Class Note for ECOL 600B at UA
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Date Created: 02/06/15
Spring 2003 ECOL 600A Evolution Core Birky 4 Evolutionary Genetics Read Futuyma Chap 22 pp 625635 except section titled Phylogenetic Insights Graur amp Li Chap 3 discusses alignment and correcting for multiple hits in much more detail than we will need Chap 4 pp 997123 except section titled Similarity pro les pp 139714Z1467163 Note Nancy Moran will be lecturing on molecular evolution so we will only touch on some basic theory and phenomena You ll probably want to read some of the above in more detail for her section of the course Speciation and the Transition from Population Genetics to Evolutionary Genetics This section is concerned with longeterm evolution ie evolutionary divergence of species Some of the basic factors that determine variation within a species also control divergence of different species mutation drift selection sex Difference is time scale Diagram below shows gene lineages during speciation in asexual haploid organism or genome e g animal mitochondria When speciation begins eg with separation of population into to subpopulations by permanent geographic barrier the two subpopulations include individuals that are more closely related to individuals from the other clade polyphyletic paraphyletic When speciation is complete they are reciprocally monophyletic and are distinct clades Lineage sorting is complete This process takes about 4Ne generations in a haploid population Measuring evolutionary divergence at the sequence level 1 For each species sequence one copy of a gene 2 Align the sequences this is usually done with computer assistance 3 Calculate the sequence difference sequence difference d sites with mismatches total sites sequence identity l 7 d number of sites without mismatches total sites A site is occupied by a base or amino acid in both sequences gaps are ignored sequence similarity proportion of sites where the amino acids are identical or are believed to be selectively equivalent amp interchangeable because they have similar physical properties or are in fact often substituted 5pm 2am ECOL S A Evaluuan Care Buky A amp B are reciprocally monophyleuc A A A A B B B B AampBare paraphyleuc A A A A B B B B AampBare polyphyleuc AA AA BB BB 5pm 2am ECOL S A Evaluuan Care Buky A cumme the sequence dwzrgenoe amine mnemedfax muluple has ammmrgta an evaluuanary madd The nmplenxs39he IWampCmtaxmadel see Brut Walsh slecture hates mm sequmces K r g ma 7 gm omn m have calculaums are dam szparately m synanymaus and nanxynanymnus mum at m 2quot caan panum vs 14 and 2m caan pannans Aaahcncmmmmm Aascmncscmcamm mnvergem A A quot Vex2mm D6PPgtD E n amncmmmmm mump e dwergem Calculating evolmjonzry mes KT nth Spent divexgzncz ume theme uf evaluuan KZT 5pm 2am ECOL snnA Evaluuan ch Buky Usua y K m m hp uhmmuans per ml hr per hp and T m m years Sh E1 m hp uhmtuuans per ml per year A nut an dxmmxmna analysts Dam gel Lhathp uhmtuuans per ml per year 1 up same asbpsuh sntexyearsaxbp uh sx at Xyears mlbpsuh sueyear Thu mphmm whm yhu are dhmg dmmhmj analysts 1 e mung hm expresnans h equauans wALh a mmmhm m determine up dmuzrmuns a u nd mun Fax Example In this case we have Km hp uh sxue and Tm years Sh Ez lgsuhs 1 hpth has Xyears mesxyears A dimming my 2MB sum 5 ABETT BA BTABETTEBA ancestur lt mmmagm specves a ABETT BA 557m nzzw u2moz K34MH pwzmwza 2T0232X22 My53 x m ghpsuhspersnepergear The best am anE mm framvntehrales fur whmhwe have aphhdrmnmd But even therethe emmaushave very large uncenme mm and mvenehxateshave aphhx rm retard muaargamsm have almaxt mm hde mdrmfexsxnmhexA Mya KS7 52 TA xl s EZKSZ Assxm Sammmzswe mngetTfmmhmgeugraphy m emm Trm aparantefmmT fur xtshaxt Repmnmive mums and variation 22 mm mm examples Evalunanary mg afhasepan uhmtuum are gmexa y hmquot ht m m m 7xoep1fm39 RNA Vu39uses whmh evnlve hum three mders hr magmtude mm Vanauan m evaluuunary rates parallels vanaum m dwexmy AM u humming are m hp uhmtunans per ml per year unless athzrwlse mud Spring 2003 ECOL 600A Evolution Core Birky Evolutionary rates vary among organisms and lineages rodents 79 X 10 9 primates 13 X 10 9 22 X 10 9 Evolutionary rates vary among genomes following are synonymous substitution rates