mtDNA-M from Africa- **Not** from India- April2016

[djoser-xyyman]

The is another ground breaking paper. In 2015 things were a bit slow. It seems like in 2016 things are picking up. What is the paper about and why is it ground breaking? The devil is in the details. Their premise is that mtDNA Haplogroup M exited Africa not from the Southern Route(horn of Africa) but through the Levant and over North Asia then into South Asia etc . Typical of Europeans they do the bait and switch. They used a mixture of genetics and archeology to come to that conclusion. They acknowledge that mtDNA-M is older inAfricans/ Oceania/Australians and East Asians compared to India and Arabia but then switch to Archeology to explain the migration path between China and Oceania/Australia. If you don't read carefully you will miss that trick they pulled.

But any astute reader will filter FACT from FICTION. ,.....There are some intriguing FACTS gleaned from the paper.


1. There is further confirmation that mtDNA-M is of African origin, albeit India has a higher frequency
2. M1 is older in Africa compared to European and Asia versions
3. M1 is found right across the African Sahel into SSA areas like Senegal
4. There are sub-clades of mtDNA-M that surrounds the Indian Ocean including lands off the East African coast. Madagascar and Seychelles come to mind
5. There are sub-clades of mtDNA-M found in distant populations such as Andaman Islanders, Australians and Madagascans


I don’t want to sound crazy. But the pattern is hard to ignore so I have to say it. Incredulous as it may sound. But there seem to be a land-bridge across or in the Indian Ocean. The phylogeographic pattern points to that. This is one of several studies that suggest that as the only likely scenario.


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Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia - Patricia Marreroa1 - April2016


modern humans to colonize the Old World. At this respect, it is pertinent to mention that a
recent whole-genome analysis comparing the ancient Eurasian component present in
Egyptians and Ethiopians pointed to Egypt and Sinai as the more likely gateway in the
exodus of modern humans out of Africa (Pagani et al., 2015). Furthermore, after a
thoroughly revision of the evidence in support of a northern route signaled by mtDNA
macrohaplogroup N (Fregel et al., 2015), we realized that the phylogeny and
phylogeography of mtDNA macrohaplogroup M fit better in a northern route
accompanying N than in a southern coastal route as was previously suggested (Maca-Meyer

et al., 2001). In fact, M in the Arabian Peninsula, the source of our experimental data seems
to have a recent historical implantation as in all western Eurasia. The unexpected detection
of M lineages in Late Pleistocene European hunter-gatherers (Posth et al. 2016), possibly
mirrors the back migration into Africa of haplogroup M1 that most probably arrived to
Northern Africa through western Eurasia, in Paleolithic times (Olivieri et al., 2006;
González et al., 2007; Pennarun et al., 2012). The founder age of M in India is younger than
in eastern Asia and Near Oceania and so, southern Asia might better be perceived as a
receiver more than an emissary of M lineages. In this study, we built a more conciliatory
model for the history of Homo sapiens in Eurasia that might attract the reluctant East Asian
position on the premises of only an early exit from Africa and only a sole northern route
across the Levant, followed by early modern humans to colonize the Old World.

[djoser-xyyman]

Material and methods

Sampling information
A total of 206 samples from unrelated Saudi healthy donors belonging to mtDNA
macrohaplogroup M were analyzed in this study, 163 of them have been previously
published (Abu-Amero et al., 2008); (Fregel et al., 2015). To fully characterize these M
lineages, 17 complete mtDNA genomes from Saudi samples were sequenced. In addition, 7
unpublished complete mtDNA genomes, belonging to macrohaplogroup M, from preceding
studies were included (Tanaka et al., 2004; González et al., 2007). Only individuals with
known maternal ancestors for at least three generations were considered in this study. We
included in the analysis 4107 published complete or nearly complete mtDNA genomes
belonging to macrohaplogroup M of Eurasian and Oceania origin. To accurately establish
the geographic ranges of the relatively rare M haplogroups, we screened 73,215 partial

Previous published data compilation
Sequences belonging to specific M haplogroups were obtained from public databases such



Results and discussion
Haplogroup M in western Eurasia with emphasis on Saudi Arabia

