**Core Concept**
Identical twins, also known as monozygotic twins, are formed when a single fertilized egg (zygote) splits and develops into two separate embryos. Despite their identical genetic makeup, they may still exhibit differences due to various factors.

**Why the Correct Answer is Right**
The correct answer is related to the concept of **epigenetic variation**. Epigenetic changes refer to chemical modifications to DNA or histone proteins that do not alter the underlying DNA sequence but can affect gene expression. These changes can occur randomly or in response to environmental factors, leading to differences in gene expression between identical twins. For example, the process of **DNA methylation**, which adds a methyl group to specific DNA sequences, can influence gene expression and contribute to epigenetic variation.

**Why Each Wrong Option is Incorrect**
* **Option A:** Mitochondrial DNA variation - Mitochondrial DNA is inherited solely from the mother, but identical twins can still share the same mitochondrial DNA.
* **Option B:** Y-chromosome variation - Since identical twins are female, they do not have a Y-chromosome.
* **Option C:** Genetic mutations - Genetic mutations can occur in the DNA sequence, but epigenetic variation refers to changes in gene expression rather than the underlying DNA sequence.

**Clinical Pearl / High-Yield Fact**
It's essential to remember that identical twins, despite their identical genetic makeup, can still exhibit differences due to epigenetic variation. This concept has important implications for understanding the development of complex diseases and the impact of environmental factors on gene expression.

**Correct Answer:** D. Epigenetic variation