tag:blogger.com,1999:blog-230849252024-03-12T22:18:34.773-06:00Yann Klimentidis' Weblogon evolution, genetics, human diversity, evolutionary ecology, physiology and more...Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.comBlogger561125tag:blogger.com,1999:blog-23084925.post-23664600580374213032012-03-16T09:17:00.002-06:002012-03-16T10:27:16.319-06:00Predicting pigmentation phenotypes with genetic information<h1 class="articleTitle"></h1><span>This is a very short paper and their methods are fairly simplistic. They pick some SNPs from the literature, and count the number of homozygous SNPs related to various pigmentation phenotypes.<br />Henry Louis Gates and "Extinct Paleo-Eskimo" are both predicted to have red hair!<br /></span><span style="font-weight: bold;"><br /><a href="http://onlinelibrary.wiley.com/doi/10.1002/ajhb.22263/abstract">Predicting homo pigmentation phenotype through genomic data: From neanderthal to James Watson</a></span><br />Caio C S Cerqueira, Vanessa R Paixão-Côrtes, Francis M B Zambra, Francisco M Salzano, Tábita Hünemeier, Maria-Cátira Bortolini<br /><span style="font-weight: bold;">American Journal of Human Biology</span>. Early View<h2 id="productTitle"></h2><span style="font-weight: bold;">Abstract</span>:<br /><blockquote style="color: rgb(102, 102, 102);">Background:Human pigmentation is regulated by several genes acting at different stages of melanin formation. Functional and association studies have elucidated the role of several of these genes in pigmentation phenotypes. Forensic and evolutionary studies can benefit from this knowledge.<br />Objectives:To evaluate the reliability of the prediction of pigmentation phenotypes using a large database of genetic markers in individuals with known phenotypes; and from this try to predict the pigmentation phenotype of prehistoric Homo specimens and of contemporary individuals whose visible phenotypes are not known.<br />Methods:We compared predicted and observed phenotypic data through an analysis of 124 single nucleotide polymorphisms in 33 genic and seven intergenic regions of 30 subjects, five of them prehistoric, whose complete nuclear genomes are available in UCSC and PSU UCSC public databases.<br />Results:For the molecular predicted versus observed phenotypes, the percentage of agreement was as follows: freckles: 91; skin: 64; hair: 44; eyes: 36; total: 59; while the molecular predicted versus probable (no visible observation available; inferences based on ethnic population characteristics) it was, respectively, 83, 60, 42, 67, and 63. The difference between two sets is statistically nonsignificant (P = 0.75).<br />Conclusion:To our knowledge, this is the first article to examine the effect of a large number of genetics markers for phenotype prediction. The approach could be useful for forensic applications, as well as for the determination of possible phenotypes of extinct prehistoric individuals.</blockquote>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com5tag:blogger.com,1999:blog-23084925.post-33350164231288017352011-10-21T09:53:00.004-06:002011-10-24T09:23:41.772-06:00Antagonistic pleiotropy - the case for BRCA mutations<h1 id="article-title-1"></h1>In a natural fertility population, these authors find that carriers of BRCA mutations have more children, shorter birth intervals, a later end to child-bearing, and "excess post-reproductive mortality risks".<br /><br /><a href="http://rspb.royalsocietypublishing.org/content/early/2011/10/06/rspb.2011.1697.abstract?papetoc"><span style="font-weight: bold;">Effects of BRCA1 and BRCA2 mutations on female fertility</span></a><br />Ken R. Smith, Heidi A. Hanson, Geraldine P. Mineau, and Saundra S. Buys <span style="font-weight: bold; color: rgb(102, 102, 102);"><br /></span><cite><abbr title="Proceedings of the Royal Society B: Biological Sciences" class="slug-jnl-abbrev"><span style="font-weight: bold;">Proc. R. Soc. B</span> </abbr></cite><span class="slug-metadata-note ahead-of-print">Published online before print <span class="slug-ahead-of-print-date">October 12, 2011</span></span><blockquote><span style="font-weight: bold; color: rgb(102, 102, 102);">Abstract </span><br /><span style="color: rgb(102, 102, 102);">Women with BRCA1/2 mutations have a significantly higher lifetime risk of developing breast or ovarian cancer. We suggest that female mutation carriers may have improved fitness owing to enhanced fertility relative to non-carriers. Here we show that women who are carriers of BRCA1/2 mutations living in natural fertility conditions have excess fertility as well as excess post-reproductive mortality in relation to controls. Individuals who tested positive for BRCA1/2 mutations who linked into multi-generational pedigrees within the Utah Population Database were used to identify putative obligate carriers. We find that women born before 1930 who are mutation carriers have significantly more children than controls and have excess post-reproductive mortality risks. They also have shorter birth intervals and end child-bearing later than controls. For contemporary women tested directly for BRCA1/2 mutations, an era when modern contraceptives are available, differences in fertility and mortality persist but are attenuated. Our findings suggest the need to re-examine the wider role played by BRCA1/2 mutations. Elevated fertility of female mutation carriers indicates that they are more fecund despite their elevated post-reproductive mortality risks. </span></blockquote><span style="color: rgb(102, 102, 102);"></span>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com9tag:blogger.com,1999:blog-23084925.post-533532124735041502011-10-20T09:35:00.003-06:002011-10-20T09:41:30.167-06:00Taino and African ancestry in Puerto RicansHere's a news story about a talk given at the latest ASHG/ICHG meeting. Bustamante et al. have been looking at admixture among Puerto Ricans (apparently the latest addition to the 1000 Genomes project), and specifically looking at the lengths of DNA segments belonging to different groups in order to infer the temporal and geographic patterns of historical admixture.<br /><a href="http://www.nature.com/news/2011/111014/full/news.2011.592.html?WT.ec_id=NEWS-20111018"><span style="font-weight: bold;">Rebuilding the genome of a hidden ethnicity</span></a><h1 class="heading entry-title"></h1>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com1tag:blogger.com,1999:blog-23084925.post-55677916728269119722011-06-16T05:53:00.000-06:002011-06-16T08:20:36.780-06:00Persistence hunting - is it really possible?<a href="http://johnhawks.net/node/15462">Here's an interesting post from John Hawks' blog</a> about a magazine article about running, evolution (and hunting?) enthusiasts who try to see how hard it would be to track a pronghorn in New Mexico.<br />Apparently they failed. I'm still not convinced that this really debunks the theory that this type of hunting is possible or was important in our evolutionary history, but pretty cool to see people trying it...sounds like fun!Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com4tag:blogger.com,1999:blog-23084925.post-46248119497652989372011-02-22T07:22:00.000-07:002011-02-22T08:23:56.341-07:00Scientists like to "fondle their problems"I thought this was a funny quote from an interesting article in Nature discussing the fact, that despite the identification of many disease-relevant proteins, "75<span class="mb">%</span> of protein research still focuses on the 10<span class="mb">%</span> of proteins that were known before the genome was mapped".<br /><br />This is actually probably mostly driven by the conservative nature of funding sources.