1.IB BiologyOption DD5 Phylogeny and SystematicsAll syllabus statements IBO 2007All images CC or public domain or link to original material.Jason de Nys http://en.wikipedia.org/wiki/File:Tree_of_life_SVG.svg

2. "The affinities of all the beings of the same class havesometimes been represented by a great tree... Asbuds give rise by growth to fresh buds, and these ifvigorous, branch out and overtop on all sides many afeebler branch, so by generation I believe it has beenwith the great Tree of Life, which fills with its deadand broken branches the crust of the earth, andcovers the surface with its ever branching andbeautiful ramifications."Charles Darwin, 1859Charlie sure could spit out a quotable piece of writing 3. D.5.1 Outline the value of classifying organismsIdentification of OrganismsUnknown organisms are easily identified if data about organismsis organised. Classification allows for the creation of keys.Remember 5.5Classification? 4. Evolutionary LinksClassification allows us to see evolutionaryrelationships. Organisms that are grouped together share a lot ofsimilar features (homologous structures). These sharedcharacteristics help us see how organisms have evolved from acommon ancestor. e.g. Llamas wereoriginally compared to sheep but a study oftheir morphology laterplaced them in the camel familyhttp://www.flickr.com/photos/mrapplegate/2423991076/ http://www.flickr.com/photos/doug88888/3458057235/ 5. Prediction of CharacteristicsCharacteristics that are shared by organisms within agroup would be expected to be found in otherspecies that are closely related.e.g. no doubt more fossilsthat can be categorised inthe Homo genus will befound.We can expect them tohave relatively big brains(crazy Hobbit findsexcepted!) http://commons.wikimedia.org/wiki/File:Hominins_2002.png 6. D.5.2 Explain the Biochemical evidence provided by the universality of DNA and proteinstructures for the common ancestry of living organisms 1) All known organisms use DNA as genetic material The genetic code is universal. Gene sequences inserted in different organisms express the same proteinshttp://commons.wikimedia.org/wiki/File:Bdna.gif 7. 2) The same 20 amino acids are used to make all proteinshttp://commons.wikimedia.org/wiki/File:Protein_primary_structure.svg 8. 3) Most amino acids can exist in left or right- handed forms, i.e. as mirror images Yet all living things useleft-handed amino acids It is believed that this was a chanceoccurrence in the oldest common ancestor The panspermia hypothesis may help explain this asmore amino acids found in meteorites are left-handedthan right-handed http://commons.wikimedia.org/wiki/File:Chirality_with_hands.jpg 9. 4) Cytochrome c is a protein involved in theelectron transport chain.It consists of 100-104 amino acids and isfound in plants, animals, and manyunicellular organismsIt is too complex to have evolvedindependently and so must come from acommon ancestor Furtherevidence of commondescenthttp://en.wikipedia.org/wiki/File:Cytochromec.png 10. D.5.3 Explain how variations in specific molecules can indicate phylogenyTaking the example of the protein cytochrome c.It is not identical in all species because singlepoint mutations in the DNA that codes for it canlead to different amino acids making up theprotein.Both humans and chimpanzees have the identicalcytochrome c molecules, while rhesus monkeysshare all but one of the amino acids: the 66thamino acid is isoleucine in the former andthreonine in the latter.This suggests that humans and chimpanzees are I didnt want to bemore closely related to each other than to rhesusmonkeys closely related tostinking humansanyway! http://www.flickr.com/photos/stuffinhergoose/571672799 11. TOK Read this article: Closer to man than ape What reasons are given for including chimps in genusHomo? Do you think humanswill ever be reclassified Pan? 12. This is part of a molecularphylogeny of all of the livingprimates.It clearly shows chimpanzees (Pan)as being more closely related tohumans than to gorillas.It was made bycomparing 34,927base pairssequenced from54 genes takenfrom each of asingle species ineach genus. 