tag:blogger.com,1999:blog-21947313033259698852011-09-06T01:55:59.693-07:00Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.comBlogger431100tag:blogger.com,1999:blog-2194731303325969885.post-86942199737681725872009-01-24T16:54:00.000-08:002009-01-24T17:09:15.522-08:00

Copy number at CCL3L1 is one of the genetic predictors of HIV susceptibility in humans (Gonzalez et al), with individuals with copy number higher than the population median being less susceptible. A new paper at PLoS Genetics shows that the gene is also copy number variable in rhesus macaque, and that this variation is also responsible for differences between individuals in susceptibility (to SIV

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com44tag:blogger.com,1999:blog-2194731303325969885.post-51013037513201547212009-01-23T07:54:00.000-08:002009-01-23T08:00:11.706-08:00

A interesting article in Science on using the (mainly vertically transmitted) human pathogen bacteria Helicobacter pylori to reconstruct the peopling of the Pacific. Which I guess is a finer-scale followup to a previous paper doing this for worldwide populations.

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com2tag:blogger.com,1999:blog-2194731303325969885.post-54918742829148042772009-01-21T18:54:00.000-08:002009-01-21T19:18:21.436-08:00

There's an interesting opinion piece at Nature by Aravinda Chakravarti. The part on populations and race covers some pretty familiar ground, but the article is obviously aimed at a more general audience. I'm not really sure what the "population view dominates in genetics" means. I think geneticists use population labels as handy identifiers, which can sometimes lead to some confusing/misleading

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com2tag:blogger.com,1999:blog-2194731303325969885.post-72174321323753443242009-01-09T09:05:00.000-08:002009-01-09T09:07:57.801-08:00

I use R pretty much constantly, so I was pleased to see it getting some attention in the NYT (see also Mailund, Hawks, and Dechronization). There is also a followup post by the article's author here.One of the best things about R is that it is freely available, this is a huge boon to any kind of statistical research as most other statistical packages are prohibitively expensive putting them out

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com6tag:blogger.com,1999:blog-2194731303325969885.post-61511919142002768992008-12-10T21:30:00.000-08:002008-12-10T21:39:17.470-08:00

Nature has a whole slew of reviews on the current progress and prospects of mapping the genetic determinants of phenotypic variation:Association mapping in humans (here)Mapping behavioral traits in mouse (here)Genetic variation in malaria (here)Mapping in plants (here)and how we should use natural variation to learn about biological systems (here)quite a fun reading list.

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com1tag:blogger.com,1999:blog-2194731303325969885.post-35536549898187166742008-12-06T16:51:00.000-08:002008-12-06T16:59:05.707-08:00

A new article by Price et al. looks at the effects of cis and trans acting variation on gene expression. A number of studies have approached the genetics of gene expression in humans by doing GWA mapping of the genetic determinants of the expression of a gene (usually many genes measured on a microarray). However, this approach is strongly biased towards finding signals in cis. The cis region

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com4tag:blogger.com,1999:blog-2194731303325969885.post-60968398532729737492008-09-17T10:33:00.000-07:002008-09-17T10:42:00.257-07:00

Just a quick link to a NYT Q&A session with Amy Harmon, who got the Pulitzer for her DNA age series. Her recent article on challenges of teaching evolution in the States has generated a lot of the questions focus on the media and creationism.

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com1tag:blogger.com,1999:blog-2194731303325969885.post-59247973056331323102008-08-31T17:15:00.000-07:002008-09-01T05:08:22.301-07:00

Two recent papers use of high density SNP chips to show counter intuitively that you can locate the geographic origin of a person to within a few hundred miles using only genetic data (Novembre et al., hat tip to gnxp), and that you can detect whether a person has contributed to the pooled data of a genome-wide association (GWA) scan (homer et al, hat tip to gnxp and the The Spitoon). Both of

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com4tag:blogger.com,1999:blog-2194731303325969885.post-90375914945668168762008-08-31T15:17:00.000-07:002008-08-31T15:20:18.611-07:00

A paper just out in Nature Genetics (Myers et al) extends what we know about how local sequence determines recombination hotspot activity (hotspots are 1-2kb regions where recombination happens far more frequently than in the surrounding region). The location of recombination hotspots along the genome can be inferred from linkage disequilibrium (LD), as LD represents the joint action of genetic