The lack of ancient and autochthonous mtDNA M lineages in western Eurasia is, at least,
surprising if we think that the out of Africa colonization of the Old World by modern
humans began through that region. Indeed, the presence of haplogroup M1 lineages in
Mediterranean Europe and the Middle East has been explained as the result of secondary
spreads of this haplogroup from northern Africa where it had a Paleolithic implantation
(Olivieri et al., 2006; González et al., 2007; Pennarun et al., 2012). Likewise, the presence
of eastern Asian M lineages belonging to C, D, G and Z haplogroups, mainly in Finno-
Ugric-speaking populations of north and eastern Europe, seems to be the footprints of
successive westward migration waves of Asiatic nomads occurred from Mesolithic period
to historic times, as documented by the Magyar occupation of the Carpathian basin at the
9th century (Lahermo et al., 2000; Tambets et al., 2004; Ingman and Gyllensten, 2007;
Nádasi et al., 2007; Tömöry et al., 2007; Lappalainen et al., 2008; Derenko et al., 2010,
2012; Der Sarkissian et al., 2013). South Asian influences on the west have been also
detected by the presence of M4, M49 and M61 Indian lineages in Mesopotamian remains
(Witas et al., 2013). In addition, ancestral mtDNA links between European Romani groups
and northwest India populations were evidenced by the sharing of M5a1, M18, M25 and
M35b lineages (Gresham et al., 2001; Kalaydjieva et al., 2001; Malyarchuk et al., 2008;
Mendizabal et al., 2011; Gómez-Carballa et al., 2013).

[djoser-xyyman]

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7% of the Saudi maternal gene pool (Abu-Amero et al., 2007, 2008). Of the 206 M

haplotypes sampled in Saudi Arabia (Table S1), 53% belong to the northern African M1 haplogroup,
being both eastern African M1a and northern African M1b branches well represented (Table S1 and
Figure S1). This fact contrasts with the sole presence of eastern M1a representatives in Yemen
(Vyas et al., 2015). Therefore, most probably, M1b lineages reached Saudi Arabia from the Levant. M
lineages with indubitable Indian origin account for 39% of the Saudi M pool, whereas the resting
8% has, most probably, a southeastern Asian source. The geographic origin of the Indian
contribution seems not to be biased as 53% of the lineages might be assigned to eastern and 47% to
western Indian regions (Metspalu et al., 2004; Chandrasekar et al., 2009; Maji et al., 2009).
However, the fact that the two M lineages characteristic of the Andaman aborigines (Endicott et
al., 2003; Thangaraj et al., 2005; Barik et al., 2008) are present in the Saudi sample deserves
mention. The isolate Ar2461 (Table S1) has the diagnostic mutations of the Andaman branch M31a1 in
the regulatory (249d, 16311) and in the coding (3975, 3999) regions. On the other hand, the
complete mtDNA sequence of Ar1076 (Figure S1) belongs to the M32c Andamese branch, matching another
complete sequence reported for Madagascar (Dubut et al., 2009). It must be stressed that this
branch has been steadily found in all mtDNA reports on Madagascar (Hurles et al., 2005; Tofanelli
et al., 2009; Capredon et al., 2013). Although at first these haplogroups were taken as evidence
that the indigenous Andamanese represent the descendants of the first out-of-Africa dispersal of
modern humans (Endicott et al., 2003; Thangaraj et al., 2005), more recent studies support a late
Paleolithic colonization of the Andaman Islands (Palanichamy et al., 2006; Wang et al., 2011).
About the possible origin of these settlers, it must be mentioned that different branches of M31
have been found in
northeastern India, Nepal and Myanmar (Thangaraj et al., 2006; Reddy et al., 2007; Barik
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[djoser-xyyman]