<br />From the authors:<br /><blockquote style="color: rgb(102, 102, 102);">Granting systems must be more daring, institutions must foster and reward risk, and the entire biomedical community must play down the legacy of the literature and let new evidence guide research. Genome-wide tools such as the DNA microarrays used in association studies have allowed geneticists to ignore preconceived ideas about disease mechanisms and pursue a remarkably successful broad-brush approach; this approach should be embraced more generally.</blockquote><h1 class="article-heading"></h1><a href="http://www.nature.com/nature/journal/v470/n7333/full/470163a.html"><span style="font-weight: bold;">Too many roads not taken</span></a> <br />Aled M. Edwards, Ruth Isserlin, Gary D. Bader, Stephen V. Frye, Timothy M. Willson & Frank H. Yu<br /><span style="font-weight: bold;">Nature</span> Volume: 470, Pages:163–165<dl class="citation"><dd></dd></dl>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com3tag:blogger.com,1999:blog-23084925.post-82893699127422379482011-02-20T12:47:00.003-07:002011-02-20T13:01:16.482-07:00Wolpoff interviewed by RazibHere's a very interesting video of a discussion between Razib Khan and Milford Wolpoff.<br />They cover a pretty wide range of topics, but mostly centered on the multiregional model of human evolution, with some discussion about the "sociology of science" weaved in throughout.<br /><br /><embed type="application/x-shockwave-flash" src="http://static.bloggingheads.tv/ramon/_live/players/player_v5.2-licensed.swf" flashvars="diavlogid=34366&file=http://bloggingheads.tv/diavlogs/liveplayer-playlist-ramon/34366/00:00/63:05&config=http://static.bloggingheads.tv/ramon/_live/files/offsite_config.xml&topics=false" allowscriptaccess="always" id="bhtv34366" name="bhtv34366" width="380" height="288"></embed>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com1tag:blogger.com,1999:blog-23084925.post-70935889699710604212011-01-27T08:40:00.002-07:002011-01-27T11:47:22.894-07:00Jared Diamond on type-2 diabetes in IndiaThe latest issue of Nature has a piece by Jared Diamond about the diabetes epidemic in India, and how some aspects of its pathology are unique among Indians as compared to other groups.<br /> <div class="top-links"> <p class="article-type"><span class="journal-title"></span></p></div><a href="http://www.nature.com/nature/journal/v469/n7331/full/469478a.html"><span style="font-weight: bold;">Medicine: Diabetes in India</span></a> <br />Jared Diamond<br /><span style="font-weight: bold;">Nature</span> Volume: 469, Pages:478–479 : 27 January 2011<br /><br />Some of the more interesting points:<br /><span style="color: rgb(102, 102, 102);"></span><blockquote><span style="color: rgb(102, 102, 102);">In 2010, the average age-adjusted prevalence of diabetes in India was 8</span><span style="color: rgb(102, 102, 102);" class="mb">%</span><span style="color: rgb(102, 102, 102);">, higher than that in most European countries</span></blockquote><blockquote style="color: rgb(102, 102, 102);">In India, as in the West, diabetes is ultimately due to chronically high levels of blood glucose, and some of the clinical consequences are similar. But whereas Westerners think of type 2 diabetes as an adult-onset disease appearing especially after the age of 50, Indians (and Chinese, Japanese and Aboriginal Australians) with diabetes exhibit symptoms at an age one or two decades younger than that. <span style="font-weight: bold;">The age of onset in India has been shifting towards ever-younger people</span> even within the past decade9 — among Indians in their late teens, 'adult-onset' diabetes already manifests itself more often than does 'juvenile-onset' diabetes. <span style="font-weight: bold;">In Britain, the prevalence of type 2 diabetes is 14 times higher in Asian than European children</span>. And although obesity is a risk factor for diabetes both in India and in the West, <span style="font-weight: bold;">the disease appears at a lower threshold of obesity in India</span>, as is also the case in China, Japan and other Asian countries.<br /><br /><span style="font-weight: bold;">Symptoms also differ between Indians and Westerners</span>: Indians with diabetes are less likely to develop blindness and kidney disease, but much more likely to suffer coronary artery disease at a relatively young age<br /></blockquote>He stresses the difference in prevalence between rich and poor Indians, and discusses how these differences are the opposite of what we observe in the US and Europe, for example, where socio-economic status is positively correlated with health.<br />Given <a href="http://www.nature.com/nature/journal/v423/n6940/full/423599a.html">Jared Diamond's past speculation</a> on the evolutionary and/or genetic causes of these types of epidemics, I thought he might have expounded on that, <a href="http://ije.oxfordjournals.org/content/36/1/226.full">as others have</a>, but alas, he didn't.Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com4tag:blogger.com,1999:blog-23084925.post-41522817436553684602011-01-20T14:14:00.001-07:002011-01-20T14:14:00.101-07:00Selection can increase genetic diversity - the example of Somali camel herders<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://1.bp.blogspot.com/_dRj9DN75euI/TTieIRKpJFI/AAAAAAAAB1Q/av_HXNgl3UM/s1600/somalia-239.jpg"><img style="float: right; margin: 0pt 0pt 10px 10px; cursor: pointer; width: 200px; height: 150px;" src="http://1.bp.blogspot.com/_dRj9DN75euI/TTieIRKpJFI/AAAAAAAAB1Q/av_HXNgl3UM/s200/somalia-239.jpg" alt="" id="BLOGGER_PHOTO_ID_5564371204500431954" border="0" /></a>The interesting finding here is that diversity in the LCT/MCM6 region is increased rather than reduced among those who are lactose tolerant compared to those who are lactose intolerant. Unlike in Europe where a single mutation swept through much of the population, among this East African population, there are several mutations that arose on different haplotype backgrounds that have a similar phenotypic effect. The result is that genetic diversity in this genomic region is increased. The authors have a pretty good discussion about the possible reasons for the patterns they observe.<br />These types of examples, albeit simplistic compared to other traits, are great for our basic understanding of the genetic basis of complex traits, and for our understanding of the genetic avenues leading to adaptation.<br /><br /><a href="http://www.ncbi.nlm.nih.gov/pubmed/19937006?dopt=Abstract"><span style="font-weight: bold;">Multiple rare variants as a cause of a common phenotype: several different lactase persistence associated alleles in a single ethnic group.</span></a><br />Ingram CJ, Raga TO, Tarekegn A, Browning SL, Elamin MF, Bekele E, Thomas MG, Weale ME, Bradman N, Swallow DM.<span style="font-weight: bold;"></span><br /><a style="font-weight: bold;" title="Journal of molecular evolution.">J Mol Evol.</a> 2009 Dec;69(6):579-88.<br /><blockquote style="color: rgb(102, 102, 102);"><span style="font-weight: bold;">Abstract:</span>Persistence of intestinal lactase into adulthood allows humans to use milk from other mammals as a source of food and water. This genetic trait has arisen by convergent evolution and the derived alleles of at least three different single nucleotide polymorphisms (-13910C>T, -13915T>G, -14010G>C) are associated with lactase persistence in different populations. Each allele occurs on an extended haplotype, consistent with positive directional selection. The SNPs are located in an 'enhancer' sequence in an intron of a neighboring gene (MCM6) and modulate lactase transcription in vitro. However, a number of lactase persistent individuals carry none of these alleles, but other low-frequency single nucleotide polymorphisms have been observed in the same region. Here we examine a cohort of 107 milk-drinking Somali camel-herders from Ethiopia. Eight polymorphic sites are identified in the enhancer. -13915*G and -13907*G (a previously reported candidate) are each significantly associated with lactase persistence. A new allele, -14009*G, has borderline association with lactase persistence, but loses significance after correction for multiple testing. Sequence diversity of the enhancer is significantly higher in the lactase persistent members of this and a second cohort compared with non-persistent members of the two groups (P = 7.7 x 10(-9) and 1.0 x 10(-3)). By comparing other loci, we show that this difference is not due to population sub-structure, demonstrating that increased diversity can accompany selection. This contrasts with the well-documented observation that positive selection decreases diversity by driving up the frequency of a single advantageous allele, and has implications for association studies.