Allele frequency

Allele frequency

• 1.
  PRESENTATION TITLE FACTORS INITIATINGMICROEVOLUTION BY CHANGING GENE FREQUENCIES SUBJECT EVOLUTION AND PRINCIPLES OF SYSTEMATIC ZOOLOGY SUBMITTED BY AFTAB BADSHAH ROLL NO 11 B.S ZOOLOGY, SEM 6TH SUBMITTED TO MAM HADIA TILA DEPTT: ZOOLOGY UCSS DATED APRIL 24, 2015 ( FRIDAY)
• 2.
  [2] Evolution Evolution, also knownas descent with modification, is the change in heritable phenotype traits of biological populations over successive generations. Scientifically evolution can be defined as “a change in the gene pool of a population from generation to generation by processes like mutation, natural selection, and genetic drift.” Micro evolution Microevolution is evolution on a small scale — within a single population. That means narrowing our focus to one branch of the tree of life. If you could zoom in on one branch of the tree of life scale — the insects, for example — you would see another phylogeny relating all the different insect lineages. If you continue to zoom in, selecting the branch representing beetles, you would see another phylogeny relating different beetle species. You could continue zooming in until you saw the relationships between beetle populations. For animals, it's fairly easy to decide what a population is. It is a group of organisms that interbreed with each other — that is, they all share a gene pool. So for our species of beetle, that might be a group of individuals that all live on a particular mountaintop and are potential mates for one another. Biologists who study evolution at this level define evolution as a change in gene frequency within a population. What is meant by Gene Pool It is a term which refers to constitution of all copies of every type of allele at every locus in all members of the population. Simply gene pool is the collection of all alleles of all genes possessed by members of a population. If only one allele exists for a particular locus in a population, that allele is said to be fixed in the gene pool, and all individuals are homozygous for that allele. But if there are two or more alleles for a particular locus in a population, individuals may be either homozygous or heterozygous. Occurrence of different allelic forms of a gene in a population is called polymorphism.
• 3.
  [3] What Is MeantBy Gene Frequency Allele frequency, or gene frequency, is the proportion of a particular allele (variant of a gene) among all allele copies being considered. It can be formally defined as the percentage of all alleles at a given locus in a population gene pool represented by a particular allele. In other words, it is the number of copies of a particular allele divided by the number of copies of all alleles at the genetic place (locus) in a population. It is usually expressed as a percentage. In population genetics, allele frequencies are used to depict the amount of genetic diversity at the individual, population, and species level. It is also the relative proportion of all alleles of a gene that are of a designated type. Explaining Gene Frequency Given the following: 1. a particular locus on a chromosome and the gene occupying that locus 2. a population of N individuals carrying n loci in each of their somatic cells (e.g. two loci in the cells of diploid species, which contain two sets of chromosomes) 3. different alleles of the gene exist 4. one allele exists in a copies Then the allele frequency is the fraction or percentage of all the occurrences of that locus that is occupied by a given allele and the frequency of one of the alleles is a / (n*N). For example, if the frequency of an allele is 20% in a given population, then among population members, one in five chromosomes will carry that allele. Four out of five will be occupied by other variant(s) of the gene. Note that for diploid genes the fraction of individuals that carry this allele may be nearly two in five (36%). The reason for this is that if the allele distributes randomly, then the binomial theorem will apply: 32% of the population will be heterozygous for the allele (i.e. carry one copy of that allele and one copy of another in each somatic cell) and 4% will be homozygous (carrying two copies of the allele). Together, this means that 36% of diploid individuals would be expected to carry an allele that has a frequency of 20%. However, alleles distribute randomly only under certain assumptions, including the absence of selection. When these conditions apply, a population is said to be in Hardy–Weinberg equilibrium. The frequencies of all the alleles of a given gene often are graphed together as an allele frequency distribution histogram, or allele frequency spectrum. Population genetics studies the different "forces" that might lead to changes in the distribution and frequencies of alleles—in other words, to evolution. Besides selection, these forces include genetic drift, mutation and migration. How Can We Check If A Population Is Evolving The hereditary process alone does not produce evolutionary change. In large bi-parental populations, allelic frequencies and genotypic ratios attain an equilibrium in one generation and remain constant thereafter unless disturbed by recurring mutations, natural selection, migration,
• 4.
  [4] nonrandom mating, orgenetic drift (random sorting). Such disturbances are the sources of micro- evolutionary change. Conditions for Hardy-Weinberg Equilibrium The Hardy-Weinberg approach describes a hypothetical population that is not evolving. But in real populations, the allele and genotype frequencies often do change over time. Such changes can occur when at least one of the following five conditions of Hardy-Weinberg equilibrium is absent: 1. No mutations. The gene pool is modified if mutations alter alleles or if entire genes are deleted or duplicated. 2. Random mating. If individuals tend to mate within a subset of the population, such as their near neighbors or close relatives (inbreeding), random mixing of gametes does not occur, and genotype frequencies change. 3. No natural selection. Differences in the survival and reproductive success of individuals carrying different genotypes can alter allele frequencies. 4. Extremely large population size. The smaller the population, the more likely it is that allele frequencies will fluctuate by chance from one generation to the next (a process called genetic drift). 5. No gene flow. By moving alleles into or out of populations, gene flow can alter allele frequencies. The Hardy-Weinberg law is a logical consequence of Mendel’s first law of segregation and expresses the tendency toward equilibrium inherent in Mendelian heredity. Let us select for our example a population having a single locus bearing just two alleles T and t. The phenotypic expression of this gene might be, for example, the ability to taste a chemical compound called phenylthiocarbamide. Individuals in the population will be of three genotypes for this locus, T/T, T/t (both tasters), and t/t (non-tasters). In a sample of 100 individuals, let us suppose that we have 20 of T/T genotype, 40 of T/t genotype, and 40 of t/t genotype. We could then make a table showing the allelic frequencies (remember that every individual has two copies of the gene): Genotype Number of individuals Copies of the T allele Copies of the t allele T/T 20 40 0 T/t 40 40 40 t/t 40 0 80 Total 100 80 120 Of the 200 copies, the proportion of the T allele is 80/200 = 0.4 (40%), and the proportion of the t allele is 120/200 = 0.6 (60%). It is customary to use “p” and “q” to represent the two allelic frequencies. The genetically dominant allele is represented by p, and the genetically recessive by q. p = frequency of T allele = 0.4
• 5.
  [5] q = frequencyof t allele = 0.6 therefore p + q = 1 Having calculated allelic frequencies in the sample, let us determine whether these frequencies will change spontaneously in a new generation of the population. Assuming that mating is random (gametes are sampled independently in pairs), each individual will contribute an equal number of gametes to the “common pool” from which the next generation is formed. Frequencies of gametes in the “pool” then will equal the allelic frequencies in the sample: 40% of the gametes will be T, and 60% will be t (ratio of 0.4:0.6). Both ova and sperm will, of course, show the same frequencies. The next generation is formed: ♂ ♀ T = 0.4 t = 0.6 T = 0.4 TT = 0.16 Tt = 0.24 t = 0.6 Tt = 0.24 tt = 0.36 Collecting genotypes, we have: Frequency of T/T = 0.16 Frequency of T/t = 0.24 + 0.24 = 0.48 Frequency of t/t = 0.36 Next, we determine the values of p and q from the randomly mated populations. From the table above, we see that the frequency of T will be the sum of genotypes T/T, which is 0.16, and one- half of the genotype T/t, which is 0.24: T (p) = 0.16 + 0.24 = 0.4 Similarly, the frequency of t will be the sum of genotypes t/t, which is 0.36, and one-half the genotype T/t, which is 0.24: t (p) = 0.36 + 0.24 = 0.6 The new generation bears exactly the same allelic frequencies as the parent population! Note that there has been no increase in the frequency of the genetically dominant allele T. Thus, in a freely interbreeding, sexually reproducing population, the frequency of each allele would remain constant generation after generation in the absence of natural selection, migration, recurring mutation, and genetic drift. Mathematically it is recognize that the genotype frequencies T/T, T/t, and t/t are actually a binomial expansion of (p + q)2 ( p + q )2 = p2 + 2pq + q2 = 1 After statistical deliberation it is clear that the equilibrium calculations give expected frequencies, which are unlikely to be realized exactly in a population of finite size. For this reason, finite population size is a cause of evolutionary change.