13. D.5.4 Discuss how biochemical variations can be used as an evolutionary clockAn evolutionary clock involvescalculating the time since speciesdiverged by comparing thenumber of differences in theirDNA and/or protein sequences.Scientists who originated the ideacalibrated the amino aciddifferences in haemoglobin withtimes derived from the fossilrecord. http://commons.wikimedia.org/wiki/File:Nature_Clock.gif 14. The assumption is that these changes occur at a regular rate.(which may not always be the case)Therefore if species A had 5 differences from species B and 10differences from species C, then the lineages for A and C musthave split twice as long ago as for A and B C BA Time 15. D.5.5 Define clade and cladisticsCladistics (From theancient Greek for"branch") is a method ofclassifying species oforganisms into groupscalled clades, whichconsist of an ancestororganism and all itsdescendants (andnothing else).Wikipediahttp://www.flickr.com/photos/aussiegall/4149475009/ 16. For example, birds, dinosaurs, crocodiles, and all descendants (living http://www.flickr.com/photos/kev http://www.flickr.com/photos/mo http://www.flickr.com/photos/tam or extinct) of theirom/photos/emraya/2929959881/most recent common ancestorform a clade Wikipedia 17. Characteristics change over time,thus the amount of change canhelp determine relationshipsGroups of organisms aredescended from a commonancestorThere is a branching pattern in theevolution of species and when asplit occurs, two distinct specieseventuate. 18. HairShelledeggsEach clade Amniotic Eggis determined by Four Limbscommon characteristics Bony Skeletonof its members that aredifferent from that of the Vertebrateother species from whichit has divergedhttp://bridgeurl.com/xrmmmk/all 19. These traits which tie the clades togetherare called shared derived charactershttp://www.flickr.com/photos/29448992@N08/2970804257/ 20. D.5.6 Distinguish, with examples, between analogous and homologous characteristicsHomologousstructures areinherited from acommon ancestor http://www.flickr.com/photos/opoterser/4189239614/ 21. e.g. The fly on the previous page andthe mosquito on this page havemouthparts adapted to their foodsources but the basic componentswere inherited from a commonancestor Other examples include pentadactyl limbs and finches beakshttp://www.flickr.com/photos/kclama/102002644/ 22. Analogous structures have similar form and function due to convergentevolution, they do not stem from a common ancestor Batshttp://www.flickr.com/photos/tjt195/105694980/ 23. birdshttp://www.flickr.com/photos/patrickwilken/112947862/ 24. and bugs all have wings for flight that evolvedindependently Other examples include: -Streamlined shape for dolphins , sharks and ichthyosaurs -Long snout and tongue for capturing ants on the anteater and echidna http://www.flickr.com/photos/hhoyer/3758550410/sizes/o/in/photostream/ 25. D.5.7 Outline the methods used to construct cladograms and the conclusions that can be drawnfrom them ANDD.5.8 Construct a simple cladogram These two cladograms are identical (although they dont look it) The shape and the order of the terminal nodes does not matter. The only information to be gathered from the cladograms below is the order ofnesting of sister clades and the relative relatedness of specieshttp://commons.wikimedia.org/wiki/File:Identical_cladograms.svg 26. Out group: Definesthe ancestralTerminal nodesSister clades: have acharacters common ancestorHumanChimpGorilla ChimpHumanGorilla Nodes: Common ancestors Root 27. Branches on acladogram can bescaled or unscaled.If the branches arescaled, the lengthof the branch oftenindicates how muchevolutionarychange hasoccurred in aspecies since it splitfrom its sister cladeat the last node http://www.ncbi.nlm.nih.gov/About/primer/phylo.html 28. Rooted cladogramsshow evolutionaryrelationships.Unrooted trees justshow therelationshipsbetween cladeshttp://www.ncbi.nlm.nih.gov/About/primer/phylo.html 29. Cladograms are made by compiling data on homologous characteristics shared by species. These characteristics can be structural, physiological and/or biochemical. With increasing taxa comes increasing complexity.Number of taxa23 45 6 789 10NPossible numberof rooted 1 3 15 105 945 10,395 135,135 2,027,025 34,459,425 1*3*5*7*...