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

Trombetta B, D'Atanasio E, Massaia A, Myres NM, Scozzari R, Cruciani F, Novelletto A - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus

Dated tree including 104 subjects plus the Ust'-Ishim [27] and Loschbour [28] specimens (arrowed).These latter were used as calibration points, by means of normally distributed priors with means 45,000 and 7,205 years ago, respectively. The 95% C.I.'s for the age of each node are represented as grey bars. The clade corresponding to Hg E1b1b-M35 has been collapsed since it is discussed in detail in a dedicated paper [65]. Groups of branches discussed in the text and in Table 4 are shadowed: a) deep branches; b) terminal branches with rho < = 20; c) terminal branches with length < = 10 mutations. Note that the positioning of the root is the result of the Bayesian process and not of the assessment of ancestral/derived states in branch 0 based on an outgroup (e.g. the chimpanzee).
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pone.0134646.g002: Dated tree including 104 subjects plus the Ust'-Ishim [27] and Loschbour [28] specimens (arrowed).These latter were used as calibration points, by means of normally distributed priors with means 45,000 and 7,205 years ago, respectively. The 95% C.I.'s for the age of each node are represented as grey bars. The clade corresponding to Hg E1b1b-M35 has been collapsed since it is discussed in detail in a dedicated paper [65]. Groups of branches discussed in the text and in Table 4 are shadowed: a) deep branches; b) terminal branches with rho < = 20; c) terminal branches with length < = 10 mutations. Note that the positioning of the root is the result of the Bayesian process and not of the assessment of ancestral/derived states in branch 0 based on an outgroup (e.g. the chimpanzee).

Mentions: Then, we considered four classes of tree branches, corresponding to different time windows (greyed in Fig 2): very recent branches with a length of 10 mutations or less (approximately equivalent to the last 9.3 ky); recent branches defined as those that coalesce at nodes with an average distance from the tip (rho) of 20 mutations or less; deep African branches lying between the A0-T node and any node older than 68 kya; all other branches, lumped in a group of medium antiquity. Hg A00 was excluded as it crosses all ages and is represented by a single individual. Also in all of these partitions, the regions C and E (Table 1) showed the highest numbers of mutations/100 kb. Non-proportionality as compared to the amount of sequenced positions for each bin was replicated in the four time windows and reached significance for the deep (p = 0.003) and intermediate (p = 2.0 × 10−11) branches (Table 4).


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

Trombetta B, D'Atanasio E, Massaia A, Myres NM, Scozzari R, Cruciani F, Novelletto A - PLoS ONE (2015)

Dated tree including 104 subjects plus the Ust'-Ishim [27] and Loschbour [28] specimens (arrowed).These latter were used as calibration points, by means of normally distributed priors with means 45,000 and 7,205 years ago, respectively. The 95% C.I.'s for the age of each node are represented as grey bars. The clade corresponding to Hg E1b1b-M35 has been collapsed since it is discussed in detail in a dedicated paper [65]. Groups of branches discussed in the text and in Table 4 are shadowed: a) deep branches; b) terminal branches with rho < = 20; c) terminal branches with length < = 10 mutations. Note that the positioning of the root is the result of the Bayesian process and not of the assessment of ancestral/derived states in branch 0 based on an outgroup (e.g. the chimpanzee).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4520482&req=5

pone.0134646.g002: Dated tree including 104 subjects plus the Ust'-Ishim [27] and Loschbour [28] specimens (arrowed).These latter were used as calibration points, by means of normally distributed priors with means 45,000 and 7,205 years ago, respectively. The 95% C.I.'s for the age of each node are represented as grey bars. The clade corresponding to Hg E1b1b-M35 has been collapsed since it is discussed in detail in a dedicated paper [65]. Groups of branches discussed in the text and in Table 4 are shadowed: a) deep branches; b) terminal branches with rho < = 20; c) terminal branches with length < = 10 mutations. Note that the positioning of the root is the result of the Bayesian process and not of the assessment of ancestral/derived states in branch 0 based on an outgroup (e.g. the chimpanzee).
Mentions: Then, we considered four classes of tree branches, corresponding to different time windows (greyed in Fig 2): very recent branches with a length of 10 mutations or less (approximately equivalent to the last 9.3 ky); recent branches defined as those that coalesce at nodes with an average distance from the tip (rho) of 20 mutations or less; deep African branches lying between the A0-T node and any node older than 68 kya; all other branches, lumped in a group of medium antiquity. Hg A00 was excluded as it crosses all ages and is represented by a single individual. Also in all of these partitions, the regions C and E (Table 1) showed the highest numbers of mutations/100 kb. Non-proportionality as compared to the amount of sequenced positions for each bin was replicated in the four time windows and reached significance for the deep (p = 0.003) and intermediate (p = 2.0 × 10−11) branches (Table 4).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus