25 research outputs found

    Mediterranean Y-chromosome 2.0—why the Y in the Mediterranean is still relevant in the postgenomic era

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    <p><b>Context:</b> Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour.</p> <p><b>Objective:</b> For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available.</p> <p><b>Methods:</b> A systematic literature search on Y-chromosomal studies in the Mediterranean was performed.</p> <p><b>Results:</b> Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations.</p> <p><b>Conclusions:</b> There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.</p

    Microsatellite data of core and edge populations of Coenagrion scitulum in Western Europe

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    Genotype data of Coenagrion scitulum individuals from five core and five edge populations. Samples were collected in the field and the extracted DNA was genotyped for twelve microsatellite loci

    Y chromosome CNV discovery in a Norwegian population.

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    <p>A. Signal intensity plot (Log 2 ratio) for a control male without CNV variants. Signals from each of the 8179 probes are represented by one dot. B. Regions of the Y chromosome containing ampliconic and palindromic sequences are represented by colored arrows using the same nomenclature as in Repping et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137223#pone.0137223.ref041" target="_blank">41</a>]. The same colors were used to represent the signal intensity of the corresponding regions in the rest of the figure. Not all ampliconic sequences are covered by SNP/CN probes in the array. The lower part of Fig 2B includes only detectable regions. C to I. Signal intensity plots (Log 2 ratio) for different type of CNVs discovered in a Norwegian population. The lower part of each subfigure shows the name of each CNV following the nomenclature used in Repping et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137223#pone.0137223.ref041" target="_blank">41</a>]. Staples delineate the positions of duplications (on the top of the figure) or deletions (on the bottom). J. Signal intensity plot for a previously undescribed duplication hereby named P6 dupl.</p

    Principal component analysis of Y chromosome specific SNP variation between haplogroups.

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    <p>A. The figure shows the graphical representation of the first two eigenvectors after PCA analysis. Y-axis corresponds to the first vector explaining 24.1% of the variation and X-axis explains 13.4% of the remaining variation. Each dot represents the results from one individual and the colour represent each HG as denoted by letters in the figure. The plus symbols in black denote individuals for which HG determination was ambiguous. The black triangles denote individuals for which no HG could be assigned. B. The results from the individuals carrying the blue-grey dupl are represented in blue, while the results from individuals carrying “blue-grey like dupl.” are in red. All cases are included within the NO-M214(xM175) haplogroup. In total 11 individuals carry these variants (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137223#pone.0137223.t001" target="_blank">Table 1</a>) but they are superimposed in the figure, due to high similarity between their HG.</p

    qPCR validation of the newly discovered P6 duplication.

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    <p>Amplification plots for a female (green), a control male (purple) and a male with P6 dupl. (blue) are shown for markers RH38681 (A), sY1081 (B) and sY933 (C). D. Intensity signal plot (Log 2 ratio) for an individual with P6 dupl. showing that markers sY1081 and sY933 are positioned within the duplicated region, while RH38681 is located outside.</p

    Distribution of CNV patterns that were significantly overrepresented in one haplogroup only.

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    <p>Each part of the figure shows the graphical representation of the first two eigenvectors after PCA analysis A. The figure shows PCA values for individuals with P3 dupl. significantly overrepresented in haplogroup E-M96. B. Individuals with b2/b3 del. significantly overrepresented in haplogroup NO-M214(xM175). C. Individuals with gr/gr del. (c8) significantly overrepresented in haplogroup D-M174. This CNV is also present in other haplogroups. D. Individuals with gr/gr dupl. (c9) + distal dupl. significantly overrepresented in haplogroup J-P256.</p

    Distribution and frequency of CNV patterns significantly overrepresented within haplogroups.

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    <p>The table shows the distribution of CNV patterns among haplogroups for ten variants that showed overrepresentation in one or more haplogroups. Ambiguous individuals, for which haplotype determination was not possible, are shown in the table for completeness, but they were not included in the statistical analysis. The p-values after Pearson Chi-Square analysis, likelihood ratio and Fisher’s exact test are shown at the bottom of the table, together with the total amount of each CNV type. The % frequency is derived from CNV type observations divided by 1506 individuals for which haplogroup could be determined. The stars mark values that are significant with the standard residual indicated in parenthesis. (Ind.) individuals, (dupl) duplication, (del) deletion and (nd) not done.</p><p>Distribution and frequency of CNV patterns significantly overrepresented within haplogroups.</p

    Sample distribution and frequency of any CNV in each haplogroup.

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    <p>From a total of 1718 individuals, 1506 could be assigned to specific haplogroups based on a limited set of phylogenetically informative Y-SNPs within the Affymetrix 6.0 arrays. The table shows the distribution among haplogroups for these individuals, as well as the frequency of CNVs within each haplogroup. The highest frequency (95%) of CNVs was found among individuals of NO-M214(xM175) haplogroup.</p><p>Sample distribution and frequency of any CNV in each haplogroup.</p

    Haplotype networks based on statistical parsimony using partial cytochrome <i>c</i> oxidase subunit 1 sequences.

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    <p>The network above (a) comprises all sequences from nine African countries obtained during this study or a previous study [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003998#pntd.0003998.ref038" target="_blank">38</a>]. For each phylogeographic group, the number of sequences (Nseq), the number of haplotypes (Nhap), the nucleotide diversity (<i>Π</i>) and the haplotype diversity (<i>h</i>) with standard deviations (SD) are given. The network below (b) comprises sequences obtained from different villages in Northwest Senegal (1993–2007), Southeast Senegal (2011) and Southwest Mali (2007). Each pie diagram represents a haplotype (i.e. unique sequence) and dots represent haplotypes that were either not sampled or went extinct and can thus be regarded as mutational steps. The sizes of the pie diagrams are in relation to the log transformed number of sequences that represent the respective haplotypes, and the colors indicate the location or year of sampling.</p

    Pairwise <i>F</i><sub>ST</sub> estimates between <i>Schistosoma mansoni</i> samples from Mali and Senegal.

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    <p>Kokry = short for Kokry-Bozo. Rtoll = short for Richard Toll.</p><p>* = significant for permutation of genotypes among villages at the nominal level of 0.05.</p><p>** = significant for permutation of genotypes among villages at the nominal level of 0.001 (i.e. Bonferroni corrected). na = not applicable.</p><p>Estimates were obtained for microsatellite dataset DMS1 (below diagonal) and DMS2 (above diagonal). Note that samples with less than 10 parasites were not included to avoid biased estimation, and that samples from Richard Toll from 1993 and 1994 were pooled.</p