</blockquote>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com5tag:blogger.com,1999:blog-23084925.post-2676205118677770682010-10-27T09:06:00.003-06:002010-10-27T14:36:36.143-06:00How/why did selection for lactase persistence occur and spread?Interesting, albeit speculative, hypothesis for the origins of the selective advantage associated with lactase persistence. Basically, looks like there is evidence for increased reliance on milk products and dairy animals at the same time as a sudden cold and dry spell - about 8,000 years ago.<br /><a href="http://www.sciencemag.org/cgi/content/summary/329/5998/1465?sa_campaign=Email/toc/17-September-2010/10.1126/science.329.5998.1465">Link to new story in Science</a><br /><br />...on a related note, see a post by <a href="http://blogs.discovermagazine.com/gnxp/2010/10/volkerwanderung-back-with-a-vengeance/">Razib pointing</a> to a story about "<a href="http://www.spiegel.de/international/zeitgeist/0,1518,723310,00.html">How Middle Eastern Milk Drinkers Conquered Europe</a>".Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com3tag:blogger.com,1999:blog-23084925.post-70105908584475857932010-10-16T07:36:00.000-06:002010-10-16T09:25:43.800-06:00Selection in fruitflies - what kind of genomic signatures does it leave?<h1 class="article-heading"></h1>We are pretty confident that we know what signatures of selection look like for some loci in humans (skin color, lactase etc...) but how about less clear-cut/subtle cases which may represent the majority of cases? This experiment gives us some much needed insight into what signatures of selection we might expect for most instances of natural selection<span style="font-weight: bold;">.</span><span style="font-weight: bold;"><br /><br /><a href="http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature09352.html">Genome-wide analysis of a long-term evolution experiment with Drosophila </a></span><br />Molly K. Burke, Joseph P. Dunham, Parvin Shahrestani, Kevin R. Thornton, Michael R. Rose & Anthony D. Long<br /><span style="font-weight: bold;">Nature </span>2010<br /><span style="font-weight: bold;"></span><blockquote style="color: rgb(51, 51, 51);"><span style="font-weight: bold;">Abstract:</span> Experimental evolution systems allow the genomic study of adaptation, and so far this has been done primarily in asexual systems with small genomes, such as bacteria and yeast. Here we present whole-genome resequencing data from Drosophila melanogaster populations that have experienced over 600 generations of laboratory selection for accelerated development. Flies in these selected populations develop from egg to adult ~20% faster than flies of ancestral control populations, and have evolved a number of other correlated phenotypes. On the basis of 688,520 intermediate-frequency, high-quality single nucleotide polymorphisms, we identify several dozen genomic regions that show strong allele frequency differentiation between a pooled sample of five replicate populations selected for accelerated development and pooled controls. On the basis of resequencing data from a single replicate population with accelerated development, as well as single nucleotide polymorphism data from individual flies from each replicate population, we infer little allele frequency differentiation between replicate populations within a selection treatment. Signatures of selection are qualitatively different than what has been observed in asexual species; in our sexual populations, adaptation is not associated with ‘classic’ sweeps whereby newly arising, unconditionally advantageous mutations become fixed. More parsimonious explanations include ‘incomplete’ sweep models, in which mutations have not had enough time to fix, and ‘soft’ sweep models, in which selection acts on pre-existing, common genetic variants. We conclude that, at least for life history characters such as development time, unconditionally advantageous alleles rarely arise, are associated with small net fitness gains or cannot fix because selection coefficients change over time.<br /></blockquote>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com1tag:blogger.com,1999:blog-23084925.post-71032136901140738652010-09-09T08:33:00.006-06:002010-09-10T16:54:06.727-06:00More loci to explain eye color variation, but still not great prediction<p class="citation"></p><h1 class="title"></h1>Here they do a GWAS for a continuous/refined eye phenotype based on hue and saturation. The authors find three new loci in addition to the other known loci, and are able to explain 50% of the variance in an independent (I think) sample of Dutch individuals. HERC2 alone explains 45% or so of the variance.<br /><br />Regarding prediction of eye color categories:<br /><blockquote style="color: rgb(102, 102, 102);">The accuracy in predicting 3-category eye color was 0.92 for blue, 0.74 for intermediate, and 0.93 for brown,...<br /></blockquote>There is some discussion about the limited quality of the photos due in part to the un-standardized lighting conditions.<br />I wonder how much better prediction would have been in a more diverse sample.<br /><br /><a href="http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000934"><span style="font-weight: bold;">Digital quantification of human eye color highlights genetic association of three new loci.</span></a><br />Liu F, Wollstein A, Hysi PG, Ankra-Badu GA, Spector TD, Park D, Zhu G, Larsson M, Duffy DL, Montgomery GW, Mackey DA, Walsh S, Lao O, Hofman A, Rivadeneira F, Vingerling JR, Uitterlinden AG, Martin NG, Hammond CJ, Kayser M.<br /><br /><span style="font-weight: bold;">PLoS Genetics</span> 2010 May 6;6:e1000934.<br /><span style="font-weight: bold; color: rgb(102, 102, 102);"></span><blockquote><span style="font-weight: bold; color: rgb(102, 102, 102);">Abstract: </span><span style="color: rgb(102, 102, 102);">Previous studies have successfully identified genetic variants in several genes associated with human iris (eye) color; however, they all used simplified categorical trait information. Here, we quantified continuous eye color variation into hue and saturation values using high-resolution digital full-eye photographs and conducted a genome-wide association study on 5,951 Dutch Europeans from the Rotterdam Study. Three new regions, 1q42.3, 17q25.3, and 21q22.13, were highlighted meeting the criterion for genome-wide statistically significant association. The latter two loci were replicated in 2,261 individuals from the UK and in 1,282 from Australia. The </span><i style="color: rgb(102, 102, 102);">LYST</i><span style="color: rgb(102, 102, 102);"> gene at 1q42.3 and the </span><i style="color: rgb(102, 102, 102);">DSCR9</i><span style="color: rgb(102, 102, 102);"> gene at 21q22.13 serve as promising functional candidates. A model for predicting quantitative eye colors explained over 50% of trait variance in the Rotterdam Study. Over all our data exemplify that fine phenotyping is a useful strategy for finding genes involved in human complex traits.