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
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)
Theodosious Dobzhansky
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…”
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 -
PRIMATES
Prosimians Tarsiers Anthropoids
New-world Monkeys
Old-world Monkeys
Hominoids
Pongids (apes)
Hominids (humans)
Primate Classification
Note: Primate classification is undergoing rapid change. This is a simplified version of one of several taxonomies.
PRIMATES - Hominoids
Chimpanzee
(Pongid)
Gorilla
(Pongid)
Orangutan
(Pongid)
Human
(Hominid)
The known fossil record of hominids also showing ourselves and the chimpanzee
Skull cast used in DE Grade 10 NSE unit
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
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
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.
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
http://www.newscientist.com/article/dn16224-neanderthal-genome-already-giving-up-its-secrets.html
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.cell.com/abstract/S0092-8674(08)00773-3
What is surprising, puzzling or paradoxical about?
The number of protein coding genes in:E. coli (bacterium) 4,377 Saccharomycetes (yeast) ~ 5,000Neurospora (fungus) ~10,000 Drosophilia (fruit fly) ~13,600C. elegans (nematode) ~20,000 Arabidopsis (plant) ~ 25,000Zea 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.
There are about 90,000 different proteins in the human body.
Humans have 46 chromosomes, chimps have 48.
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%
The other 98% of the genome
Short Tandem RepeatsSTR’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
The other 98% of the genome
Short Tandem Repeats
February 8, 2006
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.
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.
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.
MtDNA Genome
Mitochondrial Eve – The Initial StudyRebecca 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”
UNIVERSAL MATERNAL ANCESTOR (Eve)
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.
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.
Determining age using ‘molecular clocks’
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
“The availability of the near complete chromosome sequence now provides new avenues for investigating human evolution.”
XY
mt DNA markers
Y markers
National Geographic
Genographic Project
Y Haplogroups
of the World
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.
New York Times December 10, 2006
DNA Gatherers Hit a Snag: The Tribes Don't Trust ThemBy 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 ScienceSome 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.
Opposition to the Genographic Project
The other 98% of the genome
PSEUDOGENES (FOSSIL GENES)
Unitary
Duplication
Retro or Processed
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.
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.
The other 98% of the genome
Pseudogenes and Vitamin C
Gene 1
Enzyme 1
Gene 2
Enzyme 2
Gene 3
Enzyme 3
DB C Vitamin CA
GULOgene
Gulo Enz
Vitamin C
Not so in primates…
Portion of Working GULO Gene in Rat:
Matching GULO Pseudogenes in 4 PrimatesNote Deletion
In most mammals
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.
The other 98% of the genome
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.
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.
Epigenesis
Epigenetics refers to changes in gene expression due to mechanisms other than changes in DNA sequence