Squirrels, Eels, Algae and Ardi: A Clarification

The "First human ancestor", which the ABC reports looked "like a squirrel" is of course not to be mixed up with the "Human Family's Earliest ancestor", namely Ardipithecus ramidus or “Ardi”, which Smithsonian.com tells us is a "... a female who lived 4.4 million years ago”. Not that this is to be confused with the Telegraph’s 'earliest human ancestor', a “prehistoric eel-like creature discovered in a Canadian shale bed has been identified as the earliest known ancestor of man", or indeed the ABC's "Oldest Human ancestor", an "elusive, single-cell creature evolved about a billion years ago and did not fit in any of the known categories of living organisms - it was not an animal, plant, parasite, fungus or alga, they say."

I hope this clarifies who our first, oldest and earliest ancestors really were.

Birds are Fish

Birds really are dinosaurs, and a sparrow or a blackbird is every bit as much a dinosaur as Tyrannosaurus or Stegosaurus (Dr. Dave Hone, Guaridian online 6 September, 2012)

birds r relly fish cause i askd my cous and he sed so. fish are animals with 4 legs, scales & a hed. everifin wif 4 legs, scales & a hed is a fish, like cats, sparros and Barry. dinasaurs r fish wif fevhvers so a bird iz relly a fish-dinasaur coz dinasaurs r like small fish in a klassafikayin like vis:

• animals (birds & shit)
• fish (animals wif scales)
• dinasaurs (fish wif fevhers)
• birds (dunno)

vat klassafikayin tellz u vat birds r fish wif fevhers.

uno other animals r spinless like worms & bugs & shit. so r plankton & trees i guess so va klassafikayin of bugs r:

• animals (uva stuff)
• spinless (like trees)
• worms (veges wif eyes)
• bugs (worms wif legs)

vis klassafikayin tells ya vat bugs r wormies wif legs.

sum idiots fink vis is rong, but all my mates rekon its right. i ave a lot of mates & in a democracy the majority rules: bugs r worms & birds r fish!

Publications for 2011

Below is our list of publications for 2011. For those with no access to the links, will be happy to provide pdf copies on request.

Cecca, F., Morrone, J.J. and Ebach, M.C. (2011). Biogeographical convergence and time-slicing in cladistic biogeography: Concepts and methods. In P. Upchurch; A. McGowan & C. Slater (eds.), Palaeogeography and Palaeobiogeography: Biodiversity in Space and Time. Taylor & Francis (CRC Press), Boca Raton, Florida, pp. 1-12. 

Ebach, M.C. (2011). Taxonomy and the DNA Barcoding Enterprise. Zootaxa, 2742: 67–68. 

Ebach, M.C. (2011). Biogeógrafos del mundo... ¡uníos!: un camino hacia la unificación. Revista de Geografía Norte Grande, 48: 5-10. 

Ebach, M.C., de Carvalho M.R. and Nihei, S.S. (2011). Saving Our Science from Ourselves: The Plight of Biological Classification. Revista Brasileira de Entomologia, 55: 149–153. 

Ebach, M.C., de Carvalho, M.R. and Williams, D.M. (2011). Opening Pandora’s Molecular Box. Zootaxa, 2946: 60—64. 

Ebach, M.C. and Williams, D.M. (2011). A Devil's Glossary for Biological Systematics. History and Philosophy of the Life Science,s 33: 251—258. 

Ebach, M.C., Valdecasas, A.G. and Wheeler, Q.D. (2011). Impediments to Taxonomy and Users of Taxonomy: Accessibility and Impact Evaluation. Cladistics, 27: 550–557. Levkov, Z. and 

Williams, D.M. (2011). Fifteen new diatom (Bacillariophyta) species from Lake Ohrid, Macedonia. Phytotaxa, 30: 1—41. 

