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 -
Primate Classification
PRIMATES
Prosimians
Tarsiers
New-world
Monkeys
Note: Primate classification is
undergoing rapid change. This
is a simplified version of one of
several taxonomies.
Anthropoids
Old-world
Monkeys
Hominoids
Pongids
(apes)
Hominids
(humans)
PRIMATES - Hominoids
Gorilla
(Pongid)
Chimpanzee
(Pongid)
Human
(Hominid)
Orangutan
(Pongid)
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
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.
NEANDERTHAL GENOME
December 2008
Half of nuclear DNA sequenced from bone
sample. Some Preliminary Results:
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/S00928674(08)00773-3
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.
http://www.newscientist.com/article/dn16224neanderthal-genome-already-giving-up-its-secrets.html
What is surprising, puzzling or paradoxical about?
The number of protein coding genes in:
E. coli (bacterium) 4,377
Neurospora (fungus) ~10,000
C. elegans (nematode) ~20,000
Zea mays (corn) ~50,000
Saccharomycetes (yeast) ~ 5,000
Drosophilia (fruit fly) ~13,600
Arabidopsis (plant) ~ 25,000
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.
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 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 13loci 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.
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.
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”
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.
Determining age using ‘molecular clocks’
Example of Calculation
For mtDNA, the calibration was set at the humanchimp 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.
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.”
National Geographic
Genographic Project
mt DNA markers
Y markers
Y Haplogroups
of the World
The International HapMap Project is a multicountry 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.
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.
The other 98% of the genome
Unitary
PSEUDOGENES
(FOSSIL GENES)
Mutated non-functional genes
~19,000 (estimate in 2003)
Duplication
Released from constraints of
natural selection.
Accumulated mutations serve as
fossil bed for studying
evolutionary past.
Retro or
Processed
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.
The other 98% of the genome
Pseudogenes and Vitamin C
A
Gene 1
Gene 2
GULO
gene 3
Gene
Enzyme 1
Enzyme 2
Gulo Enz3
Enzyme
B
C
In most mammals
Not so in primates…
Vitamin
C
D
Vitamin C
Portion of Working GULO Gene in Rat:
Matching GULO Pseudogenes in 4 Primates
Note Deletion
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.
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