- Cryptic Species
- Human Inversion Under Selection
- The Cambrian Explosion Never Happened
- On the origin of life
- Random Mutation and Natural Selection
- The Genotype and the Phenotype and How to Measure Divergence
- Can You Marry Your Half-Sister's Daughter?
- Species Sampling for Whole Genome Sequencing
- A Few Words on Speciation
- Mean Fitness, Genetic Load, and the Misapplication of Population Genetics Metrics
- Why Study Speciation Genes?
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Best of the Archives
Tips for Purchasing a Llama
The Science Creative Quarterly offers up some tips for purchasing a guard llama . Apparently, this is a legitimate concern, as the author cites five related articles (although I'm not sure if they are real publications, and I'm not ambitious enough to find out for myself). Among the concerns is overqualification (yes, llamas come with different skill sets):
There is nothing worse than an overqualified llama. For instance a llama, trained in the delicate arts of diplomacy, will become depressed and distant if it is only given the task of guarding your ’86 Chevy Cavalier from any would-be vandal. Consequently, it will probably let its guard down and you will be left with a llama with very low self-esteem and an antennae-less ’86 Chevy Cavalier with the words “Wash me” scrawled onto the dirt caked rear windshield.
There's the Onion and Sports Pickle ; SCQ may be our equivalent source of science humor.Read full post >>
Republican Fear Factor
In this week's cartoon , Tom Tomorrow introduces us to Fear Factor, neo-con style. Among the things Republicans are scared of:
- They're terrified that their wives could get an abortion without their permission.
- They're terrified that their religious beliefs might be undermined by secular society.
- They're terrified that heterosexuality itself will be undermined by gay marriage.
It seems obvious to me that these are irrational fears, but it's not obvious to a large portion of this country. These fears manifest themselves in bigotry and oppression of others. Women are denied the right to any abortion regardless of the conditions. Certain religious beliefs (or religion in general) are endorsed by government, and in situations in which everyone is given fair treatment they claim oppression. A loving couple is denied the right to marry because they don't fit what a small minority has deemed the appropriate union (in my opinion, marriage as an institution should not receive government endorsement, but I'm a bit jaded).
A little background on where I stand on abortion: I think that any first trimester abortion should be allowed regardless of the conditions. There should be no restrictions, and they should be easily accessible. Anything after the first trimester should require the woman to show adverse health risks associated with pregnancy. She should not need to jump through loops to show she is at risk, and these abortions should also be easily accessible. I think I stand in the mainstream on this issue.
The last two Republican fears aren’t so easy to mock. One of them is the fear of terrorists. Terrorism is a legitimate concern, although the threat of terrorisms is often blown out of proportion and used to manipulate the general public. The comic isn’t mocking our fear of terrorism, but how the neo-cons use it for their own benefit. They take advantage of the average American's fear that terrorist will blow up their suburban neighborhood. They then use that fear to strip us of civil liberties in the name of anti-terrorism.
As opposed the first three examples (abortion, religion, and gays), it’s not so much the fear of terrorism that is the problem, but the response to that fear. It’s exaggerated and aimed in the wrong direction. We see the same thing in the final fear: “BIRD FLU”. As Tara so nicely pointed out, there may be a rational fear of a pandemic. The paradox is, if immunologists treat it properly (by vaccinating the public and preventing the virus from entering the country), then it appears that all of their work was for not because there was no epidemic. If they fail to act, then the disease may spread and they look like buffoons for not acting. Either way, they lose (there is the possibility that they do not respond and the disease does not spread, in which case they come out on top).
What concern me most are the rational fears to which the administration provides an inadequate response. Abortion, secularism, and gay marriage are important issues, but not nearly as significant as a bungled response to terrorism and pandemic. Of course, if we can’t adequately respond to regular old influence , what makes us think that the response to bird flu will be any better? Maybe it will be used as a scare tactic with no substantive strategy planned in response (see the government’s response to terrorism).Read full post >>
50 People Who Suck
46. Bruce Chapman
Charges: Founder of the misnamed “Discovery Institute.” Despite its pioneering title, Chapman’s organization seeks to make one of the world’s oldest, dumbest ideas the prevailing ideology. Seems to believe a petition signed by 400 PhDs and professors is convincing proof of Intelligent Design’s widespread acceptance. A lazy dissembler, he blames the lack of actual research and peer-reviewed articles on ID on academic “blackballing.” Right, ‘cause Galileo had it easy. Chapman’s sole trailblazing achievement in the field of academic inquiry has been in proving scientists can be even smugger-when driven by theology.
