Recently in Genetics Category

First we had genomics. Then we had proteomics. Then we had metabolomics.¹ Now we have poetryomics. Or at least we have the poetryome.

A new project sponsored by The Economic and Social Research Council (ESRC) -- a UK-based organization for research and training in social and economic issues -- aims to change that. Comprised of contributions from writers, scientists, and others around the world, The Human Genre Project seeks to spread the word about human genomics through short stories, reflections and poems.

I rather like "the telomeric tale of the mouse's tail (after carroll)" by shardcore.

Larry writes

There may have been a time in the past when scientists imagined a static genome that only changed slowly over millions of years. However, beginning in the 1960's we began to see the genome as a much more dynamic entity. The first evidence of this kind of genome came with the discovery of huge amounts of variation between individuals in a species.

I have to disagree with his interpretation of history here. In the next paragraph he writes

This was followed by the discovery of transposons and junk DNA.

I'll grant the junk DNA part, but Barbara McClintock described mobile elements in the 1940s, even though it took the rest of the world 30 years to catch on.¹ He then mentions "chromosomal rearrangements such as inversions, duplications, and translocations." Of course, these had been known since at least the 1910s. Chromosomal rearrangements played a vital role in establishing Thomas Hunt Morgan's chromosomal theory of heredity, and the basic data the Theodosius Dobzhansky used in many of his studies of Drosophila pseudoobscura were the frequencies of different inversion types.

I am positive Larry knows these things. He just forgot about them temporarily, so this is a friendly reminder.

Update: La Nacion has an article featuring the work (en Español).

Normally I wouldn't make a big deal about one of my own papers, but I'm making an exception this time because it involves a really nice piece of work by a graduate student for whom I served as an associate advisor. Uzay Sezen collected seedlings of the palm Iriartea deltoidea in Costa Rica from two secondary forest plots that his major advisor, Robin Chazdon, has been using for long-term studies of forest regeneration. He genotyped the seedlings and all reproductive trees in the plots using AFLPs, and he inferred the parentage of the seedlings. From these data was able to determine the spatial pattern of recruitment into the secondary forest.¹

Like many animal-dispersed trees, seedlings of Iriartea deltoidea tend to be found in clumps. Such clumps are often centered around reproductive I. deltoidea individuals, suggesting that the clumps represent seeds derived from the closest reproductive individual.

Well, you can probably guess where this is going from the way I set that up. That's not what we found at all. Instead (quoting from the abstract)

Few seedlings were offspring of the closest reproductive trees. Seedling patches observed beneath reproductive trees originate from dozens of parental trees. Observed patterns of seedling distribution and spatial genetic structure are largely determined by the behaviour of vertebrate seed dispersers rather than by spatial proximity to parental trees.

If you'd like to read more, here's a link to a copy of the paper at the website of the Proceedings of the Royal Society of London, Series B.² Enjoy!

What's mouse-ear cress, and why should you care whether it's perennial?

Mouse-ear cress (better known to scientists as Arabidopsis thaliana) is a little weed in the mustard family that has become the most studied plant in the world in the last thirty years. Its genome has been fully sequenced, and a tremendous amount is known about the underlying molecular mechanisms that are responsible for variation in many of its traits. It's become a "model organism" for many studies in plant genetics, plant molecular biology, plant physiology, plant ... anything. Why?

Well, Arabidopsis thaliana is small, easy to grow, and it has a small genome. It can complete its entire life cycle in six weeks, so scientists can get through eight generations a year, which is very important if you're doing genetics experiments that require several generations to complete. In the wild, it's an annual (occasionally a biennial, depending on when it flowers and when seeds germinate). And because it's so small you can grow hundreds in a growth chamber in the corner of a lab, keeping the growing conditions quite uniform and growing a lot of individuals. For these reasons and more this little plant has an entire web site of its own. The Arabidopsis Information Resource provides a database of genetic and molecular biology data, as well as links to a variety of other Arabidopsis resources and information about the Arabidopsis research community. In short, by working on Arabidopsis, plant biologists and plant geneticists can take advantage of a lot of work that other people have already done to ask very sophisticated and complicated problems using the most powerful tools of genetics and molecular biology. Which brings us finally to the topic of this post, perennial mouse-ear cress.
 
Wait! Perennial mouse-ear cress? Didn't I tell you a few sentences ago that it's an annual, or sometimes a biennial?

Tim Whitehead links to this story from yesterday's New York Times in which two high school  students found that 25% of the fish sold as sushi in New York are misidentified.

[O]ne-fourth of the fish samples with identifiable DNA were mislabeled. A piece of sushi sold as the luxury treat white tuna turned out to be Mozambique tilapia, a much cheaper fish that is often raised by farming. Roe supposedly from flying fish was actually from smelt. Seven of nine samples that were called red snapper were mislabeled, and they turned out to be anything from Atlantic cod to Acadian redfish, an endangered species.

