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Title: Can the new mtDNA Phylogenic tree tell us anything about Y DNA migrations
Post by: Heber on April 06, 2012, 10:33:02 AM
Dienekes has an interesting commentary on the new mtDNA phylogenetic tree.

"The Cambridge Reference Sequence is dead, long live the RSRS! Let's hope for a smooth transition.

The supplement (the paper itself is open access).

Table S5 within the supplement is very interesting, as it contains age estimates for the nodes of the new mtDNA phylogeny, and places the common mtDNA ancestor of humans (represented by the new reference sequence) at ~177,000 years.

The age of L3 (~67,000 years) is a useful sanity check of the time depth estimates, and it corresponds with the onset of Marine Isotope Stage 4.

Another useful check is for that of haplogroup H (~13,000 years), consistent with a late Paleolithic origin and Neolithic expansion of this haplogroup."

The two main Eurasian macrohaplogroups M (~50,000 years) and N (~59,000 years) also appear appropriately dated on the cusp of the major Paleolithic expansion of humans across Eurasia. The higher age of N may indeed correspond to an earlier split (this haplogroup is shared by all Eurasians), whereas M has a more contained distribution (largely lacking in West Eurasians), and may have spread later. The age of haplogroup U (~47,000 years), which is the oldest West Eurasian lineage also seems to correspond appropriately to the arrival of the earliest modern humans in Europe.

Related: PhyloTree Build 14.

The American Journal of Human Genetics, Volume 90, Issue 4, 675-684, 6 April 2012 doi:10.1016/j.ajhg.2012.03.002

A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root

Doron M. Behar et al.

Mutational events along the human mtDNA phylogeny are traditionally identified relative to the revised Cambridge Reference Sequence, a contemporary European sequence published in 1981. This historical choice is a continuous source of inconsistencies, misinterpretations, and errors in medical, forensic, and population genetic studies. Here, after having refined the human mtDNA phylogeny to an unprecedented level by adding information from 8,216 modern mitogenomes, we propose switching the reference to a Reconstructed Sapiens Reference Sequence, which was identified by considering all available mitogenomes from Homo neanderthalensis. This “Copernican” reassessment of the human mtDNA tree from its deepest root should resolve previous problems and will have a substantial practical and educational influence on the scientific and public perception of human evolution by clarifying the core principles of common ancestry for extant descendants.

My own maternal haplogroup is H1C1
From the supplementary tables I get the age of my mtDNA ancestors as

H - 12,846
H1 - 9,888
H1C - 6,448
H1C1 - 3,518

What is interesting is that H age is consistent with a late Paleolithic origin and Neolithic expansion of this haplogroup. This is similar to the story of M269.

When I compare this mtDNA aDNA found in sites in Europe I find that H probably migrated from

H - Iberia
H1 - France
H1C - Isles
H1C1 - Ireland

This is coincidentally similar to the supposed migration path of my Y ancestors M269, L23, L5, L11, P312 to L21 and L21 supposed arrival in Ireland about 3,700.

Has anyone studied the overlapping migrations of mtDNA and Y.

Title: Re: Can the new mtDNA Phylogenic tree tell us anything about Y DNA migrations
Post by: Maliclavelli on April 06, 2012, 10:21:08 PM
Yes, your hypothesis could be likely, but also mine:


I am waiting that my hypotheses are verified by aDNA:

Y: not only many hg. G were Italian (Oetzi) and others
    from R1b1* to at least R-L51 overwhelmingly Italian

mt: now the demonstrated U5b3 is about 10,000 years old
      about H we shall consider my hypotheses about R0a/b, R0a1, HV4 etc.
      we are always trying to know the origin of an American adopted, whose ancestry
      is overwhelmingly Italian (autosomal 60%) whose mtDNA H could be the witness
      of the most ancient one

My K is now K1a1b1e (6000 years old)
That of my wife and sons from Sicily is K1c1f
That of my father is H41a.

Title: Re: Can the new mtDNA Phylogenic tree tell us anything about Y DNA migrations
Post by: Heber on April 07, 2012, 04:50:48 AM
Complete Mitochondrial Genomes Reveal Neolithic Expansion into Europe

This is an interesting study, supported by good aDNA, which shows the expansion of Neolithic farmers H at 9K BCE and the expansion of PGM Mesolithic hunter gatherers U at 20K and 10K BCE.  The Balkens, Italy and Iberia appear to have played a key role in the expansion. It appears to confirm that H mtDNA played the same and parallel role as R1b-M269 Y DNA expansion. Question, did R-M269 and H expand together?

"In both datasets, the direct comparison of skyline plots between the H-type and the U-type mtDNAs (Figure 3) reveals a population increase for individuals carrying the H-type starting around 9,000 YBP and continuing to the present, whereas the U-type shows a population expansion between 20,000 and 10,000 YBP with a putative period of slight decrease between 6,000 and 5,000 YBP."