Exhibit A: Held high-level positions under Reagan and Bush, Sr. Is not a scientist.
Sentence: Infested and colonized by scabies mites: eyeless, brainless parasites unique to humans—perfect evolved to afflict us. Succumbing to the maddening itch, Chapman skins himself alive.
40. Tom Cruise
Charges: Criminal narcissism. After mega-lawyer Bert Fields threatened to sue The BEAST over Cruise’s inclusion in last year’s Loathsome List , we responded by giving him the editorial finger , and bracing ourselves for the legal spanking of our lives. Instead, the episode seemed to trigger a cascading ego crisis, culminating in a rapid and irrecoverable image downgrade from exalted idol to ridiculous buffoon. From his laughable claim of psychological expertise to his worst acting performance ever—as a man in love—Cruise simply cracked up on camera in 2005, and a public hitherto willing to overlook his obsessively inauthentic personality and comical religious affiliation had finally had enough. Cruise is a perfect example of a person who is simultaneously in love with and completely unfamiliar with himself, living in perpetual fear of self-actualization, and asserting a legal right to live free of criticism. A guy who can do whatever the hell he wants, yet chooses to devote his life to maintaining the public perception that he is somebody else.
Exhibit A: “I care man, I care. I care about you. I care about your children. I care about these people here in this room. Every one of you. And I...I mean it. That is not just some words to me. That is a promise.” Seriously, can’t even act like a human being.
Sentence: A lifetime of forced, joyless sex with famously beautiful women, only to have his colossal gay porn library posthumously bequeathed to the Smithsonian by bitter, unloved offspring.
39. Dr. David Hager
Charges: A Bush appointee to the FDA who was the key figure in its rejection of emergency oral contraceptive Plan B as an over the counter drug, which Hager bragged was the second time in fifty years the FDA has ruled against the overwhelming approval of its own advisory committee. The author of books like Stress and the Woman’s Body and As Jesus Cared for Women, Hager repeatedly sodomized his ex-wife for years against her will, alternately apologizing for or denying it when confronted by her, offering excuses like “You asked me to do that” and “Oh, I didn’t mean to have anal sex with you; I can’t feel the difference,” she told The Nation. Seems a bit fishy, a supposed authority on women’s health who can’t detect such a significant distinction with his most sensitive instrument.
Exhibit A: “My official comment is that I decline to comment.”
Sentence: A three-day group ramming by the multi-dildoed Oregon chapter of NOW, after which Hager will walk with a pronounced limp, never to regain control of his sphincter, and discover himself to be inexplicably pregnant.
37. Donovan McNabb
Charges: Played so poorly that his demoralized and alienated teammates yearned for the return of ego-vampire Terrell Owens. A chocolate commodity so inoffensive he makes Hershey bars look militant. Responded indignantly to loopy criticism from the head of the Philly NAACP, but laughed off Rush Limbaugh’s racist broadsides. Choked in the fourth quarter of Super Bowl; this year he enjoyed the worst fourth quarter passer rating in the league. Made over $11,000,000 in 2004.
Exhibit A: Logged only significant playing time this season with his mom in soup commercials.
Sentence: Peon at a Campbell’s Soup cannery in China. Flogged routinely for underperformance.
33. Johnny Damon
Charges: Any baseball player with highlights in his hair should be faced with the same penalty system applied to those using performance-enhancing steroids. It’s ruining the game. And if a ball player is going to grow a beard, it should be a Charlie Manson/Thurman Munson scraggle of bushy whiskers, not a neatly manicured and softly conditioned frame for your pretty face. The only thing that got Damon to step into line and quit hair-farming was a 52 million dollar check from the New York Yankees. Boston prayed for the multi-bladed Gillette that officially made him a Yankee to slip while gliding over his Adam’s apple and spill his lifeblood into the bathroom sink.
Exhibit A: Going from the Red Sox to the Yankees is like fucking the guy that murdered your husband.
Sentence: Killed by barrage of hurled D cell batteries when he takes the field at Fenway next season.
