Such expressions as that famous one of Linnæus, and which we often meet with in a more or less concealed form, that the characters do not make the genus, but that the genus gives the characters, seem to imply that something more is included in our classification, than mere resemblance. I believe that something more is included; and that propinquity of descent,—the only known cause of the similarity of organic beings,—is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our classifications (Darwin, 1859, p. 413f).

Saturday, 17 July 2010

New Book: Beyond Cladistics

Beyond Cladistics: The Branching of a Paradigm

Edited by David M. Williams and Sandra Knapp

Available worldwide

Third title in the Species and Systematics Book Series, published by the University of California Press

Pre-publication Sale! Save 20% if you order directly from UC Press!

Click here to see other titles in the Species & Systematics Book series.

Tuesday, 6 April 2010

Awareness in Classification 2

In response to Michael from last 'Awareness in Classification' post

Several relationships are proposed, some conflict with others:
    1. Bird - dinosaur
    2. Humans - Apes
    3. Bird - non-avian dinosaur
    4. Human - non-human ape
In examples 1 and 2 above dinosaur implies some distinct group of animals, as does apes. In examples 3 and 4 above 'non-avian' stands for 'not-bird', and 'non-human' stand for 'not human'. Thus,
    5. Bird - not bird
    6. Human - not human
It is tempting to explore the idea of what a 'not bird' might be (resisting exploring what a 'not-human' might be): a flower, a rabbit, a house...

Another relationship might be:
    7. Vertebrate-invertebrate
    8. Vertebrate-not vertebrate
It is tempting to explore the idea of what a 'not vertebrate' might be: a flower, a rabbit, a house...

One might argue that context is all important. Of course, a 'not vertebrate' doesn't mean a flower. Well, once again, what does it mean? 'Not vertebrates' are paraphyletic. One might re-classify all 'not vertebrates' as vertebrates, thus making 'not vertebrates' monophyletic (One might re-classify birds as dinosaurs making them monophyletic). Does this mean, now, that birds are invertebrates? Prokaryotes are paraphyletic. One might re-classify all 'prokaryotes' as eukaryotes, thus making 'prokaryotes' monophyletic. Does this mean, now, that birds are prokaryotes?

Words do indeed have multiple meanings. A taxon name is best associated with a relationship. Then the meaning can be empirically explored.

Sunday, 28 March 2010

Awareness in Classification 1

Our recent post reveals a few things we believe are simply misunderstandings:
    1) Paraphyletic groups and their reality
    2) Taxa descending from other taxa
    3) Phylocode adjustements to make taxa monophyletic.
Let's change to a more general issue, that of invertebrates. Are invertebrates real? No. Wikipedia begins:
    "An invertebrate is an animal without a backbone. The group includes 95% of all animal species - all animals except those in the Chordate subphylum Vertebrata..."
Can invertebrates be defined? Yes. We could list all taxa that are included within and then list as absent all the characters vertebrates have: "An invertebrate is an animal without a backbone" -- but anything can be so defined. Are invertebrates monophyletic? No. They are paraphyletic, they exclude vertebrates. But if we include vertebrates within them, then do they become monophyletic? Yes, but then that is chordates. Are vertebrates descended from invertebrates? It's a nonsense question as invertebrates do not exist in any meaningful way - from nothing comes something?

Now, replace the terms 'invertebrate' for 'dinosaur' and 'vertebrate' for 'bird'.

To say dinosaurs are amniotes is like saying invertebrates are animals. Both true but neither telling us what dinosaurs actually are (lots of thing are amniotes). Are dinosaurs monophyletic? Are inverterbrates monophyletic?

Friday, 26 March 2010

The Mystery of the Siberian Pinkie: When Classification goes Wrong

ResearchBlogging.orgBiological classification is often misunderstood and misused in the scientific literature and especially in the media:
    “... birds are dinosaurs” (New York Times, 2010).
    “Humans are apes” (Dawkins, 2010 in The Australian).
    “Scientists have identified a previously unknown type of ancient human through analysis of DNA from a finger bone unearthed in a Siberian cave” (BBC News Online).
These slogans, popular with the public, are completely misinformed and provide inaccurate information about biological classification. Let’s start with birds are dinosaurs.

The slogan assumes we know something about the classification of dinosaurs, namely that they include birds. This assumption derives from a cladogram that shows that some dinosaurs (feathered therapods) are more closely related to birds than they are to other dinosaurs (see Gauither et al., 1998).

Moreover, birds are diagnosed as any amniote that possesses feathers, meaning that therapods are birds. The slogan then should instead read “some dinosaurs are birds”. This then begs the question “what are dinosaurs?”

The phrase “Humans are apes” has been used quite often as a slogan, most notably by Richard Dawkins. Like the dinosaur bird example, it assumes that we know something about human classification. In fact, the term ‘ape’ refers to:
    “... any of two families (Pongidae and Hylobatidae) of large tailless semi-erect primates (as the chimpanzee, gorilla, orangutan, or gibbon) ...” (Merriam-Webster Online Dictionary, 2010).
Humans on the other hand belong to the Hominidae. In classification and in common usage, we are hominids and not apes. So why the confusion?

