Course Title:
Evolutionary Biology
(BINF 206)
Credit hours: 3
Course Instructor: Bishnu Maya KC, PhD
Evaluation scheme
Internal Evaluation: (25)
Two internal tests: (15)
One presentation and attendance: 10
Final evaluation : 75
…………………………………….
TOTAL : 100
MECHANISM OF EVOLUTION
Course content (12 hrs):
Mutation, Inheritance of Variation, Rates and Effects of Mutations, Estimating Mutation
Rates, Epigenetic Inheritance
Genotypes and Phenotypes, selection on a quantitative trait, Artificial Selection,
Genetic Architecture of Quantitative Traits
Random Genetic drift and selection, Genealogy of Genes, Gene flow and genetic
divergence, evolution of dispersal range, Signatures of Adaptation in genes
Speciation, Allopatric and sympatric speciation, Reproductive barriers, Patterns of
speciation
MUTATION (REVIEW)
*Refer to slides 22, 23 and 24 of 2.2# Preliminary mechanism of evolution
1. Mutation theory
First proposed by:
Hugo de Vries (1901)
Gist:
Sudden changes called mutations in the chromosome or genes acquired
from parents is the cause of variation in offspring
Mutation may be germline (inheritable) or somatic (non-inheritable)
MUTATION (REVIEW)
Pre-axial polydactyly Fasciation
Hemophilia (Royal disease) Down syndrome Heterochromia
Albinism
Polymelia Progeria Chimerism
MUTATION (TYPES)
Point mutation Synonymous
(Gene mutation) Non-synonymous
Mutation Deletion
Duplication
Inversion
Structural mutation
(Chromosomal Translocation
mutation)
Fusion
Fission Euploidy
Heteroploidy
Aneuploidy
MUTATION
1. Point mutation
• Point mutation occurs when a single nitrogenous nucleotide base is changed from
one of its four possible states (A, T, C, G in eukaryotes and A, U, C, G in
prokaryotes)
• It is the simplest type of mutation
• They are always gene mutations and never chromosome mutations
These changes may or may not affect protein synthesis. On this basis, they are further
classified into:
A) Synonymous (silent) mutation: Do not affect protein synthesis
B) Non-synonymous (replacement) mutation: Affect protein synthesis
MUTATION
1. Point mutation (contd…)
Qn. How does change in nucleotide base affect protein synthesis?
The information regarding protein synthesis from the nucleotide is read by the cell
in form of codons
Each codon is a set of 3 nucleotide bases
The synthesis of 1 amino acid is correlated to one or
multiple such codons
This correlation is determined by the universally shared
genetic code present in all living organisms
If the point mutation occurs in a codon such that it is non-
synonymous, the synthesis of an amino acid is altered which
affects protein synthesis
MUTATION
Consider the codon: GAG, associated with the amino
Example:
acid Glutamine present in β-hemoglobin in humans
• If a point mutation puts base A in place of the 3rd base G, the codon becomes GAA
• It was found that GAA also correlates to Glutamine i.e., this mutation is synonymous
• However, if the middle base A is replaced by the base T, the codon becomes GTG
• It was found that GTG correlates to Valine instead i.e., this mutation is non-synonymous
Change from Glutamine to Valine in β-hemoglobin causes sickle-cell anemia in humans
MUTATION
1. Point mutation (contd…)
Point mutation can also be classified as follows:
A. Deletion mutation:
Single nucleotide base is deleted/removed from the codon of a gene
B. Insertion mutation:
Single nucleotide base is inserted/added to the codon of a gene
C. Substitution mutation:
Single nucleotide base is replaced by another base in the codon of a gene
Example: Consider a wild-type DNA strand: ATG ACC AGG TC
1 2 3 4
Deletion: ATG ACA GGT C
Deletion of 3rd base C from codon 2
Insertion: ATG ACA CAG
GTC Addition of A as 3rd base in codon 2
ATG ACT AGG TCA Substitution of 3rd base C by T in codon 2
Substitution:
MUTATION
2. Structural mutation
• Structural mutation occurs as a change in more than one nucleotide bases at once
• They can bring change in:
Structure of chromosome
Number of chromosome
We classify them as follows on the basis of mode of action:
Structural mutation
Deletion Duplication Inversion Translocation Fusion Fission Heteroploidy
Euploidy
Aneuploidy
MUTATION
A. Deletion
During chromosome replication, a segment of the chromosome is left out (deleted)
This deletion can be of either of the two types:
Terminal deletion: Intercalary deletion:
Terminal portion of the Middle portion of the
chromosome is deleted chromosome is deleted
Entire chromosome is split Entire chromosome is split
into 2 into 3
THINK AND WRITE #1: Cystic fibrosis, Cri du chat syndrome, etc. are well-known diseases caused by
deletion mutations. What are their effects? Are they hereditary? If yes, how can they be prevented from
being inherited by the following generation?
