Links that won't waste your time, Sept. 17 edition

Gene Expression contributor p-ter expresses his (un)excitement about the Ventrome:

In terms of haplotype reconstruction, the authors make a number of dubious claims about the importance of their advances. It is not true, as stated in the introduction, that genome-wide association studies rely on phased haplotypes for analysis. In fact, most of the ones I have seen do nothing more than simply count up genotypes at each SNP in cases and controls and perform a chi-squared test. In most cases, haplotype-level analyses is simply not done. This may change in the future, of course, but it's difficult to see how what they've done (note they aren't even able to make ideal haplotype inference with the data) is that exciting.

Personally I can't understand why people are calling it the "Craigome". I suppose that's supposed to go along with the "personalized" medicine part. If it's personal, it must use your first name! That should give aid and comfort to the telemarketers, I suppose -- or maybe the genome muckety-mucks have been deploying cameras on the hucksters' sidelines!

Then again, somebody has surely thought it through. Maybe it's about Watson -- the "Watsonome" sounds like some kind of assisted living arrangement. Oooh -- you know George Church is next! I've got "Georgeome" on my mind!

Horsing around

Meanwhile, Brian Switek of Laelaps tells the changing story of horse evolution. This is a great article full of references and classic reconstructions of horse phylogeny, and Switek reviews some classics:

The 1966 edition of Romer's Vertebrate Paleontology fairs better overall, but is still found wanting. The same straight-line illustration I just mentioned is found in the section treating perissodactyls as a group, and the skeletons of Eohippus, Mesohippus, and Hippidion are shown left to right across pages 266 and 267. While the text does mention an overall diversity of forms, as well as using certain genera for the "type" from which modern horses evolved, the overall visual impression of simple anagenesis remains. Again, I doubt the casual reader picked up Romer's book for light nightly reading, but it is strange that the progressive ideas about evolution during that time are so poorly represented.

The versions of horse phylogeny from the 1970s and 1980s bear a strong resemblance to various hominid phylogenies that have emerged in the last 20 years. The theme of the essay is how the original unilineal picture of horse evolution became the current "bushy" version, and it's a good account. As for hominids --- well, keep in mind that the bushy horse phylogeny extends back to the Eocene. Horse phylogeny in the Pliocene and Pleistocene is not exactly a fractal version of the larger picture. Still, there were speciations of Equus during this time period, including the current diversity and some extinct horses.

Guts and sex

Carl Zimmer puts together three recent stories about gene duplications, including the human amylase-diet connection. I'll be posting on that one later this week, and Zimmer's account of erstwhile digestive proteins in the reproductive tracts of female Drosophila is a fascinating addition:

As gene copies build up in a genome, some of them can take on new jobs. And here is where the fly sex comes in. In some species of Drosophila flies, the males and females wage a biochemical war of the sexes. The males can boost their reproductive success by manipulating their female mates. They do so with a cocktail of chemicals mixed into their seminal fluid. Some of the chemiicals stimulate the production of eggs, some chemicals create a big mass in the reproductive tract that may make it harder for a female fly to mate with another male. Females produce chemicals of their own to counteract the male chemicals. You'd expect that mutations that gave either the male or the female an edge in this arms race would be strongly favored. And in the August issue of PLOS Genetics, scientists published a list of female reproductive proteins that show strong signs of natural selection. A dozen of these proteins are proteases--they are good at slicing other proteins apart. The flies only make these proteases in their reproductive tract, and yet the proteins are not closely related to other proteins made in the reproductive tract. Instead, their closest relatives are families of proteases that the flies make in their guts in order to digest food.

OK, maybe fascinating isn't the right word. I guess it depends how close you are to lunchtime. Or bedtime. Ewww.

"Previvors'" tales

Amy Harmon in the New York Times writes the story of breast cancer "previvors," women who have tested positive for one or more risk mutations, and must choose whether to take preventative measures such as prophylactic surgery:

Her father, who once feared he would lose his wife to cancer, encouraged the surgery. Her sister reminded her that cancer might be cured in a few years if she could wait.
Her aunt said she hated to see her niece embrace a course of action akin to "leechings of the Dark Ages." A cousin declined even to take the DNA test.

The article is illustrated by a pedigree that shows the affected family members. In this form, you can really sense the feeling of dread, seeing four generations of women ticked off the chart.

EyeOnDNA asks about the effects of the new BRCA1 and BRCA2 tests, which are intended to inform people of their carrier status for breast cancer susceptibility alleles:

This past week we saw the unveiling of a controversial general advertising campaign for the Myriad BRACAnalysis genetic test for breast and ovarian cancer susceptibility. One oft-quoted statistic in relation to the test states that "only 30,000 of more than 250,000 American women estimated to carry a mutation in BRCA1 or a related gene, BRCA2, have so far been tested." Myriad hopes to increase the number of mutation carriers detected. But what kind of counseling and support will women receive if they test positive? (emphasis in original)

Hsien puts the question in context by referencing Harmon's account.