tag:blogger.com,1999:blog-37148773.post6037499953233561789..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Does natural selection constrain neutral diversity?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger117125tag:blogger.com,1999:blog-37148773.post-49572299876537911222019-04-09T02:47:42.151-04:002019-04-09T02:47:42.151-04:00One more reason to mention here. Our finding of hi...One more reason to mention here. Our finding of higher MAC or genetic diversity in patient populations relative to normal controls is unexpected under the presently popular neutral paradigm. Why? Because different racial groups are well known to have different level of genetic diversities. Neutral theory explains it as to mean different evolutionary times and would predict that given enough time whites would reach the same level of high genetic diversity as blacks. Our finding says no.Gnomonhttps://www.blogger.com/profile/17161251198271813257noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-90376537199763524342019-03-29T23:24:42.620-04:002019-03-29T23:24:42.620-04:00Sorry, just noticed your great comments.Our result...Sorry, just noticed your great comments.Our results show patient population has greater genome wide variation or MAC than normal matched populations. Our latest paper on this is about lung cancer. If what you said is true that only a few deleterious SNPs are the cause of disease rather than the collective effect of all SNPs, you would not expect to see our finding. Yuan et al 2014 has address this: "Do the results here mean an additive effect of large numbers of MAs in MAC action and hence non-neutrality of most MAs? Many major effect risk alleles of diseases are known to be minor alleles [18], which may plausibly imply<br />that the effect of MAC may be mediated by a few known major effect risk alleles rather than large numbers of minor effect MAs. But this may not necessarily be the case. The effect of MAC was in fact abolished or weakened by major effect MAs such as kras2 mutation in lung cancer or npr-1 mutation in brood size as found here. Furthermore, MAC<br />preferentially affects traits with larger number of known<br />additive QTLs [34]. Obviously, the more the number of QTLs involved in a trait, the less the individual effect of each QTL on the trait. Thus, MAC-linked traits are expected to have more additive minor effect SNPs as risk alleles than those not linked to MAC."<br /><br />ref. <br />Lei et al., Collective effects of common SNPs and risk prediction in lung cancer. Heredity 121, pages537–547 (2018) https://www.nature.com/articles/s41437-018-0063-4 <br /><br />Yuan et al, Scoring the collective effects of SNPs: association of minor alleles with complex traits in model organisms Science China Life Sciences 57, pp 876–888Gnomonhttps://www.blogger.com/profile/17161251198271813257noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-72147530101516551402015-11-02T09:21:38.198-05:002015-11-02T09:21:38.198-05:00Hello gnomon. I just read the paper you linked ab...Hello gnomon. I just read the paper you linked above after having bookmarked this thread several months ago. Sorry I'm late to the party. <br /><br />I'm very interested interested in the amount of strict nucleotide-specific functional DNA in the human genome. In the paper your team writes:<br /><br />> "For calculating MAC [minor allele content], the number of informative SNPs used for each panel ranged from ~120 to ~151000. Since the SNPs used here are largely selected in a non-biased way, the number of SNPs used should not significantly affect the calculation of MAC. Indeed as shown for the BXD mouse panel, MAC calculated from ~51000 SNPs were highly similar to those calculated using two different non-overlapping sets of 1000 SNPs randomly selected from the ~51000"<br /><br />Suppose only 1 in 20 SNP's affect function, indicating something like 5% of the genome is nucleotide specific functional. If this is true wouldn't you have still gotten the same result. Since a set of 1000SNP's would still on average have 50 function-altering SNP's? Apologies if I'm missing something obvious here.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-41894444410316356052015-04-29T05:24:38.576-04:002015-04-29T05:24:38.576-04:00I remain in your debt. Thank you!I remain in your debt. Thank you!Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-89129081349588282172015-04-28T22:53:32.021-04:002015-04-28T22:53:32.021-04:00TomI now understand that you are reiterating Rahzi...Tom<i>I now understand that you are reiterating Rahzib Khan’s<br /><br />“…there is a correlation between the power of selection on the genome and inferred effective population size. I say inferred because they had to use species range and size as proxies.”</i><br /><br />Actually, no, I was pointing out an additional assumption that applies if you want to demonstrate (rather than infer) a genetic Allee effect: that you would need to measure fitness. Increased average fitness seems to be a reasonable assumption if positive and negative selection cause the result in Corbett-Detig et al., but as I pointed out there are other possible explanations as well, so an assumption of increased fitness alone is not totally convincing. As you have pointed out, those differences might not be measurable, but this only serves to limit the strength of any conclusions we might have.<br /><br />Tom: <i>I find Razib Khan’s characterization of ”the extremism of some of the anti-selectionists” somewhat amusing. I take it you and Razib Khan are in agreement that these results are “intriguing” but do not (yet?) constitute proof positive in settling the debate.</i><br /><br />I agree with that, yes.<br /><br /><i>In other words, we can conclude that the “anti-selection extremists” may have lost a significant battle (perhaps maybe, that is) but have not yet lost the war</i><br /><br />If we define this "anti-selection extremism" to encompass the POV that selection is sufficiently rare that it does not influence genetic diversity, then I would say yes, this paper is a blow to that world view. However, I'd point out that this paper is one in a long line all suggesting the same thing--that genetic diversity has upper bounds that do not reflect the levels predicted at mutation-drift equilibrium for given census population sizes. What this paper does is make a reasonable case for positive and negative selection being a major cause of this boundedness, rather than neutralist perspectives that might emphasise limits to Ne through population factors and periodic bottlenecking.. Paul McBridehttps://www.blogger.com/profile/09953009288824698018noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-30358514800915941472015-04-28T21:57:03.877-04:002015-04-28T21:57:03.877-04:00Hi Paul
To answer your first question, I was resp...Hi Paul<br /><br />To answer your first question, I was responding to your statement:<br /><i>“If positive selection is mutation limited (i.e. there is a waiting time for the arrival of beneficial mutations) then larger populations should produce a greater number of positive mutations.”</i><br /><br />I immediately wondered if we could possibly be opening the door to a repertoire of exaptations, some subset of which that could provide delayed positive selection at a higher hierarchical level i.e the species level. <br /><br />As mentioned elsewhere, my favorite candidate for one such exaptation that POSSIBLY could prove to provide positive selection at the higher hierarchical level of “species selection” happens to be bulk DNA aka junk DNA. The inspiration for this hunch (and I insist it is merely a hunch) would be Peter Fraser’s work on the non-random orientation of the X chromosome where the folding of Chromatin and exposure of different active regions to the “periphery” is dependent on the differentiation status of the cell type which fascinates me. That means, some of the chromatin must serve some nondescript “function” as bits and pieces are either exposed or sequestered. <br />http://www.bbsrc.ac.uk/news/health/2013/130925-pr-x-shape-chromosome-structure/<br /><br />But as I mentioned above, I am speaking more from intuition than conviction, I really have a lot more reading to do on the subject before wading in on that topic again. I really should not have gone there.<br /><br />You also stated earlier that:<br /><br /><i>“Finally, and this is particularly important for the interpretation of an Allee effect, the authors have not demonstrated any correlation with fitness.”