MUTATION
B. Duplication
A part of the chromosome is present in excess along with the normal
chromosomal composition
Such additional parts form a loop and reside on the chromosome
E.g. Mutation of ovoid eye of Drosophila into bar eye
There are 3 types of duplication:
• Intra-chromosomal (Tandem)
Duplicated portion resides within the chromosome in varying configurations
• Inter-chromosomal (Transpose)
Portion of one chromosome duplicates and attaches to another chromosome
• Extra-chromosomal
If the duplicated chromosome consists of centromere, it acts as an independent
chromosome
MUTATION
B. Duplication (contd…)
• The figure shows chromosome ABCD.EFGH
(full stop indicates centromere)
• Here, portion BCD undergoes duplication
Intra-chromosomal
duplications
Inter-chromosomal
duplication
MUTATION
C. Inversion: A part of the chromosome detaches and
reattaches but in the opposite configuration
Qn. How does inversion originate in a chromosome?
Consider a chromosome 1-2-3-4-5-6
This chromosome undergoes partial folding, due to which:
• the intermediate portion 3-4-5 reverses its configuration
• the terminal portions 1-2 and 6 remain in original state
At the site of contact during folding, breakage takes place
due to which:
• terminal ends 1-2 and 6 are separated
• reversed intermediate portion 5-4-3 acts as a bridge
New chromosome 1-2-5-4-3-6 forms
MUTATION
D. Translocation
• A portion of the chromosome is transferred to another non-homologous chromosome
• Neither net gain nor net loss of genes takes place. Only rearrangement occurs
It is of the following 3 types:
Simple translocation: Terminal portion of one chromosome is added to the terminal
end of another
Shift translocation: Terminal portion of one chromosome is added to the
intermediate region of another
Reciprocal translocation: Mutual exchange of terminal portion of chromosome
takes place
MUTATION
The figure shows reciprocal translocation of segment of
Example#1:
Chromosome 4 into Chromosome 20
Rearrangement of chromosomes 4:20 has shown
to be a causal agent of osteoporosis in children
MUTATION
The figure shows reciprocal translocation of segment of Chromosome
Example#2:
8 into Chromosome 14, which causes Burkitt’s Lymphoma
Jaw tumor in a child:
A common symptom of Burkitt’s
Lymphoma
(Cancer of the lymphatic system)
MUTATION
E. Fusion
2 non-homologous chromosomes combine into 1 chromosome
F. Fission
1 chromosome splits into 2
Fusion and fission are responsible not only
for change in composition of chromosomes
but also the number of chromosomes in the
karyotype
MUTATION
G. Heteroploidy (Gk. Hetero = many, ploid = unit)
The structural mutation by which the number of whole chromosomes is changed is known
as heteroploidy
It may be of the following types:
Heteroploidy
Euploidy Aneuploidy
MUTATION
Euploidy
If basic set of chromosomes in an organism consists of ‘n’ number of chromosomes, a
case of polyploidy involves the genome consisting “xn” number of chromosomes, where
x is a whole number (1, 2, 3, ….)
• 1n is a case of monoploidy, 2n of diploidy, 3n triploidy and so on
• Cases of euploidy other than monoploidy are called polyploidy in general
• It is generally more common in plants than in animals
MUTATION
2. Structural mutation (contd…)
Qn. How does polyploidy occur?