16. R Kelly
Charges: As if videotaping himself urinating on an underage girl wasn’t bad enough, Kelly decided to follow up by inflicting the worst piece of music in American history upon the public consciousness. Kelly claims he is a genius for squeezing out what are so far 12 installments of his “hip hopera,” “Trapped in the Closet” like so many virtually identical turds, with no variation in musical content and a story line so patently terrible that it soon became the subject of a parody-frenzy involving Saturday Night Live, South Park, Mad TV, Jimmy Kimmel, and the Upright Citizens brigade, among many others. Even his good songs all seem to be about fucking underage girls.
Exhibit A: Seriously—pissing on an underage girl.
Sentence: Trapped in a closet. Eventually dies of thirst.
There are also some good "bend over and fuck me" Democrats, like Hillary Clinton and Joe Loserman, and your usual stable of Republican colostomy bags. Don't miss the surprise at #4.
Does Being a Horse Count as an Ethnicity
A high school teacher who happens to be a Pittsburgh Steelers fan (or is he a Steelers fan who happens to be a teacher?) made one of his students take a midterm exam on the floor last Friday because that student was wearing a Denver Broncos John Elway jersey. The kid didn't get the memo: if you're gonna wear a John Elway jersey, go with the Orange Crush look, not the ugly ass angry horsey jersey .
Is Everyone On Earth Named Steve Smith?
In honor of our favorite punt returner who's quarterback can't get him the ball, here is list of all of the Steve Smith's I know of. Feel free to add more in the comments.
Here's the Carolina Panthers wide receiver (the guy who's quarterback can't get him the ball) and Chad Johnson 's junior college teammate that inspired this list. This dude's got a pretty bad-ass tattoo on his upper arm; that distinguishes from the other Steve Smiths. He's the only Steve Smith playing in the NFL (for now), but not the only football playing Steve Smith.
Steve Smith is also the #2 receiver on the USC Trojans. This Steve Smith will be playing in the NFL in two years, only adding to the confusion of players playing the same position with the same name (see here for another example). It doesn't help that USC's Steve Smith is an undersized receiver, meaning not only do Steve Smith and Steve Smith play the same position, they play the same position in the same way.
At least this Steve Smith plays a different sport than the previous two Steve Smiths. Well, technically he no longer plays his sport professionally. Looking at him in the USA Basketball uniform reminds me of how Steve Smith never quite lived up to expectations. This is the opposite of Steve Smith the Panther, who was never supposed to amount to anything, but ended up a pro-bowl quality receiver.
This Steve Smith (actually, Stephen A. Smith) used to be a respectable sports writer. Now he's become a sports talking head and D-list celebrity. Oh, and he writes his columns on a Blackberry . And he's really annoying when he opens his mouth and tries to talk -- not a good quality for a TV personality (but, surprisingly, one that a lot of TV personalities share).
Ok, so Steve Smith is not a real person, but what is "real" anyway? He's a character on American Dad . . . you know, that show that comes on after Family Guy . Never mind.Read full post >>
Weekly Random Ten (22 January 2006)
Alright, we're gonna try something new with the evolgen Weekly Random Ten. Here's the new rule: I get 10 songs worth of time to write an entry. I've used this as a rough guideline for the random ten in the past, but I never put it in writing. Once the last note in the last song is played, I must stop writing -- even if it's in mid sentence.
So, I'm sitting in front of the TV in between playoff games. I blew my pick in the first game. Looks like I went with the wrong road underdog to win. I still think the Panthers can win, but it will be quite a feat if both road dogs win in the conference championship. At least neither Delhomme nor Hasselbeck have a goofy beard -- of course, Hasselbeck's got that bald thing going against him.
I'm gonna do that stupid sports commentator thing and stand by my pick in the second game despite how things have changed. Does that piss anyone else off? An expert analyst will pick a team to win the Super Bowl at the beginning of the season. Then, halfway through the season, the team falls to 4-4, and they're still saying, "I picked them at the start of the season and I'm standing by my pick." That just shows you're too stupid to realize you were wrong and don't know how to reevaluate your position with further evidence. It's bullheaded; it's stupid. At least they're only talking heads (talking about sports, even), and not politicians responsible for making important decisions about the country. It would really suck if politicians were so stubborn and refused to change their stance on an important issue like war in light of new information . . . oh, wait, nevermind. Asshats.
Ok, I've got a couple more songs to kill. How about the size of the American flag that they busted out for the national anthem at the start of the Seahawks game. They love America a lot more than I do. Shit. All that's missing is an F-14 flyover and a huge fireworks display. That would really show those terrorist bastards. Why does the beginning of a sporting event turn into a caricature of patriotism, or even a celebration of a military state. By the way, the Seahawks have the fugliest uniforms ever.
