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Plural Lineages

*/Plural Lineages in the Human mtDNA Genome/*  

At the time I wrote */Age and Origin of the Human Species/*,
published research on the mitochondrial genome could not support
conclusions regarding human origins. Accordingly, I had to leave it an
open question. The cited research by Awadalla, Eyre-Walker, and others,
was challenged. Innan and Nordborg review the follow-on studies of
recombination.                                                   
http://walnut.usc. edu/~magnus/papers/InnanNordborg02-MBE.pdf
<http://walnut.usc.edu/~magnus/papers/InnanNordborg02-MBE.pdf>
Bottom line, there may well be some recombination, but you can't prove
it the way Awadalla tried to.

For the purposes of this discussion it isn't necessary to even
understand what recombination in mtDNA means, let alone the details of
how it is accomplished: we can simply treat it as an 'object' in this
analysis.

There has been unanimous and vociferous insistence in the media, on
one critical afrocentrist assumption: all modern human mtDNA is 'so
similar' that it *had* to have come from a single woman. This is known
to the public as the 'African Eve' theory, and researchers speak of the
same idea as 'a single genealogy for the mtDNA genome'. Far from
/proving/ the out-of-Africa theory, that assumed 'single source of all
modern mtDNA' is an absolutely *necessary* pre-condition for their
theory of afro-replacement to be true. However, *there is a /fundamental
reason/ to reject the claim that all human mtDNA is *'*so similar*'*
that it must come from one woman!*

Consider this sentence, [italic emphasis mine] from the first
paragraph of the Innan & Nordborg paper, *"The argument for
/recombination/ is based on the observation that the pattern of
polymorphism in mtDNA is incompatible with a /single genealogicaltree/
and /unique mutations/."* Thus, there are three things that might
account for the observed pattern of polymorphisms: 1) recombination, 2)
more than one lineage, or 3) multiple mutations at /many/ sites. Look at
Figure 2 <#Fig.2 minus text.jpg>of the Innan paper and you will see that
the possibly recombined or repetitively mutated sites are scattered
throughout the genome, and do not occur only in the hypervariable
region. Note that the quote from Innan & Nordborg implies that *the
/less/ recombinationor repetitive, same-site mutation has affected the
mitochondrial genome, then the LESS likely it is that there is a
/single/ genealogy for the human mtDNA genome. *In other words, unless
there has been enough repetitive mutation or recombination to account
for the observed pattern of polymorphism, then *not all* mtDNA is from
the same source, as claimed by proponents of the 'African Eve' or
African radiation-and-replacement theories.

On the other hand, *the more recombination, or repetitive mutation
that has occurred, then the more Eve*'*s age has been
under-estimated*/./ That is true because the effect of *either* repeated
mutations at one site *or* recombination is to make the mtDNA genome
appear *younger* than it really is. If we knew Eve's era from historical
or anthropological data, we could compare that date with the one derived
from the mtDNA coalescence algorithm. The difference between the
calculated coalescence result and the historical date would reveal the
combined effect of recombination and repetitive mutation. *If that
combined effect is obviously insufficient to account for the observed
pattern of polymorphism, then we may infer a plural genealogy for the
human mtDNA genome. *

There is nothing in the historical or anthropological record to
independently establish the era of (a supposed) human speciation   in
Africa. However, the situation in Eurasia is very different. There we
can calibrate the coalescence date of Eurasian strains of mtDNA with an
historical event, anthropological evidence, and research on the human
y-chromosome. Thus we can infer the effect (hence extent) of
recombination and repeated mutations, by comparing those other dates
with the result of the mtDNA coalescence calculation. *If the fit on all
these dates is fairly close* we can be assured that little recombination
or repetitive mutation has occurred, hence *the observed pattern of
polymorphism must be interpreted to reveal plural genealogy for the
mtDNA genome.*

Refer to the Mishmar paper at,                             
http://www.pnas.org/cgi/reprint/100/1/171.pdf (second full paragraph,
right-hand column, on the first page) for a brief description of the M
and N mtDNA lineages. Technically, one can't say that these are
'Eurasian specific' lineages, /only/ because they have found their way
into the African population. Note Mishmar's admission concerning the
afrocentrists' assertion that M and N evolved/diverged in North Africa.
This paper's authors come about as close to admitting that is
implausible as they can, while remaining politically correct and
afro-orthodox. On the afro-view, M and N lineages diverged from the
African Eve's lineage, while on my view they are the oldest surviving
Eurasian lineages. One's view as to the origin of the M and N lineages
doesn't affect the argument I am making in regard to determining the
relative contribution of repeated mutation and/or recombination versus
plural genealogy.

*     Mishmarcalculates the M and N lineages are /both/ 65,000 years
old, *and there was a lot going on in Eurasia around -65 kyr. *The last
common /paternal/ ancestor of Europeans lived at -59 kyr*, as calculated
from y-chromosome data. So we have a date for the male counterpart of
Eurasian Eve, /calculated from a different genome/ at a date within 10%
of agreement. Then, 'modern' *human artifacts are found in Eurasia by
-50 kyr.* Allowing for the fact that it is unlikely that we have found
the very first artifacts, and that people may have been genetically
modern for awhile before developing human (Homo /sapiens sapiens/)
culture, those dates are in remarkable agreement. Add to that,
*radiation into Australia by anatomically modern humans* may have
occurred before -60 kyrs, and no doubt that radiation took some millennia.

