Reconsideration of the “Out of Africa” Concept as Not Having Enough Proof

doi:10.4236/aa.2014.41004

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Advances in Anthropology

2014. Vol.4, No.1, 18-37

Published Online February 2014 in SciRes (http://www.scirp.org/journal/aa) http://dx.doi.org/10.4236/aa.2014.41004

Reconsideration of the “Out of Africa” Concept as

Not Having Enough Proof

Anatole A. Klyosov

The Academy of DNA Genealogy, Newton, USA

Email: aklyosov@comcast.net

Received November 25th, 2013; revised December 23rd, 2013; accepted January 18th, 2014

Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the

original work is properly cited. In accordance of the Creative Commons Attribution License all Copyrights ©

2014 are guarded by law and by SCIRP as a guardian.

This is an overview of the “Out of Africa” (OOA) concept and the concept is based upon experimental

data. The article shows that said concept is based on data which are—as a rule—interpreted by the OOA

proponents in a one-sided manner, that is to “prove” the OOA concept. The Y-chromosomal haplogroup

tree in its most ancient part includes a number of nodes-haplogroups, which in the current classification

are named A0-T, A1, and A1b. Bearers of those haplogroups are not identified in Africa or elsewhere.

However, those three haplogroups are assigned by the proponents of the OOA “by default” to be the

“African” haplogroups, which “automatically” makes all non-Africans “African descendants”. In fact,

each of the three haplogroups represents a split into African and non-African haplogroups. As a result, the

evolution (Y-chromosomal) tree produced at least five waves of migrants to Africa (haplogroups A00, A0,

A1a, A1b1, and B), while the rest of the tree consists of four non-African (by origin) haplogroups, that is

A0-T, A1, A1b, and BT, along with the downstream subclades of the latter. The tree is confirmed by the

analysis employing STR (Short Tandem Repeat) and SNP (Single Nucleotide Polymorphism) mutations

of the Y-chromosome. Indeed, according to many data, the tree shows a deep split between African and

non-African (by origin) lineages. The last split, from haplogroup A1b (into African A1b1 and non-Afri-

can—by origin—B) occurred 160,000 ± 12,000 years before present. Haplogroup B is by origin a non-

African haplogroup, which is very distant—time-wise—from haplogroups A, by at leas t 250 - 30 0 thou-

sand years, an d could not possibly have descended from haplogroups A 1a or A1b1, or their subclades. A

similar pattern is observed with the mtDNA haplogroup tree, which shows a deep split between African

L0 and non-African (by origin) haplogroups L1-L 6. T he article sh ow s how recent OOA studies (as well

as earlier ones) employ biased interpretations to artificially “prove” the OOA concept. The a r tic le shows

that the same data can be—and more justifiably—interpreted as incompatible with the OOA concept, and

giving support for a “into Africa” concept. It seems that from times of Neanderthals (seemingly having

pale skin and fair hair, based on the identified Neanderthal MCR1 melanocortin receptor), our ancestors,

of both Africans and non-Africans current populations, lived outside of Africa, apparently in Eurasia or

maybe in Europe.

Keywords: Y-Chromosome; mtDNA; Mutations; Haplotypes; Haplogroups; STR; SNP; Out-of-Africa;

Into-Africa; SHV-1 (Simplex Herpes Virus)

Introduction

The origin of humans is one of the most intriguing and ex-

citing subjects in science, philosophy, view of life. And, at the

same time, it is one of the most complicated ones.

The thing is that there was not a single and direct experiment

thus far which would firmly and reliably answer where on the

planet and when our direct ancestor, fitting the anthropological

description of a species Homo sapiens and/or the term “ana-

tomically modern human” (AMH), first appeared. Every term

in the above sentence is not clearly defined and is in fact

“floating”. When fossils are found, how to determine if t hey

belong to “the most ancient” Homo sapiens and/or AMH, when

tomorrow some more ancient relics might be found? How reli-

able are (paleo) archaeological dates, which are commonly not

reliable at all, and are always disputed by other specialists (see

the last section of this paper)? There are dozens of anthropo-

logical features that, one way or another, describe the species

Homo sapiens and the AMH; however, the theory is one thing

(albeit there is no classification which would have been em-

braced by all the experts), b ut to apply all those features con-

currently, in reality, is practically impossible. Typically, onl y

some skeletal fragments of an ancient hominin are found, and

for the most ancient bone remains some archaic features are

typically observed (see below). The next step is a matter of

interpretation, often a rather arbitrary choice whether it was

Homo sapiens or its predecessor or something else . Those in-

terpretations are often rather far from being unbiased.

Here a judgement and honesty of a scientist step in. Bets are

high—every new skeleton or its fragments, that are pronounced

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A. A. KLYOSOV

“the most ancient of all known” and related to Homo sapiens or

AMH, becomes the worldwide sensation, with all due conse-

quences such as prestigious scientific awards, large financial

grants, elections to prestigious academies, etc. Unfortunately,

these enticements may foster distortions, incomplete or incor-

rect data assessment, and may resu lt in biased conclusions. The

new and phenomenal discovery, described in academic and

other editions, is then eagerly sensationalized by the popular

press. Datings are often exaggerated, archaic features are re-

touched, and as a result it becomes comp licated determining

where the real data is. Cross-examinations, which are badly

needed in many cases, are very rare. This is the most obvious in

the area of “Out of Africa”, where for some mysterious reason

very m any authors seem to exhibit extrapolated, incomplete, or

otherwise overinterpreted data to show that the “Out of Africa”

concept has no alternatives, as reflected by standard repeats at

the beginning of many papers—“As it is known, anatomically

modern humans came out of Africa”. Here are a few out of

many examples:

“Human origins: out of Africa” (title of the paper; Tattersal,

2009).

“Human evolution out of Africa” (from the title of the paper;

Stewart & Stringer, 2012).

“The origin of patrilineal diversity in Africa” (from the title

of the paper; Cruciani et al., 2011).

“African origin of modern humans in East Asia” (from the

title of the paper; Ke et al., 2001).

“…anatomically modern humans arrived in Europe from an

African source at least 45,000 years a go” (Moorjani et al.,

2011).

“Modern humans are generally thought to have originated in

eastern Africa” (Henn et al., 2011).

“It is now well accepted that anatomically modern humans

(AMH) originated in Africa (Hammer et al., 2011).

“Africa, the ancestral homeland of all modern humans” (La-

chance et al., 2012).

“…the expansion of anatomically modern humans out of

Africa, at approximately 44,000 years ago” (Underhill et al.,

2000).

“Modern humans evolved in Africa around 200 thousand

years ago” (Campbell and Tishkoff, 2010).

“…anatomically modern humans originated in a small, iso-

lated population in Africa 150,000-200 thousand years ago”

(Patin et al., 2009).

“sub-Saharan and northeastern Africa, the most likely source

region and corridor to the rest of the world” (Arredi et al.,

2004).

“an expansion originated in Africa” (Ramachandran et al.,

2005).

“There is a broad concensus that Africa was the birthplace of

Homo sapiens—and what have been referred to as “anatomi-

cally moden humans” (AMH) (the first sentence of the paper,

Rito et al., 2013).

There are d ozens and probably hundreds of others, and there

is no need to quote more of them. As this paper shows, they are

incorrect, or unjustified, or ungrounded, or j ust uncritically

repeat each other. According to the authors, the “Out of Africa”

ancient migration might have happened some 50,000 years ago

(ya), or 70,000 ya, or 100,000 ya, or maybe 150,000 ya, or

200,000 ya, etc. This paper illustrates what kind of data those

authors actually obtained, and how they (data) are b ent to

“prove” the “Out of Africa” exodus.

Before the 1980s there was almost no discussion on the

“African origin of modern man”, the subject was rather mar-

ginal. There were two reasons why those discussions could n ot

have been considered seriously. First, it was agreed upon that a

rather remot e ancestor of the modern man was Homo erectus,

which had appeared more than a million years ago, possibly in

Africa, however, it was known that it then spread all over Eura-

sia. Therefore it was recognized that Homo sapiens could ha ve

appeared in any region of Eurasia. Second, it was recognized

that Neanderthal, the nearest cousin of AMH, had not lived in

Africa. Therefore a common ancestor of the AMH and Nean-

derthal, who lived on different accounts between 300 and 600

thousand years ago, could not have lived in Africa as well.

Neanderthal had a fair (pale) skin (see below), therefore an

African origin of man would require an arrival of a fair-skin

direct ancestor of AMH in Africa, say, 300 - 500 thousand

years ago, an evolution-driven acquisition of a black skin, oth-

erwise he would not have survived in Africa, then his exodus

from Africa and an independent back conversion of his black

skin to a fair one . To defend such an awkward suggestion a

smart hypothesi s has been invented about a rol e of vitamin D in

an evolution-driven conversion of black skin to white in the

course of the suggested migration of humans out of Africa.

Clearly, there could not have been any possible mating of the

out-of-Africa black migrants with fair-skin people outside of

Africa, since they w ere not supposed to be any at that time.

Said hypothesis of vitamin D-driven conversion of blacks to

whites has never been tested or experimentally confirmed, and

still remains a hypothe sis.

The Cann et al. (1987) “Seminal” Paper on

“Out of Africa”

As a result, un til the middle of 1980s, a talk on the African

origin of AMH was not considered really serious. An important

event happened in 1987, when Nature published a paper by

Rebecca Cann and co-authors (Cann et al., 1987) from Univer-

sity of California, Berkeley, entitled “Mitochondrial DNA and

human evolution”. The paper was rather weak not only by con-

temporary criteria, but also by those, in the 1980s, and o ne can

only wonder how that paper got through the Nature reviewers,

if there were any. It would be enough just to mention that the

Abstract, published prior the main text, said that the mtDNA

studied in the paper, “stem from one woman who is postulated

(!-AK) to have lived about 200,000 years ago, probably (!-AK)

in Africa”.

The paper opened the gates, figuratively speaking. An ex-

citement of the mass media that the Africans happened to be

our ancestors was overwhelming. The ancient African woman,

mother of all, was immediately baptized “mitochondrial Eve”,

and world leading magazines have provided their glossy covers

for that informations and assumed portraits of the “Eve”. Since

then a non-stop treatment of t he public opinion continues, if it

is not growing. This has become a commonly attested opinion,

a consensus, to argue with which is alike arguing over a verdict

on the thermodynamically impossible perpetuum mobile.

So, what was in the paper by Rebecca Cann et al. in 1987?

How it all began? Let us take a look.

The experimental part of the paper presents a mapping of

mtDNA samples of 145 plac entas (mainly from US hospitals)

and two cell lines derived from a B lack American and a South

African, as follows:

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A. A. KLYOSOV

-20 Africans (representing the Sub-Sahara region, as the pa-

per stated); however, “only two of them were born in sub-Sa-

haran Africa, the other 18 are Black Americans, who bear many

non-African nuclear genes probably contributed mainly by

Caucasian males”, according to the paper,

-34 Asians (originated from China, Vietnam, Laos, the Phil-

ippines, Indonesia and Tonga),

-46 Caucasians (originating from Europe, North Africa, and

the Middle East),

-21 aboriginal Australians, and

-26 aboriginal New Guineans.

