Tuesday, May 30, 2006

Trichoplax mitochondrial genome sequenced

In press at PNAS is the report of the sequence of the mitochondrial genome sequence of the very unusual metazoan Trichoplax adhaerens. Trichoplax is odd because it is an extremely simple version of a multicellular organism. It has no real organs, no axis of symmetry, a very small nuclear genome and only four distinct cell types.

This has led to the hypothesis that it is a basal metazoan. That is the first lineage to diverge from all the other metazoans. There could of course be other explanations for the apparent simplicity of Trichoplax such as it is a result of a loss of various features found in its ancestors. The mitochondrial genome sequence seems to confirm that Trichoplax is indeed a basal metazoan.

The mitochondrial genome is the largest yet discovered in metazoans at 24-kb, although this is smaller than the largest mitochondrial genome yet discovered in eukaryotes. That distinction goes to Reclinomonas americana a protozoon with a genome of 69-kb. The genome also shares features found in different branches of metazoa such as sponges and cnidarians and features that seem to be unique to all animals such as a lack of ribosomal protein genes. It seems that the Trichoplax mtDNA resembles the ancestoral condition of metazoa supporting its basal position.

Trichoplax adhaerens is a fascinating organism and with a nuclear genome on the way it seems likely to reveal more interesting discoveries.


Stephen L. Dellaporta, Anthony Xu, Sven Sagasser, Wolfgang Jakob, Maria A. Moreno, Leo W. Buss, and Bernd Schierwater.
Mitochondrial genome of Trichoplax adhaerens supports Placozoa as the basal lower metazoan phylum
PNAS published May 26, 2006, 10.1073/pnas.0602076103

Pharyngula::Trichoplax adhaerans.

Trichoplax: my favorite animal (PDF)

The Trichoplax story (PDF)

PDFs from Bernd Schierwater lab

Friday, May 26, 2006

Stuff Roundup 26/06

Stuff on the web/in the news that has caught my eye recently.


There was a letter sent by several leading doctors to the Times calling for the use only of medicine "based on solid evidence" and attacking bogus quackery such as homeopathy. This of course sent the quacks into a fit. It has been well covered at: Skeptico, Skepchick and rhetorically speaking.

Good news from oxford: Oxford lab injunction tightened. See also the Scientific activist's post on a Pro-test meeting.


A fabulous review of the ediacaran is in press at Earth science reviews :

The Vendian (Ediacaran) in the geological record: Enigmas in geology's prelude to the Cambrian explosion
In Press, Corrected Proof, http://dx.doi.org/10.1016/j.earscirev.2005.08.004
G.J.H. McCall.

It's 229 pages long and very comprehensive

The January-February 2006 issue of Comptes Rendus Palevol is available for free and contains loads of fascinating papers on human prehistory and evolution.

The International Journal of Biological Sciences has a nice series of papers on Amphioxus, see also the special issue (freely available) of Canadian Journal of Zoology on Protochordata.

The Quarterly Review of Biology has a free sample issue with an interesting paper on the origin of life: 'Small Molecule Interactions were Central to the Origin of Life'.


Carnivals: Skeptics' Circle, I and the Bird and Tangled Bank.

Dracorex hogwartsia a cool new dinosaur has been announced see the Hairy Museum of Natural History and another post.

No genes were lost in the making of this whale from Pharyngula,

The most freaky of all mammals: rabbits from Darren Naish.

Lovely pictures of Squid and Jellyfish from BibliOdyssey.

Monday, May 22, 2006

Bear Gulch website

Damocles serratus a fossil shark from Bear Gulch

I have just found this lovely website: Fossil fishes of Bear Gulch

"The Bear Gulch Limestone (Mississippian of Montana) is what is known as a lagerst├Ątte, a well-bedded sequence of limestone layers containing an extremely well-preserved assemblage of fossils. This deposit has yielded one of the most diverse and well preserved fossil fish assemblages in the world. We have excavated approximately 130 species of fish from this deposit over the last 35 years. The site also contains well preserved arthropods, sponges, starfish, conulariids, worms, and other soft-bodied organisms, as well as brachiopods, bryozoans, and molluscs. The Bear Gulch fossils are so well preserved that they provide a window into the life of the Mississippian that has never been available before. This site is dedicated to bringing you and the fishes of the Mississippian together."

It has some amazing pictures, drawings and infromation about the lovely fossils that have been found at Bear Gulch. In addition to fish there are also fossil invertebrates, plants and enigmas. There is just so much content here the creators deserve alot of praise.

See also:

Whitey Hagadorn, 2002, Bear Gulch: An exceptional Upper Carboniferous plattenkalk, in Bottjer, D.J., et al., eds., Exceptional Fossil Preservation: A Unique View on the Evolution of Marine Life: Columbia University Press, New York, p. 167-183. (PDF)

Sunday, May 21, 2006

Fungal mimics

Mimicry is a fascinating and widespread phenomenon where one organism gains some benefit by resembling another organism or thing. This resemblance can take many forms including visual, chemical and molecular mimicry.

