DNA analysis almost 100 years after the crime solves the mystery.
In 1917, after the Bolshevik Revolution in Russia, the members of the Romanov family, the ruling family for several hundred years, were captured. Most of the members were executed and buried in a mass grave. However, the two youngest children were not buried with the rest of their families.
History told of a separate burial for these two children, Alexei and one of his sisters.
However, rumors persisted well into the 20th century that one or both of these children escaped and lived the remainder of their lives in hiding. One "famous" woman, Anna Anderson, a Polish claimed that she was Anastasia Romanov. She wasn't the only one. During the 20th century over 200 people claimed to be one of the missing Romanov's.
In 1991 the missing grave was discovered and most of the Romanov's identified by DNA analysis; however, the last two children were not in the grave.
PLoS ONE. Coble et al. report on the finding of a 2nd grave in 2007 and the identification of the 2 skeletons contained therein as the remains of Alexei Romanov and one of his sisters. It can't be confirmed whether the female was Maria or Anastasia.
So, how do they identify the remains and determine lines of inheritance? They do DNA testing from several different loci in the genome, but one of the most common methods for determining line of ancestry is sequencing of mitochondrial DNA.
Mitochondria are the energy producers in our own cells. Most of the chemical reactions that result in the burning of compounds to create our own energy takes place inside these small organelles located within each of our cells.
Evolutionarily speaking, mitochondria are very old, and evolved from the earliest merging of cells together--one to house the genome, and one to house the energy machinery. An historical artifact of this merger is that mitochondria actually contain their own DNA, and their own ribosomes for making protein from it. A mitochondrial genome (mtDNA) is much smaller in size than the human genome, but is important for cellular function. the mtDNA encodes proteins needed for energy production, and there are genetic diseases ascribed to mutations in mtDNA.
The mitochondrion have many similarities to bacterial cells, even though they cannot survive outside of host cells.
So, with that background of mitochondria is the explanation that sequences of mtDNA will allow you to determine maternal lines of descent. While each of our genomes is an amalgam of the genomes of both our father and mother, the genome contained within each of our mitochondria is only from our mother. The mother contributes the egg, which along with its DNA component contains all the other organelles to allow cells to grow and divide. The sperm provided by the male only provides the second half of the genetic code--and that gets delivered to the nucleus, not to the mitochondrion.
So, the sequence of mtDNA, which is present in all of us, can determine our maternal line of descent. This was one of the powerful tools used to identify the remains of the Romanov children and determine they were the children of Tsarina Alexandra Romanov.