An average of 370 restriction sites were surveyed, repre-

senting about 9% of the 16,569 base-pair human mtDNA ge-

nome. The authors estimated the extent of nucleotide sequence

divergence for each pair of individuals, which ranged from 0 to

1.3 substitutions per 100 base pairs, with an average sequence

divergence of 0.32%. However, the authors wanted to show that

these differences were the largest ones in the Africans, t here-

fore all five populations were divided into “region-specific

clusters”, taking into account pairwise differences in each pop-

ulation. It turned out that:

-46 European mtDNA split to 36 clusters,

-34 Asian mtDNA split to 27 clusters,

-21 Australian mtDNA split to 15 clusters,

-26 New Guinean split to 7 clusters,

-However, 20 African mtDNA have postulated to be in only

one cluster, “assuming that Africa is the source, there is only

one African cluster” (quotation from the paper).

Those who understand what the authors did-probably would

not want to read further. Because then the authors began to

calculate which population is the oldest one, and this was the

main purpose for splitting the populations into clusters. The

idea was to calculate age of populations, taking into account the

divergence between clusters within each population, and the

Africans gave, of course, the highest “age”, since they were

postulated to have only one cluster. As a result, the diversity

(mean pairwise distance within clusters) was as follows:

-Africa 0.36%

-Asia 0.21%

-Аustralia 0.17%

-New Guinea 0.11%

-Еurope 0.09%

Then the authors translated those “divergencies” into years,

namely when the respective territories were populated (average

age of clusters). For these, the following “calibrated” chrono-

logical indications were taken: a minimum of 30,000 years ago

for New Guinea, 40,000 years ago for Australia, and 12,000

ago for the New World; from this, the mean rate of mtDNA

divergence between humans occurred between 2% and 4% (that

is 2 - 4 mutations per each 100 nucleotides) per million years.

From here, the authors calculated the average age of clusters as

-Africa 90 - 180 thousand years

-Asia 53 - 105

-Аustralia 43 - 85

-New Guinea 28 - 55

-Еurope 23 - 45

It was done in a rather crude way and using a circular argu-

ment, however, the authors obtained a reasonable set of ages

(partly due to the circular argument). As it will be shown below,

other authors, including the author of this paper, obtained more

direct figures for the African lineages to be started at 141,500 ±

15,600 ya (Cruciani et al., 2011), 160,000 ± 12,000 years ago

(Klyosov and Rozhanskii, 2012a), plus a few archaic African

lineages (haplogroups A0 and A00) at about 180,000 and

210,000 ya, respectively; Asian and European lineages com-

bined (haplogroup BT) at about 64,000 ya (ibid.), Australia—at

about 45 - 5 0,000 ya, and the most ancient bone residues of

AMH in Europe are dated by about 45,000 ya (Benazzi et al.,

2011; Higham et al., 2011). C learly, t he authors (Cann et al.,

1987) have done their calculations with accuracy plus-minus

100%, however, they got a reasonable pattern.

In the same way the authors (Cann et al., 1987) calculated

that the common ancestor of all surviving mtDNA types existed

143 - 285 kya, and since the common ancestor of all African

mtDNA lived, according to their calculations, 90-180 kya (that

is it was younger, though withing the margin of error), then “its

founders may have left Africa at about the same time”.

That is, the authors (Cann et al., 1987) have calculated t hat

non-Africans arose from a more recent common ancestor than

the African one, and postulated (sic!) that their ancestor came

out of Africa. The authors concluded, as indicated in the Ab-

stract, that one woman, a common ancestor of all mtDNA, “is

postulated (!) to have lived about 200,000 y ears ago (this is a

transformation of the value of 143-285 thousand years ago—

AK), probably (!) in Af rica”.

This was the beginning of an avalanche of similar papers,

similar in types of justifications of their conclusions. Very soon

that concept spread widely in the Western media and was

cheerfully supported by the mass media, by population genetic-

ists, in scien ce in general and among the “masses”. In almost no

time a general understanding was that the “Out of Africa”

theory was totally, completely, and irreversibly proven by strict

scientific means. In reality, there were practically no other ge-

netic justifications.

Alternative Explanations, and Typical Mistakes

of the “Out of Africa” Concept

This paper shows that dozens of academic genetic articles

which “support” the Out of Africa concept suffer from a simple

set of common mistakes. Data in none of them actually support

the concept. Most of the papers have good data and at least

questionable interpretations. Some h ave erroneous da ta and

interpretations. How could it have happened? Apparently, lack

of critical thinking. Lack of desire to analyze alternative solu-

tions. All which define good science.

A principal mistake which constantly haunts population ge-

neticists is that they typically take a higher “genetic diversity”

as an indication to the ancestry, compared to those populations

which ha ve lower “genetic diversity”. For example:

-Hellenthal et al. (2008), “the haplotype diversity is highest

in Africans,”

-Campbell and Tishkoff (2010), “Africa not only has the

highest levels of human genetic variation in the world but also

contains a considerable amount of linguistic, environmental

and cultural diversity.”

The list in fact can continue almost infinitely. In reality,

highest diversity does not by any means represent a homeland,

unless the homeland ha s been totally isolated and has not been

affected by populations from outside. New York City has a

higher diversity than Boston, but that doesn’t mean that New

York City is a homeland for Boston. Diversity quite commonly

is a result of mixing, and Africa is a home of highly mixed

populations, including quite ancient and rather recent popula-

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A. A. KLYOSOV

tions, migrated to Africa in the last few millennia (see below).

“Into Africa” migrations greatly increase the diversity there.

Bearers of R1b-V88, which arrived in Africa on its migratory

way along the Mediterranean Sea (Cruciani et al., 2010) and

their descendants who currently reside in Cameroon and Chad,

also contributing to diversity in Africa. So, diversity by itself

does not support the idea of a common homeland in this context.

Practically the same thing is expressed in a recent paper by Rito

et al. (2013): “… the region of highest diversity may differ for

different marker systems and, despite having been commonly

used as such, is not necessarily informative about the place of

speciation.”

Some academic papers appear from time to time which de-

scribe migrations “into Africa”. For example, a recent paper in

Nature in August 2013 (Hayden, 2013) describes migrations

into Africa 3000 and 900 - 1800 years ago. Did they add to the

“genetic diversity” in Africa? Sure they did. Furthermore, they

migrated to the Sub-Saharan region, where Cann et al. (1987)

sampled mtDNA and found a “high genetic diversity.”

The same is related to a common mistake which is exempli-

fied by Atkinson (2011) in a recent article in which he asserts

that “human genetic and phenotypic diversity declines with

distance from Africa ··· underpinning support for an African

origin of modern humans ··· local language diversity ··· points

to parallel mechanisms shaping genetic and linguistic diversity

and supports an African origin of modern human languages.”

This effort to shore up the Out of Africa hypothesis also fails.

Since haplogroups A and BT diverged from the same α-haplo-

group (Figure 1), this does not mean tha t the younger lineage

descended from the older. Our research shows that they parall el

to each other such as two te eth in the proverbial fork. They

descend not from each other, but from a common ancestor who

in this particular case was the α-haplogroup (A1b in the current

classification).

Haplogroup R1a (20,000 ya) and haplogroup R1b (16,000 ya)

(Klyosov & Rozhanskii, 2012b; Klyosov, 2012), arose in Cen-

tral Asia (ibid.). Both are younger than haplogroup A

(~160,000 ya) but they are not descended from haplogroup A.

A boy is not a descendant of hi s olde r brother. They b oth hav e a

common ancestor, which is their father. The fact that the In-

do-European (IE) languages are younger than the click lan-

guages does not prove that IE languages descended from click

languages or that Africa is a homeland of the languages of man.

Obviously, to consider “genetic diversity” one should know

the population genesis, their history, and not formally and “li-

nearly” compare their “diversity”. This is a systemic problem

with population studies.

A lower diversity in non-Africans compared to Africans is

explained in Figure 1. About 64,000 ya (64,000 ± 6000 ya)

non-Africans went through a severe population bottleneck.

Through some cataclysm, yet unidentified, almost all non-Af-

ricans have perished, and only a small group of them survived.

Y-chromosomal genealogical lineages of practically all present-

day non-Africans and some Africans (haplogroup B through T)

coalesce to that small group of survivors. Two hypothes es have

the highest rank—Toba eruption ~70,000 ya, the most violent

volcano eruption on Earth for the last 100,000 years, and cool-

ing (probably but not necessarily connected to the eruption) in

the Northern Hemisphere. According to climatologists, a cata-

strophy rank of the cooling is significantly higher compared to

the Toba eruption.

Figure 1 shows that the “diversity” of the left branch (the

Figure 1.

Haplogroup tree of the H. sa piens Y-chromosome derived from haplo-

types and subclades. This diagram shows the most recent common

ancestors (TMRCAs) of H. sapiens as described in this study. To pre-

pare this tree, 7415 haplotypes from 46 subclades of 17 major haplo-

groups have been analyzed. The timescale on the vertical axis shows

thousands of years from the common ancestors of the haplogroups and

subclades. The tree shows the α-haplogroup, which is ancestral to both

the African and non-African haplogroups (equivalent to A1b in the

curreny classification), its co mmon ancestor lived 1 60,000 ± 12,000 ya),

and the β-haplogroup, which is equivalent to haplogroup BT in the

current classification (its common ancestor lived 64,000 ± 6000 ya).

Haplogroups F through R (which includes T) represent Europeoids

(Caucasoids) who arose ~58,000 years before the present. The Mongo-

loid and Austronesian haplogroup C split ~36,000 ya; the Middle East-

ern haplogroups D and E split ~42,000 ya (Klyosov & Rozhanskii,

2012a). The tree does not show the archaic African lineages A00 and

A0 (the last has replaced the lin eag es A1 b o n th e lef t), wh ich are sho wn

on the updated tree in Figure 4.

Africans today) is higher compared to the right branch (non-

African), however, the African branch is not ancestral with

respect to non-African branch. Both have a common ancestor,

the alpha-haplogroup of about 160,000 ya. As one can see, the

figure explains all the data by Cann et al. (1987) without any

“Out of Africa” concept. Other proofs of the validity of Figure

1 will be shown.

Popularization of the “Out of Africa” Concept

Soon after the Cann et al. (1987) publication a figure of

70,000 ya appeared as a date of “Out of Africa” exodus of

AMH. That figure became a cliché in almost every article in

which the Out of Africa hypothe sis has been mentioned. In fact,

the dating was “floating” as well. In reality, none of the dates

was a product of serious calculations, if any calculations at all.

There was not any methodology of calculations of the “Out of

Africa” date, except those with a margin of error plus-minus

100% (at least), and even those were based on crude assump-

tions, as it was shown above with the example of the Cann et al.

(1987) paper. Here are a number of other examples of the dat-

ing:

“50 thousand years ago” (Jobling & Tyler-Smith, 2003).

“50 thousand years ago” (Thomson et al, 2000).

“50 - 60 thousand years ago” (Shi et al., 2010).

“50 - 60 thousand years ago” (Mellars, 2011).

“50 - 70 thousand years ago” (Hudjasov et al., 2007).

“50 - 70 thousand years ago” (Stoneking & Delfin, 2010).

“60 thousand years ago” (Li & Durbin, 2011).

OPEN ACCESS 21

A. A. KLYOSOV

“60 thousand years ago” (Henn et al., 2011).

“60 thousand years ago” (Wei et al., 2013).

“60 - 70 thousand years ago” (Ottoni et al., 2010).

“60 - 80 thousand years ago” (Forster, 2004).

“54 ± 8 thousand years ago” (Forster et al., 2001).

“60 thousand years ago” (Stewart & Stringer, 2012).

“45 - 50 thousand years ago” (Fernandes et al., 2012).

“50 - 65 thousand years ago” (Behar et al., 2008).

