School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA.
Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA.
Am J Phys Anthropol. 2020 Sep;173(1):34-49. doi: 10.1002/ajpa.24041. Epub 2020 Mar 14.
Epigenetic mechanisms influence the development and maintenance of complex phenotypes and may also contribute to the evolution of species-specific phenotypes. With respect to skeletal traits, little is known about the gene regulation underlying these hard tissues or how tissue-specific patterns are associated with bone morphology or vary among species. To begin exploring these topics, this study evaluates one epigenetic mechanism, DNA methylation, in skeletal tissues from five nonhuman primate species which display anatomical and locomotor differences representative of their phylogenetic groups.
First, we test whether intraspecific variation in skeletal DNA methylation is associated with intraspecific variation in femur morphology. Second, we identify interspecific differences in DNA methylation and assess whether these lineage-specific patterns may have contributed to species-specific morphologies. Specifically, we use the Illumina Infinium MethylationEPIC BeadChip to identify DNA methylation patterns in femur trabecular bone from baboons (n = 28), macaques (n = 10), vervets (n = 10), chimpanzees (n = 4), and marmosets (n = 6).
Significant differentially methylated positions (DMPs) were associated with a subset of morphological variants, but these likely have small biological effects and may be confounded by other variables associated with morphological variation. Conversely, several species-specific DMPs were identified, and these are found in genes enriched for functions associated with complex skeletal traits.
Overall, these findings reveal that while intraspecific epigenetic variation is not readily associated with skeletal morphology differences, some interspecific epigenetic differences in skeletal tissues exist and may contribute to evolutionarily distinct phenotypes. This work forms a foundation for future explorations of gene regulation and skeletal trait evolution in primates.
表观遗传机制影响复杂表型的发育和维持，也可能有助于物种特异性表型的进化。就骨骼特征而言，人们对这些硬组织的基因调控知之甚少，也不知道组织特异性模式与骨骼形态有何关联，或者在不同物种之间有何差异。为了开始探索这些主题，本研究评估了五种非人类灵长类物种骨骼组织中的一种表观遗传机制，即 DNA 甲基化，这些物种的骨骼形态和运动方式存在差异，代表了它们的进化群体。
首先，我们测试骨骼 DNA 甲基化的种内变异是否与股骨形态的种内变异相关。其次，我们确定了 DNA 甲基化的种间差异，并评估了这些谱系特异性模式是否有助于物种特异性形态的形成。具体来说，我们使用 Illumina Infinium MethylationEPIC BeadChip 来鉴定狒狒（n=28）、猕猴（n=10）、长尾黑颚猴（n=10）、黑猩猩（n=4）和绒猴（n=6）股骨小梁骨中的 DNA 甲基化模式。
显著的差异甲基化位置（DMPs）与部分形态变异相关，但这些可能具有较小的生物学效应，并且可能与与形态变异相关的其他变量混淆。相反，鉴定出了几个物种特异性的 DMP，这些 DMP 存在于与复杂骨骼特征相关的功能丰富的基因中。
总的来说，这些发现表明，尽管种内表观遗传变异与骨骼形态差异没有直接关联，但骨骼组织中存在一些种间的表观遗传差异，这些差异可能有助于进化上不同的表型。这项工作为未来在灵长类动物中探索基因调控和骨骼特征进化奠定了基础。
