Sardinia! Sardinia! Did AMH originate there?

[djoser-xyyman]

Having explored other forums recently I decided to join a few. To see what I am up against. To my surprise at one of the forum the “experts” are really laymen. Novices. …and that was a popular genetic testing site. Nevertheless I had a few discussions which led me to create this thread. During the discussion a few things were brought up that I decided to dig further into. And I came across these papers. I am not sure why or how I missed this when they were first published These papers put so many thing in perspective. I knew Sardinia was inportant in AMH exit out of Africa but I am beginning to see it is a lot more important than I first thought. This is the first time it as been reported that Sardinia harbor one of the deepest clade of our species. Hg-A. If fact it is unique to Sardinia. We found out recently that Sardinians also harbor their own unique version of R-V88 found in the Central African regions(3 “Slaves” in the Caribbean study). Furthermore Sardinia harbors the closest matching clade, on record, to Otzi Alps Iceman. We also know that Otzi matches closest to Sardinians through AIM/SNPs.



So here are excerpts from the two studies. Hit me up with any questions.


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Francalacci P, Morelli L, Angius A, Berutti R, Reinier F, Atzeni R, Pilu R, Busonero F, Maschio A, Zara I et al. 2013. Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny. Science 341(6145): 565-569.



Ancient DNA analysis

The reliability of the phylogenetic rate was assessed using a sequence coming from an ancient mummified sample (Ötzi) of known age, radiocarbon dated to 5,300 years old (9). This sequence belongs to a clade of haplogroup G encompassing a Tuscan, a Corsican and 8 Sardinian samples (table S3). It shares with the other samples 10 derived SNPs, while it is not possible to assign the allelic status to other 17 SNPs lacking of a readable signal in the ancient sample. Another 8 SNPs, showing the ancestral allele, separate the Ötzi sequences from the Tuscan, Corsican and Sardinian cluster, which presents the derived allele. Subsequently, the Tuscan sequence separates from the Sardo-Corsican ones. In addition, the Ötzi sequence shows 15 singletons, although this number is likely underestimated, considering the poor coverage of ancient DNA. Applying our phylogenetic rate (one mutation every about 200 years), the date for the MRCA between Ötzi and the Sardo- Corsican samples ranges from about 9,000-12,500 years ago (depending on the assignment of the 17 SNPs of unknown status) (fig. S6). The number of Ötzi’s singletons indicates a separate evolution of at least 3,000 years, resulting in an estimated age of 6,000 years at its lower limit, approaching the actual age of the specimen. However, this estimate is older and thus does not conflict with our phylogenetic rate, whereas a younger age would have contradicted it

[djoser-xyyman]

Archaeological context

The long history of human settlement in Sardinia is illustrated by the known Mesolithic to Late Neolithic period archaeological sites (Figures S7). The first direct evidence of modern Homo sapiens in Sardinia dates back to upper Paleolithic, with a human phalanx discovered at Corbeddu cave (Central Eastern Sardinia) and radiocarbon dated to ~20,000 years ago (BP) (30). However, based on the available evidence, this early peopling remained isolated. Sardinia began to be substantially inhabited during the Mesolithic (10,500-8,000 years BP),


Genetic variation within the male-specific portion of the Y chromosome (MSY) can clarify the origins of contemporary populations, but previous studies were hampered by partial genetic information. Population sequencing of 1204 Sardinian males identified 11,763 MSY single-nucleotide polymorphisms, 6751 of which have NOT previously been observed.


Recently, high-coverage Y chromosome sequencing data from 36males from different worldwide populations (5) assessed 6662 phylogenetically informative variants and estimated the timing of past events, including a putative coalescence time for modern humans of ~101,000 to 115,000 years ago


We generated a high-resolution analysis of the MSY from population sequencing of 1204 Sardinian males (8). We used a hierarchical approach and, to be consistent with previous work (5), focused on approximately 8.97 mega– base pairs (Mbp) from the Y chromosome in the X-degenerated region. We inferred 11,763 MSY phylogenetically informative single-nucleotide polymorphisms (SNPs), detected in at least two individuals and unequivocally associated with specific haplogroups and sub-haplogroups; 6751 of these SNPs had not thus far been reported in PUBLIC Databases

[djoser-xyyman]

The average number of derived alleles in the 1204 males is 1002.6 (T21.2 SD) which, consistent with a neutral evolution of these Y polymorphisms, shows a remarkable uniformity of the branch length.


