Thursday, July 12, 2012

Dimly lit taxa - guest post by Bob Mesibov

The following is a first for iPhylo, a guest post by Bob Mesibov. Bob

Rod Page introduced 'dark taxa' here on iPhylo in April 2011. He wrote:

The bulk of newly added taxa in GenBank are what we might term "dark taxa", that is, taxa that aren't identified to a known species. This doesn't necessarily mean that they are species new to science, we may already have encountered these species before, they may be sitting in museum collections, and have descriptions already published. We simply don't know. As the output from DNA barcoding grows, the number of dark taxa will only increase, and macroscopic biology starts to look a lot like microbiology.

Rod suggested that 'quite a lot' of biology can be done without taxonomic names. For the dark taxa in GenBank, that might well mean doing biology without organisms – a surprising thought if you're a whole-organism biologist.

Non-taxonomists may be surprised to learn that a lot of taxonomy is also done, in fact, without taxonomic names. Not only is there a 'dark taxa' gap between putative species identified genetically and Linnaean species described by specialists, there's a 'dimly lit taxa' gap between the diversity taxonomists have already discovered, and the diversity they've named.

Dimly lit taxa range from genera and species given code names by a specialist or a group of collaborators, and listed by those codes in publications and databases, to potential type specimens once seen and long remembered by a specialist who plans to work them up in future, time and workload permitting.

In that phrase 'time and workload permitting' is a large part of the explanation for dimly lit taxa. Over the past month I created 71 species of this kind myself. Each has been code-named, diagnostically imaged, databased and placed in code-labelled bottles on museum shelves. The relevant museums have been given digital copies of the images and data.

The 71 are 'species-in-waiting'. They aren't formally named and described, but specialists like myself can refer to the images and data for identifying new specimens, building morphological and biogeographical hypotheses, and widening awareness of diversity in the group to which the 71 belong.

'Time and workload permitting'. Many of the 71 are poor-quality or fragmented museum specimens from which important morphological data, let alone sequences, cannot be obtained. Fresh specimens are needed, and fieldwork is neither quick nor easy. In my special corner of zoology, as in most such corners in zoology and botany, the widespread and abundant species are all, or nearly all, named. The unnamed rump consists of a huge diversity of geographically restricted and uncommon species. There are more than 71 in that group of mine; those are just the rare species I know about, so far.

'Time and workload permitting'. A non-taxonomist might ask, 'Why don't you just name and describe the 71 briefly, so that the names are at least available, and the gap between what's known and what's named is narrowed?' The answer is simple: inadequate descriptions are the bane of taxonomy. There are hundreds of species in my special group that were named and inadequately described long ago, and which wind up on checklists of names as 'nomen dubium' and 'incertae sedis'. Clearing up the mysteries means locating the types (which hopefully still exist) and studying them. That slow and tedious study would better have been done by the first describer.

Cybertaxonomic tools can help bring dimly lit taxa into full light, but not much. The rate-limiting steps in lighting up taxa are in the minds and lives of human taxonomists coping with the huge and bewilderingly complex diversity of life. It's not the tools used after the observing and thinking is done, it's the observing and thinking.

In their article 'Ramping up biodiversity discovery via online quantum contributions' (, Maddison et al. argue that the pace of naming and description can be increased if information about what I've called dimly lit taxa is publicly posted, piece by piece, 'publish as you go', on the Internet. In my case, I would upload images and data for my 71 'species-in-waiting' to suitable sites and make them freely available.

Excited by these discoveries, amateurs and professionals would rush to search for fresh specimens. Specialists would drop whatever else they were doing, borrow the existing specimens of the 71 from their repositories and do careful inventories of the morphological features I haven't documented. Aroused from their humdrum phylogenetic analyses of other organisms, molecular phylogeny labs would apply for extra funding to work on my 71 dimly lit taxa. In no time at all, a proud team of amateurs and specialists would be publishing the results of their collaboration, with 71 names and descriptions.

Shortly afterwards, flocks of pigs would slowly circle the 71 type localities, flapping their wings in unison.

Memo to Maddison et al. and other would-be reformers: the rate of taxonomic discovery and documentation is very largely constrained by the supply of taxonomists. You want more names, find more namers.