Common Design vs. Common Descent

I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.

Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.

If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.

One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.

Since I think there is promising evidence for YFR, I don’t think too much about common design vs. common descent. If the Earth is old, but the fossil record is young, as far as I’m concerned the nested hierarchical patterns of similarity are due to common design.

That said, for the sake of this discussion I will assume the fossil record is old. But even under that assumption, I don’t see how phylogenetics solves the problem of orphan features found distributed in the nested hierarchical patterns of similarity. I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).

Phylogeny is a nice superficial explanation for the pattern of taxonomic nested hierarchy in sets of proteins, DNA, whatever so long as a feature is actually shared among the creatures. That all breaks down however when we have orphan features that are not shared by sets of creatures.

The orphan features most evident to me are those associated with Eukaryotes. Phylogeny doesn’t do a good job of accounting for those. In fact, to assume common ancestry in that case, “poof” or some unknown mechanism is indicated. If the mechanism is unknown, then why claim universal common ancestry is a fact? Wouldn’t “we don’t know for sure, but we believe” be a more accurate statement of the state of affairs rather than saying “universal common ancestry is fact.”

So whenever orphan features sort of poof into existence, that suggests to me the patterns of nested hierarchy are explained better by common design. In fact there are lots of orphan features that define major groups of creatures. Off the top of my head, eukaryotes are divided into unicellular and multicellular creatures. There are vetebrates and a variety of invertebrates. Mammals have the orphan feature of mammary glands. The list could go on and on for orphan features and the groups they define. Now I use the phrase “orphan features” because I’m not comfortable using formal terms like autapomorphy or whatever. I actually don’t know what would be a good phrase.

So whenever I see an orphan feature that isn’t readily evolvable (like say a nervous system), I presume God did it, and therefore the similarities among creatures that have different orphan features is a the result of miraculous common design not ordinary common descent.

3,738 thoughts on “Common Design vs. Common Descent

  1. First the neighbor joining tree, shark rooted. The computed caption:

    Figure. Evolutionary relationships of taxa
    The evolutionary history was inferred using the Neighbor-Joining method [1]. The optimal tree with the sum of branch length = 0.51346098 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (150 replicates) are shown next to the branches [2]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the JTT matrix-based method [3] and are in the units of the number of amino acid substitutions per site. The analysis involved 15 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 513 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [4].

    1. Saitou N. and Nei M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.
    2. Felsenstein J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
    3. Jones D.T., Taylor W.R., and Thornton J.M. (1992). The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8: 275-282.
    4. Tamura K., Stecher G., Peterson D., Filipski A., and Kumar S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution30: 2725-2729.
    Disclaimer: Although utmost care has been taken to ensure the correctness of the caption, the caption text is provided “as is” without any warranty of any kind. Authors advise the user to carefully check the caption prior to its use for any purpose and report any errors or problems to the authors immediately (www.megasoftware.net). In no event shall the authors and their employers be liable for any damages, including but not limited to special, consequential, or other damages. Authors specifically disclaim all other warranties expressed or implied, including but not limited to the determination of suitability of this caption text for a specific purpose, use, or application.

    click link to see enlarged image:
    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/shark_rooted_nj_tree_v1.png

  2. Next the ML tree, with computed caption:

    Figure. Molecular Phylogenetic analysis by Maximum Likelihood method
    The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [1]. The tree with the highest log likelihood (-3272.3912) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 15 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 513 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [2].

    1. Jones D.T., Taylor W.R., and Thornton J.M. (1992). The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8: 275-282.
    2. Tamura K., Stecher G., Peterson D., Filipski A., and Kumar S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution30: 2725-2729.
    Disclaimer: Although utmost care has been taken to ensure the correctness of the caption, the caption text is provided “as is” without any warranty of any kind. Authors advise the user to carefully check the caption prior to its use for any purpose and report any errors or problems to the authors immediately (www.megasoftware.net). In no event shall the authors and their employers be liable for any damages, including but not limited to special, consequential, or other damages. Authors specifically disclaim all other warranties expressed or implied, including but not limited to the determination of suitability of this caption text for a specific purpose, use, or application.

    Click link below to see enlarged image:
    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/shark_rooted_tree_ml_tree_v1.png

  3. John Harshman: Ah, but every nucleotide substitution is an orphan base.

    Exactly. I was taking Sal’s definition of orphan as something “not present in everything else” or “taxonomically restricted to group/species X”.This can be applied even to single nucleotide mutations.

