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4. Chromosomal disorders
We used the fraction of reads mapping to the X and Y chromosome vs. the autosomes (X-ratio
vs. Y-ratio) as implemented in ANGSD (44) to determine the genetic sex for each individual. We
also found two individuals with chromosomal disorders, which we briefly describe here:
4.1 XXY aneuploidy (Klinefelter syndrome) in individual CLL011
The Syndrome originally described in (109) consisted of gynecomastia and aspermatogenesis. It
was previously thought to be a hormonal disorder until (110) defined the syndrome as
chromosomal disorder caused by an extra X chromosome in genetically male individuals (47,
XXY). The symptoms and traits are tall stature, hypogonadism, fertility problems and sometimes
difficulties in learning. The prevalence is 1 in 650 male births (111).
The individual CLL011 shows an X-ratio (see Materials and Methods, table S1.1) of 0.80,
similar to genetically female individuals, but a Y-ratio of 0.46, similar to genetically male
individuals, which is indicative of an XXY karyotype. Levels of mtDNA contamination are low
(0.36%) and render female contamination unlikely (fig. S1, table S1.1), while the commonly
used ANGSD method for male individuals is not applicable in this case. Individual CLL011 is
reported anthropologically as an adult individual but no further morphological details were
given. Other aDNA studies have also reported XXY cases recently (58, 112).
4.2 Trisomy X (Triple-X syndrome) in individual ALM062
The trisomy X or triple-X syndrome was described (110) as chromosomal disorder caused by an
extra/supernumerary X chromosome in genetically female individuals (47, XXX). Clinical
symptoms are often absent or unnoted, and, if present, are variable and usually related to delayed
speech development and psychiatric disorders, early growth with longer legs and sometimes
infertility (113, 114). The prevalence is approximately 1 in 1000 female births (110).
The neonatal individual ALM062 shows a Y-ratio of 0.01, as expected for genetically female
individuals, but a X-ratio of 1.18, consistent with 1.5 higher than males and 0.5 times higher than
females, and thus indicative of an XXX karyotype. Levels of mtDNA contamination are
sufficiently low (0.4%) to exclude additional female contamination (fig. S1, table S1.1).
5. Kinship
We used three different methods to estimate the degree of kinship based on genome-wide from
the newly typed individuals, including LcMLkin (47)(fig. S2A and fig. S2B), PWMR (48), fig.
S2C) and READ (49), table S1.5, table S1.6 and table S1.7) for pseudo-haploid data (see
methods). We also confirmed the 1st or 2nd degree related pairs by way of f3-outgroup statistics of
the form f3(ind1, ind2; Mbuti) (fig. S2D)
6. Population group labels
For the co-analyzed Middle Late Neolithic (MLN) and Copper Age (CA) Iberian individuals
from previous publications, we kept the labels as used in (7), and followed the chronological and
geographical naming scheme for our newly reported individuals, resulting in
SE/SW_Iberia_CA (Southeast, Southwest) (table S2.1).
For the Bronze Age (BA) Iberian individuals, we used the same principle (7), resulting in
N/NE/C/SE/SW _Iberia_BA (North, Northeast, Northwest, central, Southeast, Southwest).
Concerning the group SE_Iberia_BA, we pooled individuals, who are assigned to the El Argar
group as SE_Iberia_BA_Argar and those associated with the Valencian BA as
SE_Iberia_BA_Valencian. In order to explore the groupings at higher resolution, we kept
individuals from the site Molinos de Papel separated (MolinosPapel_EBA), as it is one of the
earliest sites that shows Argaric features in the archaeological record (e.g. intramural burials,
double burials, presence of a silver ornament), but cannot be considered a typical El Argar
hilltop settlement nor funerary context). We further grouped the few individuals from the
extended territory of a late phase El Argar group (Cerro de la Virgen in Granada) as
CerroVirgen_Late_Argar, already reported in (7). We also grouped the published (7) and
newly reported individuals from the site Cabezo Redondo in Alicante separately as
SE_CabezoRedondo_BA, as this site in the Valencian territory also shows Argaric features. The
main El Argar sites, La Almoloya and La Bastida (Bastida_Argar), were also analyzed
separately, to allow for temporal grouping. Individuals from La Almoloya were further divided
according to settlement phases as Almoloya_Argar_Early and Almoloya_Late_Argar.
Outlier individuals already reported in (7) were tagged with different labels (C_Iberia_CA_Afr
from Camino de las Yeseras and SW_Iberia_BA_Afr from Loma del Puerco) and not included
in any CA or BA groups. We also analyzed the new outlier individual from the site Zapatería
(ZAP002) independently. For the remainder of the prehistoric European groups, we kept labels
as used in the respective publications (table S2.1).