• Autopolyploids:
Such species are naturally polyploids
Cynodon dactylon
e.g. Dubo (Cynodon dactylon)
• Induced polyploids:
Chemical (e.g. colchicine) or radiation (e.g. X-ray) treatment may be used
They interfere with spindle fibres of mitotically dividing meristematic cells
Induction of
polyploidy using
colchicine
MUTATION
Example: Whole genome duplication (tetraploidy)
• Gametes are formed by meiotic cell division by which they carry a haploid genome
even if the parental genome is diploid
• In some exceptional cases, the gametes carry the diploid genome
• If such diploid gametes fertilize, a tetraploid generation arises that is an entirely
new species compared to the parental generation
THINK AND WRITE #2: What differentiates
a species from another? On this basis,
establish why the tetraploid generation is
considered a different species than its
parental diploid generation.
MUTATION
Aneuploidy
Change in chromosomal number due to addition or removal of certain chromosomes
from a genome is known as aneuploidy
• Monosomy: If usual chromosome set is 2n, a case of monosomy alters it to 2n-1
• Nullisomy: Diploid 2n chromosome set is altered to 2n-2
• Trisomy: Diploid 2n chromosome set is altered to 2n+1
• Tetrasomy: Diploid 2n chromosome set is altered to 2n+2
Down syndrome Turner syndrome is
(Trisomy-21) is a case a case of
of trisomy where an monosomy where
additional copy of one X chromosome
chromosome 21 is is absent in
present. females
RATE OF MUTATION (µ)
The probability that an offspring will bear a mutation is mathematically represented
as the Rate of Mutation, denoted by the symbol (µ)
µ can be calculated per DNA base pair (bp), per locus and per genome
µ varies greatly with species
Organism µ per bp This shows that rate of mutation of viruses is almost
1000000 times greater than that of bacteria. This
Bacteria ∼10-9-10-10 is a main reason why developing cure to viral
Viruses ∼10-3 -10-5 diseases is such a big challenge in the medical field
while anti-biotics have successfully been developed
THINK AND WRITE #3: In the same organism,
µ per genome is much greater than µ per bp.
Why do you think so?
RATE OF MUTATION (ESTIMATION)
A. Phenotype screening (most primitive)
A large number of individuals from a laboratory population is inspected (screened) by
an examiner who looks to see how many individuals show changes due to mutation
𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑚𝑢𝑡𝑎𝑡𝑒𝑑 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠
µ is determined by: µ =
𝑡𝑜𝑡𝑎𝑙 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠
Drawbacks:
µ per base pair cannot be determined
Not all mutations may be observed by the examiner or even expressed by the organism
Only specific kinds of organisms suitable for the laboratory can be studied
B. Phylogenetic method
2 species that shared a common ancestor ‘t’ generations ago will have mutated 2µt
𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑡𝑜𝑡𝑎𝑙 𝑚𝑢𝑡𝑎𝑡𝑖𝑜𝑛𝑠
times in that particular segment. µ =
2𝑡
Drawbacks:
It requires information about no. of generations which may not be accurately available
Portions of the genome that evolved due to natural selection cannot be studied
RATE OF MUTATION (ESTIMATION)
C. Mutation accumulation
It is a more accurate modification of phylogenetic method in which a founder
population is bred in the laboratory by eliminating natural selection so that the only
cause of variation is mutation. µ is determined by the same formula as B.
Drawbacks:
Lab-bred organisms tend to show fewer mutations
Only specific kinds of organisms suitable for the laboratory can be studied
D. DNA sequencing (least expensive and most effective)
The DNA of the parents is sequenced at ‘n’ sites for ‘t’ generations and variation
𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑜𝑏𝑠𝑒𝑟𝑣𝑒𝑑 𝑚𝑢𝑡𝑎𝑡𝑖𝑜𝑛𝑠
caused by mutation is searched. µ =
𝑛𝑡
Drawbacks:
Change of mutation in specifically studied gene is very small
A close approximation is provided and not the exact value
EFFECTS OF MUTATION
Based on the effects shown by the mutation, it may be of the following types:
Types of Mutation
(On the basis of effects shown)
Synonymous Non-synonymous
(Negligible effect) (Significant effect)
Deleterious Beneficial
mutations mutations
In case of point mutations, only non-synonymous mutations show significant effects
while synonymous mutations have almost no effect on an organism’s fitness
EFFECTS OF MUTATION
A. Deleterious mutations
Most mutations are deleterious i.e., decrease the fitness of the organism
This effect is mathematically represented by the survival coefficient (s)
Example: Analysis of survival coefficient after 560 mutations in Saccharomyces
cerevisiae (Yeast) *Examples of well-known deleterious mutations have been
th
included in the 5 slide as well
The adjoining graph shows that most of the non-
synonymous mutations showed deleterious effect as
selection coefficient becomes negative
If value of s becomes -0.15 due to a mutation, it
indicates that the mutation decreased the survival by
15%
NOTE: Stop codons are groups of 3
nucleotide bases, or simply codons, that
terminate (stop) the process of protein
synthesis.
