Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences

Abstract

Background: Comparisons of maternally-inherited mitochondrial DNA (mtDNA) and paternally-inherited non-recombining Y chromosome (NRY) variation have provided important insights into the impact of sex-biased processes (such as migration, residence pattern, and so on) on human genetic variation. However, such comparisons have been limited by the different molecular methods typically used to assay mtDNA and NRY variation (for example, sequencing hypervariable segments of the control region for mtDNA vs. genotyping SNPs and/or STR loci for the NRY). Here, we report a simple capture array method to enrich Illumina sequencing libraries for approximately 500 kb of NRY sequence, which we use to generate NRY sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). We also obtained complete mtDNA genome sequences from the same individuals, allowing us to compare maternal and paternal histories free of any ascertainment bias. Results: We identified 2,228 SNPs in the NRY sequences and 2,163 SNPs in the mtDNA sequences. Our results confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA, although the differences are not as large as previously suggested. More importantly, we find substantial regional variation in patterns of mtDNA versus NRY variation. Model-based simulations indicate very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations. We also find that the ratio of female effective population size to male effective population size (N f /N m ) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in N f than N m .

Human Y-chromosome variation in the genome-sequencing era

“…alignment to the reference genome) possible only in the unique regions of the chromosome; these discontinuous segments dispersed along the MSY add up to about 10 Mb in total length (Box 1). Some studies have enriched specifically for 0.5-3.7-Mb subsets of these regions [22][23][24] , whereas others have sequenced the entire genome and subsequently extracted the relevant reads bioinformatically 4,20,[25][26][27] . Sequencing depth (the number of sequence reads covering a particular genomic position) is also important, because the low depth used in several early studies is likely to result in less efficient discovery of rare variants that are present in just one or a few individuals; as these variants lie on terminal branches of the phylogeny, such branches would be that occur in the male germline 132 .…”

Coevolution of genes and languages and high levels of population structure among the highland populations of Daghestan

“…Several studies suggest that sex-specific processes throughout paternal and maternal history indicate consistently larger effective population sizes for females than for males, which are roughly half that of females [62][63][64] . Higher variance of male reproductive success, existence of polygyny, and warfare with high male mortality rates may have produced different male versus female demographic histories in the Daghestani highlands.…”

Y chromosome of Aisin Gioro, the imperial house of the Qing dynasty

“…Mongolian and Manchu samples [19] ; M401 and M546 were found in Mongolian and many related populations, especially the "star cluster", which was suspected to be the clan of Genghis Khan, also belongs to the clade C3b2b1-M401 [18] ( Fig. 3); and F5483/SK1074 from Orochon and Daur samples [20] .…”