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

<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. <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. <b>Methods:</b> A systematic literature search on Y-chromosomal studies in the Mediterranean was performed. <b>Results:</b> Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations. <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.