Molecular Evolution Stat 246 Spring 2002 Week 6a 1 Evolution using molecules Our DNA is inherited from our parents more or less unchanged Molecular evolution is dominated by mutations that are neutral from the standpoint of natural selection Mutations accumulate at fairly steady rates in surviving lineages We can study the evolution of macro molecules and reconstruct the evolutionary history of organisms using their molecules 2 Some important dates in history billions of years ago Origin of the universe 15 4 Formation of the solar system 4 6 First self replicating system 3 5 0 5 Prokaryotic eukaryotic divergence 1 8 0 3 Plant animal divergence 1 0 Invertebrate vertebrate divergence 0 5 Mammalian radiation beginning 0 1 86 CSH Doolittle et al 3 4 Two important early observations Different proteins evolve at different rates and this seems more or less independent of the host organism including its generation time It is necessary to adjust the observed percent difference between two homologous proteins to get a distance more or less linearly related to the time since their common ancestor 5 Insects h V ertebrates g Carp Lamprey Reptiles Fish f ab cd e Reptiles 200 Mammals 220 Birds Reptiles Mammals Corrected amino acid changes per 100 residues Rates of macromolecular evolution j i 10 Fib rin op ep tide 1 1 s MY 180 160 140 120 6 7 8 9 Evolution of 5 the globins in b lo g o Y m M e H 8 5 100 80 60 40 4 3 20 Separation of ancestors of plants and animals Paleocene 200 300 400 500 600 700 Huronian Algonkian Cambrian Ordovician Silurian Devonian Permian Triassic Jurassic Cretaceous Eocene Miocene Oligocene 100 Carboniferous 2 0 Pliocene 1 c me hro toc y C MY 0 20 800 900 1000 1100 1200 1300 1400 Millions of years since divergence After Dickerson 1971 6 Different rates of change for different proteins Protein PAMs 100 residues Theoretical a 10 8 Pseudogenes years lookback time 400 45 c Fibrinopeptides 90 200 c Lactalbumins 27 670 c Lysozymes 24 750 c Ribonucleases 21 850 c Hemoglobins 12 1 5 d Acid proteases 8 2 3 d Triosephosphate isomerase 3 6 d 18 d Phosphoglyceraldehyde dehydrogenase Glutamate dehydrogenase 2 9 1 b d a PAMs Accepted point mutations b c Useful lookback time 360 PAMs Million years d Billion years Doolittle 1986 7 Rates of change in protein families Protein Rate Fibrinopeptides 90 Growth hormone Ig lambda chain C region 27 Epidermal growth factor Somatotropin 30 27 27 26 25 Pancreatic ribonuclease 21 Haptoglobin alpha chain 20 Lipotropin beta Serum albumin Phospholipase A 2 Protease inhibitor PST1 type Prolactin Pancreatic hormone Carbonic anydrase C Lutropin alpha chain Hemoglobin alpha chain Hemoglobin beta chain Lipid binding protein A II 21 19 Myelin basic protein percent 100My a Melanotropin beta Alpha crystallin A chain Endorphin Cytochrome b Insulin 5 16 16 12 12 Lactate dehydrogenase Adenylate cyclase 5 0 4 8 4 5 4 4 3 6 3 4 3 2 2 8 Vasoactive intestinal peptide 2 6 Glyceraldehyde 3 P DH 2 2 Cytochrome C Plant ferredoxin Collagen Troponin C skeletal muscle Glutamate DH 7 4 5 6 3 5 9 8 8 4 5 9 Plastocyanin Neurophysin 2 Alpha crystallin B chain 8 5 6 2 4 3 10 8 7 7 3 Calcitonin Corticotropin 17 8 9 Acid proteases Trypsin 17 Myoglobin Nerve growth factor 7 0 Triosephosphate isomerase 18 9 8 Amyloid A Parvalbumin 19 Gastrin Animal lysozyme 7 4 BPTI Protease inhibitors 31 Lactalbumin Thyrotropin beta chain 33 Ig gamma chain C region Complement C3a Rate Parathyrin 37 Lutropin beta chain Protein 37 Ig kappa chain C region Kappa casein a Glucagon Histone H2B Histone H2A Histone H3 Ubiquitin Histone H4 From Nei 1987 Dayhoff et al 1978 2 5 2 2 1 9 1 7 1 5 1 5 1 2 0 9 0 9 0 5 0 14 0 1 8 0 1 Beta globins orthologues 10 20 30 40 BG human M 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 bovine M A A F K BG macaque BG platypus BG chicken BG shark N T S G G N I N L W A Q L I G A C A A I 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 50 60 70 80 BG human R 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 bovine A N D S N M K BG macaque BG platypus BG chicken BG shark S N A S A G A T S G A K N A N S T I L M R T S G A V K N Y G N L K E F T A C S Y G E A T L G V A V T G 90 100 110 120 BG human N 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 bovine D A K V R N BG macaque BG platypus BG chicken BG shark Q K D K N R I V R S I N S Q D I I I A S D V S Q T D K K A E E V S K A K C F V E G I L L K 130 BG human 140 K E F T P P V Q A A Y Q K V V A G V A N A L A H K Y H BG macaque Q BG platypus D S E W L S H G BG bovine BG chicken BG shark V L D F R D E C W L R V H R D K A Q T I W E Y F G V V D I S K E means same means deletion reference as sequence 9 Beta globins Uncorrected pairwise distances DISTANCES between protein sequences Calculated over 1 to 147 Below diagonal Above diagonal hum observed number of differences number of differences per 100 amino acids mac bov pla chi sha 5 16 23 31 65 23 30 62 hum mac 7 17 bov 23 24 pla 34 34 39 chi 45 44 52 sha 91 88 91 27 37 65 29 64 42 61 90 87 10 Beta globins Corrected pairwise distances DISTANCES between protein sequences Calculated over 1 to 147 Below diagonal observed number of differences Above diagonal estimated number of substitutions per 100 amino acids Correction method Jukes Cantor hum hum bov pla chi sha 5 17 27 37 108 …
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