Mooi, R.D., Williams, D.M., and Gill, A.C. (2011). Numerical cladistics, an unintentional refuge for phenetics – a reply to Wiley et al. Zootaxa, 2946: 17—28. 

Williams, D.M. (2011). Synedra, Ulnaria: definitions and descriptions – a partial resolution. Diatom Research, http://dx.doi.org/10.1080/0269249X.2011.587646 

Williams, D.M. and Gill, A.C. (2011). ‘Adventures in the fish trade’ by Colin Patterson, edited and with an introduction by David M. Williams & Anthony C. Gill. Zootaxa, 2946: 118—136. 

Williams, D.M. and Kociolek, J.P. (2011). An overview of diatom classification with some prospects for the future. The Diatom World (Sebach, J & Kociolek, JP, eds), pp. 47—91.

 

Agnosticism in Comparative Biology

Gnostic adj. of or relating to knowledge (from gnōstos meaning 'known')

Agnostic adj. a person who believes that nothing is known on some topic, either at the present, or in principle

In the philosophy of religion and recent public debates over atheism, a distinction is made of the difference between believing in God (theism) and not believing in God (atheism), but a third option, agnosticism is often regarded as the equivocation or uncertainty about whether or not there is a God. In fact, agnosticism is the denial that the existence of a God can be known one way or the other, and that we should stick to the facts we do know. Agnostics reject gnosticism of either kind. In biology, there are similar matters to consider.

Tweeted Histories I #Homology

@Goethe1824 I can relate a worm and a man via a third thing! I'll write a poem about it!
@sexy_Blumnbch What?
@henrich.B if you hang a human skeleton next to that of bird, you can compare their structures #Bronn1858

@Darwinathome's birdy

@sexy_Blumnbch Eww!
@MonsterMoa nah! what you want is a bauplan. #Owen1849
@Swiss_Pride What evidence have you got? You need space, time as well as form! #Agassiz1859
@Embryo.boy I think he means comparing embryos and how they develop #Gegenbaur1859
@Swiss_Pride no I don't!
@Darwinathome I found a birdy!
@MonsterMoa just compare the forearms of bats, humans and whales. See? Analogy!
@RayL Don’t just compare: find the origin of things. Homology? Bah! Homogeny!
@asagray I like @Darwinathome's birdy. Can u send photo?
@Stammbaum Origins, we need origins! My own Stammbaum gives origins; now all is homogeny
@Darwinathome can someone tell @Stammbaum to leave me alone?
@RayL Not all is homogeny, some comparisons are not true: homoplasy!
@Stammbaum Who cares. I have lots of stammbaume, one for every creature. All with homogeny, homoplasy and homology
@naefnotnaf @Stammbaum got it wrong. You can't mix phylogeny and systematics #Naef1919
@naefnotnaf homology is a systematic relationship separate from phylogeny
@angry_mayr Typologist!
@Zimmermann no it's not! homology is a transformational relationship.
@a.remane or a process #Remane1952
@willi Why not compromise? Use @naefnotnaf's systematics for taxa and @Zimmermann for their characters! #Hennig1950
@ggsimp what about ancestors? Homology is similarity between the bits of us and ancestors
@sokal_123 you mean overall similarity at a node? #SokalSneath63
@willi no, special similarity, that is synapomorphy #Hennig66
@angry_mayr Cladist!
@nelson_usa perhaps it's a non-transformational relationship? #NelsonPlat81
@beaty.boy Pattern Cladist!
@Colin82 non-transformational but based on similarity #Patterson82 
@ron.brady forget similarity, homology is simply an affinity. See @Goethe1824
@normlovesspiders homology is a three-item relationship regardless what is based on
@hennig_superstar %$#%! Homology is synapomorphy?
@k.nixon homology = synapomorphy + symplesiomorphy #NixonCarp11

The Autonomous Algorithm: Malpractice in Theory

In our last post we introduced the topic of the Autonomous Algorithm, a black box that acts as the foundation for a theory and method. In this post we explain what we mean by theory and method and why we believe that no tool can function as a logical foundation. Doing so is a form of malpractice.

