MAJOR CREDIT SEMINAR

on

MITOCHONDRIAL DNA : A TOOL

FOR EVOLUTIONARY STUDIES

Presented by
Dr. Ashok Chaudhary
P-2506
PhD scholar
Div. of AGB
 OUTLINE

Introduction

mtDNA structure and function

Maternal transmission of
heteroplasmy
Evolutionary significance of mtDNA
heteroplasmy
Evolutionary growth of different livestock
species by mtDNA

Conclusion
 Mitochondria

It is remnants of ancestral bacterial

endosymbionts

Found in nearly all eukaryotic cells.

It is membrane-bound cell organelles

(mitochondrion, singular) that generate
chemical energy needed to power the
cell's biochemical reactions.

Chemical energy is stored in a small Structure of Mitochondria

molecule called adenosine triphosphate
(ATP)
 Structure of mtDNA

• 1963 – Mitochondrial DNA

was first detected
(N. M. K. Nass and S. Nass, 1963)

• Next 30 years the complete

mtDNA sequence [approx.
17,000 base pairs (bp)] was
OXPHO
determined in many species S
(Anderson et al., 1981)

• Vertebrate cells in culture appear to have 1000-5000 molecules of the

circular mitochondrial genome (Shmookler Reis and Goldstein, 1983)
 D-loop region

origin of heavy-
 Mammalian mtDNA can be arranged as unicircular
strand replication
monomers, unicircular dimers or catenated forms

(Clayton, 1982)

 The non-coding regions in the mtDNA molecule Light-strand

contains the regulatory elements for replication and Promoter

transcription are known as "D-loop"

 The displacement loop or "D-loop" is a separation

of strands in a specific region of the mtDNA.

 It contain 1123-bp stretch of DNA is often in a origin of light-

strand replication
single stranded configuration
Molecular events of mtDNA
(Moraes et al.,2002) expression and replication.
 Function
Mitochondria is Powerhouse of the cell OXPHOS – Oxidative phosphorylation

Mitochondria ATP

Other function such as :

 Apoptosis (Sinha et al.,2013)

 Ageing (Bratic et al.,2013)

 Signalling (Chandel et al.,2015)

 Metabolic homeostasis and biosynthesis of important macromolecules such as

lipids and heme (Cheng et al.,2013)
 Major difference between Nuclear DNA and mtDNA

Nuclear DNA Mitochondrial DNA

Location Nucleus of cell Mitochondrial Matrix

Size 3.2 billion bp 17000 bp

Structure Antiparallel double helix, Linear Double stranded, Circular

Copy number One set per cell Hundred to thousand per cell

Recombination Yes No

Mutation Lower mutation rate Higher mutation rate

Encoding gene Approximately 20000 Only 37 genes

Inherited From both parents From mother only

Introns Present Absent

 SPECIATION
Slow process
• Evolving in geographic
isolation for extended
periods

SPECIES
EVOLUTION
Continuous process
Influenced by
 Environment and surroundings
 Genetic interactions
 To understand the evolution and phylogenetic relationships of domestic
animal species

Various markers used to comprehend the evolutionary

relationships

Autosomal Y-chromosome sequence

microsatellites

Mitochondrial DNA sequencing

 Maternal transmission of heteroplasmy

A group of genes within an organism that was inherited

together from a single parent Haplotype

Strict maternal Single mtDNA Homoplasmic

transmission of mtDNA haplotype individuals

Simultaneous presence of two or more types Heteroplasmic

of mtDNA in the same individual individuals
 Heteroplasmy

 The uniparental transmission of the mtDNA used as a genetic marker

 The scarce evidence for mtDNA heteroplasmy in the late 1980s and 1990s
attracted attention
 Heteroplasmy was considered as an interesting exception of the strict
maternal mtDNA inheritance.
 Recently, heteroplasmy has been extensively studied
 Heteroplasmy was more widespread than it was previously believed,
particularly as low frequency variants
(Parakatselaki et al., 2021)
 Sources of Heteroplasmy

Somatic mutagenesis during an Through leakage of paternal mtDNA in

individual’s lifetime the zygote during fertilization

• It is most prevalent source

• Higher mutation rate & huge copy
number of mtDNAs is expected to
create variants of mtDNA
(Stewart et al.,2021)

• These variants differ from the

common haplotype in one or few • Paternal leakage can be considered
SNPs (Li et al.,2015) as an inherent inadequacy
(Parakatselaki et al., 2021)
 Heteroplasmy and mtDNA as Genetic Marker
Heteroplasmy could potentially affect the validity of mtDNA as a
marker in three ways.

First way

mtDNA mtDNA
Haplotype Haplotype
A&B A&B

Only Haplotype A Only Haplotype B

By chance
amplified & amplified &
sequenced sequenced

Two individuals are genetically different

Second way

• Heteroplasmy can lead to interlineage recombination, which cannot exist under

the strict asexual mtDNA transmission.