EFFECTS OF MUTATION
B. Beneficial mutations
Mutations are rarely beneficial
Examples:
In primitive humans, the enzyme
lactase (digests lactose) was
present only during childhood.
A mutation thousands of years
Sickle-cell anemia is generally ago allowed specific groups of Pesticide resistance caused by
deleterious, but is beneficial in humans to be lactose tolerant mutation is beneficial in the
malaria-endemic regions in adulthood as well perspective of pests
INHERITANCE OF VARIATION
Variation may be somatic or germline. Germline variations are inherited to successive
generations which is what drives evolution forward
Such germline variations present in the gametes may be inherited through sexual
reproduction by any of the following means:
Inheritance
Asexual Sexual
inheritance inheritance
Nuclear Extra-nuclear
inheritance inheritance
INHERITANCE OF VARIATION
Asexual inheritance
Asexual inheritance mechanism is common in prokaryotes and viruses. It is explained by
a phenomenon called Horizontal Gene Transfer (HGT), that may occur:
I) II)
I) By conjugation:
The bacteria come in direct contact and exchange DNA
II) By transformation:
The naked DNA of dead bacterium remains left
over which is acquired by another living III)
bacterium
III) By viral infection (transduction):
A virus that infected bacterium A and then
bacterium B can transfer portion of the bacterial
genome from A into B
INHERITANCE OF VARIATION
Sexual inheritance
It is common in eukaryotes where meiotic division of true nucleus and cytoplasm occurs
A. Nuclear inheritance
Inheritance involves chromosomes present in the nucleus as hereditary material
• They tend to follow Mendelian laws of inheritance
• They may also be sex-linked
Nuclear inheritance occurs mainly due to:
I) Segregation:
Alleles of the genotype segregate during gamete formation and only 1 of them is
selected
II) Recombination:
Homologous chromosomes synapse, cross over and give entirely new recombinant
chromosomes during gamete formation by meiosis
INHERITANCE OF VARIATION
A. Nuclear inheritance (contd…)
A gamete consists of only 1 of the 2 alleles
Both homozygous and heterozygous offspring form from
heterozygous parents
Crossing over
INHERITANCE OF VARIATION
B. Extra-nuclear inheritance (Epigenetic inheritance)
Such inheritance is caused due to action of genetic material present beyond the
nucleus of the cell
It is also known as epigenetic inheritance
They tend to disobey Mendelian laws of inheritance
• Extra-nuclear genetic material may include:
Cellular organelles (e.g. chloroplasts, mitochondria, etc.)
Cytoplasmic RNA
Endosymbionts, etc.
INHERITANCE OF VARIATION
B. Extra-nuclear (Epigenetic) inheritance contd…
Inheritance by cytoplasmic RNA
During fertilization, male gametes contribute only the nucleus while female gametes
contribute almost all of their cytoplasm
If substances (such as RNA produced during oogenesis) responsible for variation are
present exclusively in the ooplasm of the female gametes, the inheritance shows a
Maternal Effect
Qn. What is a Maternal Effect?
