tag:blogger.com,1999:blog-37148773.post8676201562450970244..comments2024-03-19T00:24:23.577-04:00Comments on <center>Sandwalk</center>: What's the Difference Between a Human and Chimpanzee?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger33125tag:blogger.com,1999:blog-37148773.post-13371887095981533782016-10-08T05:28:07.762-04:002016-10-08T05:28:07.762-04:00Hello,
This reference might help..
http://www.na...Hello,<br /><br />This reference might help..<br /><br />http://www.nature.com/nature/journal/v429/n6990/abs/nature02564.html<br /><br />Cheers,<br />KarlJ.Karlhttps://www.blogger.com/profile/00924584014848026429noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-61234333224238653982015-01-10T04:19:20.717-05:002015-01-10T04:19:20.717-05:00As I mentioned in the blog post you linked to (reg...As I mentioned in the blog post you linked to (regarding Demuth's paper about gene families), the author of that study made some huge mistakes, and they were pointed out by Laurent Duret:<br /><br />http://www.plosone.org/annotation/listThread.action?root=8729<br /><br />Basically, Demuth's paper should be discarded.<br /><br />I have tried to replicate Duret's objection, but unfortunately the format of the gene family identifiers has changed, and there is no mapping between the old format and the new.Glennhttps://www.blogger.com/profile/03419669114209732527noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-23146456337536521842012-01-31T14:34:49.854-05:002012-01-31T14:34:49.854-05:00I think what I would do is to see differences in c...I think what I would do is to see differences in characters, and guess that differences big enough for me to see are big enough to make some relevant fitness difference to the organism. I would suspect non-neutrality but be suspicious of any particular just-so-story, particularly given the real possibility that these changes are side-effects of changes in other characters.<br /><br />For molecular changes I would certainly suspect neutrality, but of course that depends on exactly where they are -- for example, if a change was in the active site of an important enzyme my eyebrows would raise.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-48841660151840462182012-01-30T15:53:20.227-05:002012-01-30T15:53:20.227-05:00I said nothing about "concluding" anythi...I said nothing about "concluding" anything. In the absence of any evidence to the contrary I assume, as a working hypothesis, that the trait is neutral. That's all I assume. It's the null hypothesis. I will happily change my mind as soon as I see some evidence of adaptation.<br /><br />Adaptationists, on the other hand, assume that the trait is adaptive and then they "assume" some kind of adaptive just-so story to explain their assumption. They reject neutrality out of hand. I don't know why they do that, do you?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-67666735434320393492012-01-29T21:46:11.015-05:002012-01-29T21:46:11.015-05:00Why do you feel it's necessary to come up with...<i>Why do you feel it's necessary to come up with an adaptive explanation of some sort? Why not assume that it's accidental until there's evidence to the contrary?</i><br /><br />Great, so the less information we have, the more strongly we can conclude in favor of neutrality ...Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-3363744800389837082012-01-29T20:21:26.836-05:002012-01-29T20:21:26.836-05:00Joe, don't take this the wrong way but when yo...Joe, don't take this the wrong way but when you say ...<br /><i>Many of these changes can also be side effects of selection for other traits. My ability to roll my tongue is the result of changes in muscles in the tongue, changes that may have noticeable effects on fitness for other reasons than the issue of rolling.</i><br /><br />Why do you feel it's necessary to come up with an adaptive explanation of some sort? Why not assume that it's accidental until there's evidence to the contrary?<br /><br />Is there any evidence at all that people who can roll their tongues are more (or less) fit than people who can't?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-61332953350074419062012-01-29T09:02:14.054-05:002012-01-29T09:02:14.054-05:00We usually stick out our tongues and try to roll t...<i>We usually stick out our tongues and try to roll them. Many students can't roll their tongues so we discuss whether tongue-rolling ability affects fitness. Then we talk about the shape of our lips, our earlobes, English ankles, and male pattern baldness. How many of these heritable morphological traits affect fitness?<br /><br />The point is not to dispute the fact that many morphological differences between closely related species are adaptive. The point is to question whether all of it is adaptive and what we should adopt as out null hypothesis when trying to decide.