• 6.
  [6] Factors Initiating EvolutionaryChanges Any population which fails in Hardy-Weinberg equilibrium undergoes evolutionary changes. These evolutionary changes are brought about by the following agencies which tend to alter the gene frequencies of the population Mutation. Mutations are changes in the structure of genes and chromosomes. The Hardy-Weinberg theorem assumes that no mutations occur or that mutational equilibrium exists. Mutations, however, are a fact of life. Most importantly, mutations are the origin of all new genes and a source of variation that may prove adaptive for an animal. Mutation counters the loss of genetic material from natural selection and genetic drift, and it increases the likelihood that variations will be present that allow a group to survive future environmental shocks. Mutations are random events, and the likelihood of a mutation is not affected by the mutation’s usefulness. Organisms cannot filter harmful genetic changes from advantageous changes before they occur. The effects of mutations vary enormously. Most are deleterious. Some may be neutral or harmful in one environment and help an organism survive in another environment. Mutational equilibrium exists when a mutation from the wild-type allele to a mutant form is balanced by mutation from the mutant back to the wild type. This has the same effect on allelic frequency as if no mutation occurred. Mutational equilibrium rarely exists, however. Mutation pressure is a measure of the tendency for gene frequencies to change through mutation. Gene Flow The Hardy-Weinberg theorem assumes that no individuals enter a population from the outside (immigrate) and that no individuals leave a population (emigrate). Immigration or emigration upsets the Hardy-Weinberg equilibrium, resulting in changes in gene frequency (evolution). Changes in gene frequency from migration of individuals are gene flow. Although some natural populations do not have significant gene flow, most populations do. Natural Selection Natural selection can change both allelic frequencies and genotypic frequencies in a population. Although the effects of selection are often reported for particular polymorphic genes, we must stress that natural selection acts on the whole animal, not on isolated traits. An organism that possesses a superior combination of traits will be favored. An animal may have traits that confer no advantage or even a disadvantage, but it is successful overall if its combination of traits is favorable. When we claim that a genotype at a particular gene has a higher relative fitness than others, we state that on average that genotype confers an advantage in survival and reproduction in the population. If alternative genotypes have unequal probabilities of survival and reproduction, Hardy-Weinberg equilibrium is upset. Non-random Mating If mating is nonrandom, genotypic frequencies will deviate from Hardy-Weinberg expectations. For example, if two different alleles of a gene are equally frequent, we expect half of the genotypes to be heterozygous and one-quarter to be homozygous for each of the respective alleles.
• 7.
  [7] If we havepositive assortative mating, individuals mate preferentially with others of the same genotype, such as albinos mating with other albinos. Matings among individuals homozygous for the same allele generate offspring that are homozygous like themselves. Matings among individuals heterozygous for the same pair of alleles produce on average 50% heterozygous offspring and 50% homozygous offspring (25% of each alternative type) each generation. Positive assortative mating increases the frequency of homozygous genotypes and decreases the frequency of heterozygous genotypes in a population but does not change allelic frequencies. Preferential mating among close relatives also increases homozygosity and is called inbreeding. Whereas positive assortative mating usually affects one or a few traits, inbreeding simultaneously affects all variable traits. Strong inbreeding greatly increases chances that rare recessive alleles will become homozygous and be expressed. Inbreeding alone cannot change allelic frequencies in the population, only the ways that alleles are combined into genotypes. Genetic drift The changes in allele frequencies in a population due to random fluctuations is simply termed as genetic drift. As a matter of chance, the frequencies of alleles found in gametes that unite to form zygotes vary from generation to generation. Over the long run, genetic drift usually results in either the loss of an allele or its fixation at 100% in the population. The process is random with regard to particular alleles. Genetic drift can lead to the loss or fixation of deleterious, neutral, or beneficial alleles. The rate at which this occurs depends on the population size and on the initial allele