As shown in a schematic tree (Fig. 1), all of the most common Y-chromosome haplogroups previously detected in Europe are present in our sample (Table 1), with the sole exception of the northernmost Uralic haplogroup N. The first bifurcation separates the mostly sub-Saharan haplogroup A (7 individuals, 0.6%in our sample) from the others. Haplogroup E (132, 11.0%) is present with its European clade, characterized by the presence of the M35 marker, together with a small number of individuals belonging to themainly African clade E1a. The rare haplogroup F (7, 0.6%) is related to haplogroup G (131, 10.9%), which shows a private Sardinian- Corsican clade whose ancient roots have been found in an Eneolithic sample from the Italian Alps (9). Haplogroup I (490, 40.7%) is of special interest because it is mostly represented by the I2a1a clade, identified by theM26 marker, which is at high frequencies in Sardinia (10) but is rare or absent elsewhere (11). Haplogroup J (161, 13.4%) is observed with its MAIN subgroups; and the super-haplogroup K is present with the related


Related L and T branches (36, 3.0%), with a single individual of haplogroup Q (1, 0.08%) and with the more common haplogroup R (239, 19.9%) occurring mostly as the western European M173- M269 branch. Almost half of the discovered SNPs (4872) make up the skeleton of the phylogenetic tree and constitute the root of the main clades. The skeleton includes*** lineages that are unbranched for most of their length***, with ramifications only in the terminal portion. This indicates an early separation of the clades, followed by new variability generated during subsequent expansion events.

To estimate points of divergence between Sardinian and continental clades, we sequenced two samples from the Basque Country and northern Italy, belonging to haplogroup I, and two, from Tuscany and Corsica, belonging to haplogroup G. We also analyzed the sequence of the so-called Iceman Ötzi (9), together with 133 publicly available European sequences from the 1000 Genomes Project database and those SNPs from the International Society of Genetic Genealogy (ISOGG) database detected outside Sardinia.

Considering two other ***basal*** lineages encompassing ***only*** Sardinian samples, we can infer that when the I2a1a sub-haplogroup entered Sardinia, it had already differentiated into four founder lineages that then accumulated private Sardinian variability. Two other founder clades show similar divergence after entry into the island: one belonging to haplogroup R1b1c (xV35) (whose differentiation is identified contrasting the Sardinian data with the ISOGG and 1000 Genome data), and the other to haplogroup G2a2b-L166 (identified by divergence from a sequenced Corsican sample).

The initial expansion of the Sardinian population, used for calibration, is marked by six clades belonging to three different haplogroups, with an average variation of around 35 to 40 SNPs, representing the ancient founder core of modern Sardinians. Our data further suggest a more intricate scenario of Sardinian demographic history. Specifically, clades of E, R, and G that show Sardinian specific variability of 25 to 30 SNPs are consistent with further expansion in the Late Neolithic (~5500 to 6000 years ago) (Table 1). Additional variation putatively arrived with groups of individuals carrying other haplogroups (namely the I clades different from I2a1, J, and T).

[djoser-xyyman]

[djoser-xyyman]

[djoser-xyyman]

[djoser-xyyman]

So the big question is ...what does this all mean?

1. The Sardinians carry a UNIQUE branch of the deepest male haplogroup ie A found is Khoe-San, Ethiopians, and Berbers. Mbos being the deepest with A00.
2. Sardinians also carry UNIQUE branches of the old R1b-V88 clade found also in central Africans.
3. Sardinians carry branches of PN2 that has NOT yet diversified. The San also carry the same along with Great Lakes and some Berbers.
4. The Maasai, MKK, carry the ancestral form of the hg-A3 found in Sardinians and Ethiopians.
5. Interestingly the Sardinians carry, along with R-V88, R1b-M269, R1a, L and Q, along with hg-F.
6. In addition there version of hg-G is related to Otzi Alps Ice man.
7. Sardinians carry ancestral versions of hg-I


You tell me. what does this all mean?

[djoser-xyyman]

[djoser-xyyman]

Off course I am kidding about the origin thing. But undoubtedly it was an important stepping stone.