</i><br /><br />I thank you for your later clarification:<br /><br /><i>“…interpreting the Corbett-Detig et al. paper explicitly in terms of Allee effects is that there is only an inference of an effect on mean population fitness based on population-genetic theory--there is not a demonstration that such an effect occurs in practice.”</i><br /><br />I now understand that you are reiterating Rahzib Khan’s<br /><br /><i>“…there is a correlation between the power of selection on the genome and inferred effective population size. I say inferred because they had to use species range and size as proxies.”</i><br /><br />I find Razib Khan’s characterization of <i>”the extremism of some of the anti-selectionists”</i> somewhat amusing. I take it you and Razib Khan are in agreement that these results are <b>“intriguing”</b> but do not (yet?) constitute proof positive in settling the debate.<br /><br />In other words, we can conclude that the “anti-selection extremists” may have lost a significant battle (perhaps maybe, that is) but have not yet lost the war.<br /><br />Thank you for helping me out with possible implications to the Allee Effect. I learned a lot on this thread and I remain in your debt!<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-1023621643743098822015-04-27T18:55:11.579-04:002015-04-27T18:55:11.579-04:00Tom: I now wonder out loud whether that statement ...Tom: <i>I now wonder out loud whether that statement would have significant implications when that logic is extrapolated (along the lines first suggested by Gould) to any long-term potential positive bulk effects of so-called junk DNA (as I hinted above).</i><br /><br />Unless I am misunderstanding exactly where you are going with that--and please explain further if I am--I don't see how. I was referring to the production of positive mutations under the assumption of mutation-limited selection. Incidentally, there is some evidence that this is a fair assumption in many natural populations, although Ohta (1972) also provided some theoretical reasons why it might not always be the case. Either way, the rate of production of beneficial mutations is a distinctly population-genetic phenomenon--the production of new mutations is increased because of great Nc. If there is a connection to bulk effects of junk DNA and species selection I am not sure what it is.<br /><br /><i>I am not certain I exactly understand your point.</i><br />My point is that one of several caveats in interpreting the Corbett-Detig et al. paper explicitly in terms of Allee effects is that there is only an inference of an effect on mean population fitness based on population-genetic theory--there is not a demonstration that such an effect occurs in practice. Combined with the other caveats (i.e. that selection is not definitively the cause of the bounded genetic diversity), I am just pointing out for balance what some of the assumptions are that would go into interpreting their result as a genetic Allee effect. Hope that helps.<br /><br /><i>Perhaps it does not matter, given genes can be fixed at extremely low low (presumably undetectable) selection coefficients</i><br />Perhaps, although if we can't know either way, then we need to be cautious in our interpretations. Paul McBridehttps://www.blogger.com/profile/09953009288824698018noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-29715047704904283052015-04-27T10:12:15.680-04:002015-04-27T10:12:15.680-04:00Hi again Paul,
Remembering that I am an aging hig...Hi again Paul,<br /><br />Remembering that I am an aging high school teacher out of my depth here; I was hoping you could elaborate a little on your very last sentence:<br /><br /><i>Finally, and this is particularly important for the interpretation of an Allee effect, the authors have not demonstrated any correlation with fitness.</i><br /><br />I am not certain I exactly understand your point.<br /><br />Perhaps it does not matter, given genes can be fixed at extremely low low (presumably undetectable) selection coefficients as explained here: <br />http://sandwalk.blogspot.ca/2014/12/how-to-think-about-evolution.htmlTom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-49106164872862821772015-04-27T05:18:24.310-04:002015-04-27T05:18:24.310-04:00Hi Paul
I am in awe. Thank you.
