Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny

Abstract

Genetic variation within the male-specific portion of the Y chromosome (MSY) can clarify the origins of contemporary populations, but previous studies were hampered by partial genetic information. Population sequencing of 1204 Sardinian males identified 11,763 MSY single-nucleotide polymorphisms, 6751 of which have not previously been observed. We constructed a MSY phylogenetic tree containing all main haplogroups found in Europe, along with many Sardinian-specific lineage clusters within each haplogroup. The tree was calibrated with archaeological data from the initial expansion of the Sardinian population ~7700 years ago. The ages of nodes highlight different genetic strata in Sardinia and reveal the presumptive timing of coalescence with other human populations. We calculate a putative age for coalescence of ~180,000 to 200,000 years ago, which is consistent with previous mitochondrial DNA-based estimates.

Fig. 1. Phylogenetic tree of the 1209 (1204 Sardinians and 5 non-Sardinians) Y-chromosome sequences

The bifurcations AT, BT, CT, and DE have been inferred because of the absence of individuals belonging to haplogroups B, C, and D in our sample. Colored branches represent different Y-chromosome haplotypes. The number of polymorphisms for the main branches is shown in black; the average number of SNPs of sub-haplogroups is given in blue. The sub-haplogroups are named according to ISOGG nomenclature. The left axis indicates the number of SNPs from the root. The asterisk indicates the calibration point. The colored dots indicate private Sardinian clusters with an average number of SNPs in the range of 35 to 40 in red, 25 to 30 in green, and 7 to 12 in blue. The black dots indicate clusters with an average number of SNPs in the range of 70 to 120. The arrow indicates the position on the tree of the Ötzi, Tuscan, and Corsican samples. The gray box is enlarged in Fig. 2.

Fig. 2. Phylogenetic tree of the 492 (490 Sardinians and 2 non-Sardinians) Y-chromosome sequences belonging to haplogroup I

The number of polymorphisms for the main branches is shown in black; the average number of SNPs of sub-haplogroups is shown in blue. The sub-haplogroups are named according to ISOGG nomenclature. The red dots indicate Sardinian private clades, labeled in Greek letters as in Table 1. The black dots indicate clusters with an average number of SNPs in the range of 70 to 120. The arrows indicate the position of the northern Italian and Basque samples on the tree. The asterisk indicates the calibration point.