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In general, ancient and contemporary Native Americans were predicted to have intermediate/brown eyes, black hair, and intermediate/darker skin pigmentation.
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Read More »Since the last decade, many studies have aimed to develop tools capable of predicting externally visible characteristics (EVCs) of an individual by analyzing only its genetic material. Over the past few years, we faced a great advance in understanding the molecular mechanisms underlying melanin biosynthesis. Thus pigmentation phenotypes, such as eye, hair and skin color, became the most promising EVCs for DNA prediction [1]. The IrisPlex system, developed in Europe, was the first tool tested and validated for this matter [2]. It includes six SNPs from different genes that are highly correlated with human iris color. Then, 18 new markers capable of predicting hair color were included, composing the HIrisPlex system [3]. Later, a new version of the tool was developed, the HIrisPlex-S system [4]. It includes 41 markers (40 SNPs and one INDEL) capable of predicting eye, skin and hair color simultaneously. Along with that, a different research group developed other five sets of predictive tools that compose the Snipper app suite version 2.5: three for eye (with 7, 13, and 23 SNPs), one for hair (with 12 SNPs), and one for skin color prediction (with 10 SNPs) [[5], [6], [7]]. Both HIrisPlex-S and Snipper were developed for European populations, but presented satisfactory results when tested elsewhere [4,8]. Other predictive tools for pigmentation traits have also been proposed, such as the one proposed by Hart et al., consisting of eight SNPs for eye and skin color prediction and also the one proposed by Allwood et al., consisting of four SNPs for eye color prediction [9,10]. These tools were primarily developed to assist crime investigations, helping to find the perpetrator in cases with inconclusive STR analysis. However, these tools are also useful for mass disaster victim identification, particularly in situations that lack reference DNA profiles to be compared with the one retrieved from the victim. In addition to the good performance of the prediction systems in Europe, new possibilities have come into view, such as the prediction of pigmentation phenotypes from ancient and contemporary skeletal remains. The HIrisPlex system has already been used in a few studies of this kind. One study used this tool to successfully predict pigmentation phenotypes from skeletal remains of World War II victims buried in mass graves in Slovenia in spite of possible DNA degradation over time [11]. The HIrisPlex system was also used to predict phenotypes from bone and tooth samples collected from individuals deceased between the 12th century and present time. They concluded that HIrisPlex is a sensitive system applicable to both ancient and contemporary samples [1]. Finally, another study used HIrisPlex to help in identification of the remains of King Richard III of England, deceased in 1485 [12]. Likewise, the Snipper sets for eye, hair and skin color prediction were used to determine phenotypic characteristics from a Chalcolithic sample (3480 ± 30 years before present) found in Asturias, Northern Iberia. The results indicated that the individual presented brown eyes (using the 13 SNPs set), light blond hair and white skin, and that it is possible to obtain phenotypic information from a critical ancient sample dating back more than 3000 years [13]. Given the recent availability of ancient DNA and whole-genome sequencing (WGS) data from Native Americans [[14], [15], [16], [17], [18]], the possibility of predicting Native American’s EVCs has come into view. In this study, we retrieved genotype information on 61 SNPs from the HIrisPlex-S [4] and Snipper sets [[5], [6], [7]] from WGS data from 20 contemporary and 22 ancient Native American samples, in order to predict skin, hair and eye color of each sampled individual. Given the absence of information concerning pigmentation phenotypes of ancient Native Americans, any attempts to provide consistent predictions from DNA would provide invaluable insights for anthropological purposes.
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