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 15 4 Origin of the universe 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 f g h i V ertebrates Insects Carp Lamprey abcde Reptiles Fish 200 Birds Reptiles Mammals Reptiles 220 Mammals Corrected amino acid changes per 100 residues Rates of macromolecular evolution j 10 160 140 120 Fibrin op 1 1 M eptides Y 180 6 7 89 5 Evolution of the globins in ob l og Y m M He 5 8 100 80 40 me chro Cyto MY 20 0 4 Pliocene Miocene Oligocene Eocene Paleocene 100 200 300 Algonkian Cambrian Devonian Silurian Ordovician Jurassic Triassic Permian Cretaceous 0 Carboniferous 20 3 2 400 500 600 1 c Separation of ancestors of plants and animals Huronian 60 700 800 900 1000 1100 1200 1300 1400 Millions of years since divergence After Dickerson 1971 6 Different rates of change for different proteins Protein PAMsa 100 residues 108 years Pseudogenes 400 Fibrinopeptides 90 Lactalbumins 27 Lysozymes 24 Ribonucleases 21 Hemoglobins 12 Acid proteases 8 Triosephosphate isomerase 3 Phosphoglyceraldehyde dehydrogenase 2 Glutamate dehydrogenase 1 Theoretical lookback timeb 45c 200c 670c 750c 850c 1 5d 2 3d 6d 9d 18d a PAMs Accepted point mutations b Useful lookback time 360 PAMs c Million years 7 Rates of change in protein families Protein Ratea Protein Rate Fibrinopeptides Growth hormone Ig kappa chain C region Kappa casein Ig gamma chain C region Lutropin beta chain Ig lambda chain C region Complement C3a Lactalbumin Epidermal growth factor Somatotropin Pancreatic ribonuclease Lipotropin beta 3 5 Haptoglobin alpha chain Serum albumin Phospholipase A2 Protease inhibitor PST1 type Prolactin Pancreatic hormone Carbonic anydrase C Lutropin alpha chain Hemoglobin alpha chain Hemoglobin beta chain Lipid binding protein A II Gastrin Animal lysozyme Myoglobin Amyloid A Nerve growth factor Acid proteases Myelin basic protein 90 37 37 33 31 30 27 27 27 26 25 21 21 Thyrotropin beta chain Parathyrin Parvalbumin BPTI Protease inhibitors Trypsin Melanotropin beta Alpha crystallin A chain Endorphin Cytochrome b5 Insulin Calcitonin Neurophysin 2 Plastocyanin 7 4 7 3 7 0 6 2 5 9 5 6 5 0 4 8 4 5 4 4 4 3 3 6 20 19 19 18 17 17 16 16 12 12 10 9 8 9 8 8 9 8 7 8 5 8 4 7 4 Lactate dehydrogenase Adenylate cyclase Triosephosphate isomerase Vasoactive intestinal peptide Corticotropin Glyceraldehyde 3 P DH Cytochrome C Plant ferredoxin Collagen Troponin C skeletal muscle Alpha crystallin B chain Glucagon Glutamate DH Histone H2B Histone H2A Histone H3 Ubiquitin Histone H4 3 4 3 2 2 8 2 6 2 5 2 2 2 2 1 9 1 7 1 5 1 5 1 2 0 9 0 9 0 5 0 14 8 0 1 0 1 Beta globins orthologues 10 BG human BG macaque BG bovine BG platypus BG chicken BG shark 60 70 80 100 110 120 NLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFG Q K D A K V RN D K NR IV R S I N SQ DI II A S DV SQ TD KK AEE V S K AKCF VE GILLK 130 BG human BG macaque BG bovine BG platypus BG chicken BG shark 40 RFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLD S N A N DS N MK A SAG A TS G A KN A N S T IL M R TS G AVKN Y GNLKEFTACSYG E A T LGVAVT G 90 BG human BG macaque BG bovine BG platypus BG chicken BG shark 30 MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQ N T M A A F K SGG N IN L W A QLI G A C A A I WSEV LHEI TT KSIDKHSL AK A MFI T 50 BG human BG macaque BG bovine BG platypus BG chicken BG shark 20 140 KEFTPPVQAAYQKVVAGVANALAHKYH Q VL DF R D S E W L S H G D EC W L RV H R DK A QT IWE YFGV VD ISKE means same as reference sequence means deletion 9 Beta globins Uncorrected pairwise distances DISTANCES between protein sequences Calculated over 1 to 147 Below diagonal observed number of differences Above diagonal number of differences per 100 amino acids hum mac bov pla chi sha 5 16 23 31 65 hum mac 7 17 23 30 62 bov 23 24 27 37 65 pla 34 34 39 29 64 chi 45 44 52 42 61 sha 91 88 91 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 mac bov pla chi sha hum 5 17 27 37 108 mac 7 18 27 36 102 bov 23 24 32 46 110 pla 34 34 39 34 106 chi 45 44 52 42 98 sha 91 88 91 90 87 11 UPGMA tree BG shark BG chicken BG platypus BG bovine BG macaque BG human 12 Alu sequences globin2 Alu 1 Knight et al 1996 hum 1 hum 2 hum 3 chimp bonob goril orang C C G G A C A G G A A A C 10 A C T C T G G G A A A T T A G G A G T G G C C 20 A C G T 80 T T C C C C G A G A A C T C C T 140 G G G T C G T G G G C G A A C C 260 G C A A C A A T hum 1 hum 2 hum 3 chimp bonob goril orang A T C A C C T G A 70 G G hum 1 hum 2 hum 3 chimp bonob goril orang T A A A A A T A C 130 A A A G A A A A T C G A 200 C T T 250 T C C A G C C T G G hum 1 hum 2 hum 3 chimp bonob goril orang G C T G A G G C 190 A G G hum 1 hum 2 hum 3 chimp bonob goril orang C C A T C C T G C A C A G C C …
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