 hours

D.5.1D.5.1Outline the value of classifying Outline the value of classifying organisms.organisms.

This refers to natural classification:This refers to natural classification:

How organisms How organisms trulytruly grouped grouped together in together in naturenature

• Identifying unknown organisms, using Identifying unknown organisms, using ID keyID key

• How organisms related evolutionarily How organisms related evolutionarily (DNA evidence for current species; (DNA evidence for current species; anatomical for fossils b/c no DNA)anatomical for fossils b/c no DNA)

• Predicting characteristics similar to Predicting characteristics similar to those found in related organismsthose found in related organisms

D.5.2D.5.2Explain the biochemical evidence Explain the biochemical evidence provided by the universality of DNA and provided by the universality of DNA and protein structures for the common ancestry protein structures for the common ancestry of living organisms.of living organisms.• Supports Mendel’s, Darwin’s ideasSupports Mendel’s, Darwin’s ideas• Universality…genetic engineeringUniversality…genetic engineering

– Not possible unless have a common ancestor!Not possible unless have a common ancestor!

• All proteins in all living organisms use All proteins in all living organisms use same 20 amino acidssame 20 amino acids– Can engineer organism to synthesize a new Can engineer organism to synthesize a new

protein never made beforeprotein never made before– All are left-handed…no right-handed ones!All are left-handed…no right-handed ones!

TOK: The universality of DNA and the genetic code had a TOK: The universality of DNA and the genetic code had a profound effect on Marshall Nirenberg and other pioneering profound effect on Marshall Nirenberg and other pioneering biochemists, as it showed that humans were part of the biochemists, as it showed that humans were part of the overall tree of life and were not set apart genetically. This overall tree of life and were not set apart genetically. This must affect the way in which we view ourselves and the rest must affect the way in which we view ourselves and the rest of the living world.of the living world.

D.5.3 Explain how variations in specific D.5.3 Explain how variations in specific molecules can indicate phylogeny.molecules can indicate phylogeny.

• Phylogeny: study of evolutionary past Phylogeny: study of evolutionary past of a speciesof a species

• Most similar = most closely relatedMost similar = most closely related• Molecular evidenceMolecular evidence

– PolypeptidesPolypeptides• Hemoglobin, cytochrome C (mitochondrial), Hemoglobin, cytochrome C (mitochondrial),

chlorophyllchlorophyll

• DNA sequencing (nuclear, mitochondrial)DNA sequencing (nuclear, mitochondrial)• Compare!Compare!

TOK: Variations are partly due to mutations, which are TOK: Variations are partly due to mutations, which are unpredictable and chance events, so there must be unpredictable and chance events, so there must be caution in interpreting them.caution in interpreting them.

D.5.4 Discuss how biochemical variations D.5.4 Discuss how biochemical variations can be used as an evolutionary clock.can be used as an evolutionary clock.

• Mutations occur each generationMutations occur each generation• Differences accumulate steadily, Differences accumulate steadily,

graduallygradually• EstimateEstimate time 2 related species split time 2 related species split• Count # differences in molecules (base Count # differences in molecules (base

pairs)pairs)– More diff = longer since splitMore diff = longer since split– Use mathematical model to infer time periodsUse mathematical model to infer time periods

• Example in book—p. 451Example in book—p. 451• ESTIMATE! Compare to morphological ESTIMATE! Compare to morphological

data, etc.data, etc.

TOK: We must be careful not to suggest that this clock moves on TOK: We must be careful not to suggest that this clock moves on at a constant and invariable rate, so interpretation of data here at a constant and invariable rate, so interpretation of data here must be very carefully done, with the uncertainties made clear.must be very carefully done, with the uncertainties made clear.

D.5.5 Define D.5.5 Define clade & cladisticsclade & cladistics..

• Cladistics: grouping taxa according Cladistics: grouping taxa according to recently evolved characteristicsto recently evolved characteristics

• Primitive traits (plesiomorphic) Primitive traits (plesiomorphic) – Same structure & function, evolved Same structure & function, evolved

earlyearly

• & derived traits (apomorphic)& derived traits (apomorphic)– Same structure and function, but Same structure and function, but

evolved more recently as modification of evolved more recently as modification of previous traitprevious trait

• shared by organismsshared by organisms more recent vs more distant splitsmore recent vs more distant splits

D.5.5 Define D.5.5 Define clade & cladisticsclade & cladistics..

• Clade:Clade:– Group with certain derived traits, Group with certain derived traits,

different from the group it splits withdifferent from the group it splits with– (2 groups are 2 separate clades) (2 groups are 2 separate clades)

• Monophyletic:Monophyletic:– Most recent ancestor & all Most recent ancestor & all

descendantsdescendants

D.5.6 Distinguish, with examples, between D.5.6 Distinguish, with examples, between analogous characteristics & homologous analogous characteristics & homologous characteristicscharacteristics..

• AnalogousAnalogous– Same function but not necessarily same Same function but not necessarily same

structurestructure– Not derived from common ancestorNot derived from common ancestor– Wings: pterosaurs, birds, insects, batsWings: pterosaurs, birds, insects, bats– Not in same clade of “flight”; must consider Not in same clade of “flight”; must consider

many other differencesmany other differences– Fins: dolphin, shark (mammal vs fish)Fins: dolphin, shark (mammal vs fish)

• HomologousHomologous– From same part of Common ancestorFrom same part of Common ancestor– Pentadactyl limb (human, bat, whale)—same Pentadactyl limb (human, bat, whale)—same

general formatgeneral format– Eyes (molluscs to birds)Eyes (molluscs to birds)

D.5.7 Outline the methods used to D.5.7 Outline the methods used to construct cladograms and the conclusions construct cladograms and the conclusions that can be drawn from them.that can be drawn from them.• Cladogram: visual diagram to show evolutionary Cladogram: visual diagram to show evolutionary

relationshipsrelationships

• List organisms to be includedList organisms to be included• List characteristics of eachList characteristics of each

– Morphological, biochemical, etc.Morphological, biochemical, etc.• Search for commonalities and differences, make a Search for commonalities and differences, make a

table (- , +)table (- , +)– Derived traitsDerived traits

• Place accordinglyPlace accordingly• Node (split) = new species/cladeNode (split) = new species/clade• Ancestral trait = common to all (primitive Ancestral trait = common to all (primitive

characteristic)characteristic)• Fewest derived traits = bottom of cladogramFewest derived traits = bottom of cladogram

– ““Oldest” in evolutionary termsOldest” in evolutionary terms• Most Most top top

– Most recent to evolveMost recent to evolve

D.5.8 Construct a simple D.5.8 Construct a simple cladogram.cladogram.

Morphological or biochemical data Morphological or biochemical data can be used.can be used.

Example –p. 455Example –p. 455

D.5.9 Analyse cladograms in D.5.9 Analyse cladograms in terms of phylogenetic terms of phylogenetic relationships.relationships.Example from classExample from class

• AncestorAncestor• Primitive characteristicPrimitive characteristic• Timeline of sortsTimeline of sorts• Close on cladogram branches = Close on cladogram branches =

closely related vs farther apartclosely related vs farther apart• Lines on cladogram = derived Lines on cladogram = derived

characteristicscharacteristics– All organisms above it share the char.All organisms above it share the char.

D.5.10 Discuss the relationship between cladograms and the classification of living organisms.• Derived characteristics @ 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