Mitochondrial DNA in Taxonomy and Phylogeny

• 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.

• 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

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.

• 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).

• 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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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

• 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.

• 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”).

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.

• 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.

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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

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.

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.

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.

• 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.

• 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

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).

• 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.

• 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.

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.

mt DNA in evolutionary studies

T h e M i t o c h o n d r i a l E v e T h e o r y

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.

• 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).

• A c c o r d i n g t o t h e m o s t c o m m o n i n t e r p r e t a t i o n o f t h e m i t o c h o n d r i a l D N A d a t a , t h e t i t l e s b e l o n g t o t h e s a m e h y p o t h e t i c a l w o m a n .

• T h e l i v i n g h u m a n s w h o s e m i t o c h o n d r i a l l i n e a g e s b r a n c h e d e a r l i e s t f r o m t h e t r e e a r e i n d i g e n o u s A f r i c a n s .

• T h e l i n e a g e s o f i n d i g e n o u s p e o p l e o n o t h e r c o n t i n e n t s a l l b r a n c h o f f f r o m A f r i c a n l i n e s .