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0tag:blogger.com,1999:blog-2194731303325969885.post-11173839761329155602008-08-20T17:11:00.000-07:002008-08-20T18:01:54.622-07:00

A freakonomics blog piece on the FBI's DNA match probabilities (via Genome-technology). There is also some interesting correspondence (1,2,3) in Nature Reviews Genetics on the reliability and use of Low Copy Number DNA forensic profiling (i.e. using trace amounts of DNA), which briefly discusses the difficulties posed by contamination and allele drop out. When I get a minute I'll have to go and

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com1tag:blogger.com,1999:blog-2194731303325969885.post-38151422943292517192008-08-17T15:32:00.000-07:002008-08-17T15:38:28.471-07:00

A new paper, just out in Nature Genetics, by Zody and Jiang et al. looks at the evolutionary history of the ~1Mb 17q inversion. This inversion was first described by Stefansson et al.. Stefansson et al. found the normal allele H1 was present in many populations but that the inverted allele H2, seemed to have increased rapidly in frequency in Europeans, perhaps due to positive selection, in

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0tag:blogger.com,1999:blog-2194731303325969885.post-23750398789296493272008-08-15T19:41:00.001-07:002008-08-16T08:32:05.432-07:00

I just spotted that the author of the right-handed snakes paper, I wrote about a while ago (see here), has videos on his website of the snakes and snails in action.

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0tag:blogger.com,1999:blog-2194731303325969885.post-91520465288076155332008-08-07T11:47:00.000-07:002008-08-07T11:54:56.618-07:00

Two new papers mapping fine-scale recombination rates:The first ( Mancera et al , see here for a commentary from Michael Lichten) maps recombination events in yeast tetrads using very high density genotyping. One of the most interesting points from an evolutionary perspective is that they claim to find direct evidence of biased gene conversion (repairing of G/C-A/T heterozygotes in gene

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0tag:blogger.com,1999:blog-2194731303325969885.post-56326053623545814722008-07-29T11:54:00.000-07:002008-07-29T11:59:05.067-07:00

Males leave more than sperm when they copulate with a female, they also leave a bunch of seminal proteins that are involved in sperm competition and sexual conflict. The problem in studying this system is that it is hard to distinguish between those proteins already present in the female and those deposited by the male during copulation. An new paper (Findlay et al.) uses a clever technique to

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0tag:blogger.com,1999:blog-2194731303325969885.post-91650088167895158232008-07-27T12:49:00.000-07:002008-07-27T13:08:14.863-07:00

Happy birthday to PLoS Genetics. There's an article giving various facts and thanks here . PLoS Genetics has quickly become a great journal for evolutionary genetics and genetics in general. I think it ranks very favorably along with journals like Genetics, Genome research and Nature Genetics (though it carries fewer of the big/successful association studies than the latter).

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com1tag:blogger.com,1999:blog-2194731303325969885.post-10749540208798281842008-07-06T14:52:00.000-07:002008-07-06T15:18:37.040-07:00

I've not posted for a while as I've been away at conferences and I'm been trying to catch up with the work I've missed. I'll try to keep my posts more regular and I hope I've not dropped off people's lists (if I was on them to begin with).What stops a species from extending its range indefinitely, why does a species not adapt and spread to every environment it encounters? This question has

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0tag:blogger.com,1999:blog-2194731303325969885.post-43127109095612295212008-04-25T17:07:00.000-07:002008-04-25T17:22:29.560-07:00

I was thinking about blogging about the paper on metal tolerance evolution in Arabidopsis halleri via a cis-regulatory change (Hanikenne et al), but I see that gnxp has already done so here. So I thought in the vein of the 'cis-regulatory vs protein' evolution debate, I would point people towards a recent paper (Scalliet et al and here for a commentary) looking at a phenotypic change involving a

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0tag:blogger.com,1999:blog-2194731303325969885.post-17037985558317756872008-04-21T10:03:00.000-07:002008-04-21T12:04:13.547-07:00

