tag:blogger.com,1999:blog-37148773.post1224433293940027995..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: What did Joe Felsenstein say about sex?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger59125tag:blogger.com,1999:blog-37148773.post-87855676419995956842015-11-16T09:15:16.090-05:002015-11-16T09:15:16.090-05:00Fixed it. Sorry for leaving the error up for so lo...Fixed it. Sorry for leaving the error up for so long. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-46509349888574420212015-11-16T06:20:07.869-05:002015-11-16T06:20:07.869-05:00@Larry
There's a typo in:
"As John Maynar...@Larry<br />There's a typo in:<br />"As John Maynard-Smith pointed out in 1968, when genes/alleles are in linkage disequilibrium then recombination does not result in a change in allele frequencies (i.e. evolution)."<br /><br />Must be: "... linkage equilibrium..."<br />Joachim Dagghttps://www.blogger.com/profile/00985198925581721229noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-53783407648884193002014-05-27T13:05:49.701-04:002014-05-27T13:05:49.701-04:00OK – again I must be missing something!
I always ...OK – again I must be missing something!<br /><br />I always understood that Bacteria often display the linkage equilibrium (for all intents and purposes) of sexual populations.<br /><br />For example:<br />http://www.pnas.org/content/90/10/4384.full.pdf<br /><br />What am I missing?<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-50978323147384428192014-05-27T12:34:10.704-04:002014-05-27T12:34:10.704-04:00Right, thanks again, Joe. As my question here did ...Right, thanks again, Joe. As my question here did not show up for some hours, I thought this discussion was over and sent you the e-mail. Therefore the - er - crossover (overlap:-).<br /><br />Joachim Dagghttps://www.blogger.com/profile/00985198925581721229noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-16266163953362873742014-05-27T09:46:27.231-04:002014-05-27T09:46:27.231-04:00@Alan: There are cases like Drosophila where ther...@Alan: There are cases like <i>Drosophila</i> where there is no crossing-over in males. So crossing-over is not inevitable. Furthermore most organisms go to a great deal of trouble to outcross. That is difficult and expensive. Wouldn't they be a lot better off just producing diploid eggs by mitosis?<br /><br />As for what "is sex", I have always preferred to talk of the evolution of recombination. Saying you are going to explain "sex" implies to the reader that you are discussing why the sexes are different, and they are likely to be very disappointed when they discover what you are really discussing. It is a good way to sell books, though.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-58748449213466406472014-05-27T07:29:25.631-04:002014-05-27T07:29:25.631-04:00@Joachim For me, that are not asexual genotypes bu...@Joachim <i>For me, that are not asexual genotypes but sexual genotypes lacking crossing-over and the additional recombination that comes with it.</i><br /><br />This chimes with the point I've been making. To explain sex, one first needs to explain cyclic syngamy and reduction. Recombination could be the reason for that cycle, though I rather doubt it, and I am puzzled by the general insistence that homologous recombination is what sex <i>is</i>, rather than something it <i>has</i>, with a near-universal role in the cytological control of segregation. The fact that there is reciprocal exchange in 50% of DSB's is not necessarily the 'desired' result of crossover. It's a mechanical link which provides tension as the bivalents are teased apart by opposing spindles. Crossover and non-crossover resolution products are inevitable given the essential blindness of the process as to which upstream strand 'belongs' to which downstream one. There is no fundamental reason for a gene to 'care' which partners it ends up with. AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-37355270852571136572014-05-26T12:54:53.757-04:002014-05-26T12:54:53.757-04:00As it happens, Joachim Dagg also sent me a persona...As it happens, Joachim Dagg also sent me a personal email with the same content. I have answered him: in brief the simulation had only one cromosome pair, so independent segregation of chromosomes would not bring about recombnation in the no-crossing-over case. It was thus a fair simulation of recombination versus no recombiation. PS: the 1976 Y&F paper can be read free at the Genetics web site (www.genetics.org), as is their policy with papers older than a few years/Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-43945253644451321132014-05-26T04:12:49.799-04:002014-05-26T04:12:49.799-04:00@Joe Felsenstein
You wrote: "In the Yokoyama ...@Joe Felsenstein<br />You wrote: "In the Yokoyama and Felsenstein 1976 paper we simulated a case where a population had (initially) 50% asexual individuals, and 50% sexuals who could cross with each other. The simulation showed that the sexuals fixed more often than the asexuals. So that was a case where the boundary was traversible -- simply by change of frequency of the two types.<br /><br />(I should add that the case did not have Maynard Smith's phenomenon of the "cost of sex", so it avoided that serious issue)."<br /><br />As I understood that paper, you considered a recombination modifier locus that switches recombination between homologous chromosomes (due to crossing-over) on or off depending on genotype. <br /><br />Let's take the simpler case, where the allele for crossing-over is recessive, a, and only the genotype aa will have recombination between homologous chromosomes due to crossing over.