We used the fraction of reads mapping to the X and Y chromosome vs. the autosomes (X-ratio
vs. Y-ratio) as implemented in ANGSD (44) to determine the genetic sex for each individual. We
also found two individuals with chromosomal disorders, which we briefly describe here:
4.1 XXY aneuploidy (Klinefelter syndrome) in individual CLL011
The Syndrome originally described in (109) consisted of gynecomastia and aspermatogenesis. It
was previously thought to be a hormonal disorder until (110) defined the syndrome as
chromosomal disorder caused by an extra X chromosome in genetically male individuals (47,
XXY). The symptoms and traits are tall stature, hypogonadism, fertility problems and sometimes
difficulties in learning. The prevalence is 1 in 650 male births (111).
The individual CLL011 shows an X-ratio (see Materials and Methods, table S1.1) of 0.80,
similar to genetically female individuals, but a Y-ratio of 0.46, similar to genetically male
individuals, which is indicative of an XXY karyotype. Levels of mtDNA contamination are low
(0.36%) and render female contamination unlikely (fig. S1, table S1.1), while the commonly
used ANGSD method for male individuals is not applicable in this case. Individual CLL011 is
reported anthropologically as an adult individual but no further morphological details were
given. Other aDNA studies have also reported XXY cases recently (58, 112).
4.2 Trisomy X (Triple-X syndrome) in individual ALM062
The trisomy X or triple-X syndrome was described (110) as chromosomal disorder caused by an
extra/supernumerary X chromosome in genetically female individuals (47, XXX). Clinical
symptoms are often absent or unnoted, and, if present, are variable and usually related to delayed
speech development and psychiatric disorders, early growth with longer legs and sometimes
infertility (113, 114). The prevalence is approximately 1 in 1000 female births (110).
The neonatal individual ALM062 shows a Y-ratio of 0.01, as expected for genetically female
individuals, but a X-ratio of 1.18, consistent with 1.5 higher than males and 0.5 times higher than
females, and thus indicative of an XXX karyotype. Levels of mtDNA contamination are
sufficiently low (0.4%) to exclude additional female contamination (fig. S1, table S1.1).
5. Kinship
We used three different methods to estimate the degree of kinship based on genome-wide from
the newly typed individuals, including LcMLkin (47)(fig. S2A and fig. S2B), PWMR (48), fig.
S2C) and READ (49), table S1.5, table S1.6 and table S1.7) for pseudo-haploid data (see
methods). We also confirmed the 1st or 2nd degree related pairs by way of f3-outgroup statistics of
the form f3(ind1, ind2; Mbuti) (fig. S2D)
6. Population group labels
For the co-analyzed Middle Late Neolithic (MLN) and Copper Age (CA) Iberian individuals
from previous publications, we kept the labels as used in (7), and followed the chronological and
geographical naming scheme for our newly reported individuals, resulting in
SE/SW_Iberia_CA (Southeast, Southwest) (table S2.1).
For the Bronze Age (BA) Iberian individuals, we used the same principle (7), resulting in
N/NE/C/SE/SW _Iberia_BA (North, Northeast, Northwest, central, Southeast, Southwest).
Concerning the group SE_Iberia_BA, we pooled individuals, who are assigned to the El Argar
group as SE_Iberia_BA_Argar and those associated with the Valencian BA as
SE_Iberia_BA_Valencian. In order to explore the groupings at higher resolution, we kept
individuals from the site Molinos de Papel separated (MolinosPapel_EBA), as it is one of the
earliest sites that shows Argaric features in the archaeological record (e.g. intramural burials,
double burials, presence of a silver ornament), but cannot be considered a typical El Argar
hilltop settlement nor funerary context). We further grouped the few individuals from the
extended territory of a late phase El Argar group (Cerro de la Virgen in Granada) as
CerroVirgen_Late_Argar, already reported in (7). We also grouped the published (7) and
newly reported individuals from the site Cabezo Redondo in Alicante separately as
SE_CabezoRedondo_BA, as this site in the Valencian territory also shows Argaric features. The
main El Argar sites, La Almoloya and La Bastida (Bastida_Argar), were also analyzed
separately, to allow for temporal grouping. Individuals from La Almoloya were further divided
according to settlement phases as Almoloya_Argar_Early and Almoloya_Late_Argar.
Outlier individuals already reported in (7) were tagged with different labels (C_Iberia_CA_Afr
from Camino de las Yeseras and SW_Iberia_BA_Afr from Loma del Puerco) and not included
in any CA or BA groups. We also analyzed the new outlier individual from the site Zapatería
(ZAP002) independently. For the remainder of the prehistoric European groups, we kept labels
as used in the respective publications (table S2.1).