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admixture • North Africa • population history • Africa • Neandertal DNA • introgression •

population structure

The North African Neandertal

descendants
18 Oct 2012

A new paper by Federico Snchez-Quinto and colleagues reports on

comparisons of North African population samples with the Neandertal
DNA project data Sanchez-Quinto:2012. The paper shows that North
African populations also carry a substantial trace of Neandertal
ancestry, like living populations outside of Africa, much more than
populations of sub-Saharan Africa.

One of the main findings derived from the analysis of the

Neandertal genome was the evidence for admixture between
Neandertals and non-African modern humans. An alternative
scenario is that the ancestral population of non-Africans was
closer to Neandertals than to Africans because of ancient
population substructure. Thus, the study of North African
populations is crucial for testing both hypotheses. We analyzed a
total of 780,000 SNPs in 125 individuals representing seven
different North African locations and searched for their
ancestral/derived state in comparison to different human
populations and Neandertals. We found that North African
populations have a significant excess of derived alleles shared
with Neandertals, when compared to sub-Saharan Africans. This
excess is similar to that found in non-African humans, a fact that
can be interpreted as a sign of Neandertal admixture.
Furthermore, the Neandertal's genetic signal is higher in
populations with a local, pre-Neolithic North African ancestry.
Therefore, the detected ancient admixture is not due to recent
 Near Eastern or European migrations. Sub-Saharan populations
are the only ones not affected by the admixture event with
Neandertals.

The interesting aspect of the paper is that the authors attempted to

separate the ancestry of North African samples into a pre-Neolithic
indigenous African component, and a residual component that
represents more recent gene flow into North Africa, from all sources.
The historic movement into North Africa has been fairly
cosmopolitan, involving sub-Saharan Africans, Arabs, Medieval
Europeans, Romans, Carthaginians and many other peoples. Snchez-
Quinto and colleagues used the ADMIXTURE program to try to sort
out a pre-Neolithic indigenous component and analyze that
specifically for Neandertal similarity.

Unsurprisingly, the fraction of estimated sub-Saharan African

ancestry in each population sample was inversely correlated with the
estimated Neandertal ancestry. That is, the more a population looks
like sub-Saharan Africans, the less Neandertal it has.

Here’s what’s surprising: When they sorted out parts of the genome in
Tunisians that ADMIXTURE determines to be most likely from pre-
Neolithic North Africans, they found these parts of the genome had
more Neandertal ancestry than typical of the CEU sample of northern
European ancestry. Is it possible that ancient North Africans had more
Neandertal similarity than today’s Europeans?

Snchez-Quinto and colleagues suggest that the Neandertal ancestry in

this population came in Upper Paleolithic times from the Near East.
That is possible, or some of the Neandertal similarity may reflect
ancient African population structure. Really I think we will have to do
a finer analysis of chromosome blocks to examine the subset of shared
Neandertal derived alleles that reflect introgression versus
incomplete sorting from the ancestral African population. It will be
very interesting to examine more closely the mixture of population
history within Egypt, through which most Near Eastern pre-Neolithic
population movement must have come.

The authors note that the distribution of Neandertal similarity outside

Africa increases with distance from Africa.

A previous study [26] observed that the similarity to Neandertals

increases with distance from Africa and suggested this could be
explained by SNP ascertainment bias plus a strong genetic drift
in East Asian populations. Nonetheless more complex,
population-biased, ascertainment schemes might have additional
effects (i.e bottlenecks), but these are not expected to
significantly increase the rate of false positives in admixture tests
[31]. The Tunisian population has been reported to be a genetic
isolate [17] so it is plausible that part of the signal detected is
actually due to genetic drift. However, this should not affect the
other North African groups in our study. Finally, given that SNP
arrays are based on common alleles and probably the relevant
admixture information is encoded within the rare and very rare
alleles, the potential bias, if anything, will underestimate ancient
hominid admixture signals, as shown in previous studies [2],[3].

This pattern was also observed by Meyer and colleagues earlier this
year Meyer:Denisova:2012, and I discussed it in my post on that paper
(“Denisova at high coverage”). Both papers note that ascertainment
bias may contribute to this pattern. I added that Meyer and colleagues
had assumed that genes found in sub-Saharan African populations
could not have come from Neandertals, which greatly biased their
estimates against Europe and West Asia, considering historical and
prehistoric gene flow across the Sahara and along the Indian Ocean
coast. So I’m not yet accepting the relative numbers of Neandertal
ancestry from different populations, as we don’t know that they have
all come from consistent assumptions. In particular, an elevated
amount of Neandertal ancestry in China – this paper puts it almost as
double the amount of Neandertal ancestry in northern Europeans – is
unlikely. There is no pattern of bottlenecks that can give rise to that
excess without additional population mixture, and hard to see where
such population mixture would have happened without also affecting
the ancestors of Europeans. Instead, we have some work to do in
reducing the biases on these comparisons.

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John Hawks is the Vilas-Borghesi Distinguished Achievement

Professor of Anthropology at the University of
Wisconsin—Madison. I work on the fossil and genetic record of
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