The largely qualitative morphological characters used in traditional taxonomy have unfortunately proven to be poor indicators of evolutionary relationship among coral species. Consequently, we need additional and alternative lines of evidence with which to test species hypotheses. Molecular methods, in combination with quantitative morphological characters, have proven highly successful to date in a number of taxa, including many corals.
One of the keys to a robust taxonomy is therefore to be able to define the genetics of each nominal species. At present, we cannot extract molecules from most of the type material, because most specimens have been bleached to remove their tissue for ease of storage. Indeed, this might never be possible. Therefore, we need a new specimen from which we can extract DNA to serve as the molecular archetype of each nominal species. Hence, the focus of Project Phoenix on collecting topotypes of all the nominal species in the order. Topotypes are specimens collected from the same type location as the holotype. In addition to a careful comparison with the type material, collecting from as close as possible to where the original specimen was collected is the best way to make sure the specimen is from the nominal species.
Collecting topotypes also allows us to get field images of each species to facilitate future identification for ecological surveys. It is often very difficult to imagine what a specimen might look like in the field based on the skeleton of the holotype. Indeed, some field characters, such as colour, are proving highly useful for differentiating some species in the field at some locations.
Topotypes can also supplement other aspects of the type material, including morphology. For example, many nominal species have been described from small fragments, thus limiting the morphological characters that can be captured from the type such as branch length, branch thickness, angle between branches etc. Traditional morphological approaches have been largely qualitative and it is important to note that quantitative morphological approaches still have a very important role to play in determining species boundaries in corals.
Methods to collect and curate scleractinian coral topotypes are summarised here.
For sequencing and data processing, we generally follow the PHYLUCE pipeline by Faircloth (2015).