This presentation details on the application of mitochondrial DNA in Taxonomy and Phylogenetic studies.

2. • Mitochondria (singular: Mitochondrion) are membrane-
bound organelles found in the cytoplasm of almost all eukaryotic cells .
• It’s primary function is to generate large quantities of energy in the form
of adenosine triphosphate (ATP).
• Mitochondria are typically round to oval in shape and range in size from
0.5 to 10 μm.
• In addition to producing energy, mitochondria store calcium for
cell signaling activities, generate heat and mediates cell growth and
death.

3. • The only eukaryotic organism known to
lack mitochondria is oxymonad
Monocercomonoides spp.
• Mitochondria are unlike other cellular
organelles in that they have two
distinct membranes, a unique genome
and reproduce by binary fission.
These features indicate that
mitochondria share an evolutionary past
with prokaryotes .
Monocercomonoides

4. Mitochondrial Genome
• Mt genome consists of a circular
chromosome 16.5kb in size that is located
in the mitochondrial matrix .
• Most cells contain at least 1000 mtDNA
molecules distributed among hundreds
of individual mitochondria.
• It contains 37 genes, and encodes 2 types
of rRNA and 22 types of tRNAs.

5. • Genes encode 13 proteins that are subunits
of enzymes of oxidative phosphorylation.
• The remaining 74 polypeptides of the
oxidative phosphorylation complex are
encoded by the nuclear genome.
• In most multicellular organisms, the
mtDNA - or mitogenome - is organized as a
circular, covalently closed, double-
stranded DNA.
• For human mitochondrial DNA 100-10,000
separate copies of mtDNA are usually
present per cell (egg and sperm cells are
exceptions).

6. • The two strands of mtDNA are differentiated
by their nucleotide content, with a guanine-
rich strand referred to as the heavy strand (or
H-strand) and a cytosine-rich strand referred
to as the light strand (or L-strand).
• The light strand encodes 28 genes, and the
heavy strand encodes 9 genes for a total of 37
genes.
• Of the 37 genes, 13 are for proteins
(polypeptides), 22 are for transfer RNA (tRNA)
and two are for the small and large subunits
of ribosomal RNA (rRNA).
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8. Barcode of life
• In 2003, Paul Hebert from the University
of Guelph in Ontario, Canada, proposed
“DNA bar-coding” as a way to identify
species.
• Biological specimens were identified using
morphological features like the shape, size
and color of body parts. In some cases a
trained technician could make routine
identifications using morphological keys,
but in most cases an experienced
professional taxonomist is needed.
Paul Herbert

9. • If a specimen is damaged or is in
an immature stage of
development, even specialists may
be unable to make
identifications.
• Barcoding solves these problems
because even non-specialists can
obtain barcodes from tiny
amounts of tissue. This is not to
say that traditional taxonomy
has become less important.

10. • Rather, DNA barcoding can serve a dual purpose as a new tool in the
taxonomists toolbox supplementing their knowledge as well as being an
innovative device for non-experts who need to make a quick
identification.
• The gene region that is being used as the standard barcode for almost all
animal groups is a 648 base-pair region in the mitochondrial
Cytochrome C oxidase 1 gene (“CO1”).

11. COI is proving highly effective
in identifying birds, butterflies,
fish, flies and many other
animal groups.
COI is not an effective barcode
region in plants because it
evolves too slowly, but two
gene regions in the chloroplast,
matK and rbcL, have been
approved as the barcode regions
for plants.

14. • The Database:
There are currently two main barcode databases.
– The International Nucleotide Sequence
Database Collaborative is a partnership among
GenBank in the U.S., the Nucleotide Sequence
Database of the European Molecular Biology
Lab in Europe, and the DNA Data Bank of
Japan.
– Barcode of Life Database (BOLD) was created
and is maintained by University of Guelph in
Ontario. It offers researchers a way to collect,
manage, and analyze DNA barcode data.
• The Data Analysis:
Specimens are identified by finding the closest
matching reference record in the database.

15. A 648-bp region (the Folmer region) of the mitochondrial cytochrome c
oxidase subunit I (COI) gene was proposed as a potential 'barcode’.
To date, the Barcode of Life Data Systems database includes almost 2,000,00
barcode sequences from over 160,000 species of animals, plants, and fungi.

16. • Taxonomy- the science of classifying
living things according to shared
features has always been a part of
human society.
• Identifying organisms has grown in
importance as we monitor the
biological effects of global climate
change and attempt to preserve
species diversity in the face of
accelerating habitat destruction.

17. • We know very little about the
diversity of plants and animals,
let alone microbes, living in
many unique ecosystems on
earth.
• Less than two million of the
estimated 5-50 million plant
and animal species have been
identified.

