We were able to obtain
well-preserved endogenous DNA from a cranial vault fragment
of ind3, the results of which have already been published24.
In the case of ind1 and ind2, we sampled their petrous bones.
After enriching for 1,240,000 single-nucleotide polymorphisms
(SNPs), we obtained 722,470 SNPs on chromosomes 1–22
(1.772× average coverage) for ind1 by pooling data from two nonUDG-treated libraries (each SNP with a coverage of at least one
sequence) (Table 1 and Supplementary Data 1). We recovered
264,795 SNPs (0.282× coverage) for ind2 by pooling data from
four UDG-treated libraries (Table 1 and Supplementary Data 1).
Both individuals in Burial 1 were consistent with being genetic
males based on the ratio of sequenced reads aligning to the X
and Y chromosomes (Table 1). Low contamination estimates
(0–1.353%) and high deamination frequencies (ind1: 29.6%; ind2:
10.6%) support the authenticity of the recovered sequences
(Table 1).
To assess kinship and genetic affinities we carried out
population genetic analyses of the three individuals together
with previously published Eurasian Upper Palaeolithic and Mesolithic individuals. First, we analysed ind1 and ind2 using
f3- and f4-statistics. The individuals have genetic affinities similar
to those described by Fu et al. for ind3 (ref. 24). All three KremsWachtberg individuals share most alleles with each other, and
then with individuals from the Gravettian population cluster
named after the site of Dolní Věstonice (Czech Republic,
~100 km northeast)24 (Fig. 3a/b and Supplementary Data 2).
The Burial 1 boys share significantly more alleles with ind3 than
they do with any other Upper Palaeolithic/Mesolithic specimens
analysed, except for Věstonice13 for whom the signal is nonsignificant (Z = −1.477, Fig. 3a and Supplementary Data 2),
which points at close genetic ties between individuals from the
two contemporaneous sites.
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