Mitochondrial DNA in Taxonomy and Phylogeny
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Mitochondria are essential organelles in eukaryotic cells, primarily responsible for energy production and various cellular functions. They have a unique genetic makeup and reproduce through binary fission, indicating a shared evolutionary history with prokaryotes. DNA barcoding, particularly using mitochondrial DNA, has become a vital tool for species identification, aiding in biodiversity monitoring and conservation efforts.
Mitochondrial DNA in Taxonomy and Phylogeny
- 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). 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 1% 99%DNA
- 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.