Rod Page at iPhylo draws attention to a new paper in Systematic Biology (Costello et al 2011) estimating the total number of species. They come to a much lower figure than a previous paper (Camilo Mora et al 2011). Rod said something interesting that linked in to my thoughts on species numbers.

“The fuss over the number of bacteria and archaea seems to me to be largely a misunderstanding of how taxonomic databases count taxa. Databases like Catalogue of Life record described species, and most bacteria aren’t formally described because they can’t be cultured. Hence there will always be a disparity between the extent of diversity revealed by phylogenetics and by classical taxonomy.”

These papers seem to be estimating the number of species that would be formally described if we carried on as we have been. The interesting thing is how this relates to the actual number of species that exist. I wonder what the slope of the line of increasing number of species formally described and the slope of informal ‘descriptions’ (eg from DNA) would look like? After all surely we are only really interested in the number of species in nature, not in our catalog of nature. Studies of the change in our estimates of a parameter are always less interesting and useful than the parameter itself, species number in this case.

Cryptic Species

Even putting consideration of bacteria and archaea aside, use of population level DNA barcoding has revealed large numbers of cryptic species. These are often, as you might expect, among small dull-looking taxa where its hard to tell them apart by eye (although we do also find cryptic species in very well characterised groups such as birds, and mammals).

My feeling is that it is very rare indeed for the outputs of DNA barcoding to lead to formal descriptions of species. This is partly because those scientists do not have suitable training and partly because species description is a very difficult and frustrating task.

Meiofaunal Community Sequencing

Meiofaunal community sequencing has suggested very large increases of biodiversity of eukaryotes compared to morphological approaches. Studies of nematodes for example reveals very large numbers of (conservatively judged) Operational Clustered Taxonomic Units (likely species or higher level groupings). The work of Si Creer and colleagues is particularly informative.

Remarkably, along only an 800 m transect, we detected 182 Nematoda OCTUs, compared with 450 species of Nematode that have been described from around the entire British Isles. From a geographical perspective, these data represent the discovery of 40% of the previously known phylum richness from a transect that represents 0.004% of the length of the British coastline (~17,820 km, Ordnance Survey). (Fonseca et al. 2010)

Yes we can argue about what is a species. Yes there can be problems with defining taxa by % sequence divergence alone. But really these would be fine-scale adjustments, its hard to get away from the fact that lots of lines of evidence suggest that there are a lot of undescribed species. Don’t forget that this isn’t DNA barcoding, this is species identification and discovery. Often when extensive geographic sampling is carried out on these small organisms they may additionally fall into cryptic species assemblies. So cryptic species complexes may be overlaid on top of this realisation that much/most biodiversity is undiscovered.

Will these species ever be described?

Will these species ever be described? No, they won’t. Almost none of these will ever be described formally, and yet they exist, they comprise a very important component of our ecosystems. This problem is not going to go away, and will likely get more evident with high throughput environmental sequencing. The approaches to estimating species numbers need to be more explicit (especially towards the press) about what they are actually counting. They are not counting species numbers, but the frequency with which people write up species descriptions, and I would argue that DNA barcoding and environmental sequencing remove any plausible correspondence between these two rates.

You could of course take the view that a species only exists when it has been formally described. I’m sure formal description is a good thing, but irrespective of their official status these species do exist, they do contribute to actual biodiversity, they do interact in networks, they do harm/help our soil, crops, livestock, and health. Unlike King Canute at some point we have to respond to the flood in a practical manner, and counting described species as if they were true estimates of species numbers is starting to look rather naive.

I don’t want to criticise these groups too much. I like anyone who has a go at species diversity estimation, and Camilo Mora et al in particular do look at links between described and actual species numbers, and it is always difficult to get the subtleties of your work over in the press. Its just that I am yet to really see this important difference come over in the reporting of this work, nor have I really seen many biologists (at coffee time, or the web) who see it. We are making the assumption that species description in birds and mammals represent ‘small beasties’, and that pre-molecular estimates are representative of post-molecular. Do you feel comfortable with those assumptions? I don’t really have new suggestions how we should estimate the true number of eukaryotic species on our planet, but we need to think much more broadly and critically about how we should estimate this. And don’t even get me started on the overlooked bacterial and achaean diversity…

References

Camilo Mora, Derek P. Tittensor, Sina Adl, Alastair G. B. Simpson, Boris Worm. How Many Species Are There on Earth and in the Ocean?. PLoS Biol 9(8): e1001127.doi:10.1371/journal.pbio.1001127

Mark J. Costello, Simon Wilson and Brett Houlding. Predicting total global species richness using rates of species description and estimates of taxonomic effort. Syst Biol (2011) doi:10.1093/sysbio/syr080

Gómez, A et al Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon. Proceedings of the Royal Society B: Biological Sciences 274, no. 1607 (January 2007): 199. doi:10.1098/rspb.2006.3718

Fonseca, Vera G,  et al. Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nature communications 1 (January 2010): 98. doi:10.1038/ncomms1095

Creer, S et al. Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Molecular Ecology 19 Suppl 1 (March 2010): 4-20. doi:10.1111/j.1365-294X.2009.04473.x.