For all the non-philosophers reading this post, we define theory as a set of mathematical principles on which an activity is based. The set of principles that underlie the study of geophysics is that radio waves and sound waves for instance have different levels of penetration. When a sound wave is reflected it can tell us the density and depth of an object, like a rock. These principles are based on physics, and not on the actual program that models the depth and density of rock. Doing that would be putting the cart before the horse. If we change the way we model the results of our acoustic test, we do not change the underlying principles of physics.

A method is a procedure to accomplish something. Methods are generally activities that can be done by pen and paper (although sometimes they are easier when automated) in which we determine the steps, for instance, to find out how to tell what is beneath a particular surface. The implementation is the tool that is used to do implement the method. This is usually as a computer algorithm. So, an algorithm is a tool that is based on a method that is underpinned by a theory. Seems simple enough, but this is often misinterpreted.

The Autonomous Algorithm

The S&B Blog will be running a series of posts dealing with the rise of the black box and the fall of the foundations of systematics.

The Timetree of Life: A product
of the Autonomous Algorithm?

Presently, the majority of systematic analyses are constructed in the same way - a matrix is assembled and fed into a computer that then produces a branching diagram. Students of systematics are taught how to produce this branching diagram, using the algorithm, without context to the foundations of systematics. The result is a whole new generation of computer users ignorant of the basic fundamentals of systematics, such as theory (i.e., homology, monophyly), history (i.e., why we do what we do) and methodology (i.e., how to find homologs and construct a cladogram by hand). This also results in an increased dependency on algorithms, which in turn creates a new systematic history and theory that revolves around algorithms rather than concepts. The former black box, which implemented basic algorithms to find approximations of cladograms, is now totally autonomous to the theory, method and history that had gone into its creation. We call this the Autonomous Algorithm.

Willi Hennig (1913 - 1976)

The great entomologist Willi Hennig (1913—1976), founder of ‘Phylogenetic Systematics’, was born on this day. Had he lived, he’d be 98.

So Long, and Thanks for All the Fish

It’s time to say goodbye to Paraphyly Watch, paraphyly, holophyly and all who sailed in them. It was fun while it lasted but all good things must come to an end and, alas, as you can see, we are moving on, redesigning, removing and rolling on. The year 2010 witnessed a spate of relevant papers to the Watch but time and inclination prevent us from devoting ourselves to their contents and absorbing their message. Save one last remark.

For us, organisms and taxa, taxa and areas call our attention, and our time might be more usefully spent elsewhere, doing these other things. It is these other things our blog will now be chiefly devoted, such that we might find subjects worthy of study, particularly classification and all its implications. Evolution is one such implication. Evolution, too, is a subject we find of interest. Hennig devoted many pages to the subject of classification – and evolution, as it happens. Our view contrasts with that of Cavalier-Smith:

“Real evolution often ignores Germanic cladistic logic; its messiness and lack of rules makes classification an art where compromise is necessary and rigid formalism harmful” (Cavalier-Smith 2010, p. 115).

German logic? ‘Real’ evolution? Classification as ‘art’? Cavalier-Smith continues:

“I agree with Mayr (1974), Halstead (1978) and others that the Hennigian perspective impedes realistic scientific discussion of phylogenetic history, because of its evolutionarily unrealistic formalism based on an intellectually impoverished view of the complexities of actual phylogenies, especially its failure to come to grips with evolutionary transformation, the reality of ancestors, and not least its dogmatism” (Cavalier-Smith 2010, p. 116).

“Realistic scientific discussion of phylogenetic history”? Cavalier-Smith embraces paraphyly; it looms large in his many works, they are sprinkled liberally among his various, ever-changing classifications, his artworks(Cavalier-Smith 2010, p. 115, fig. 1). An aversion to paraphyletic groups is, of course, anti-evolutionary:

“Cladistic aversion to paraphyletic groups, and lumping of paraphyly and polyphyly as ‘non-monophyly’, are logically flawed and anti-evolutionary” (Cavalier-Smith 2010, p. 117, legend to fig. 2).

