**2. Haplotype terminology**

A review of current literature reveals a staggering collection of terms synonymous with haplotypes, as listed in Table 1.


**Table 1.** Terminology

Even if it were possible to define the various neologisms, it seems certain that confusion will remain until there is recognition of the conceptual background.

We introduced the term *ancestral haplotypes* to emphasise the persistence of the founding pool [3, 4]. Such haplotypes are conserved over thousands of generations; they allow identification of remote ancestors and their contributions to the creation of individual members of the species with their diseases. Unfortunately, others use the same term in different ways and even in the opposite sense, that is, to refer to *the single* original haplotype which is presumed to have mutated to give rise to all the so-called variants now present. Indeed, as just one example of the problem, the reader has to be able to interpret the following: "we identified all nonredun‐ dant haplotypes with a frequency of ≥10% and consisting of at least 10 SNPs, which are likely to represent the nonrecombinant descendants from a single ancestor" [5].

To yet further confound matters, increasingly, the term *haplotype* is being used to describe any combination of alleles or markers, such as SNPs, without regard to their reproducibility, inheritance, polymorphism or biological significance. Currently, there are conflicting methods of detection. The problems appear to be increasing as ephemeral concepts diverge and as claims for better approaches focus on just one or another competing technology or bioinfor‐ matic package.

Several other aspects are clear.


nately, and amazingly, there is now uncertainty as to how to define the haplotypes. For example, a recent paper urges international collaboration to avoid fragmentation [7]. It would be wise to avoid neologisms and such redefinitions without clarity of meaning.