That's enough from me for now. Here are the ten songs I listened to while writing this crappy entry:
- Sublime - Get Out!
- Gorillaz - Feel Good Inc.
- Living End - So What
- 311 - Light Years
- Tilt - Bad Seed
- The Hives - A.K.A. I-D-I-O-T
- NOFX - Eat the Meek
- Jurassic 5 - React
- The Ataris - Neilhouse
- Pete Townshend - Let My Love Open the Door
Last Second Picks
Pittsburgh Steelers at Denver Broncos
Who I want to win: I'm a Raiders fan, so I hate the Broncos. There is no way I can pull for them. That means that I'm rooting for the Steelers by default. Plus, how can you not be for Troy Polamalu and his hair . And I live in Steelers country, so it's hard to not get sucked into the black and gold fever.
Who I think will win: On a neutral field, the Steelers would win. Too bad this game is being played at
Carolina Panthers at Seattle Seahawks
Who I want to win: Ever wonder what a seahawk is ? Of course, the Panther is one of the archetypes of conservation genetics. I would be happy to see either of these teams go to the Superbowl. I'm kinda sick of Sean Alexander, though. If Alexander plays well, I wanna see the Panthers win. If Alexander sucks it up big time, go Seahawks.
Who I think will win: The Panthers have won their last five road games (including two playoff road wins). There is no way they can win another road game. There is no way they make it to the Super Bowl. There is no way I'm not picking the Panthers. Yes, the Panthers will win. Plus, when I see someone as tall as I am excelling at receiver in the NFL, I can't help but pull for him.
Enjoy the games. Read full post >>
"Proof" is a word that only applies to mathematics and liquor.I now return you to your regularly scheduled podcast . . . Read full post >>
Haven't You Seen My Movies?
There's a motherfucking snake on the motherfucking plane . . . motherfuckers!
YES THEY DESERVED TO DIE!!! AND I HOPE THEY BURN IN HELL!!!
If you don't get it, you need to get it . Read full post >>
One Bourbon, One Scotch, and One Double Black Diamond
Miller tried to clarify his statements, explaining that he didn't actually drink on race mornings, but that, on occasion, he'd arrived at the start with a hangover from the night before.So, Bode goes out and wins the downhill on Saturday, gets hammered that night, then shows up for the Slalom with some knockin' in his noggin. Sounds ok to me. Rage on Bode, rage on. Read full post >>
More Sunday Afternoon NFL Blogging
Adrian Peterson the Chicago Bear (left) and Adrian Peterson the Oklahoma Sooner (right).
One thing that comes with having a good season is increased TV coverage. I've seen a lot more of the Chicago Bears this year (and now in the playoffs), and I've become familiar with some of their players. When I heard that Adrian Peterson was their running back, I thought, "Wow, he wasn't at Oklahoma very long." It turns out there are two Adrian Petersons. In a couple of years, Adrian Peterson , the younger, will be starring in the NFL, only adding to the confusion.
At least the Jason/Jayson Williams had the decency to stand out by playing different positions. Additionally, only Jayson Williams was charged with manslaughter, only one of the Jason Williams has the motorcycle riding skills of Kellen Winslow Jr., and only one of the Jason Williams tokes with Randy Moss . Read full post >>
Why The Patriots Lost
Toni Tony Tone & A Tribute to Troy
But I'm gonna be a total asshole and claim Tony Dungy should shoulder a lot of the blame. Sure, his son just died . And, yeah, the dude's a man of faith (whatever the hell that's worth). But Dungy's got a bit of Ewing theory going for him, seeing as how the Tampa Bay Buccaneers won a Super Bowl the year after firing Dungy. Dungy deserves some props for turning the Bucs into winners and leading them to the playoffs, but he's gonna be remember as a guy who couldn't win it all.
The Dungy-Manning pairing may make it impossible for the Colts to ever make it to the Super Bowl. The Patriots seemed to be Manning's NFL version of the Florida Gators, but this year (following one of the best starts to season in NFL history) the Colts couldn't even win a single playoff game. It's another year and another flop in the playoffs for Dungy and Manning. I wonder if Dungy never bothered to come back to Indianapolis after his son died or if Peyton got injured while his offensive line could not protect him, would the Colts have fared better in the Playoffs?