*(2N-3)cladograms So software is often used to find the best possible tree that has the fewest evolutionary steps. 30. This cladogram forbacteria iscomputergenerated 31. 1) Compile a table of the characters being compared CharactersShark Frog KangarooHumanVertebrae X X X XTwo pairs of limbsX X XMammary glandsX XPlacentaX Modified from: http://www.bu.edu/gk12/eric/cladogram.pdf 32. 2) Use the data to constructa Venn diagram, Vertebrae:Start with the Sharkcharacteristic Two Pairs ofshared by allLimbs: Frogtaxa in the Mammarybiggest circleGlands:and work KangarooinwardsPlacenta: Human 33. 3) Convert the Venn diagram into a cladogramSharkFrogKangaroo HumanPlacenta Mammary Glands LungsVertebrae 34. Now you try! Make a Venn diagram for this data.CharactersSponge Jellyfish Flatworm Earth- Snail Fruit fly Starfish HumanwormCells with flagella XX XXX X XXSymmetry X XXX X XXBilateral symmetry XXX X XXMesodermXX X XXHead develops first XX XAnus develops firstXXSegmented bodyXXCalcified shellXChitinous ExoskeletonXWater Vascular systemXVertebrae X 35. It should lookCells with flagella: SpongesomethingSymmetry: Jellyfishlike this:Bilateral symmetry: Flatworm MesodermHead develops first Anus develops firstSegmented Body: Earthworm WaterCalcifiedVascularVertebrae: Shell:system:HumanChitinousSnailStarfish exoskeleton: Fruit flynow makethe cladogram 36. It should look something like this: Flat-Sponge Jellyfish worm Snail Earthworm Fruit fly Starfish HumanCalcifiedWatershellChitinous vascular shell system VertebraeSegmented body Head developsfirstAnus develops firstSome of thecharacteristics in thedata table were unnecessaryMesodermfor the construction of thisBilateral symmetrycladogram. SymmetryFlagellaCan you identify them? 37. Unnecessary to use two characteristics todifferentiate between Starfish and Human.Either would do the trickFlat-SpongeJellyfish worm SnailEarthwormFruit fly Starfish HumanCalcified Watershell Chitinous vascularshell system Vertebrae Segmented bodyHead develops first Anus develops firstUnnecessary to differentiate Snail.Snail is the only species with head Unnecessary to useMesodermdevelops first and withouttwo characteristics Bilateral symmetryto split lineagessegmented bodySymmetry Flagella 38. D.5.9 Analyse cladograms in terms of phylogenetic relationships AB C DOf the three nodes, 3 is most recent and 1 3occurred earliest.Node 3 is the most recent 2common ancestor for C and DNode 2 is the most recent common 1 ancestor for B and CNode 3 is the common ancestor of all taxaAnd so on 39. D.5.10 Discuss the relationship between cladograms and the classification of living organismsMammals have theunique homologouscharacteristic ofproducing milkThey form a cladehttp://www.flickr.com/photos/chavals/3720930469/ 40. Likewise, birds share thecommon characteristic offeathersThey too form a cladehttp://www.flickr.com/photos/bestrated1/47581481/ 41. LizardTortoiseReptiles, as a group, consist of the crocodilians, lizards and snakes, tortoises and turtlesand tuatara.However, they are not a clade.One of them is actually moreTuataraclosely related to birds.Crocodile Care to guess which one? http://www.flickr.com/photos/audreyjm529/155024495/ http://www.flickr.com/photos/mg-muscapix/3288435589/ http://www.flickr.com/photos/8363028@N08/2665814123/ http://www.flickr.com/photos/sidm/5253662054/ 42. Crocodiles are more closely relatedto birds than to lizards!Monophyletic: A recent common ancestor and all itsdescendantsParaphyletic: Does not include all descendants from acommon ancestorPolypheletic: A group of organisms that does notWhat this doesntinclude the most recent common ancestorshow is that birds arethe last descendants ofthe dinosaurs!http://en.wikipedia.org/wiki/File:Phylogenetic-Groups.svg 43. *ornithologists study birds, herpetologists study amphibians and reptilesherp is a polyphylatelic grouping whereas birds are monophylatelicFish are paraphylatelicDinosaurs are paraphylatelic http://xkcd.com/867/ 44. Further information: An excellent series that coversmost of the contentThe tree of lifeSir David AttenboroughAmazing site, not to be missed!+ BBC = Brilliant