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DNA: THE ULTIMATE FORENSIC RECORD OF EVOLUTION (Beyond Stones and Bones)

DNA: THE ULTIMATE FORENSIC RECORD OF EVOLUTION (Beyond Stones and Bones). How molecular genetics is expanding our understanding of the tree of life. Page from Darwin's notebooks around July 1837 showing his first known sketch of an evolutionary tree. The Year 2009

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DNA: THE ULTIMATE FORENSIC RECORD OF EVOLUTION (Beyond Stones and Bones)

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  1. DNA: THE ULTIMATE FORENSIC RECORD OF EVOLUTION (Beyond Stones and Bones) How molecular genetics is expanding our understanding of the tree of life Page from Darwin's notebooks around July 1837 showing his first known sketch of an evolutionary tree.

  2. The Year 2009 Marks the bicentennial of Charles Darwin’s birth. (Born Feb. 12, 1809) and the 150th anniversary of the publication of the Origin of Species (1st edition published 1859)

  3. "Nothing in biology makes sense except in the light of evolution" Theodosious Dobzhansky

  4. In the Descent of Man, Darwin: Declared the chimpanzee and gorilla our closest living relatives based on anatomical similarities, and he made this prediction: “It is, therefore probable….our early progenitors lived on the African continent…”

  5. Nature of Science “Scientific knowledge is simultaneously reliable and tentative. Having confidence in scientific knowledge is reasonable while realizing that such knowledge may be abandoned or modified in light of new evidence….. .” NSTA Position Statement “The Nature of Science” July 2000 Titcomb Basin, Wind River Mtns, Wyoming -

  6. Primate Classification PRIMATES Prosimians Tarsiers Anthropoids New-world Monkeys Old-world Monkeys Hominoids Pongids (apes) Hominids (humans) Note: Primate classification is undergoing rapid change. This is a simplified version of one of several taxonomies.

  7. PRIMATES - Hominoids Gorilla (Pongid) Chimpanzee (Pongid) Human (Hominid) Orangutan (Pongid)

  8. The known fossil record of hominids also showing ourselves and the chimpanzee Skull cast used in DE Grade 10 NSE unit

  9. What is a genome? All the DNA contained in an organism or a cell, which includes both the chromosomes within the nucleus and the DNA in mitochondria. All of the biological information (DNA) needed to build and maintain a living example of that organism. National Center for Biotechnology Information

  10. The Human Genome Project • Draft completed April 2003, refined in 2006 • International effort • Cost $3 billion • ~ 3 billion base pairs • Haploid set of DNA • Early draft indicated ~ 30000 – 35000 protein coding genes • Current estimate puts number of protein coding genes at ~ 20,500

  11. Chimp Genome Sequenced in 2005 • 3 billion base pairs in sequence • 96% of chimp & human DNA sequences are identical • 1.2% difference when considering single base pair substitutions • additional 2.7% difference considering duplications and rearrangements A chimpanzee named Clint was the source of the DNA for the genome study. Clint lived at the Yerkes Primate Research Center near Atlanta until he died in 2004 at the age of 24.

  12. NEANDERTHAL GENOME December 2008 Half of nuclear DNA sequenced from bone sample. Some Preliminary Results: Lacked genes for lactose tolerance, increased fertility, and microcephalin which is linked to bulging brains in humans. Did they interbreed with modern humans? Probably not. Europeans and Africans appear to have equal numbers of genetic differences with Neanderthals, suggesting that the first anatomically modern humans to arrive in Europe replaced Neanderthals. August 2008 A complete mitochondrial (mt) genome sequence was reconstructed from bone of a 38,000 year-old Neandertal individual. Analysis establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 + or - 140,000 years. http://www.newscientist.com/article/dn16224-neanderthal-genome-already-giving-up-its-secrets.html http://www.cell.com/abstract/S0092-8674(08)00773-3

  13. What is surprising, puzzling or paradoxical about? The number of protein coding genes in: E. coli (bacterium) 4,377 Saccharomycetes (yeast) ~ 5,000 Neurospora (fungus) ~10,000 Drosophilia (fruit fly) ~13,600 C. elegans (nematode) ~20,000 Arabidopsis (plant) ~ 25,000 Zea mays (corn) ~50,000 Humans & most mammals ~20,500 Protein coding genes make up about 2% of the human genome. All organisms (archaea, bacteria, eukaryotes) share ~ 500 genes. Humans have 46 chromosomes, chimps have 48. There are about 90,000 different proteins in the human body.

  14. The other 98% of the genome Transposable Elements and Evolution All 7 Alu elements in Human and Chimp hemoglobin are in exactly same place. The DNA sequences in the 7 Alu elements range in similarity from 94.7% to 98.9%

  15. The other 98% of the genome Short Tandem Repeats STR’s (short tandem repeats) and VNTR’s (variable tandem repeats) are used in forensics and genealogy The FBI has chosen 13 specific STR loci to serve as the standard for CODIS. The likelihood that any two individuals (except identical twins) will have the same 13-loci DNA profile can be as high as 1 in 1 billion or greater. STR repeats for D81179 Locus In this example the STR TCTA is repeated 12 times

  16. The other 98% of the genome Short Tandem Repeats Y-Chromosome and Mitochondrial DNA and the Search for Ancestry

  17. February 8, 2006

  18. Love You, K2a2a, Whoever You Are Amy Harmon New York Times January 22, 2006 Amy Harmon’s mtDNA has the genetic marker of one of the four founding mothers of a large part of today’s Ashkenazi Jewish population. Harmon discusses some of the positive outcomes as well as troubling issues surrounding genetic genealogy.