The phenomena by which the characters of the offspring depends discriminately on
the mother’s character despite dominance/recession and independent assertion of
gametes during fertilization is known as Maternal Effect
INHERITANCE OF VARIATION
B. Extra-nuclear (Epigenetic) inheritance contd…
Example: Clockwise (dextral) and anti-clockwise (sinistral) coiling of shells of Lymnaea
Lymnaea (Great pond snail) is a mollusk bearing spirally coiled shells. When viewed
from apex of the shell, the following might be observed:
• EITHER, the spiraling is clockwise (known as dextral spiraling)
• OR, the spiraling is anti-clockwise (known as sinistral spiraling)
• Dextral allele (S+) is considered wild-type while sinistral allele (S) is considered
mutant allele
Lymnaea Sinistral (left) & Dextral (right)
INHERITANCE OF VARIATION
B. Extra-nuclear (Epigenetic) inheritance contd…
Example: Clockwise (dextral) and anti-clockwise (sinistral) coiling of shells of Limnaea
Maternal effect can be seen in F1 generation of cross between S+S+ and SS snails
Case-I.
Genotype of male parent is SS and female is S+S+
• Dextral coiling is observed in F1 generation P
• Mendel’s 1st law is obeyed
• Maternal effect is absent
Case-II.
Genotype of male parent is S+S+ and female is SS
• Sinistral coiling is observed in F1 generation F1
• Mendel’s 1st law is disobeyed
• Maternal effect is present +S SS+
Case-I S Case-II
(Dextral) (Sinistral)
INHERITANCE OF VARIATION
B. Extra-nuclear (Epigenetic) inheritance contd…
Inheritance by endosymbionts
Micro-organisms present symbiotically within the living cell are known as
endosymbionts
Such endosymbionts can have physical or chemical actions by which character of the
particular host cell differs
The inheritance of such characters through gametes depends on how long exposure
cytoplasm if provided during fertilization/conjugation
Photosynthetic prokaryote
Chloroplasts and mitochondria were parasitic Chloroplast
Eukaryotic cell
prokaryotes that later developed endo-symbiontic
relation with the host eukaryote cell. This explains
their semi-autonomous nature, presence of 70s
ribosome, circular DNA, etc.
Mitochondria
Anaerobic prokaryote
INHERITANCE OF VARIATION
B. Extra-nuclear (Epigenetic) inheritance contd…
Example: Killer strain of Paramecium aurelia
Some individuals of the species Paramecium aurelia secrete a lethal poison called
paramecin that is lethal to other Paramecium individuals
Such species are said to bear the “killer” (K) strain and others bear the non-lethal
sensitive (k) strain
Paramecin is actually formed due to the
presence of endo-symbiont bacteria
Caedobacter taeniospiralis (also known as
Kappa particles) in their cytoplasm
INHERITANCE OF VARIATION
B. Extra-nuclear (Epigenetic) inheritance contd…
Example: Killer strain of Paramecium aurelia
P. aurelia reproduces sexually by process of conjugation
i.e., paramecia of opposite mating types come in direct
contact and exchange nuclei
Conjugation of paramecia
If the period of conjugation is elongated, there is
sufficient time for the kappa particles to also be
exchanged
Hence, ¼ daughters will contain killer (KK) strain
INHERITANCE OF VARIATION
B. Extra-nuclear (Epigenetic) inheritance contd…
Inheritance by cytoplasmic organelles
Some organelles (e.g. plastids and mitochondria) also possess genetic material that
may influence inheritance
Example: Color inheritance in Mirabilis jalapa (four o’clock plant)
Unlike most other higher plants, Mirabilis jalapa consists of 3 types of branches:
• Fully green (presence of chloroplast)
• Fully white/pale (absence of chloroplast)
• Variegated/multi-colored (presence of
chloroplast and leucoplast)
INHERITANCE OF VARIATION
B. Extra-nuclear (Epigenetic) inheritance contd…
Example: Color inheritance in Mirabilis jalapa (four o’clock plant)
Mirabilis jalapa undergoes cross-pollination
It was found that the offspring had the same color as the
flowering branch regardless of the pollen’s genotype:
Flowering branch Pollen Offspring
Green Green / White/ Variegated Green
White Green / White/ Variegated White
Variegated Green / White/ Variegated Variegated
This Maternal Effect is seen due to the THINK AND WRITE #4: Are Sex-linked
inheritance of color by extra-nuclear Inheritance and Maternal Effect the same
genetic material present in the chloroplasts thing? Why or why not?