Tim headlines his entry "More fake fish", which is true, but it's not what interests me.

Whenever I lecture about quantitative genetics, I always talk about height in humans as an example of a trait influenced by the expression of many genes. Since I teach at the University of Connecticut, I often show the pair of photographs in this article from Genetice¹, because (a) it shows a nice bell curve of heights and (b) it allows me to show how the environment can influence the expression of quantitative traits.² I talk about Nilsson-Ehle's results on kernel color in wheat as an example of how multiple genes³ may influence the expression of a phenotype.

Now thanks to recent work described in Nature Genetics I can give students a best guess as to how many genes influence height variation in humans. The answer?

Human population geneticists have enormous numbers of polymorphic markers at their disposal. The HapMap project, for example, makes data from 3.2 million mapped single nucleotide polymorpisms freely available on its website. That's one SNP every kb on average. Those working on model organisms, like Drosophila or Arabidopsis don't have quite that much information available, but they have complete genome sequences and access to a wide variety of genomic tools.

Those of us working on non-model groups, like the plant genus Protea have a much more limited set of tools available to us. There are a few widely used chloroplast and nucelar sequences in plants – matK, rbcL, the trnL-trnF intron, ITS, ETS, waxy, and a few more. But identifying new possibilities has been very tedious and has had a low probability of success.

Now nunatak at The Beagle Project Blog points out a paper in PLoS One that I missed. The technology described there – Diversity Arrays Technology (DArT) – seems quite promising.

Olivier Jaillon and colleagues report a high-quality draft genome for the wine grape, Vitis vinifera in today's issue of Nature. Many gene families related to the characteristics of wine have been extensively duplicated: the family of genes encoding stilbene synthases includes 43 identified genes and 89 copies of terpene synthases have been identified. Stilbene synthatses are involved in the synthesis of resveratrol, the compound that has been associated with health benefits from red wine. Terpene synthases are involved in synthesis of a variety of resins, essential oils, and aromatics – compounds that are essential components of the taste and aroma of wine. It seems likely that these extensive duplications are the result of selection for favorable wine-producing characteristics during the domestication of wild grapes.

That's the recent evolutionary story. There's also an ancient one referred to in the tilte of this post. Jaillon and colleagues present evidence that many dicots are paleohexaploids. It's long been known that polyploidy played an important role in evolution of flowering plants, and it is now becoming clear that some of the earliest dicots may have been polyploid and that many extant eudicots are paleohexaploids..

We already know that bacteria swap genes among themselves so readilty that Ford Doolittle, among others, argue that relationships among them is better described by a network than by an evolutionary tree. We also already know that many genes that were part of the original photosynthetic symbiont that evolved into the chloroplast in green plans have been transferred to the nucleus (e.g., tufA). We even already know that many groups of animals host endosymbiotic bacteria belonging to the genus Wolbachia and that these bacteria sometimes play an important role in reproductive isolation between species (e.g., in the wasp Nasonia).

In today's Science Julie C. Dunning Hotopp and her co-authors report multiple cases in which Wolbachia genes have been transferred to the nucleus of their host. In Drosophila ananassae almost the entire genome (ca. 1 mb) had been transferred, and that about 2% of the transferred genes are transcribed. In Nasonia they identified only small transfers (<500 bp).

ThIs study raises one very intriguing question: Is lateral gene transfer (relatively) common only from endosymbiotic bacteria to hosts or is it (relatively) common among all bacteria? As the authors point out, “[w]hole eukaryote genome sequencing projects routinely exclude bacterial sequences on the assumption that these represent contamination.” As a result, current whole-genome sequences can't be used to answer this question. Only the time-consuming experimental approach Hotopp and her colleagues used can determine whether the bacterial sequences detected in whole-genome projects are truly contamination, or if they represent nuclear copies of bacterially-derived DNA.

We appraised 432 sex-difference claims in 77 eligible articles. Authors stated that sex comparisons were decided a priori for 286 claims (66.2%), while the entire sample size was used in 210 (48.6%) claims. Appropriate documentation of gene-sex interaction was recorded in 55 claims (12.7%); documentation was insufficient for 303 claims and spurious for the other 74. Data for reanalysis of claims were available for 188 comparisons. Of these, 83 (44.1%) were nominally statistically significant at a P = .05 threshold, and more than half of them (n = 44) had modest P values between .01 and .05. Of 60 claims with seemingly the best internal validity, only 1 was consistently replicated in at least 2 other studies. (Patsopolous et al. Journal of the American Medical Association 298:880-893; 2007 – abstract)

Nature (“Let down by the statistics”) and Science (“Epidemiologist sees flaws in papers on genes and gender”) report on the study. David Balding sums it up this way in Nature: “This paper reveals an entire industry of prominently reported results that are largely unjustified and probably mostly false.”