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This 15 page Class Notes was uploaded by Oma Larkin on Friday October 23, 2015. The Class Notes belongs to BIOL 404 at University of Idaho taught by Erica Rosenblum in Fall. Since its upload, it has received 40 views. For similar materials see /class/227882/biol-404-university-of-idaho in Biology at University of Idaho.
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Date Created: 10/23/15
BIOL 404 Molecular Evolution introduction to the Course Dr Erica Bree Rosenblum Universityor Idaho Course Sections 1 Foundations history early evolution building blocks of life etc H Microevolution mutation selection drift recombination etc 111 Macroevolution genomic architecture genomic evolution IV New horizons synthesis current topics Course Structure Lectures Monday Wednesday Friday 330 420 Office hours Monday Wednesday 230 330 at LSS 359 Or by appointment Course Assignments Exams Two midterms One nal Term project Grant proposal Peer review Participation Paper presentation Discussion and participation Course Materials Textbooks Grauer and Li required Additional Reading Primary literature Website httppeopleibestuidahoedubreeBIOL40 4html Check often Note Power points will be posted after the fact as study aids but this does not eliminate the need to take notes Please save paper when you print What is molecular evolution Molecular evolution is the process of change over time at the scale of DNA RNA and proteins The field integrates evolutionary biology molecular biology and population genetics We are interested in patterns and processes being vs becoming We will discuss theory and application Why study molecular evolution There is an entire molecular world out there The total amount of DNA in living organisms if strung end to end is on the order of 10 25 km That is 10 times the diameter of the known universe Molecules are the gears that make all of life tick Why study molecular evolution To understand the genetic basis of biological diversity Why study molecular evolution To understand the evolutionary history of life on earth History is written in the molecules Why is Mol Evol relevant to the real world Conservation applications Populariun six genlliK warmthquot Time gt Genetic variation can be correlated with extinction risk httpevolutionbel39keleyedu Why is Mol Evol relevant to the real world HlVl Tim M Medical applications What are the origins of HIV HM gum M HID1 gulp it How do we design appropriate treatments given drug resistance 2222quot httpevolution berkeleyedu Why is Mol Evol relevant to the real world Agricultural applications of v i z i l n v W1 d teosinte domestlc corn Evolutionary history of domestic crops arti cial selection d viral disease resistance genes httpIevolutionberkeleyedu Why is Mol Evol relevant to the real world Legal applications A mums lrnm 2 St a a mum mm 1 DNA evidence used in criminal trials man prominent cases clearing and implicating suspects mm new mm a Why is this eld particularly important now Base pans loci studied Sequences in GenBank 7 an nun un 60 00 inuuaun 125 2mm an 1 man 55 mun ZEUS man was 39r39eal Data GenBank Hierarchical Levels of Evolution What evolves Anything that functions as a replicator and an interactor Genes Genomic hierarchies introns exons gene families regulation Genomes gene interactions pliotrophy epistasis Individuals organismal development Populations Species Lineages ancestordescendent line Our course focuses at the genesgenomes level but has implications all the way up the tree Hierarchical Levels of Evolution Micro and macro evolution are mechanisticale linked Muxnu Gun r Gunmu rm nw mm 38 bllllon years Macroevoluhon Nahum StIccllun mm levulmum hen v edulevnhmarv Unit I FOUNDATIONS 4 Historical perspectives Foundations gt Early evolutlon 3 uLp m k quot r t39 39 I a r H it a Hg 4 39Eg39 H a 2 z 5 39 if P I t 1 n V 1 I quotIquot A u 1139 E A i H 8 1 f I Fmrnation Stable Plobiotit F ro RHA mm rst EMA Diversi cation of Eartlquot hymnSphere Hmmistly world world pmtein life of life I 1 l f N W l39 5 1425 14 3E 36 gasping5mm Reading For today intro Grauer and Li introduction For Wednesday history Dobzhansky 1964 Biology Molecular and Organismic Darwin 1859 Origin of Species Chapter III Struggle for Existence optionall if tlatson and Crick A structure for DNA For Friday early evolution Rivera and Lake 2004 The ring of life Robison 2005 J umpstarting a cellular world optional Doolittle ooo Uprooting the tree of lite Means we will read and discuss in class BlOL 404 Molecular Evolution Diversiw Statistics I Di Erica Bree Rosenblum Universltyorldaho Diversity Statistics H ete rozygosity Single locus expected heterozygosity or gene diversity in h 1 Z x 2 Summation ofthe 1 frequency of each allele i 139 1 for all alleles at locus m Multi locus expected heterozygosity or gene diversity 1 Summation of the ene H 1n 2 h g diversity for each locus 139 for all loci considered 11 11 H etc rozygosity Heterozygosity is population size dependent lg uvlnnu Also note that under pure drift gene diversity will decrease by 12Ne per generation Loss of l39leterolygoslty We can measure loss of heterozygosity as a result of population structure with Wright s F statistics F 1 Observed heterozygosity Expected frequency of heterozygotes under HWE F statistics always go from O to 1 High F suggests lower than expected heterozygosity or higher than expected inbreeding F statistics F inbreeding coef cient the probability that 2 alleles in the same individual are identical by descent 3y 0 m 0 x Q 00 KL x 4 Note IBD can i39elkartz idenuoal By Descent or more commonly lsulan on F statistics F inbreeding coefficient the probability that 2 alleles in the same individual are identical by descent If you have inbreding the probability of identity by descent increases Average yield 0 am Why do we care about measuring inbreeding Inbreeding depression reduction in fitness due to inbreeding 70 l Mechanisms l homozygosing of L4 deleterious recessives g overdomlnance 3 40 l l 30r a l 39 