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وراثة العشائر Population genetics

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مشروووووع الوراثه

  1. 1. POPULATION GENETICS
  2. 2. •Population geneticsGenetic structure of a population.clan..Group of individuals of the same species that can interbreed.
  3. 3. POPULATION GENETICS•Genetic structure of a population•Group of invdividuals of thesame species thet can interbreed
  4. 4. Why is gentic variation important?1-Gene pool = is the complete set ofunique alleles in a species orpopulation2-Genetic variation increase = the genepool = increases3-Potential for change in geneticstructure4-Genotype
  5. 5. •5-adaptation to environmental change•6-Conservation•7-Divergence of populations8-BiodiversityWhy is genetic variation important ?Variation survivalNo variation Extinction !!Globalwarming
  6. 6. Why is genetic variation important?migration or lsolationVariationNo variationnorthsouthnorthSouth
  7. 7. WHY IS GENETIC VARIATIONIMPORTANT•Variation migration or isolation divergenceNO VARIATION NO DIVERGENCE!!northsouthnorthsouth
  8. 8. POPULATION GENETICS•Genetic structure of a population•1-alleles•2-genotypes•Group of individuals of the same species thet can interbreed•patterns of genetic veriaton in populations changeticstructure through time•Describing genetic structure•1-Genotype frequencies•2-allele frequencies
  9. 9. •distributionallele frequencyPopulation genetics is the study ofand change under the influence of the four main evolutionarygeneandmutation,genetic drift,natural selectionprocesses:It also takes into account the factors of.flow.population structurepopulation subdivision and,recombinationandadaptationIt attempts to explain such phenomena as.speciation•Population genetics was a vital ingredient in the emergence ofIts primary founders were.modern evolutionary synthesisthewho also laid,R. A. FisherandS. HaldaneJ. B.,Sewall Wrightquantitativethe foundations for the related discipline of.genetics•Traditionally a highly mathematical discipline, modernpopulation genetics encompasses theoretical, lab and fieldwork.
  10. 10. •Fundamentals•.peppered mothbodied form of the-is the whitetypicaf.betulariaBiston•Biston betularia f. carbonaria is the black-bodied form of the pepperedmoth.•Population genetics is the study of the frequency and interaction ofalleles and genes in populations A sexual population is a set ofThis impliestogether.breedorganisms in which any pair of members can]otherthat all members belong to the same species and live near each•For example, all of the moths of the same species living in an isolatedforest are a population. A gene in this population may have severalofphenotypesalternate forms, which account for variations between thethe organisms. An example might be a gene for coloration in moths thatis the complete set ofgene poolblack and white. A:alleleshas twofor an alleleallele frequencyalleles for a gene in a single population; theis the fraction of the genes in the pool that is composed of that allele (forexample, what fraction of moth coloration genes are the black allele).occurs when there are changes in the frequencies of allelesEvolutionwithin a population; for example, the allele for black color in a populationof moths becoming more common.
  11. 11. •Hardy–Weinberg principle•geneticwill only cause evolution if there is enoughselectionNatural,geneticsMendelianin a population. Before the discovery ofvariationBut with blending.blending inheritanceone common hypothesis wasinheritance, genetic variance would be rapidly lost, making evolution byprovides theWeinberg principle-Hardynatural selection implausible. TheMendeliansolution to how variation is maintained in a population withAccording to this principle, the frequencies of alleles.inheritance(variations in a gene) will remain constant in the absence of selection,mutation, migration and genetic drift The Hardy-Weinberg "equilibrium"refers to this stability of allele frequencies over time.•A second component of the Hardy-Weinberg principle concerns theeffects of a single generation of random mating. In this case, thegenotype frequencies can be predicted from the allele frequencies. For: theallelesexample, in the simplest case of a single locus with twoa and their frequenciesrecessiveis denoted A and thedominant alleleare denoted by p and q; freq(A) = p; freq(a) = q; p + q = 1. If the genotypefrequencies are in Hardy-Weinberg proportions resulting from randomin thehomozygotesfor the AA2p=(AA)freqmating, then we will havepopulation, freq(aa) = q2 for the aa homozygotes, and freq(Aa) = 2pq for.heterozygotesthe
  12. 12. •Natural selection•make it more likely for antraitsselection is the fact that someNaturalPopulation genetics describes.reproduceto survive andorganismofpropensity or probabilityas afitnessnatural selection by definingsurvival and reproduction in a particular environment. The fitness is.selection coefficient+s where s is the1normally given by the symbol w=or the observable characteristics,phenotypesNatural selection acts onbasis of any phenotype whichgenetically heritableof organisms, but thegives a reproductive advantage will become more common in aIn this way, natural selection converts).allele frequencypopulation (seepopulationdifferences in fitness into changes in allele frequency in aover successive generations.•Before the advent of population genetics, many biologists doubted thatsmall differences in fitness were sufficient to make a large difference toevolution Population geneticists addressed this concern in part bySelection can overcome genetic drift.genetic driftcomparing selection toWhen.effective population sizedivided by the1when s is greater thanthis criterion is met, the probability that a new advantageous mutanttime until fixation ofs The2is approximately equal tofixedbecomessuch an allele depends little on genetic drift, and is approximately[)/s.sNproportional to log(