“50 - 60 thousand years ago” (Cann, 2013).

“60 thousand years ago” (Chiaroni et al., 2009).

“50 - 75 thousand years ago” (Patin et al., 2009).

“50 thousand years ago” (Edmonds et al., 2004).

“45 thousand years ago” (Moorjani et al., 2011).

“50 - 70 thousand years ago” (Xue et al., 2005).

“70 - 80 thousand years ago” (Majumder, 2010).

“40 thousand years ago” (Campbell & Tishkoff, 2010).

“50 thousand years ago” (Poznik et al., 2013).

“60 thousand years ago” (Rito et al., 2013).

“55 - 70 thousand years ago” (Soares et al., 2009).

“between 40 and 70 thousand years ago” (Sahoo et al., 2006).

“between 35 a nd 89 thousand year s ago” (Underhill et al.,

2000).

“between 80 and 50 thousand years ago” (Yotova et al.,

2011).

“between 50 and 100 thousand years ago” (Hublin, 2011).

“between 27 - 53 and 58 - 112 thousand years ago” (Carrigan

& Hammer, 2006).

“70 - 60 thousand years ago” (Curnoe et al., 2012).

“~110 thousand years ago” (Francalacci et al., 2013).

“200 thousand years ago” (Hayden, 2013).

In fact, there is no date which would have been justified and

supported by experimental data. Those datings above do not

make any sense. They were just made up.

Let us slow down with the critique, and take a look at what

do we have, regarding Africans and non-Africans. If present-

day non-Africans did not descend from Africans, then who

were their ancestors? Where did Africans come from? Whe re

did non-Africans come from? Figu re 1 shows that they had a

common ancestor (Y-chromosome) around 160,000 years ago.

Archaeology and paleoanthropology data of African skeletal

residue would not tell us much about African and non-African

origins. The y are interesting and educational, however, we do

not know if bearers of those bones had offspring, and not just

offspring but survived until our times. If not—they are not our

ancestors. T he y might belong to terminated lineages. Unless we

know haplogroups and haplotypes of those skeletal remains, we

know nothing on their contribution to the present d ay human-

kind. Besides, we do not know where bearers of those skeletal

remains came from. It might well be that their close ancestors

have migrated to Africa from elsewhere. Indeed, if “Out of

Africa” was possible, equally possible were “into Africa” mi-

grations, and we know that they occurred. Many datings of

ancient skeletal remains are incorrect, and some examples are

given bel ow. Many skeletal residues claimed as Homo sapiens

or “Anatomically Modern Humans” have noticeable archaic

features, and their assignment to Homo sapiens is questionable

or flatly incorrect (more about it in t he last section of this pa-

per). Many findings concern not skeletal remains but settle-

ments (claimed as those of Homo sapiens), sea or river shells,

stone tools. It is often unknown who left those artifacts, and red

ochre, found there, also does not mean much, since it is known

that Neanderthals used ochre for their purposes. Neanderthals

of Eurasia also employed stone tools.

The question regarding common ancestors of Africans and

non-Africans can be solved preferably by considering their

DNA. When data obtained are supported by archaeology and

anthropology, it is great, however, there are not much data;

nonetheless, let us look at them.

Data on DNA in the context of this stu dy can be considered

in three ways, which ideally must be compatible. They are: 1)

haplotypes and haplogroups of Y-chromosome of m en, 2)

mtDNA, and 3) genome dat a . The last set of data is actually a

pattern of practically irreversible mutations (SNPs) in the DNA,

which can be interpreted with respect of evolution of humans,

since it shows dynamics and direction of mutations in the

course of evolution. For example, genomes of Neanderthal and

present-day man show many identical mutations, which are also

present in the DNA of chimpanzee. It means that those muta-

tions were inherited from a common ancestor of chimpanzee

and man. Therefore, if we have SNPs which we see in Nean-

derthal but not in chimpanzee, it might mean that Neanderthal

is our direct ancestor. Those mutations are either not found or

they are questionable. The situation with Neanderthal as our

ancestor is not clear and conflicting data obtained earlier are

currently under reconsideration. Recently announced 1% - 4%

as allegedly inherited in modern man from Neanderthal are also

under reconsideration.

Africans and non-Africans ha ve plenty of common SNP mu-

tations from a common ancestor of Homo with chimpanzee.

Those SN Ps are not particularly interesting for a question

whether non-Africans have descended from Africans, or vise

versa. Those common mutations should be filtered out. Another

question does present a particular interest: do non-Africans

have SNPs which are observed in Africans but not in chimpan-

zee?

The above is a critical question, an answer to which repre-

sents a cornerstone in studying evolution of present-day hu-

mankind. An answer thus far is a resounding no.

What Do Actual Exp eri men tal Data Tell Us? An

Alternative and More Plausible Explanation

What do actual experimental da t a tell us on SNP mutations

in Africans and non-Africans? Let us begin with haplotypes and

haplogroups of man extrapolated to times more than 100,000

years ago; and we have to extrapolate since we do not have

experimental data on excavated haplogroups and haplotypes of

those times, in Africa and elsewhere. That is why the “Out of

Africa” concept and its “supportive” data are always based on

conjectures, extrapolations, and as we show in this paper, those

conjectures are alway s based on very questionable, or flatly

wrong assumptions. Furthermore, “Out of Africa” proponents

seem to not ha ve considered eq ually reasonable, alternative

explanations, as it is shown below.

We do not have experimental data for haplogroups and hap-

lotypes at more than 100,000 ya, because it is a very complex

technical (and scientific) task; in the course of those times hu-

man DNA is degraded almost completely, chemically and par-

ticularly under effect of microorganisms. DNA of a Neander-

thal (female) of 45,000 ya was isolated and sequenced; however,

to isolate and sequence, even partially, D NA of a man of

160,000 ya is a task, orders of magnitude more complex.

How do we do those “extrapolations”? One needs to deter-

mine haplotypes in a random selection of contemporary men, of

OPEN ACCESS

A. A. KLYOSOV

the Y-chromosome under study. A selection should be taken

from among bearers of certain haplogroups or their subclades,

that is among men which are united by a certain set of SNPs.

They are relatives, according to their common haplogroups or

subclades, and a set of their haplotypes allows us to calculate

rather reliably when their common ancestor lived.

For example, there is a good representative group of males

among contemporary Africans, which according to the ISOGG-

2014 (International Society of Genetic Genealogy) classifica-

tion form subclade A1b1b2b (third line from the bottom in the

tree of haplogroups A00/A0/A, see below). This tree shows the

hierarchy of haplogroup A subclades, t hat is, in a way, the evo-

lution of haplogroup A. The tree evolves via branching: the first

one which split off the trunk was the most ancient haplogroup

A00, its sub-branches (subclades) are unknown as yet. The

trunk continues with haplogroup A0-T, which split into two

subclades, A0 and A1; A1 in its turn split into A1a and A1b;

A1b split into A1b1 and BT.

Haplogroup BT (beta-haplogroup in Figure 1), as it will be

shown below, is very remote from haplogroups of the series

“A”, bearers of which now live in Africa. Those a re haplo-

groups A00, A0, A1a, and A1b1 with subclades, shown in the

haplogroup A tree below (to which haplogroup BT is added in

the lower part). Those four haplogroups can indeed be consi-

dered as the African ones—by origin or by arrival to Africa

more than 100,000 years ago. Other three haplogroups. A0-T,

A1, and A1b, have not been found in Africa (or elsewhere), we

see them only deep back in time, as ancestral haplogroups, each

split into an African lineage (A0, A1a, and A1b1, respectively),

and presumably non-African lineages (A1, A1b, and BT).

There is no data which allow to call A0-T, A1, A1b, and BT as

“African haplogroups”.

Let us take a look again, more specifically, how the haplo-

group tree branches, how each branch forms a fork, and how

one “tooth” of each fork leaves (migrates) to Africa, and anoth-

er stays elsewhere, and forms a next fork. In other words, mi-

grations to Africa have occurred by waves. The whole pattern

can be presented as a non-African “trunk”, which has produced

splits, one side of which were leaving to Africa. Those splits

can be tentatively numbered:

- Split 1: The trunk, which arose from common ancestors

with primates (chimpanzee, gorilla, orangutan, macaqua,

etc.) splits into Neanderthal (300 - 600 kya) and the rest of

the trunk; Neanderthal—as far as we know—was not of an

African Homo species, and the rest of the trunk, therefore,

was also presumably a non-African Homo species;

- Split 2: Around 210 kya the trunk split into the most ancient

(thus far) Homo sapiens haplogroup A00 (now African) and

the rest of the trunk (presumably non-African); all bearers

of A00, identified thus far, belong to an African tribe Mbo

in Cameroon, or are Afro-Americans, presumably des-

cended from the same tribe (Mendez et al ., 2013); t he last

paper did not mention their anthropology;

- Split 3: The trunk then reaches haplogroup A0-T (presume-

bly no n-African), which around 180 kya split into haplo-

groups A0 (now African) and A1 (presumably non-Afri-

can);

- Split 4: Haplogroup A1 split into А1а (presumably mi-

grated to Africa, though A1a bearers now live in Africa, in

the Midle East, an in Europe) and A1b (presumably stayed

not in Africa);

- Split 5: Haplogroup A1b split into A1b1 (presumably mi-

grated to Africa) and ВТ (beta-haplogroup in Figure 1),

which was not an African haplogroup and it is very remote

from them.

This series of splits was never under consideration by pro-

ponents of the “Out of Africa” concept. It has never been pub-

lished and discussed.

Now, let us present an important statement.

Splits 3, 4, and 5 occurred from haplogroups A0-T, A1, and

A1b, respectively.

-Split 3 produces A0, bearers of which now live in Africa,

and A1, bearers of which are not identified as yet. Non-Afri-

cans descended from A1, and have not descended from African

A0; A0 mutations are absent in non-Africans.

-Split 4 produces A1a, bearers of which now live in Africa,

and A1b, bearers of which are not identified as yet. Non-Afri-

cans descended from A1b, and have not descended from Afri-

can A1a; A1a mutations are absent in non-Africans.

-Split 5 produces A1b1, bearers of which now live in Africa

(as well as in the Middle East and Europe), and BT, from which

all non-African haplogroups descended, including haplogroups

the most numerous in Europe-R1a, R1b, I1, I2, N1c1. Most

Europeans and Asians descended from BT, and have not des-

cended from “African” A1b1. A1b1 mutations are absent in

most of non-Africans.

So, what is left from the “Out of Africa” concept?

In order to “prove” that anatomically modern ancestors of all

people on the planet came out of Africa, proponents of the

OOA concept claim all the three node haplogroups-A0-T, A1

and A1b “African”. The fact that none of them is found in

Africa is of no concern for the proponents. Af ter such a claim

the proponents say—look, all non-African haplogroups des-

cended from the African A0-T, A1 and A1b. The “Out of Afri-

ca” concent is “proven”.

This, of course, is not a proof. It is much more likely that

those three haplogroups are not African, and their bearers lived

elsewhere. Then a connection between an ancestor of a pale

skin Neanderthal (see below) and pale skin contemporary non-

Africans is easy to explain. Equally easy to explain migrations

of bearers of haplogroups A0, A1a, A1b1 to Africa, after they

split from the respective non-African haplogroups A0-T, A1,

A1b. Equally easy to explain huge time (mutational) distances

between African and non-African haplogroups, because they

descended from ve ry ancient (160,000 ya) common ancestors,

and not from each other; in the latter case the distances between

their haplogroups would be around 60 - 70 kya, and in reality

they are 250 - 300 kya, as shown below. Non-African lineages

principally could not descend from African ones, when the time

between them reaches 250 - 300 thousand years. The propo-

nents of the OOA concept constantly announce that the OOA

exodus was 60 - 70 thousand yea rs ago. They do not know that

the actual distance there is 4 - 5 times higher.