So, let's stop treating Dungy like a sacred cow -- the dude's got more choke in him than Michelle Kwan. Yeah, I went there. Whatcha gonna do about it?
Oh, and my boy Troy was all over the place today. Even if he can't catch, the man can defend the pass better than any other safety out there. Don't let anyone cut those Samson locks ; his hair is the secret to his power. Read full post >>
Detecting Natural Selection (update)
Happy Friday the 13th
It's Friday, January Thirteenth. Don't walk under no ladders. Don't let no black cats walk in your path. And don't shake hands with no lepers.
Ok, I made that last one up. Read full post >>
Fuck You, Rate My Professor
The Best Things Ever Since Anything Ever
- Vince Young's limp wristed throwing style .
- Live-action Mike Tyson Punch Out.
- How to throw a party in your parents' house when you're home for the holidays.
This Is What Happens When You're Culturally Illiterate
Brigitte Nielson, on the other hand, earned fame in the 1980s for her appearance in Beverly Hills Cop II, her marriage to Sylvester Stallone, and her fling with Mark Gastineau. She disappeared (as much as a 6 foot 1 inch, platinum blonde, Dane can disappear) from the limelight until she co-starred in the television opiate, VH1's The Surreal Life. It was during her time on that show that she "fell in love" with Public Enemy's Favor Flave. They then starred in a spinoff show devoted to their disturbing relationship. Apparently, they're splitsville, and Brigitte is planning to marry some guy half her age even though she still hasn't completed the divorce with her previous husband.
Birgit and Brigitte have something in common: both had careers as singers . . . Birgit far more successful and talented. Read full post >>
NFL Playoff Picks
Washington Redskins at Seattle Seahawks
Who I want to win: That's easy: the Redskins. If you paid attention, you'd know that I'm pulling for the racist epithets to go all the way just so I can watch Clinton Portis play dress up. That, and I have a hard time pulling for a bald quarterback .
Who I think will win: The Seahawks will probably win seeing how they have the best running back in the NFL (yes, better than Southeast Jerome), and the 'Skins set the record for fewest yards in a playoff win .
New England Patriots at Denver Broncos
Who I want to win: Neither team. I'm hoping an avalanche buries the city of Denver this weekend, and the game gets cancelled, so the winner of the other AFC divisional game gets an automatic trip to the Super Bowl. I'm sick of the Patriots -- they beat my beloved Raiders in the tuck game. I hate the Broncos (and the Chiefs) because I'm a Raiders fan.
Who I think will win: The fucking Patriots. They always win these games. Even though Denver beat them earlier in the season. Even though Denver had a better regular season. Even though New England has a bunch of injured players. New England will still win.
Pittsburgh Steelers at Indianapolis Colts
Who I want to win: Colts, I guess. The Steelers busted up Carson Palmer's knee. They also knocked off the Bengals, which means no more Chad Johnson touchdown celebrations.
Who I think will win: The Colts have a better defense, a better offense, and home field advantage. They also have a Manning at quarterback, which means look out for the choke. That said, I still think the Colts will win.
Carolina Panthers at Chicago Bears
Who I want to win: I'm apathetic about this one. When in doubt, pull for the underdog. So , let's go Panthers. Besides, if the Bears win, the final score will be 5-3. At least if the Panthers win there's a chance that some points will be scored.
Who I think will win: The Bears are favored, but I think the Panthers will pull it out. The Bears have a great defense and no offense. The Panthers have a solid defense and an ok offense. Unless the Bears D puts up two scores, they ain't gonna win.
There they are, my picks. Let's see how I do. Read full post >>
Evolgen Jumps the Shark
In announcing its move to the new Seed Media Group blog consortium, Science Blogs , Dispatches from the Culture Wars proclaimed that Ed is Selling Out , conjuring up images of Pete Townshend and Roger Daltrey hawking deodorant and baked beans on an album cover . I too am moving over to Science Blogs, but while Ed may be doing it for the money, evolgen’s move over to Seed is motivated by sheer masochism. You see, I’m jumping the shark, shooting myself in the foot so to speak.
Don’t expect evolgen to ever be the same again. This humble little blog is movin’ on up to the east side (to a deluxe website in the sky) to live with George and Weezie. You can say that we finally got a piece of the pi (bad, nay, horrible science joke).