4 200 0 25 0150 075 xio Inbreeding coeffiuent F Why do we care about measuring inbreeding An aside on inbreeding avoidance adaptations Heterostyly self incompatibility Why do we care about measuring inbreeding An aside on inbreeding avoidance adaptations Heterostyly self incompatibility Sex biased dispersal Why do we care about measuring inbreeding An aside on inbreeding avoidance adaptations Heterostyly self incompatibility Sex biased dispersal Selffertilization avoidance in hermaphrodites Why do we care about measuring inbreeding An aside on inbreeding avoidance adaptations Heterostyly self incompatibility Sex biased dispersal Selffertilization avoidance in hermaphrodites Why do we care about measuring inbreeding However there is also plenty of evidence for assortative mating dad39s heigm ay mom s heigBl l I I I I I I I I I5140145150155150165Honsi 0 Unear m Why do we care about measuring inbreeding Calculating inbreeding coef cients can also tell us about population structure Why do we care about measuring inbreeding Calculating inbreeding coef cients can also tell us about gene ow F statistics We can calculate several different F statistics I individual S sub pop T total pop F statistics We can calculate several different F statistics FIS Inbreeding coef ofIndividuals quot within Subpopulations 339 eg high Fis if you ave sampled a single clutch as your subpop F statistics We can calculate several different F statistics FIS Inbreeding co ef of Individuals within 39a Subpopulati ons For outcrossing organisms Fis is usually very small lt001 F statistics We can calculate several different F statistics FIT Inbreeding coef of Individuals within total population N ot us ed very commonly F statistics We can calculate several different F statistics Inbreeding coef of Subpops 1 within Total pop eg high FST if you have limited migration between subpops F statistics We can calculate several different F statistics Inbreeding coef of Subpops within Total pop Fst is variable in na ur populations 0 panmixis 1 isolation F statistics Equilibrium value for F st depends on migration rate and surprise surprise population size 1 V 4N 1 A suiprisingly low amount of migration 1 migrant per generation will raise Fst to 02 Note There ere additional F st like measures for different data types Gtst Phist etc F statistics Fst in natural populations From Morjan and Rieseberg review A 300 pm 7 Artlmat Frequency F statistics We can estimate Fst and corresponding multilocus measures from genetic data As always we will likely Violate some assumptions of our island model 0 H O No selection No mutation All pops are same size All pops contribute equally O to migrant poo Migration is random with respect to distance F statistics We can estimate Fst and corresponding multilocus measures from genetic data There are other models OOOOOO of population structure you can use ie I I stepping stone models 9 Q CID Q CID Additional considerations Additional considerations Although we think about migration at the organismal level in fact gene ow may not be equal across all loci For example introgression gs gig 3 Se t g 3 F statistics Not always easy to estimate gene ow from molecular data Hergdlry ung H7425 Pecand a Ddqu rm mm H Nowrm 999 Short Review Indirect measures of gene flow and migration F31 14Nm 1 MICHAEL E WHmocK39r a UAViD E MCCAULEY fDepanmmtoIZDoiayy Umwrsljof nmh Comm Vanmuva arm Eoagy yamm Linnun N swile remake 372 m dlflirully uf dimly mummy gm Hm has m m mmmun use ui mum mum exunpuhmd rmm gm ixsquenry dam Thusv mmm am mm mm at I4 1 umwmml quotVENAI at me grnuur minute mung pupi nums and m usnd m 50 u numim nr 124 ampnndaandtD pmmnD39 15 LISA imd m Hump muse 355wquot um surh mm mom i when mulled quannuuvs inmmausu to he gained ahan dispuml i mum in 1 Guam u is pn m m m n is or w my nigmuh sunsnrmi entering a m um F mu hm iramL mI m an mumw lmmv pupal on par ponrmuon Linimummiv um mamaluuml onquot model uudurlylng um immluilmi quot12km uwn Inningka Keywords allozymm dlxpurni F gm aw Huilwrl unmahsur assumpunns mi populations am vary ikniv measures dennn Additional considerations Additional considerations Although we think about migration at the organismal level in fact gene ow may not be equal across all loci For example introgression 2 Q s 2 3 Additional considerations Additional considerations Although we think about migration at the organismal level in fact gene ow may not be equal across all loci For example 1ntrogress1on Additional considerations Additional considerations Although we think about migration at the organismal level in fact gene ow may not be equal across all loci From Morjan and Rieseberg review Mean animal mitochondrial Fst 045 Mean animal nuclear Fst 020 Additional considerations Additional considerations Even small numbers of migrants can spread advantageous alleles and keep populations cohesive I mn 1 W100 39 L39 IMm mnwxl l 009000 For example Even for tiny migration rates and modest selection coefs you can get spread of advantageous alleles Additional considerations Additional considerations Even small numbers of migrants can spread advantageous alleles and keep populations cohesive 1 0000000 n IDLXAX39J WCCOO a i 1003quot men For example 1003000 But mutations with really low selection Genevalians Additional considerations Additional considerations Although small numbers of migrants are thought to homogenize populations local adaptation can proceed despite relatively large amounts of gene ow For example 10000 coefs act like neutral alleles and have a hard 109m time spreading across subdivided pops won O n Nm Selection coemcienl s 0 0m 0 Earless Lizard Fence Lizard Whipta Lizard Earless Lizard Fence Lizard Wail Iin AF LPs 19 unlinked loci AFLPS 3 37 bands 5000 bp 50 bands at i 41 Ml r in M C 1 1 MC i 1 ELF LP Additional considerations Additional considerations Conservative vs creative role for gene ow Does gene ow retard local adaptation by introducing maladapted alleles 01 Does gene ow facilitate adaptation by allowing the spread of advantageous alleles