  19. MtDNA and Y- Chromosome Studies • mtDNA comparisons along maternal lines of descent trace all modern humans to a woman (Eve) who lived in Africa less than 200,000 years ago. • Y-chromosome studies along paternal lines indicate that all modern humans alive today are descended from a man (Adam) who lived in Africa about 60,000 years ago.

  20. MtDNA Genome • Maternally inherited • 16,569 base pairs encode 37 genes involved in energy production and storage. • Polymorphisms in the D-loop or hypervariable region are useful in human diversity studies. This is a non-coding region.

  21. Mitochondrial Eve – The Initial Study Rebecca Cann, Mark Stoneking, and Allan Wilson, Nature, 1987. • Sequenced mtDNA from the placentas of 147 women from many populations from the around earth. • In their analysis, they assumed that if two mtDNA sequences shared a polymorphism, then they shared a common ancestor. • By building up a network of the 147 sequences, they were able to infer ancestral relationships between the women. THEIR CONCLUSION: “All these mitochondrial DNA’s stem from one woman who is postulated to have lived about 200,000 years ago, probably in Africa”

  22. UNIVERSAL MATERNAL ANCESTOR (Eve)

  23. Determining the age of lineages using ‘molecular clocks’ • Assumptions: • Nucleotide changes occur over time at a regular clock-like rate. • Groups separated by 20 nucleotide changes have common ancestors twice as old as those separated by 10 nucleotide changes. • The rate of nucleotide change can be determined • To calibrate a molecular clock, researchers use the time of a lineage split for which there is a high degree of confidence about when it occurred.

  24. Determining age using ‘molecular clocks’ Example of Calculation For mtDNA, the calibration was set at the human- chimp split 6 million years ago. Chimps and humans differ by about 12% in their mtDNA. Thus rate of change of hominid mtDNA is about 2% per million years. The average total divergence of contemporary human sequences is about 0.4%. Thus the divergence time is about 200,000 years.

  25. THE HUMAN Y CHROMOSOME: AN EVOLUTIONARY MARKER COMES OF AGE Mark A. Jobling & Chris Tyler-Smith Nature Reviews Genetics 4, 598-612 01 Aug 2003 X Y “The availability of the near complete chromosome sequence now provides new avenues for investigating human evolution.”

  26. National Geographic Genographic Project mt DNA markers Y markers

  27. Y Haplogroups of the World

  28. The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings. Using the information in the HapMap, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors.

  29. Opposition to the Genographic Project New York Times December 10, 2006 DNA Gatherers Hit a Snag: The Tribes Don't Trust Them By AMY HARMON The Genographic Project has come to a standstill in North America. Indigenous leaders fear that genetic ancestry information could jeopardize land rights and other benefits that are based on the notion that their people have lived in a place since the beginning of time. CBS News October 10, 2006 Mad At Science Some Activists Say The Genographic Project Is Undermining Indigenous Cultures The Indigenous Peoples Council on Biocolonialism says taking samples from indigenous groups undermines their belief systems. Here, the Genographic Project's leader, Dr. Spencer Wells, performs a cheek swab from a participant in Chad. 

  30. The other 98% of the genome Unitary PSEUDOGENES (FOSSIL GENES) Mutated non-functional genes ~19,000 (estimate in 2003) Released from constraints of natural selection. Accumulated mutations serve as fossil bed for studying evolutionary past. Duplication Retro or Processed

  31. The other 98% of the genome Human GULO Unitary Pseudogene and Vitamin C Mice and many mammals have a functional GULO gene that is involved in producing vitamin C. The GULO gene in primates is a non-functional pseudogene. How might this have happened? Use it or lose it. Fossil genes are exactly what we would predict to evolve as a consequence of continued mutation in the absence of natural selection. Fossil genes mark changes in lifestyle and when we can spot and track these genes it is possible to reconstruct ancestry. With some exceptions humans and chimps have same pseudogenes in the same place, and on average are 98% identical.

  32. GULO gene Gene 3 Gene 2 Gulo Enz Enzyme 3 Enzyme 2 The other 98% of the genome Pseudogenes and Vitamin C In most mammals Gene 1 Not so in primates… Enzyme 1 A B C Vitamin C D Vitamin C Portion of Working GULO Gene in Rat: Note Deletion Matching GULO Pseudogenes in 4 Primates

  33. The other 98% of the genome HEMOGLOBIN DUPLICATION PSEUDOGEGES Humans have 13 copies of genes that encode hemoglobin. Only 4 function in adults. These genes are located in two clusters, A & B. About 30% of psi-beta DNA sequence is mutated.

  34. Other Pseudogenes Cytrochrome c genes (49 in humans) Color vision (opsin) genes (correlated to olfaction) Olfactory genes (mice have 1,400) 18% fossilized in mice, lemurs, and New World monkeys that lack color vision. 29% fossilized in Old world Monkeys 33% fossilized in apes, chimps, and orangutans 50% fossilized in humans Use it or lose it.

  35. The Alternative Genome The old axiom “one gene, one protein” no longer holds true. The more complex an organism, the more likely it became that way by extracting multiple proteins from individual genes. The genes of mice and humans are 88% alike. Many of the ways we differ from rodents arise from how we edit our genetic information.

  36. Epigenesis Epigenetics refers to changes in gene expression due to mechanisms other than changes in DNA sequence

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