The barcode of life: Cataloguing the natural world

[ This article by Paul Willis, was published on January 5 2012, last updated on April 2 2012. ]

A still from the LIFE 2.0 exhibition at RiAus

Here is perhaps the most fundamental question in biology, one that has more complicated answers than you might think and one whose answers are changing as technology marches forward.

What is a species?

Intuitively and naively, it sounds like a simple question to answer. Non-biologists can readily tell apart several thousand ‘species’ of animal, plant and fungi. There’s little debate that there are two living species of elephant, the African and the Asian, or that we form a species distinct from our closest relatives the chimpanzees. But take a closer look and the lines become blurred. There are phenomena such as ring species that change through a continuum across their range and the end points are two separate species.

The classic biological definition of a species is a population of organisms that are sexually isolated from all others. Members of a group can have sex with each other and produce viable offspring and, once again, for most cases, this is fine and a very workable definition. But life isn’t really divided up into many millions of groups that we call species. We only see it as such because we lack the temporal vision that lets us see populations of organisms changing through time. Life is a single four dimensional organism, a theme I’d like to return to in a future blog post. Where this manifests itself in our 3D world and where it confounds our attempt to define species by sexual isolation is where one ‘species’ is undergoing speciation to become two. Thus we can get two closely related species coming together to produce sexually inert hybrids. Once again the lines around species boundaries blur.

As a palaeontologist, sexual isolation as a definition of species is completely useless. With the best will in the world there is no way I can test the sexual reproductive capacities of the fossils I study. I rely on a completely different species concept, one based on the shapes (morphology) of the fossils I study. If I look at a new specimen of a fossil crocodile that appears to differ in size, shape or other features from all other known crocodiles, I have to make a call as to if that represents this being a new species or if there is some other explanation for the aberrant form. To make this decision I compare skulls and bones from living crocodilians to get an idea of how much variation in form can be expected within a species and then project that information back onto my fossil. I then have to make an argument that the differences represent a different species of crocodile or perhaps a new genus or even sub family. Then the fun really begins working out how this new species fits into the bigger, known picture of crocodilian evolution – something else I’ll leave for a future essay.

Then there is genetics where a species is not judged by reproductive prowess or morphological expression but as identifiable sections of genetic code. In genetics a species is defined as a group of organisms with a high level of genetic similarity but there are debates as to what the ‘high level’ is.

A recent article from the BBC looks at how these differences in species concepts have caused us to rethink the question “How many species of humans are there?”. Meanwhile, back in Adelaide, we recently saw a whole conference given over to the latest phase of cataloguing life. It’s called DNA barcoding and it’s a logical extension of the genetic definition of species. It’s about identifying unique subsets of DNA code that allow you to say here we have a unique ‘species’.

In November last year great minds of biological science met to discuss the latest techniques and applications of DNA barcoding. It is a fascinating area and we filmed a whole discussion on the subject, available here. Its applications for identifying not only the diversity of life out there in the world but also tracking illegal forest or fishery products or finding new compounds for pharmaceuticals and other uses are astounding. If you want to get to the front of the line in understanding the cutting edge of biology, then you really should take a look at this video.

I certainly learnt a lot from hosting that debate! The ability through genetic technologies of being able to take a bulk sample from the wild and work out how many different species are present greatly amplifies the number of species we now know about. In fact many species identified this way are micro-organisms that have never been seen by the human eye. Rather than giving them a formal name and description as in my old school of taxonomy, species can be placed in ‘bins’ with clinical-sounding numbers instead of names. Each bin contains the identity of a population of organisms that share a unique and identifiable bit of DNA. Thus we are able to catalogue the natural world at an astounding rate and with a previously unthought-of precision.

DNA barcoding is the future of the most foundational block of biology. For too long taxonomists have been derided as the stamp-collectors of science, neatly dividing up life into workable units. DNA barcoding has pumped steroids into taxonomy and reinforced its command of understanding just who and what we share this planet with. It’s awesome technology applied to the nature of life.

By Dr Paul Willis @Fossilcrox