János Podani (2010) echoes the sentiment:

“For pattern cladists, paraphyly is a less useful concept, because paraphyly together with polyphyly are “explanations for non-groupings, or more accurately, excuses for the absence of monophyly” (Williams, 2007). Paraphyletic and polyphyletic groups are therefore referred to “non-monophyletic groups” (Williams & Ebach, 2007; definition P4). For pattern cladists, non-monophyletic groups do not exist, being unnatural (“nongroups”). The approach is an evidently non-evolutionary one, paraphyly and polyphyly having very different evolutionary implications (Cavalier-Smith, 2010)” (Podani 2010, 1014).

Non-evolutionary? Anti-evolutionary?

Hörandl & Stuessy, when summarising the various concepts of paraphyly, understood it as a tool for classification – and evolution. For them “Cladistics put considerations of evolution, i.e., phylogeny, back into classification” – but left a bit out. They cite, with approval, Podani. With respect to monophyletic classification they suggest it “neglects important evolutionary processes” – which must be ‘Real’ evolution (Hörandl & Stuessy 2010, p. 1646)

The statements above, from Cavalier-Smith, Podani, Hörandl & Stuessy: Are any true, or even any part of them true?

It is time to say goodbye to Paraphyly Watch and paraphyly. It is time to devote our attention to classification, what we see is the saviour of comparative biology, maybe even all of biology.

Cavalier-Smith, T. 2010. Deep phylogeny, ancestral groups and the four ages of life. Phil. Trans. R. Soc. B 365: 111—132, doi: 10.1098/rstb.2009.0161

Hörandl, E. & Stuessy, T.F. 2010. Paraphyletic groups as natural units of biological classification. Taxon 59: 1641—1653.


Podani, J. 2010. Monophyly and paraphyly: A discourse without end? Taxon 59: 1011—1015.

A Makeover

You like it? The Blogger Template Designer calls it "Simple". We like it and hope that it is easier on the eye.

Above you will see our new design, a 'Chtenopteryx ontogeny motif', and below that, an additional quote that will change from time-to-time (this month it's Darwin).

We hope to hear from you, dear Systematics & Biogeography reader, especially those can enlighten us on the ontogeny in the header above. You will be hearing from us.

Adventures with my DNA Barcoder

"But humanity is bioilliterate. Yes, there is a high priest for the name and natural history of some species. That person, however, is almost never standing by your side. But with Google, can you get it? No, there is no hole in your computer or handheld into which to insert the biobit to link through Google. Who is going to give you that name in the dark, the rain, the backyard, or the rain forest? True bioliteracy is being able to link what humanity knows to the biodiversity in hand, eye, or mouth, and build on it. What is the cost to let all seven billion of us read wild biodiversity, now? The barcorder in the back pocket" (Janzen, 2010, Biotropica, 42:540-542).

Thursday, 25th
I am so excited! Today I bought my DNA Barcoder from the gift shop at my local natural history museum. It comes with a two page booklet that tells me I need 6 AAA batteries and something to barcode.

Friday, 26th
I went down to the university to show my new barcoder to my sister. She needs lots of fresh tissue to do her molecular work and always complains that her specimens are either too old or contaminated. "Not with this!" I told her. She looked at me and my barcoder and started laughing. Stuck-up cow.

Saturday, 27th
Today is my first barcoding day (it rained all week, so there was nothing to barcode). I barcoded my cat, which it turns out, is 'human'. Perhaps it's because humans and cats are closely related? Perhaps I need something more distantly related?