et al., 2008; Fornarino et al., 2009; Wang et al., 2011). Inasmuch as M32c, it has been also
detected in Indonesia (Hill et al., 2007) and in Malaysia (Haslindawaty et al., 2010;
Maruyama et al., 2010). Another interesting link involving India, Saudi Arabia and the
Mauritius Island is the case of haplogroup M81,defined in PhyloTree.org Build16 (van
Oven and Kayser, 2009). It was first detected as a sole sequence in a LHON patient from
India (Khan et al., 2013). The Saudi sample Ar567 shares with this Indian sequence
substitutions 215, 4254, 6620, 13590, 16129 and 16311 and, in addition, it shares
substitutions 151, 6170, 7954 and 16263 with a complete sequence from the Mauritius
Island (Fregel et al., 2014). At first sight, four different mutations occurring in a short
segment of 11 bp, from positions 5742 to 5752, differentiate the Mauritius from the Saudi
sequence. However, a closer inspection reveals they represent only two additional shared
mutations differently interpreted: the loss by transversion to G of a C at position 5743 in the
Ma12 reading corresponds to a deletion of C in the same position in the Ar567 lecture, and
the loss of a G by transition to A at position 5746 in Ma12 corresponds to an A insertion at
position 5752 in Ar567. Therefore, both sequences can be only distinguished by transition
12522 present in the Saudi sample and absent in Ma12 (Figure S1). Curiously, these
affinities between samples from Saudi Arabia and those from Indian Ocean islands near the
African shores can be extended to the Saudi Q1a1 sequence Ar196 (Table S1), which has
exact matches only with MA405 sample from Madagascar (Capredon et al., 2013), and to
the presence in Saudi Arabia (Fregel et al., 2015) and Mauritius (Fregel et al., 2014) of
different lineages belonging to the Indian branch (M42b) for which a deep link with the
Australian M42a branch has been detected (Kumar et al., 2009). Other lineages present in
the Saudi mtDNA pool, as M20, E1a1a1 or M7c1 point to specific arrivals from
southeastern Asia. Interesting as these affinities and provenances are, the fact that all these


However, after extensive
phylogenetic and phylogeographic analyses for this marker (Metspalu et al., 2004; Olivieri
et al., 2006; Sun et al., 2006; González et al., 2007; Pennarun et al., 2012), this supposed
India to Africa connection was not found. The detection in southeast Asia of new lineages
that share with M1 the 14110 substitution (Kong et al., 2011; Peng et al., 2011), gave rise to


). M1 is found from Portugal and Senegal in the west to the
Caucasus, Pakistan and Tibet at the east and, from Guinea-Bissau and Tanzania in the south
to Russia at the north (Kivisild et al., 2004; Olivieri et al., 2006; Gonder et al., 2007;
González et al., 2007, 2007; Zhao et al., 2009; Malyarchuk et al., 2010; Pennarun et al.,
2012; Yunusbayev et al., 2012; Siddiqi et al., 2014) but, its highest diversity is found in
Ethiopia and the Maghreb as the isolates detected at the borders are lineages derived from
M1a branch in Russia and Tanzania and M1b branch in Guinea Bissau and Tibet. The
geographic range of M20 and M51 largely overlaps, showing a common wide are

However, the actual representatives
of M1, from the Levant to the Tibet, are derived lineages with ancestors in Africa. Until
now, basal lineages of M1 have not been detected in any of the northern or southern
hypothetical paths.

Furthermore, unlike southeastern Asia
and Australia, autochthonous M lineages have not been detected to the west of South Asia.
It might be adduced that later expansions from the West replaced the M lineages in those
regions, however, massive expansions of western mtDNA lineages in India have not been
detected, instead it has been pointed out that most of the extant mtDNA boundaries in

Secondly, whenever it has been compared, the founder age
of M in India is significantly (p = 0.002) younger than those in Eastern and Southeastern
Asia and Australo-melanesian centers (Table 1). It has been argued that this could be due to
an uneven distribution and sampling of M lineages in India (Sun et al., 2006; Thangaraj et
al., 2006). However, when the same weight is given to every lineage, independently of their
respective abundance (Table 1), the founder age slightly diminish in India and raises in East
Asia compared to their respective weighted founder ages. Recently, it has been admitted
that the initial radiation of macrohaplogroup M could have occurred in eastern India or
further east following the southern route (Mellars et al., 2013). In fact, the possibility that

