1. 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

2. Hofreiter, Nat.Rev.Genet. 2:353, 2001
8 clones of PCR-amplified mtDNA from
26,000 year old cave-bear bone
“Note that direct sequencing would lead to ambiguous results at least at two positions (arrows)”
Forms of DNA damage likely to
affect ancient DNA
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

3. Nature,1993
- but in fact this turned out to be contaminating “modern” DNA
In some cases, mistakes were due to organellar DNA fragments (pseudogenes) integrated into “modern” nuclear genome

4. Ancient DNA studies (1984 – 2004)
Willerslev & Cooper Proc Roy Soc 272:3, 2005

5. Dispersal of modern human populations
Hartl & Jones Fig
Stoneking Nature Rev Genet 12:603, 2011
“Out-of-Africa mitochondrial Eve” hypothesis
... Y chromosome data are also in agreement

6. Relationship between Neanderthals and “modern humans”?
First modern humans appeared ~ 200,000 years ago
Our closest known relatives are Neanderthals who lived from ~ 600,000 to ~30,000 years ago
1997 – S. Paabo – PCR amplified & sequenced mitochondrial DNA (D-loop region, 379 bp) from skull and compared to 986 living humans
Krings, Cell 90: 19, 1997
(from skeleton discovered in cave in Germany in 1856)
~ 3 x more differences between human-Neanderthal than human-human
and no particular similarity between Neanderthal-European human
2000 – mtDNA of Neanderthals from Croatia & the Caucasian Mountains region also analyzed
Estimate of divergence time: 550,000 – 690,000 yr
(using chimpanzee as outgroup)
… suggesting that Neanderthals were evolutionary dead-end
Hofreiter, Nat.Rev.Genet. 2:353, 2001
(ie. branch that became extinct without any direct genetic contribution to modern human lineage)

7. 2002 “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

8. Chimpanzee outgroup too distant? “long branches attract” phenomenon
Figure 5.28

9. 2006 – two studies report 1 million bp from Neanderthal nuclear genome
Science 314: 1071, 2006
2007

10. 2008 – first complete Neanderthal mitochondrial genome (16 kb)
2007 – nuclear gene for pigmentation suggests Neanderthals had red hair
Neanderthals ... They're Just Like Us?
National Geographic
2008 – first complete Neanderthal mitochondrial genome (16 kb)
2010 – draft sequence of Neanderthal nuclear genome (> 4 billion bp from 3 individuals !!)
New rapid sequencing techniques
2011 – mitochondrial DNA analysis from Neanderthal family of 12 individuals dated to ~ 49,000 years ago
Providing anthropological insights into kinship structure, mating behaviour…

11. Inferences about evolutionary relationships from genomic data
Stoneking Nature Rev Genet 12:603, 2011
“The genomes provide evidence of gene flow between the three lineages after anatomically modern humans left Africa, drastically changing our view of human evolution.”
“Red arrows mark genetic evidence of interbreeding among different populations. Black arrows mark suggested or possible additional gene flow.”
Lalueza-Fox & Gilbert Curr Biol 21:R1002, 2011

12. Stedman Nature 428:415, 2004

13. MYH16 (member of myosin
multi-gene family)
Stedman Nature 428:415, 2004

14. Compared rates of non-synonymous vs. synonymous nt substitution
to assess degree of functional constraint
Stedman Nature 428:415, 2004