I am intrigued ...Hi Paul<br /><br />I am in awe. Thank you.<br /><br />I am intrigued with your suggestion:<br /><br /><i>If positive selection is mutation limited (i.e. there is a waiting time for the arrival of beneficial mutations) then larger populations should produce a greater number of positive mutations.</i><br /><br />I hope I understand you correctly. I now wonder out loud whether that statement would have significant implications when that logic is extrapolated (along the lines first suggested by Gould) to any long-term potential positive bulk effects of so-called junk DNA (as I hinted above). <br /><br />But now I am in really over my head, and I need to warn you. That subject is a particularly sensitive on e on this forum and in the past has provoked acrimony.<br /><br />Thanks again for providing such a detailed answer to Larry’s original question above.<br /><br />Best and grateful regards<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-9446812577709169872015-04-27T00:45:10.079-04:002015-04-27T00:45:10.079-04:00Hi Tom,
They have certainly found evidence for a ...Hi Tom,<br /><br />They have certainly found evidence for a reasonably strong correlation between range/body size and the strength of linked selection. I have given a number of caveats as to why I wouldn't expect the relationship between range and population size to be generally so strong across such taxa, but there is also no reason why the relationship wouldn't be qualitatively right in most cases (which is what would be important for a discussion of Allee effects). <br /><br />Yes, I think that this could possibly be interpreted as an example of an Allee effect. If positive selection is mutation limited (i.e. there is a waiting time for the arrival of beneficial mutations) then larger populations should produce a greater number of positive mutations. Larger populations should probably see overall fewer fixations of slightly deleterious alleles (i.e. stronger background selection). Both of these factors should increase average fitness. Because selective sweeps from positive mutations, and background selection against negative ones both reduce Ne, these effects limit neutral diversity. Based on the authors' logic, the very fact that neutral diversity appears to be bounded, rather than scaling freely with Nc, is an Allee effect because they attribute it to two selective effects that at least slow degradation of population fitness and might increase it.<br /><br />It is worth pointing out that there are other quite plausible factors that could prevent the scaling of genetic diversity with Nc (e.g., see Maruyama and Kimura, 1980). It is also worth noting that while the authors have used actual genetic diversity, their estimation of linked selection is only based around the potential for selective sweeps and background selection given the density of functional sites. Finally, and this is particularly important for the interpretation of an Allee effect, the authors have not demonstrated any correlation with fitness.Paul McBridehttps://www.blogger.com/profile/09953009288824698018noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-30651756840512734262015-04-26T22:31:50.108-04:002015-04-26T22:31:50.108-04:00Hi Paul
Thank you - very interesting!
So if I un...Hi Paul<br /><br />Thank you - very interesting!<br /><br />So if I understand you correctly, these intriguing findings suggest the correlation between species range and size and Nc would in fact appear to be strong. Meanwhile, natural selection constrains levels of neutral genetic diversity moreso in species with large Nc than small Nc.<br /><br />Furthermore, by definition, an Allee effect is a positive association between absolute average individual fitness and population size over some finite interval.<br /><br />Is it possible that the authors may in fact have inadvertently stumbled across an indirect measure of the Allee Effect which has hitherto proven elusive and difficult to do? ... or is that a bridge too far?<br /><br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-57148350969821760452015-04-26T19:11:09.994-04:002015-04-26T19:11:09.994-04:00To continue the conversation, part of my work deal...To continue the conversation, part of my work deals with correlations between range size and population size. Before talking about correlations between range/population/density, it is important to define what is meant by range size. Many of the widely available estimates of range size for vertebrate species (e.g., through IUCN) are estimates for the extent of occurrence (EOO), which is the smallest convex polygon drawn around all of the observation points made for that species. Provided the whole range is encapsulated, this approach overestimates the actual range of the species, because almost certainly some habitat interpolated between points will not be occupied, or will have only a low density from accidentals. On the other