Cool Stuff that I Have Been Meaning to Blog . . .

There are quite a few articles sitting around on my desktop waiting for me to write about them. It's gotten to the point where I just need to unload them on the blogosphere. Click through below the fold for some cool stuff from the scientific literature.

• More on Neutrality from Laurence Hurst and Colleagues -- I just wrote about the nearly neutral theory, and here is an analysis of selection on silent sites in the human genome. Is this a coincidence or was this article subconsciously on my mind? From the abstract:

  "At least in species with large populations, even synonymous mutations in exons are not neutral. By contrast, in mammals, neutrality of these mutations is still commonly assumed. However, new evidence indicates that even some synonymous mutations are subject to constraint, often because they affect splicing and/or mRNA stability."

  The difference, here, is that selection is not operating on translational efficiency like it does in Drosophila, Caenorhabditis, or yeast.

• Stephen Scherer and Colleagues Give Us a Review of Structural Variation in the Human Genome -- Let's see, I've written about this before a few times. There was the human inversion under natural selection. Now we realize that we all differ from each other by multiple chromosomal rearrangements and other structural 'aberrations'. And if you take out chunks of our genome it may not matter. Enough of the linking to myself, here's what the authors have to say:

  "Rapidly accumulating evidence indicates that structural variants can comprise millions of nucleotides of heterogeneity within every genome, and are likely to make an important contribution to human diversity and disease susceptibility."

  A combination of new technologies (whole genome sequencing, hybridization arrays) has led us to realize how common structural variation is within natural populations. But I think the most important factor that has led to the discovery of these 'aberrations' is the realization that they are so common. Now that we know they're there, everyone is looking for them.

• An Odd Model of Mutagenesis -- Rather than the classic model of constant mutation, Jeffrey Schwartz postulates that mutation rates depend on environmental stresses. Sure, UV irradiation and chemical mutagens can induce mutations. But Schwartz argues that organisms evolve in response to the environment by increasing mutation rates. I don't know what else to say about this; it's quite, um, interesting.

• Centromeric Shifts in Genus Equus (from Razib at Gene Expression, who wants me to comment on this) -- Centromeric shifts can accompany Robertsonian fusions. This phenomenon has been mostly studied in marsupials. Razib writes:

  "Anyway, I know aneuploidy is usually the problem, but I think there will be some really interesting stuff coming out of this area."

  I don't think aneuploidy is that big of a deal. I think the rearrangements suppress genetic flux between karyotypes allowing for the accumulation of genetic isolating factors on rearranged chromosomes (see here). This is the case in Drosophila, and has not been rejected in mammals.

• Undoing Speciation -- This is what happens when you prematurely define populations or races as species:

  "Historically, six small lakes in southwestern British Columbia each contained a sympatric species pair of three-spined sticklebacks (Gasterosteus aculeatus). These pairs consisted of a 'benthic' and 'limnetic' species that had arisen postglacially and, in four of the lakes, independently. Sympatric sticklebacks are considered biological species because they are morphologically, ecologically and genetically distinct and because they are strongly reproductively isolated from one another . . .Our morphological analysis showed a clear breakdown between benthics and limnetics . . . Bayesian analyses of population structure in a sample collected in 1994 indicated two genetically distinct populations in Enos Lake, but only a single genetic population was evident in 1997, 2000, and 2002. In addition, genetic analyses of samples collected in 1997, 2000, and 2002 showed strong signals of 'hybrids'; they were genetically intermediate to parental genotypes. Our results support the idea that the Enos Lake species pair is collapsing into a hybrid swarm."

  It would be premature to define a hybrid storm as a collapse of species, as well, so let's hold up on that. I'll leave the concept of species to John Wilkins, but I'm a lumper, so I'm not too quick create more species. Personally, I don't think it's very rewarding to define species (or, at least, to argue about what are 'true' species). I find it far more interesting to study species pairs at various stages of isolation and determine the isolating barriers that exist at those stages. Whether or not these sticklebacks are species is not as interesting as studying how environmental factors can break down early isolating barriers.