Sunday, 28th
I barcoded an ant that I found crawling behind the sofa. The barcoder tells me it's a fungus. I see no other ants. Later on I find a honey bee trapped in my kitchen window. It comes up as a 'geranium'. The barcoder really needs to be calibrated or something.

Wednesday, 1st
Finally, a hot and sunny day! I tried to entice a bird with bread crumbs. No luck.

Thursday, 2nd
Couldn't get close enough to the house sparrows in my park to barcode them. I barcoded various trees in the arboretum. Amazing! The barcoder gets it right every time. There was only one plant sign in the whole park that was wrong!

Sunday, 5th
What a day! Yesterday morning I found a whip snake sunning itself on my porch. I managed to barcode it before it bit me in self defense. Luckily the hospital knew which anti-venom to use because my trusty barcoder got it right again!

Tuesday, 7th
I’m going to be famous! I barcoded a cicada and found that it was 7 different species! I rushed down to the local natural history museum to tell them of the news. Perhaps they can name a news species after me? Apparently the museum barcodes species from all over world and no longer employs taxonomists (the ones who describe new species). A barcoding technician pointed out several local amateur entomological groups I could join. "That's where you find taxonomists now" he said. Perhaps I’ll try Google.

Publications for 2010

Below is our list of publications for 2010. For those with no access to the links, will be happy to provide pdf copies on request.

Christenhusz, MJM., Baker, W., Chase, MW., Fay, MF., Lehtonen, S., Van Ee, B., Von Konrat, M., Lumbsch, T., Renzaglia, KS., Shaw, J., Williams, DM and Zhang, Z-Q. (2010). The first anniversary of Phytotaxa in the International Year of Biodiversity. Phytotaxa, 15: 1–8.
 
Ebach, M.C. (2010). Paleobiological Revolution: Essays on the Growth of Modern Paleontology. Systematic Biology, 59: 753-755.
 
Ebach, M.C. (2010). A new book on biogeography. Cladistics, 26: 560-562.
 
Ebach, M.C. and de Carvalho M.R. (2010). Anti-intellectualism and the DNA Barcoding Enterprise. Zoologia, 27: 165-178 [access free pdf here]. 
 
Ebach, M.C. and Williams D.M. (2010). Aphyly: A Systematic Designation for a Taxonomic Problem. Evolutionary Biology, 37: 123-127.
 
Ebach, M.C. and Williams D.M. (2010). Systematics and Biogeography: Cladistics and Vicariance. Systematic Biology, 59: 612-614.
 
Parenti, L.R. and Ebach, M.C. (2010). Wallacea Deconstructed. In D.M. Williams & S. Knapp (eds.), Beyond Cladistics: The Branching of a Paradigm. University of California Press, Berkeley, pp. 303-318.
 
Reid, G. and Williams, D.M. (2010). Notes on the genus Semiorbis Patrick with a description of a new species. Diatom Research, 25: 355—365.
 
Toyoda, K, Nagumo, T. and Williams, DM. (2010). A new marine monoraphid species, Achnanthes pseudolongipes sp. nov. From Miyagi, Japan. Diatom Research, 25: 185—193.
 
Tuji, A, Williams, D.M, Sims, P.A, and Tanimura, Y. (2009) [2010] An Illustrated Catalogue of Type Specimens from the H.M.S. Challenger Voyage in Castracane’s Slide Collection in the Natural History Museum, London. In: Joint Haeckel and Ehrenberg project: Re-examination of the Haeckel and Ehrenberg Microfossil Collections as a Historical and Scientific Legacy Y. Tanimura and Y. Aita, eds). National Museum of Nature and Science Monographs, No. 40, pp. 7—11.
Williams, D.M. (2010). Historical biogeography, microbial endemism and the role of classification: everything is endemic. In Biogeography of microorganisms.  Is everything small everywhere? (Fontaneto, D, ed.), Cambridge University Press, Cambridge, pp. 11—31.
 
