Perretti Silvia, Santos Patrícia, Vizzari Maria Teresa, Tassani Enrico, Benazzo Andrea, Ghirotto Silvia, Barbujani Guido
Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44121, Italy.
Department of Environmental Sciences and Prevention, University of Ferrara, Ferrara 44121, Italy.
Proc Natl Acad Sci U S A. 2025 Jul 22;122(29):e2502158122. doi: 10.1073/pnas.2502158122. Epub 2025 Jul 15.
Light eyes, hair, and skins probably evolved several times as dispersed from Africa. In areas with lower UV radiation, light pigmentation alleles increased in frequency because of their adaptive advantage and of other contingent factors such as migration and drift. However, the tempo and mode of their spread is not known. Phenotypic inference from ancient DNA is complicated, both because these traits are polygenic and because of low sequence depth. We evaluated the effects of the latter by randomly removing reads in three high-coverage ancient samples, the Paleolithic Ust'-Ishim from Russia, the Mesolithic SF12 from Sweden, and the Neolithic I5077 from current Croatia. We could thus compare three approaches to pigmentation inference, concluding that for suboptimal levels of coverage (<8×), a probabilistic method estimating genotype likelihoods leads to the most robust predictions. We then applied that protocol to 348 ancient genomes from Eurasia, describing how skin, eye, and hair color evolved over the past 45,000 y. The shift toward lighter pigmentations turned out to be all but linear in time and place, and slower than expected, with half of the individuals showing dark or intermediate skin colors well into the Bronze and Iron ages. We also observed a peak of light eye pigmentation in Mesolithic times, and an accelerated change during the spread of Neolithic farmers over Western Eurasia, although localized processes of gene flow and admixture, or lack thereof, also played a significant role.
浅色眼睛、头发和皮肤可能是在从非洲扩散的过程中多次进化而来的。在紫外线辐射较低的地区，浅色色素沉着等位基因的频率增加，这是由于它们的适应性优势以及其他偶然因素，如迁移和基因漂变。然而，它们扩散的速度和模式尚不清楚。从古代DNA进行表型推断很复杂，这既是因为这些性状是多基因的，也是因为序列深度较低。我们通过随机去除三个高覆盖率古代样本中的读数来评估后者的影响，这三个样本分别是来自俄罗斯的旧石器时代乌斯季-伊希姆人、来自瑞典的中石器时代SF12以及来自现在克罗地亚的新石器时代I5077。因此，我们可以比较三种色素沉着推断方法，得出结论：对于次优覆盖水平（<8×），一种估计基因型可能性的概率方法能得出最可靠的预测。然后，我们将该方案应用于348个欧亚大陆古代基因组，描述了过去45000年里皮肤、眼睛和头发颜色是如何演变的。结果表明，向浅色色素沉着的转变在时间和地点上几乎不是线性的，而且比预期的要慢，直到青铜时代和铁器时代，仍有一半个体表现出深色或中间色皮肤。我们还观察到中石器时代浅色眼睛色素沉着出现峰值，在新石器时代农民向欧亚大陆西部扩散期间变化加速，不过局部的基因流动和混合过程，或缺乏这些过程，也起到了重要作用。