</span></blockquote><br /><p class="auth_list"></p>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com2tag:blogger.com,1999:blog-23084925.post-30283541786947440572010-04-26T08:04:00.005-06:002010-04-26T18:59:42.828-06:00Diet, disease, and pigment variation in humansSome interesting hypotheses about the relationships between skin pigmentation, vitamin D, and immune response in Europe.<br /><br /><a href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WN2-4YWS6F4-2&_user=446477&_coverDate=04%2F20%2F2010&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000020378&_version=1&_urlVersion=0&_userid=446477&md5=069a475eb0fc9e7f6c115c75b0485255"><span style="font-weight: bold;">Diet, disease and pigment variation in humans.</span></a><br /><span style="font-weight: bold;">Med Hypotheses. </span>2010 Apr 19. [Epub ahead of print]<br /><span style="font-weight: bold;"></span><blockquote style="color: rgb(51, 51, 51);"><span style="font-weight: bold;">Abstract</span>: There are several hypotheses which explain the de-pigmentation of humans. The most prominent environmental explanation is that reduced endogenous vitamin D production due to diminished radiation at higher latitudes had a deleterious impact on fitness. This drove de-pigmentation as an adaptive response. A model of natural selection explains the high correlations found between low vitamin D levels and ill health, as vitamin D's role in immune response has clear evolutionary implications. But recent genomic techniques have highlighted the likelihood that extreme de-pigmentation in Eurasia is a feature of the last 10,000years, not the Upper Pleistocene, when modern humans first settled northern Eurasia. Additionally the data imply two independent selection events in eastern and western Eurasia. Therefore new parameters must be added to the model of natural selection so as to explain the relatively recent and parallel adaptive responses. I propose a model of gene-culture co-evolution whereby the spread of agriculture both reduced dietary vitamin D sources and led to more powerful selection on immune response because of the rise of infectious diseases with greater population densities. This model explains the persistence of relatively dark-skinned peoples at relatively high latitudes and the existence of relatively light-skinned populations at low latitudes. It also reinforces the importance of vitamin D as a micronutrient because of the evidence of extremely powerful fitness implications in the recent human past of pigmentation. Copyright © 2010. Published by Elsevier Ltd.</blockquote><div class="abstract_text"><p></p></div>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com9tag:blogger.com,1999:blog-23084925.post-663000002520016852010-03-11T08:39:00.000-07:002010-03-11T08:41:41.412-07:00Does Usain Bolt lack the ACTN3 R577X polymorphism?<div class="fulltext-TITLE"><span class="fulltext-IT">...that's the question that pops into my mind after reading the title and abstract. I wonder if they genotyped the elite of the elite (Bolt, Powell) or just the "elite"? It looks like they did:<br /></span><blockquote style="color: rgb(51, 51, 51);">Forty-six of these international athletes had won medals at major international competition or held sprint world records. </blockquote><span class="fulltext-IT">Nevertheless, <a href="http://yannklimentidis.blogspot.com/2007/11/actn3-in-west-vs-east-african-athletes.html">another negative finding</a> on the association between the ACTN3 fast twitch muscle fiber, "sprint" genotype and sprint phenotypes.</span><span class="fulltext-IT"> In fact, two of the elite-elite Jamaican sprinters were homozygous for the slow-twitch variant! They acknowledge that the power to detect a difference here is pretty low because of the very low frequency of the ACTN3 R5777X polymorphism in West Africans.</span><span class="fulltext-IT">.. so much for<a href="http://yannklimentidis.blogspot.com/2008/11/ny-times-article-on-testing-kids-for.html"> personalized prediction of sports ability</a></span>, at least for now.<span class="fulltext-IT"> I say just look at your big toe... does it extend out farther than your second toe? if so, you could probably be pretty fast.<br />Given these results, Usain probably does lack the ACTN3 polymorphism, but on the other hand, he could be the one of the two out of the 46 elite-elite sprinters who is homozygous for it.<br /><br />P.S. - gotta love the senior author's name!<br /><br /></span></div><span style="font-weight: bold;"></span><a href="http://www.ncbi.nlm.nih.gov/pubmed/20010124?dopt=Abstract"><span style="font-weight: bold;">ACTN3 and ACE Genotypes in Elite Jamaican and US Sprinters</span></a><br />SCOTT, ROBERT A; IRVING, RACHAEL; IRWIN, LAURA; MORRISON, ERROL; CHARLTON, VILMA; AUSTIN, KRISTA; TLADI, DAWN; DEASON, MICHAEL; HEADLEY, SAMUEL A.; KOLKHORST, FRED W.; YANG, NAN; NORTH, KATHRYN; PITSILADIS, YANNIS P.<br /><span style="font-weight: bold;"></span><blockquote style="color: rgb(51, 51, 51);"><span style="font-weight: bold;">ABSTRACT</span> The angiotensin-converting enzyme (ACE) and the [alpha]-actinin-3 (ACTN3) genes are two of the most studied "performance genes" and both have been associated with sprint/power phenotypes and elite performance. Purpose: To investigate the association between the ACE and the ACTN3 genotypes and sprint athlete status in elite Jamaican and US African American sprinters. Methods: The ACTN3 R577X and the ACE I/D and A22982G (rs4363) genotype distributions of elite Jamaican (J-A; N = 116) and US sprinters (US-A; N = 114) were compared with controls from the Jamaican (J-C; N = 311) and US African American (US-C; N = 191) populations. Frequency differences between groups were assessed by exact test. Results: For ACTN3, the XX genotype was found to be at very low frequency in both athlete and control cohorts (J-C = 2%, J-A = 3%, US-C = 4%, US-A = 2%). Athletes did not differ from controls in ACTN3 genotype distribution (J, P = 0.87; US, P = 0.58). Similarly, neither US nor Jamaican athletes differed from controls in genotype at ACE I/D (J, P = 0.44; US, P = 0.37). Jamaican athletes did not differ from controls for A22982G genotype (P = 0.28), although US sprinters did (P = 0.029), displaying an excess of heterozygotes relative to controls but no excess of GG homozygotes (US-C = 22%, US-A = 18%). Conclusions: Given that ACTN3 XX genotype is negatively associated with elite sprint athlete status, the underlying low frequency in these populations eliminates the possibility of replicating this association in Jamaican and US African American sprinters. The finding of no excess in ACE DD or GG genotypes in elite sprint athletes relative to controls suggests that ACE genotype is not a determinant of elite sprint athlete status.<table id="fulltext-body"><tbody><tr><td class="fulltext-body-paragraph"><p class="fulltext-ABSTRACT fulltext-INDENT"></p></td></tr></tbody></table></blockquote><table id="fulltext-body"><tbody><tr></tr></tbody></table>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com7tag:blogger.com,1999:blog-23084925.post-11053632170536897002010-03-11T05:11:00.002-07:002011-02-20T13:05:04.566-07:00More than one molecular way to adaptively change a phenotype<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://4.bp.blogspot.com/_dRj9DN75euI/S5hbfWNcE6I/AAAAAAAABqk/5__0J4uI19M/s1600-h/white-sands-lizard.jpg"><img style="margin: 0pt 0pt 10px 10px; float: right; cursor: pointer; width: 320px; height: 213px;" src="http://4.bp.blogspot.com/_dRj9DN75euI/S5hbfWNcE6I/AAAAAAAABqk/5__0J4uI19M/s320/white-sands-lizard.jpg" alt="" id="BLOGGER_PHOTO_ID_5447204343400633250" border="0" /></a>The authors report on their finding of different mutations in the same gene MC1R affecting different molecular pathways on the way to lighter pigmentation in lizards. There are several likely examples of molecularly divergent phenotypic convergence in humans, some of which may originate in the same gene: MC1R - skin color in Europeans and E. Asians, LCT - lactase persistence in Europe, Middle East, and E. Africa, and probably, adaptation to high altitude in E. Africa, Andes, and Himalayas.