The naming of Phragmites haplotypes

The genus Phragmites includes several species, of which only Phragmites australis has a worldwide distribution. It has been several decades since the last formal taxonomic examination of the genus and a number of recent genetic studies have revealed novel diversity and unique lineages within the genus. In my initial work on genetic variation in Phragmites (Saltonstall in Proc Nat Acad Sci 99:2445-2449, 2002), I came up with a naming scheme for identifying chloroplast DNA haplotypes which combined unique sequences at two loci, designated by numbers, to form haplotypes, designated by letters. Here I describe this naming system in more detail, explain how it has evolved over time as more genetic data has become available, provide a summary of all haplotypes currently available on GenBank, and address some common misunderstandings about how the haplotypes are named.