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

<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

Cat mtDNA fragments

Nine ND5 gene fragments were amplified via multiplex PCR and either sequenced by NGS in bulk following the “aMPlex Torrent” workflow, or reamplified individually by nested PCR and sequenced by pyrosequencing (see Ottoni et al, 2017, Nature Ecol Evol in press). The nine sequences obtained by “aMPlex Torrent” for each specimen were concatenated using a 10 N intervening spacer. For the specimen sequences that were obtained only by pyrosequencing, the N spacer was extended to allow alignment of all sequences. The coordinates of the fragments, excluding primers, numbered according to the Felis silvestris mtDNA reference sequence (NC001700) are: Frag_7: 12918-12961; Frag_2: 13052-13102; Frag_8: 13263-13333; Frag_3: 13513-13569; Frag_4: 13746-13807; Frag_1: 13945-13980; Frag_5: 14004-14012; Frag_9: 14170-14228; Frag_6: 15071-15131

Cat Taqpep gene fragments

Three fragments allowing genotyping of the T139, D228 and W841 codons of the Taqpep genes controlling the Macquerel or Blotched Tabby coat color pattern were concatenated for each specimen using a 10 N intervening spacer. The coordinates of the fragments, excluding primers, numbered according to the Felis silvestris Taqpep gene (LOC101101437) from the genomic sequence NC018723 are: T139: 21887-21926; D228: 22154-22180; W841: 80673-80731

Principal component analysis (PCA), together with a biplot, of 14 West-African population samples, (a) inclusively and (b) exclusively the Ghanaian C1 population sample, based on the Y-SNP frequencies using the phylogeny given in S3 Fig.

<p>The cumulative proportion of plot (a) is 0.92 for the first two principal components (PC1: 0.83; PC2: 0.09), and of plot (b) is 0.81 for the first two principal components (PC1: 0.45; PC2: 0.36). The nomenclature and the references of the population samples are available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141510#pone.0141510.s012" target="_blank">S1 Table</a>. </p

Geographic location of all population samples along the Bight of Benin and the rest of the West-African coast analysed in the study.

<p>The nomenclature and the references of the population samples are available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141510#pone.0141510.s012" target="_blank">S1 Table</a>.</p

Principal component analysis (PCA) of ten West-African population samples and the HapMap YRI sample based on the Y-SNP frequencies using the phylogeny given in S2 Fig.

<p>The cumulative proportion of the plot is 0.90 for the first two principal components (PC1: 0.63; PC2: 0.27). In this analysis the Ghanaian C1 population sample was excluded from the analysis. The nomenclature and the references of the population samples are available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141510#pone.0141510.s012" target="_blank">S1 Table</a>.</p