<br /><br />The cool thing about this paper is that they use cell culture to find that even though the mutations are in the same gene, they result in lighter pigmentation through different molecular pathways.<br /><br /><a href="http://www.pnas.org/content/107/5/2113.abstract"><span style="font-weight: bold;">Molecular and functional basis of phenotypic convergence in white lizards at White Sands </span></a><br />Erica Bree Rosenblum, Holger Römpler, Torsten Schöneberg, and Hopi E. Hoekstra<br /><span style="font-weight: bold;">PNAS</span> February 2, 2010 vol. 107 no. 5 2113-2117 <cite><span class="slug-pages"></span></cite><span style="font-weight: bold;"></span><blockquote style="color: rgb(51, 51, 51);"><span style="font-weight: bold;">Abstract:</span> There are many striking examples of phenotypic convergence in nature, in some cases associated with changes in the same genes. But even mutations in the same gene may have different biochemical properties and thus different evolutionary consequences. Here we dissect the molecular mechanism of convergent evolution in three lizard species with blanched coloration on the gypsum dunes of White Sands, New Mexico. These White Sands forms have rapidly evolved cryptic coloration in the last few thousand years, presumably to avoid predation. We use cell-based assays to demonstrate that independent mutations in the same gene underlie the convergent blanched phenotypes in two of the three species. Although the same gene contributes to light phenotypes in these White Sands populations, the specific molecular mechanisms leading to reduced melanin production are different. In one case, mutations affect receptor signaling and in the other, the ability of the receptor to integrate into the melanocyte membrane. These functional differences have important ramifications at the organismal level. Derived alleles in the two species show opposite dominance patterns, which in turn affect their visibility to selection and the spatial distribution of alleles across habitats. Our results demonstrate that even when the same gene is responsible for phenotypic convergence, differences in molecular mechanism can have dramatic consequences on trait expression and ultimately the adaptive trajectory. </blockquote><div class="section abstract" id="abstract-1"><p id="p-3"></p> </div>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com2tag:blogger.com,1999:blog-23084925.post-67341223473891269062010-03-02T20:45:00.000-07:002010-03-02T21:46:50.605-07:00Chinese prefer darker-skinned pigs and MC1R tells part of the story<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://4.bp.blogspot.com/_dRj9DN75euI/S43l0QvbHrI/AAAAAAAABl0/YlGIF-m2Yog/s1600-h/pig.jpg"><img style="margin: 0pt 0pt 10px 10px; float: right; cursor: pointer; width: 320px; height: 218px;" src="http://4.bp.blogspot.com/_dRj9DN75euI/S43l0QvbHrI/AAAAAAAABl0/YlGIF-m2Yog/s320/pig.jpg" alt="" id="BLOGGER_PHOTO_ID_5444260210570632882" border="0" /></a>I'm not yet able to get full text access to this paper, but after looking into the related literature, I was suprised to see that there is quite a lot out there. Given that variation in MC1R was selected upon to lighten skin in Europeans, I was somewhat surprised to see the opposite happen in pigs.<br />Spaniards also <a href="http://en.wikipedia.org/wiki/Jam%C3%B3n_ib%C3%A9rico">like black pigs</a>.<br />By the way, I'm not too fond of the term "artificial" in this type of context.<br /><br /><span style="font-weight: bold;"><a href="http://www.nature.com/hdy/journal/vaop/ncurrent/abs/hdy2009191a.html">Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication.</a></span><br />Li J, Yang H, Li JR, Li HP, Ning T, Pan XR, Shi P, Zhang YP<br /><span style="font-weight: bold;">Heredity.</span> 2010 Feb 24. [Epub ahead of print]<br /><span style="font-weight: bold; color: rgb(51, 51, 51);"></span><blockquote><span style="font-weight: bold; color: rgb(51, 51, 51);">Abstract:</span><span style="color: rgb(51, 51, 51);"> Black coat colour is common in Chinese indigenous domestic pigs, but not among their wild ancestors, and it is thus presumed to be a 'domestication trait.' To determine whether artificial interference contributes to morphological diversification, we examined nucleotide variation from 157 Chinese domestic pigs and 40 wild boars in the melanocortin receptor 1 (MC1R) gene, which has a key role in the coat pigmentation of Sus scrofa. Compared with a pseudogene GPIP, our results showed that the joint effects of demography and selection have resulted in markedly low genetic diversity of MC1R in Chinese domestic pigs. Coalescent simulation and selection tests further suggest that the fixation of two non-synonymous substitutions associated with black colour is the result of artificial selection. In contrast, a much higher genetic diversity and only a single non-synonymous substitution were found among the wild boars, suggesting a strong functional constraint. Moreover, our conclusion is consistent with the preference for black colour in the ancient Chinese sacrificial culture. This case provides an interesting example of a molecular evaluation of artificial livestock selection and its associated cultural impact in ancient China.</span></blockquote><span style="color: rgb(51, 51, 51);"></span>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com2tag:blogger.com,1999:blog-23084925.post-69746347472020341292010-02-28T05:57:00.001-07:002011-08-09T14:02:14.694-06:00Predicting hair, eye, and skin color from a small set of SNPs<h1 class="title"></h1>They examined the association between 75 SNPs in 24 genes and skin, eye and hair color among 789 people of various ethnic backgrounds. Since this is for forensic purposes, they were looking for a small set of SNP markers (i.e. 3) that could reliably predict these pigmentation phenotypes, independent of ethnic origin.<span style="font-weight: bold;"> </span>Their sample consisted mostly of individuals of European descent<span style="font-weight: bold;">, </span>but a decent number of several other ethnic groups<span style="font-weight: bold;">.
<br />
<br />Hair color:</span>
<br />SLC45A2, SLC24A5 and MC1R - R squared: 76.3% (one SNP per gene listed)
<br /><span style="font-weight: bold;">Skin color:</span>
<br />SLC24A5, SLC45A2, ASIP - R squared: 45.7% ... interaction term of ASIP and SLC45A2 increased r-squared to 49.6% (one SNP per gene listed)
<br /><span style="font-weight: bold;">Eye color:</span>
<br />HERC2, SLC24A5, SLC25A2 - R squared: 76.4%... (HERC2 appears to be doing the vast majority of the explaining)
<br />
<br />The obvious remaining question from all this is how high does the proportion of variance explained go if you use information from all markers together. Anyway, it appears that, as they mention, five SNPs in five genes account for much of the variation.
<br />Given that most subjects were Eur, it would have been nice to see the extent to which they were driving the results, by for example, doing the same analysis only on them. In other words how different would the results be if most subjects were African or Native American etc...?
<br />I did not know that HERC2 is adjacent (5' side) to OCA2, and contains a promoter region for OCA2.
<br />
<br /><a href="http://www3.interscience.wiley.com/journal/123279996/abstract"><span style="font-weight: bold;">Predicting Phenotype from Genotype: Normal Pigmentation</span></a>
<br />Valenzuela RK, Henderson MS, Walsh MH, Garrison NA, Kelch JT, Cohen-Barak O, Erickson DT, John Meaney F, Bruce Walsh J, Cheng KC, Ito S, Wakamatsu K, Frudakis T, Thomas M, Brilliant MH.