  13. 13. Genetic drifttheThat is,samplingrandomcaused byallele frequenciesis a change indriftGeneticalleles in the offspring are a random sample of those in the parents Genetic drift maycause gene variants to disappear completely, and thereby reduce genetic variability. Inwhich makes gene variants more common or less common,natural selectioncontrast todepending on their reproductive success the changes due to genetic drift are not driven byenvironmental or adaptive pressures, and may be beneficial, neutral, or detrimental toreproductive success.The effect of genetic drift is larger for alleles present in a smaller number of copies, andsmaller when an allele is present in many copies. Vigorous debates wage amongscientists over the relative importance of genetic drift compared with natural selection.held the view that genetic drift plays at the most a minor role inRonald FisherMotoo1968evolution, and this remained the dominant view for several decades. Inwhich claimsneutral theory of molecular evolutionrekindled the debate with hisKimurathat most of the changes in the genetic material are caused by neutral mutations andgenetic drift The role of genetic drift by means of sampling error in evolution has beenwho argue that selection on linked sites is,ProvineWillandGillespieJohn Hcriticized bya more important stochastic force.orbranching processesThe population genetics of genetic drift are described using eitherapproaches are usuallyfrequency Thesedescribing changes in allelediffusion equationaapplied to the Wright-Fisher and Moran models of population genetics. Assuming geneticdrift is the only evolutionary force acting on an allele, after t generations in manyreplicated populations, starting with allele frequencies of p and q, the variance in allelefrequency across those populations is
  14. 14. •tation•in the formgenetic variationis the ultimate source ofMutationof new alleles. Mutation can result in several different types ofchange in DNA sequences; these can either have noor prevent the gene from,product of a geneeffect, alter thesuggestDrosophila melanogasterfunctioning. Studies in the flythat if a mutation changes a protein produced by a gene, thiswill probably be harmful, with about 70 percent of thesemutations having damaging effects, and the remainder beingeither neutral or weakly beneficial
  15. 15. •Mutations can involve large sections of DNA becomingTheserecombinationgeneticusually through,duplicatedduplications are a major source of raw material for evolving newgenes, with tens to hundreds of genes duplicated in animalfamiliesMost genes belong to largeryearsgenomes every millionNovel genes are produced by severalancestrysharedofof genesmethods, commonly through the duplication and mutation of anancestral gene, or by recombining parts of different genes toact asdomainsHere,functionsform new combinations with newmodules, each with a particular and independent function, thatcan be mixed together to produce genes encoding new proteinswith novel properties For example, the human eye uses fourcolor visiongenes to make structures that sense light: three forall four arose from a single ancestral;night visionand one forentireadvantage of duplicating a gene (or even angeneAnotherthis allows one gene;redundancyis that this increases)genomein the pair to acquire a new function while the other copyperforms the original function Other types of mutationoccasionally create new genes from previously noncoding DNA
  16. 16. •In addition to being a major source of variation, mutation mayalso function as a mechanism of evolution when there aredifferent probabilities at the molecular level for differentmutations to occur, a process known as mutation bias If twogenotypes, for example one with the nucleotide G and anotherwith the nucleotide A in the same position, have the same fitness,but mutation from G to A happens more often than mutation fromA to G, then genotypes with A will tend to evolve Differentinsertion vs. deletion mutation biases in different taxa can lead tothe evolution of different genome sizes Developmental ormorphologicalmutational biases have also been observed infirst theory of-phenotypeexample, according to theevolutionForgeneticmutations can eventually cause the,evolutioninduced by theof traits that were previouslyassimilationenvironment
  17. 17. •Mutation bias effects are superimposed on other processes. Ifselection would favor either one out of two mutations, but thereis no extra advantage to having both, then the mutation thatoccurs the most frequently is the one that is most likely tobecome fixed in a population Mutations leading to the loss offunction of a gene are much more common than mutations thatproduce a new, fully functional gene. Most loss of functionmutations are selected against. But when selection is weak,mutation bias towards loss of function can affect evolution Forare no longer useful when animals live in thepigmentsexample,darkness of caves, and tend to be lost This kind of loss offunction can occur because of mutation bias, and/or because thefunction had a cost, and once the benefit of the functiondisappeared, natural selection leads to the loss. Loss ofduring laboratory evolutionbacteriumability in asporulationappears to have been caused by mutation bias, rather thannatural selection against the cost of maintaining sporulationability When there is no selection for loss of function, the speedat which loss evolves depends more on the mutation rate than itthat it is drivenindicatingsizeeffective populationdoes on themore by mutation bias than by genetic drift.
