Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree

Scozzari, Rosaria; Massaia, Andrea; D’Atanasio, Eugenia; Myres, Natalie M.; Perego, Ugo A.; Trombetta, Beniamino; Cruciani, Fulvio

doi:10.1371/journal.pone.0049170

Cited by 29 publications

(44 citation statements)

References 41 publications

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“…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-African branches (subclades, haplogroups), leading to a common ancestor of both, when moved back in time.…”

Section: Figurementioning

confidence: 50%

“…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 "Out 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.…”

Section: Snp Mutations Show That Non-africans Are Not Descendants Of mentioning

confidence: 99%

“…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 haplogroup A, which the authors (Scozzari et al, 2012) call all "African", apparently by definition. All other subclades, except one, are related to haplogroup B, which the authors also call "African", again by definition.…”

Section: Figurementioning

confidence: 99%

“…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.…”

Section: Figurementioning

confidence: 99%

“…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 Figure 2, and briefly announce that "it supports the 'Out of Africa' theory".…”

Section: Figurementioning

confidence: 99%

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

Klyosov¹

2014

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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-African-by origin-B) occurred 160,000 ± 12,000 years before present. Haplogroup B is by origin a nonAfrican haplogroup, which is very distant-time-wise-from haplogroups A, by at least 250 -300 thousand years, and could not possibly have descended from haplogroups A1a 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-L6. The article shows how recent OOA studies (as well as earlier ones) employ biased interpretations to artificially "prove" the OOA concept. The article 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.

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Section: Figurementioning

confidence: 50%

Section: Snp Mutations Show That Non-africans Are Not Descendants Of mentioning

confidence: 99%

Section: Figurementioning

confidence: 99%

“…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.…”

Section: Figurementioning

confidence: 99%

Section: Figurementioning

confidence: 99%

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

Klyosov¹

2014

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Multiplex genotyping assays for fine‐resolution subtyping of the major human Y‐chromosome haplogroups E, G, I, J, and R in anthropological, genealogical, and forensic investigations

et al. 2013

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Inherited DNA polymorphisms located within the nonrecombing portion of the human Y chromosome provide a powerful means of tracking the patrilineal ancestry of male individuals. Recently, we introduced an efficient genotyping method for the detection of the basal Y-chromosome haplogroups A to T, as well as an additional method for the dissection of haplogroup O into its sublineages. To further extend the use of the Y chromosome as an evolutionary marker, we here introduce a set of genotyping assays for fine-resolution subtyping of haplogroups E, G, I, J, and R, which make up the bulk of Western Eurasian and African Y chromosomes. The marker selection includes a total of 107 carefully selected bi-allelic polymorphisms that were divided into eight hierarchically organized multiplex assays (two for haplogroup E, one for I, one for J, one for G, and three for R) based on the single-base primer extension (SNaPshot) technology. Not only does our method allow for enhanced Y-chromosome lineage discrimination, the more restricted geographic distribution of the subhaplogroups covered also enables more fine-scaled estimations of patrilineal bio-geographic origin. Supplementing our previous method for basal Y-haplogroup detection, the currently introduced assays are thus expected to be of major relevance for future DNA studies targeting male-specific ancestry for forensic, anthropological, and genealogical purposes.

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Seeing the Wood for the Trees: A Minimal Reference Phylogeny for the Human Y Chromosome

et al. 2013

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During the last few decades, a wealth of studies dedicated to the human Y chromosome and its DNA variation, in particular Y-chromosome single-nucleotide polymorphisms (Y-SNPs), has led to the construction of a well-established Y-chromosome phylogeny. Since the recent advent of new sequencing technologies, the discovery of additional Y-SNPs is exploding and their continuous incorporation in the phylogenetic tree is leading to an ever higher resolution. However, the large and increasing amount of information included in the "complete" Y-chromosome phylogeny, which now already includes many thousands of identified Y-SNPs, can be overwhelming and complicates its understanding as well as the task of selecting suitable markers for genotyping purposes in evolutionary, demographic, anthropological, genealogical, medical, and forensic studies. As a solution, we introduce a concise reference phylogeny whereby we do not aim to provide an exhaustive tree that includes all known Y-SNPs but, rather, a quite stable reference tree aiming for optimal global discrimination capacity based on a strongly reduced set that includes only the most resolving Y-SNPs. Furthermore, with this reference tree, we wish to propose a common standard for Y-marker as well as Y-haplogroup nomenclature. The current version of our tree is based on a core set of 417 branch-defining Y-SNPs and is available online at http://www.phylotree.org/Y.

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Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree

Cited by 29 publications

References 41 publications

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

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

Multiplex genotyping assays for fine‐resolution subtyping of the major human Y‐chromosome haplogroups E, G, I, J, and R in anthropological, genealogical, and forensic investigations

Seeing the Wood for the Trees: A Minimal Reference Phylogeny for the Human Y Chromosome

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