Therefore when I describe splits/forks above, I write “pre-

sumably non-African haplogroup” A0-T, A1, A1b.

As it is shown below, haplogroup BT is very remote time-

wise from haplogroups A and their subgroups. From the haplo-

types analysis it seems that a whole series of haplogroups,

namely A00, A0, A1a, and A1b1 ha ve moved to Africa from

non-African regions, locations of which remain unknown; most

likely they might have been in Europe or Asia. In other words,

there have been at least four “into Africa” migrations since

some 200,000 ya (haplogroup A00), then about 180,000 ya

(haplogroup A0), the n about 160,000 (haplogroup A1a), and

OPEN ACCESS 23

A. A. KLYOSOV

then about 70,000 ya (haplogroup A1b1). Of course, there have

been migrations into Africa at later times, described for exam-

ple, by Hayden (2013), which increased a high genetic diversity

in Africa. Those haplogroups of the A series and their down-

stream subclades, such as A0a, A0b, A0a1, A0a2, A0a1a,

A01a1b (see flowchart below), can be considered as “African”,

albeit not necessarily by appearance there, but since they live in

Africa now.

Let us consider subclade A1b1b2b-M13, which in the Hap-

logroup A FTDNA Project

http://www.familytreedna.com/public/Haplogroup_A/defaul

t.aspx?section=yresults

is the most numerous.

The subclade splits into two main branches of A1b1b2b,

Arabic and European. Who was a common ancestor of these

two branches and where did he live, we do not know, however,

as we have assumed above, he might have lived in Europe or

Asia, and his descendants c ould have moved to Africa. Or he

could equally have li ved in Africa and his

A common ancestor of Homo and chimpanzee

(...)

• Neanderthal

(...)

• A00 L1236

• A0-T L1085

• • A0 V148, V149

• • A0a L979

• • • A0a1 V150

• • • • A0a1a V151, V169, Р114

• • • • A0a1b L1289

• • • A0a2 L981, V203

• • • A0b L1035

• • A1 V168

• • • A1a M31, P82, V4

• • • A1b P108, V221

• • • • A1b1 L419

• • • • A1b1a V50

• • • • A1b1a1 M14, L968

• • • • • • A1b1a1a M6, M196

• • • • • • A1b1a1a1 P28

• • • • • • A1b1a1a2 L963

• • • • • • • A1b1a1a2a M114

• • • • • • • A1b1a1a2b P262

• • • • A1b1b M32

• • • • • A1b1b1 M28

• • • • A1b1b2 V160

• • • • • A1b1b2a M51

• • • • • • A1b1b2a1 P291

• • • • • • • A1b1b2a1a P102

• • • • • • • A1b1b2b M13

• • • • • • A1b1b2b1 M118

• BT V31, M91, SRY10831.1

descendants moved to South Arabia and Europe. The general

logic of the subclade t ree, described above, makes it unlikely

that a co mmon ancestor of A1b1 arose in Africa (see Split 4

and Split 5 above). What we do know is that available haplo-

types of the A1b1b2b-M13 subclade represent a rather shallow

(time-wise) branch, which apparently has passed a population

bottleneck. However, the available haplotypes provide a va lua-

ble source of information, since they place their branch into the

space of all haplotypes of mankind.

Analysis of those A1b1b2b haplotypes, performed with help

of very “slow”, most stable 22 markers of Y-chromosome

(Klyosov, 2011; Klyosov and Rozhankii, 2012a), shows that a

common ancestor of the Arabic branch of the subclade

A1b1b2b had the following base haplotype:

12 11 11 9 11 10 10 9 12 12 7 12 8 0 13 11 16 9 14 9 11 11

(A1b1b2b, Arabic)

while a common ancestor of the European branch had the fol-

lowing:

12 11 11 9 11 10 10 9 12 12 7 10 8 0 13 11 16 10 14 9 11 11

(A1b1b2b, European)

Three mutations between them place their common ancestors

to 3/0.006 = 500  536 generations apart, that is 13,400 years,

and their common ancestor lived about 13,400/2 = 6700 years

ago plus an average “age” of the two branches, which finally

makes about 7170 years to their common ancestor (principles of

calculations are described in [Kly osov, 2011; Kly osov and Roz-

hanskii, 2012a]; 0.006 is t he mutation rate constant for the 22

marker haploty pes, in mutations per haplotypes per conditional

generation of 25 years), with margins or error pl us -minus 5%.

Let us compare the above two base haplotypes with that for

the African haplogroup A00 (it was calculated based on 95

marker h aplotypes of men of Mbo tribe, who live in Cameroon

[Mendez et al., 2013]):

13 11 12 10 11 16 10 9 14 14 8 8 8 9 12 11 12 8 12 12 11 11

(A00)

Here we see a difference in 30 and 29 mutations, respectively,

which places their common ancestors (A00 and A1b1b2b) apart

by a minimum of 286 - 308 thousand years, therefore, their

common ancestor (that is, of haplogroup A00) lived about 210

thousand ya. A number of mutations correlates with time not

linearly, but exponentially, due to back mutations, and the cal-

culations should include a correction for back mutations

(Klyosov, 2009, 2012).

If we compare those base haplotypes for A00 and two

branches of A1b1b2b with that of haplogroup B (Klyosov and

Rozhanskii, 2012a)

11 12 11 11 11 10 11 8 16 16 8 10 8 12 10 11 15 8 12 11 12 11

(B)

then we see 29 mutations between A00 and B, and practically

the same—29 and 27 mutations, respectively—between B and

the A rabic and European branches of A1b1b2b. Thi s again

corresponds to 286 - 248 thousand years between common

ancestors of haplogroups A and B.

This tremendous distance between haplogroups A and B

cannot allow haplogroup B to descend from haplogroup A. The

two have a common ancestor, who lived about 160,000 years

ago (see Figure 1).

Thus, haplogroup B is very remote from haplogroup A, by

27-29-30 mutations. However, it is not very remote from Euro-

pean (to some extent) haplogroups R1a and R1b, by only 12

and 10 mutations, respectively, from their subclades R1a-Z280

and R1b-M269:

11 12 13 11 11 12 11 9 15 16 8 10 8 12 10 12 12 8 12 11 11 12

(R1b-M269)

12 12 11 11 11 11 11 8 17 17 8 10 8 12 10 12 12 8 12 11 11 12

(R1a-Z280)

This again is explained by Figure 1, in which haplogroups B

and R sit in the same cluster, and all of them are remote from

haplogroups A.

The base haplotypes of R1a-Z280 and R1b-M269 are sepa-

rated by only 8 mutations, whic h corresponds to t he time to

their most recent common ancestor, that is haplogroup R1, of

OPEN ACCESS

A. A. KLYOSOV

about 26,000 ya. A c ommon ancestor of haplogroup B lived

about 50,000 ya, and he did not descent from haplogroup A.

Haplogrops A and B possess two independent DNA-genealogy

lineages, which arose from the alpha-haplogroup 160,000 ya.

Debates of the Last Two Years over

Figure 1 above

When the paper which contained Figure 1 and its interpreta-

tion was publi shed in May 2012 in Advances in Anthropology,

it was met with total silence in academic media. There was not

a single objection or critique in academia, or any positive

comment, despite the paper having been downloaded 10,895

times (as of January 18, 2014, according to the AA counter).

However, active discussion among population geneticists took

place on related Internet forums. Specif ically, four main con-

clusions of the paper met negative reception among the popula-

tion geneticists:

1) African and non-African DNA lineages split about

160,000 ya, and there is a large corresponding “genetic” (muta-

tional) distance between them,

2) non-African DNA lineages did not descend from “African”

haplogroups A00, A0, A1a, and A1b1,

3) haplogroups A1, A1b, and BT did not come “Out of Afri-

ca”, and

4) there were not a ny “Out of Africa” migrations which

would have been derived non-African AMH from African

AMH. In reality, they both split from their common AMH

about 160,000 ya. There have been many “out of Arica” and

“into Africa” reciprocal migrations, as well as many “out of

Europe” and “into Europe” migrations, and “out of Asia” and

“into Asia” migrations, and none of them can be considered as

a deci sive one or the only one in shaping AMH, or Homo sa-

piens for that matter.

The most active forum critics have announced that Figure 1

and the respective conclusions totally co ntradict the “Out of

Africa consensus”, and equally conflict with all published dia-

grams, flowcharts, and haplogroup trees, obtained with Y-DNA,

mtDNA and genome studies. They hav e also announced that

non-African lineages descended from haplogroups A (and their

subclades), hence, African. They have announced t hat Figure 1

disagrees with the evolution of mtDNA, in which ancestors of

non-African (current) lineages also came out of Africa, which is

“logical”, since male and female haplogroups should have been

coming from Africa together, concurrently.

Each and all of those announcements were mistaken. As it

happens often, the opponents did not wa nt or could not under-

stand that ther e were not any contradictions or conflicts. The

data whic h they quoted were generally right, but the opposition

interpretations of the published “Ou t of Africa” studies were

incorrect. Let us consider it more attentively.

The Latest Book Human Evolutionary Genetics

(by Jobling, Hollox, Hurles, Kivisild, and

Tyler-Smith, 2014) Presents Right

Data but Wrong Conclusions

The new book, Human Evolutionary Genetics, by Jobling,

Hollox, Hurles, Kivisild, and Tyler-Smith (2014), chapter 9

“Origins of Modern Humans”, section “Mitochondrial DNA

phylogeny”, p. 304. Quotation: “This has some striking features:

Complete separation of African and non-African lineages”. T he

next section—“Y-chromosomal phyloge ny”, p. 305. Quotation:

“Although less detailed than the mtDNA phylogeny, its struc-

ture shows close parallels: Complete separation of African and

non-African lineages”.

As we see, there are not any contradictions with Figure 1

above. However, the authors of the book employ old interpreta-

tions, by quoting papers of 2000, on both mtDN A and Y-

chromosome. They consider Y-chromosomal haplogroup B

“African” (see calculations above that haplogroup B could not

possibly be “African” by origin, since it is tremendously distant

from haplogroups A), and continue that it “contains both Afri-

can and non-African lineages”. Is it a valid argument? Haplo-

group R1b also contains both African and non-African lineages

(Cruciani et al., 2010), and many R1b bearers lived for thou-

sands of years in Cameroon and Chad regions. It is not enough

to say “African” without defining, did they arise in Africa or

migrated there.

Figure 1 shows that haplogroup B forms a cluster with

non-African haplogroups, and we described above that hapl o-

group B is very remote from haplogroups A. So why do the

authors of the quoted book call haplogroup B “African”? Only

because many haplogroup B bearers live in Africa now. Former

Europeans live in America now, however, the y can hardly be

defined as Native Americans. If haplogroups contain both Afri-

can and non-African lineages, how may that be equated with

“Out of Africa”? Why not—equally logically—“into Africa”?

TMRCA for the branch conta ining both African and non-Afri-

can lineages is described in the book as 52 ± 28 kya (mtDNA)

and 31 - 79 kya (Y-DNA), while Figure 1 gives for the origin

of BT haplogroup 64 ± 6 kya. There is not any contradiction.