<br /><a href="javascript:AL_get(this,%20'jour',%20'J%20Forensic%20Sci.');" title="Journal of forensic sciences."></a><span style="font-weight: bold;">J Forensic Sci.</span> 2010 Feb 11. [Epub ahead of print]
<br /><p class="aff"></p><div class="abstract_text"><p><span style="font-weight: bold;"></span></p><blockquote style="color: rgb(51, 51, 51);"><span style="font-weight: bold;">Abstract:</span>Genetic information in forensic studies is largely limited to CODIS data and the ability to match samples and assign them to an individual. However, there are circumstances, in which a given DNA sample does not match anyone in the CODIS database, and no other information about the donor is available. In this study, we determined 75 SNPs in 24 genes (previously implicated in human or animal pigmentation studies) for the analysis of single- and multi-locus associations with hair, skin, and eye color in 789 individuals of various ethnic backgrounds. Using multiple linear regression modeling, five SNPs in five genes were found to account for large proportions of pigmentation variation in hair, skin, and eyes in our across-population analyses. Thus, these models may be of predictive value to determine an individual's pigmentation type from a forensic sample, independent of ethnic origin.</blockquote><p></p></div>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com3tag:blogger.com,1999:blog-23084925.post-29509344328242015602010-02-15T11:49:00.005-07:002010-02-15T18:33:12.602-07:00Predicting lactase persistence from genetic data ... not yet!<p class="citation"><a href="javascript:AL_get(this,%20'jour',%20'BMC%20Evol%20Biol.');" title="BMC evolutionary biology."></a></p>...especially in Africa, SE Europe, and parts of Asia.<span style="font-weight: bold;"><br /></span>It seems like their genetic information consists of the four SNPs that are so far known to be associated with lactase persistence. <span style="font-weight: bold;"><br /><br /><a href="http://www.ncbi.nlm.nih.gov/pubmed/20144208?dopt=Abstract">A worldwide correlation of lactase persistence phenotype and genotypes</a></span><br />Itan Y, Jones BL, Ingram CJ, Swallow DM, Thomas MG<br /><span style="font-weight: bold;">BMC Evol Biol.</span> 2010 Feb 9;10(1):36. [Epub ahead of print]<br /><blockquote style="color: rgb(51, 51, 51);"><span style="font-weight: bold;">ABSTRACT:</span> BACKGROUND: The ability of adult humans to digest the milk sugar lactose - lactase persistence - is a dominant Mendelian trait that has been a subject of extensive genetic, medical and evolutionary research. Lactase persistence is common in people of European ancestry as well as some African, Middle Eastern and Southern Asian groups, but is rare or absent elsewhere in the world. The recent identification of independent nucleotide changes that are strongly associated with lactase persistence in different populations worldwide has led to the possibility of genetic tests for the trait. However, it is highly unlikely that all lactase persistence-associated variants are known. Using an extensive database of lactase persistence phenotype frequencies, together with information on how those data were collected and data on the frequencies of lactase persistence variants, we present a global summary of the extent to which current genetic knowledge can explain lactase persistence phenotype frequency. RESULTS: We used surface interpolation of Old World lactase persistence genotype and phenotype frequency estimates obtained from all available literature and perform a comparison between predicted and observed trait frequencies in continuous space. By accommodating additional data on sample numbers and known false negative and false positive rates for the various lactase persistence phenotype tests (blood glucose and breath hydrogen), we also apply a Monte Carlo method to estimate the probability that known lactase persistence-associated allele frequencies can explain observed trait frequencies in different regions. CONCLUSION: Lactase persistence genotype data is currently insufficient to explain lactase persistence phenotype frequency in much of western and southern Africa, southeastern Europe, the Middle East and parts of central and southern Asia. We suggest that further studies of genetic variation in these regions should reveal additional nucleotide variants that are associated with lactase persistence.</blockquote><div class="abstract_text"><p></p></div>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com4tag:blogger.com,1999:blog-23084925.post-58774843022820446482010-01-24T14:00:00.001-07:002010-01-24T15:29:22.040-07:00Signatures of selection in dog breeds<h1 id="article-title-1"></h1>10 breeds, 21,000 SNPs, breed-specific Fst.<br /><br />Their most notable hits:<br />HMGA2 and IGF1R (size)<br />SILV, MITF (coat color and texture)<br />CDH9, DRD5, HTR2A (behavior)<br />SOX9 (skeletal morphology)<br />FTO, SLC2A9, SLC5A2 (physiology)<br /><br />Unfortunately they only use Fst to detect evidence of selection. It would have been interesting to try out some haplotype or other tests of selection, but they were probably constrained by the total number of SNPs they had.<br /><br />Most interestingly:<br /><blockquote style="color: rgb(51, 51, 51);">Similar to analyses of selection in natural populations (23), we find that genes involved in immunity and defense are also significantly overrepresented in the 155 candidate selection<br />regions. This is somewhat surprising, as natural and artificial selection would not necessarily be expected a priori to act on similar classes of genes, and suggests that immune related genes are pervasive targets of selection because of their critical role in pathogen defense or propensity for pleiotropic effects (24).</blockquote>...also:<br /><blockquote style="color: rgb(51, 51, 51);">We note that as an initial foray into comparative selection mapping, of the 1,506 genes located in putatively selected regions in dogs, 169 overlap with genes located in well-supported selected regions in humans (10). Although this result should be interpreted with caution, as the specific targets of selection are generally not known with certainty in either dogs or humans, it does raise the intriguing possibility that recent selection has influenced common loci in both the human and dog lineages.</blockquote><a href="http://www.pnas.org/content/107/3/1160.abstract?etoc"><span style="font-weight: bold;">Tracking footprints of artificial selection in the dog genome</span></a><br />Joshua M. Akey, Alison L. Ruhe, Dayna T. Akey, Aaron K. Wong, Caitlin F. Connelly, Jennifer Madeoy, Thomas J. Nicholas, and Mark W. Neff<br /><span style="font-weight: bold;">PNAS</span> January 19, 2010 vol. 107 no. 3 1160-1165<br /><span style="font-weight: bold;"></span><blockquote style="color: rgb(51, 51, 51);"><span style="font-weight: bold;">Abstract</span>: The size, shape, and behavior of the modern domesticated dog has been sculpted by artificial selection for at least 14,000 years. The genetic substrates of selective breeding, however, remain largely unknown. Here, we describe a genome-wide scan for selection in 275 dogs from 10 phenotypically diverse breeds that were genotyped for over 21,000 autosomal SNPs. We identified 155 genomic regions that possess strong signatures of recent selection and contain candidate genes for phenotypes that vary most conspicuously among breeds, including size, coat color and texture, behavior, skeletal morphology, and physiology. In addition, we demonstrate a significant association between HAS2 and skin wrinkling in the Shar-Pei, and provide evidence that regulatory evolution has played a prominent role in the phenotypic diversification of modern dog breeds. Our results provide a first-generation map of selection in the dog, illustrate how such maps can rapidly inform the genetic basis of canine phenotypic variation, and provide a framework for delineating the mechanistic basis of how artificial selection promotes rapid and pronounced phenotypic evolution. </blockquote><div class="section abstract" id="abstract-1"><p id="p-4"></p> </div>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com2tag:blogger.com,1999:blog-23084925.post-77000013287117333002010-01-19T12:30:00.007-07:002010-01-19T14:19:18.529-07:00More on the genetics of European farmers vs. hunter-gatherersContinuing on the theme from the last post, here is a paper that just came out in PLoS Biology. It seems to come to the same conclusion as the <a href="http://yannklimentidis.blogspot.com/2010/01/genetics-of-hunter-gatherers-and-early.html">Science one that used ancient mtDNA</a>...sort of. The results conflict since the Bramanti one finds discontinuity in mtDNA lineages, while this paper doesn't. So the Bramanti paper finds little evidence for continuity in mtDNA lineages, while this one finds that there is some continuity in mtDNA lineages, at least compared to the Y-chromosome. The two papers use different sources of data and different methods, which could somehow explain the discrepancy.