Williams, D.M, Chudaev, D.A, Lomonosov, M.V and Gololobova, MA.. (2010). Punctastriata glubokoensis spec. nov., a new species of ‘Fragilarioid’ diatom from lake Glubokoe, Russia. Diatom Research, 24: 479—485.
Williams D.M. and Ebach, M.C. (2010). Molecular Systematics and the Blender of Optimization: Is There a Crisis in Systematics? Systematics and Biodiversity, 4:481-484. 
 
Williams, D.M, Ebach, M.C. and Wheeler, Q.D (2010). Beyond belief: the steady resurrection of phenetics. In D.M. Williams & S. Knapp (eds.), Beyond Cladistics: The Branching of a Paradigm. University of California Press, Berkeley, pp. 169-197.
 
Williams, DM and Kociolek, JP. (2010). Classifications of Convenience: The Meaning of Names. Diatom Research 25: 213—216. Williams, DM and Morales, EM. (2010). Pseudostaurosira medliniae, a new name for Pseudostaurosira elliptica (Gasse) Jung et Medlin. Diatom Research 25: 225—226.
 
Yanling Li, Williams, D.M, Metzeltin, D., Kociolek, J.P. and Zhijun Gong (2010). Tibetiella pulchra gen. nov. et sp. nov., a new freshwater epilithic diatom (Bacillariophyta) from River Nujiang in Tibet, China. Journal of Phycology, 46: 325—330.

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.

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

or:

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

or

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.

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?

The Mystery of the Siberian Pinkie: When Classification goes Wrong

Biological 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”.

References

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

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.

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 (mcebach@gmail.com).

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

Paraphyly Watch 2009: Pewter Leprechaun Awards Ceremony

Albert Hall, London.

Thousands of people gather outside in the snow, lining up and waiting to get in to what is tipped to be a star-studded awards ceremony. Inside, we see seats slowly being filled, hear the humdrum of excited voices and the clink of champagne glasses. The air is electric with excitement.

[Announcer] Welcome to the most awaited event of the year! Thousands of people are lining up outside to see the winner of the 2009 Pewter Leprechaun. The Hall is sold out and rumors have it that hawkers are selling tickets for over £1000. The air is tense and the crowds excited by the news that this year nominations are a close tie. Walking up to the booth I saw several of the judges looking tired and worn from the week-long debate as to who will be this year’s winner. We also have several famous scientists in the crowd. There I see ... I think ... is it Aristotle? Possibly. Since the introduction of the Simpson-Darlington Time Machine many international and temporal guests are able for the first time to visit on a whim. I guess it could be Plato ... err ... not to sure. Yes, there is the guest of honor Aristotle, carrying the ceremonial Great Chain of Being ladder - the Scala Naturae itself. He will of course be chairing the session from the right of the stage.

This year’s nominees are:

Martin D. Brazeau on ‘The braincase and jaws of a Devonian ‘acanthodian’ and modern gnathostome origins’ published in Nature (2009, 457:305-308)

Dennis P. Gordon on ‘Towards a management hierarchy (classification) for the Catalogue of Life’ a Draft Discussion Document published in Species 2000 & ITIS Catalogue of Life Annual Checklist (2009, on CD-ROM)

Donald R. Prothero on the ‘Evolutionary Transitions in the Fossil Record of Terrestrial Hoofed Mammals’ published in Evolution, Education and Outreach (2009, 2:289-302)

Todd F. Stuessy and Christiane Konig on the ‘Classification should not be constrained solely by branching topology in a cladistic context’ published in Taxon (2009, 58:347-348)

János Podani on the ‘Taxonomy versus evolution’ by also published in Taxon (2009, 58:1049-1053)

The audience is seated and the lights dim

[Announcer] I see that the lights are dimming and...

Applause

[Announcer] ... rapturous applause for the man himself - the father of paraphyly and host for tonight - Ernst Haeckel! He is walking onto stage, completely out-fitted in tweeds and ... is that a duck hanging from his belt....?

