Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females

Poznik, G. David; Henn, Brenna M.; Yee, Muh Ching; Śliwerska, Elżbieta; Euskirchen, Ghia; Lin, Alice A.; Snyder, M; Quintana-Murci, Lluı́s; Kidd, Jeffrey M.; Underhill, Peter A.; Bustamante, Carlos D.

doi:10.1126/science.1237619

Cited by 244 publications

(243 citation statements)

References 47 publications

(37 reference statements)

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“…The marker Z280 was not used as it maps to duplicated ampliconic tracts. map 101-bp sequencing reads to the hg19 human reference, and we called genotypes across 9.99 Mb and estimated coalescence times using a rate of 1 SNP accumulating per 122 years as described in Poznik et al 4 …”

Section: Whole Y-chromosome Sequencingmentioning

confidence: 99%

“…[1][2][3][4][5] The International Society of Genetic Genealogy 10 has aggregated these variants and those discovered with previous technologies into a public resource that population surveys can leverage to further elucidate the geographic origins of and structure within haplogroups. [6][7][8][9][10][11][12][13] Y-chromosome haplogroup R (hg R) is one of 20 that comprise the standardized global phylogeny.…”

Section: Introductionmentioning

confidence: 99%

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The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

Underhill¹,

Poznik²,

Rootsi³

et al. 2014

Eur J Hum Genet

138

137

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,23R1a-M420 is one of the most widely spread Y-chromosome haplogroups; however, its substructure within Europe and Asia has remained poorly characterized. Using a panel of 16 244 male subjects from 126 populations sampled across Eurasia, we identified 2923 R1a-M420 Y-chromosomes and analyzed them to a highly granular phylogeographic resolution. Whole Y-chromosome sequence analysis of eight R1a and five R1b individuals suggests a divergence time of B25 000 (95% CI: 21 300-29 000) years ago and a coalescence time within R1a-M417 of B5800 (95% CI: 4800-6800) years. The spatial frequency distributions of R1a sub-haplogroups conclusively indicate two major groups, one found primarily in Europe and the other confined to Central and South Asia. Beyond the major European versus Asian dichotomy, we describe several younger sub-haplogroups. Based on spatial distributions and diversity patterns within the R1a-M420 clade, particularly rare basal branches detected primarily within Iran and eastern Turkey, we conclude that the initial episodes of haplogroup R1a diversification likely occurred in the vicinity of present-day Iran.

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Section: Whole Y-chromosome Sequencingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

Underhill¹,

Poznik²,

Rootsi³

et al. 2014

Eur J Hum Genet

138

137

View full text Add to dashboard Cite

show abstract

“…1 Binary markers such as SNPs (single-nucleotide polymorphisms) have low mutation rates,~10 − 8 per base per generation, 2 and represent often unique events in human evolution. STRs (short tandem repeats) are multiallelic markers and most have a mutation rate of 10 − 3 -10 − 4 per generation.…”

Section: Introductionmentioning

confidence: 99%

Y-chromosome diversity in Catalan surname samples: insights into surname origin and frequency

et al. 2015

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The biological behavior of the Y chromosome, which is paternally inherited, implies that males sharing the same surname may also share a similar Y chromosome. However, socio-cultural factors, such as polyphyletism, non-paternity, adoption, or matrilineal surname transmission, may prevent the joint transmission of the surname and the Y chromosome. By genotyping 17 Y-STRs and 68 SNPs in~2500 male samples that each carried one of the 50 selected Catalan surnames, we could determine sets of descendants of a common ancestor, the population of origin of the common ancestor, and the date when such a common ancestor lived. Haplotype diversity was positively correlated with surname frequency, that is, rarer surnames showed the strongest signals of coancestry. Introgression rates of Y chromosomes into a surname by non-paternity, adoption, and transmission of the maternal surname were estimated at 1.5 − 2.6% per generation, with some local variation. Average ages for the founders of the surnames were estimated at~500 years, suggesting a delay between the origin of surnames (twelfth and thirteenth centuries) and the systematization of their paternal transmission. We have found that, in general, a foreign etymology for a surname does not often result in a non-indigenous origin of surname founders; however, bearers of some surnames with an Arabic etymology show an excess of North African haplotypes. Finally, we estimate that surname prediction from a Y-chromosome haplotype, which may have interesting forensic applications, has a~60% sensitivity but a 17% false discovery rate.

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“…First, this estimate is more than double the oldest previous estimate of 141 500±15 600 ya, 3 and is hugely larger than all the other previous or subsequent estimates, which ranged from 46 000 to 160 000 ya. [4][5][6][7][8] Second, it significantly predated the most ancient mitochondrial DNA, which Poznik et al 7 had recently estimated to be only slightly younger than the Y chromosome (mtDNA:99 000-148 000 vs Y:120 000-156 000 ya). Third, this TMRCA estimate is 142 000 years older than the oldest known anatomically modern human, estimated to be 196 000±2000 years old.…”

Section: Introductionmentioning

confidence: 99%

The ‘extremely ancient’ chromosome that isn’t: a forensic bioinformatic investigation of Albert Perry’s X-degenerate portion of the Y chromosome

Elhaik

Tatarinova

Klyosov³

et al. 2014

Eur J Hum Genet

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Mendez and colleagues reported the identification of a Y chromosome haplotype (the A00 lineage) that lies at the basal position of the Y chromosome phylogenetic tree. Incorporating this haplotype, the authors estimated the time to the most recent common ancestor (TMRCA) for the Y tree to be 338 000 years ago (95% CI ¼ 237 000-581 000). Such an extraordinarily early estimate contradicts all previous estimates in the literature and is over a 100 000 years older than the earliest fossils of anatomically modern humans. This estimate raises two astonishing possibilities, either the novel Y chromosome was inherited after ancestral humans interbred with another species, or anatomically modern Homo sapiens emerged earlier than previously estimated and quickly became subdivided into genetically differentiated subpopulations. We demonstrate that the TMRCA estimate was reached through inadequate statistical and analytical methods, each of which contributed to its inflation. We show that the authors ignored previously inferred Y-specific rates of substitution, incorrectly derived the Y-specific substitution rate from autosomal mutation rates, and compared unequal lengths of the novel Y chromosome with the previously recognized basal lineage. Our analysis indicates that the A00 lineage was derived from all the other lineages 208 300 (95% CI ¼ 163 900-260 200) years ago.

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Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females

Cited by 244 publications

References 47 publications

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

Y-chromosome diversity in Catalan surname samples: insights into surname origin and frequency

The ‘extremely ancient’ chromosome that isn’t: a forensic bioinformatic investigation of Albert Perry’s X-degenerate portion of the Y chromosome

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