tag:blogger.com,1999:blog-1871542942842750523.post4397464159086409486..comments2023-07-24T10:40:57.739-04:00Comments on dechronization: Software Review: Structure 2.2 GUIGlorhttp://www.blogger.com/profile/17707197225963721646noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-1871542942842750523.post-52001466821390608402008-07-10T15:31:00.000-04:002008-07-10T15:31:00.000-04:00Awesome program, indeed. Nature sometimes departs ...Awesome program, indeed. Nature sometimes <A HREF="http://en.wikipedia.org/wiki/Hardy-Weinberg_principle#Deviations_from_Hardy-Weinberg_equilibrium" REL="nofollow">departs from HWE</A> and locks a high number of alleles in homozygous combinations. That along with high levels of gene flow (Fst<0.05) can make Structure see one genetic cluster. There's also the issue of unsampled (a.k.a. ghost) populations that <A HREF="http://www.montpellier.inra.fr/URLB" REL="nofollow">GeneClass2</A> deals well with. But I'm departing from the original posting. <BR/><BR/>I believe Mark's referring to results obtained after <A HREF="http://dx.doi.org/10.1098/rspb.2007.0248" REL="nofollow">his 2007 paper</A>.sergios-orestis kolokotronishttps://www.blogger.com/profile/05492639186814501804noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-54708509671632030072008-07-07T18:58:00.000-04:002008-07-07T18:58:00.000-04:00One thing I will mention is that structure has all...One thing I will mention is that structure has allowed us to determine that different species of darters are having limited interspecific sex. However enough to transfer mt genomes, but not enough for the introgression of autosomal alleles.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-26962497331825851802008-07-07T18:57:00.000-04:002008-07-07T18:57:00.000-04:00My comment was not meant as a critique of structur...My comment was not meant as a critique of structure. Mark, what type of data did you use in your leech analysis, and how much data (e.g. number of genes, or microsats, etc.)?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-25764418050058330662008-07-07T18:39:00.000-04:002008-07-07T18:39:00.000-04:00Is this work on leeches published? I just did a q...Is this work on leeches published? I just did a quick check on your web page and web of science and didn't see anything obvious.Glorhttps://www.blogger.com/profile/17707197225963721646noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-83820348053013333912008-07-07T18:32:00.000-04:002008-07-07T18:32:00.000-04:00Assumptions or not, STRUCTURE (without the GUI) wa...Assumptions or not, STRUCTURE (without the GUI) was central to our determination that various incipient species of leeches just weren't having sex. The GUI's nice, but the output from the command line is very easy to interpret.<BR/>SiddallMark Siddallhttps://www.blogger.com/profile/15569596998437017042noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-19523344127175612702008-07-07T11:06:00.000-04:002008-07-07T11:06:00.000-04:00Which assumptions do you find most troubling? I'm...Which assumptions do you find most troubling? I'm concerned that the model is designed specifically to identify disjunct populations and can't distinguish among alternative models of population structure (e.g., isolation by distance versus population fragmentation). Nevertheless, it seems no more assumption laden than other methods in population genetics.Glorhttps://www.blogger.com/profile/17707197225963721646noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-26027332110354078132008-07-07T09:01:00.000-04:002008-07-07T09:01:00.000-04:00We have been using structure for the past year to ...We have been using structure for the past year to examine patterns of introgression among freshwater fish species. There are some hefty assumptions that come with the model, and users should familiarize themselves with the theory backing the method.Anonymousnoreply@blogger.com