Did you even read it?
"To obtain quantitative inferences about the genetic relationships among the ancient and present-day individuals, we used qpAdm (35, 36), which provides a flexible framework for testing admixture models and estimating mixture proportions. Guided by the PCA, we began by using three groups of individuals—present-day Dinka (28), ancient Chalcolithic-period individuals from Israel (25), and the ~4500 BP forage from Mota, southern Ethiopia (24)—to represent distinct components of ancestry plausibly found in ancient and present-day eastern Africans, with present-day western Africans among the outgroups (21). We note that the use of these proxy groups in qpAdm modeling does not imply an assumption that they are directly ancestral to the true sources contributing to the individuals we analyzed. Instead, for a model to be properly formulated, the reference groups only need to be more closely related to the true sources than are the outgroups, without substantially different admixture (35). Thus, for example, ancestry related to the Chalcolithic Israel reference individuals could plausibly have originated anywhere in northeastern Africa or the Levant, and could have been present in northeastern Africa for many thousands of years. We use the Chalcolithic individuals in this study because we lack genetic data from a phylogenetically adjacent reference group from Egypt, Sudan/South Sudan, or the Horn."
Its just as likely that Chalcolitic Israel is East African. It cannot even be said that its from the Levant with certainty.