Reply to Mendez et al: the ‘extremely ancient’ chromosome that still isn’t

Elhaik, Eran; Tatarinova, Tatiana V.; Klyosov, Anatole A.; Graur, Dan

doi:10.1038/ejhg.2014.227

Cited by 3 publications

(3 citation statements)

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“…In fact, this requires that mutation and substitution rates could be equated. The recent availability of autosomal, genome-wide estimates of the de novo mutation rate [ 12 – 14 ] prompted some authors [ 4 , 11 ] to adopt it as a base to calculate a substitution rate for the Y-chromosome, with due adjustments.This operation is not free of assumptions (thoroughly discussed in the Supplemental text of Scozzari et al[ 4 ]) and is currently a subject of vivid debate [ 15 – 17 ]. Specifically, there are several unknowns.…”

Section: Introductionmentioning

confidence: 99%

Regional Differences in the Accumulation of SNPs on the Male-Specific Portion of the Human Y Chromosome Replicate Autosomal Patterns: Implications for Genetic Dating

et al. 2015

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Factors affecting the rate and pattern of the mutational process are being identified for human autosomes, but the same relationships for the male specific portion of the Y chromosome (MSY) are not established. We considered 3,390 mutations occurring in 19 sequence bins identified by sequencing 1.5 Mb of the MSY from each of 104 present-day chromosomes. The occurrence of mutations was not proportional to the amount of sequenced bases in each bin, with a 2-fold variation. The regression of the number of mutations per unit sequence against a number of indicators of the genomic features of each bin, revealed the same fundamental patterns as in the autosomes. By considering the sequences of the same region from two precisely dated ancient specimens, we obtained a calibrated region-specific substitution rate of 0.716 × 10-9/site/year. Despite its lack of recombination and other peculiar features, the MSY then resembles the autosomes in displaying a marked regional heterogeneity of the mutation rate. An immediate implication is that a given figure for the substitution rate only makes sense if bound to a specific DNA region. By strictly applying this principle we obtained an unbiased estimate of the antiquity of lineages relevant to the genetic history of the human Y chromosome. In particular, the two deepest nodes of the tree highlight the survival, in Central-Western Africa, of lineages whose coalescence (291 ky, 95% C.I. 253–343) predates the emergence of anatomically modern features in the fossil record.

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Section: Introductionmentioning

confidence: 99%

Regional Differences in the Accumulation of SNPs on the Male-Specific Portion of the Human Y Chromosome Replicate Autosomal Patterns: Implications for Genetic Dating

et al. 2015

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“…Indeed, the calculations based on this Y lineage implied that the ancestor of the Y chromosome of all present-day men and the Y chromosome Mbo had lived in Africa 340,000 years ago [45]. This predates largely the date for the "mitochondrial Eve", the mother of all present-day maternal lineages, and the most ancient fossils of Homo sapiens.Even if the date is more likely to be closer to 208,000, as proposed by a later analysis [46] using a Y mutation rate in line with more recent calculations [39], this is still a surprising result. How can it be explained?…”

Section: Genetic Exchanges Between Archaic Populationsmentioning

confidence: 53%

Tracing the origin of our species through palaeogenomics

Geigl

Bennett

Grange

2015

BIO Web of Conferences

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Abstract. The recent breathtaking progress in whole genome sequencing technology allows access to the genomes both of ancient organisms and populations, including those now extinct. Despite the heavy degradation and the extremely low quantities of ancient DNA, it is sometimes possible to sequence an entire genome from a fossil. This enterprise has been successful in the case of fossilized remains from Neanderthals, a lineage of hominids that lived in Europe for 200,000 years and disappeared 30,000 years ago. An even greater surprise was the genome that has been obtained from a small finger bone preserved in a cave in the Siberian Altai Mountains. This genome revealed the existence of a human lineage previously unknown from the fossil record. The corresponding population mixed with the Neanderthals and the ancestors of the present day populations of South-East Asia. These hybridization events left different traces in the non-African human populations emphasizing the fact that we are genomic mosaics. The comparison of the different genomes also gives hints to how the genome of present-day populations was shaped and helps us to better understand which parts of our genetic make-up are responsible for the biological features of H. sapiens.

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“…In fact, there is recent evidence suggesting that natural selection is involved in the maintenance of genetic variation involving copy number variants [65]. This is an area where some controversy remains, following the discovery of a new lineage (haplogroup A00) in 2013, revisions of the estimated TMRCA have been suggested [66][67][68][69].…”

Section: Specific Particularities Of the Msy In Relation To Human Population Historymentioning

confidence: 99%

The Y Chromosome: A Complex Locus for Genetic Analyses of Complex Human Traits

Parker

Erzurumluoglu

Rodriguez

2020

Genes

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The Human Y chromosome (ChrY) has been demonstrated to be a powerful tool for phylogenetics, population genetics, genetic genealogy and forensics. However, the importance of ChrY genetic variation in relation to human complex traits is less clear. In this review, we summarise existing evidence about the inherent complexities of ChrY variation and their use in association studies of human complex traits. We present and discuss the specific particularities of ChrY genetic variation, including Y chromosomal haplogroups, that need to be considered in the design and interpretation of genetic epidemiological studies involving ChrY.

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Reply to Mendez et al: the ‘extremely ancient’ chromosome that still isn’t

Cited by 3 publications

References 4 publications

Regional Differences in the Accumulation of SNPs on the Male-Specific Portion of the Human Y Chromosome Replicate Autosomal Patterns: Implications for Genetic Dating

Regional Differences in the Accumulation of SNPs on the Male-Specific Portion of the Human Y Chromosome Replicate Autosomal Patterns: Implications for Genetic Dating

Tracing the origin of our species through palaeogenomics

The Y Chromosome: A Complex Locus for Genetic Analyses of Complex Human Traits

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