was previous to the detection of M clades with very deep
ages in southeast Asia (Kong et al., 2011; Peng et al., 2011; Zhang et al., 2013). In turn, the
founder age for M in Oceania is significantly older than the ones estimated for East Asia (p
= 0.004) and for Southeast Asia (p = 0.032). This decreasing age gradient moving
westwards is in accordance with the hypothesis that carriers of macrohaplogroup M
lineages colonized India from the East instead the West. It could be argued that South Asia
was colonized very early by the southern eastward coastal expansion of modern humans out
of Africa but those primitive mtDNA lineages were extinguished by genetic drift and the
subcontinent recolonized latter from eastern groups left on the way to Australia. However,
this argument is in contradiction, first, with the suggestion, based on past population size
prediction deduced from mtDNA variation, that approximately 45 and 20 kya most of
humanity lived in southern Asia (Atkinson et al., 2008), and second, with the mean founder
age of macrohaplogroup R in South Asia (62.5 ±3.5 ky) that is significantly older (p =


Actually, the southern component is most prevalent in the Andamanese. Of particular interest is the
fact that when populations of Southeast Asia and Near Oceania were incorporated to these
genome wide analyses, the Andaman Islanders showed a closer affinity with southeast
rather than South Asian populations (Chaubey and Endicott, 2013; Aghakhanian et al.,
2015). It is evident that our mtDNA interpretation and the autosomal results give a very
similar picture. Furthermore, independent support for the existence of an early center of
primitive modern humans in southeastern Asia, that originated very early expansions, has
come recently from improved phylogenetic resolution analysis of the Y-chromosome KM526
haplogroup. It has been detected a rapid diversification process of this haplogroup in
Southeast Asia-Oceania with subsequent westward expansions of the ancestors of
haplogroups R and Q that make up the majority of paternal lineages in Central Asia and
Europe (Karafet et al., 2014).

[zarahan]

Good find. Keep up the good work. based on this the theorized "backflow" from India to Africa
is not as strong as some think. From this new study:

"About the origin of the North African haplogroup M1
The existence of haplogroup M lineages in Africa was first detected in Ethiopian
populations by RFLP analysis (Passarino et al., 1998). Although an Asian influence was
contemplated to explain the presence of this M component on the maternal Ethiopian pool,
the dearth of M lineages in the Levant and its abundance in south Asia gave strength to the
hypothesis that haplogroup M1 in Ethiopia was a genetic indicator of the southern route out
of Africa. In addition, it was pointed out that probably this was the only successful early
dispersal (Quintana-Murci et al., 1999). However, the limited geographic range and genetic
diversity of M in Africa compared to India was used as an argument against this hypothesis
(Maca-Meyer et al., 2001; Roychoudhury et al., 2001; Metspalu et al., 2004; Olivieri et al.,
2006; Thangaraj et al., 2006; González et al., 2007), instead proposing M1 as a signal of
backflow to Africa, most probably from the Indian subcontinent. However, after extensive
phylogenetic and phylogeographic analyses for this marker (Metspalu et al., 2004; Olivieri
et al., 2006; Sun et al., 2006; González et al., 2007; Pennarun et al., 2012), this supposed
India to Africa connection was not found. "


It appears that M then had initial development, or if not the full haplogroup itself- various root types
of M first appeared in Africa- with these basal roots being refined over time into a distinct "M"
within Africa, or if outside- somewhere between Africa and India. M1 could be a variant developing within Africa.
This "root type" or "proto-M" model within Africa finds support from Bandelt 2006:

"These indicate that the root of L3 gives rise to a multifurcation from a
single haplotype producing a number of distinct subclades... The
simplest explanation for this geographical distribution [haplogroups M
and N], however, is an expansion of the root type within East Africa,
where several independent L3 branches thrive, including a sister group
to L3, christened L4 (Kivisild et al. 2004; Chap. 7), followed by
divergence into haplogroups M and N somewhere between the Horn of
Africa and the Indian subcontinent. Since neither the L3 root type nor
any other descendants survive outside Africa, the root type itself must
have become extinct during a period of genetic drift in the founder
population as it diversified into haplogroups M and N, if the
diversification was outside Africa. If on the other hand the
diversification was indeed within East Africa, then Haplogroups M and
N must have either been carried out of Africa in their entirety or
subsequently have become extinct within Africa, with the singular
exception of the derived M1."
- Hans-Jürgen Bandelt et. 2006. EDS. Human Mitochondrial DNA and
the Evolution of Homo sapiens.