<br />Razib's already <a href="http://scienceblogs.com/gnxp/2010/01/european_man_the_farmer.php#more">all over</a> this.<br /><br /><span style="font-weight: bold;"></span><a href="http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000285"><span style="font-weight: bold;">A Predominantly Neolithic Origin for European Paternal Lineages</span></a><br />Patricia Balaresque, Georgina R. Bowden, Susan M. Adams, Ho-Yee Leung, Turi E. King, Zoë H. Rosser, Jane Goodwin, Jean-Paul Moisan, Christelle Richard, Ann Millward, Andrew G. Demaine, Guido Barbujani, Carlo Previderè, Ian J. Wilson, Chris Tyler-Smith, Mark A. Jobling<br /><span style="font-weight: bold;">PLoS Biology</span> 8(1): e1000285. <br /><span style="font-weight: bold;"></span><blockquote style="color: rgb(51, 51, 51);"><span style="font-weight: bold;">Abstract:</span> The relative contributions to modern European populations of Paleolithic hunter-gatherers and Neolithic farmers from the Near East have been intensely debated. Haplogroup R1b1b2 (R-M269) is the commonest European Y-chromosomal lineage, increasing in frequency from east to west, and carried by 110 million European men. Previous studies suggested a Paleolithic origin, but here we show that the geographical distribution of its microsatellite diversity is best explained by spread from a single source in the Near East via Anatolia during the Neolithic. Taken with evidence on the origins of other haplogroups, this indicates that most European Y chromosomes originate in the Neolithic expansion. This reinterpretation makes Europe a prime example of how technological and cultural change is linked with the expansion of a Y-chromosomal lineage, and the contrast of this pattern with that shown by maternally inherited mitochondrial DNA suggests a unique role for males in the transition.</blockquote>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com2tag:blogger.com,1999:blog-23084925.post-86024902600925417322010-01-09T06:09:00.000-07:002010-01-09T08:04:53.893-07:00Genetics of hunter-gatherers and early farmers in EuropeI'm back, and will try to be more regular about posting. This paper came out a few months ago in Science and I've been meaning to look at it for a while.<br />They examine the Fst in mtDNA sequence between hunter-gatherer samples (13,400 to 2,300 ago) in Central Europe, from more recent individuals (and modern Europeans). I guess they must use archaeological or other evidence to determine their subsistence pattern.<br />They get an Fst of 0.163, which is indeed remarkably high - although do we really know what to expect when comparing populations over time? To answer this, they perform some simulations, and reject the hypothesis that this Fst could have been due to a process of population continuity.<br />Along with their discussion of the haplotype differences betwee the hunter-gatherers and farmers, this result is pretty interesting and suggests a migration of early farmers into central Europe and replacement of hunter-gatherers.<br />Proto-Indo-Europeans?<br /><br /><a href="http://www.sciencemag.org/cgi/content/abstract/326/5949/137"><span style="font-weight: bold;">Genetic discontinuity between local hunter-gatherers and central Europe's first farmers.</span></a><br />Bramanti B, Thomas MG, Haak W, Unterlaender M, Jores P, Tambets K, Antanaitis-Jacobs I, Haidle MN, Jankauskas R, Kind CJ, Lueth F, Terberger T, Hiller J, Matsumura S, Forster P, Burger J.<br /><span style="font-weight: bold;">Science</span> 2009 Oct 2;326(5949):137-40.<br /><span style="font-weight: bold;"></span><blockquote style="color: rgb(102, 102, 102);"><span style="font-weight: bold;">Abstract:</span> After the domestication of animals and crops in the Near East some 11,000 years ago, farming had reached much of central Europe by 7500 years before the present. The extent to which these early European farmers were immigrants or descendants of resident hunter-gatherers who had adopted farming has been widely debated. We compared new mitochondrial DNA (mtDNA) sequences from late European hunter-gatherer skeletons with those from early farmers and from modern Europeans. We find large genetic differences between all three groups that cannot be explained by population continuity alone. Most (82%) of the ancient hunter-gatherers share mtDNA types that are relatively rare in central Europeans today. Together, these analyses provide persuasive evidence that the first farmers were not the descendants of local hunter-gatherers but immigrated into central Europe at the onset of the Neolithic.</blockquote>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com8tag:blogger.com,1999:blog-23084925.post-6781642478587341592009-09-14T05:07:00.000-06:002009-09-14T07:16:19.391-06:00Are Uyghurs a recent or ancient population?<h2> </h2>They are basically seeing whether there are many private haplotypes in the Uyghur population compared to East Asian and European populations. They don't find this to be the case, thus suggesting that Uyghurs are the result of a recent admixture process.<br /><br /><a href="http://mbe.oxfordjournals.org/cgi/content/abstract/26/10/2197?etoc"><span style="font-weight: bold;">Haplotype-Sharing Analysis Showing Uyghurs Are Unlikely Genetic Donors </span></a><br />Shuhua Xu, Wenfei Jin and Li Jin<br /><span style=""></span><span style="font-weight: bold;">Molecular Biology and Evolution </span>2009 26(10):2197-2206<br /><blockquote style="color: rgb(51, 51, 51);"><span style="font-weight: bold;">Abstract: </span>The Uyghur (UIG) are a group of people primarily residing in Xinjiang of China, which is geographically located in Central Asia, from where modern humans were presumably spread in all directions reaching Europe, east, and northeast Asia about 40 kya. A recent study suggested that the UIG are ancestry donors of the East Asian (EAS) gene pool. However, an alternative hypothesis, that is, the UIG is an admixture population with both EAS and EUR ancestries is also supported by our previous studies. To test the two competing hypotheses, here we conducted a haplotype-sharing analysis (HSA) based on empirical and simulated data of high-density single nucleotide polymorphisms. Our results showed that more than 95% of UIG haplotypes could be found in either EAS or EUR populations, which contradicts the expectation of the null models assuming that UIG are donors. Simulation studies further indicated that the proportion of UIG private haplotypes observed in empirical data is only expected in alternative models assuming that UIG is an admixture population. Interestingly, the estimated ancestry contribution of 44%:56% (EAS:EUR) based on HSA is consistent with our previous estimation with STRUCTURE analysis. Although the history of UIGs could be complex, our method is explicit and conservative in rejecting the null hypothesis. We concluded that the gene pool of modern UIGs is more likely a sole recipient with contribution from both EAS and EUR.</blockquote>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com5tag:blogger.com,1999:blog-23084925.post-31913608696868991532009-09-01T12:35:00.002-06:002009-09-01T12:46:57.878-06:00Human mutation rate estimatevia <a href="http://www.cell.com/current-biology/abstract/S0960-9822%2809%2901454-7">this story at Nature News</a>, their estimate based on Y chromosome is 100-200 new mutations per genome per generation, or about one mutation in every 30 million bases, which is in agreement with previous indirect estimates. Apparently this is the first direct measurement of the human mutation rate.