The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes

Skaletsky, Helen; Kuroda-Kawaguchi, Tomoko; Minx, Patrick; Cordum, Holland S.; Hillier, LaDeana W.; Brown, Laura G.; Repping, Sjoerd; Pyntikova, Tatyana; Ali, Johar; Bieri, Tamberlyn; Chinwalla, Asif T.; Delehaunty, Andrew; Delehaunty, Kim D.; Du, Hui; Fewell, Ginger A.; Fulton, Lucinda A.; Fulton, Robert S.; Graves, Tina; Hou, Shunfang; Latrielle, Philip; Leonard, Shawn; Mardis, Elaine R.; Maupin, Rachel; Mcpherson, John Douglas; Miner, Tracie L.; Nash, William E.; Nguyen, Christine; Ozersky, Philip; Pepin, Kymberlie H.; Rock, Susan M.; Rohlfing, Tracy; Scott, Kelsi; Schultz, Brian; Strong, Cindy; Tin-Wollam, Aye Mon; Yang, Shiaw-Pyng; Waterston, Robert H.; Wilson, Richard K.; Rozen, Steve; Page, David C.

doi:10.1038/nature01722

Cited by 1,901 publications

(2,347 citation statements)

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“…This estimate is consistent with estimates derived from human-chimpanzee Y chromosome analyses (1.5 Â 10 À9 À2.1 Â 10 À9 substitutions per nucleotide per year) under the assumption of a divergence time range of 5-7 million years. 16,17 A substitution rate estimate of 1 Â 10 À9 substitutions per nucleotide per year is a widely accepted estimate. For example, Wei et al 18 applied this rate to estimate that the time depth of the Y-chromosomal tree was B101 000-115 000 years, and dated the lineages found outside Africa to 57 000-74 000 years.…”

Section: Resultsmentioning

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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Section: Resultsmentioning

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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“…95% of Y chromosome genomes are male‐specific, containing 23 million base pairs of male‐specific euchromosome (Skaletsky et al., 2003). Y chromosome genetic analysis plays an important role in the research of human male evolution, complementary medicine, and forensic genetics (Jobling & Tyler‐Smith, 2003).…”

Section: Discussionmentioning

confidence: 99%

Linking Y‐chromosomal short tandem repeat loci to human male impulsive aggression

Yang

Cao

et al. 2017

Brain and Behavior

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IntroductionMen are more susceptible to impulsive behavior than women. Epidemiological studies revealed that the impulsive aggressive behavior is affected by genetic factors, and the male‐specific Y chromosome plays an important role in this behavior. In this study, we investigated the association between the impulsive aggressive behavior and Y‐chromosomal short tandem repeats (Y‐STRs) loci.MethodsThe collected biologic samples from 271 offenders with impulsive aggressive behavior and 492 healthy individuals without impulsive aggressive behavior were amplified by PowerPlexRY23 PCR System and the resultant products were separated by electrophoresis and further genotyped. Then, comparisons in allele and haplotype frequencies of the selected 22 Y‐STRs were made in the two groups.ResultsOur results showed that there were significant differences in allele frequencies at DYS448 and DYS456 between offenders and controls (p < .05). Univariate analysis further revealed significant frequency differences for alleles 18 and 22 at DYS448 (0.18 vs 0.27, compared to the controls, p = .003, OR=0.57,95% CI=0.39–0.82; 0.03 vs 0.01, compared to the controls, p = .003, OR=7.45, 95% CI=1.57–35.35, respectively) and for allele 17 at DYS456 (0.07 vs 0.14, compared to the controls, p = .006, OR=0.48, 95% CI =0.28–0.82) between two groups. Interestingly, the frequency of haploid haplotype 22‐15 on the DYS448‐DYS456 (DYS448‐DYS456‐22‐15) was significantly higher in offenders than in controls (0.033 vs 0.004, compared to the control, p = .001, OR = 8.42, 95%CI =1.81–39.24). Moreover, there were no significant differences in allele frequencies of other Y‐STRs loci between two groups. Furthermore, the unconditional logistic regression analysis confirmed that alleles 18 and 22 at DYS448 and allele 17 at DYS456 are associated with male impulsive aggression. However, the DYS448‐DYS456‐22‐15 is less related to impulsive aggression.ConclusionOur results suggest a link between Y‐chromosomal allele types and male impulsive aggression.

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“…10 The high level of similarity between certain regions of Y and X chromosomes/autosomes 16,17 can blur signals of genotyping Y-SNPs, as can the very high proportion of ampliconic repeats that are often highly similar to each other (usually 499.9% identity). 16,17 Consequently, we employed specific quality controls and excluded the following data in 117 male samples: (1) Y-SNPs with heterozygous alleles; (2) Y-SNPs genotyped with a missing rate more than 5%; and (3) known Y-SNPs with identical genotypes (ie, invariants).…”

Section: Data Filteringmentioning

confidence: 99%

Retrieving Y chromosomal haplogroup trees using GWAS data

Peng

Fan

et al. 2013

Eur J Hum Genet

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Phylogenetically informative Y chromosomal single-nucleotide polymorphisms (Y-SNPs) integrated in DNA chips have not been sufficiently explored in most genome-wide association studies (GWAS). Herein, we introduce a pipeline to retrieve Y-SNP data. We introduce the software YTool (http://mitotool.org/ytool/) to handle conversion, filtering, and annotation of the data. Genomewide SNP data from populations in Myanmar are used to construct a haplogroup tree for 117 Y chromosomes based on 369 high-confidence Y-SNPs. Parallel genotyping and published resequencing data of Y chromosomes confirm the validity of our pipeline. We apply this strategy to the CEU HapMap data set and construct a haplogroup tree with 107 Y-SNPs from 39 individuals. The retrieved Y-SNPs can discern the parental genetic structure of populations. Given the massive quantity of data from GWAS, this method facilitates future investigations of Y chromosome diversity.

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The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes

Cited by 1,901 publications

References 50 publications

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

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

Linking Y‐chromosomal short tandem repeat loci to human male impulsive aggression

Retrieving Y chromosomal haplogroup trees using GWAS data

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