It seems that I’m writing a taxonomy blog these days…
In this week’s edition of Nature (subscription required; sorry), an editorial discusses a possible part of the solution to this problem: automating the process of species identification.
The vast majority of species on Earth aren’t easily distinguishable to the naked eye. Often, only one or two individuals in the world—increasingly more frequently, they’re professors emeriti—possess the expertise to identify species in a given taxonomic group. And, worryingly, when species ID comes down to somewhat subjective characters, different scientists may ID things completely differently in blind tests. So, wouldn’t it be wonderful if we could have a computer do all the work for us?
Automated identification has begun to happen. The thing is, one first has to develop the procedure before it can be automated. It’s almost certainly going to be specific to the taxon in question—wing measurements may identify parasitoid wasps with 100% accuracy, but be meaningless for, say, fruit flies. It also requires that the species in question be described already,* though it might also flag any specimens that didn’t “fit” into any species as potential new species or hybrids.
Now, suppose the character in question was not wing shape but a gene. That’s the idea behind DNA barcoding, which aims to identify every species on earth by sequencing a single region of the genome. (In animals, the region in question is the mitochondrial gene COI.) This is an idea that has really taken off, though it’s not without controversy. I personally think it’s a great idea, if applied correctly.
But barcoding and high-throughput phenomics won’t solve the taxonomy problem on their own. It’s often said that both will free up time that traditional taxonomists would normally spend identifying specimens (for museums, forensics, curious people, non-specialists in their field), thus allowing them to tackle the problem of discovering and describing species (called alpha taxonomy) in the first place. But it’s not just time that taxonomists need—they need more taxonomists. More people with the knowledge to diagnose new species, more people to collect them, more people to write up the formal descriptions. But there is little or no money for this—it tends to go towards barcoding—and even less interest in becoming a full-time taxonomist, even as many of them are retiring.
There are many components to a workable solution here, including the training of “parataxonomists” in biodiversity hotspots and collaboration with amateurs. I want to make a modest little proposal of my own: enlist that most useful of laboratory denizens, the undergrad.
There are quite a few species that we know exist, but haven’t formally described. Typically they’re sitting in jars on museum shelves waiting for a specialist to get around to them. In a summer of lab work, an undergrad could easily learn the major morphological traits used to diagnose species in a given group, and characterize them for at least a couple of new species. The P.I., if he or she has described several species in a genus, might have a sort of “template” for a formal description of related species. Then it’s just a matter of coming up with names.
This would get some much-needed alpha taxonomy done, and give an undergrad the chance to get something published, even if it’s in an obscure journal. Publications don’t just look good for grad school applications—they’re probably an asset for med school as well. I imagine the chance to get published might even make some students consider volunteering for a project if there were no funding available. This plan also increases the chances that some unsuspecting student will get really excited about taxonomy, and at least consider becoming a taxonomist him/herself.
For the record, I did something like this myself as an undergrad. It was a side project of some of my summer research and resulted in my first publication. And, since my supervisor (a) already had the specimens, and already knew that they were undescribed species, and (b) has described a ton of species in the genus, so knew what to look for, it wasn’t that time-consuming: I got through two species in about 6 weeks. That’s pickled fish to submitted paper. It’s in a pretty obscure little journal, but for an undergrad, that really doesn’t matter!
*Although one could envision a more general program that could take a whole slate of measurements, then form clusters of specimens that might be species. I’m almost certain this has already been done. It would require post hoc checks to determine whether the clusters actually corresponded to species.