tag:blogger.com,1999:blog-37148773.post668326641538311099..comments2024-03-18T09:58:09.828-04:00Comments on <center>Sandwalk</center>: Coelacanths Evolve More Slowly?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger39125tag:blogger.com,1999:blog-37148773.post-52396622702081965772013-11-07T04:52:42.517-05:002013-11-07T04:52:42.517-05:00I'm a bit late to this discussion, but I'm...I'm a bit late to this discussion, but I'm writing something on this for the museum where the picture on this blog post was taken (Oxford). I don't quite get their method: is the protein tree based on the amino acid sequence or the underlying ATCG code? If the latter (as I would guess from their choice of model), why is there no estimate of synonymous vs nonsynonymous evolution. This might show whether the slow rate is due to low mutation (few synonymous changes predicted) or to strong purifying selection (normal rate of accumulation of synonymous changes).<br /><br />Also, is there likely to be an ascertainment bias in the genes chosen? Picking those that *can* be easily compared means you will undoubtedly chose conserved sequences. But this should equally apply to the tetrapod and coelacanth linages, unless the filled-out tetrapod tree was used to infer a basal sequence for the tetrapods. Anonymoushttps://www.blogger.com/profile/12097380772105203428noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-53607480800328291752013-04-22T18:26:47.083-04:002013-04-22T18:26:47.083-04:00If. In other words, no. I merely say that it's...If. In other words, no. I merely say that it's 1) unnecessary to say everything you think you need to and 2) possible to find several ways of saying what you actually do need to.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-51415693489776273052013-04-22T17:58:30.118-04:002013-04-22T17:58:30.118-04:00So if I understand you correctly, your results sec...So if I understand you correctly, your results section in its entirety would read something like this: "The phylogeny can be seen in figure 2"?Alex SLhttps://www.blogger.com/profile/00801894164903608204noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-85576890104839011572013-04-22T09:40:18.369-04:002013-04-22T09:40:18.369-04:00I find it hard to imagine why you would have to de...I find it hard to imagine why you would have to describe 20 nodes in a results section rather than allowing the tree to speak for itself, but there are still alternatives available. "X is the sister group of Y"; "X is outside Y"; "Y and Z form a clade that excludes X"; and so on. The perceived difficulty of combining accuracy and good writing is not an excuse.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40088144863637383652013-04-22T06:30:32.610-04:002013-04-22T06:30:32.610-04:00The problem remains that there is only one way of ...The problem remains that there is only one way of describing a tree left that is not considered misleading, and repeating the same phrase twenty times in a row in your results section looks like pretty bad writing and is seriously off-putting.Alex SLhttps://www.blogger.com/profile/00801894164903608204noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-77210379785729289292013-04-22T03:11:47.174-04:002013-04-22T03:11:47.174-04:00(The claim that their results support changes in f...(The claim that their results support changes in fixation probabilities of protein coding genes.)Konradhttps://www.blogger.com/profile/06867375994008638278noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-38778635980968483042013-04-22T03:09:22.307-04:002013-04-22T03:09:22.307-04:00Larry: where do they actually make that claim? I s...Larry: where do they actually make that claim? I saw speculation, but no actual claim. And as I pointed out above, they present (presumably without realizing) results against such a claim.Konradhttps://www.blogger.com/profile/06867375994008638278noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-69312632002617723002013-04-21T20:36:26.476-04:002013-04-21T20:36:26.476-04:00I think it's misleading because it can't h...I think it's misleading because it can't help but reference a great chain of being that doesn't exist. Even if you explain that there are different possible chains, it amounts to the same thing. The fact is that we are taking one fork of a basal divergence and calling it the main line of evolution and arbitrarily calling the other a side branch. If hagfish are basal vertebrates, then other vertebrates are basal hagfish, which sounds silly. The other meaning of "basal" is "less diverse than its sister group", which is also silly. Best dispensed with.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10479161675537218422013-04-21T17:37:50.200-04:002013-04-21T17:37:50.200-04:00So the term is not misleading at all if you use it...So the term is not misleading at all if you use it or explain it right. Some lay people are still thinking of the Great Chain of Being, so TONS of scientific terms are going to be "misleading" for these people. Starting with "evolution".El PaleoFreakhttps://www.blogger.com/profile/11323149141956089390noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60028407023342592962013-04-21T14:31:44.937-04:002013-04-21T14:31:44.937-04:00Yes, if I had been a reviewer of this article I...Yes, if I had been a reviewer of this article I'd have asked for more explanation, and I would have made them give confidence intervals for meaningful parameters instead of (or alongside) p-values in their tests for rate differences. No more of this misleading "significantly slower" talk.