</i><br /><br />Many of these changes can also be side effects of selection for other traits. My ability to roll my tongue is the result of changes in muscles in the tongue, changes that may have noticeable effects on fitness for other reasons than the issue of rolling.<br /><br />The question was not whether <i>all</i> morphological differences are neutral -- surely they are not. Previously we were discussing whether the fraction neutral was more like 90% or more like 10%.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-86012997694114509992012-01-28T09:58:14.504-05:002012-01-28T09:58:14.504-05:00Well, how much of it would have how much effect on...<i>Well, how much of it would have how much effect on fitness? You seem to know (somehow). </i><br /><br />I don't know but I want students to think about the possibility that much of it may be non-adaptive. There's a huge misconception out there that all (or almost all) morphological changes have to affect fitness and my goal is to challenge that assumption. <br /><br />We usually stick out our tongues and try to roll them. Many students can't roll their tongues so we discuss whether tongue-rolling ability affects fitness. Then we talk about the shape of our lips, our earlobes, English ankles, and male pattern baldness. How many of these heritable morphological traits affect fitness?<br /><br />The point is not to dispute the fact that many morphological differences between closely related species are adaptive. The point is to question whether all of it is adaptive and what we should adopt as out null hypothesis when trying to decide.<br /><br />In humans, the hair on our heads just keeps growing and growing. That doesn't happen in the other apes. How do we explain this difference? Do we immediately assume that there must be some adaptive significance to having long hair and beards or do we assume that it could be non-adaptive, putting the onus on the adaptationists to prove their case? <br /><br />And what about the relative lack of hair on the rest of our bodies? Is that an accident due to neoteny or does it require some elaborate just-so story about sun and savannahs?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-6654555981701037582012-01-27T20:36:54.100-05:002012-01-27T20:36:54.100-05:00The probability of fixation is about 2s. If s is 0...<i>The probability of fixation is about 2s. If s is 0.0000025 then the probability of fixation is about 0.000005 or 0.0005%. In other words, the allele will be lost 99.999% of the time.<br /><br />The time to fixation is (2/s)ln(2N). For an allele with such a low fixation coefficient the time will be about one million generations or approximately 10 million years.<br /><br />The selection coefficients are going to have to be much higher if we're going to explain a significant numbers of morphological changes as adaptations.</i><br /><br />There are two issues: significant numbers of morphological changes, or significant numbers of loci differing between humans and chimps. You've got me on the latter, but I think you are in a terribly weak position on the former. Most of the differences will be due to the allele substitutions of larger effect, because these both have higher probability of fixation <i>and</i> have more effect on the character. Thus the changes that account for a morphological difference are 4x as likely to be due to a substitution that has 2x larger effect. <br /><br /><i>In class, I ask my students to look around them at all of the heritable variation in morphological traits that we see today in a modern multicultural society. How much of that variation is likely to be adaptive or thought have been adaptive in the recent past (<50,000 years)?<br /><br />Not much, if you are being honest. Isn't it likely that much of the morphological variation that became fixed in the past was also non-adaptive?</i><br /><br />Well, how much of it would have how much effect on fitness? You seem to know (somehow). Considering a trait that is a quantitative character, and considering how much genetic variance it has and how large the selective effect is of a one-standard-deviation change, you can do some calculations. But it looks like you are relying on impressions. <br /><br /><i>That doesn't rule out significant adaptations. I'm just trying to get people to realize that the vast majority of changes at the molecular level are non-adaptive and that may also be true for most morphological changes.</i><br /><br />I agree about the molecules, anyway.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-86597927028695919332012-01-26T12:52:51.027-05:002012-01-26T12:52:51.027-05:00Of course, in deriving the minimum non-neutral sel...Of course, in deriving the minimum non-neutral selection coefficient, I may have forgotten to consider diploidy, ie 1/2N not 1/N ...Allan Millernoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-48941466527385132552012-01-26T11:31:55.839-05:002012-01-26T11:31:55.839-05:00The time to fixation is (2/s)ln(2N). For an allele...