"The high frequency of H-type mtDNAs in European Neolithic populations and its complete absence in pre-Neolithic hunter-gatherers suggests that H-type mtDNAs arrived with early farmers in Europe. The population size increase observed between 9,000 and 5,000 YBP likely represents the population expansion that accompanied the Neolithic revolution."

The Neolithic transition from hunting and gathering to farming and cattle breeding marks one of the most drastic cultural changes in European prehistory. Short stretches of ancient mitochondrial DNA (mtDNA) from skeletons of pre-Neolithic hunter-gatherers as well as early Neolithic farmers support the demic diffusion model where a migration of early farmers from the Near East and a replacement of pre-Neolithic hunter-gatherers are largely responsible for cultural innovation and changes in subsistence strategies during the Neolithic revolution in Europe. In order to test if a signal of population expansion is still present in modern European mitochondrial DNA, we analyzed a comprehensive dataset of 1,151 complete mtDNAs from present-day Europeans. Relying upon ancient DNA data from previous investigations, we identified mtDNA haplogroups that are typical for early farmers and hunter-gatherers, namely H and U respectively. Bayesian skyline coalescence estimates were then used on subsets of complete mtDNAs from modern populations to look for signals of past population expansions. Our analyses revealed a population expansion between 15,000 and 10,000 years before present (YBP) in mtDNAs typical for hunters and gatherers, with a decline between 10,000 and 5,000 YBP. These corresponded to an analogous population increase approximately 9,000 YBP for mtDNAs typical of early farmers. The observed changes over time suggest that the spread of agriculture in Europe involved the expansion of farming populations into Europe followed by the eventual assimilation of resident hunter-gatherers. Our data show that contemporary mtDNA datasets can be used to study ancient population history if only limited ancient genetic data is available.

Archaeological evidence suggests that agrarian societies emerged in Western Asia around 11,000 years before present (YBP) [1] and rapidly spread reaching South Eastern Europe by approximately 9,000 YBP [2]. The transition from pre-Neolithic hunter-gatherer societies to Neolithic farming and cattle breeding is often called the Neolithic revolution and marks one of the most pronounced cultural changes in European prehistory [3], [4] that can be observed in the archaeological record all over Europe [5]. By around 5,000 YBP almost all populations in mainland Europe practiced agriculture. There are two main hypotheses for how Neolithic cultures spread across Europe. The first, suggests cultural transmission as the main factor, i.e. that the new technologies and subsistence strategies were learned from neighbouring groups [6]. The second hypothesis suggests an expansion of farmer populations from the Near East into Europe, replacing most of the pre-Neolithic hunter-gatherer populations. This population replacement model, termed demic diffusion, is conceived as population spread and expansion, with limited admixture with resident populations.

Recently, mitochondrial DNA (mtDNA) from skeletal remains of European early farmers and late hunter-gatherers has been retrieved [7]–[13]. The frequency of mtDNA haplogroups, defined by substitutions shared by related mtDNA types ( tree build 12), in early farmers across Europe [7], [10]–[13] was found to be overall similar to those in modern Europeans (Figure 1, Figure S4, Figure S5), while pre-Neolithic hunter-gatherers appear to be quite distinct (Figure 1). In particular, 83% (19 out of 23) of hunter-gatherers analyzed to date carry mtDNAs belonging to haplogroup U [9], [10], [14] and none of the hunter-gatherers fall in haplogroup H. In contrast, haplogroup U has been found in only 13 of 105 (around 12%) individuals from early farming cultures of Europe and it occurs in less than 21% of modern Europeans, while haplogroup H comprises between 25% and 37% of mtDNAs retrieved from early farming cultures (Figure S4) and is in about 30% of contemporary Europeans (Figure 1). The mtDNA data thus suggest that the pre-Neolithic populations in Europe were largely replaced by in-coming Neolithic farming groups, with a maximum mtDNA contribution of around 20% from pre-Neolithic hunter-gatherers [8]–[10]. The genetic contribution of pre-Neolithic hunter-gatherers to later Neolithic populations is furthermore supported by a similar frequency of U subhaplogroups (U5, U4, K and U2) that were found in pre-Neolithic hunter-gatherers (Figure S3) and are still the most common U-subhaplogroups in modern Central Europeans (Figure S5).

Title: Re: Can the new mtDNA Phylogenic tree tell us anything about Y DNA migrations
Post by: Maliclavelli on April 07, 2012, 05:55:14 AM
I have discussed this paper elsewhere and am disliked by the presence of Svante Paabo (a genius in his field) amongst the authors, but I think having demonstrated on this forum and elsewhere that:
1)   there were in Europe mtDNA R0a’b, R0a1*, HV1a’b’c, HV4 etc., not derived from Arabia
2)   there were YDNA R1b1* etc. not derived from the Caucasian one but ancestor of the European subclades (see again R-L51*: 4% in Central-North Italy, 0,3% Eastwards).

If this is true, also mtDNA H  could have been born in Europe. Not everything we find in Europe has come from elsewhere.