Module No.

and Title Module 3 Evolutionary Processes

Module Overview
Module
Objectives/Outcomes
Lessons in the Module
This module discusses the mechanism on how traits
frequencies of dominant and recessive alleles change over a
small and large populations. You will learn also baseline
models of the changes in alleles when evolutionary drivers
are not operating and what will happen to the frequencies of
allele if natural selection, mutation, non-random mating are
present.
1. Describe the mechanism of population genetics.
2. Describe the evolution in finite population.
3. Discuss evolution at multiple loci.
4. Describe evolution of the genome.
Lesson 1 The Genetics of Population
Lesson 2 Evolution in Finite Population
Lesson 3 Evolution at Multiple Loci
Lesson 4 Genome Evolution

Lesson 2 Lesson 2 Evolution in Finite Population

Learning Outcomes Describe the evolution in finite population.

INTRODUCTIONS

From the previous lesson, we learned that allele frequencies of a large population do not
change over time in the absence of evolutionary processes such as natural selection, mutation,
and non-random mating after attaining fixation. If there are observed changes in allele
frequencies, it is usually very close to the expected frequencies. This assumption is generally
based on Hardy–Weinberg Model. Further, we learned also that when each evolutionary
process is operating, allele frequencies may eventually change. For instance, when natural
selection is operating, selection coefficient (s) is measured to obtain the fitness reduction of
phenotypes from a certain environment. In this sense, the larger the s the stronger the action
of natural selection on an allele frequency in the population. The allele with larger s changes
the frequencies faster and would eventually reach fixation earlier.
However, what do you think will happen to allele frequencies in a small population? In a small
population, the realized frequencies will not always be close to the expected frequencies.
Entirely different from the frequencies in a large population. A null model for a small
population that serves as the baseline, counterpart of the Hardy-Weinberg Model, is the
Wright-Fisher model. We will further learn the details below about how frequencies of alleles
will be changing.

ABSTRACTION

Understanding Wright-Fisher Model

This model is similar to Hardy-Weinberg Model, but in this case, it only serves as a baseline on a
small population in the expected changes of genotype frequencies over time in the absence of
selection, migration, mutation, and nonrandom
mating. Probabilities of the changes in allele
frequencies (genetic drift) in small populations are
assumed based on the model. This is a null model for
a small population which assumes that:
1. Natural selection is not operating on the trait or
traits affected by the locus in question.
2. Mating in the population is random concerning the
locus in question.
3. No mutation is occurring.
4. There is no migration into the population from
other populations.
What is the effect of Genetic Drift on Allele
Frequencies?
In a small population, allele frequencies change
randomly. This is called genetic drift. The following
are the effect of drift in a small population:
1. It causes allele frequencies to fluctuate over time
even in the absence of evolutionary processes. The
rate of fluctuations depends on the size of the
population. Drift is more powerful in smaller
Figure 1. Simulation of allele frequencies based on populations thus it causes larger allele frequency.
different populations. Supposedly, the frequency of the A1 allele is neutral
 at 0.5 (Figure 1). At a population of 10, the allele could go to fixation at less than 40
generations: at a population size of 100, the allele could go to fixation within 100
generations; and at 1000 generations the allele frequency would just remain at 50%.
The result as reflected in Figure 1 is based on 10 different simulations.
2. Genetic drift reduces genetic variation in a population. Alleles are lost at a faster rate in
small populations. When all alternative alleles have been lost, one allele becomes fixed
in the population. This means that one allele already replaced all other alternative
alleles in the loci. In this sense, variability is reduced.

3. It causes heterozygosity to decrease within a population over time and increases

homozygosity. Remember that one allele is favored over time because of drift and it
could go to fixation. Therefore, the alternative alleles will decrease and over time will be
lost in the population. As this happens, genetic diversity among the population is
substantially decreased. This is the reason why rare or declining population of animals
needs to increase their genetic diversity. Low genetic diversity could endanger a
population, especially during a catastrophic event.
4. Genetic drift causes a divergence between populations over time. You have to
remember that genetic drift causes random fluctuation of allele frequencies in a small
population. It occurs based on chance events. Because it is a random process, it is
unpredictable which allele could be fixed in certain sub-populations. When several
populations are fixing different allele alternatives, it will result in divergence of
populations over time. For instance, if a small population of a bird species is distributed
in 10 hypothetical islands of Pujada bay where migration is limited to none, over time
due to genetic drift allele frequencies fluctuate randomly. Because it is random and
based on chance events, it is unpredictable what allele will be fixed in each island-
meaning each island population might have a different allele.

