tag:blogger.com,1999:blog-3248412803814730250.post958118977848021253..comments2024-03-17T01:48:59.504-07:00Comments on The Theropod Database Blog: Peters' dinosaur phylogeny fails finale part 1 - The ProblemsMickey Mortimerhttp://www.blogger.com/profile/08831823442911513851noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-3248412803814730250.post-87638954840390851182013-03-29T18:58:00.389-07:002013-03-29T18:58:00.389-07:00They usually don't come up because authors are...They usually don't come up because authors are usually better at forming characters. Again I use my "number of presacral vertebrae divided by number of sacral vertebrae, answer rounds to an - even number (0); odd number (1)" fictional example. If this were in an analysis, you wouldn't say it doesn't matter how or why it's supposed to work, you'd say there's no way such a character could be genetically controlled.<br /><br />Your philosophy toward character choice and coding in general is far too blase. You can't trust the phylogeny to "come out in the wash", certainly not with 228 characters. What you don't seem to realize is that (even when correctly coded), your choice of characters (and taxa) does skew the suite. If you "just want to see what happens" when using those characters, great, but then don't pretend it's giving you a well supported phylogeny.Mickey Mortimerhttps://www.blogger.com/profile/08831823442911513851noreply@blogger.comtag:blogger.com,1999:blog-3248412803814730250.post-34841930558430414802013-03-24T06:54:13.587-07:002013-03-24T06:54:13.587-07:00What developmental mechanism do you know that work...What developmental mechanism do you know that works in straight lines between elements formed at different times? <br /><br />The why and how questions never come up in phylogenetic analysis. IF the tibia was longer than the femur in a near legless taxon and in a cursor, that's a convergence. Wings, or a Carapace, as a trait, is a convergence. How they develop is not germane to scoring. It all comes out in the wash. The suite is what counts. And the choice of traits can skew the suite. That's one reason why I haven't added traits for the last 150 or so added taxa. I just want to see what happens with what I got. D.P.https://www.blogger.com/profile/13009843520057633239noreply@blogger.comtag:blogger.com,1999:blog-3248412803814730250.post-37183837902167986292013-03-20T01:16:18.122-07:002013-03-20T01:16:18.122-07:00Regarding interphalangeal lines, I said it doesn&#...Regarding interphalangeal lines, I said it doesn't matter if these could be objectively identified (choosing the right angle to put each phalanx and metapodial from adjacent ones) or are functionally useful (as the roughly straight line between first phalanges on manual digits II-V is when we hold a golf club, as you say). My issue with them being used as characters is that morphological characters are basically stand-ins for mutations that could be inherited. Characters have to be heritable to make sense to use, and all we inherit from our parents' (in cultureless species like basal dinosaurs) is mutations. So what kind of mutation could code for metacarpals II and III lining up with phalanx I-1? We know how limbs form in archosaurs. Check Figure 4 of Wagner and Gauthier (1999). Digit IV forms, the next distal carpal splits off and III forms from that, then distal carpal II and digit II forms, then distal carpal I and digit I branches from that. For interphalangeal lines to be heritable, there would need to be a straight line in the embryo that told the mesenchyme when to disintegrate between future bones. What developmental mechanism do you know that works in straight lines between elements formed at different times?<br /><br />Similarly, the problem with the different hands in my figure isn't convergence. I expect some convergence in any tree. The problem is I fail to see how the two hands are similar in any way development or evolution could account for. Sure us humans can make a line from two bones and say it falls at a certain place in another bone, but just like with my vertebral equation character, I don't see how these two conditions are something nature could arrive at using the same mutations.<br /><br />"Higher taxa" do indeed have that shelf, if you mean the archosaurs examined here. Turfanosuchus, Gracilisuchus, Shuvosaurus, Effigia, Herrerasaurus, Panphagia, Pisanosaurus and Heterodontosaurus all seem to have it, for instance. It could be convergent with Proganochelys for all I know, but that's the feature prior authors were coding for, not any shelf determinable from lateral view.