• Recombination will mix the evolutionary histories of the different parts of mtDNA
molecule and introduce noise in phylogenies
(Schierup et al.,2000)

Third way

• False heteroplasmy due to comparisons between nuclear (NUMT) and

real mtDNA sequences or between solely NUMT sequences, which
obviously will lead to incorrect results.

(Parakatselaki et al., 2021)

Evolutionary significance of mtDNA
heteroplasmy
 The Mitochondrial Paradox

Maternal transmission of
Lack of inter-lineage mtDNA
recombination.

Deleterious mutation Death of

Homoplasmic individuals
accumulation individual

Muller’s ratchet
(Muller et al.,1964)

 Because it has survived for

more than two billion years and
Escaped
selection acts efficiently, as
ratchet
suggested by the very low
dN/dS ratio, particularly in
animal’s mtDNA
(Soares et al.,2013)
mtDNA
 Mechanism to escape muller’s retchet
 Many mechanisms of mtDNA to escape Muller’s ratchet

1 Genetic bottleneck (Zhang et al.,2018)

2 Focal replication of mtDNA (Wai et al.,2008)

3 Focal destruction of mtDNA (Diot et al.,2016)

Packaging of mtDNA into larger segregating

4 units (Cao et al.,2009)

• Non-mutually exclusive hypothesis - mtDNA overcomes Muller’s ratchet by

allowing a low rate of paternal leakage, which leads to recombination with
the maternal lineage (Greiner et al.,2015)
 mtDNA bottleneck
Offspring’s
Mitochondrial DNA
• Rapid shifts in
heteroplasmy were
first observed in
pedigrees of Holstein
cows

(Ashley et al.,1989)

• Similar observations seen in numerous vertebrate and invertebrate species

including Drosophila, zebrafish, mice and humans

• These observations led to the suggestion that there was a genetic bottleneck
during the maternal transmission of mtDNA (Zhang et al.,2018)
 Characteristic of mtDNA

That make it an ideal marker for evolutionary studies

1. Small genome size

2. Maternal inheritance

3. Haploid

4. Absence of recombination

5. Extremely low probability of paternal mtDNA leakage

6. Higher mutation rate as compared to the nuclear DNA

7. Change mainly through mutation rather than recombination

Evolutionary growth of different livestock
species by mtDNA
 Cattle
Bos primigenius
large parts of Eurasia and
Northern Africa
(van.,2005) Bos taurus
First domestication in
Upper Euphrates
Valley - 10,000 –11,000
years ago
(Ajmone et al.,2010)
Bos indicus
Second domestication in
Indus Valley – 8000 –
10000 years ago
(Ajmone et al.,2010)

African taurine cattle

Third domestication in
Northeast African region

(Kataria et al.,2021)
 Genesis of modern mitochondrial haplogroup

Bos
primigenius

I R
I1 B. indicus
T Q
P ups
B. taurus gro
a plo
rh
rare
I2 c h
Mu

T1 T2 T3 T4
(Zeder et al.,2006)
Domestication centre of cattle
 Domestication centre of cattle
Taurine mtDNA
Taurine mtDNA haplogroup T3
haplogroup T4
Northern Asia

Eastern Asia
Southwest Asia
and China
Southeast Asia
Southwest Asia
T, T1, T2 &
T3
Haplogroups I1 and I2
• Hotspot of zebu cattle
Taurine mtDNA (B. indicus) mtDNA
haplogroup T1 diversity

• Predominance in Africa
(Chen et al.,2010)
 Evolutionary growth of Buffalo

Phylogenetic analysis of buffaloes of India, China, and Bangladesh shown following

five haplogroups

Buffalo haplogroups

SA1 SA2 SA3 SB1 SB4

(Wang et al.,2017)
Domestication of Riverine buffalo
Domestication of Riverine buffalo

23.2 %

Size of the circle: Proportional to the

number of animals represented
Length of line: Number of mutational
steps.

(Kumar et al.,2007)
Evolutionary changes in Goat
 Evolutionary changes in Goat

Caprine genetic diversity across the globe

(Haplogroup)

22
Haplotype
identified
A B C D F G

Caprine genetic resources of India

Predominant in India (Naderi et al.,2007)
 Geographic distribution of mtDNA haplotype

 Consistent with reports from different continents and countries

that haplogroup A has the widest distribution and is present in
>90% of domesticated goats in all over world (Naderi et al.,2007)
Geographic distribution of mtDNA haplotype in India

(Diwedi et al., 2020)

 Application of mtDNA marker

In phylogenetic
01 In animal breeding 02
analyses

03 In forensic 04 In disease diagnosis

medicine

(Slaska et al.,2014)
 Conclusion

Mitochondrial DNA, by virtue of the number of studies available and various other
advantages, is far more practical than nDNA for phylogeographic surveys

Heteroplasmy is proved to be important for the evolution and the survival of mtDNA
itself

mtDNA analysis gives an understanding of the history and genetic structure, which in
future may help in prioritization and designing of the conservation plans

There is need of further in-depth research in order to understand the uniparental

transmission of mtDNA and the functional and evolutionary role of heteroplasmy
THANK
YOU