Location and structure of palindrome P6, showing positions of PSVs analysed.

<p>a) Idiogram of Y chromosome, showing positions of the 8 palindromes, with structure and coordinates (in GRCh37) of P6 below. b) Position and nature of the differences between the arms of P6, indicating the 10 SN-PSVs analysed, and the positions of PCR primers used in arm-specific amplifications. STSs marking the arm boundaries are also shown (with ‘sY’ prefixes). Asterisks indicate the two SN-PSVs identified from a haplogroup O3a chromosome.</p

Recognition of gene conversion, co-conversion and inversion events.

<p>a) Existence of three genotypes at a hypothetical PSV indicates that gene conversion has taken place, if recurrent mutation is neglected. Genotyping the PSV in a phylogenetic context, and applying the principle of maximum parsimony, allows the recognition of: b) Haplogroup descending from an ancestor in which the PSV mutation has not yet arisen (G/G), and is therefore uninformative; c) Haplogroup descending from an ancestor in which the PSV mutation has arisen (G/A), but shows no variation, and therefore no evidence for gene conversion; d) Haplogroup descending from an ancestor in which the PSV mutation has arisen, and shows evidence of at least two bidirectional conversion events (G/G and A/A); e) Recognition of co-conversion of more than one PSV requires ‘phase’ information, as does (f) recognition of inversions.</p

Inter-specific sequence divergence in arms and spacers of palindrome P6.

a<p>2×2 contingency table, Chi-square test with Yates correction.</p

Patterns of P6 nucleotide replacements in the human and chimpanzee lineages.

a<p>2×2 contingency table, Chi-square test with Yates correction.</p>*<p>p-value<0.05.</p>**<p>p-value<0.01.</p

Schematic representation of the inversions identified within three haplogroups.

<p>The approximate position of each inversion is indicated by a red cross.</p

Gene conversion violates the stepwise mutation model for microsatellites in y-chromosomal palindromic repeats.

The male-specific region of the human Y chromosome (MSY) contains eight large inverted repeats (palindromes), in which high-sequence similarity between repeat arms is maintained by gene conversion. These palindromes also harbor microsatellites, considered to evolve via a stepwise mutation model (SMM). Here, we ask whether gene conversion between palindrome microsatellites contributes to their mutational dynamics. First, we study the duplicated tetranucleotide microsatellite DYS385a,b lying in palindrome P4. We show, by comparing observed data with simulated data under a SMM within haplogroups, that observed heteroallelic combinations in which the modal repeat number difference between copies was large, can give rise to homoallelic combinations with zero-repeats difference, equivalent to many single-step mutations. These are unlikely to be generated under a strict SMM, suggesting the action of gene conversion. Second, we show that the intercopy repeat number difference for a large set of duplicated microsatellites in all palindromes in the MSY reference sequence is significantly reduced compared with that for nonpalindrome-duplicated microsatellites, suggesting that the former are characterized by unusual evolutionary dynamics. These observations indicate that gene conversion violates the SMM for microsatellites in palindromes, homogenizing copies within individual Y chromosomes, but increasing overall haplotype diversity among chromosomes within related groups

Sample description.

<p>Long., longitude; Lat., latitude. <i>n</i>_X, <i>n</i>_A, <i>n</i>_Y and <i>n</i>_mt: sample size for X-linked, autosomal, Y-linked and mitochondrial markers, respectively.</p

Diagram representing the relative values of expected genetic differentiation for autosomal markers and for X-linked markers .

<p>In the red upper right triangle, the <i>F</i>_ST estimates for autosomal markers are higher than for X-linked markers. In this case, <i>N</i>_f/<i>N</i> is necessarily larger than 0.5. In the blue region of the figure, the <i>F</i>_ST estimates for autosomal markers are lower than for X-linked markers. The white plain line, at which , represents the set of (<i>N</i>_f/<i>N</i>, <i>m</i>_f/<i>m</i>) values where the autosomal and X-linked <i>F</i>_ST estimates are equal. In this case , if <i>N</i>_f = <i>N</i>_m, then the lower effective size of X-linked markers (which would be three-quarters that of autosomal markers) can only be balanced by a complete female-bias in dispersal (<i>m</i>_f/<i>m</i> = 1). Conversely, if <i>m</i>_f = <i>m</i>_m, the large female fraction of effective numbers compensates exactly the low effective size of X-linked markers only for <i>N</i>_f = 7<i>N</i>_m. Last, if <i>m</i>_f = <i>m</i>_m/2, then the autosomal and X-linked <i>F</i>_ST estimates can only be equal as the number of males tends towards zero.</p

Human sex-specific demography inferred from genetic data.

<p>This table summarizes the observed patterns of sex-specific differences in demographic parameters reported in a number of recent studies. The first column lists the location of the sampled populations, or indicates whether the study is conducted at a global scale. The second column gives the markers used, and the third column indicates the statistical methods employed. The fourth column provides indications on social organization, available a priori for the populations under study. In the fifth and sixth columns, the authors' interpretations of sex-specific differences in demographic parameters are given, with respect to skewed gene flow and/or effective numbers.</p>a<p>Indications on social organization, marriage rules, etc., as provided by the authors.</p>b<p>The differences in demographic parameters between males and females, as inferred by the authors, are given in terms of sex-biased gene flow, and skewed effective numbers; the authors' interpretation to the observed pattern is given in parentheses, when available.</p>c<p>Single nucleotide polymorphisms.</p>d<p>Analysis of molecular variance <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000200#pgen.1000200-Excoffier2" target="_blank">[69]</a>.</p>e<p>Not available (no detailed information given by the authors concerning social organization, marriage rules, etc.).</p>f<p>Short tandem repeats.</p>g<p>Time to the most recent common ancestor.</p>h<p>mtDNA and NRY were not sampled in the same individuals or populations.</p>i<p>The authors discussed a possible difference in demographic parameters between males and females, but considered it as negligible.</p>j<p>The authors did not consider this pattern.</p>k<p>Food-producer populations.</p>l<p>Hunter-gatherer populations.</p>m<p>Monte Carlo Markov chain method to estimate population sizes and migration rates <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000200#pgen.1000200-Beerli1" target="_blank">[70]</a>.</p>n<p>Variance in Reproductive Success.</p>o<p>population-mutation parameter.</p

Level of diversity and differentiation for NRY markers and mtDNA.

<p>We calculated the total allelic richness (<i>AR</i>) (over all populations) and the expected heterozygosity <i>H</i>_e<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000200#pgen.1000200-Nei1" target="_blank">[55]</a> using Arlequin version 3.1 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000200#pgen.1000200-Excoffier1" target="_blank">[56]</a>. Genetic differentiation among populations was measured both per locus and overall loci, using Weir and Cockerham's <i>F</i>_ST estimator <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000200#pgen.1000200-Weir1" target="_blank">[57]</a>, as calculated in Genepop 4.0 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000200#pgen.1000200-Rousset2" target="_blank">[58]</a>. We calculated the total number of polymorphic sites, the unbiased estimate of expected heterozygosity <i>H</i>_e<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000200#pgen.1000200-Nei1" target="_blank">[55]</a>, and <i>F</i>_ST using Arlequin version 3.1 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000200#pgen.1000200-Excoffier1" target="_blank">[56]</a>.</p