frequencies. Eventually, one of the alleles is eliminated and the other is fixed at 100%. At this point, the allele has become monomorphic and cannot fluctuate any further. By comparison, the allele frequencies in the large population fluctuate much less, because random sampling error is expected to have a smaller effect. Nevertheless, genetic drift leads to homozygosity even in large populations, but this takes many more generations to occur. Certain circumstances can result in genetic drift having a significant impact on a population. Two examples are the founder effect and the bottleneck effect. The Founder Effect When a few individuals become isolated from a larger population, this smaller group may establish a new population whose gene pool differs from the source population; this is called the founder effect. The founder effect might occur, for example, when a few members of a population are blown by a storm to a new island. Genetic drift, in which chance events alter allele frequencies, will occur in such a case if the storm indiscriminately transports some individuals (and their alleles), but not others, from the source population. The Bottleneck Effect A sudden change in the environment, such as a fire or flood, may drastically reduce the size of a population. A severe drop in population size can cause the bottleneck effect, so named because the population has passed through a “bottleneck” that reduces its size (Figure 23.10). By chance alone, certain alleles may be overrepresented among the survivors, others may be underrepresented, and some may be absent altogether. Ongoing genetic drift is likely to have substantial effects on the gene pool until the population becomes large enough that chance events have less impact. But even if a population that has passed through a bottleneck ultimately recovers in size, it may have low levels of genetic variation for a
• 8.
  [8] long period oftime—a legacy of the genetic drift that occurred when the population was small. Human actions sometimes create severe bottlenecks for other species Example Detecting Micro-evolutionary Change As defined microevolution is a change in gene frequency in a population and a population is a group of organisms that share a common gene pool — like all the individuals of one beetle species living on a particular mountaintop. Imagine that you go to the mountaintop this year, sample these beetles, and determine that 80% of the genes in the population are for green coloration and 20% of them are for brown coloration. You go back the next year, repeat the procedure, and find a new ratio: 60% green genes to 40% brown genes. You have detected a micro-evolutionary pattern: a change in gene frequency. A change in gene frequency over time means that the population has evolved. Imagine that you observe an increase in the frequency of brown coloration genes and a decrease in the frequency of green coloration genes in a beetle population. Any combination of the mechanisms of microevolution might be responsible for the pattern, and part of the scientist's job is to figure out which of these mechanisms caused the change: Some "green genes" randomly mutated to "brown genes”, although since any particular mutation is rare, this process alone cannot account for a big change in allele frequency over one generation. Some beetles with brown genes immigrated from another population, or some beetles carrying green genes emigrated.
• 9.
  [9] When the beetlesreproduced, just by random luck more brown genes than green genes ended up in the offspring. In the diagram, brown genes occur slightly more frequently in the offspring (29%) than in the parent generation (25%). Beetles with brown genes escaped predation and survived to reproduce more frequently than beetles with green genes, so that more brown genes got into the next generation.
• 10.
  [10] REFERENCES 1. Cell biology,molecular biology, genetics, evolution and ecology by P.S Verma and V.K Agarwal ; multicolor edition; chapter 7; population genetics and evolution page 888---- 901. 2. Campbell biology 10th edition by Reece, Urry, Cain, Wasserman, Minorsky and Jackson; unit 4; mechanisms of evolution; chapter 23 “the evolution of populations”; page 484---- 542. 3. Integrated principles of zoology 14th edition by Hickman, Roberts, Keen, Larson, I’Anson, Eisenhour; part 2, continuity and evolution of life; chapter 6, organic evolution; page 126---130. 4. Miller-Harley Zoology 5th edition; part 1, Biological principles; chapter 5, evolution and gene frequencies; page 64---69. 5. Concepts of genetics by Robert J. Brooker, part VI, chapter 25; population genetics; page 614---640 6. Principles of genetics 6th edition by Snustad and Simmons; chapter 23; population genetics page 634---638. 7. en.wikipedia.org/wiki/Allele_frequency 8. www.slideshare.net 9. www.acedemia.edu.pk