  18. 18. •Evolution of mutation rate•Due to the damaging effects that mutations can haveon cells, organisms have evolved mechanisms suchthe,mutations Thereforeto removeDNA repairasoptimal mutation rate for a species is a trade-offbetween costs of a high mutation rate, such ascosts ofmetabolicdeleterious mutations, and themaintaining systems to reduce the mutationrate, such as DNA repair enzymes Viruses that useRNA as their genetic material have rapid mutationrates which can be an advantage since these viruseswill evolve constantly and rapidly, and thus evade theimmunedefensive responses of e.g. the humansystem
  19. 19. •Gene flow and transfer•is the exchange of genes betweenflowGenepopulations, which are usually of the same species Examplesof gene flow within a species include the migration and then. Genepollenbreeding of organisms, or the exchange ofhybridtransfer between species includes the formation of.horizontal gene transferorganisms and•Migration into or out of a population can change allelefrequencies, as well as introducing genetic variation into apopulation. Immigration may add new genetic material to theof a population. Conversely, emigrationgene poolestablishedmay remove genetic material. Population genetic models canbe used to reconstruct the history of gene flow betweenpopulations.
  20. 20. •Reproductive isolation•between two diverging populations are required forbarriers to reproductionAs, gene flow may slow this process bybecome new speciesthe populations tospreading genetic differences between the populations. Gene flow is hinderedby mountain ranges, oceans and deserts or even man-made structures such]genes, which has hindered the flow of plantGreat Wall of Chinaas the•most recentDepending on how far two species have diverged since their, it may still be possible for them to produce offspring, ascommon ancestorare generallyhybridsSuchmulesmating to producedonkeysandhorseswith, due to the two different sets of chromosomes being unable to pair upinfertile. In this case, closely related species may regularlymeiosisduringinterbreed, but hybrids will be selected against and the species will remaindistinct. However, viable hybrids are occasionally formed and these newspecies can either have properties intermediate between their parentspecies, or possess a totally new phenotype The importance of hybridization inof animals is unclear, although cases have been seen innew speciescreatingstudied-being a particularly wellgray tree frogtheanimals withmany types ofexample Hybridization is, however, an important means of speciation in(having more than two copies of each chromosome) ispolyploidyplants, sincetolerated in plants more readily than in animals Polyploidy is important inhybrids as it allows reproduction, with the two different sets of chromosomeseach being able to pair with an identical partner during meiosis Polyploids alsoinbreeding depressionhave more genetic diversity, which allows them to avoidin small populations
  21. 21. •Genetic structure•Because of physical barriers to migration, along with limited), andvagilitytendency for individuals to move or spread (tendency to remain or come back to natal place), natural populations rarely all interbreed asphilopatry(etBuston) (panmixyconvenient in theoretical random models (al., 2007). There is usually a geographic range within whichto one another than thoserelatedindividuals are more closelyrandomly selected from the general population. This isdescribed as the extent to which a population is geneticallystructured (Repaci et al., 2007). Genetic structuring can be, speciesclimate changecaused by migration due to historical.habitator current availability ofrange expansion
  22. 22. •Horizontal Gene Transfer•Horizontal gene transfer is the transfer of genetic material fromone organism to another organism that is not its offspring; thismedicine, this contributes toInbacteriais most common among, as when one bacteriaantibiotic resistancethe spread ofacquires resistance genes it can rapidly transfer them to otherspecies Horizontal transfer of genes from bacteria toandcerevisiaeSaccharomyceseukaryotes such as the yeastthe adzuki bean beetle Callosobruchus chinensis may alsohave occurred An example of larger-scale transfers are the, which appear to have received arotifersbdelloideukaryoticcanVirusesplantsrange of genes from bacteria, fungi, andalso carry DNA between organisms, allowing transfer of genesscale gene transfer has-Large]domainsbiologicaleven acrossandeukaryotic cellsalso occurred between the ancestors ofandchloroplastsprokaryotes, during the acquisition ofmitochondria
  23. 23. •Epistasis•, the phenotypic effect of an allele at one locusepistasisBecause ofmay depend on which alleles are present at many other loci. Selectiondoes not act on a single locus, but on a phenotype that arises throughdevelopment from a complete genotype.•), the theoretical task for population1974(LewontinAccording togenetics is a process in two spaces: a "genotypic space" and a"phenotypic space". The challenge of a complete theory of populationgenetics is to provide a set of laws that predictably map a populationtakesselection), where1Pspace (phenotype) to a1G(genotypesofplace, and another set of laws that map the resulting population (P2)genetics can predictMendelian) where2Gback to genotype space (the next generation of genotypes, thus completing the cycle. Evenmolecularaspects ofMendelian-leaving aside for the moment the non, this is clearly a gargantuan task. Visualizing thisgeneticstransformation schematically:
  24. 24. (adapted from Lewontin 1974, p. 12). XDlaws, the aspects of functionalepigeneticrepresents the genetic and1T, that transform a genotype into phenotype. We willdevelopmentbiology, oris the transformation due2T".phenotype map-genotyperefer to this as the "to natural selection, T3 are epigenetic relations that predict genotypes basedon the selected phenotypes and finally T4 the rules of Mendelian genetics.In practice, there are two bodies of evolutionary theory that exist inparallel, traditional population genetics operating in the genotype space and, operating inanimal breedingandplanttheory used inbiometricthephenotype space. The missing part is the mapping between the genotypeand phenotype space. This leads to a "sleight of hand" (as Lewontin terms it)whereby variables in the equations of one domain, are consideredparameters or constants, where, in a full-treatment they would betransformed themselves by the evolutionary process and are in realityfunctions of the state variables in the other domain. The "sleight of hand" isassuming that we know this mapping. Proceeding as if we do understand itis enough to analyze many cases of interest. For example, if the phenotypescale is-) or the timecell disease-sickleone with genotype (-to-is almost onesufficiently short, the "constants" can be treated as such; however, there aremany situations where it is inaccurate.
  25. 25. •Linkage•, the effect of an allele at onelinkage equilibriumIf all genes are inat other loci. Ingene poollocus can be averaged across thewithlinkage disequilibriumreality, one allele is frequently found ingenes at other loci, especially with genes located nearby on the samebreaks up this linkage disequilibrium tooRecombinationchromosome., where an allele at one locus risesgenetic hitchhikingslowly to avoidto an allele under selection at alinkedto high frequency because it isnearby locus. This is a problem for population genetic models thattreat one gene locus at a time. It can, however, be exploited as aselectivevianatural selectionmethod for detecting the action of.sweeps•, linkage isasexual populationsIn the extreme case of primarilycomplete, and different population genetic equations can be derivedMost]63[and solved, which behave quite differently to the sexual case., are asexual. The population genetics ofbacteria, such asmicrobeslays the foundations for tracking the origin andmicroorganisms.pathogensand deadly infectiousantibiotic resistanceevolution ofPopulation genetics of microorganisms is also an essential factor fordevising strategies for the conservation and better utilization ofbeneficial microbes (Xu, 2010).
  26. 26. •Modern evolutionary synthesis•The mathematics of population genetics were originally developed as the. According to Beattymodern evolutionary synthesisbeginning of the(1986), population genetics defines the core of the modern synthesis. In thefirst few decades of the 20th century, most field naturalists continued to believethat Lamarckian and orthogenic mechanisms of evolution provided the bestexplanation for the complexity they observed in the living world. However, asthe field of genetics continued to develop, those views became less tenableDuring the modern evolutionary synthesis, these ideas were purged, and onlyevolutionary causes that could be expressed in the mathematical framework ofpopulation genetics were retained Consensus was reached as to whichevolutionary factors might influence evolution, but not as to the relativeimportance of the various factors•, a postdoctoral worker in T. H. Morgans lab, hadDobzhanskyTheodosiusgeneticists suchRussianbeen influenced by the work on genetic diversity by. He helped to bridge the divide between the foundationsChetverikovSergeiasdeveloped by the population geneticists and the patterns ofmicroevolutionofGenetics andbook1937observed by field biologists, with hismacroevolutionexamined the genetic diversity of wildDobzhansky.the Origin of Speciespopulations and showed that, contrary to the assumptions of the populationgeneticists, these populations had large amounts of genetic diversity, withmarked differences between sub-populations. The book also took the highlymathematical work of the population geneticists and put it into a moreaccessible form. Many more biologists were influenced by population geneticsvia Dobzhansky than were able to read the highly mathematical works in theoriginal
  27. 27. •Selection vs. genetic drift•Fisher and Wright had some fundamental disagreements and acontroversy about the relative roles of selection and drift continuedfor much of the century between the Americans and the British.•,ecological genetics, the pioneer ofE.B. FordIn Great Britaincontinued throughout the 1930s and 1940s to demonstrate thepower of selection due to ecological factors including the ability tosuch asgenetic polymorphismsmaintain genetic diversity through. Fords work, in collaboration with Fisher,blood typeshumancontributed to a shift in emphasis during the course of the modern]driftgeneticovernatural selectionsynthesis towards•, and of theirtransposable elementsRecent studies of eukaryoticnonadaptive, point again to a major role ofspeciationimpact onand geneticMutationdriftgeneticandmutationprocesses such asdrift are also viewed as major factors in the evolution of genomecomplexity
  28. 28. •Population geneticsGenetic structure of a population.clan..Group of individuals of the same species that can interbreed.
