1Introduction to molecular evolutionLecture 13, Statistics 246March 4, 20042Evolution using molecules:implicit assumptionsOur DNA is inherited from our parents more or less unchanged.Molecular evolution is dominated by mutations that are neutralfrom the standpoint of natural selection.Mutations accumulate at fairly steady rates in surviving lineages.We can study the evolution of (macro) molecules and reconstructthe evolutionary history of organisms using their molecules.3Some important dates in history(billions of years ago)Origin of the universe 15 ±4Formation of the solar system 4.6First self-replicating system 3.5 ±0.5Prokaryotic-eukaryotic divergence 1.8 ±0.3Plant-animal divergence 1.0Invertebrate-vertebrate divergence 0.5Mammalian radiation beginning 0.1 86 CSH Doolittle et al.4The three kingdoms5Two important early observationsDifferent proteins evolve at different rates, and this seemsmore or less independent of the host organism, including itsgeneration time.It is necessary to adjust the observed percent differencebetween two homologous proteins to get a distance more orless linearly related to the time since their common ancestor.( Later we offer a rational basis for doing this.)An striking early version of these observations is next.6Evolution ofthe globinsHemoglobinFibrinopeptides1.1 MY5.8 MYCytochrome c20.0 MYSeparation of ancestorsof plants and animals12346789105MammalsBirds/ReptilesReptiles/FishCarp/LampreyMammals/ReptilesV ertebrates/Insectsa220200180160140120100806040200200100 300 400 500 600 700 800Millions of years since divergenceAfter Dickerson (1971)Corrected amino acid changes per 100 residues900 1000 1100 1200 1300 1400bcde f h ig jHuronianAlgonkianCambrianOrdovicianSilurianDevonianPermianTriassicJurassicCretaceousPaleoceneOligoceneMiocenePlioceneEoceneCarboniferousRates of macromolecular evolution7Protein aPAMs/100 residues/108 years Theoretical lookback timebPseudogenes 400 45cFibrinopeptides 90 200cLactalbumins 27 670cLysozymes 24 750cRibonucleases 21 850cHemoglobins 12 1.5dAcid proteases 8 2.3dTriosephosphate isomerase 3 6dPhosphoglyceraldehyde dehydrogenase 2 9dGlutamate dehydrogenase 1 18d______________________________________________________________________________________aPAMs, Accepted point mutations (explained shortly). bUseful lookback time = 360 PAMs.cMillion years. dBillion years. From Doolittle 1986Different rates of change for different proteins8Rates of change in protein familiesProtein RateaProtein RateFibrinopeptides 90 Thyrotropin beta chain 7.4Growth hormone 37 Parathyrin 7.3Ig kappa chain C region 37 Parvalbumin 7.0Kappa casein 33 BPTI Protease inhibitors 6.2Ig gamma chain C region 31 Trypsin 5.9Lutropin beta chain 30 Melanotropin beta 5.6Ig lambda chain C region 27 Alpha crystallin A chain 5.0Complement C3a 27 Endorphin 4.8Lactalbumin 27 Cytochrome b54.5Epidermal growth factor 26 Insulin 4.4Somatotropin 25 Calcitonin 4.3Pancreatic ribonuclease 21 Neurophysin 2 3.6Lipotropin beta 21 Plastocyanin 3.5Haptoglobin alpha chain 20 Lactate dehydrogenase 3.4Serum albumin 19 Adenylate cyclase 3.2Phospholipase A219 Triosephosphate isomerase 2.8Protease inhibitor PST1 type 18 Vasoactive intestinal peptide 2.6Prolactin 17 Corticotropin 2.5Pancreatic hormone 17 Glyceraldehyde 3-P DH 2.2Carbonic anydrase C 16 Cytochrome C 2.2Lutropin alpha chain 16 Plant ferredoxin 1.9Hemoglobin alpha chain 12 Collagen 1.7Hemoglobin beta chain 12 Troponin C, skeletal muscle 1.5Lipid-binding protein A-II 10 Alpha crystallin B-chain 1.5Gastrin 9.8 Glucagon 1.2Animal lysozyme 9.8 Glutamate DH 0.9Myoglobin 8.9 Histone H2B 0.9Amyloid A 8.7 Histone H2A 0.5Nerve growth factor 8.5 Histone H3 0.14Acid proteases 8.4 Ubiquitin 0.1Myelin basic protein 7.4 Histone H4 0.1apercent/100My From (Nei, 1987; Dayhoff et al., 1978)9Some terminologyIn evolution, homology (here of proteins), means similarity due tocommon ancestry.A common mode of protein evolution is by duplication. Dependingon the relations between duplication and speciation dates, wehave two different types of homologous proteins. Loosely,Orthologues: the “same” gene in different organisms;commonancestry goes back to a speciation event.Paralogues: different genes in the same organism; commonancestry goes back to a gene duplication.Lateral gene transfer gives another form of homology.10Beta-globins (orthologues)10 20 30 40M V H L T P E E K S A V T A L W G K V N V D E V G G E A L G R L L V V Y P W T Q BG-human- . . . . . . . . N . . . T . . . . . . . . . . . . . . . . . . . . . . . . . . BG-macaque- - M . . A . . . A . . . . F . . . . K . . . . . . . . . . . . . . . . . . . . BG-bovine- . . . S G G . . . . . . N . . . . . . I N . L . . . . . . . . . . . . . . . . BG-platypus. . . W . A . . . Q L I . G . . . . . . . A . C . A . . . A . . . I . . . . . . BG-chicken- . . W S E V . L H E I . T T . K S I D K H S L . A K . . A . M F I . . . . . T BG-shark50 60 70 80R F F E S F G D L S T P D A V M G N P K V K A H G K K V L G A F S D G L A H L D BG-human. . . . . . . . . . S . . . . . . . . . . . . . . . . . . . . . . . . . N . . . BG-macaque. . . . . . . . . . . A . . . . N . . . . . . . . . . . . D S . . N . M K . . . BG-bovine. . . . A . . . . . S A G . . . . . . . . . . . . A . . . T S . G . A . K N . . BG-platypus. . . A . . . N . . S . T . I L . . . M . R . . . . . . . T S . G . A V K N . . BG-chicken. Y . G N L K E F T A C S Y G - - - - - . . E . A . . . T . . L G V A V T . . G BG-shark90 100 110 120N L K G T F A T L S E L H C D K L H V D P E N F R L L G N V L V C V L A H H F G BG-human. . . . . . . Q . . . . . . . . . . . . . . . . K . . . . . . . . . . . . . . . BG-macaqueD . . . . . . A . . . . . . . . . . . . . . . . K . . . . . . . V . . . R N . . BG-bovineD . . . . . . K . . . . . . . . . . . . . . . . N R . . . . . I V . . . R . . S BG-platypus. I . N . . S Q . . . . . . . . . . . . . . . . . . . . D I . I I . . . A . . S BG-chickenD V . S Q . T D …
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