The case of the unreliable SNP: Recurrent back-mutation of Y-chromosomal marker P25 through gene conversion

Adams, Susan M.; King, Turi; Bosch, Elena; Jobling, Mark A.

doi:10.1016/j.forsciint.2005.06.003

Cited by 36 publications

(28 citation statements)

References 22 publications

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“…Typing methods for six of these markers (P25, P297, M335, M18, M73, and M269) were described earlier. 18,28,[30][31][32][33] The marker P25, which has been shown to be liable to back mutation by gene conversion, 34 was analyzed in the Asian samples from CEPH and in the R1b (R-M343) chromosomes lacking any other internal mutation.…”

Section: Molecular Analysismentioning

confidence: 99%

Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages

et al. 2010

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Although human Y chromosomes belonging to haplogroup R1b are quite rare in Africa, being found mainly in Asia and Europe, a group of chromosomes within the paragroup R-P25* are found concentrated in the central-western part of the African continent, where they can be detected at frequencies as high as 95%. Phylogenetic evidence and coalescence time estimates suggest that R-P25* chromosomes (or their phylogenetic ancestor) may have been carried to Africa by an Asia-to-Africa back migration in prehistoric times. Here, we describe six new mutations that define the relationships among the African R-P25* Y chromosomes and between these African chromosomes and earlier reported R-P25 Eurasian sub-lineages. The incorporation of these new mutations into a phylogeny of the R1b haplogroup led to the identification of a new clade (R1b1a or R-V88) encompassing all the African R-P25* and about half of the few European/west Asian R-P25* chromosomes. A worldwide phylogeographic analysis of the R1b haplogroup provided strong support to the Asia-to-Africa back-migration hypothesis. The analysis of the distribution of the R-V88 haplogroup in 41800 males from 69 African populations revealed a striking genetic contiguity between the Chadic-speaking peoples from the central Sahel and several other Afroasiatic-speaking groups from North Africa. The R-V88 coalescence time was estimated at 9200-5600 kya, in the early mid Holocene. We suggest that R-V88 is a paternal genetic record of the proposed mid-Holocene migration of proto-Chadic Afroasiatic speakers through the Central Sahara into the Lake Chad Basin, and geomorphological evidence is consistent with this view.

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Section: Molecular Analysismentioning

confidence: 99%

Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages

et al. 2010

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“…Thus, the branches defined by the M18 and M335 mutations might descend from P297(+) chromosomes. The P25 marker represents a paralogous sequence variant (PSV): three copies of the P25 sequence lie within palindromic repeats, with the mutation at P25 on one copy (Adams et al 2006). P25 is also known to undergo reversion by gene conversion.…”

Section: Caveatsmentioning

confidence: 99%

New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree

et al. 2008

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Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.

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“…The YCC nomenclature labels reflect the exclusion of the P25 SNP from the phylogeny given its innate instability. 44 The asterisk (*) refers to the unresolved status of the phylogenetic haplogroups beyond the specified marker. (b) Approximate locations of the 118 studied populations appear as circles on the map that are proportional to sample sizes, the smallest n¼9 and the largest n¼522.…”

Section: The Phylogenetic Relationships Of Rs9786140 [M412] Rs9786194mentioning

confidence: 99%

A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe

Myres¹,

et al. 2010

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The phylogenetic relationships of numerous branches within the core Y-chromosome haplogroup R-M207 support a West Asian origin of haplogroup R1b, its initial differentiation there followed by a rapid spread of one of its sub-clades carrying the M269 mutation to Europe. Here, we present phylogeographically resolved data for 2043 M269-derived Y-chromosomes from 118 West Asian and European populations assessed for the M412 SNP that largely separates the majority of Central and West European R1b lineages from those observed in Eastern Europe, the Circum-Uralic region, the Near East, the Caucasus and Pakistan. Within the M412 dichotomy, the major S116 sub-clade shows a frequency peak in the upper Danube basin and Paris area with declining frequency toward Italy, Iberia, Southern France and British Isles. Although this frequency pattern closely approximates the spread of the Linearbandkeramik (LBK), Neolithic culture, an advent leading to a number of pre-historic cultural developments during the past r10 thousand years, more complex pre-Neolithic scenarios remain possible for the L23(xM412) components in Southeast Europe and elsewhere.

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The case of the unreliable SNP: Recurrent back-mutation of Y-chromosomal marker P25 through gene conversion

Cited by 36 publications

References 22 publications

Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages

Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages

New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree

A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe

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