Distinguishing Father from Brother
I will clarify your question a little. We start with two men, Dave and John. We know Dave and John are related, either as brothers, or parent-child. Can we use genetics to work out their relationship?

If Dave and John are brothers they will have the same mtDNA, the DNA in the mitochondria, because mitochondria are maternally inherited. They should have the same Y chromosome, because they have the same father (the Y comes from the father, and males have one Y to pass on, therefore they each received the same Y).

If Dave (John) is John's (Dave's) father, then they should have different mtDNA because they have different mothers (assuming that Dave (John) didn't have a child with his mother or sister, and that mtDNA is variable within the population). They would have the same Y chromosome, because that is paternally inherited.

If Dave and John have the same X chromosome it would be indicative of the same mother (there is a 50% probability that two male siblings will have the same X chromosome, while the probability of a father and son having the same X chromosome would be determined by variability of the X chromosomes within the population).

For the autosomal part of the genome, each parent carries two copies of each gene. This means that, in each gene, there is the potential for four different alleles, with two of those being passed to the offspring. For example, at gene $A$ the mother may have alleles $A_1$ and $A_2$, while the father has $A_3$ and $A_4$. The offspring receives one copy from each parent, with equal probability. The probability that a son receives $A_3$ from the father is 50%. The probability that a second son receives the same $A_3$ allele is 50%. Therefore, both father-son and brother-brother relationships have a coefficient of relationship of 0.5.

In summary, the mtDNA will liekly be the best indicator, but it is only indicative, it is possible (but highly unlikely in most modern societies) for father and son to share the same mtDNA.



You could, in principle, work out whether Dave is John's son or his father. For example (a really over simplified example), look at the diagram below. You first look at Dave's sequence and one chromosome in a pair has the sequence AAAAAAAAAA (Red chromosome) while the other has GGGGGGGGGG (Yellow chromosome). You then look at John's sequence and find one chromosome with the sequence TTTTTTTTTT (Green chromosome) and one with the sequence AAAAGGGGGG (Red &amp; Yellow Chromosome). John could have received the AAAAGGGGGG chromosome from Dave after Dave's red and yellow chromosome recombined, while it is not possible that John is the father of Dave. John's green chromosome came from his mother.