10,000 genomes.

Lots of genomes going to be sequenced. Some of the members of the group are colleagues at Guelph. Very cool. That is all.

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

Genome 10K Community of Scientists

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10 000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16 203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60 000 living species). In this proposal, we present precise counts for these 16 203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.




Evolver Zone.

Readers of this blog will soon notice some changes. This is because the Evolver Zone site has now been launched, and Genomicron will be fit within it. For now, it will remain a separate blog at this same location, but the look will be updated shortly. Meanwhile, have a look at the resource of multimedia and information about software, databases, journals, and web links at Evolver Zone (www.evolverzone.com).

TravelBlogue, or How to live vicariously through one’s student.

The very first post here was called “My grad student made me do it“, and explained that a then-newly-arrived PhD student in my lab was a blogger and got me interested in blogging. He is still a blog author, and most recently has posted a very enjoyable series about his travels from more or less the bottom to the top of the USA/Canada parts of North America looking for aquatic creatures. I personally did not get to go anyplace exciting this summer, but it has been great having the option to live vicariously, especially as he was most recently at one of the coolest (literally?) places on Earth: Devon Island in the high Arctic. Follow his adventures:

Florida to Guelph:

Guelph to Thompson:


Resolute and True Love

  • Coming soon

A pronounced affection for parasites.

According to Peter Olson of the Natural History Museum in London, “All free-living organisms host one or more parasites”. This can be taken two ways, both of them generally true: a) that each individual multicellular organism hosts at least one individual parasite within its body, and b) that each free-living species plays host to at least one species of parasite that attacks it exclusively. Consider this second point for a moment. For each free living species there is one or more (usually several more) parasite species — that is, as a category (polyphyletic, obviously), parasites may very well be the most diverse types of organisms on the planet.

On the other hand, most parasites are much smaller than their hosts, and so it has typically been assumed that they contribute a negligible fraction to any particular ecosystem’s total biomass. Nuh-uh. In a report published in Nature this week, Kuris and colleagues presented five years’ worth of analyses of estuaries in California and Baja California in which they measured the amount of biomass made up of parasites and free-living organisms.

In sum, Kuris et al. (2008) examined 138 species of infectious agents, 199 species of free-living animals (including invertebrates as well as fishes and birds), and 15 species of free-living plants in their study. They found that plants contributed the most biomass to all three of the estuaries they studied, followed by groups such as snails, bivalves, and crabs. Parasites made up only about 0.2% to 1.2% of the animal biomass of each environment, and on average parasite groups had biomasses 1000 times lower than the average free-living group. However, as Kuris et al. (2008) report,

Certain parasitic groups dominated the parasite biomass, reaching levels similar to those of common free-living groups. For instance, the biomass of trematode worms was comparable to that of the fishes, burrowing shrimps, polychaetes or small arthropods. In all estuaries, trematode biomass exceeded bird biomass by threefold to ninefold.

In other words, parasites make up a larger fraction of the living matter in these environments than do the top predators. In particular, parasites that castrate their hosts (i.e., prevent them from diverting resources into reproductive effort) were the most abundant. The world is not fishy or feathery, it is fluky.

So, whereas the famous quote attributed to J.B.S. Haldane that if there is a creator he must have “an inordinate fondness for beetles” still applies, it may be that he has an even more pronounced affection for parasites. Especially the castrating sort.


Kuris, A.M., R.F. Hechinger, J.C. Shaw, K.L. Whitney, L. Aguirre-Macedo, C.A. Boch, A.P. Dobson, E.J. Dunham, B.L. Fredensborg, T.C. Huspeni, J. Lorda, L. Mababa, F.T. Mancini, A.B. Mora, M. Pickering, N.L. Talhouk, M.E. Torchin, and K.D. Lafferty. 2008. Ecosystem energetic implications of parasite and free-living biomass in three estuaries. Nature 454: 515-518.

Update: For more detailed discussions, see Not Exactly Rocket Science and keep your eyes open for a post at The Loom.

Species-Scape: very cool, but…

Larry Moran directs us to have a look at Species-Scape at the Cornell website. It’s great.


1. It has one group of “prokaryotes”, Kingdom Monera, which is pretty old school. (Same goes for “Protists“). You don’t like dividing the Archaea and Bacteria? Ok, but how about a note that many people now consider this one of the deepest divisions of life? If they can mention something as esoteric to most readers as the phylogenetic species concept, surely they could include a brief line about, you know, phylogenetic groupings at the highest level.

2. And I quote:

This is a taxonomic view of life on earth — based on systematic classifications — which challenges our typical “mammal-centric” understanding of the world around us. Today there is increasing awareness of the enormous diversity of life on earth, but few people probably appreciate the fact that the Species-Scape is completely dominated by multilegged (more than 4 legs) and legless animals, fungi and microbes. Mammals, with a mere 4,000 species, are dwarfed by “lower” animals.

Do we really have to use a misconception to correct a misconception?

Biodiversity databases.

The recent launch of the Encyclopedia of Life has generated quite a bit of excitement. It is my hope that advances such as this will help to make information about the millions of species that inhabit the planet accessible to everyone. It is the ultimate in open access science. In keeping with this, here is a list of biodiversity databases that are freely available to anyone. (I am sure to have missed some and I left out many taxon-specific pages — please leave me a comment or send me an email if you know of any other major resources and I will update the compilation).