hand, area of occupancy (AOO) is based only on areas where direct observations have been made, with minimal interpolation based on habitat availability. Because this is far more intensive, there are few range-wide estimates of AOO for species. However, AOO is more ecologically meaningful, and it has a strong and positive correlation with population density--the larger the range as estimated by AOO, the higher the density. This correlation is considered strong enough that it alone is widely used to make conservation decisions (i.e. threat categories) about population size. <br /><br />EOO does not have a clear correlation with population density. Therefore, independent estimates of density are needed to compare population sizes of different species using only range. Using direct population estimates for well-studied groups (e.g. birds) it is possible to show that population size and EOO correlate quite well after correcting for body size, but in my experience this works well only for reasonably similar species (e.g. within families of birds). <br /><br />The authors estimated their own EOOs using the GBIF database. For bird and mammal species, separate estimates have already been made, which allows for some comparisons. In some cases there are two- or three-fold differences between theirs and the previous estimates. So, before even trying to translate range size into population size, it needs to be acknowledged that range size estimates themselves are only rough estimates of true range. Further, I would be very surprised if the breadth of species used in the discussed PLOS Biology study could possibly lend itself to accurate Nc estimates based on EOO and body size, even if their EOO estimates were extremely good estimates of the true ranges. An extra hurdle: to find the correlations that they did, their estimates for population size would have to be representative of long-term population size, as it takes many generations for mutation-drift equilibrium to be reached in large populations.<br /><br />With all of this criticism said, the correlation they detect between range/body size and the "effect of selection" on genetic diversity is fascinating, and in line with expectations if they had reasonable population size estimates. Perhaps they were lucky; perhaps the estimates actually work out quite well for some reason across deep divergences like this, maybe because of the scale of the comparisons (I don't know--I work with much closer relationships than this); or perhaps there is an unmeasured explanatory factor involved. Paul McBridehttps://www.blogger.com/profile/09953009288824698018noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63778048541935375812015-04-26T15:05:36.293-04:002015-04-26T15:05:36.293-04:00Of course I meant to say
Presuming identical Bio...Of course I meant to say <br /><br />Presuming identical Biomass – smaller species of fish that exhibit shoaling over a large range by definition would demonstrate higher Nc than larger species of fish under identical circumstancesTom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28858970130596571872015-04-26T07:48:15.484-04:002015-04-26T07:48:15.484-04:00just as a postscript:
Re: “body size”
Presuming ...just as a postscript:<br /><br />Re: “body size”<br /><br />Presuming identical Biomass – shoals of smaller fish by definition would demonstrate higher Nc than shoals of larger fish.<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10754054566491501552015-04-26T07:34:34.899-04:002015-04-26T07:34:34.899-04:00Hi John
Let’s go back to Larry’s original questio...Hi John<br /><br />Let’s go back to Larry’s original question.<br /><br /><i>Razib Khan is an adaptationist and he's discovered a paper that gets him very excited: Selectionism Strikes Back!...<br /><br />...It is impossible for someone like me to evaluate this paper. Can someone take a look to see if it's valid?</i><br /><br />You will note above that I cited Razib Khan and was merely taking Khan at his word:<br /><br /><i> As the figure above shows <b>there is a correlation between the power of selection on the genome and inferred effective population size</b>. I say inferred because they <b>had to use species range and size as proxies</b>. Obviously this isn’t perfect, but I suspect that the utilization of these proxy variables only diminishes the correlation. The authors admit that there is a lot of work to be done, but this is just the first step.</i><br /><br />Now I cite your reaction to all this:<br /><br /><i>It should be obvious that the correlation between species range and size (body size?) and population size is fairly weak, and the correlation between population size and population density is even weaker.</i><br /><br />Thank you for helping me out and answering Larry's question above. <br /><br />So I guess that would mean the original PLoS paper does not pose a threat to what Kahn deems <i>"the extremism of some of the anti-selectionists"</i><br /><br />Moving on, you ask:<br /><br /><i>And I still don't see what the Allee effect could have to do with any of this.