  29. 29. Migration..Migration is the movement of individuals in or out of a population.Selection..Selection is the primary factor driving evolution..
  30. 30. Genetic Drift..Genetic drift is the random in allele frequencies.
  31. 31. •HOW does genetic structure change?•Changes in allele frequencies and genotype frequencies through time.•
  32. 32. MutationNatural selection Genetic drift Non-random matingMigration
  33. 33. MUTATIONHowever ,the rate of mutation is quite low:for any given gene,about 1 copy in104_106 is a new mutation.>>>-Mutations provide the necessary rawmaterial for evolutionary change ,but bythemselves new mutations do not have ameasurable effect on allele or genotypefrequencies
  34. 34. MigrationMigratMigration is necessary to keep a speciesfromfragmenting.Migration is necessary to keep a speciesfrom fragmenting into several differentspecies>
  35. 35. SelectionSelection is the primaryfactor driving evolution... Genes that conferincreased fitness tend totake over a population..Selection can occur at manyplaces in the life cycle: theembryo might be defective, thefetus might not survive tobirth, the immature offspringmight be killed, the individualmight not be able to find amate or might be sterile.
  36. 36. Fitness is a function of thegenotype. We will definethe “relative fitness” of thebest genotype as equal to1.0, and the fitnesses of thetwo other genotypes asequal to or less than 1.
  37. 37. •Resistance to antibacterial soap•NATURAL SELECTIONGeneration 1:1.00 not resistant0.00 resistantApplication or using antibacterialsoap can kill the bacteria.
  38. 38. NATURALSELECTIONResistance to antibacterial soapGeneration 1:1.00 not resistant0.00 resistantGeneration 2:0.96 not resistant0.04 resistantOne bacteria get mutatedand resist soapmutation!
  39. 39. •Natural selectionResistance to antibacterial soap•Generation 1:1.00 not resistant•0.00 resistant•Generation 2:0.96 not resistant•0.04 resistant•Generation 3:0.76 not resistant0.24 resistantResistant bacteria reproduce and grow innumber. On the other hand the non resistantbacteria decreased in number.
  40. 40. Natural selectionResistance to antibacterial soap•Generation 1:1.00 not resistant0.00 resistant•Generation 2:0.96 not resistant0.04 resistant•Generation 3:0.76 not resistant0.24 resistant•Generation 4:0.12 not resistant0.88 resistantThe resistant bacteria dominate thepopulation
  41. 41. •Natural selection can cause•populations to diverge•Divergence
  42. 42. Genetic DriftGenetic drift is therandom changes inallele frequencies.Genetic drift occursin all populations, butit has a major effecton small populations.For Darwin and the neo-Darwinians, selection was theonly force that had a significanteffect on evolution. More recentlyit has been recognized thatrandom changes, geneticdrift, can also significantlyinfluence evolutionary change. Itis thought that most major eventsoccur in small isolatedpopulations.
  43. 43. Genetic driftGlobal Disaster
  44. 44. NON-RANDOM MATING
  45. 45. •random change in allele frequencies that occurs in small populations•1: gene pool { }•Equilibrium { }•genetic drift { }•Inbreeding { }•combined genetic information of all the members of a particular population•Mutation { }•genetic drift { }•gene pool { }•Migration { }
  46. 46. •continued breeding of individuals with similar characteristics•migration•inbreeding•gene pool•population

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