Most of the science content of evolgen will be posted at my new Science Blogs url (http://www.scienceblogs.com/evolgen). Bookmark that link, write it down, tattoo it on your ass, or do whatever you need to do to remember my new internet location. But don’t lose this url . My current plan is to continue posting non-science related stuff here at Blogger (and we will maintain this site as an archive of previous evolgen posts) such as the apathetically enjoyed Weekly Random Ten and some stuff on sports and pop culture. While most of the science content will be posted over at Science Blogs, I will keep posting my Detecting Natural Selection series at Blogger.
Given the shift in focus of this blog, and the fact that the Science Blogs site will contain the bulk of the evolution and genetics that make up evolgen, I will be moving the description “AT THE CONVERGENCE OF EVOLUTION AND GENTICS” over to the Science Blogs version of evolgen. The Blogger version of evolgen will now be known as:
Clash, Culture and Science
The name comes from the title of a Rancid song ( Cash, Culture and Violence ), with some slight modifications. “Clash” refers to the only band that matters , but also the general idea of confrontation, disagreement, and antagonism. You will be seeing more posts on things that piss me off (ala another mad biologist you may be familiar with), and these will not be limited to intelligent design creationism. As you may have noticed, I am a pop-culture whore. You can expect a lot of posts on this guilty pleasure (along with some posts on sports ) in the “Culture” section of Clash, Culture and Science. Finally, I would be remiss to leave out any “Science” writing. While the new Science Blogs version of evolgen will have the bulk of the science content, Clash, Culture and Science will also have a science angle.
I’m not the only one to jump the shark (or sell out, whatever the case may be). Here are some friends of evolgen that will be joining me over at Science Blogs:Dispatches from the Culture Wars
Living the Scientific Life Read full post >>
Give the British Some Spare Time . . .
The application (known as iSpecies, which I don't think has anything to do with iMac , iBook , iPod , or I, Robot ) is available here .
(via Rod Page's blog ) Read full post >>
Are Deletions Deleterious? Part 2
The approach I previously described uses allele and genotype frequencies to identify clusters of SNPs that are not in Hardy-Weinberg equilibrium. This involves analyzing all of the SNPs in the entire population simultaneously. Another approach, described in the paper from Jonathan Pritchard ’s group, uses known relationships of family members (so called “parent-offspring trios”) to identify SNPs that are transmitted from parents to offspring in a non-Mendelian fashion. They start with the observation that individuals carrying a deletion at a SNP locus will appear to be homozygous when genotyped at that SNP (this same assumption was made by Altshuler). They then examined the progeny from the parent-offspring trios for individuals that are homozygous for a particular SNP (note: there will be a lot of homozygous SNPs in any one individual) and see if they could have inherited the same allele from each of their parents. For example, if the parents are genotyped as “AA” and “TT” at a particular SNP, and their child is genotyped as “AA”, either there was a mutation in the germline of the TT parent (changing one of the T alleles to A), or the TT parent is actually “T-“ (where the “-“ means that parent is missing a second copy of the SNP). If one of the parents is T- then the child’s genotype is actually “A-“, and that child inherited the deletion from the parent with the genotype T-.
Figure 1. Examples of four of the seven types of trio genotype configurations used in this analysis.
The true genetic state of each individual is depicted within his or her pedigree symbol. The called genotype, when it differs from the true genotype, is shown outside the pedigree symbol. The three upper configurations (A and C) all result in mendelian incompatibilities. We define 'Type I mendelian incompatibilities' as those that are compatible with a deletion transmitted from parent to child and 'Type II mendelian incompatibilities' as those that are incompatible with the deletion model. Key to figure: A: mendelian incompatibility, genotypes compatible with a deletion transmitted from the mother; C: mendelian incompatibility, genotypes incompatible with a transmitted deletion; E: no mendelian incompatibility, genotypes compatible with a deletion transmitted from the mother (but not the father); G: no mendelian incompatibility, genotypes incompatible with a transmitted deletion. Candidate deletion regions are runs of consecutive SNPs with at least two Type I mendelian incompatibilities and other SNPs that are compatible with a deletion; all the SNPs must suggest transmission from the same parent. See further details in Methods.
