The Derived FOXP2 variant was shared with Neanderthals.

Krause et al, 2007

Introduction
Homo Neanderthalensis and Homo Sapiens shared a common ancestor approximately 400,000 years ago. Neanderthals display distinctive physical characteristics and evolved mainly in Europe and Western Asia. Modern humans are thought to have evolved in Africa and then spread to other parts of the world.

Introduction - FOXP2 and Language

No other existing animals have the same capacity for language as Homo sapiens. Therefore, knowing when and under what evolutionary pressures our capacity for language evolved is of great interest. FOXP2 is the only gene known to have a specific role in the development of language and speech. Inactivation of one copy of FOXP2 leads to deficits in orofacial movements and linguistic processing similar to those seen in individuals with adult-onset Brocas aphasia.
Brocas aphasia = damage to the Brocas area of the brain causing an inability to produce fluent speech.

 FOXP2 is among the 5% most conserved proteins in mammals. But... Two amino acid substitutions (located in exon 7) have been fixed in the human lineage since the split with chimp common ancestor. Analysis using human diversity data around exon 7 suggests that a recent selective sweep occurred (ending within last 200,000 years). This suggests that the two substitutions are associated with the rise of modern language ability.

Aim and Methods

AIM: To analyse genotype of Neanderthals at the two substitution positions in exon 7 (nucleotide positions 911 and 977). They used PCR to amplify DNA from ancient remains. They combined the control primers with different primers for the gene and performed multi step multiplex PCR.

Partial sequence alignment of FOXP2 Gene. The three primer pairs used to retrieve the two substitutions from the Spanish Neandertals.

Many controls were used to ensure authenticity of results.

1) Analysed ratio of Neanderthal to modern human mtDNA in regions where they differ. Ended up using two bones for this comparison (from Spain).

2)

Controls for detecting human nuclear DNA contamination use genomic sequence data from 38,000 year old Neanderthal to identify key sequence positions on autosomes and X that are ancestral (identical to chimp sequence and different to humans).
Took advantage of detailed modern human Y chromosome phylogeny: (the time to its recent ancestor is more recent than the divergence from Neanderthals). You would expect the Neanderthal Y chromosome to fall outside the variation of the modern human Y.

3)

Results and Discussion

Not all the control primers yielded products because of such a small amount of DNA. But:

They found that the FOXP2 allele in the Neanderthal samples was the same as that in modern humans (they share the same two substitutions). Which previously was shown to have been subject to a selective sweep.
This sequence variant is a G to T substitution, not commonly associated with ancient DNA damage, therefore likely to represent a genuine allele present in the Neandertals.

Results of the multiplex PCRs on the two Spanish Neandertals. Products carrying ancestral allelic states = red , derived allelic states = green, Neandertal-specific state = blue , no products were obtained = grey.

There are three possible explanations for this:

1. Gene flow between Neanderthals and Homo Sapiens. 2. The FOXP2 haplotype was present in the common ancestor and then was later positively selected for in humans after their divergence from Neanderthals. 3. The selective sweep occurred earlier than previously thought about 300,000-400,000 years ago.

1.

Gene flow between Neanderthals and Homo Sapiens. However, neither the maternally inherited mtDNA nor the paternally inherited Y chromosome shows evidence of gene flow from modern humans into Neandertals or of subsequent contamination of their remains. Other autosomal variation tests failed to detect any gene flow.

2. The FOXP2 haplotype was present in the common ancestor and then was later positively selected for in humans after their divergence from Neanderthals. The relevant haplotype needs to be at a considerable frequency in the ancestral population in order to obtain the high frequencies in Neandertals. However, the higher the variant frequency before positive selection, the less likely it is to detect a signature of a selective sweep. Hence, this scenario is unlikely.

3. The selective sweep occurred earlier than previously thought about 300,000-400,000 years ago.
Given a divergence time of chimpanzees and humans (6.5 million years), the fixation of the sweep would have occurred within the last 260,000 years. Other evolutionary factors could further increase the variance on these time estimates, making it possible that the sweep started or occurred in the common ancestral population of Neandertals and modern humans.

This is the most likely

Conclusion
The third explanation is most likely: These genetic changes and the selective sweep predate the common ancestor (300,000400,000 years ago) of modern humans and Neandertals. Neandertals carried a FOXP2 protein identical to that of presentday humans in the only two positions that differ between human and chimpanzee. These changes were present in the common ancestor of modern humans and Neandertals. This is in contrast to more recent age estimates of the selective sweep based on extant human diversity data. Thus, these results illustrate the usefulness of retrieving direct genetic information from ancient remains for understanding recent human evolution. This demonstrates that the Neanderthal genome can be used to provide information on the timing of genetic changes in human lineage relative to the divergence of Neanderthals.