The same authors provide with the TMRCA for the entire

mtDNA phylogeny of 172 ± 50 kya, for the entire Y-DNA

phylogeny of 40 - 140 kya. Cruciani et al. in their recent work

(2011) gave the TMRCA for African lineages of 141.5 ± 15.6

kya. Figure 1 above (Klyosov and Rozhanskii, 2012a) shows

160 ± 12 kya for the split between African and non-African

lineages. There is not any conflict.

With respect to Y-chromosome the authors of the book

symmetr ically provide the same interpretations as those in the

case of mtDNA. If a branch contains both “African DNA”

(since their bearers live there now) and non-African DNA, it is

not enough to claim that they migrated “Out of Africa”. The

same conclusion, albeit in a more careful form, can be seen at

the end of the book’s chapter. The authors write on the OOA—

“Interpretations of almost all sources of evidence are hotly

debated and it is difficult to identify a consensus view about

many topics”. However, after it—“Genetic diversity is higher

in Africa than on other continents, which is consistent with a

longer period of evolution in Africa…”. Agai n, it is a typical

mistake of population geneticists. It should have been add-

ed—“… or a mix in Africa of many DNA-lineages from an-

cient to recent times”. Mixing gives diversity, not necessarily

“a longer period of evolution”.

Another quote: “Most phylogenies of individual loci show a

root in Africa…”. Do they? Phylogenies never show “a root”.

They show a direction of evolution, unrooted. “… this is seen

particularly clearly in the well-resolved phylogenies of mtDNA

and the Y chromosome”. In reality, it is shown below that the

well-resolved phylogenies of both mtDNA and th e Y-chromo-

some do not indicate “a root in Africa”. It is a common and

unjustified stretch, as Figure 1 above shows. The final conclu-

sion of the authors “The current consensus view is therefore …

an out-of-Africa model…” Is there really “consensus”?

OPEN ACCESS 25

A. A. KLYOSOV

An Apologetic Follow-Up of the Cann et al.

(1987) Paper

It is of interest to follow the development of “ideas” ex-

pressed in the Cann, Stoneking and Wilson (1987) paper, which

I have discussed above. A follow-up paper came out after four

years (Vigilant et al., 1991), with two former authors, Stone-

king and Wilson, along with three new co-authors, absent Cann.

This new paper (1991) informs, that the Cann et al. (1987)

proposal “that all contemporary human mtDNAs trace back…

to the ancestral mtDNA present in an African population some

200,000 years ago” was at first “rejected because of confusion

over conceptual issues”, and mentions “perceived weaknesses

of the Cann et al. study”. Among those weaknesses the authors

(Vigilant et al., 1991) count “it used an indirect method of

comparing mtDNAs…; used a small sample made up largely of

African Americans to represent Native African mtDNAs; used

an inferior method … for placing the common DNA ancestor on

the tree of human mtDNA types; gave no statistical justification

for inferring an African origin of human mtDNA variation; and

provided an inadequate calibration of the rate of human

mtDNA evolution”. In other words, its authors recognized the

weakness of the paper (Cann et al., 1997) tha t formed a ground

for the “Out of Africa” concept. However, the concept was

already accepted by the “consensus”, and it was too late to turn

it back. Therefore, the 1991 paper aimed at throwing the Cann

et al. (1987) paper out as a weak one, but justified the concept

itself.

So what was the “justification” aimed at showing that Afri-

can mtDNA is ancestral with respect to the non-Afri can

mtDNA in the follow-up paper? This is again a repetition of the

common fundamental mistak e by the proponents of the OOA

concept, that if one population is more ancient then the other,

the firs t must be an ancestral with respect to the second one.

My u ncle is old er than me, but he is not my ancestor.

In conclusion of the paper (1991), the authors wrote: “our

study provides the strongest support yet for the placement of

our common ancestor in Africa some 200,000 years ago”. In

reality, as the reader will now hopefully appreciate, that was the

“strongest support” that the surviving branch of people who

now live in Africa is more ancient than that of people who now

live not in Africa (see Figure 1). This “proof” has nothing to do

with an ancestry. For a verification of an ancestry, one has to

compare the SNPs and hapl otypes of the populations. The

authors of both the 1987 and 1991 papers did not compare any

haplotypes, as well as most population geneticists presently do

not.

SNP Mutations Show That Non-Africans Are

Not Descendants of Africans of Haplogroups A

and B. Instead, They Have a Common Ancesto r

of About 160,000 Years Ago

Let us take a look at a recent paper by Scozzari et al. (2012)

that some consider as an exemplary study of African genome

and justification of the “O ut of Africa” concept. Indeed, the

paper designed a new, upgraded African haplogroup/subclade

tree with a transition to the non-African part of the tree, that is

to CT haplogroup. The last part of the tree is represented in

Figure 1 by the right-hand side containing a set of lineages,

related to C to R2 haplogroups. Scozzari et al. call it “the recent

‘Out of Africa’ CT clade”. In conclusion, the authors claim—

“Our data provide a highly resolved branching in the Afri-

can-specific portion of the Y tree and support the hypothesis of

an origin in the north-western quadrant of the African conti-

nent for the human MSY diversity”. The Scozzari et al. (2012)

tree is shown in Figure 2.

Let us pay attention to some important features of the tree in

Figure 2. It starts (rather, cont inues the evolution trunk of hu-

man Y-chromosome) in the upper left-hand si de of the tree, and

immedia tely reaches the first fork at haplogroup A0-T (the

name of the haplogroup is not shown on the tree). We see a

split of A0-T into haplogroups A1b (it is A0 now according to

the new nomenclature) with its subclades, which go “up”, on

the top of the t re e, and A1, wh ich goes “down”. In other words,

we see a departure of a first African branch (A0) from the

“main tree”. None of non-African groups (haplogroup CT,

among them) descends from that departed haplogroup A0

(=A1b in the graph above). It should be noted that the Scozzari

paper employs an obsolete nomenclature (of 2011), the current

nomenclature (2013) uses A0 in place of the old A1b, with its

SNPs V148, V149 and others, listed in the upper pa rt of the tree.

Their positions are clarified in the haplogroup A tree above in

the text (section “What do actual experimental data tell us?).

The ne xt fork took place at haplogroup A1, into “African”

haplogroups A1a and A1a1 with its downstream SNPs M31,

Р82, V4, and others, on the one hand, and the res t of the tree,

on t he other. None of non-African groups (haplogroup CT,

among them) descend from the second “African” branch (A1a

and its subclades).

The third fork is represented by appearance of haplogroup

A1b in its current nomenclature. It sends asi de “African” hap-

logroups А2 and А3 (now they are A1b1a and A1b1b) with

downstream subclades; currently both of them are covered by

haplogroup A1b1 with its downstream SNPs V249/L419,

which further splits apart into subclades A1b1a-V50 (former

А2) and A1b1b-M32 (former А3), both are with their subclades.

Among the latter is subclade A1b1b2b-M13, haplotypes have

considered above, and consists of the Arabic and European

DNA lineages. Another branch of said fork of haplogroup A1b

is haplogroup BT, shown in the lower part of the tree in Figure

2. It is obvious that haplogroup BT does not descend from the

“African” haplogroups having index “A”, since all of them are

positioned in the upper part of the tree in Figure 2, which BT is

in the lower part. The word “African” we have to place in quo-

tation marks, since among their haplogroups and subclades are

the A rabic and European haplotypes; Europeans are mainly

from England, Ireland, Scotland, Turkey; Arabian branch is

composed mainly by haplotypes from Saudi Arabia, as well as

by haplot ypes from England, Switzerland, Finland, and other

countries.

One can notice, of course, that ancestors of bearers of the

contemporary European and Asian haploty pes of haplogroup A

could have migrated out of Africa; however, it can be equally

suggested that they could have migrated into Africa. Therefore,

those arguments do not support the “Out of A fr ica” concept,

they are rather mute. For some mysterious reason only the “Out

of Africa” alternative finds support among proponents of the

concept.

Figure 2 shows that the non-African haplogroup CT (th e

lowest line in Figure 2) does not descend from “African”

branches of haplogroup A, nor from haplogroup B with its sub-

clades. CT leaves aside all the “African” haplogroups. If we

follow the time direction (that is from left to right in Figure 2),

the mutation (SNP) flow, leading to haplogroup CT, comes

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A. A. KLYOSOV

Figure 2.

The deepest portion of th e hu man Y-chromoso me accord ing to Sco zzari et al.’s (20 12) paper. The internal structure of some haplogroup B sub-clades

is not shown (black triangles). One can see that more than a half of lineages are related to haplo group A, which th e autho rs (Scozzari et al., 201 2) call

all “African”, apparently by definition. All other subclad es, except one, are related to h aplogroup B, which the authors also call “African”, again by

definition. Haplogroup CT in the lower right-hand side contains, according to the authors of the study, 19 DNA lineages, all non-African. From

Scozzari et al. (2012) with permission.

from the main trunk of the Y-chromosome evolution, that is

from the short bar in the upper left part of the tree, then passes

through haplogroup A0-T (there are no indications that A0-T is

an “African” haplogroup); then through haplogroup A1 (simi-

larly, there is no indication that it is an “African” haplogroup);

then through haplogroup A1b, which is also non-African; then

through non-African haplogroup BT, and appears as haplo-

group CT. Thus, all three “African” branches (А0, А1а, А1b1)

on this evolution route split off from the “main trunk” (though

it is a relative term here) via the respective deviations, forks,

etc.

We have considered the Scozzari et al. (2012) paper in such

detail, because this kind of analysis is practically absent in the

literature. The typical manner is to show a tree, such as in Fig-

ure 2, and briefly announce that “it supports the ‘Ou t of Africa’

theory”. On the contrary, it does not support the “Out of Africa”

concept. There is no contradiction in Figures 1 and 2. They

both show the same dynamics of evolutionary development of

the haplogroups, namely their repeated split into “African” and

“non-African” branches. A difference between the trees in

Figures 1 and 2 is only in that the Figure 2 shows subclades of

haplogroup A in more detail, and Figure 1 shows haplogroups

between B and R2 in more detail. Also, Figure 2 (from Scoz-

zari et al.) lacks the chronological scale, that Figure 1 shows.

In order to illustrate the similarity of Figures 1 and 2, Figure 3

shows both of them, next to each other, oriented in the same

direction.

Both trees shown in Figures 1 and 2 do not reveal recently

discovered haplogroup A00, which arose around 210,000 ya. It

is shown in Figure 4, along with updated nomenclature. The

current nomenclature is given in accord with ISOGG-2014.

http://www.isogg.org/tree/ISOGG_HapgrpA.html

The pattern is now clarified. There is no contradiction or

conflict between the trees of Y-chromosome haplogroups

shown in Figure 1 (Klyosov and Rozhanskii, 2012a) and in

Figure 2 (Scozzari et al., 2012). All data as well as all known

others show a deep mutational difference and a deep separation

between African and non-Af rican branches (subclades, haplo-

groups), leading to a common ancestor of both, when moved

back in time. These data do not reveal an “African” origin of

AMH, at least during 30,000 - 500,000 ya. Instead, the data

show a split between African and non-African lineages about

160,000 years ago.

Let us take a look again at the above discussed paper by

Scozzari et al. (2012). At which moment did a statement of the

African origin of mankind appear there? What was it based

upon?

That “Out of Africa” statement appears as soon as in the

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A. A. KLYOSOV

Figure 3.