</i><br /><br />Let’s stop talking in abstractions and cite specific examples such as the evolution of shoaling and schooling in Fish populations which would be a paradigm of the Allee effect.<br /><br />There must be an adaptive and polygenetic component to swarming behavior. I wanted you to agree that left to their own devices, shoaling and schooling fish (for example) will demonstrate a high Nc over time if they have a large range, and all as an adaptive advantage of the Allee effect. <br /><br /><b>TM:</b> <i> Any species exhibiting Allee over a large range ie. that simultaneously exhibited a large population density AND a large range would be definition exhibit a large Nc.</i> <br /><br />For the sake of argument, let’s just for the moment assume that that contention is in fact correct, then Allee does indeed<i> have a lot to do with any of this.</i><br /><br />According to Neutral Theory, Razib Khan poses a problem:<br /><br /><i>…natural selection removes more variation at linked neutral sites in species with large Nc than those with small Nc and provides direct empirical evidence that natural selection constrains levels of neutral genetic diversity across many species.</i><br /><br />This should not be happening. <br /><br />There are a number of trivial reasons why the Allee effect would reduce variation such as the "oddity effect". <br /><br />I cite from Wikepedia:<br /><br /><i>The "oddity effect" posits that any shoal member that stands out in appearance will be preferentially targeted by predators. This may explain why fish prefer to shoal with individuals that resemble themselves. The oddity effect would thus tend to homogenize shoals.</i><br /><br />http://en.wikipedia.org/wiki/Shoaling_and_schooling#How_fish_school<br /><br />In other words, the “oddity effect” would confound Neutral Theory expectations for apparently trivial reasons that only apply to those prey species demonstrating an Allee effect.<br /><br />And not just the “oddity effect”… there are other consequences, but that’s enough for now.<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-33105614253336499202015-04-26T05:12:14.029-04:002015-04-26T05:12:14.029-04:00@Peer Terborg
I don't agree with Gnomon and so...@Peer Terborg<br />I don't agree with Gnomon and so do you (I suspect you missed that point).<br />Shi Huangs Ideas certainly are at odds with your "frontloading ideas", he is an evolutionist.<br />If I you think that I am wrong, I'd like you to elaborate why do you think that the "brilliant analysis" of an evolutionist can be compatible with your point of view. <br />There is a lot at stake! You could disprove the first axiom of creationism research!<br /><br />First Axiom of Creationism-Research:<br />Shit attracts flies.<br /> Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-2349250271584651012015-04-25T16:25:05.140-04:002015-04-25T16:25:05.140-04:00It should be obvious that the correlation between ...It should be obvious that the correlation between species range and size (body size?) and population size is fairly weak, and the correlation between population size and population density is even weaker. And I still don't see what the Allee effect could have to do with any of this.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-58754162752808366032015-04-25T12:50:49.077-04:002015-04-25T12:50:49.077-04:00Hi again John… and again thank you for your patie...Hi again John… and again thank you for your patience and your indulgence<br /><br />Regarding your question<br /><br /><i> You are missing the difference between "neutral" and "nearly neutral". </i><br /><br />I admit I am climbing a steep Ebinghus curve here. I did refer to Razib Khan’s citation of <br /><br />http://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution<br /><br />… but that is no guarantee I have indeed mastered the concept.<br /><br /><i>Also, the way you quantify diversity may influence what you find. What do *you* mean by "diversity"?</i><br /><br />Agreed - refer to my earlier posts (down below) regarding “<i>proxy</i>” variables.<br /><br />By <i>” diversity”</i> I was deferring to the original definition on the first sentence of the original PLoS paper<br /><br /><i>The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size (Nc).</i><br /><br />http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002112<br /><br />FTR – I actually have spent quite some time composing my thoughts before typing! That said, I may clearly be over my head and out of my league and I thank you for your efforts to aid my understanding of this interesting question.<br /><br />Best and warmest regards<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-48477122449160186312015-04-25T12:36:55.892-04:002015-04-25T12:36:55.892-04:00Hi again John
Your question:
What paper?