<br /><br />But my point was just that this effect, by itself, (especially if it were due to slightly lower mutation rate, perhaps via fewer hotspots) would not really be that earthshaking. <br />LJUnknownhttps://www.blogger.com/profile/15295365056966230651noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-36124991230241125942013-04-21T08:18:26.627-04:002013-04-21T08:18:26.627-04:00We can't even say "basal lineage" wh...<i>We can't even say "basal lineage" when a lineage is basal??<br />This is going too far...</i><br /><br />You can, but it all depends... We primates are basal primatomorphs (from the colugos' point of view). Primatomorphs are basal euarchonts (with respect to tree-shrews). Euarchonta are basal Euarchontoglires (with respect to rodents and lagomorphs), etc., etc... with the ancestors of Tetrapoda ending up as basal sarcopterygians (if you ask the coelacanth).Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-29684523337574058512013-04-21T07:39:19.619-04:002013-04-21T07:39:19.619-04:00We have known that the error rate of DNA replicati...We have known that the error rate of DNA replication/repair is under genetic control for almost fifty years. <br /><br />We also know that the error rate in most lineages has been approximately constant for hundreds of millions of years in spite of the fact that variation can arise from time to time.<br /><br />It's possible that some clades have evolved an efficient replication/repair system that's twice as good as that in almost all other species but it's not the most parsimonious explanation of the data. Besides, the paper implies that the overall mutation rate in these fish isn't much different than in other species.<br /><br />Note that the authors aren't invoking changes in mutation rate. They are claiming that the results support changes in the fixation propabilities in coelacanth protein-encoding genes. That's extremely unlikely, don't you agree? Would you have allowed this paper to be published with that kind of explanation and no mention of other possibilities or of the fact that this conflicts with a lot of theory and data?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-88827424532892340812013-04-21T06:38:00.349-04:002013-04-21T06:38:00.349-04:00You know, I sometimes think the same. I hate it ho...You know, I sometimes think the same. I hate it how you cannot describe your phylogeny anymore without the reviewers throwing a bucket of red ink at the manuscript. Every phrase except "X is sister group to Y, and in Y A is the sister group of B" appears to be considered unscientific now, but it makes for very obnoxious writing.<br /><br />I think that "basal" still makes sense because you always have a perspective: that of your current study group. When you study primates, the rodents are a basal branch; when you study rodents, the primates are a basal branch. Still, the problem is with the laypeople whose perspective is nearly invariably a great chain of being leading up to humans...Alex SLhttps://www.blogger.com/profile/00801894164903608204noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-75932359410460368282013-04-21T05:05:11.935-04:002013-04-21T05:05:11.935-04:00We can't even say "basal lineage" wh...We can't even say "basal lineage" when a lineage is basal??<br />This is going too far...El PaleoFreakhttps://www.blogger.com/profile/11323149141956089390noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-16305619095222058152013-04-20T17:30:54.693-04:002013-04-20T17:30:54.693-04:00Larry, so we agree that the mutation rate (error r...Larry, so we agree that the mutation rate (error rate - repair rate) can vary with the locus. The existence of the hot spots you mention is evidence for this. There is also evidence of different mutation rates in different chromosomes of the same organism, and different mutation rates in different species. There is even variation in mutation rates between genotypes:<br /><br />labs.eeb.utoronto.ca/agrawal/publications/nps_afa_pnas_2012.pdf<br /><br />All of this suggests that mutation rate is under partial genetic control, and so it is certainly possible that the coelacanth has a lower mean mutation rate than most other vertebrates. <br /><br />I have no opinion about whether it really does have a lower rate, though.<br /><br />LJUnknownhttps://www.blogger.com/profile/15295365056966230651noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-27160947576357557792013-04-20T15:28:21.679-04:002013-04-20T15:28:21.679-04:00@Lou Jost
The mutation rate is mostly determined ...@Lou Jost<br /><br />The mutation rate is mostly determined by the error rate of DNA replication. There are a few hotspots but the error rate is pretty much the same throughout the entire genome.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-91858128319196751322013-04-20T11:08:14.795-04:002013-04-20T11:08:14.795-04:00No, different mutation rates per base aren't d...No, different mutation rates per base aren't distributed at random across the genome. Mutation rates are properties of particular loci. These are actual mutation rates I am talking about, not a rate based on what's left after purifying selection. Those loci under no selection pressure often mutate more rapidly than loci which are under high selective pressure.