18. • Scientists agree that the yearly rate of extinction has increased from
about one species per million to 100-1,000 per million.
• This means that thousands of plants and animals are lost each year.
Most of these have not yet been identified.

19. • Classical taxonomy falls short in
this race to catalog biological
diversity before it disappears.
• Specimens must be carefully
collected and handled to
preserve their distinguishing
features.
• Differentiating subtle
anatomical differences between
closely related species requires
the subjective judgment of a
highly trained specialist – and
few taxonomists are available
these days.

20. • mt DNA allows non-experts to
objectively identify species – even from
small, damaged, or industrially processed
material.
• A “DNA barcode” is a unique pattern of
DNA sequence that identifies each living
thing.
• Short mt DNA barcodes, about 700
nucleotides in length, can be quickly
processed from thousands of specimens
and unambiguously analyzed by computer
programs.

21. • The International Barcode of
Life (iBOL) organizes
collaborators from more than
150 countries to participate in a
variety of campaigns to census
biodiversity.
• The 10-year Census of Marine
Life, completed in 2010,
provided the first comprehensive
list of more than 190,000 marine
species and identified 6,000
potentially new species.

22. • DNA barcodes showed that a well-
known skipper butterfly
(Astraptes fulgerator), identified in
1775, is actually ten distinct species.
• DNA barcodes have revolutionized
the classification of orchids, a
complex and widespread plant
family with an estimated 20,000
members.

23. • Twenty years of research have established the utility of mitochondrial DNA
sequences in differentiating among closely-related animal species.
• Four properties make mitochondrial genomes especially suitable for identifying
species.

24. There are 100-10,000 more copies of mitochondrial than
nuclear DNA per cell, making recovery, especially from small
or partially degraded samples, easier and cheaper.

25. Relatively few differences within
species in most cases. Small
intraspecific and large
interspecific differences signal
distinct genetic boundaries
between most species, enabling
precise identification with a
barcode.

26. Introns, which are non-coding
regions interspersed between
coding regions of a gene, are
absent from mitochondrial
DNA of most animal species,
making amplification
straightforward.
Nuclear genes are often
interrupted at places by
introns, making amplification
difficult or unpredictable.

27. • DNA barcodes are also used to
detect food fraud and products
taken from conserved species.
• Working with researchers from
Rockefeller University and the
American Museum of Natural
History, students from Trinity
High School found that 25% of 60
seafood items purchased in
grocery stores and restaurants in
New York City were mislabeled as
more expensive species.

28. • One mislabeled fish was the
endangered species, Acadian
redfish.
• Another group identified three
protected whale species as the
source of sushi sold in California
and Korea.
• However, using DNA barcodes to
identify potential biological
contraband among products
seized by customs is still in its
infancy. Dr. Sanal George

30. In an effort to find correspondence between traditional
species boundaries established by taxonomy and those
inferred by DNA bar coding, Herbert and co-workers
sequenced DNA barcodes of 260 of 667 bird species that
breed in N. America( Herbert et.al. 2004).

31. • They found that every one of the
260 species had a different COI
sequence.
• COI variations between species
averaged 7.93% whereas variation
within species averaged 0.43%.
• In four cases there were deep
intraspecific divergences indicating
possible new species.
• Herbert et.al.’s results reinforce
and strengthen the case for DNA
bar coding.

32. • Assigning specimens to known species using only a tiny
piece of tissue.
• Discovering new variation within what were presumed to be
single species.
• Documenting the biodiversity of poorly known taxonomic
groups and poorly sampled geographical regions.

34. Comparisons show we differ
from one another by only 1 or 2
nucleotides out of 648, while we
differ from chimpanzees at 60
locations and gorillas at 70
locations.

35. mt DNA in evolutionary studies
The Mitochondrial Eve Theory

36. Was thought up by Rebecca Cann,
Mark Stoneking, and Allan Wilson in
1987.
Mitochondrial Eve Theory
States that the mitochondrial DNA in
all humans is inherited from one
common female ancestor.
There are many theories of human
evolution, but this is one of the more
supported theories with evidence to
back it up.

37. • The University of California Berkley used
restriction enzymes to track the lineage of
women from around the world.
• From the findings of scientists it suggested
that there were two separate groups, such as
Sub-Saharan Africans and North Africans.
• The information from these studies was then
used to come up with a mutation rate for
Mitochondrial DNA to trace back to the
most recent common ancestor (MRCA).

38. • According to the most
common interpretation of
the mitochondrial DNA
data, the titles belong to
the same hypothetical
woman.
• The living humans whose
mitochondrial lineages
branched earliest from the
tree are indigenous
Africans.
• The lineages of indigenous
people on other
continents all branch off
from African lines.