<br /><br /><a href="http://www.cell.com/current-biology/abstract/S0960-9822%2809%2901454-7"><span style="font-weight: bold;">Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree</span></a><br />Yali Xue, Qiuju Wang, Quan Long, Bee Ling Ng, Harold Swerdlow, John Burton, Carl Skuce, Ruth Taylor, Zahra Abdellah, Yali Zhao, Asan, Daniel G. MacArthur, Michael A. Quail, Nigel P. Carter, Huanming Yang and Chris Tyler-Smith<br /><span style="font-weight: bold;">Current Biology</span>, 27 August 2009<br /><span style="font-weight: bold;"></span><blockquote style="color: rgb(102, 102, 102);"><span style="font-weight: bold;">Abstract: </span>Understanding the key process of human mutation is important for many aspects of medical genetics and human evolution. In the past, estimates of mutation rates have generally been inferred from phenotypic observations or comparisons of homologous sequences among closely related species [1,2,3]. Here, we apply new sequencing technology to measure directly one mutation rate, that of base substitutions on the human Y chromosome. The Y chromosomes of two individuals separated by 13 generations were flow sorted and sequenced by Illumina (Solexa) paired-end sequencing to an average depth of 11 or 20, respectively [4]. Candidate mutations were further examined by capillary sequencing in cell-line and blood DNA from the donors and additional family members. Twelve mutations were confirmed in 10.15 Mb; eight of these had occurred invitro and four invivo. The latter could be placed in different positions on the pedigree and led to a mutation-rate measurement of 3.0x10-8 mutations/nucleotide/generation (95% CI: 8.9x10-9 7.0x10-8), consistent with estimates of 2.3x10-8 - 6.3x10-8 mutations/nucleotide/generation for the same Y-chromosomal region from published human-chimpanzee comparisons [5] depending on the generation and split times assumed.</blockquote>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com1tag:blogger.com,1999:blog-23084925.post-7503603777037738492009-08-30T16:54:00.004-06:002009-08-31T08:05:18.929-06:00Got some performance enhancing polymorphisms?<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://1.bp.blogspot.com/_dRj9DN75euI/SpvYTDCTpbI/AAAAAAAAAmM/baBgIYIIFV0/s1600-h/usain+bolt+100+berlin.jpeg"><img style="margin: 0pt 0pt 10px 10px; float: right; cursor: pointer; width: 320px; height: 197px;" src="http://1.bp.blogspot.com/_dRj9DN75euI/SpvYTDCTpbI/AAAAAAAAAmM/baBgIYIIFV0/s320/usain+bolt+100+berlin.jpeg" alt="" id="BLOGGER_PHOTO_ID_5376128401940915634" border="0" /></a>First of all, gotta love the term "Performance Enhanding Polymorphisms" (PEPs). This is a review paper describing what we know about the genetics of athletic performance. They focus on ACE, ACTN3, MSTN, NOS3 and several other genes. In light of recent performances, and just out of curiosity, let's get some genotypes on these three people:<br />Usain Bolt<br />Lance Armstrong<br />Michael Phelps<br /><br /><a href="http://arjournals.annualreviews.org/doi/abs/10.1146/annurev-genom-082908-150058"><span style="font-weight: bold;">Genetics of Athletic Performance</span></a><br />Elaine A. Ostrander, Heather J. Huson, and Gary K. Ostrander<br /><span style="font-weight: bold;">Annual Review of Genomics and Human Genetics</span> Vol. 10: 407-429 <span style="font-weight: bold;"></span><blockquote style="color: rgb(102, 102, 102);"><span style="font-weight: bold;">Abstract:</span> Performance enhancing polymorphisms (PEPs) are examples of natural genetic variation that affect the outcome of athletic challenges. Elite athletes, and what separates them from the average competitor, have been the subjects of discussion and debate for decades. While training, diet, and mental fitness are all clearly important contributors to achieving athletic success, the fact that individuals reaching the pinnacle of their chosen sports often share both physical and physiological attributes suggests a role for genetics. That multiple members of a family often participate in highly competitive events, such as the Olympics, further supports this argument. In this review, we discuss what is known regarding the genes and gene families, including the mitochondrial genome, that are believed to play a role in human athletic performance. Where possible, we describe the physiological impact of the critical gene variants and consider predictions about other potentially important genes. Finally, we discuss the implications of these findings on the future for competitive athletics.</blockquote><div class="abstractSection"><p class="last"></p> </div>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com1tag:blogger.com,1999:blog-23084925.post-89587983662339372622009-08-28T07:40:00.004-06:002009-08-28T07:52:51.593-06:00Geographical origin and dating of the lactase persistence alleleSee <a href="http://dienekes.blogspot.com/2009/08/lactase-persistence-spread-with.html">Dienekes' blog post</a> about a new paper that purports the origin of the lactase persistence allele to be somewhere in the Austria/Czech Republic area, around 7,500 years ago.<br />From the abstract:<br /><span style="color: rgb(102, 102, 102);"></span><blockquote><span style="color: rgb(102, 102, 102);">Using data on −13,910*T allele frequency and farming arrival dates across Europe, and approximate Bayesian computation to estimate parameters of interest, we infer that the −13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly in association with the dissemination of the Neolithic Linearbandkeramik culture over Central Europe. Furthermore, our results suggest that natural selection favouring a lactase persistence allele was not higher in northern latitudes through an increased requirement for dietary vitamin D.</span> </blockquote>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com0tag:blogger.com,1999:blog-23084925.post-88421565692878664512009-08-22T12:30:00.002-06:002009-08-22T12:44:00.579-06:00A set of AIMs that can distinguish within continents<span style="font-size:+1;"><b></b></span><a href="http://www.biomedcentral.com/1471-2156/10/39/abstract/"><span style="font-weight: bold;">An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels.</span></a><br />Nassir R, Kosoy R, Tian C, White PA, Butler LM, Silva G, Kittles R, Alarcon-Riquelme ME, Gregersen PK, Belmont JW, De La Vega FM, Seldin MF.<br /><span title="BMC genetics."><a href="javascript:AL_get(this,%20'jour',%20'BMC%20Genet.');"></a></span><span style="font-weight: bold;">BMC Genet.</span> 2009 Jul 24;10(1):39.<br /><span style="font-weight: bold;"></span><blockquote style="color: rgb(102, 102, 102);"><span style="font-weight: bold;">ABSTRACT</span>: BACKGROUND: Case-control genetic studies of complex human diseases can be confounded by population stratification. This issue can be addressed using panels of ancestry informative markers (AIMs) that can provide substantial population substructure information. Previously, we described a panel of 128 SNP AIMs that were designed as a tool for ascertaining the origins of subjects from Europe, Sub-Saharan Africa, Americas, and East Asia. RESULTS: In this study, genotypes from Human Genome Diversity Panel populations were used to further evaluate a 93 SNP AIM panel, a subset of the 128 AIMS set, for distinguishing continental origins. Using both model-based and relatively model-independent methods, we here confirm the ability of this AIM set to distinguish diverse population groups that were not previously evaluated. This study included multiple population groups from Oceana, South Asia, East Asia, Sub-Saharan Africa, North and South America, and Europe. In addition, the 93 AIM set provides population substructure information that can, for example, distinguish Arab and Ashkenazi from Northern European population groups and Pygmy from other Sub-Saharan African population groups. CONCLUSION: These data provide additional support for using the 93 AIM set to efficiently identify continental subject groups for genetic studies, to identify study population outliers, and to control for admixture in association studies.</blockquote>Yann Klimentidishttp://www.blogger.com/profile/08967411331213363781noreply@blogger.com0