Cavalli-Sforza and colleagues used Principal Component Analysis (PCA) to summarize general spatial patterns of human allele frequencies across continents into maps. They interpreted peaks in these PCA maps to indicate sources of colonization, e.g. Neolithic expansions etc. However, a new paper by Novembre and Stephens (Novembre and Stephens 2008) questions this interpretation. They show that many

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com3tag:blogger.com,1999:blog-2194731303325969885.post-13011207360813295352008-04-12T13:54:00.000-07:002008-04-12T14:03:35.622-07:00

A really neat paper (Loeuillet et al.) in PLoS Biology identifying a candidate SNP for cellular susceptibility to the HIV-1 virus. The paper adding to our growing knowledge of the genetics of HIV susceptibility (see a review of the paper by David Goldstein).Rather than investigating this in patients with the disease, the paper initially measures how susceptible different cell lines are to HIV.

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com6tag:blogger.com,1999:blog-2194731303325969885.post-61035348352220449272008-04-06T18:59:00.000-07:002008-04-06T19:23:59.118-07:00

Just a few thoughts on genome-wide association studies, prompted by Genetic Future's recent posts on the low returns of some genome-scans (here and the here). Now meta-analysis of combined studies will get us a long way towards getting small effect alleles without the expense of typing additional cases (and we've seen quite a bit of this already), as will methods for studying epistatic

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com2tag:blogger.com,1999:blog-2194731303325969885.post-30799274837143434992008-04-05T07:25:00.001-07:002008-04-05T09:05:28.218-07:00

A summary by PZ Myers of Coyne and Wray's keynote speeches on evodevo. It sounds like it would have been fun to see, particularly the dueling t-shits (one is quoted in the title of this post). I think that Coyne is right that the only real way to know where selected changes occur and what type of mutations they are is to do very detailed follow-up work. I thought I would give a link to a

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com2tag:blogger.com,1999:blog-2194731303325969885.post-1709708431885824772008-04-02T21:06:00.000-07:002008-04-02T22:11:41.563-07:00

A quick post about Hay et al, which I spotted thanks to Pondering Pikaia (Nature news also has a piece on it). I think that this paper is interesting but I think there are some issues in the interpretation. The paper estimates the mtDNA mutation rate of tuatara (an ancient lineage of reptile living on New Zealand), and find that the mtDNA mutation rate is one of the highest estimated so far. The

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com1tag:blogger.com,1999:blog-2194731303325969885.post-50269592122186018422008-03-26T12:17:00.000-07:002008-03-27T17:08:55.761-07:00

The best way to learn about demography from population genetic data is to look at multiple unlinked regions (a common theme over at the evolgen blog). The distribution of frequencies in a populations of neutral alleles at SNPs (the site frequency spectrum), is informative about population history. For example an excess of low frequency mutations is consistent with recent population growth, as

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0tag:blogger.com,1999:blog-2194731303325969885.post-27698116390874995782008-03-23T12:12:00.000-07:002008-03-23T12:23:22.144-07:00

A short but nice article by Doris Bachtrog, looking at whether there is a faster mutation rate in males compared to females in Drosophila. Studies of a number of vertebrates have shown a faster rate of substitution on the Y compared to the X at putatively neutral sites, thus suggesting a faster male mutation rate (as under neutrality the substitution rate is the mutation rate). This high rate of

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com2tag:blogger.com,1999:blog-2194731303325969885.post-69063770363672175952008-03-21T12:27:00.000-07:002008-03-21T14:36:38.388-07:00

Just a quick note to point people towards a paper (Yanoviak et al) that gives an amazing example of a parasite inducing mimicry in their host. The nematode parasite is transmitted to ant larvae via bird droppings, which the ant larvae are fed on. The parasite makes the ant's abdomen bright berry red, and also makes the ant hold its abdomen up in the air. This attracts birds to eat the berry-like

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0tag:blogger.com,1999:blog-2194731303325969885.post-82910935254675279332008-03-19T08:44:00.000-07:002008-03-19T09:06:06.772-07:00

There's a really interesting paper by Sean Carroll's group in Cell ( Jeong et al. ) on pigmentation differences between two closely related species of Drosophila (D. santomea and D yakuba). D santomea has a small range and is restricted high altitudes on the island of São Tomé, while Yakuba is more widespread and lives at lower altitudes on São Tomé. The species can hybridize, and form a natural