It begins to look like that -65kyr coalescence date is right on
target, and we could claim there is /no/ influence from recombination
and repeated mutation, so all the sites reflected in Figure 2 are
evidence for plural genealogies: QED! However, that would be
disingenuous, because I believe there has been /some/ recurrent
mutation, though it is possible they have fully accounted for it in
their model, and /some/ recombination, which they probably have /not/
explicitly factored in. So, I would expect that coalescence date to be a
little more recent than the era of a genetically significant event,
which actually *caused* modern humans to differentiate from a relatively
advanced population of archaic sapiens.

One reason we can expect the loss of lineages existing before the
modern type differentiated, is that there could have been a population
'bottle-neck' associated with speciation itself. Moreover there must
have been a severe population loss in temperate or higher latitudes when
Mt. Toba erupted around -74kyrs and caused a nuclear winter in Eurasia.
That savage selection event alone would account for the loss of archaic
Eurasian mtDNA lineages. *It may be significant that the two oldest
Eurasian mtDNA lineages are the same age. *The fact that they both date
from the same era makes it more plausible that ancient lineages were
lost in a specific selection event and/or population bottleneck rather
than only through 'lineage sorting'. It is comparatively *un*likely that
/two/ mtDNA lineages would /simultaneously/ diverge from a putative
African lineage, and /both/ (but /only/ they) migrate from Africa and
survive to the present. It is far more reasonable and parsimonious to
assume that no archaic Eurasian lineages survived two severe
bottlenecks, and subsequent lineage sorting, in the indigenous Eurasian
population.

So, even if we assume that the actual population constriction
occurred prior to the coalescence date, and associate it with the
obvious selection event of Toba's eruption, the -65kyr coalescence date
still calibrates quite closely. If we compare the dates, we note that
-65 kyrs is only about 12% less than the putative genetically
significant date of -74 kyrs. So we can see that both recombination and
repeated mutations can only have had a small effect on the calculation
of a coalescence date, hence there are *not* many sites in the mtDNA
genome that have experienced recombination or repeated mutation. *But,
look at Figure 2 <#Fig.2 minus text.jpg>,* where it is evident that
*many* of the sites show evidence of *either *recombination or repeated
mutation, *or else they are evidence of more than one genealogy for the
mtDNA genome!* Accordingly, *most* of the sites graphed in Figure 2
/*must* be considered as evidence for more than one mtDNA genealogy./
Therefore, *M and N lineages are /not /derived from the African genome,
but represent the oldest, surviving lineages of the Eurasian types.*
Hence M and N are Eurasian specific lineages that only entered Africa
through radiation, rather than coming /from/ Africa 

In conclusion, *recombination and repetitive mutations are /not
enough/*(by a wide margin) *to explain the observed pattern of
polymorphisms in the mtDNA genome.* Therefore, *there is /more than one/
genealogy*: there are two Eurasian maternal lineages, associated with
the speciation of modern humans (Homo /sapiens sapiens/) in Eurasia, and
another, African lineage. This falsifies the 'Afro-radiation and
replacement' theory, and the politically correct shibboleth that 'we are
all Africans'. As explained in */Age and Origin of the Human Species,/*
the evidence already pointed to a recent, Eurasian origin for modern
humans. *Only the /assertion/ of a single genealogy for mtDNA could be
construed as evidence of African replacement, and that assumption is
revealed as unjustified.*

Mishmar et al, is probably correct to attribute variation, in
lineages derived from M and N, to natural selection. One supposes they
theorize that mtDNA selection took place in the last 50kyrs (Wallace's
date for an African radiation, quoted in NYT, "Ice Age Ancestry") in
order to accommodate their theory to the constraints of assuming an
African origin for modern humans. However, it is more plausible that
such selection took place in very ancient times (when pre-human species
were adapting to a cold climate) and was only *retained */at high
latitudes/, among people living at low culture levels, as the
adaptations come at a fitness cost, and thus were lost when and where
physical adaptations were superseded by elaborated clothing and shelter,
in the temperate zone and the recent era.

FIG. 2 Evidence for recurrent mutation
or recombination (or both)  in human mtDNA (data of Ingman et al.
2000).  Each point represents the comparison between a pair of
polymorphic sites. The point is black if the pattern of polymorphism for
the pair of loci is such that either recombination must have occurred
between the loci or recurrent mutation affected at least one of the
loci. The point is white otherwise.

If recombination has occurred, and (importantly) the probability of
recombination increases with distance between sites, white points are
expected to be clustered along the diagonal (because recombination is
less likely to have effected closely linked sites). Recurrent mutations,
on the other hand, might be expected to give rise to a pattern that does
not depend on the distance from the diagonal, leading to black "crosses"
against a white background. The D-loop is visible as a cluster of such
crosses in the upper right corner (position 0 corresponds to the first
position after the D-loop)

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