A mini review in FEMS Microbiology Letters (1) has stimulated my interest in the little known mimetic interactions of plants and fungi.

There are several ways that fungi can imitate plants and manipulate them or use them to manipulate other organisms. One particularly fascinating mechanism is the production of ‘pseudoflowers’ that is structures formed from the leaves of a plant infected by fungi that resemble flowers, they also smell like flowers and exude sweet liquid as a reward. This liquid contains fungal spores and when pollinating insects land on the pseudoflowers they pick up spores and transfer them to other flowers that the fungus can then infect. I am just amazed by this type of manipulation, it will be fascinating to learn just how this remarkable feat is achieved and how it evolved.

(A) Uninfected flowering Euphorbia cyparissias plant and (B) E. cyparissias infected by the rust fungus Uromyces pisi. (2)

Pseudoflower of an Arabis produced by the fungus puccinia monoica (3)

Fungi can also act as molecular mimics tricking the host plant into thinking that they are grains of pollen. This allows them a fantastic entry route into the plant bypassing the physical barriers found in the rest of the plant. The Stigmas of plants have evolved to capture pollen grains from the air. The normal pollen floats in the air in a similar ways to fungal spores and so end up on stigmas in a similar way. There is also some evidence that molecules on the surface of the growing fungus contain similar molecules to pollen. A similar trick is accomplished by several pathogens where surface molecules resemble those of the host.

While writing this I saw an interesting post at Thomasburg walks via the carnival of animalcules. I am not sure if they are flower mimics, they certainly look like flowers. It would be interesting to find out if they attracted pollinating insects to disperse them, or if in this case the resemblance to flowers in coincidental.


1) Mimicry in plant-parasitic fungi
Henry K. Ngugi & Harald Scherm
FEMS Microbiol Lett 257 (2006) 171–176

American Journal of Botany 87(1): 48–55. 2000.

3) Floral mimicry by a plant pathogen
B. A. Roy
Nature 362, 56 - 58 (04 March 1993) ; doi:10.1038/362056a0


Monday, May 15, 2006

Tutankhamun archive to go online

According to The Guardian the whole of the archive related to the excavation of the tomb of Tutankhamun is goinf to be made available online:

"Between 1922 and 1930, at least 5,398 objects were removed. Carter and his colleagues made meticulous index cards, notes and sometimes drawings of each find, and kept diaries and records of their progress. All of which went to Oxford, where they have been preserved since Carter's death in 1939.

From then, research progress has been slow, Dr Jaromir Malek, of the Griffith Institute in Oxford, told a Bloomsbury Academy conference in London last Saturday. "We came to the conclusion that probably 20% of the material had been properly published, and if the current rate of progress was going to continue it would probably take another 200 years," he said.

The Oxford archive, as it stands, will be entirely online within two years."

Here are links to what is currently available:

Tutankhamun: Anatomy of an Excavation is ambitious in its scope but simple in its aims: to make the complete records of Howard Carter's excavation of the tomb of Tutankhamun available on these web pages.

The Search for Tutankhamun. (Howard Carter's records of the five seasons of excavations, financed by Lord Carnarvon, in the Valley of the Kings 1915 - 1922).

The state of British butterflies

A new report called 'The state of butterflies in Britian and Ireland' by the charity Butterfly Conservation has just been resleased.

It present s a mixed picture of the state of british butterflies. Some have done quite well but many other gave continued to decline. It seems that generalists who can cope with different environments are doing quite well but specialists that rely on particular habitats have done badly. There is also evidence of range expansion of some species probably because of climate change. This is ok for species that are able to move to a new habitat, if you are a species that relies on a small patch of habitat then it's bad news.

Hopefully this survey will provide clues as to how our butterflies can be conserved and unline the importance of climate change to many species.

Some of the data from the BBC:

Painted Lady (+31%)
Red Admiral (+30%)
Marsh Fritillary (-32%)
White-letter Hairstreak(-68%)
Pearl-bordered Fritillary (-77%)
High Brown Fritillary (-82%)
Source: Butterfly Conservation, figures for 1995-2004 survey, compared to 1970-1982

Thursday, May 11, 2006

Friday, May 05, 2006

New Ediacaran type fossil

Stromatoveris (click for bigger)

In the current issue of Science (5 May 2006) There is a description of an amazing new fossil from the Chenjiang lagerstatte in China (1).

I have written about the Ediacaran (Vendian) and the strange organisms before, and although many organisms remain mysterious this fossil seems to resolve one of the most puzzling aspects of the Ediacaran – how are they related to later organisms and their modern descendants.

One of the characteristic organisms of the Ediacaran is the ‘frondose’ fossils such as Charnia (also here) and this new fossil Stromatoveris is of the frondose type.