I cit...Hi again John<br /><br />Your question:<br /><br /><i> What paper?</i><br /><br />I cite below the relevant bit from Razib Khan's<br /><br />http://www.unz.com/gnxp/selectionism-strikes-back/?utm_source=rss&utm_medium=rss&utm_cam<br /><br /><i>Why would you use species range as a proxy for population?</i><br /><br />That relevant bit would be<br /><br /><i>As the figure above shows there is a correlation between the power of selection on the genome and inferred effective population size. I say inferred because they had to use <b>species range</b> and size as <b>proxies</b>. Obviously this isn’t perfect, but I suspect that the utilization of these proxy variables only diminishes the correlation. The authors admit that there is a lot of work to be done, but this is just the first step.</i><br /><br />Your question:<br /><br /><i> why would you use population as a proxy for population density?</i><br /><br />Any species exhibiting Allee over a large range ie. that simultaneously exhibited a large population density AND a large range would be definition exhibit a large Nc.<br /><br />As I mentioned above, I do not think this should prove a problem for the champions of Neutral Theory.<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63374309900056544072015-04-25T12:24:22.432-04:002015-04-25T12:24:22.432-04:00Hi John
First a prequel
I only recently became a...Hi John<br /><br />First a prequel<br /><br />I only recently became aware of the Allee effect when attempting to summarize the regulation of complex Biological systems from the level of Gene Regulation (example lambda bacteriophage lysogeny) to Ecosystems (the Allee Effect) and was struck by the fact that positive feedback is egregiously misrepresented in standard introductory textbooks.<br /><br />"Positive Feedback" plays a very important role in maintaining "set points"; often-as-not before quick transitions to some new "commitment step" as presciently elucidated by Jacob and Monod as far back in 1961. Positive feedback does not always accelerate to some "terminal event".<br /><br />Ergo, my ongoing interest in Allee effects. All such considerations become VERY complex when actually attempting to determine the ubiquity of Allee Effects. When reading Larry's post, I immediately wondered out loud whether the authors had unknowingly stumbled across an indirect measure of Allee. Mind you my maths skills are woefully inadequate to take that line of conjecture further on my own.<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-17941753016953102332015-04-24T20:10:41.384-04:002015-04-24T20:10:41.384-04:00What paper? Why would you use species range as a p...What paper? Why would you use species range as a proxy for population? And even more, why would you use population as a proxy for population density?John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-49888828529693190062015-04-24T20:08:25.047-04:002015-04-24T20:08:25.047-04:00You are missing the difference between "neutr...You are missing the difference between "neutral" and "nearly neutral". Also, the way you quantify diversity may influence what you find. What do *you* mean by "diversity"?John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-65766190745474318992015-04-24T17:15:22.895-04:002015-04-24T17:15:22.895-04:00Hi again John
You say:
The Allee effect doesn...Hi again John<br /><br />You say:<br /><br /><i>The Allee effect doesn't predict large population sizes in the abstract, or larger population sizes than other species. </i><br /><br />I agree, unless of course "species range" is employed as a "proxy" for Nc as was done in this paper.Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-4341589799960958942015-04-24T16:59:42.848-04:002015-04-24T16:59:42.848-04:00First things first.
John, you say:
At higher po...First things first.<br /><br />John, you say:<br /><br /><i> At higher population sizes, purifying selection is more effective and nearly neutral diversity should be reduced; what more is needed?</i><br /><br />But is that not the whole point? What you just described is not supposed to be happening if (and I quote Razib Khan)<i> "the extremism of some of the anti-selectionists"</i><b>[sic] </b>were correct.<br /><br />I cite directly from Larry’s cited link: <b>Selectionism Strikes Back!</b><br /><br />http://www.unz.com/gnxp/selectionism-strikes-back/?utm_source=rss&utm_medium=rss&utm_cam<br /><br /><i>Assuming the neutral theory of molecular evolution you’d expect that you’d have more genetic diversity in species with larger population sizes,…</i> <br /><br />…not less. <br /><br />So what am I missing?<br /><br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-12716878340605959672015-04-24T16:56:08.020-04:002015-04-24T16:56:08.020-04:00I am going to beg deference of that question until...I am going to beg deference of that question until I am up to speed on the writings of Gregory et al. <br /><br />I would like to revisit so-called higher orders of selection as advocated by Gould et al, such as at the species level, but not just now.<br /><br />I am not ready just now.Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.com