The new smallest genome among animals.

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I have seen both some of the largest and smallest genomes among animals (well, I have seen stain bound to their DNA, at least). The largest report remains that of the marbled African lungfish, Protopterus aethiopicus, at a gigantic 132Gb (about 40 times more than humans). Some authors argue that this is an overestimate, but regardless they have huge genomes that are undoubtedly much, much larger than those of any mammal.

Until recently, the smallest animal genome size was reported to occur in some root-knot nematodes of the genus Meloidogyne (~ 30Mb) or perhaps in the placozoan Trichoplax adhaerens (~ 40Mb). I tended to have doubts about the nematode estimates because they were derived using older methodology. However, my colleague Serge Morand and his co-authors now report an even smaller genome in a plant-parasitic nematode based on estimates using modern flow cytometry techniques. In particular, the genome size of Pratylenchus coffeae is estimated at about 19Mb, making it the smallest so far found in a metazoan.


Assuming that the lungfish value is reliable, this extends the overall range of genomes sizes in animals to almost 7,000-fold.

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References:

Leroy, S, S. Bouamer, S. Morand, and M. Fargette. 2007. Genome size of plant-parasitic nematodes. Nematology 9: 449-450.

Image from http://nematode.unl.edu/pracoff7.jpg


Funny picture place holder.

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I must apologize — it has been a long time since I have posted, despite there being all sorts of interesting new things to talk about with regard to genomics and evolution. It’s teaching and grant season, which means I will probably continue to be a part-time blogger at most for another couple of weeks. I have lots to write about [1], but no time — so please bear with me.

One item of note, I have been invited to contribute regularly to Scitizen. I may also reconsider being a featured blogger at Scientific Blogging once things calm down later in the semester. In any event, it is nice to see that Genomicron is being appreciated.

Some of my fellow science bloggers (for me, that’s a small s / small b since I have not been called up to the big leagues by Seed!) are working on a paper to discuss the role of blogging for scientists. I can say that blogs have turned out to be useful for all three major components of a prof’s job, namely service (as public outreach), research (as a source of discussions of and links to interesting papers), and teaching. An example of the latter happened this morning. I was checking out Retrospectacle [2] and came across the picture below. When I stopped laughing, I decided to add it to the lecture I will be giving on kin selection today, which includes a section on sibling conflict and parent-offspring conflict. Sometimes a picture is worth 1,000 words, evn if teh words iz spelld all rong. Enjoy.


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Notes

1) This includes finally responding to a meme, namely the one on the evolution of Genomicron as tagged by Sandwalk.

2) Shelley Batts needs votes to get a scholarship — help her out, won’t you?


Congratulations, Mr. Zimmer.

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Carl Zimmer has been awarded a National Academies 2007 Communication Award, and I for one am very pleased. Carl is a fine example of what I, as a scientist, believe a science writer should be. He cares deeply about getting the details right, but is able to convey even complex ideas in an accessible and entertaining way. He provides clear refutation of any claims that one cannot be both readable and accurate. Oh, and he quoted me accurately and obviously listened to what I had to say about my area of research.

It is also good to see that the National Academies recognized not only his printed stories, but also contributions on his blog.

And so I happily say: Congratulations, Mr. Zimmer!


Terrible science writing in The Skeptic magazine.

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Speaking of misleading headlines, The Skeptic, which is a fine publication produced by Australian Skeptics and which, to my knowledge, does not itself contain any terrible science writing, has reprinted my blog post Anatomy of a Bad Science Story as an article in the latest issue (with permission, of course).

Have a look, and if you’re in the Land of Oz (or, presumably, anywhere), why not join Australian Skeptics and get the full magazine on a regular basis?

Click for full size view.

This just in: DNA barcoding is not the be all and end all of the universe.

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I want to share a few quotes about DNA barcoding. Some of these are from critics of barcoding (Roe and Sperling 2007) and some are from proponents of DNA barcoding (Hebert and Gregory 2005). For fun, see if you can guess which is which, and then see if you can guess why critics keep saying the same thing despite what barcoding actually involves.

This shortfall suggests that mtDNA is not as universally successful as suggested by DNA-barcoding advocates. Additional markers are clearly essential to clarify species boundaries, providing additional support for an integrative, multilocus approach to delimiting species.