<br /><br />Unless I'm seriously mistaken, the genotypes Aa and AA should still have the recombination due to segregation of homologous chromosomes during meiosis and subsequent gamete fusion. <br /><br />For me, that are not asexual genotypes but sexual genotypes lacking crossing-over and the additional recombination that comes with it.<br /><br />That's also, why your disclaimer in parentheses is necessary. IMHO you did not pit asexual mutants against sexuals but two extreme recombination modifier alleles against each other. <br /><br />Did I overlook something?Joachim Dagghttps://www.blogger.com/profile/00985198925581721229noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-8009676318688979442014-03-14T18:22:37.106-04:002014-03-14T18:22:37.106-04:00Sorry about that, then.Sorry about that, then.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40501652640025351102014-03-14T12:23:09.761-04:002014-03-14T12:23:09.761-04:00Mmm. I was not so much trying to explain any eleme...Mmm. I was not so much trying to explain any element but to get things the 'right way out'. I perceive a further confusion now because of the two senses in which 'cross' could be taken - 'crossover' or simply getting two diploids to make another. <br /><br />Without syngamy/reduction, you don't get an opportunity to do recombination, nor much out of it. It puzzles me why the consequences of those elements seem so secondary - to the point where people exclude them from their definition of sex. We don't need to be slaves to definition, of course. But cyclic haploidy/diploidy with two different diploids providing each gamete seems to be a sufficient 'minimal' definition of outcrossing sex, without going near recombination. In early evolution, this may be all there was. <br /><br />Of course despite that context, very few modern mitoses do without 1-chiasma-per-chromosome. This does argue for a substantial cytological role. It's not just Poisson-distributed across the genome (nor even the chromosome) for example. On the other hand, in the few achiasmate meioses that do occur species make sure that crossover does occur in the other sex, so it's probably not <i>just</i> about cytology. AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-50608565332310834012014-03-14T11:46:43.998-04:002014-03-14T11:46:43.998-04:00Joe - the quote was from Larry's piece. No nee...Joe - the quote was from Larry's piece. No need to apolgise! AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-22697784952627969012014-03-14T11:43:27.255-04:002014-03-14T11:43:27.255-04:00There have been theories that concentrated on syng...There have been theories that concentrated on syngamy and reduction to explain outcrossing. Those effects would then not explain recombination.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-47319930036958939432014-03-14T11:42:06.140-04:002014-03-14T11:42:06.140-04:00Yes. Linkage equilibrium. Sorry.Yes. Linkage equilibrium. Sorry.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-39645214730865899202014-03-14T07:36:43.913-04:002014-03-14T07:36:43.913-04:00As John Maynard-Smith pointed out in 1968, when ge...<i>As John Maynard-Smith pointed out in 1968, when genes/alleles are in linkage disequilibrium then recombination does not result in a change in allele frequencies (i.e. evolution).</i><br /><br />Shouldn't that be linkage equilibrium?AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-71631639645987277952014-03-14T07:18:19.846-04:002014-03-14T07:18:19.846-04:00Thats why worms/snails are so numerous despite bei...<i>Thats why worms/snails are so numerous despite being slow moving creatures.</i><br /><br />Robert's world is so wonderfully Ptolemaic.judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-45125489645107794852014-03-13T18:58:24.546-04:002014-03-13T18:58:24.546-04:00Why would Joe Frankenstein write about sex..? He h...Why would Joe Frankenstein write about sex..? He has no idea, and nobody else has an idea... Why doesn't he write about the real sex, the wild one.... oh yeah... that one ..ummmmmm what's wrong with Joe? He no like siks...?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-75992996814729589912014-03-13T15:55:37.486-04:002014-03-13T15:55:37.486-04:00I didn't notice anyone mentioning moths. But e...I didn't notice anyone mentioning moths. But earthworms, and snails don't "breed alone". They defy that order of God and sinfully engage in bisexual sex with other bisexual sinners. They do not self-fertilize, having at least that much respect for Divine Law. So yes, I guess the Fall is the only possible explanation for their evil behavior.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-6101113116551157372014-03-12T21:24:02.807-04:002014-03-12T21:24:02.807-04:00Joe Felsenstein
The segregation of sexual traits i...Joe Felsenstein<br />The segregation of sexual traits into male and female dominates nature and especially large nature. the few exceptions, I understand its few, can be dismissed as adaptations in a post fall world.<br />Indeed moth worms and snails must breed alone in order to reproduce quickly which is a order from God. Thats why worms/snails are so numerous despite being slow moving creatures.<br />the purpose of sex and sexual identity, except in people, is simply reproduction. <br />A creator had a idea that reproduction is best served by segregated sexual traits in a creature type and so male/female.<br />No evidence at all it evolved. Its just guessing. Robert Byershttps://www.blogger.com/profile/05631863870635096770noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-51889638689272516622014-03-12T17:53:57.238-04:002014-03-12T17:53:57.238-04:00You have raised many of the arguments that people ...You have raised many of the arguments that people have raised for evolution of "sex" (recombination with outcrossing). These scenarios are among those that are proposed to embody the two great classes of models: the Fisher/Muller and the Sturtevant/Mather.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-80963690633548206672014-03-12T16:04:33.629-04:002014-03-12T16:04:33.629-04:00@ Joe