Coalescent Theory and the genealogy of genes

We trace evolutionary relationships of
organisms and identify common ancestry using
a phylogenetic relationship shown in a
phylogenetic tree. Now, if we try to
understand changes and relatedness of allele
frequencies, we will trace alleles following the
Coalescent theory. This theory is used to
determine the genealogy of genes. This means
that the analysis is done at the level of the
genes. Genealogical relationships in a
population help better understand deeper
how genetic drift operates and how it
influences variation in a population. Allelic
Figure 2. Coalescent theory
differences among a set of gene copies at the same locus must have arisen by mutation after
the coalescent point for this set of gene copies. For example tracing the origin of gene copies of
I,ii, iii on figure 2. You will see that mutations occur subsequently on the red dots (coalescent
point) giving rise to the three alternative gene copies. Any allelic differences among a set of
gene copies at the same locus must have arisen by mutation after the coalescent point for this
set of gene copies.
Demography, Biogeography, and Drift
Changes in a population are definitely on the actual number of individuals (demography). The
census population size or the actual count of the population size can massively affect or reduce
the effective population size. Effective population
size is the number or quantity of the population
that could best represent the genetic composition
of the population. The census population size is
relatively difficult to determine since it changes
from generation to generation and so drift varies
as well. Hence to determine the probable changes
in a population in terms of genetic frequencies,
effective population size is used as a concept to
account for the differences of rate drift to
understand key population parameters. Two
important processes that can affect effective
population size are the population bottleneck and
founder effect. The concept of effective population size is used by a geneticist to understand
key population parameters in accounting for the rate of drift, such as expected heterozygosity,
change over time.
Ne= Effective population size
Nm= Breeding Male population
Nf= Breeding female population

Kindly follow this example: The remaining population of Philippine Eagles is only 1000.
Assuming that the breeding population of the male is 300 and the female has 400 individuals,
what is the effective population of the Philippine Eagles?

Figure 2 This means that among the 1000

individuals, the effective population of the
Critically Endangered Philippine is only
Ne= 4(300)(400) = 480,000 = 685.7
686 individuals.
 300+400 700

Census population relatively

fluctuates. There is a certain
period that population size
drastically changes, becomes
so small. The period of small
population size is called
POPULATION BOTTLENECK.
Within this period, allele
frequencies dramatically
change. For instance, an allele
Figure 3. Population bottleneck. might be lost when an
organism is experiencing this
period or certain alleles might be fixed in the population. This may lead also to the divergence
between populations since allele frequencies will eventually differ before and after the
bottleneck. Looking at figure 3 example, during a bottleneck event, due to chance events you
will notice that a surviving population would only have some of the alleles while other alleles
are significantly lost. As a result, allele frequency will greatly differ before and after the
bottleneck. This event also causes divergence in the population. For instance, assuming that the
Philippine Tamaraw population undergoes population bottleneck, allele frequencies before and
after the bottleneck will drastically change. Some alleles of the Philippine Tamaraw might be
lost and one allele of a gene will reach fixation.
Kindly read the following articles:
Population Dynamics, Herd Behavior, and Genetic Analysis of the Critically Endangered
Tamaraw (Bubalus mindorensis): A Mini-Review
FOUNDER EFFECT on the other hand refers to the change in allele frequencies that results from
the sampling effects that occur when a small number of individuals from a large population
initially colonize a new area and found a new population. This usually happens to some species
of plants brought by birds to some isolated areas like islands. Individuals colonizing an island
usually represent only a subset of the genes from the mainland. For instance, an organism
colonizing an island that carries an allele frequency of R=0.3, r=07 may change to R=0.6 and
r=04 over time in the island.
It is important to note that in a finite population when drift is operating-alleles eventually
become entirely homozygous. However, mutations provide continuous genetic variation, and
the loss of heterozygosity due to drift is balanced by mutation as new mutation arises.

Neutral Theory of Molecular Evolution

Mutations maintain genetic variations even if genetic drift alters heterozygosity in a small
population. This provides balance as new mutation arises. Mostly, mutations occur by changing
genes or a new gene arises. However, there are also changes within the molecular level known
as molecular evolution. This involves DNA or RNA sequences that change over time, and how
the amino acid sequences that compose proteins change over time. This helps us better
understand the changes in the sequences of nucleic acid over time that may generate changes
in the phenotypic level. This was proposed by Kimura (1961). This theory proposes that:
1. Most of the variation present within a population is selectively neutral. This means that the
changes caused by mutations are neutral and do not affect mostly the functions of the genes.
2. Most of the changes in DNA or amino acid sequence over time are selectively neutral.
We have to understand that there are differences in an amino acid sequence that do not
manifest phenotypic differences called cryptic molecular variation. There are mutations also
that subsequently substitute alleles. Allelic substitution occurs when a new allele arises by
mutation and is subsequently fixed in the population. Allelic substitutions can be synonymous
or nonsynonymous mutations. Synonymous substitutions or silent mutations are mutations
that do not result in changed amino acid and does not alter the sequence of the protein
encoded. This means that a protein product remains the same even if there’s a mutation along
with nucleic sequences. The amino acid product remains the same. However, nonsynonymous
mutations are mutations that do change the amino acid sequence but can cause changes in the
way protein functions.
Application
Kindly read the following articles and answer the questions below:
a) Genetic diversity of the Critically Endangered Philippine Eagle Pithecophaga jefferyi (Aves:
Accipitridae) and notes on its conservation
b) Mitochondrial DNA Haplotype Analysis of the Endemic and Critically Endangered Philippine
Cockatoo (Cacatua haematuropygia P.L.S. Müller, 1776)

Questions:
1) Describe the current status of the genetic diversity of the Philippine Eagle, Philippine
Cockatoo, and Philippine Tamaraw.
2) Which of the three species is currently experiencing an extreme population bottleneck?
Why?

CLOSURE

Congratulations!