The taxonomy crisis: nothing left to discover?

In his post Taxonomy - crisis, what crisis? Rod Page reported on a new publication by Lucas et al (in press) which contains some really provocative findings:

• There is no decrease in the number of taxonomists, yet no 'taxonomy crisis'
• Instead there is an increase of taxonomists since 1900
  
• But there is a decline in the number of species descriptions per taxonomist

This is really interesting, especially when we remember the recently published estimates on the total number of species on Earth (ca. 8.7 Mio, Mora et. al 2011) which have also been used by the authors to illustrate the significance of taxonomists:

describing Earth's remaining species may take as long as 1,200 years and would require 303,000 taxonomists at an approximated cost of US$364 billion. With extinction rates now exceeding natural background rates by a factor of 100 to 1,000, our results also suggest that this slow advance in the description of species will lead to species becoming extinct before we know they even existed.

So what happened, are taxonomists getting lazy nowadays?

Lucas et. al. (in press) propose a different explanation:

[...] the currently decreasing numbers of species described per taxonomist over the past 50 years probably represents the effect of a declining pool of missing species.

Wait a moment.. are there too little species left to discover, thus the estimates above completely wrong?
Interesting, but the members of the TAXACOM list propose some other explanations, such as: 'we know hundreds of new species but publishing this is not funded anymore' etc.

Hard times for taxonomists...


References:

Lucas N. Joppa, David L. Roberts, Stuart L. Pimm The population ecology and social behaviour of taxonomists Trends in Ecology & Evolution doi:10.1016/j.tree.2011.07.010

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

Welcome in the post-taxonomic world

Rod Page reports on the growing number of unclassified and 'name less' GenBank entries in is new post 'Dark taxa: GenBank in a post-taxonomic world'.

A new ancestry for elephants

Changes in names and taxonomical classification are a common occurrence as our knowledge of species living and extinct expands. In fact, around 10% of all taxonomic names are changed every year (Nimis, 2001). The changes are mainly in the realm of microbiology where morphology is difficult to apply, but rarely in the realm of charismatic megafauna, e.g. elephants.

However, there has been a long ranging dispute on whether the African savannah elephant and the African forest elephant are merely subspecies of the African elephant (Loxodonta Africana), or whether the genus Loxodonta needs to be re-organised.

Recent work by Rohland et al. (2010) compared genetic markers of the genomes of the iconic woolly mammoth (Mammuthus primigenius) and the American mastodon (Mammut americanum) with the modern African savanna elephant, African forest elephant, and Asian elephant.

A surprising finding from our study is that the divergence of African savanna and forest elephants—which some have argued to be two populations of the same species—is about as ancient as the divergence of Asian elephants and mammoths. Given their ancient divergence, we conclude that African savanna and forest elephants should be classified as two distinct species.

As we see, there is no certainty in taxonomy. And there goes my favourite example of a stable taxonomic name.

Literature

Nimis, P. L. (2001), A tale from Bioutopia - Could a change of nomenclature bring peace
to biology's warring tribes?, Nature, 413(6851), 21, doi:10.1038/35092637.

Rohland N, Reich D, Mallick S, Meyer M, Green RE, et al. (2010) Genomic DNA Sequences from Mastodon and Woolly Mammoth Reveal Deep Speciation of Forest and Savanna Elephants. PLoS Biol 8(12): e1000564. doi:10.1371/journal.pbio.1000564

Boring latin names are banished

This funny link just came in via the taxacom list:

Dudley UnEarthed :

On the lower floor the museum has its major interpretative displays in a recently refurbished gallery called ‘Dudley Unearthed’. The gallery features two time lines, one showing the place of the famous Silurian Geology of the area in the history of the Rocks of Britain and the other showing the place of the industrial revolution in the human history of the area.
Boring latin names are banished but if you want more information just ask !

Well... generally applied, this would solve much of our taxonomy troubles ;)

Vertebrates and their vertebrae

Looking at modern vertebrates, their number of vertebrae varies remarkably. While some snakes have of the order of 300 vertebrae (all thoracic vertebrae), some turtles only have 18 vertebrae in total - from neck to tail. Then, in mammals the number of vertebrae and their functional division is remarkably constant.

In a recent study Johannes Müller (Berlin Natural History Museum) and co-workers surveyed 436 recent and extant amniote taxa to study the development of vertebrae in response to environmental pressure, body mass and genetic factors.