I met John Maynard Smith personally and re...@ Joe<br /><br /> I met John Maynard Smith personally and remember him discussing this very question with my wife and my wife’s supervisor many many years ago in my wife’s supervisor’s kitchen… the details are long lost in the mists of time.<br /><br />I do remember something along the lines that clonal expansion is efficient at generating large numbers quickly, a useful trait in situations of intense competition but sex is useful when “circumstances change”… That is as much as I can remember.<br /><br />Let’s see if I can take it from there…<br /><br />Why is sex beneficial? The most likely advantage of sex is that it increases a parent’s chances of producing offspring that can survive.<br /><br />Sex must be beneficial for small populations subject to Genetic Drift allowing them to escape Muller’s ratchet?<br /><br />i.e. In a small population subject to genetic drift - the burden of accumulating deleterious mutations may eventually cause some populations to go extinct (bad luck of the draw due to drift, as it were).<br /><br />Sexual reproduction short-cuts Muller’s ratchet. E.g. two individuals each with one copy of some deleterious mutation will produce offspring that are free of either mutation 25% of the time.<br /><br />ITMT I am about to teach Taxonomy and I am reminded that so-called “primitive” organisms (forgive me – you know I mean “basal” for “primitive”) employ asexual reproduction in constant environments as their default setting and sexual reproduction kicks in under scenarios of environmental stress.<br /><br />In other words; if environment changes, not only may offspring be poorly adapted but ALL offspring will be poorly adapted because they are identical.<br /><br />Zygospores are quiescent resting bodies awaiting environmental conditions to return to "normal" ...<br /><br />or alternatively...<br /><br />...allow recombination resulting in novel variable offspring, some of which can to adapt to the “new normal”. <br /><br />I can imagine zygospores as some evolutionary quiescent exaptation that eventually gave rise to sexual reproduction… the exaptation possibly being DNA repair.<br /><br />Why is sex beneficial? Parent’s chances of producing offspring that can survive competition are greatly enhanced, remembering that each generation produces far more progeny than can possibly survive.<br /><br />Again, this appears too easy… what am I getting wrong?<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-19987421194052575302014-03-12T14:02:08.018-04:002014-03-12T14:02:08.018-04:00I may have misunderstood what 'crosses' wi...I may have misunderstood what 'crosses' with what. But it rather illustrates my point. I'm not sure why syngamy and reduction don't count as 'sex', but recombination is seen as diagnostic. It seems wholly the wrong way round to me. AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-72579357035111175052014-03-12T09:59:31.519-04:002014-03-12T09:59:31.519-04:00I don't think that is quite what I would call ...I don't think that is quite what I would call a 'traversible boundary'! Grey squirrels are eliminating red in the UK, but one would not suggest that a boundary is being traversed. <br /><br />The boundary I had in mind is that whereby a sexual lineage gives rise to an asexual one, or vice versa. Traversal in the two directions is mechanistically distinct, and not symmetrical in most relevant parameters. Starting from a homogeneous equilibrium ignores this (in simpler models).AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-25843220828139475292014-03-12T09:34:50.189-04:002014-03-12T09:34:50.189-04:00Yes, because beneficial variants will compete with...Yes, because beneficial variants will compete with each other if they arise in different genetic backgrounds (linkage disequilibrium). Sexual reproduction will remedy this situation more rapidly than competence and viral infection can.Corneelhttps://www.blogger.com/profile/02884855837357720225noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-7299883204253533262014-03-12T09:00:46.240-04:002014-03-12T09:00:46.240-04:00Did you know that earthworms and snails blatantly ...<i>Did you know that earthworms and snails blatantly violate God's decree about the sexes being in separate individuals? They are evil.</i><br /><br />And fish. That's why I cook them. Serves them well.<br /><br /><br />Pedro A B Pereirahttps://www.blogger.com/profile/15195139833344839287noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-59647053033726556392014-03-12T08:33:39.750-04:002014-03-12T08:33:39.750-04:00The mechanisms for the evolution of recombination ...The mechanisms for the evolution of recombination (with outcrossing), which is what we are calling "sex", give an advantage to a little but of recombination, but that advantage decreases as one adds more recombination.<br /><br />At the same time, there are counteracting forces of natural selection against recombination when it breaks up disequilibrium of favorably interacting genes. So one can imagine a balance between these forces and an optimum level of recombination, far short of no effective linkage.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.com