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com1tag:blogger.com,1999:blog-2194731303325969885.post-1525016568623122932008-03-07T17:35:00.000-08:002008-03-07T17:59:00.212-08:00

One of the most obvious features of our genome, is the large difference between in the X and Y chromosomes. The Y chromosome is small compared to its partner the X, much of its DNA content is made up of repetitive DNA and it codes for few genes.Much of the degeneration of the Y is thought to due to the lack of recombination on the Y chromosome. Recombination is thought to be initially suppressed

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com2tag:blogger.com,1999:blog-2194731303325969885.post-32976826724213941692008-03-02T17:16:00.000-08:002008-03-02T17:54:53.795-08:00

A paper that was published last year, that gives a wonderful example co-evolution. I'm not sure if it got much coverage (but may well be mistaken), but it really is great.Snails often have clockwise shells (which in itself, is a wonderful example of the evolution of asymmetry). The authors show that snakes that prey on these snails have evolved to have more teeth on their right mandible than

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0tag:blogger.com,1999:blog-2194731303325969885.post-57119093407156606762008-02-14T08:00:00.000-08:002008-02-14T08:04:55.188-08:00

I just read the Decode paper on reproductive success and relatedness (here. You can read other comments on it at Gene Expression here and here , and over at John Hawks. Overall I think it is a really interesting finding. One of the impressive things is that the number of grandchildren that a couple produced is still a decreasing function of relatedness out to 5 and 6 cousins. As the authors note

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com1tag:blogger.com,1999:blog-2194731303325969885.post-74154510375921081532008-02-07T17:43:00.000-08:002008-03-24T17:39:42.960-07:00

I thought I would post a few notes on the KITLG stickleback paper. Sticklebacks are a great system because many populations of marine stickleback have become isolated in flesh water lakes. A number of groups have done a lot of great work with them, and the availability of a good genetic map and draft genome is really accelerating them into a model system. The paper is really nice and maps a major

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0tag:blogger.com,1999:blog-2194731303325969885.post-89611395565690007992008-01-24T17:22:00.000-08:002008-12-11T11:13:41.918-08:00

Thought I would pop a couple of pictures up from the Pacific island paper , and briefly point out another paper on the topic. One of the debates that the paper sought to resolve is "Are Polynesians more closely related to Asian/Taiwanese populations or to Melanesians?"First a picture of the area (taken and cropped from the PLoS genetics paper, citation at the bottom), as I had trouble remembering

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0tag:blogger.com,1999:blog-2194731303325969885.post-44351248303764649012008-01-20T14:41:00.000-08:002008-01-20T16:22:18.954-08:00

For most genes in our genome both maternal and paternal copies are expressed. One notable exception from this is the X chromosome in females. To compensate for the fact that males have only a single X chromosome, female cells compensate by expressing one X chromosome (at least for the majority of genes on the X) by inactivating the other X chromosome. The choice of which X chromosome to

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com2tag:blogger.com,1999:blog-2194731303325969885.post-89517253084553355962008-01-17T17:21:00.001-08:002008-01-17T17:58:14.336-08:00

A new paper looking at the genetic structure of Pacific Islanders has just come out. The authors type nearly a thousand markers on 952 individuals from 41 Pacific populations. I've not had a chance to read the paper in any depth, but it looks really interesting. Studies of single loci such as the Y or mtDNA offer a very noisy view of human history as chance events in the history of the maternal

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com3tag:blogger.com,1999:blog-2194731303325969885.post-27858650862629242982008-01-01T17:05:00.000-08:002008-01-03T11:14:12.262-08:00

Thanks for commenting John.I think that people do not doubt that the effective population size of humans has increased, what is debatable is when and by how much.I stand by my comment that effective population sizes can not be estimated from archaeological data. The only way to truly estimate the population genetic parameter Ne is from population genetic data. It is not enough to do some

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0tag:blogger.com,1999:blog-2194731303325969885.post-51659360315878600062007-12-28T14:00:00.001-08:002007-12-28T14:14:03.167-08:00

