Source: A Genetic History of the Near East from an aDNA Time Course Sampling Eight Points in the Past 4,000 Years (
US National Library of Medicine National Institutes of Health) 2020 A.D.
From the source, “We then estimated kinship40 among our samples and found individuals SFI-43 (female) and SFI-44 (male), who lived around 500 BCE during the Iron Age III under the Persian rule, were first-degree relatives (Figure S4) and shared the same mtDNA haplogroup, T2C1 (Table S4). We kept these two individuals in the dataset for the following test and projected all ancient samples in set 2 onto a principal component analysis (PCA)41 plot based on variation in modern West, Central and South Eurasians (Figures 1 and S5). The plot differentiates between populations from the Near East, Europe, Caucasus, Russian Steppe, Central and South Asia. The ancient Lebanese (i.e., ancient individuals who lived in what is today known as Lebanon) clustered with the modern and ancient Near Easterners: the new samples clustered between the Bronze Age population (Sidon_BA) and modern Lebanese. The two first-degree relatives, SFI-43 and SFI-44, appeared as outliers and did not cluster with their contemporaries, but instead were positioned close to the Bronze Age samples. We wanted to test whether these two individuals had a genetic affinity to a population other than the ancient Lebanese. Thus, using qpWave,42,43 we selected 11 outgroups (see Supplemental Methods) that have different relationships with the populations found in set 1 and tested whether SFI-43 and SFI-44 formed a clade with any of the populations (including the ancient Lebanese) in our dataset. We found that SFI-43 only formed a clade with ancient Egyptians (Table S5), implying that she shared all of her ancestry with them or a genetically equivalent population. On the other hand, SFI-44’s ancestry appeared to be more complex because he did not form a clade with any population in our dataset, yet he appeared to share ancestry with SFI-43, ancient Egyptians, and ancient Levantines (Table S5). To better understand the relationship of SFI-43 and SFI-44 with the Lebanese and Egyptians, we projected the ancient Lebanese and ancient Egyptians onto a PCA constructed with the variation found in their modern populations. SFI-43 and SFI-44 clustered with the ancient Egyptians and were positioned between modern or ancient Lebanese and modern Egyptians, but SFI-44 was positioned closer than SFI-43 to the Lebanese (Figure S6). Because SFI-43 and SFI-44 are first-degree relatives but appear to have differences in their genetic ancestry, we tested whether SFI-44 can be modeled as a mixture of ancestries deriving from SFI-43 and any other individuals or populations in our dataset by using qpAdm.42 We found that SFI-43 could be modeled as deriving ∼70% of his ancestry from a population related to SFI-44 and ∼30% from a population related to ancient Levantines (Table S6). But these ancestry proportions do not reflect the first-degree relationship that the two individuals shared unless more than one mixture event had occurred in the family, so we created a simulated hybrid genome that represents a first-generation mixture between an ancient Egyptian and an ancient Lebanese and tested whether SFI-44 could be modeled as descending from a mixture between SFI-43 and the hybrid genome. The model showed that SFI-44 derived ∼50% of his ancestry from SFI-43 and ∼50% from an individual whose ancestry was similar to that of the hybrid genome (Table S6). Thus, these results suggest that SFI-43 was an Egyptian woman and SFI-44 was her son from a man who himself had both Egyptian and Lebanese ancestries. The structure of this family in Lebanon highlights population movements and the heterogeneous society that existed at that time, but additional sampling is needed if we are to understand whether this cross-cultural mixing was common or whether our samples were exceptional. We removed SFI-43 and SFI-44 from all following analyses in which local individuals were grouped to represent their respective time periods…(E) Haplotype segments shared between the ancient Lebanese and global modern populations. The heatmap is based on ChromoPainter’s co-ancestry matrix, and we averaged values from the modern populations over all individuals in the population. We scaled the heatmap by row to highlight the differences between the ancient individuals. Two Hellenistic individuals and one early Roman individual showed excess haplotype sharing with Central and South Asian populations compared with that of other ancient Lebanese individuals, whereas individuals SFI-43 and SFI-44 shared more segments with Africans and Egyptians. We counted between 19,073 (blue) and 19,659 (red) shared haplotype chunks in the dataset.”