New Research visitor – Dr. Marco Fondi

We are pleased to welcome a new visitor to our research group – Dr. Marco Fondi.

Dr. Fondi is joining us for six months as part of a Science Foundation Ireland funded project on understanding networks in biology.

Marco has been working at the Dipartmento di Biologia Evoluzionistica in the Laboratorio di Evoluzione Microbica e Molecolare.

In the last four or five years, Dr. Fondi has made some significant findings in the whole area of analysing gene fusions, recombination and the evolution of plasmids.

The Cambrian Conundrum: a new perspective

Together with a bunch of collaborators from the US we recently published a paper in the journal Science (1) about the Cambrian evolutionary explosion, and the origin of animals.

This is a multidisciplinary study addressing some key questions in animal evolution by merging genomic and palaeontological information.  This multidisciplinary approach was firstly advocated by Bruce Runnegar (2), one of the greatest contemporary palaeontologists, and is named Molecular Palaeontology.

From my point of view this study is of paramount importance not only because it improved our understanding of animal evolution; but also because our new paper represents the first large-scale molecular palaeobiological study and marks the coming of age of this new research paradigm.

It is difficult, to summarise this paper in few, simple words, mostly because it has so many different facets.  However, let’s simply say that Darwin considered the Cambrian evolutionary explosion (i.e. the sudden appearance of bilaterally symmetrical animals in the fossil record ~ 525 Millions of years ago) as one of the potentially most serious problems with his gradualist theory of evolution by natural selection (3).  In the fossil record, Precambrian ancestors of the Cambrian animals were unknown.  Darwin concluded that this was most likely because of gaps in the fossil record.  He went on by stating that as older rocks would have been uncovered ancestors of the Cambrian animals would have been found.  Indeed many Precambrian fossils are now known but uncontroversially recognisable ancestors of the Cambrian bilaterians have still to be found.  So, using the words of Enrico Fermi (see Ref. 4): “where are they?” This discrepancy has led many evolutionary biologists to conclude that the Cambrian explosion is, most likely, some sort of fossil preservation artefact (i.e. a taphonomic artefact).

In a series of papers published in the early sixties Linus Pauling and Emile Zuckerkandl (5) firstly suggested that historical information about living species could be found in the genetic material.  They also introduced the concept of “molecular clock”.  In simple terms, this is based on the idea that the genetic distance between two species should be roughly proportional to the time since they diverged from their last common ancestor.  Molecular clocks allow estimating divergence times among organisms in a (largely) fossil independent way (few fossils still need to be used to calibrate the clock).

Molecular clocks have long been used to try to date the animal radiation, and for a long time these methods produced results largely incongruent with the Cambrian explosion.  That is, they suggested that animals with a bilateral symmetry significantly predated their first origin in the geologic record.  Because these results are consistent with Darwin’s original hypothesis that the fossil record is highly incomplete, these results have been taken to confirm the artefactual nature of the Cambrian explosion.   However, and most importantly, these earlier studies used molecular clock methods that are now considered obsolete, and that assumed an unrealistic, fixed rate of substitution across the entire animal kingdom (see for example Ref. 6).

In our study we used modern, well performing molecular clock methods that avoid the assumption of rate constancy, a large sample of living taxa and a robust set of calibration points from the fossil record.  In this way we were able to show (see Figure) that the Cambrian explosion is not a preservation artefact but a real evolutionary event: It represents the time at which the modern animal phyla (e.g. Brachiopoda, Mollusca, Nematoda, Arthropoda and so forth) radiated.  What is surprising of the pattern we observed is that all animal Phyla seem to have independently radiated in a very short amount of time, which closely correspond to the time of the Cambrian radiation.

However, it is important to point out that the origin of the animals with bilateral symmetry is not the same as the origin of the animals.  According to our result, the latter event happened ~ 770 Millions of years ago.  This is concordant with recent results suggesting Demosponges (a groups of sponges) should have existed > 700 millions years ago (7,8).

To sum this up our results validate the reality of the Cambrian evolutionary explosion without violating the Darwinian paradigm.  So, is the Cambrian explosion real? The answer is Yes.  Does it pose a problem to the Darwinian theory of evolution? The answer is No.

 

References

1) Erwin, D.H., Laflamme, M., Tweedt S.M., Sperling, E.A., Pisani, D. and Peterson K.J. (2011). The Cambrian conundrum: Early divergence and later ecological success in the early history of animals. Science  334: 1091-1097.

2) Runnegar, B. (1986) Molecular Palaeontology. Palaeontology  29: 1-24.

3) Darwin, C. (1859) On the origin of species by means of natural selection.  John Murray, London (page 306).

4) Hart, M. H. (1975). An explanation for the absence of extraterrestrials on Earth. Q. J. R. Astron. Soc. 16:128-135.

5) Zuckerkandl and Pauling (1965) Molecules as documents of evolutionary history. J. Theor. Biol. 8:357-366.

6) Sanderson M.J., (1997) A non parametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14:1218-1231.

7) Love, G.D., Grosjean, E., Stalvies, C., Fike, D.A., Grotzinger, J.P., Bradley, A.S., Kelly, A.E., Bhatya, M., Meredith, W., Snape, C.E., Bowring, S.A., Condon, D.J., and Summons, R.E. (2009) Fossil steroids record the appearance ofDemospongiae during the Cryogenian period. Nature 457:718-722.

8) Maloof, A.C., Rose, C.V., Beach, R., Samuels, B.M., Calmet, C.C., Erwin, D.H., Poirier, G.R., Yao, N., and Simons, F.J. 2010 Possible animal-body fossils in pre-Marinoan limestones from South Australia. Nature Geoscience 3:653-659.

 

 

 

 

 

 

 

 

 

 

 

 

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H-Index, M-Index and google citations

Today I downloaded and installed the r program for analysing Google Scholar citation metrics (you can pick it up here).

There is a lot of talk about the various metrics being used to analyse the productivity of scientists and there seems to be no really good way to do it.  A simple point-statistic doesn’t do it very well.

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Post-doctoral applicants sought for IRCSET grants.

post-doc applicants wanted

We are looking for post-doctoral applicants for the upcoming IRCSET grant deadline. The name of the programme is EMPOWER and it is aimed at relatively early-stage postodoctoral applicants. Here is some of the information form the website:

EMPOWER: Government of Ireland Postdoctoral Fellowships in Science, Engineering and Technology
IRCSET will continue to offer their sought-after fellowships based at an Irish host laboratory.   The candidates must have been employed for no more than 36 months as a postdoctoral researcher before the closing date of the Call, and propose pursuing their work for 24 months at an Irish research laboratory.  They must be able to provide evidence of at least one significant research output, such as a published peer-reviewed article or equivalent intellectual property output.  For more detailed information on the eligibility criteria, please download the ‘EMPOWER Terms & Conditions’ document from the EMPOWER page.  Applications for EMPOWER will be accepted via one call for Postdoctoral Fellowships in autumn each year.

We are looking for applicants for the Pisani, Fitzpatrick and McInerney laboratories.

If you have been working in the areas of bioinformatics and/or molecular evolution, please feel free to contact us through our contact page.  The deadline for completed applications is December 7th, 2011.

Survival of the sexiest

 

 

This is to announce that on Tuesday next (the 15th of November), there will be a talk given by Dr. James McInerney in JH2 in the John Hume Building at NUI Maynooth at 7:30pm, entitled:

 

Survival of the sexiest: Why females want a mate with a good sense of humour, a brightly coloured tail and nice antlers.

 

 

The event is open to the public and is part of Science week and there is no admission charge.

 

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