There is an important distinction between “describing” and “delimiting” species, but a conflation of the two has created uneasiness about the use of DNA barcodes as the foundation of future taxonomic descriptions. We emphasize that DNA barcoding seeks merely to aid in delimiting species – to highlight genetically distinct groups exhibiting levels of sequence divergence suggestive of species status. By contrast, DNA barcodes – by themselves – are never sufficient to describe new species. At some stage, clearly divergent DNA barcodes, in combination with other information, will be used as the basis for providing a new Linnaean name and, as with any taxonomic hypothesis, this would be subject to ongoing re-evaluation. For example, in a recent survey of North American birds, the threshold for delineating probable new species was arbitrarily set at 10x the average within-species variation of the entire barcode dataset. This led to the revelation of four presumptive new species, but decisions regarding the formal recognition of these taxa are left, appropriately, to the ornithological community (notably, existing morphological and behavioural information supports these new hypotheses).

Rather than concentrating on a single character type (e.g. morphological or DNA sequence variation), a wide range of characters, including molecular data, morphology, behaviour, and geography, are integral to assessing species boundaries and delimiting species.

DNA barcoding using a single gene region does not assure complete taxonomic resolution, but it does promise proximity. Based on past results for varied animal groups, DNA barcoding will deliver species-level resolution in 95-97% of cases. When it fails, it will narrow the options to a small number of congeneric taxa (which, in many cases, could be resolved fully with additional genetic or other data).

Additional sources of data, such as morphology, host preference, geographic range and pheromone can be used when elucidating species boundaries, as this approach will improve detection of incongruence between markers, allowing insight into the process of speciation.

The synergy between DNA barcoding and studies of morphological/ecological diversity is further illustrated by the case of the skipper butterfly, Astraptes fulgerator, in which a combined morphological, natural history and barcoding approach revealed a complex of 10 species in one small area of Costa Rica. Importantly, several of these species showed a relatively small barcode divergence, but a coupling of this information with records on larval host plants and morphology illuminated the full diversity of the complex.

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References

Hebert, P.D.N. and T.R. Gregory. 2005. The promise of DNA barcoding for taxonomy. Systematic Biology 54: 582-859.

Roe, A.D. and F.A.H. Sperling. 2007. Population structure and species boundary delimitation of cryptic Dioryctria moths: an integrative approach. Molecular Ecology 16: 3617-3633.

Welcome to Mobile DNA blog.

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When I began this blog, several of the big-name bloggers were kind enough to point people in my direction. While Genomicron is not in the same league as, say, Pharyngula or Sandwalk, it has become reasonably well established. As such, it could provide at least some help to new bloggers if I make a note of their new blogs.

Case in point, Mobile DNA by Prof. Cedric Feschotte (University of Texas at Arlington). There are few things cooler in genomics than transposable elements (in my humble opinion), and this is the subject of both Prof. Feschotte’s research and his neonate blog. Let’s give him some hits so that he will be encouraged to continue sharing his insights on this topic with the rest of the blogosphere.

If anyone else has started a new blog about genomics or evolution, feel free to link to it in the comments.


Bloggers for Peer-Reviewed Research Reporting (BPR3): Why I won’t be participating (yet?).

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I am partially aware of the discussions that have been taking place about having some sort of quasi-official designation that a particular blog post is discussing peer reviewed research. I am all for improving the discourse on blogs when it comes to reporting research. Some readers may recall that I was involved in a minor row (since resolved amicably) over the way a discussion of a paper by some well respected researchers was conducted. I also don’t think blogs count as anything like peer review, and if anyone suggests otherwise, it’s probably because they don’t actually participate much in the peer review process as either an author or a reviewer.

On the other hand, I think blogs are an excellent place to discuss, disseminate, and dissect peer-reviewed articles in a way that makes them more accessible to a broader audience and opens the scientific process to view by non-specialists. My concern is simply that people could mistake what happens on blogs for how the peer review system functions.

There is now a new icon that bloggers are encouraged to use when discussing peer-reviewed research, which was the victor in an open design contest by the Bloggers for Peer Reviewed Research Reporting (BPR3):

According to their site,

Bloggers for Peer-Reviewed Research Reporting strives to identify serious academic blog posts about peer-reviewed research by developing an icon and an aggregation site where others can look to find the best academic blogging on the Net.