Plants nuclear 6 X 10 9 chloroplast Z X 10 9 mitochondrial 06 X 10 9 Primates mitochondrial m 20 X 10 9 nuclear m 5 X 10 9 Evolutionary rates vary among genes and other sequences vertebrates amino acid sequence divergences fibrinopeptides 4 X 10 9 hemoglobins l X 10 9 cytochrome c 02 X 10 9 Pseudogenes evolve faster than genes mammals pseudogenes 485 X 10 9 protein coding genes 181 X 10 9 188 rRNA genes 004 X 10 9 Z88 rRNA genes 050 X 10 9 Note the data for these genes come from different species pairs and are not exactly comparable Evolutionary rates vary among regions of a gene mammals exons total 181 X 10 9 synonymous substitutions 465 X 10 9 nonsynonymous substitutions 088 X 10 9 Explaining evolutionary rates and patterns Forces are mutation drift and directional selection Balancing selection usually doesn39t last very long after speciation exception MHL in humans and chimpanzees Key point only mutations that are fixed will contribute to differences between species E ZNuF fixations site mutations site X generation fixations mutation neutral mutations in diploids F l ZN E u Spring 2003 ECOL 600A Evolution Core Birky Substitution rate in pseudogenes and synonymous substitutions can be used as an estimate of u Often easier and more accurate than direct measurement Synonymous substitutions in highly expressed genes are subject to weak selection Summary of relationship between selection and substitution rates and diversity proportion of proportion of neutral mut39s higher 7777777777777777777777777777777777777777777777777777777 gtneutral mut39s lower E u E lt u E ltlt u promoters pseudogenes introns lst amp 2nd codon positions in synonymous sub39s 3rd codon positions noncatalytic regions catalytic site conserved sequences substitution rates and diversity highest 777777777777777777777777777777777777777777777777777777777777777777777777777777 lowest Positive selection for advantageous mutations can be detected in evolutionary studies In a gene KsKa ratio At specific sites 0 Compensating substitutions o Convergent and parallel evolution Molecular Clocks In spite of all the above variations evolutionary rates can be approximately constant over long periods of time when one looks at a single gene If one can calculate E for a gene in some lineage one can estimate the time since divergence of two other lineages by solving E KZT for T KZE Some people have pointed to cases of extreme divergence eg a few cases of hundredefold differences in E or just the high variance in E and argued that there is no clock There is the only question is whether it is good enough for its intended use the answer will be different in different cases Also in many cases it is the only game in town The really interesting and probably very deep question is why is the rate of evolution even remotely constant Why doesn39t it vary by a factor of 103 or 104 For E to be constant requires that 4 parameters be constant or vary in a nicely compensating fashion N Ne u and s Sex and Evolution Hitchhiking and background selection effects don39t affect longeterm neutral substitution rates But the fixation probability of selected mutations at a site is affected by selected mutations segregating in the background especially if they are linked to the site Hille Robertson effect awn 1n hard selecuan madd and advantagwus mutauans are mm hkdy m be 1m Selecuan bn hankgmund acts hkz name mtexfenrgwnh selemm at me Can he awed as reduced Ne Sex cauntenvls 211211 by npxaung sum A131 and A1 32 wALh A131 and A2 32 MN Email gene advantage b1 sex Namm sdeman waxks hatter wALh sex Predmmn asexual Images shauld have ngb exunmannte and W peuaummte A nut bn mutauana 1bad and esmplrg frammeltden 1n a urvwmglmeage 1n an asexual mgamvn due 41 mnpmsaurgsuhsmuuans z 41 demmental nabmbaubng Nat 11222me dbn aknnwmquzncy dmnbuuan b1 swine 1 ma n n 1 One margy selected abvantagewus uhmtuuan mm mmpensate fur sevzral weakly selecud demmzntals My mumbn Inde mte umva as a hung requues 11 s 2 11de when s 1 the man selec m mman u 1 the mmaubn rate and uhsrnpts a and 3 refer a advantagwus and demmzntal mutauans Anathexpmnt Fitness 1 quanutauvemululamsumt Sam anus b1 apmans a vw selec mla an an many demmen39als the Sam um
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