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Neanderthals
Noonan, et al. Sequencing and Analysis of Neanderthal Genomic DNA
Green, et al. Analysis of one million base pairs of Neanderthal DNA
Kristine Briedis
Journal Club 11/21/06
Neanderthals
• Most closely related
hominid group to modern
humans
• First recognized 150
years ago in Germany
• Existed 500,000 years
ago
• Lived in Europe and West
Asia
• Evolved away from
humans
• Disappeared 30,000
years ago
http://www.msnbc.msn.com/id/13154583/
Interbreeding?
• Open question if humans
and Neanderthals
cohabitated
• Overlap in their
geographical ranges and
time of existence
• Some late Neanderthal
groups adopted cultural
traits that might have
been influenced by
modern humans
DNA
• Before now, Neanderthal DNA
studies were limited to
mitochondrial DNA sequencing
(1997)
• Sequencing of nuclear
Neanderthal DNA would help
human genome annotation
and identify our most recent
genetic differences
• Two groups used a bone found
in 1980 in a cave in Croatia
• Carbon dated to 38,310 ±
2,130 years ago
http://www.nature.com/nature/journal/v444/n7117/pdf/444254a.pdf
Contamination
• Challenge to find
uncontaminated samples
• Tested >70 Neanderthal bone
and tooth samples
• Most samples were too
degraded or contaminated
• Six bones were further tested
• Amplified mtDNA that previous
studies have shown to be
different from modern humans
• Vi-80 bone (from Croatia) was
best prospect for sequencing
Sequencing Approaches
• 454 sequencing:
• “sequencing by
synthesis”
• Uses small fragments of
DNA (advantageous)
• PCR every fragment to
10m copies
• Attach DNA to bead
• Solutions of nucleotides
are progressively applied;
photons are generated as
each base is incorporated
• >1 million base pairs
• Metagenomic approach:
• Insert DNA fragments into
plasmids
• Amplify in bacteria
• Sequence inserts using
either pyrosequencing or
Sanger method
• Can be used to target
specific genes
• 65,000 base pairs
Vi-80 bone
• Recovered 254,933
unique sequences from
Vi-80 bone (Nature
group)
• Aligned sequences to
complete genomes,
environmental samples
(env database), and
GenBank set of
redundant nucelotide
sequences (nt)
Neanderthal chromosomes
Time of Divergence
• Science group:
– used SNPs to approximate when modern humans
and Neanderthals diverged
– Estimated 120,000-670,000 years, with a best guess
of 370,000
• Nature group:
– used PCR confirmed substitutions of mtDNA
– assumed human-chimp divergence 4.7-8.4 millions
years
– estimate human-Neanderthal divergence of 461,000825,000 years; best guess of 516,000 when including
nuclear DNA substitution information
Log-likelihood graphs
Nucleotide changes
• Generated 3-way alignments between Neanderthal,
human, and chimp
• Estimate 7.1%-8.2% of sequence changes between
human and chimp occurred after Neanderthal
divergence
SNP study
• Compared Neanderthal sequences to human SNP sites
• Neanderthal has derived (human SNP) allele (as
opposed to ancestral chimp allele) in 30% of all SNPs
• Possibly overestimation since SNPs analyzed are of high
frequency in human and thus are likely older
• Estimate conflicts with their population split model
• Suggests interbreeding?
• Neanderthal X chromosome shows higher level of
divergence than autosomes
• Possible gene flow from modern human males into
Neanderthals
Ancestral Population Size
• Human effective population size is around 10,000
• Chimps, gorillas, and orangutans have an effective
population size 2-4 times larger
• Effective population size of human and chimp ancestor
thought to be closer to apes than modern humans
• Estimate for Neanderthal is up to 12,000 with a best
guess of 3,000
• Indicates effective population size of hominids had
decreased prior to human-Neanderthal split
• Dependent on what split time you use (time after which
there was no more interbreeeding between groups)
Summary
• Papers describe sequencing of about
.03% of Neanderthal autosomal genes
• Groups agree that human and
Neanderthal genomes are <0.5% different
• Broad agreement on divergence time
(370,000 vs 516,000)
• Possible gene flow between human and
Neanderthal, but not definitive yet
Future Plans
• Is it possible to fully sequence genome?
• 1x coverage requires 20g of bone and 6000 runs
on the 454 sequencing platform
• Nature authors think they can make the
sequencing 10x more efficient
• Their goal is to fully sequence the Neanderthal
genome within two years
• Currently 5 million bp are available
• Science authors are targeting FOXP2 gene
– Linked to speech and language; Present in many
animals, but human version differs from chimp
Happy Thanksgiving!
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