John Hawks has recently published a post commenting on what I thought was a pretty decent post by evolgen, about the rate of adaptative vs neutral evolution. I take issue with a number of points raised in the Hawks post, and in Hawks et al. Firstly, as I discussed previously I think that Hawks et al have not shown a speed up in the rate of selective sweeps. Also there are a number of aspects

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com2tag:blogger.com,1999:blog-2194731303325969885.post-34846651227264760482007-12-22T16:15:00.000-08:002007-12-27T10:10:18.913-08:00

There is an interesting article in PNAS on the differences in inheritance in males and female Drosophila by Wayne M et al.Sexual selection is a key driving force in evolution. Sexual dimorphisms (differences between the sexes) are one of the most obvious patterns in nature, from peacocks tails to the elaborate genitalia of insects. So there is obviously a lot of interest in understanding how

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com2tag:blogger.com,1999:blog-2194731303325969885.post-46860273059360234132007-12-15T05:54:00.000-08:002007-12-15T15:30:51.007-08:00

Thank you for commenting on my post John. I appreciate you discussing your paper with me, I understand that this is a very busy time for you.My criticism of Hawks et al, is that Wang et al (nor Hawks et al) did not do sensiblesimulations, which is a concern as the false positive rate and power of the test is key to Hawks et al statements about the number of sweeps. Most previous selection-scan

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0tag:blogger.com,1999:blog-2194731303325969885.post-61242613504271393142007-12-13T13:58:00.000-08:002007-12-13T16:11:05.877-08:00

Now first of all I should say that I find the hypothesis that human evolution has sped up quite plausible. Large populations are generally more capable of responding more readily to new selection pressures, than small ones. Human populations have been exposed to (and created) a range of new environments, to which our increasing large population size may have allowed us to adapt to rapidly.However

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com1tag:blogger.com,1999:blog-2194731303325969885.post-53825466269215941422007-12-08T17:56:00.000-08:002007-12-08T18:05:44.198-08:00

a couple of interesting blog pieces Pondering Pikaia on how the globin genes of Penguins have evolved to help them dive. and Jonathan Eisen at tree of life on Nancy Moran's work on the genomes of symbionts (just out in PNAS). I saw Nancy Moran give a talk on her work (a year or two ago) and I have to agree with Eisen that she does really great and pretty work. Her talk has definitely stuck

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0tag:blogger.com,1999:blog-2194731303325969885.post-80448553416966392562007-12-08T07:00:00.000-08:002007-12-08T18:17:01.369-08:00

First of all I should start by saying that everything on this blog (about peer-reviewed research) comes with the disclaimers 'I may well have misunderstood the paper or be incorrect in my thinking' and 'I think that this is interesting and novel, but I may have missed a flaw in the author's logic or prior work on this topic'. This is especially true when I talk about papers outside my area.

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0tag:blogger.com,1999:blog-2194731303325969885.post-37716930140448603852007-12-02T10:47:00.000-08:002007-12-05T17:50:55.807-08:00

There are a couple of interesting papers (1, 2) over at PLoS biology (also discussed here ) studying a sex ratio distortion system. This is a type of mutation, which causes the sex ratio of the bearer's offspring to differ from the usual 50:50. If the mutation occurs on a sex chromosome such a mutation can be spread through the population. For example, a mutation on the X chromosome, which

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com4tag:blogger.com,1999:blog-2194731303325969885.post-48540715715567752992007-09-20T08:32:00.001-07:002007-12-02T16:30:56.475-08:00

It would be a lot of fun (although also an IRB nightmare) to involve a bunch of schools in an association study. In school we learn about tongue rolling and attached ear-lobes being classic Mendelian traits, but I don't think we (or I anyway) know the genes underlying these traits. It would be great to take classes of kids from around the country and get their teachers to phenotype them (i.e. can

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com5tag:blogger.com,1999:blog-2194731303325969885.post-91998285793723663392007-09-20T08:31:00.001-07:002007-09-20T08:31:45.258-07:00

Well here I go off into the world of blogging. I'm interested in evolution and in particular population genetics. This blog will be a collection of ideas and discussion on recent papers on evolution, population genetics and association mapping (and whatever else takes my fancy).

Ghttp://www.blogger.com/profile/05140268044719927398noreply@blogger.com0