Allele frequency

badshah

1. PRESENTATION TITLE
FACTORS INITIATING MICROEVOLUTION BY CHANGING GENE FREQUENCIES

SUBJECT
EVOLUTION AND PRINCIPLES OF SYSTEMATIC ZOOLOGY

SUBMITTED BY AFTAB BADSHAH
ROLL NO 11
B.S ZOOLOGY, SEM 6
TH

SUBMITTED TO MAM HADIA TILA
DEPTT: ZOOLOGY UCSS

DATED APRIL 24, 2015 ( FRIDAY)

2. [2]

Evolution
Evolution, also known as 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 Meant By 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, or genetic 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 = frequency of 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
= p
2
+ 2pq + q
2
= 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 Evolutionary Changes
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 have positive 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 of time—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 beetles reproduced, 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]

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7. en.wikipedia.org/wiki/Allele_frequency
8. www.slideshare.net
9. www.acedemia.edu.pk