I agree with the general notion of letting readers know that peer-reviewed research (vs., say, just someone’s opinion) is being described, but I’m afraid I can’t participate in the program as structured. Why? Because the name, “Bloggers for Peer Reviewed Research Reporting” is ambiguous — is the reporting peer reviewed? No, it isn’t, but this could give the wrong impression. In fact, the logo strongly reinforces this, reading only “Peer Reviewed Research BPR3“.

It’s a decent idea, but the impression it gives in its current manifestation is contrary to my views on the role of blogging in scientific communication.

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Update:

Evolgen is promising (threatening?) to publish original, unreviewed research on a blog. Slap the above icon on it, and this would give a very misleading impression to nonexperts. I have to oppose both developments if they are going to, in any way, appear to circumvent or undermine peer review processes. (Update: he will be using this as an educational demonstration, which I fully support… but let’s not have it go beyond that on other blogs).

BPR3 has provided a reply to this post and the comments it engendered, and to their credit they are looking at making some changes to improve the situation. Of course I will be open to participating in the future if I feel it is useful and in accordance with my views on blogging about science. I wish them luck with this.


Genomicron discovers Adaptive Complexity, and likes it.

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Via Panda’s Thumb, I have come across a blog that I wish I had known about sooner. It is Adaptive Complexity by Michael White, postdoc in the Department of Genetics and the Center for Genome Sciences at the Washington University School of Medicine, who is also a featured writer at Scientific Blogging (some readers may recall that I was invited to be a featured writer, but I ultimately decided not to commit due to time constraints).

In any case, Adaptive Complexity provides some good posts, and expresses some of the same frustrations as I do, about non-coding DNA. Some highlights:

Welcome to my blogroll and feed reader, Dr. White.


Favourite science blogs.

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As noted by, well, everybody, The Scientist is assembling a list of the bioblogosphere’s best. Here is my list of favourite blogs — this isn’t exhaustive, however, as there are many that I read regularly in addition to this (see my blogroll for more). These are just the ones that I follow most closely.

  • Pharyngula — PZ Myers’s monster chimaera between hardcore objective science and stinging anti-theism.
  • Sandwalk — Online home of Larry Moran, everyone’s favourite curmudgeonly Canuck.
  • The Loom — Proof courtesy of Carl Zimmer that science writing can be consistently top-notch.
  • Evolution…Not Just a Theory Anymore — Although I don’t care for the name (evolution will always be both a fact and a theory), Greg Laden continually offers excellent insights.
  • ERV — Sarcastic, merciless, and never boring, and she knows a heck of a lot about ERVs and HIV.
  • John Hawks Weblog — Interesting, accessible discussions about things anthropological.
  • Aetiology — Tara Smith’s launching pad for discussions on evolution and health.
  • Evolgen — Thoughts on evolutionary genetics from a grad student who knows his material.
  • Laelaps — Home of Brian Switek, one of the hardest working bloggers around, who produces top quality essays on important topics in evolutionary science.
  • The DNA Network — A great collection of blogs on the subjects of genetics, genomics, and medicine. Features great blogs like Eye on DNA, My Biotech Life, and ScienceRoll.
  • Sex, Genes & Evolution — John Logsdon’s blog about, well, sex, genes, and evolution; great stuff, and I wish there were more frequent posts.
  • Interrogating Nature — High end contributions from Chris Harrison, a bright, young scientist-in-training.
  • The Tree of Life — Genomics plus opinions from Jonathan Eisen, good stuff.
  • Barcode of Life Blog — Superb clearinghouse by Mark Stoeckle on information regarding the ever-expanding Barcode of Life initiative.
  • EvolutionBlog — Plenty of interesting insights from Jason Rosenhouse on evolution.

By the way, if you like this blog, please be sure to post a comment about it on The Scientist‘s site!


On the lookout for DAPs!

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Larry Moran and PZ have both picked up on the term “DAP“. There have already been several more examples identified outside the realm of genomics in their comments threads. As such, I think that “DAP” can be given the following broadened definition:

Dog’s Ass Plot (DAP, or Dapper):

A graphical representation of data in any field that, through a lack of clear axis labels, selective inclusion/exclusion of data, visual presentation style, and/or other questionable characteristics, generates a misleading interpretation of the data in the viewer, especially by implying an illusory pattern that is not supported by the available data.

Can you indicate an example from your own subject of study? If so, please provide a link in the comments section. Bring on the Dappers!!