Neanderthal ancestry?
Sat, 20 Nov 1999 11:56:41 +0000

Being finally settled into Houston, I am beginning to catch up on articles
which have been published over the past year.There have been a spat of
articles which shed light on the past history of human populations which
should be brought to the attention of those interested in the relationship
between modern humans and ancient populations. One article is Magnus
Nordborg, "On the Probability of Neanderthal Ancestry," Am. J. Human
Genetics, 63(1998):1237-1240

This is an analysis of the conclusions which have widely and popularly been
drawn concerning the supposed proof that Neanderthals contributed nothing
to the human genome. The conclusion is based upon the work of Matthias
Krings, who extracted Neanderthal mtDNA (Matthias Krings, et al.,
"Neandertal DNA Sequences and the Origin of Modern Humans," Cell,
90:19-30). The mtDNA is definitely not a modern haplotype, and this is
widely used by those who don't understand genetics as proof that
Neanderthals and humans didn't interbreed. Krings et al did not draw that
conclusion yet others have tried to do it.

Nordborg sets up his mathematical model with:

"Assume that Neanderthals were an isolated population for a long time,
until they encountered anatomically modern humans at time tm and merged
with them to form a single, randomly mating population, with a fraction, c,
of the population being Neanderthal. Then, the so-called replacement
hypothesis is simply that c = 0. The data in figure 1 are perfectly
consistent with this scenario; that is, the possiblitiy that the data is 1,
without interbreeding. However, this provides support for replacement only
to the extent that alternative scenarios can be shown to have a much lower
probability. Therefore, the probability of the data must be found for
different values of c>0." Magnus Nordborg, "On the Probability of
Neanderthal Ancestry," Am. J. Human Genetics, 63(1998):1237-1240, p. 1238

He then concludes:

"In cases for which we expect few ancestors at tm, the probability that
none of the 986 sampled mtDNAs came from the Neanderthal fraction of the
population does not differ much from the probability that none of the
currently existing mtDNAs did so. This latter probability is equal to the
well-known probabilityt hat an allele starting at frequency c is lost,
through drift, by time tm. Under this assumption, another question of
interest can be addressed: Given that extant humans do not carry
Neadnerthal mtDNA, what does this suggest about the rest of the genome?
For the constant-calculation-size model, for example, assume that
Neanderthals and anatomically modern humans merged 1 coalescent-time unit
ago (equivalent to tm = 68,000 years, for the population size used above)
and that Neanderthals composed 25% of the new population. Then the
probability that all Neanderthal mtDNA was lost through drift is .52 (the
probabiliyt that Neanderthal mtDNA was not in the sample [calculated as
above] is the same, to two decimal places): At the same time, each nuclear
locus, for which the coalescence-time scale is four times slwoer, would
have lost all Neanderthal alles with probability .1 and would have become
fixed for them with probability 9.8 x 10^-5. Thus 90% would still be
segregating for Neanderthal alleles.
"In conclusion, data such as those shown in figure 1 shed little light on
the issue of replacment versus interbreeding, unless the number of
ancestors of the sample was large throughout the periods of interest. This
is part of a general problem: in order to estimate gene flow, a large
sample is needed, and, in order to estimate ancient-gene flow, a large
ancient sample is needed." According to coalescent theory, large ancient
samples usually cannot be obtained by the sampling of modern pupulations."
." Magnus Nordborg, "On the Probability of Neanderthal Ancestry," Am. J.
Human Genetics, 63(1998):1237-1240, p. 1238-1239

This means that even with 25% of our ancestors being neanderthals, we would
have only a coin toss chance of having their mtDNA! Mathematically, we
could have NO Neanderthal mtDNA yet still have a significant fraction of
Neanderthal nuclear DNA! And he points out that we don't have enough data
to assess the ancient gene flow among ancient populations.

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