A comparison of haplogroup and subclades of the “African” lineages (the left part of both trees, from Figures 1 and 2), and

non-African (the tree at the top shows one combined lineage of haplogroup CT, and the tree at the bottom shows the extend ed

haplogroup BT). The tree at the bottom was published by Klyosov and Rozhanskii in May 2012, and the tree at the top was pub-

lished by Scozzari et al . in November 2012 . The tree at the top s hows that the series of “ African” haplogroup s split three times

in a row and depart from the non-African haplogroups, and that non-African haplogroups BT and CT do not descend from the

African ones. The tree at the bottom shows the same splits of “African” haplogroups from non-African (haplogroups on the

right), and indicates that the split of “African” (by the current location) from non-African occurred about 160, 000 years ago.

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A. A. KLYOSOV

Figure 4.

Haplogroup tree of the H. sa piens Y-chromosome derived from haplo-

types and subclades (see Figure 1) with an addition of the recently

discovered haplogroup A00, and with an updated nomenclature of

haplogroups and subclades compared with those in Figures 1 and 2.

The timescale on the vertical axis shows thousands of years from the

common ancestors of the haplogroups and subclades. The tree shows

the α-haplogroup, which is apparently equivalent to haplogroup A1b in

the current nomenclature, and is ancestral to both the African and

non-African haplogroups (its co mmon ancestor lived 160,000 ± 12,000

ya), and the β-haplogroup, which is equivalent to haplogroup BT in the

current classification (its common ancestor lived 64,000 ± 6000 ya).

second paragraph of the introduction, and informs on “the re-

cent ‘out of Africa’ CT clade [15]”. What was the reference [15]

which allegedly proved the state ment? It was the paper “The

1000 Genomes Project Consortium (2010) A map of human

genome variation from population-scale sequencing. Nature,

467, 1061-1073”, which does not mention “out of Africa” nor

Africa at all. It does not mention “CT clade”.

The Scorzarri (2012) paper authors (and others they refered

to) have identified some African bearers of subclades:

A0a1-V150, A0a 1a-P114, A0a1b-V151, A1a-M31, A1a-V53,

A1b1a1a2a-M114, A1b1a1a2b-P262, A1b1b1-M28, A1b1b2a-M51,

P71, A1b1b2b-M13, A1b1b2b1-M118, which they found in

“low frequencies”: one in Algeria, two in Cameroon, one in

Ghana, two in Niger, seven in South Africa, three in Ethiopia,

two in Kenya. All these subclades are located in the upper part

of the tree in Figure 2, and indeed belong to “African” sub-

clades (or they migrated to Africa relatively recently), and

NONE of BT or CT lineages descend from them. So how can

they be claimed as “ancestral” to non-African lineages? None

of actual bearers of haplogroups A0-T, A1, A1b have been

found in Africa or elsewhere. So how they can be claimed as

“African”? Just because they were assigned “A” letter in the

index?

As we see, all those conjectures by proponents of the “Out of

Africa” concept are groundless. They assume that the currently

African branches A00, A0, A1a, A1b1 descended from African

haplogroups, and those were A0-T, A1, A1b. In reality, this

has never been shown. Those haplogroups represented forks

from which A0, A1a, A1b1 split and migrated to Africa.

The authors (Scozzari et al., 2012) place the origin of haplo-

group B to the sub-Saharan region (they write-“essentially a

sub-Saharan clade). We have shown above that haplotypes of

haplogroup B are tremendously remote from “African” h aplo-

types of haplogroup A, and obviously have a non-African ori-

gin. CT does not come from haplogroup B, as it is obvious

from Figure 2. B and CT haplogroups have a common ancestor,

that is haplogroup BT (see Figures 1-3).

So, what was the major conclusion the authors (Scozzari et

al., 2012) made? As the reader ca n guess, it was that haplo-

group CT came from Africa, and not just from Africa, but

“from the north-western quadrant of the African continent”.

There, as the authors concluded, “an origin for the human MSY

diversity” is located. How come? Their subclade tree (Figure 2)

shows that CT did not descend from “African sources” that

have been identified by the authors in (current) African chro-

mosomes. All of them are in the upper segment of the tree.

Besides, as Pontius Skoglund (2013) rightly noticed, “Patterns

of genetic diversity can never provide strong evidence for t he

origin of expansions”. After study ing the genetic relationships

of populations of Khoe-San and other African populations such

as Central African Pygmies, click-speaking East African popu-

lations such as Hadza and Sandawe, the author (ibid.) wrote

“this leaves the question of modern human origins in Africa

unanswered”. Some consensus.

A recent paper by Cruciani et al. (2011) fits the same pattern

as that of other OOA proponents beginning with its title—“…

The origin of patrilineal diversity in Africa”. On what scientific

ground? On the same “ground” as explained above—they

showed that African lineages are more diverse compared with

those of non-Africans. Their SNP tree is almost the same as

those shown in Figures 1-3, and their dating of the split be-

tween African and non-African lineages of 141.5 ± 15.6 kya is

within the margin of error with 160 ± 12 kya for the tree in

Figure 1. The Cruciani et al. (2011) tree shows as follows:

about 142 kya there was a split of haplogroup A1b (A0 in the

new nomenclature) from the main trunk of the tree, then ap-

proximately 108 kya the branch A1a split off, then, about 105

kya, A2 and A3 split off (A1b1a and A1b1b, respectively, in

the new nomenclature). Subclades A0, A1a, A1b1a, and A1b1b

the authors reasonably assigned to “African”, since they were

found in four Africans. There are no objections to that, however,

those subclades are not ancestral to non-African subclades.

Then, about 75 kya, according to the authors, haplogroup BT

arose, and 39 kya haplogroup CT arose. We know that neither

BT nor CT descended from “African” haplogroups. However,

since the branching points (fork haplogroups) are designated by

the authors as “A” (A1a-T, A2-T), the authors consider them—

as default—the “African” haplogroups, hence, “Out of Africa”.

According to the authors (Cruciani et al., 2011), since “Afr i-

can” haplogroups A0 (=A1b in the outdated nomenclature),

A1a, A2 and A3 (obsolete nomenclature) arose 105 - 108 kya,

and BT arose 75 kya, a (mutation-derived) distance between

them should be about 30 - 33 kya. In fact, it is 248 - 286 thou-

sand years (see calculations above). It clearly shows that hap-

logroup B did not descend from the “African” haplogroups. It

descended from their common ancestor about 160,000 ya (see

above). The same conclusion follows from Figu re 2 by Scoz-

zario et al. (2012), and from Figure 1 (Klyosov and Rozhanskii,

2012a).

The above considerations and conclusions were related to

Y-chromosome. An overall conclusion is that all available ex-

perimental data do not show any “Out of Africa” principal mi-

grations of AMH. There are no African SNPs in Y-chromo-

somes of non-Africans. Non-African lineages and haplotypes

are tremendously distant from the African. As practically all

sources admit, there is “complete separation of African and

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A. A. KLYOSOV

non-African lineages” (see above for actual quotes). However,

it is interesting that by accepting all of it, population geneticists

continue to repeat—“Out of Africa”. On what ground? No an-

swer.

Cross-Verification of the Haplogroup Tree in

Figure 4 Employing SNPs

There is one more approach to a verification of the tree in

Figure 4, that is by employing SNPs (Single Nucleotide Poly-

morphism). SNPs, which are practically irreversible mutations,

are accumulating in Y-chromosome (as well in other pa rts of

the DNA) in the course of evolution. The longer (time-wise) the

distance between certain nodes (points) in the flowchart in

Figure 4, the more SNPs are accumulated there. It is a random,

statistical process, however, it can be quantified. The longest

single evolution line in Figure 4 belongs to haplogroup A00,

therefore, we can expect that t he present-day bearers of haplo-

group A00 reveal the highest number of SNPs from the pre-

sumed time when A00 arose (about 210,000 ya). The runner up

should be haplogroup A0. The distance between alpha- and

beta-haplogroups (that is between A1b and BT) should be rela-

tively short compared to that in A00 and A0, about 100,000

years, and then SNPs kept accumulating upon transition from

BT to more recent and contemporary haplogroups.

This is what has been confirmed, considering and counting

the SNPs. A list of the SNPs is given below; it is not the final

one, and new SNP are being discovered from time to time.

However, as a certain approximation the list works.

Haplogroup A00 is the most ancient, the most archaic, its

evolution line is the longest one. Its SNPs were discovered in

men of the Mbo tribe in Came roon (Mendez et al., 2013):

AF4, AF5, AF7, AF8, AF9, AF10, AF13, L990, L1086,

L1087, L1088, L1091, L1092, L1094, L1096, L1097, L1100,

L1102, L1103, L1104, L1106, L1107, L1108, L1109, L1110,

L1111, L1113, L1114, L1115, L1117, L1119, L1122, L1126,

L1131, L1133, L1134, L1138, L1139, L1140, L1141, L1144,

L1146, L1147, L1148, L1149, L1151, L1152, L1154, L1156,

L1157, L1158, L1159, L1160, L1161, L1163, L1233, L1234,

L1236, L1284.

Haplogroup A00 contains 59 SNPs. Sinc e A00 arose a bout

210,000 ya, then it can be estimated tha t one SNP-mutation

occurs once in 3600 years, on average, in the considered frag-

ment of Y-chromosome.

Then, as we already know, haplogroup A0-T arose on the

main trunk of the haplogroup tree, shown in Figure 4. It split

into A0 and A1, the last one continued the trunk. A0 now live

mainly in Africa. A0-T does not contain any A00 mutation.

That is, A0-T did not descend from the African haplogroup

A00. There is no data which would define A0-T as African.

Indeed, it is an ancestor of the “African” A0, as well as of the

non-African haplogroups, which passed via haplogroups BT,

then CT and so on.

There are 32 SNPs of haplogroup A0-T:

AF3, L1085, L1089, L1090, L1093, L1095, L1098, L1099,

L1101, L1105, L1116, L1118, L1120, L1121, L1123, L1124,

L1125, L1127, L1128, L1129, L1130, L1132, L1135, L1136,

L1137, L1142, L1143, L1145, L1150, L1155, L1235, L1273.

Haplogroup А0 has 51 SNPs:

L529.2, L896, L982, L984, L990, L991, L993, L995, L996,

L997, L998, L999, L1000, L1001, L1006, L1008, L1010,

L1011, L1012, L1015, L1016, L1017, L1018, L1055, L1073,

L1075, L1076, L1077, L1078, L1080, V148, V149, V152,

V154, V157, V163, V164, V165, V166, V167, V172, V173,

V176, V177, V190, V196, V223, V225, V229, V233, V239

Haplogroup A0 is 8 SNPs short compared to A00, that is A0

is about 30,000 years younger compared to A00. Indeed, А0

arose 180,000 ya, haplogroup A00 210,000 ya.

Haplogroup А1 has only 21 SNP discovered:

L985, L986, L989, L1002, L1003, L1004, L1005, L1009,

L1013, L1053, L1084, L1112, L1153, P305, V161.2, V168,

V171, V174, V238, V241, V250

Unlike the sister haplogroup A0, bearers of A1 apparently

did not survive until present time. It might be that they perished

in that cataclysm, mentioned above, which caused the bottle-

neck of the non-African population (see above). A summary

lifetime of haplogroups А0-Т, А1, and A1b (the last one has

only two SNPs, Р108 and V221) is equal to 32 + 21 + 2 = 55

SNPs, that is 55 × 3600 = 198 thousand years.

