Recent common ancestry of human Y chromosomes: evidence from DNA sequence data - PubMed (original) (raw)

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Recent common ancestry of human Y chromosomes: evidence from DNA sequence data

R Thomson et al. Proc Natl Acad Sci U S A. 2000.

Abstract

We consider a data set of DNA sequence variation at three Y chromosome genes (SMCY, DBY, and DFFRY) in a worldwide sample of human Y chromosomes. Between 53 and 70 chromosomes were fully screened for sequence variation at each locus by using the method of denaturing high-performance liquid chromatography. The sum of the lengths of the three genes is 64,120 bp. We have used these data to study the ancestral genealogy of human Y chromosomes. In particular, we focused on estimating the expected time to the most recent common ancestor and the expected ages of certain mutations with interesting geographic distributions. Although the geographic structure of the inferred haplotype tree is reminiscent of that obtained for other loci (the root is in Africa, and most of the oldest non-African lineages are Asian), the expected time to the most recent common ancestor is remarkably short, on the order of 50,000 years. Thus, although previous studies have noted that Y chromosome variation shows extreme geographic structure, we estimate that the spread of Y chromosomes out of Africa is much more recent than previously was thought. We also show that our data indicate substantial population growth in the effective number of human Y chromosomes.

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Figures

Figure 1

Figure 1

A rendition of the three gene trees, where the mutations (56 single-nucleotide substitutions) are represented by circles, and those mutations that distinguish important geographic clades are numbered 1 and 2 (see Geographic Structure of the Tree).

Figure 2

Figure 2

The likelihood curve and expected age of the MRCA in units of_N_ generations, given θ under the model of constant population size. A number of points (nine for the three genes combined) were obtained by using

genetree

, and an error function (cubic spline) was fitted between the points for the likelihood curve (expected age of the MRCA).

Figure 3

Figure 3

The likelihood surfaces and_E_[_T_MRCA] surfaces in units of _N_0 generations, given θ and β, under the exponential growth model. The three single gene surfaces used an error function to connect nine points on the likelihood curve. For the three genes combined, an error function was used where possible to connect 37 points. When the error function did not fit, linear interpolation was used. A cubic spline was used for all_E_[_T_MRCA] surfaces.

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