The key findings were:

• Early mammals (synapsids) had six cervical vertebrae and in total twenty thoracic plus lumbar vertebrae.
• The number of vertebrae is determined by somite formation and Hox-gene expression during embrional development. This also determines the position of the limbs along the spinal column.
  
• Early synapsids already showed the same number of vertebrae as recent mammals, while basal reptiles already showed a great variation in their number of vertebrae.

The paper is available on-line at PNAS:

Müller J., Scheyer T.M., Head J.J., Barrett P., Werneburg I., Ericson P.G.P., Pol D., Sánchez-Villagra M.R: Homeotic effects, somitogenesis and the evolution of vertebral numbers in recent and fossil amniotes. In: Proceedings of the National Academy of Sciences (PNAS), doi: 10.1073/pnas.0912622107

The paper comes with substantial amounts of supporting information. Unfortunately, the direct link from the article "splash page" does not work. This, again, shows the importance of using persistent identifiers like DOI for the publication of supplementary data.

Taxonomy Puzzles

In his blog Taxonomy vs. Systematics Dave Hone suspected that at least some paleontologist are not aware that systematics and taxonomy are two different things.
Even worse: As I wrote earlier both are completely ignored in a large number of paleontology related research articles! The authors of these articles do use species names but there is no 'systematics/taxonomy' section which explains the taxonomic concept of the author.

Some may now argue that this is not a problem because many species used in these investigations are so common or simple that everybody knows what is meant by species XY. But this is not true. For example it has been shown by the 'ElKef blind test' (to clarify how aprupt the K/T extinction really was) that differing taxonomic concepts can drastically reduce the comparability of scientific results (Lipps, 1997, Keller, 1997).
There are many reasons why this happens: Taxon names change, names are wrongly assigned or different reference specimen or images are used etc. The result is a big chaos of synonymies which is hard to unpuzzle. Therefore, scientists may use the same taxon name but mean totally different species.

By carefully prepared synonymy lists taxonomists traditionally try to track such taxonomic changes. With our TaxonConcept tool we have stored thousands of synonymy lists and it is often surprising how complicated it can get when e.g. synonyms of taxon names get their own synonymy lists or taxon names have been wrongly assigned. As an example, the picture on the top of this page which shows a graph of the relations of the taxon 'Archaeoglobigerina cretacea' to other taxon names which includes hundreds of other taxon names.
So, if you use taxon names in your studies try to provide some hints on what your taxonomic concept is. Otherwise you may leave future generations of with taxonomy puzzles like this.

References:

Keller, Gerta: Analysis of El Kef blind test I, Marine Micropaleontology, Volume 29, Issue 2, January 1997, Pages 89-93.

Lipps, Jere H.: The cretaceous-tertiary boundary: The El Kef blind test, Marine Micropaleontology, Volume 29, Issue 2, January 1997, Pages 65-66.

Technological Twists on Taxonomy

Browsing through Nature, I came across a book review by Kevin Kelly on "Systematics as Cyberscience: Computers, Change, and Continuity in Science" by Christine Hine. In his review Kelly takes a look at why taxonomy has been so slow to adopt the new tools provided by information technology.

"Taxonomy, the science of identification and classification of new species, has been one of the slowest disciplines to adopt computers. When most other scientists routinely use these number crunchers to detect patterns within large sets of data, why have taxonomists only recently started to use them?

The reasons are many. Foremost has been the subtle variation among closely related species, which makes quantification of their traits difficult. No computer program can outdo the highly refined judgements of a taxonomic expert who can classify from nuanced alterations even the smallest organism. Consequently, new species are identified and described in a manner that would have been familiar to Charles Darwin 150 years ago.

Second, much taxonomic information has been, and remains, parochial. The expertise required for classifying fly parasites has little in common with that for fungal species or whales. Taxonomic information occupies niches — niche being the exact biological term for these narrow confines. Specialized niches of information with their own protocols challenge computerization.

Third, the low priority given to taxonomy has meant it is perennially underfunded. High-powered computation and software come low on the list after the meagre needs of traditional taxonomy are (barely) met.

Despite these hurdles, the related field of systematics (exploring relationships between organisms over time) is rapidly transforming itself as computation becomes integral. In Systematics as Cyberscience, sociologist Christine Hine investigates the effects of computers and communication technology on the taxonomic community."

Read more ... (Sorry, no Open Access).