The paper says, "First, an allele (G) at rs12913832near the OCA2 gene, with a proven association to blue eye color in individuals of European descent, has an estimated alternative allele frequency of 49% in the Levant_ChL population, suggesting that the blue-eyed phenotype was common in the Levant_ChL," and, "Second, an allele at rs1426654 in the SLC24A5 gene which is one of the most important determinants of light pigmentation in West Eurasians is fixed for the derived allele (A) in the Levant_ChL population suggesting that a light skinned phenotype may have been common in this population, although any inferences about skin pigmentation based on allele frequencies observed at a single site need to be viewed with caution."
In other words, it says that the people from this population were probably often blue-eyed and that there is evidence they were light-skinned, but the latter is not certain. It doesn't say anything about a Japethic presence since "Japethic" is not a meaningful scientific term.