<br />LJUnknownhttps://www.blogger.com/profile/15295365056966230651noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10395412131241828792013-04-20T04:17:59.312-04:002013-04-20T04:17:59.312-04:00Just want to point out that fig 3 in the paper act...Just want to point out that fig 3 in the paper actually quantifies (a point estimate of) the proportion of sites evolving under purifying selection (blue), neutrally (yellow) and positive selection (red) on each branch of the tree, and the strength of that selection, for the gene depicted. The analysis is based on comparing synonymous and nonsynonymous rates, so can only be done for protein coding regions. Throughout the tree, purifying selection dominates, with quite a few neutrally evolving sites and an essentially negligible nr of positively selected sites. When the authors speculate about adaptation playing a role, they are ignoring this evidence.<br /><br />(Full disclosure: I'm one of the people responsible for the analysis methodology that produced this figure.)Konradhttps://www.blogger.com/profile/06867375994008638278noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54597685466872245622013-04-20T03:59:48.236-04:002013-04-20T03:59:48.236-04:00Also note that the reported effect size is not ver...Also note that the reported effect size is not very large.<br />Konradhttps://www.blogger.com/profile/06867375994008638278noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-38527300786239026662013-04-20T03:52:19.832-04:002013-04-20T03:52:19.832-04:00It is well established that mutation rate correlat...It is well established that mutation rate correlates strongly with generation time in vertebrates, and possibly also in other systems (e.g. invertebrates and plants). The reasons for the correlation are still under debate. See Thomas et al, MBE 2010, which starts with a review of some of the literature on this.Konradhttps://www.blogger.com/profile/06867375994008638278noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-64679673892310077752013-04-19T22:02:12.433-04:002013-04-19T22:02:12.433-04:00Different genes are bound to have different mutati...Different genes are bound to have different mutation rates because that's what we should expect if the background mutation is random. Small genes will be more difficult to properly measure, and might look more biased, than larger genes, for example. Then there's purifying selection. Mutations causing harm will be selected against. This is why the apparent mutation rates inside genes is lower than in the spaces between genes or in introns. Then there's how important each part of a gene's sequence might be for function. If a lot of the gene is functionally important, we will se a much lower "mutation rate" because of stronger purifying selection ... so as you can see, before talking about genetic control for mutational rates, probability and purifying selection might explain a lot about apparent differences in mutation rates. Maybe some organisms do have different mutation rates for reasons other than random events combined with purifying selection. I have not studied that too much. Maybe some have better repair mechanisms and that translates as lower mutation rates. I have not studied that too much either.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-78521108797277746832013-04-19T21:50:59.312-04:002013-04-19T21:50:59.312-04:00We know that mutation rate per base is partially u...We know that mutation rate per base is partially under genetic control, because different genes have different mutation rates per base. So I don't see that it is impossible for some lineages to evolve lower mutation rates than others. <br />Lou JostUnknownhttps://www.blogger.com/profile/15295365056966230651noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-75708014241805493892013-04-19T20:42:39.309-04:002013-04-19T20:42:39.309-04:00Exceptionally long generation times could explain ...Exceptionally long generation times could explain the data provided that coelacanth eggs are formed after 30-odd generations and then remain dormant for one hundred years. The fish would also have to produce limited amounts of sperm during that time.<br /><br />Do you have a reference?<br /> Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10684321759975660542013-04-19T19:34:28.076-04:002013-04-19T19:34:28.076-04:00It is clear that ‘living fossil’, ‘basal lineage’,...It is clear that ‘living fossil’, ‘basal lineage’, or ‘primitive extant species’ are rather misleading concepts, and that genomes keep evolving even while morphology is under stabilizing selection. Still, I thought the long-going controversy over whether evolutionary rates can differ between lineages was by now clearly decided in the affirmative.<br /><br />In my own field of botany, there appears to be some evidence that shorter generation times lead to longer branches in molecular phylograms, meaning that molecular evolution is faster in short-lived and slower in long-lived organisms. I am still a bit puzzled why that would be so - I would consider it more logical that faster growth would speed up mutation rates. On the other hand, because sex increases recombination, the number of generations per time might reasonably be expected to have an impact. Interestingly, I have also seen talks at conferences showing that carnivorous plants sometimes show very long branches compared to their non-carnivorous relatives; no idea why that is.Alex SLhttps://www.blogger.com/profile/00801894164903608204noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-70102756479663556512013-04-19T18:41:36.507-04:002013-04-19T18:41:36.507-04:00Still suspicious. According to the abstract, their...Still suspicious. According to the abstract, their relative rate tests were done with distances abstracted from the tree. So if there's an artifact, their tests would not detect it. Can you really test for a node-density effect using the posterior tree distribution? I don't actually see how.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.com