Bacteria Expect the Unexpected
Organisms ensure the survival of their species by genetically adapting to the environment. If environmental conditions change too rapidly, the extinction of a species may be the consequence. A strategy to successfully cope with such a challenge is the generation of variable offspring that can survive in different environments. Even though a portion of the offspring may have a decreased chance to survive, the survival of the species as a whole is guaranteed. For the first time scientists have now observed the evolution of such a strategy under lab conditions in an experiment with the bacterial species Pseudomonas fluorescens: A bacterial strain exposed to rapidly changing environmental conditions developed the ability to generate variable offspring without additional mutations. This new strategy ensured the survival of the bacterial strain. The results were published in NATURE. (05.11.2009).

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.

http://www.nature.com/news/2009/091104/full/462021a.html

http://www.ucsc.edu/news_events/text.asp?pid=3333

http://genome10k.soe.ucsc.edu/

Maybe this sounds silly to you.  Me too.  It also sounded silly to Hart and Grosberg (2009), who thoroughly debunk the hypothesis using data that were already easily available.  You can read a play by play of the refutation over at Jerry Coyne’s blog  Why Evolution Is True and in Scientific American.

So, if it’s already been discussed on a popular blog, why bring it up again?  Because this one relates directly to my area of research, and the subject of many a post here on Genomicron — genome size.

One of the “predictions” given in Williamson’s paper is that species of insects with complete metamorphosis (holometabolous development) will exhibit evidence of a merger of insect and onychophoran genomes, and thus have larger DNA amounts.  It so happens that a) this is bass-ackwards, and b) it is easy to find this out by checking my Animal Genome Size Database (which is what Hart and Grosberg did) or my paper in Genetica from 2002 or my book from 2005 or pretty much any decent paper on insect genome sizes in the last several years.

From Gregory (2005).

I often have to summarize reasons why people should care about genome size, as when preparing grant applications.  I never thought that I could add to this list, “refuting nutty hypotheses about the origins of caterpillars”.  I won’t, though, even if many of the data used in the comparison were generated by me or my students (including pretty much all the Lepidoptera estimates).

But, on a more positive note, this flap did draw attention to velvet worms, which are pretty cool:

References

Gregory, TR. 2002. Genome size and developmental complexity. Genetica 115: 131-146.

Gregory, TR. 2005. Genome size evolution in animals.  In: The Evolution of the Genome, ed. TR Gregory.  Elsevier, San Diego, p. 3-87.

Hart, MW and Grosberg RK. 2009. Caterpillars did not evolve from onychophorans by hybridogenesis.  Proc. Natl. Acad. Sci. USA, in press.

Williamson, D.I.  2009. Caterpillars evolved from onychophorans by hybridogenesis. Proc. Natl. Acad. Sci. USA 106:15786–15790.

Scientists — and their institutions — should resist the ever-present temptation to hype their results.

[skipping to the money quote...]

…the temptation for scientists and their institutions to spin their research to the media, or to go publicity-mongering, is always there. And — as illustrated by the excessive public-relations campaign surrounding Ida, a fossil presented as a missing link in human evolution — too many in the media will buy into the initial hype.

Such behaviour is corrosive to the process of scholarly scientific communication. Research institutions must not allow it to become the norm.

Visit www.microbialart.com for lots of intriguing artworks created using living microorganisms.

Some more creations by students in my lab:

Archaeopteryx

Galapagos Islands

Skull

Primate phylogeny

Reduced genome works fine with 2000 chunks missing

To put a figure on how much of our DNA is non-essential, Vrijenhoek and his colleagues screened the genomes of 600 healthy students, searching for chunks of DNA at least 10,000 base pairs in length that were missing in some individuals. Across all the genomes, about 2000 such chunks were missing – amounting to about 0.12 per cent of the total genome.

Some people will over-interpret this as strong evidence for a majority of “junk DNA”. Comprising only 0.12% of the genome, it isn’t. However, as these are natural deletions >10kb, it gets around the objections to the deletion studies (i.e., that the conditions in the lab weren’t the same as the challenges faced in the wild). Then again, it may be that you can have one or two deletions and be ok because there is some redundancy, but if you were missing all of these bits you’d be in trouble. Others will dismiss it as an artifact or somehow not really testing the claim (read: dogmatic assumption) that all DNA is functional, but what else is new.

Are Humans Still Evolving? Absolutely, Says A New Analysis Of A Long-term Survey Of Human Health

Byars, S., D. Ewbank, et al. (2009). Natural selection in a contemporary human population. Proceedings of the National Academy of Sciences 106, in press.