<i>The time to fixation is (2/s)ln(2N). For an allele with such a low fixation coefficient the time will be about one million generations or approximately 10 million years. </i><br /><br />Ah, this is where population genetics really confuses me! The 'simplified' time to fixation of a neutral allele is 4Ne generations, ie 400,000 (only 2 gens out from the 'complicated' time). Yet here we have an allele with a positive selection coefficient taking two and a half times as long? <br /><br />Again, the neutral chance of fixation is 1/N, so values of 2s below that become effectively neutral - they can't be <i>less</i> likely than a neutral allele to fix? ie, is the minimum value of s that would behave non-neutrally not >0.000005? <br /><br />I know it doesn't make a huge difference. And, in the wild, the computationally necessary assumption of constancy for s values over such long time periods is, I suspect, always overturned by more local effects - fluctuations in s itself.Allan Millernoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-39546744222741599402012-01-26T10:09:59.011-05:002012-01-26T10:09:59.011-05:00I fixed it. Is it clear now?I fixed it. Is it clear now?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-81713161311638498382012-01-26T10:07:38.678-05:002012-01-26T10:07:38.678-05:00Most of those errors would be base calls. A small ...Most of those errors would be base calls. A small proportion would be indels. We get a tiny fraction of 5 million. Not worth thinking about in a first approximation.<br /><br />In fact I would expect polymorphism to be a bigger source of "error". Or, if we're talking about one individual, heterozygosity. How did the genome projects handle heterozygosity anyway?jnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-89663462935876953572012-01-26T10:05:31.301-05:002012-01-26T10:05:31.301-05:00Well that pretty much settles it, don't you th...Well that pretty much settles it, don't you think?<br /><br />The creationists say that chimps and humans are only 80% identical because all of the unfinished part of the genome sequences must be different. <br /><br />Time to re-write the textbooks! :-)Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-1497008539588824962012-01-26T10:02:47.275-05:002012-01-26T10:02:47.275-05:00The probability of fixation is about 2s. If s is 0...The probability of fixation is about 2s. If s is 0.0000025 then the probability of fixation is about 0.000005 or 0.0005%. In other words, the allele will be lost 99.999% of the time. <br /><br />The time to fixation is (2/s)ln(2N). For an allele with such a low fixation coefficient the time will be about one million generations or approximately 10 million years. <br /><br />The selection coefficients are going to have to be much higher if we're going to explain a significant numbers of morphological changes as adaptations. <br /><br />In class, I ask my students to look around them at all of the heritable variation in morphological traits that we see today in a modern multicultural society. How much of that variation is likely to be adaptive or thought have been adaptive in the recent past (<50,000 years)? <br /><br />Not much, if you are being honest. Isn't it likely that much of the morphological variation that became fixed in the past was also non-adaptive? <br /><br />That doesn't rule out significant adaptations. I'm just trying to get people to realize that the vast majority of changes at the molecular level are non-adaptive and that may also be true for most morphological changes.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-85978052849993363892012-01-26T09:39:48.178-05:002012-01-26T09:39:48.178-05:00Typical error rates for "finished" genom...Typical error rates for "finished" genome sequences are on the order of 10^-4 or one error in 10,000 base pairs. That's about 300,000 sequence errors in the genome. The original chimp genome sequence was far from being "finished" when it was first published. <br /><br />First draft genomes typically have error rates of more than one in 1000 meaning that something like 3 million errors would be counted as differences in the comparison with the human genome. Many of these would be small deletions. <br /><br />Furthermore, the human genome was not a "finished" genome when the comparison was first done so there would have been sequence errors there as well.