Finally, haplogroup ВТ has 30 SNPs:

L413, L418, L438, L440, L604, L957, L962, L969, L970,

L971, L977, L1060, L1061, L1062, M42, M91, M94, M139,

M299, P97, SRY10831.1, V21, V29, V59, V64, V102, V187,

V202, V216, V235

This gi ves 30 × 3600 = 108,000 years for t he evolution of the

beta-haplogroup since the time of the divergence with the

“African” haplogroup A1b1 (160 ± 12 kya, see Figure 4) to the

bottleneck of the BT population of 64 ± 6 kya. Those 108 kya is

the distance between alpha- and b eta-haplogroups in Figure 4.

Those are years which disappeared (between A1b, that is the

alpha-haplogroup, and BT, which is the beta-haplogroup), from

the evolution of the non-African BT haplogroups. Non-Africans

popped up literally from nowhere 64 ± 6 thousand years ago,

from a viewpoint of archaeology and anthropology, as fully

developed AMH. They did not descend from Africans.

It is important that those “lost” millennia in the evolution of

the non-African DNA lineages, are cross-reproducible in the

analysis of both STRs (haplotypes, based on t hat the flow chart

in Figure 4 was composed), and SNPs, as it is shown above.

Why we do not see those excavated DNA in Eurasia is still

unknown. However, we know of excavated skeletal remains of

Homo sapiens in the Middle East, dated between 160 and 60

kya, but their haplogroup was not examined. If it happens hap-

logroup BT, with those SNPs listed above, the puzzle will be

finally solved.

Let us now look at mitochondrial DNA. There, as proponents

of “Out of Africa” say, it is more than clear. “Non-African

mtDNA all descended from African”.

Is it so?

Non-African mtDNA Do Not Descend from

African mtDN A

The recent pap e r by Behar et al. (2012) shows that in the

very beginning of the mtDNA evolution tree there is a split of

the main “stem” lineage into L0 (on t he right) and L1-L6 (on

the left). All other haplogroups in the world descended from

L1-L6.

Haplogroup L0 embrace a large series of about fifty ancient

African haplogroups, which were identified mainly in sub-

Saharan Africa, among Khoisan-speaking populations, and also

in Ethiopia and Tanzania (East Africa), in Mozambique (South-

Eastern Africa), and among Pygmies. All ot her haplogroups are

believed to descend from haplogroup L3, with an “age” of

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A. A. KLYOSOV

about 60 - 70 kya, that is approximately the same as that of

Y-chromosomal BT haplogroup. Therefore, it is quite plausible

that haplogroup L3 did not come out of Africa, but migrated

into Africa alo ng with bearers of Y-chromosomal haplogroup

BT, or B. However, which conclusion is made by Behar et al.

(2012)? Did they consider that altermative, as an equally valid

conclusion? Of course not. Their conclusion was—“Out of

Africa”. On what ground?

Behar et al. (2012) did not even consider a deep separation of

the African haplogroup L0 from all others despite their own

figure, which shows that the African haplogroup L0 is not an-

cestral with respect to all other mtDNA haplogroups (Figure 5

below).

In reality, the separation of the African haplogroup L0 at 150

- 170 kya from apparently non-African haplogroups L1-L6

(Figure 5) and the subsequent migration of haplogroup L3 (60 -

70 kya) into Africa fit nicely to the separation (split) of African

Y-chromosomal haplogroup of series A (160 kya) and non-

African (the apparent age of 64 kya after passing through a

population bottleneck, see above) with a subsequent migration

of haplogroup B to Africa.

More data has accumulated suggesting that there were a mul-

titude of ancient migrations into (and apparently from) Africa.

A recent paper in Nature (Hayden, 2013) presented data re-

garding two migrations from Eurasia to Khoisan tribes, one

3000 ya to East Africa, another 900 - 1800 ya to South Africa.

The author did not report which haplogroups were brought to

Africa by the migrants. However, there is no doubt that those

migrations have increased the “genetic diversity” among Khoi-

sans, which is believed to be the highest in Africa. Another

important feature of the data is that it points to the possibility of

ancient “migrations into Africa”, which was not and could not

be in any doubt. Sarah Tishkoff, one of the most active propo-

nents of the “Out of Africa” concept, has greeted the “into

Africa” new data, and called them “making sense”, since “arc-

haeological and linguistic studies support it” (Nature, 29, 2013,

p. 514).

Herpes Virus Migrations Are Mistakenly

Announced as Supporting the

“Out of Africa” Concept

A history with a recent publication which made a w ide press

“Using HSV-1 genome phylogenetics to track past human mi-

grations” (Kolb et al., 2013) presents a good ex ample how the

aim at “Out of Africa” distorts data interpretations and conclu-

sions of a study. The stu dy compared 31 complete and nearly

complete “globally derived” (not exactly so) HSV-1 genomic

sequences. Sources of the Herpes Simplex Virus were from

Keny a (East A f rica), China, South Korea and Japan (East Asia),

Seattle, San Francisco and Houston (USA), and Glasgow (UK).

The authors have found that the phylogenetic tree forms six

clusters (Figure 6). The clusters consist of the following sam-

ples:

I—10 samples total, of which 7 samples were from Seattle,

one from “USA” (no detail provided), one from San Francisco,

and one from Glasgow,

II—6 samples total, of which one was from China, one from

Houston (US), two from South Korea, and two from Japan,

III—two samples from Kenya,

IV—three samples from Kenya,

V—seven samples from Kenya,

VI—two samples from Kenya.

The authors of the study rounded them up and reported that

“the tree revealed a six clade pattern based on the geographical

origin of the isolates”. According to the authors, “the Euro-

pean/North American viruses fo rmed clade I, East Asian strains

formed clade II and the East African viruses comprised clades

III, IV, V and VI”. An origin of the “USA” strain was not dis-

closed, and it is not clear if they were obtained from Europeans

(by descent) or Native Americans. However, since the authors

suggested that an outlier strain (Houston) placed into the East

Asian cluster “may originally have been from the native Ame-

rindian population”, it seems that the other US-based samples

were from individuals of European descent. Nevertheless, the

authors concluded that those clusters “mirror global human

migrations” and support the “Ou t of Africa model” of human

migration. The main reason for it, as always, was an argument

of diversity, namely that “The East African derived viruses

contained the greatest amount of genetic diversity and formed

four of the six clades.”

Let us consider, as we did above, where that “diversity” is

coming from. As we have seen repeatedly above, the diversity

is coming from a common ancestor of all those lineages, shown

in Figure 6, which did not necessarily live in Africa. Some

viruses migrate to Africa with their carriers, others migrate

elsewhere. There is no indication that they descended initially

from African viruses. Figure 6 shows again a series of cascade

splits, and after each split the resulting downstream strains

move in different directions. There is no “African origin” here.

Let us follow the phylogenetic tree in more detail. A small

bar on the very left represents a common ancestor of all the

strains of the virus. We do not know where it lived. It could

have been anywhere in the world. The first split results in two

different strains: the contemporary Kenyan strain splits off, and

another strain later underwent a cascade of splits (the lower

node in Figure 6). The first “Kenya n” strain (the top two sam-

ples in Figure 6) was not ancestral to any of the later strains

considered in the study, including the European ones.

The n ext split caused again a separation of populations of the

virus, and, apparently, their human carriers, and cluster V in

Figure 6 was formed, which was also found in Kenya. There

were no non-African viruses descended from it; at least, t he y

have not been observed in the st udy.

The ne xt split produced virus E07, again found in Kenya.

There were no non-African viruses descended from it. The

authors mistakenly assigned it to cluster IV, however, it does

not belong there.

The next two splits produced clusters IV and III, again Ke-

nya n, according to the authors of the study. European or Asian

viruses did not descend from them, as well as, apparently, Eu-

ropean and Asian populations which carried those strains. With

that split the African (Kenyan) new strains were not observed in

the study. There was nothing related to “Out of Africa” there. It

was more likely “into Africa”, since the Kenyan strains were

not ancestral to the European or Asian strains, as it is obvious

from Figure 6.

The last split is into European and East-Asian strains of the

virus, that is clusters II and I, respectively. There is nothing

“American” (with respect to Native Americans) there. It is a

European cluster of the virus, carried by migrants from Europe

to America.

It is surprising that the authors of the study have not seen

such a simple explanation of the dynamics of the strains.

OPEN ACCESS 31

A. A. KLYOSOV

Figure 5.

Schematic representation of the human mtDNA phylogeny within hominine, and exemplified with Homo neanderthalinsis (on the left) and

Home sapiens (on the right). The ph ylogeny illustrating approximate divergence times of the s pecies. RNRS stands for Reconstructed Nean-

derthal Reference Seq uen ce, RSRS – for Reconstru cted Sap ien s Ref eren ce Sequ en ce. Mutate d nu cleo tide p os ition s s eparatin g th e n od es o f the

two basal human haplogroups L0 and L1’2’3’4’5’6 and their derived states as compared to the RSRS are shown. Please notice a huge split

between L0 and L1-L6 on the right. From Behar et al. (2012) with permission.

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A. A. KLYOSOV

Figure 6.

Phylogenetic tree featuring HSV-1 strains which depict the formation of six clades based on geographic origin.

Clade I includes European/North American strains (Glasgow [#17], Seattle, San Francisco, “USA”—all US are

marked in blue color), Clade II comprises East Asian strains (China [red], South Korea [purple], Japan [yellow],

and Houston, US [blue]), and III, IV, V and VI are East African (Kenya [green]). From Kolb et al. (2013) with

permission.

Apparently, they were too mu ch focusing at bendi ng the data to

fit “Out of Africa”.

The senior author of the study, Kurtis Brandt, a professor of

medical microbiology and ophthalmology, sta ted in his inter-

view: “What we found follows exactly what the … molecular

geneticists who have analyzed the human genome have told us,

about wh ere humans originated and how they spread across the

planet.”

(http://www.sci-news.com/genetics/science-herpes-virus-out-of

-africa-theo ry-01482.html). This was exactly the main problem

of the study.

In another interview Kurtis Brandt says that “the results were

quite “stunning.” He goes on to describe their findings: “We

found that all of the African isolates cluster together, all the

viruses from the Far East, Korea, Japan, China clustered to-

gether, all the viruses in Europe and America, with one excep-

tion, clustered together.”

(http://guardianlv.com/2013/10/herpes-simplex-virus-confirms-

out-of-africa-migration-of-ancient-humans/). Generally, it is

true, despite some stretches. However, it does not support the

“Out of Africa” concept at all, as it was explained above.

The paper (Kolb et al., 2013) provides one more illustration

how experimental data a re bent in order to show the desir able

“Out of Africa” conclusion by all means. This concerns calcu-

lations of t he “divergence time” for the strains. The authors

wanted to obtain 50,000 ya from the initial divergence, which

would fit the desired “Out of Africa” time, and they obtained it.

Here is how th ey came to those 50,000 ya. This is rather educa-

OPEN ACCESS 33

A. A. KLYOSOV

tional and entertaining.

The authors (Kolb et al., 2013) have reported that the re are

three significantly varying figures for the mutation rate con-

stants for Simplex and other herpes viruses, equal to 18.2 ×

10−9, 30 × 10−9 and 3 × 10−9 substitutions/site/year. To employ

all of them would hav e resulted in divergence times that dif-

fered by 30 times. The authors did not know which constant of

the three would have been a matter of choice. They decided to

take such a constant which would give them a desired and

“consentual” 50,000 ya. As a first step, the authors considered a

suggested divergence time between European and Asian popu-

lations as 23 - 45 thousand yea rs ago, as four literature sources

have claimed. The authors took an average figure from all the

four values, making it 34,000 ± 10,500 years ago. Those are

obviously lower figures compared to historical ones, since Eu-

ropean and Asian haplogroups separated not later than 55 - 60

ky (see Figure 1); however, all those calculations in the paper

were so crude—and datings, and the mutation rate constants—

that it could not have been taken seriously.

