Neanderthals Noonan, et al. Sequencing and Analysis of Neanderthal Genomic DNA Green, et al. Analysis of one million base pairs of Neanderthal DNA

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NeanderthalsNoonan, et al. Sequencing and
Analysis of Neanderthal Genomic DNAGreen, et al.
Analysis of one million base pairs of Neanderthal
DNA

• Kristine Briedis
• Journal Club 11/21/06

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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/
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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

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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/pd
f/444254a.pdf
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Contamination

• Challenge to find uncontaminated samples
• Tested gt70 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

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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
• gt1 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

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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)

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Neanderthal chromosomes
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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
  461,000-825,000 years best guess of 516,000 when
  including nuclear DNA substitution information

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Log-likelihood graphs
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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

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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

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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)

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Summary

• Papers describe sequencing of about .03 of
  Neanderthal autosomal genes
• Groups agree that human and Neanderthal genomes
  are lt0.5 different
• Broad agreement on divergence time (370,000 vs
  516,000)
• Possible gene flow between human and Neanderthal,
  but not definitive yet

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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

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Happy Thanksgiving!

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