Many scientists misuse existing terms in classification to make assumptions about evolution. Since evolution and classification are two separate issues, there is a degree of confusion. The slogan “humans are apes” is supposed to infer that humans evolved from apes or both apes and humans evolved from something else. In classification, this slogan is meaningless, unless it is meant to say that humans are members of either pongidae and hylobatidae. The same misuse of classification can be seen in a recent report of a newly discovered hominid from Siberia. The report by Krause et al (2010) states:
    “DNA sequence retrieved from a bone [the distal manual phalanx of the fifth digit, or the 'pinkie'] excavated in 2008 in Denisova Cave in the Altai Mountains in southern Siberia. It represents a hitherto unknown type of hominin mtDNA that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago (Krause et al., 2010).
mtDNA is not used in taxonomy to diagnose new species. Moreover the variability in mtDNA has been found to be high between individuals (see He et al., 2010). So what is this hullabaloo about? It appears it concerns itself over a newly discovered pinkie and there isn't much it can tell. You need more evidence than a pinkie to determine and describe a new species into an existing taxonomy. What Krause et al (2010) have found is a reconfirmation that hominid mtDNA is highly diverse. But yet, reading both Krause et al (2010) and the media, we are led to believe that a new species of hominid has been discovered. This is clearly not the case. Until further evidence is found (e.g., bones or bone fragments) and a diagnosis made can we be sure that “scientists have identified a previously unknown type of ancient human”.


Gauthier, J. A., Estes, R and de Queiroz, K 1988. A phylogenetic analysis of Lepidosauromorpha. In: R. Estes and G. Pregili (eds), Phylogenetic relationships of the lizard families. Stanford University Press, Stanford, CA, pp. 15-98.

He, Y., Wu, J., Dressman, D., Iacobuzio-Donahue, C., Markowitz, S., Velculescu, V., Diaz Jr, L., Kinzler, K., Vogelstein, B., & Papadopoulos, N. (2010). Heteroplasmic mitochondrial DNA mutations in normal and tumour cells Nature, 464 (7288), 610-614 DOI: 10.1038/nature08802

Krause, J., Fu, Q., Good, J., Viola, B., Shunkov, M., Derevianko, A., & Pääbo, S. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern Siberia Nature DOI: 10.1038/nature08976

Monday, 22 March 2010

Publications for 2009

Below is our list of publications for 2009. For those with no access to the links, will be happy to provide pdf copies on request.
    de Carvalho M.R. & M.C. Ebach 2009. Dearth of the specialist, rise of the machinist. History and Philosophy of the Life Sciences 31:467-470.
    Ebach, M.C. 2009. Goethe to Linneaus. In (eds. Wheeler, Q.D. & Knapp, S.) Letters to Linnaeus. Linnean Society, London, pp. 81-83.
    Ebach, M.C. & Williams, D.M. 2009. How objective is a definition in the subspecies debate? Nature 457:785.
    Ebach, M.C. 2009. Phylogeny. In: Brix J.H. (ed.) Encyclopedia of Time. Sage Publications Inc., Thousand Oaks, CA.
    Ebach, M.C. & Wheeler, Q.D. 2009. Cybertaxonomy. In: Brix J.H. (ed.) Encyclopedia of Time. Sage Publications Inc., Thousand Oaks, CA, pp. 252-260.
    Karthick B., Toyoda, K., Ramachandra, TV., & Williams, DM. 2009. A note on the identity of Ceratoneis iyengarii Gonzalves & Gandhi (Fragilariophyceae, Bacillariophyta). Diatom Research 24: 233-236.
    Li, Y., Williams, DM., Metzeltin, D., Kociolek, J.P., & Gong, Z. 2010. Tibetiella pulchra gen. nov. et sp. nov., a new freshwater epilithic diatom (Bacillariophyta) from River Nujiang in Tibet, China. Journal of Phycology Published Online: Dec 11 2009; DOI: 10.1111/j.1529-8817.2009.00776.x
    McNamara, K.J., Feist, R. & Ebach, M.C. 2009. Patterns of evolution and extinction in the last harpetid trilobites during the Late Devonian (Frasnian). Palaeontology, 52:11-33.
    Parenti, L.R. & Ebach, M.C. 2009. Comparative Biogeography: Discovering and Classifying Biogeographical Patterns of a Dynamic Earth. University of California Press, Berkeley.
    Parenti, L.R., Viloria, Á.L., Ebach, M.C. & Morrone, J.J. 2009. On the International Code of Area Nomenclature (ICAN): a Reply. Journal of Biogeography, 36:1619-1621.
    Stachura-Suchoples. K& Williams, DM. 2009. Description of Conticribra tricircularis, a new genus and species of Thalassiosirales, with a discussion on its relationship to other continuous cribra species of Thalassiosira Cleve (Bacillariophyta) and its freshwater origin. European Journal of Phycology 44: 477-486.
    Stachura-Suchoples, K., Williams, DM. & Jahn, R. 2009. On extinct, freshwater taxa in the genus Thalassiosira with observations on Thalassiosira species from Pliocene deposit in Oregon, U.S.A. Diatomededelingen 33: 111-113.
    Toyoda, K., Tanaka, J. & Williams, DM. 2009. A new brackish water diatom, Achnanthes secretitaeniata sp. nov. from Japan. Journal of Japanese Botany 84: 19-26.
    Tuji, A., Williams, DM., Sims, P.A. & Tanimura, Y. 2009. An Illustrated Catalogue of Type Specimens from the H.M.S. Challenger Voyage in Castracane's Slide Collection in the Natural History Museum, London. JOINT HAECKEL and EHRENBERG PROJECT: Reexamination of the Haeckel and Ehrenberg Microfossil Collectionsas a Historical and Scientific Legacy, edited by Y. Tanimura and Y. Aita, pp. 7-11. National Museum of Nature and Science Monographs, No. 40, Tokyo 2009.
    Williams, D.M. 2009. 'Araphid' Diatom Classification and The 'Absolute Standard'. Acta Botanica Croatica 68: 455-463.
    Williams, DM, Chudaev, DA, Lomonosov, MV, & Gololobova, MA. 2009. Punctastriata glubokoensis spec. nov., a new species of 'Fragilarioid' diatom from lake Glubokoe, Russia. Diatom Research 24: 479-485.
    Williams D.M. & Ebach, M.C. 2009. What, exactly, is cladistics? Re-writing the history of systematics and biogeography. Acta Biotheoretica, 57:249–268.
    Williams, DM. & Reid, G. 2009. New Species in the Genus Colliculoamphora. Williams & Reid with Commentary on Species Concepts in Diatom Taxonomy.Beihefte zur Nova Hedwigia (Eugene Stoermer Festschrift) 135: 185-200.