Although Stromatoveris seems to be of Ediacaran type it is found in early Cambrian sediments. This is strange as it is usually thought that the Ediacaran biota largely went extinct at the base of the Cambrian, although fossils such as Thaumaptilon walcotti have indicated the possibility of some survivors.

There are essentially two broad schools of opinion on the relationship of the Ediacarans, that they had a unique construction unrelated to any know type of organism or that they are related fairly closely to modern phyla. The remarkable preservation of Stromatoveris allows features to be detected that suggest that it is a relative of Ctenophores. Interestingly that does not rule out the possibility that other organisms, even ones that look superficially similar, are strange ‘giant protists’ or have a similarly unfamiliar type of construction.

Proposed phylogeny of Stromatoveris (click for bigger)

This has important implications for evolution, it seems that some modern phyla had diverged before the Cambrian, as has long been suspected on the basis of molecular dates. Another recent discovery, yet again using fossils from Chengjiang, links the Ediacaran Parvancorina with the arthropods such as trilobites (2) extending the range of another phylum back in time.


1) Lower Cambrian Vendobionts from China and Early Diploblast Evolution.
D.-G. Shu, S. Conway Morris, J. Han, Y. Li, X.-L. Zhang, H. Hua, Z.-F. Zhang, J.-N. Liu, J.-F. Guo, Y. Yao, and K. Yasui.
Science 5 May 2006: 731-734.

2) A Parvancorina-like arthropod from the Cambrian of South China.
Lin, J.P., S.M. Gon III., J.G. Gehling, L.E. Babcock, Y.L. Zhao, X.L. Zhang, S-X. Hu, J.L. Yuan, M.Y. Yu, & J. Peng. 2006.
Historical Biology 18(1): 33–45.

Wednesday, May 03, 2006

The oddness of Hyaenas

In the current issue of Nature ( 27 April 06) there is an interesting article about the reason that female Spotted hyaenas (Crocuta crocuta) are exposed to very high levels of androgens such as testosterone during the later stages of pregnancy. The answer seems to be that high levels of androgens pass on high status to the offspring of high status females. It also seems to promote aggressive and dominant behavior such as mounting (1).

This seems to be related to the extremely odd reproductive behavior and anatomy of hyenas, although the precise relationship is still a mystery.

It has long been noted that female hyaenas have very unusual genitalia with the females having an enormously enlarged clitoris giving the appearance of having male genitalia. They even have pseudo testes increasing the resemblance (2).

A female hyaena with a arrow pointing to the peniform clitoris

This structure is referred to as the ‘peniform clitoris’ :

The dissected reproductive organs of a hyaena

This would appear to be a complete mystery as this imposes a variety of costs throughout life. It makes copulation extremely difficult as intromission has to occur into the enlarged clitoris (!) if mating is difficult that is nothing to giving birth:

“Toward the end of an extended period of labor, a fetal hyena fills and stretches the clitoris (outlined by white dots) of a primiparous female. The clitoral meatus (large arrow) will eventually tear and permit birth to occur. Subsequent deliveries, through the stretched and torn clitoral meatus, are much more rapid. Note nipples (small arrows).” (2)

At least thing get slightly better with further births although I shouldn’t imagine that is much consolation for the hyaena. In fact, about 60% of first births are stillborn in a captive colony due to this peculiar anatomy; in the wild it could be even higher.

There seems to be two different processes that give rise to the female morphology. The development of the peniform clitoris begins early in development before the late burst of androgens. This shows that it is not a side effect of dominance conferring androgens. It seems like this particular avenue of development has been selected for because it is beneficial in itself. Although high levels of androgens are necessary for the complete development of the peniform clitoris (3) so there is probably some sort of co-evolution.

If there are such heavy costs of this morphology then why does it exist? There are several theories, it is probably partly to do with the increased dominance, aggression and possibly other thing like increased size/muscle mass. But there could be increased dominance without the peniform clitoris so it is likely that it has a benefit in itself, this could be because there is a lot of aggression towards young female hyaenas from siblings adult females and members of other clans and the enlarged clitoris could act to fool other hyaenas into not harming the young females (4).


1) S. M. Dloniak, J. A. French and K. E. Holekamp
Rank-related maternal effects of androgens on behaviour in wild spotted hyaenas
Nature 440, 1190-1193 (27 April 2006
) doi:10.1038/nature04540

2) Cunha GR, Wang YZ Place NJ, Liu W, Baskin L, and Glickman SE. (2003). The urogenital system of the female spotted hyena ( Crocuta crocuta ): a functional histological study.
J Morph 256:205–218. (PDF)

3) Cunha GR, Place NJ, Baskin LS, Conley AJ, Weldele ML. Cunha TJ, Wang YZ, Cao M, and Glickman SE. (2005). The ontogeny of the urogenital system of the spotted hyena (Crocuta crocuta Erxleben).
Biol Reprod 73:554-564. (PDF)

4) Muller MN & RW Wrangham.
Sexual mimicry in hyenas.
Quarterly Review of Biology. 77:3-16. (PDF)