Any run of at least two Mendelian inconsistencies was labeled as a deletion. They examined parent-offspring trios from two populations: a European derived population (CEU) harbored 345 deletions and one from Nigeria (YRI) harbored 590. Just like the other paper I described, they validated some of the deletions using quantitative PCR and confirmed that the PCR products from all 12 candidates were in fact valid. They also using an oligonucleotide microarray to test for false positives in 9 of the offspring at 93 deletions and confirmed all but 13 of the deletions (14% false positives). I won’t get into the details of it, but they assessed their power to detect deletions given the amount of polymorphism in the SNP data set, the spacing of SNPs, and the size of the deletions they were identifying.
The median deletion size was 10.6 kb and 8.5 kb in the CEU and YRI samples, respectively, and the size distribution is L-shaped (many small deletions, and a tail containing the large deletions). Most of the deletions were segregating at low frequencies, and 39% were identified in only one trio. Interestingly, some of the deletions at the same locus appear to have different breakpoints, and some deletions sit on multiple haplotype backgrounds, suggesting that certain loci have been deleted independently in multiple lineages. This is nothing new, as many factors (such as repeat sequences flanking a region) can make a particular locus more prone to deletion and duplication (more on this later).
Finally, they took a closer look at deletions that contained genes (exons and introns) and found 267 genes within their entire sample of deleted regions (201 of which were deletions of coding sequence, and 92 were completely deleted genes). There was a deficiency of SNPs in genic regions within deletions compared to genic regions with no association to a deletion, suggesting that purifying selection against haplotypes carrying deletions of genes decreases the variation at these loci. They assigned each gene to a functional class and found an overrepresentation of genes involved in immunity, sensory perception, cell adhesion and signal transduction in their set of 267 deleted genes. These functional classes are similar to those identified in screens for segmental duplications, genes with signatures of positive selection, and lineage specific gene family expansions.
I think the two most interesting finds are the reuse of deletion breakpoint regions (independent origins of the same deletion) and the analysis of functional classes. Many human diseases are the result of the deletion, duplication, or relocation of a particular genomic region. These chromosomal aberrations often occur in somatic cell lines (ie, they are not inherited per se, but the mutation happens some time during the individual’s life history). There is some aspect of heritability when it comes to these types of mutations, as you can inherit a predisposition to a certain genetic disease if you get a defective allele from one parent or you inherit a locus that is predisposed to a deleterious mutation. How can you be predisposed to get a particular mutation? Well, if you have some sort of repetitive sequence (transposable element, segmental duplication, etc) flanking a “disease gene”, that repeat can induce a genomic rearrangement that leads to some deleterious change in that disease gene. The same idea is behind the independent origins of similar deletions that Pritchard’s group proposes.
It appears that certain functional classes of proteins are more prone to rapid evolution, duplication, and deletion. One explanation for the differences in “evolvability” between classes of proteins lies in the differences in purifying selection on different genes. Let’s assume that genes that carry out a more important function than other genes are less robust to mutation (both in amino acid sequence and expression), so that changes to the copy number of particular genes will have deleterious effects. Not only will natural selection remove haplotypes that carry a deletion or duplication of that gene, it will also select against repetitive sequences flanking that gene that would allow for the duplication and deletion events to occur. We see this type of pattern when we look at the location of transposable elements (TEs) in a genome -- they are clustered in intergenic regions, although this may also be due to the effects of TEs on the expression of nearby genes. If only certain genes can withstand having rearrangement inducing repeats in their vicinity, then certain functional classes will be overly duplicated and deleted. Furthermore, some genes (such as large gene families like the odorant receptors) appear to be overly duplicated, suggesting natural selection may favor repetitive sequence near these genes (in fact, duplicated genes alone can spur on more duplication because they are repetitive sequences themselves).
If we imagine that certain classes of genes are under more purifying selection than other classes, then we can expect to see the same types of genes in the rapidly evolving class regardless of how we measure the rate of evolution (nucleotide sequence, segmental duplication, deletion, flanked by repeats, or any other technique). I hope to finish my discussion of SNPs and deletions with my next post in which I will attempt to write about linkage disequilibrium (a subject that gives me trouble).
Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK. 2006. A high-resolution survey of deletion polymorphism in the human genome. Nat Genet. 38:75-81
Hinds DA, Kloek AP, Jen M, Chen X, Frazer KA. 2006. Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet. 38:82-85
McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB Lee C, Daly MJ, Altshuler DM, & The International HapMap Consortium. 2006. Common deletion polyrmorphisms in the human genome. Nat Genet. 38: 86-92.Read full post >>