Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe

Abstract

Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.

Population Genetics and Signatures of Selection in Early Neolithic European Farmers

“…Mitochondrial DNA and Y-chromosome haplogroups of the DER individuals are generally consistent with the genetic variation reported from early Neolithic farmers ( supplementary table S1, Supplementary Material online) ( Brandt et al 2013 ; Szécsényi-Nagy et al 2015 ), and the mitochondrial genomes match the HVR-I haplotypes reported earlier ( Haak et al 2010 ). We primarily found G2a2 and H2 Y haplogroups associated with Neolithic farmers ( Lacan et al 2011 ; Haak et al 2015 ; Rivollat et al 2020 ; Rohrlach et al 2021 ). We also observed one male with the Y-chromosome I haplotype that is generally common among European HGs and therefore considered as a signal of male HG ancestry contribution but also reported in lower frequency from Iberian and French Neolithic individuals ( Lipson et al 2017 ; Rivollat et al 2020 ).…”

“…We generated genome-wide SNP capture data for ∼1.24 million variant sites (1,240k SNP array) across the genome ( Fu et al 2015 ; Mathieson et al 2015 ), mitochondrial genome capture ( Maricic et al 2010 ), Y-chromosome capture ( Rohrlach et al 2021 ) and 3 Mb immune-capture data ( Immel et al 2021 ) from N = 32 individuals. In addition, we sequenced the complete genomes of two DER individuals (DER002 2.26X and DER009 3.07X), and a local HG individual from Bad Dürrenberg, Germany (BDB001 13x), for which genome-wide SNP capture data was previously reported ( Rivollat et al 2020 ).…”

Genomic transformation and social organization during the Copper Age–Bronze Age transition in southern Iberia

“…Libraries fulfilling these criteria were retained for hybridization capture of 1.24 million informative sites (1240k SNP panel) in the human genome ( 22 ). Libraries were independently captured for mitochondrial genomes (tables S1.3 and S1.4 and text S2) [( 40 ) modified following ( 41 )] and mappable regions of the Y chromosome (table S1.1 and text S3) ( 42 ). Following standard aDNA processing pipelines ( 43 ), we quantified contamination rates at the autosomal (in males) ( 44 ) and mitochondrial levels (both genetic sexes) ( 45 ), showing low contamination estimates for the individuals in this study (<3% for nuclear and <1% for mitochondrial DNA; see Materials and Methods).…”

“…Libraries were sequenced in-house on an Illumina HiSeq 4000 platform to an average depth of 5 million reads and after demultiplexing processed through EAGER ( 43 ). After an initial quality filter based on the presence of aDNA damage and endogenous DNA higher than 0.1%, libraries were subsequently enriched using in-solution capture probes synthetized by Agilent Technologies for ~1240k SNPs along the nuclear genome and independently for the complete mitogenome ( 40 ) following ( 41 ) and mappable regions of the Y chromosome ( 42 ), both in-house protocols. The captured libraries were sequenced for 20 to 40 million reads on average using either a single end (1 × 75-bp reads) or paired end configuration (2 × 50-bp reads).…”

“…By using an in-house protocol for Y capture ( 42 ), we were able to assign Y-chromosome haplogroups in male individuals. We genotyped the Y-chromosome reads using a Y-SNP list from the ISOGG (International Society of Genetic Genealogy) dataset included in the 1240k and Y-capture probes and by using an in-house script (A.B.R.)…”