Applause ends

[Ernst Haeckel] Danke Schoen! Meine Damen und Herren! Tonight ve vill avard zi Pewter Leprechaun for 2009 to zi most admirable abuse and misuse of paraphyly. It iz my pleasu ...

Applause. Haeckel gets annoyed

[Ernst Haeckel] Aufhalten! Ve applaud at zi end! AT ZI END!

Applause ends abruptly

[Ernst Haeckel] Zat ist better. Ver vos I. Ach ja ... my pleasure to announce the vinner. Bevor I do, may vi present and bless die Pewter Leprechaun?

Haeckel looks around slightly confused. The main doors open and a procession starts at the back of the Hall

[Announcer] And we see the procession of the Pewter Leprechaun held aloft by George Gaylord Simpson. Following behind him is the Holy Order of the Lineage, Ernst Mayr, P.J. Darlington, Peter Ashlock all holding candles ... and ... there is some commotion at the back ... some shouting ... oh dear ... is that Adolf Naef? My word! Naef is attacking Simpson - he must just have read Principles of animal taxonomy during his brief visit here. He is not happy ... some more shouting ... OH! Simpson has punched Naef! The American has swiped the Swiss in a spectacular left-hook! Naef has recovered and is grabbing the Pewter Leprechaun.. has he got it? He HAS GOT IT! Mayr tackles Naef, Naef passes it on to ... Zangerl! My God, see that man run! Dodges Remane and Zimmermann ... who are discussing functional homology and ... knocks over Hennig, who was admiring Remane ... a crash-tackle by Ashlock and Zangerl looses the Leprechaun! They have lost the Leprechaun! .. It’s ... Ashlock ... picks up the leprechaun and passes it onto .... Darlington .... pushes over Hennig who just got up again ... passes it onto Mayr, back to Darlington who ... misses the catch! He has missed the catch! There is a scramble for the Leprechaun and Haeckel, yes Haeckel, joins in and ... punches out Hennig who just got up again ... and runs and leaps onto stage. What a performance from the German!

This has been a most remarkable entry for the Holy Order of the Lineage! The audience is wild with excitement. Aristotle stands up to bless the Leprechaun .. and ... it’s blessed! The Leprechaun has been blessed by the Great chain of being ladder! Haeckel struts back to the podium and puts his hand in his top pocket ... yes ... it’s a golden envelope!

[Ernst Haeckel] Meine Damen und Herren! Zi vinner of zi 2009 Pewter Leprechaun is ...

Haeckel slowly opens the envelope and pulls out a card

[Ernst Haeckel] Mein Gott!

Haeckel appears startled and looks to Aristotle holding out the card. Aristotle strains to see what is written on it. The audience titters

[Ernst Haeckel to Aristotle] Iz dis ein f*cking joke?

Aristotle shrugs. Haeckel composes himself

[Ernst Haeckel] Well ... zi judges ... have decided that the award should go to zi most prolific publisher of zi use and abuse of paraphyly. The vinner iz ... Taxon, zi journal of the International Association for Plant Taxonomy!

Audience applauds insanely

[Announcer] This is a surprise! The Pewter Leprechaun has never been awarded to a journal, in fact, it has never been awarded to anyone. I hope the nominees aren’t too disappointed. But aren’t the audience just loving it! Ernest Haeckel bows and leaves the stage. Aristotle leads the procession of the Holy Order out the Hall as the audience slowly rises in respect. Simpson and Darlington looking a bit bruised but enjoying the moment. Do I see a smile from Mayr? Err ... no, but I am sure he is loving every minute of it!

So ends the Pewter Leprechaun Awards Ceremony for 2009. We hope that 2010 brings forth a startling array of nominations. All entries can be submitted to the Systematics & Biogeography Blog via next year’s 2010 Paraphyly Watch post.

Have a Merry Christmas and a Happy New Year!