<br /><br />I'm glad you see scoring from reconstructions and mounts as a problem. With trees often differing from each other by only a few extra steps, we cannot afford to trust that wrong guesses will balance each other out. I include all references in my extensive character-by-character critique. If you lack one, ask me for it.<br /><br />For Daemonosaurus, mostly miscodings of it from what I can tell so far. At least we're on the same coast, so dinner's not implausible. ;)Mickey Mortimerhttps://www.blogger.com/profile/08831823442911513851noreply@blogger.comtag:blogger.com,1999:blog-3248412803814730250.post-27352812292103288072013-03-19T13:13:38.658-07:002013-03-19T13:13:38.658-07:00Thanks for the heads-up on the mistakes I made wit...Thanks for the heads-up on the mistakes I made with the PVL specimen attributed to Gracilisuchus. I misread right for left on the ischium and believed Romer. D.P.https://www.blogger.com/profile/13009843520057633239noreply@blogger.comtag:blogger.com,1999:blog-3248412803814730250.post-42015656123599416892013-03-19T04:25:23.000-07:002013-03-19T04:25:23.000-07:00Mickey, I appreciate your thoroughness and your in...Mickey, I appreciate your thoroughness and your insight. It 'takes a village' to create a tree. <br /><br />With regard to Parallel Interphalangeal Lines (PILs), Hone et al. (2009) actually confirmed the presence of PILs several times throughout their paper, never tested it on a taxon with more than three toes, and demanded more precision in the digital lineups than nature can provide. Some taxa are actually known by their interrupted PILs. Others are in evolutionary transition from one pattern to another. And most of the time the PILs do not become apparent until they are used (as you'll see when you make a fist or grab a golf club, but not so much when you hold your hand flat). More on the foibles, mistakes and oversights of Hone et al. (2009) were published in Peters 2010, DOI: 10.1080/08912961003663500. (Funny how the rejoinders are never noted by you guys).<br /><br />Your illustration of a possible problem in toe morphology provides keen insight, and would indeed score as a convergence in my matrix. It would not be the only convergence on the tree (the vast majority of traits used are convergent somewhere) and the suite of other characters would drown out that noise for maximum parsimony. (I sense you are using the old Larry Martin trick of "show me one character that unites birds and dinosaurs." It's always the suite of several hundred traits that provides the nesting site, not just a single or a dozen traits). <br /><br />You found an interesting coding of the mandible shelf where I thought it was not. Is that shelf the same sort of shelf (homology) seen in higher taxa? If not, that's why I scored it differently. <br /><br />I do score my matrix from reconstructions and mounts and therein lies a potential problem. If I'm not aware of some plaster, it gets scored as if real. In traits that are not real scores would tend to randomize, adding noise to the parsimony, not direction. I have often mentioned if better data is out there, please send it in. This goes double for plaster. If you have not done so, then please do so. I often find problems with my own coding and endeavor to update them. I will continue to do so as my tree evolves on its own. I am not married to the tree that I recovered, but it is the tree that I recovered and sister taxa do bear more than a passing resemblance to each other throughout the tree. Some branches are weaker. Others are quite strong. <br /><br />Your earlier tree had a series of plant-eaters preceding theropods and separating theropods from bipedal, equally carnivorous crocs. I look forward to seeing what your new tree looks like and trust that you will have found a closer model to the actual evolutionary tree of archosaurs/dinosaurs. If Daemonosaurus doesn't lead to phytodinosaurs, I'd like to know the reason why and, if more parsimonious elsewhere, I'll buy you dinner. -- Dave<br /><br /><br /><br />D.P.https://www.blogger.com/profile/13009843520057633239noreply@blogger.comtag:blogger.com,1999:blog-3248412803814730250.post-31092782316630924722013-03-16T23:39:03.014-07:002013-03-16T23:39:03.014-07:00I'm on the edge of my seat...I'm on the edge of my seat...Mike Keeseyhttps://www.blogger.com/profile/00147156174467903264noreply@blogger.com