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-80883900179243897402012-01-25T17:55:32.834-05:002012-01-25T17:55:32.834-05:00good information ... I have read and will be added...good information ... I have read and will be added to my personal knowledge... thanksbusana muslimhttp://toko-baju-muslim.comnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-2165613010145995222012-01-25T17:23:20.205-05:002012-01-25T17:23:20.205-05:00I don't actually see how you can get such sequ...I don't actually see how you can get such sequence errors in a genome that has -- what? -- 10x coverage or better. Now my usual experience is with just 1x coverage of many species, and there's a suspiciously high level of consistency in small indel placement among close relatives. So yeah, I think most of them should be just fine. (Of course I'm talking about Sanger sequencing, and pyro/454 sequencing has a much higher error rate for both base and indel calls. But the genomes in question were done the old way.) Is this really an issue? I've got to suppose that a very small proportion of reported indels are sequencing (or, more likely, amplification) errors.John Harshmannoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28107302658489749542012-01-25T11:18:34.057-05:002012-01-25T11:18:34.057-05:00OK, I'm back, having looked at Polavarapu et a...OK, I'm back, having looked at Polavarapu et al. They do not in fact say there are only 26,500 indels. They limit their search to indels between 80 and 12,000 bp. That is, they ignore all indels under 80 bp. Like many other phenomena, indels display a hollow curve distribution. Indels over 80 bp are very rare compared to shorter indels. It's likely, in fact, that 1bp indels are an absolute majority of indel events.<br /><br />So there you are, discrepancy explained: the chimp genome paper was counting all indels, while Polavarapu et al. were counting only the largest indels.John Harshmannoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-30468393189616299302012-01-25T11:14:29.804-05:002012-01-25T11:14:29.804-05:00John,
Sorry 'bout that.
I added the referenc...John,<br /><br />Sorry 'bout that.<br /><br />I added the reference and modified the text because the number reported in the paper (26,509) only refers to indels larger than 80 bp.<br /><br />It's true that there are millions of indel differences between humans and chimps. What we don't know is how many of those are real and how many are due to sequence errors. The chimp sequence is not very good.<br /><br />Are the bird genome sequences so good that you can rely on small indels of 1-5 bp?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-39592976247067921242012-01-25T11:11:41.304-05:002012-01-25T11:11:41.304-05:00Haven't read Polavarapu et al. yet (and thanks...Haven't read Polavarapu et al. yet (and thanks for posting the reference), but the chimp genome paper was based on an actual count over the entire published alignment. It's hard to see how two alignments (if that's what it is) could be different enough to account for a greater than 3 orders of magnitude difference. At the least, this demands some explanation.John Harshmannoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-42777793074343187682012-01-24T21:45:03.775-05:002012-01-24T21:45:03.775-05:00Population genetic theory says that natural select...Population genetic theory says that natural selection will be effective if the selection coefficient for that allele substitution exceeds the reciprocal of 4N. As the population size N was in the vicinity of 100,000, that says that selection if effective if s > 0.0000025. So I think the fraction is more like 90%.<br /><br />Changes that do not result in any change in visible morphology include some that change nerve function or physiology, so let's not go overboard. And no, just because we declare one pattern to be a null hypothesis does not mean we get to forget about other possibilities.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-1854397949406733822012-01-24T15:54:12.856-05:002012-01-24T15:54:12.856-05:00I think we can agree that 99.9% of all differences...I think we can agree that 99.9% of all differences are neutral since they don't involve any change in visible morphology. <br /><br />The question is, what percentage of those alleles that DO result in a visible morphology have been fixed by natural selection? I'm guessing that number would be less than 10%. What number do you prefer?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28885816376532644202012-01-24T15:50:11.980-05:002012-01-24T15:50:11.980-05:00There are many papers and many estimates. I don...There are many papers and many estimates. I don't know which one is more likely to be correct, do you?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-4365318151074520892012-01-24T14:20:15.534-05:002012-01-24T14:20:15.534-05:00So, are you saying that ... gasp ... there's s...So, are you saying that ... gasp ... there's something else besides DNA?!Anonymousnoreply@blogger.com