Friday, 12 February 2010

Australian Postgraduate Award in Biogeography Available at UNSW

An Australian Postgraduate Award (APA) is available for a PhD in the Biogeography Lab of Dr Malte Ebach at the School of Biological, Earth and Environmental Sciences, University of New South Wales. The Biogeography Lab investigates the biotic evolution of Australasia and the geographical and geological processes responsible for biotic diversification over time. We seek a highly motivated student with a good honours or Masters degree in biology/ evolutionary biology or geology/palaeontology to choose from two projects:

1. Evolution and biogeography of water-bugs of Eastern Australasia

This project, in collaboration with Professor Gerry Cassis (UNSW), examines the morphological and molecular systematic relationships of selected endemic taxa of water-bugs (Gerromorpha and Nepomorpha) in Australasia and the relationships between the biotic areas they inhabit. The broader project investigates the biotic evolution of Australasia and the geographical and geological processes responsible for biotic diversification. Requirements: Interest in evolutionary biology, taxonomy, biogeography, field work and natural history. Experience in either systematics, biogeography and molecular techniques would be an advantage.

2. Palaeozoic biogeography and trilobite evolution

This project, in collaboration with Dr John Paterson (UNE), investigates the systematic biology of Carboniferous trilobites (Proetida) and their evolutionary relationships in order to infer palaeogeographic and tectonic reconstructions. The broader project investigates the biotic evolution of Australasia and the geographical and geological processes responsible for biotic diversification.

Requirements: Interest in palaeobiology, palaeobiogeography, field work and natural history. Experience in either sedimentology, biostratigraphy and taxonomy would be desirable.

Please note that applicants must be a citizen or permanent resident of Australia.

Please direct all enquiries and applications to Dr Malte Ebach (

Tuesday, 9 February 2010

Darwin came from Essex (via Peru) says cat's DNA

From the Wollongong Herald

The DNA recovered from Charles Darwin's cat has proven that the 19th century naturalist was descended from South American Indians.

The aspirant Find-an-Ancestor Project uses the DNA from celebrity pets to map human origins. Tiddles, Charles Darwin's first tabby, is one of 30 exhumed ex-pets. "We'd never thought we'd find Tiddles, or any of the 10 cats Darwin owned during his life" says Prof. Trevor Bruce of the University of Ulladulla".

Research funded by the Geelong Anti-ageing Centre tested Tiddle's preserved DNA and discovered that Darwin's ancestors came from a small village in present-day Peru. From there they travelled directly to Essex, possibly via a land bridge made of ice, or by small raft, from France. "The evidence is astounding" says Prof. Bruce, "it is amazing how much information one can extrapolate from DNA".

Tests have led scientists to propose the 'Out of Anywhere hypothesis'. Prof. Bruce explains: "Look, it doesn't matter whose DNA you have, people just seem to originate anywhere. We had the late Liberace's budgie examined and found out that 'The Glitter Man' was descended from Eskimos".

Further research hopes to discover the centre of origin for all humans. Dr. Karen Hall hopes that this will herald a new hypothesis. "Palaeoanthropologists say that humans and apes originated in Africa. Show me one celebrity with a pet gorilla!"

You can participate in the Find-an-Ancestor Project by sending $120.00 for a 'detection kit'. The kit includes a swab and a shovel for extracting pet DNA.

Related Post: Charles Darwin's genetic history unlocked by DNA project