APPLICATIONS OF MOLECULAR PHYLOGENETICS
Archaeology/paleontology (“ancient DNA” analysis)
Conservation biology
Forensic science
Taxonomy
Power & pitfalls of PCR (polymerase chain reaction)
Rapid amplification of specific genomic regions using
very small amounts of DNA
But … damaged DNA may lead to sequence artifacts
or “ancient” DNA may be contaminated with “modern” DNA
8 clones of PCR-amplified mtDNA from
26,000 year old cave-bear bone
Forms of DNA damage likely to
affect ancient DNA
“Note that direct sequencing would lead to
ambiguous results at least at two positions (arrows)”
C/G to T/A changes due to deamination of C residues?
“Assuming neutral pH, 15oC … take about 100,000 years for hydrolytic damage
to destroy all DNA…. Some environmental conditions could extend this time limit…”
“ … to consider amplification of DNA molecules older than one million years of age
is overly optimistic.” (Svante Paabo lab)
Hofreiter, Nat.Rev.Genet. 2:353, 2001
- used 3,300 year-old DNA (bone) from
King Tutankhamun’s tomb to construct
a 5-generation family tree
Hawass J. Amer.Med.Assoc. 303:638, 2010
- malaria parasite (Plasmodium)
identified as possible cause of death
Marchant Nature 472: 404, 2011
Comparison of 3 high-throughput methods of sequencing ancient DNA
Stoneking Nature Rev
Genet 12:603, 2011
Analysis of DNA from an ancient human - Nature Feb. 11, 2010
“For the first time, the sequence of a near-complete nuclear genome has
been obtained from the tissue of an ancient human. It comes from
permafrost-preserved hair, about 4,000 years old, of a male palaeo-Eskimo
of the Saqqaq culture, the earliest known settlers in Greenland.”
“We identified 353,151 high-confidence singlenucleotide polymorphisms (SNPs), of which 6.8%
have not been reported previously.”
Rasmussen et al. Nature 463:757, 2010
Since some SNPs are reliable markers for known
phenotypes of individual humans...
... could predict that Saqqaq man had
brown eyes, non-white skin, thick dark
hair, dry ear wax and increased
susceptibility to baldness
Lambert Nature 463:757, 2010
Comparison of Saqqaq high-confidence SNPs to those
of contemporary human populations
“Principal component analysis
to capture genetic variation”
- support for migration from Siberia into New World ~ 5,500 years ago,
independent of that giving rise to modern Native Americans and Inuit.
Rasmussen et al. Nature 463:757, 2010
Dispersal of modern human populations
Hartl & Jones Fig. 14.30
Stoneking Nature Rev Genet 12:603, 2011
“Out-of-Africa mitochondrial Eve” hypothesis
... Y chromosome data are also in agreement
Are Neanderthals the direct ancestors of modern Europeans?
First modern humans appeared
~ 200,000 years ago
First known Neanderthals ~ 300,000 years ago
1856 - Neanderthal skeleton found in Germany
(~ 30,000 – 100,000 years old)
Krings, Cell 90: 19, 1997
1997 – S. Paabo – PCR amplified & sequenced mitochondrial
DNA (D-loop region, 379 bp) from skull and compared to 986
living humans
~ 3 x more differences between human-Neanderthal than human-human
and no particular similarity between Neanderthal-European human
Science 277: 176, 1997
Coalescence times – joining of genetic
lineages to common ancestor when
traced back in time
If lineages diverged ~ 600,000 years ago,
… suggests that Neanderthals were evolutionary dead-end
(ie. branch that became extinct without any direct genetic contribution
to modern human lineage)
2000 – mtDNA of Neanderthals from Croatia & the Caucasus analyzed
Hofreiter, Nat.Rev.Genet. 2:353, 2001
“A reanalysis of the ancient mitochondrial DNA”...
Gutierrez, Mol Biol Evol 19: 1359, 2002
HVI part of D-loop
HVI + HVII
Previous sequence data
High variation in substitution rate within D-loop region
- different outcome with HVI vs. HVI + HVII sequences
Chimpanzee outgroup too distant? “long branches attract” phenomenon
p.214
Figure 5.28
Sequence analysis of Neanderthal genome (Nov. 2006)
Science 314: 1071, 2006
Stedman Nature 428:415, 2004
MYH16 (member of myosin
multi-gene family)
Stedman Nature 428:415, 2004
Compared rates of non-synonymous vs. synonymous nt substitution
to assess degree of functional constraint
Stedman Nature 428:415, 2004