tag:blogger.com,1999:blog-10781944.post4303868211306318551..comments2024-03-28T00:36:36.460-07:00Comments on The Tree of Life: Open Evolution Highlights - the Population Genetics of dN/dSJonathan Eisenhttp://www.blogger.com/profile/07953790938128734305noreply@blogger.comBlogger8125tag:blogger.com,1999:blog-10781944.post-5619478290232113592009-01-26T14:24:00.000-08:002009-01-26T14:24:00.000-08:00Thanks Ed. I somehow missed yours/Eduardo's paper...Thanks Ed. I somehow missed yours/Eduardo's paper.Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-7179434967727571022009-01-26T08:25:00.000-08:002009-01-26T08:25:00.000-08:00We have previously shown there is a time-dependent...We have previously shown there is a time-dependent dN/dS gradient in bacteria as non-synonymous mutations preferentially get removed by selection (at a rate determined partially by the population size) here:<BR/>J Theor Biol. 2006 Mar 21;239(2):226-35. Epub 2005 Oct 18<BR/><BR/>so, yes, caution advised!!Ed Kurtzhttps://www.blogger.com/profile/10469130194795578722noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-4996051723674497572009-01-12T10:17:00.000-08:002009-01-12T10:17:00.000-08:00Yes, gioby, fair point. There are issues in lots ...Yes, gioby, fair point. There are issues in lots of organisms with defining coding with things like alternative splicing, overlapping genes, etc . But that does not of course mean you cannot calculate dN/dS. It means that it may not mean what you think it means (to steal some lingo from the Princess Bride). Even when you have the full transcriptome the meaning can be difficult to figure out as few regions are "on" all the time. I still view these measures as potentially useful -- just to be taken with a grain of salt.Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-67020436918442226572009-01-12T07:20:00.000-08:002009-01-12T07:20:00.000-08:00I believe that it is impossible to calculate the M...I believe that it is impossible to calculate the MacDonald's index (dN/dS).<BR/><BR/>If you look at most of the metazoans' trascriptome, you'll see that the maiority of genes have at least two or three splicing isoforms each. The latest studies say that in human, this happen for the 70% of the genes.<BR/><BR/>How can you calculate which nucleotide is coding and which is not, unless you know the full transcriptome of an organism?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-10781944.post-15036534522721664722008-12-18T14:02:00.000-08:002008-12-18T14:02:00.000-08:00APB - I think trackbacks do work in theory in PLoS...APB - I think trackbacks do work in theory in PLoS. ut some sites do not allow trackbacks. For example, Blogger/Blogspot does not allow them still I believe. So it might be the fault of how you publish your blog.Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-44590390240741743342008-12-18T13:31:00.000-08:002008-12-18T13:31:00.000-08:00This is a great paper and I'm glad to see it discu...This is a great paper and I'm glad to see it discussed. This is an off-topic comment and I apologize, but this seems like a good place to get it answered:<BR/><BR/>Why don't the trackbacks work on PLoS? (Maybe I am doing something wrong but) I have tried to use trackbacks a few times on blog posts of my own and I don't see them show up on the journal article site in PLoS. (And this post isn't linked on the paper yet either.)<BR/><BR/>I'm a giant fan of PLoS and think that its infrastructure, which permits/encourages online interaction, is awesome and holds great potential. It would be really nice to seem some of that interconnectivity working a little better.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-10781944.post-65777104749056607222008-12-16T18:17:00.000-08:002008-12-16T18:17:00.000-08:00DavidYes this seems unrealistic but they do at lea...David<BR/><BR/>Yes this seems unrealistic but they do at least hint at the problems in their conclusion: "For microbes and viruses, however, the distinction may be more opaque."Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-908163913547793322008-12-16T15:30:00.000-08:002008-12-16T15:30:00.000-08:00I see their point with the viral evolution stuff.....I see their point with the viral evolution stuff...but to characterize different strains of bacteria as coming from a single population (and thus dN/dS studies between bacterial genomes) is a tad bit unrealisticDave Baltrushttps://www.blogger.com/profile/01125408825437399383noreply@blogger.com