Since the authors took “reference” divergence times lower

than t he y should have been, the mutation rate constants must be

much higher tha n they should have been. Indeed, the adjusted

mutation rate constant was much higher than the all the four

cited from the literature, namely, 134 × 10−9 substitutions/site/

year, with an upper and lower limits of 214 × 10−9 and 74.8 ×

10−9, respectively. This can be compared to the literature’s 3×,

18.2× and 30 × 10−9 substitutions/site/year. This apparently was

not a matter of concern to the authors. The ultimate goal was

50,000 years.

Now, using this grossly inflated figure for the mutation rate

constant, the authors obtained th at the initial divergence time

for the virus occurred 50,300 ± 16,700 ya, and claimed that it

“supports the “out of Africa model” of human migrations”. A

similarly calculated date for the Eurasian strains divergence

time was 32,800 ± 10,900 ya, and time for divergence of a sin-

gle Chinese virus sample and a single Texas sample of an un-

known origin results in a divergence time of 15,760 ± 5300 ya.

The authors concluded that the last date “fits with the estimated

time period in which the North American continen t was popu-

lated from Asia”. No comments.

Based on all of it the authors claimed that “the data supports

the “out of Africa model” of human migrations”. As we have

explained above, this has nothing to do with the “Out of Africa”

concept. The mutation rate constant for the Simplex Herpes

Virus, “calculated” by the authors, exceeded three other litera-

ture values by 4.5 to 45 times. There we re no explanations from

the authors for such a discrepancy. There were no other verifi-

cations of t he obtained mutation rate constant. The authors

obtained, using that mutation rate constant, that HSV-1 and

HSV-2 diverged 2.184 ± 0.753 million years ago (please notice

the accuracy of the bot h figures in the estimate!), but this also

says practically nothing; it could have come up as 20 million

years, and it would have been a good number too. There could

have been said that it was macaque as a carrier of the virus. In

other words, any data goes in such a work. If the literature mu-

tation rate constants (or some of them) are valid, then the initial

divergence time of the HSV-1 was not 50,300 ya, but between

220 thousand and 2.2 million years ago, and also could have

been interpreted in terms of evolution of man. Indeed, every-

thing goes. But then there would not have been “Out of Africa”

“support’.

A conclusion: the experimental data by Kolb et al. (2013) are

valuable, but manipulations, “interpretations”, and conclusions,

particularly regarding “Out of Africa” have no value at all.

Anthropological Data and Datings

A peculiar situation was formed in the last few years, when

many anthropologists doubted experimental anthropology data

on evolution of man as very controversial, but pointed at gene-

ticists, that the latter “have real data” and, as they claim, it con-

firmed the “Out of Africa” concept. Many geneticists, on the

other hand, doubt experimental genetic data on evolution of

man as very controversial, unreliable and conflicting with each

other, but point at anthropologists, that they “have real data”,

and believe that anthropologists confirmed the “Out of Africa”

concept. In reality none of them confirmed the dubious (and,

actually, false) concept, however, those reciprocal bows kee p

the concept afloat.

The cornerstone mutual belief is that AMH allegedly arose in

Africa and it happened about 200,000 ya. By definition, AMH

was Homo sapiens who did not have noticeable archaic skeletal

features. Now, let us list several actual experimental observa-

tions in that regard:

-All African excavated skeletal remains dated before 36,000

ya posess noticeable archaic features,

-Ancient skeletal remains very often are so fragmentary, that

to reconstruct an appearance of ancient people even in a mi-

nimal degree is typically close to impossible,

-An anthropological pattern of skeletal remains is often sim-

ilar in Africa and elsewhere, so it is close to impossible to

firmly conclude who went where—out of Africa or into Africa,

-Very often ancient settlements produce no skeletal remains

at all, and conclusions (or rather suggestions) about “anatomi-

cally modern humans” are often made based on view and dating

of the settlements and some st one tools, however, they could be

left by archaic humans, and not AMHs or even Homo sapiens,

-Datings of ancient bones are often so questionable that few

specialists accept them literally or uncritically, or even serious-

ly.

Unfortunately, radiocarbon datings practically do not work

on times more than 40,000 years , and a recent record in that

regard was set at 60,000 years. The reason is well unders-

tood—a half-life of the radioactive isotope 14С equals to 5730

years, that is 40,000 years is equivalent to seven half-life times,

60,000 years takes more than ten half-life times. The method is

based on measurements in biological samples of a rati o of the

stable isotope 12C (and a little of 13С, concentration of which is

about 1% compared to that of 12C) and radioactive 14С, an ini-

tial content of which equals about 1 × 10−10 per cent in the

tested biological sample, and decreases with time according to

its half-life time. After 60 thousand years the content of 12C

drops from the initial 1 × 10−10 per cent by 210 times, that is by

1024 times. Modern detectors are unable to measure such low

concentrations of 12C, at least those detectors whic h are in pos-

session of archaeologists. This corresponds to 1 click per hour

per gram of the tested carbon. A natural radioactivity back-

ground is much higher.

This opens a wide probability for errors, and no t only for

“innocent errors”. Many anthropologists remember an embar-

rassing story with dishonoring and firing of a German anthro-

pologist, Professor Reiner Protsch for systematic, as it was

revealed, falsifications of dates for numerous ancient and not so

ancient skeletal relics. After cross-examination, a dating by

OPEN ACCESS

A. A. KLYOSOV

Protsch of 36,000 ya turned out to be 7500 ya, another dating of

21,300 ya occurred in fact 3300 ya, and a skeleton dated by

Protsch by 29,400 ya happened to be that of a man who died in

1750, 255 years before (Gardian,

http://www.theguardian.com/science/2005/feb/19/science.scien

cenews). The same in kind story was presented by the interna-

tional journal Archaeology

http://archive.archaeology.org/0505/newsbriefs/insider.html.

Similar stories happen in archaeology and anthropology, and

even if not through obvious (and verified and proven) falsifica-

tions, which, of course, occur in very rare cases, still a likelih-

ood for a mistake is rather high. It should be noted here that the

most ancient biological artifacts are dated not by radiocarbon,

but employing other methods, such as the argon method, in

which a ratio of 40Ar/39Ar is measured.

Overall, t h ere is not any anthropological of archaeological

proof of appearance of anatomica lly modern human in Africa,

or the “Out of Africa” migration. There is not any proof that

stone tool types found in Europe and Eurasia were brought

from sub-Sahara regions. All announcements on discoveries of

skeletal remains of AMH older than 50 kya, and more so, older

than 150 kya, in the sub-Saharan area, are distorted or incorrect

in the first place. All of them expose rather noticeable archaic

features. A good overview of this issue was recently published

in Advances in Anthropology by Australian anthropologist Ro-

bert Bednarik. A number of studies tell of absence of such

findings from south of the Sahara (e.g., Grine et al., 2007;

Grine et al., 2010). All known olde s t fossils, such as Omo Ki-

bish 1 (195 kya, Ethiopia, fragments of skull with the face, very

incomplete), Omo-2 (having a number of primitive features),

Herto (the Middle Awash region, 160 - 154 kya, very robust

and thus distinguishable from AMH), dated between 200 - 100

kya, possess archaic features (Rightmire, 2009) and cannot be

considered AMH. Many excavated remains do not have facial

bones. Even the Hofmeyr skull from South Africa, dated to 36

kya (though has no recorded archaeological associations, and

dated by application of optically stimulated luminescence and

U-series methods to sediments filling of the braincase) is fea-

tured a robust face, close to crania associated with Upper Pa-

leolithic industries in Eurasia (cited by Rightmire, 2009). Over-

all, the Hofmeyr skull posesses noticeable archaic features

(Grine et al., 2007; Rightmire, 2009; Tattersall, 2009). An

American anthropologist Rightmire (2009) noted that “neither

the Herto hominins, nor others from La te Pleistocene sites such

as Klasies River in southern Africa and Skhu_l/Qafzeh in Israel,

can be matched in living populations. Skulls are quite robust,

and it is only after ~35,000 years ago that people with more

gracile, fully modern morphology make their appearance”.

Righmire continues that the process or events underlying AMH

emergence “are poorly understood”. This conclusion was re-

peated by Hammer et al. (2011)—“…hominins with a combina-

tion of archaic and modern features persist in the fossil record

across sub-Saharan Africa and the Middle East until after ~35

kya”. In other words, multiple references by proponents of the

“Out of Africa” concept that many fossils of AMH were found

in Africa with dates between 200 and 160 kya , are at least ques-

tionable, if not untrue. Manipulations and distortions continue.

Michael Hammer, a recent proponent of the “Out of Africa”

concept, however, expressed a doubt as late as in 2013, when

the situation with “Out of Africa” became increasingly con-

fused. His recent paper in Scientific American (May 2013)

Hammer concludes as follows: “Many loose ends remain. Yet

one thing is clear: the roots of modern humans trace back to

not just a single ancestral population in Africa but to popula-

tions throughout the Old World”.

This does seem quite reasonable. Studying history of the an-

cient world, we see plenty of mobile migrations, including very

long migrations, long in terms of distance and time. When pro-

ponents of the “Out of Africa” hypothesis insist that it took

only 10 thousand years for the “Out of Africa” humans to reach

Australia, then it is hard to imagine that for the preceding 150

thousand years humans sat still in Africa and did not spread all

over the world, out of Africa and into Africa, multiple times.

How come that such a shaky concept of the one-sided “Out of

Africa” so aggressively and forcefully promoted was accepted

(but not quite) by present-day educated population in modern

countries? It should cause alarm—regarding both that aggres-

sive and overwhelming delivery of the false concept, falsely

claiming “consensus among scientists” (there was none), and

such a sheepish acceptance of that false concept by a general

population. The most alarming is the fact that the concept did

not have any proof, it was based on lies, fantasies, conjectures,

wishful thinking. How could science, largely funded by the

general population, have turned by a handful of manipulators

into an abusive tool? This is a real thing to be concerned about.

Conclusion

Ancestors of the most present-day non-Africans did not come

from Africa in the last 30,000 - 600,000 years at least. In other

words, those who migrated from Africa, or were forcefully

taken out as slaves, are not ancestors of the contemporary Eu-

ropeans, Asians, Native Americans, Australians, Polynesians.

This follows from the whole multitude of data in anthropology,

genetics, archaeology, DNA genealogy. Study of the DNA of

excavated bones of Neanderthals has shown in them MCR1

melanocortin rece ptor, in the same variant as that in modern

humans, which makes pale skin and red ha ir, observed in mod-

ern humans (Lalueza-Fox et al., 2007), though, according to the

study authors, humans did not inherit MCR1 from Neanderthals.

There was not any dat a that Neanderthals were Black Africans.

Indeed, no Neanderthals were found in Africa. Since modern

humans and Neanderthals (our cousins) have had a common

ancestor, that common ancestor likely had fair skin and light-

color hai r, and did not live in Africa. That was between 300 and

600 ky a. There is still a puzzle how our fair skin ancestors,

which split about 160,000 ya and one branch of them migrated

to Africa (see Figure 1), adjusted to African climate (which,

though, was different from today’s) and acquired a black skin

color. An answer lies, apparently, in regulation of melanin bio-

synthesis. However, it is a different sto ry.

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