    I would venture a strong guess that a gene or even organ/bio-system absense-presence-based phylogeny would correlate with phylogenies derived from orthologous genes.

  4. Rumraket:

    I would venture a strong guess that a gene or even organ/bio-system absense-presence-based phylogeny would correlate with phylogenies derived from orthologous genes.

    To the extent the “organ/bio-system absense-presence-based phylogeny” agrees with the Linnaen style typological taxonomies, the phylogenies computed for orthologous genes I expect should generally match.

    But as I’m trying to show, with the cytochrome-c, the “organ/bio-system absense-presence-based phylogeny” of the paleontologists does NOT agree with either the Linnaen style typological taxonomy NOR even the computed molecular phylogeny of cytochrome-c orthologs. The Typological Taxonomy agrees more with the computed molecular phylogeny than the narrative that we evolved from a lungfish-like, coelacanth-like creature.

  5. stcordova: But as I’m trying to show, with the cytochrome-c, the “organ/bio-system absense-presence-based phylogeny” of the paleontologists does NOT agree with either the Linnaen style typological taxonomy NOR even the computed molecular phylogeny of cytochrome-c orthologs.

    Yeah good luck with that. Try including more species btw. Do it with fifty, or a hundred (okay maybe that’s extreme). And get a wider coverage of the eukaryotes. Get some fungi, mulluscs, crustaceans, a couple of primates, some whales, some felines perhaps, some birds, some reptiles, your fish, and so on and so forth.

    Stop cherry picking.

  6. stcordova: Why is a molecular clock unwarranted, just because it doesn’t agree with a foregone conclusion? You do see the epicycles and ad hoc rationalizations piling up don’t you?

    It is an observational fact that it varies.

    You understand what “observational fact” means right?

  7. Mung,

    Similarities are indicative of common descent. Except when they aren’t. And now you are telling us that differences are also indicative of common descent. Except when they aren’t.

    This is far easier than you seem to be making it. You, who accept common descent, don’t even understand the rationale for it.

    Differences aren’t indicative of common descent. But a difference, when inherited by an entire clade, becomes a similarity in that clade.

    Species 1: AAAAA
    Species 2: AAAAB
    Species 3: AAAAB

    B is a difference when considering all 3, but a similarity when considering the latter 2. The simple inference is that all share a common ancestor which did not have B, and that 2 and 3 have a common ancestor which is not an ancestor of 1.Of course other scenarios – other phylogenies – may in fact be the reality, which is why one is better off looking at more data. But, I don’t see why the basic logic of this causes Creationists to blink so furiously.

  8. Mung,

    Is there a specific percentage of dissimilarity at which shared ancestry can no longer be inferred? If so, what is it? 50%?

    You choose. I mean, you could probably make a reasonable estimate yourself using basic statistical inference – how likely is it that a particular alignment would result from common descent rather than ‘random’ factors. This is bog standard stuff – the kind of threshold decision scientists in many fields make all the time without Creationists getting all haughty with ’em.

  9. Rumraket,

    Exactly. I was taking Sal’s definition of orphan as something “not present in everything else” or “taxonomically restricted to group/species X”.This can be applied even to single nucleotide mutations.

    Yeah, and specifically-located SINE inserts 🙂

  10. The constant molecular clock assumption is particularly unwarranted when it comes to something like cytochrome c. What’s remarkable, though, is that you can take a gene that has precious little to do with the ‘form’ of the organism (yeah, I know, apoptosis; irrelevant), and recover anything even close to the morphological tree. And do it again with another gene. Try an intron, or functional RNA, you’ll get the same. Curious, innit?

  11. Mung: Them who? What truth did they not believe?

    I don’t now, but that is the quote that Sal cited at me when I asked why God was being oblique about the evidence for design. So I guess he thinks it has some relevance in this context.

  12. Mung: But sadly, “common descent” and “unguided evolution” predict far more false trees than the one true tree.

    I thought the job of common descent was to explain how the actual distribution of distinguishing characters among species came about. You’ll get the correct phylogenetic tree as an added bonus.

    BTW, I do not see what unguided evolution has to do with this.

  13. stcordova: EXCEPT, the mammals don’t nest inside Teleostomi! Just like I said, mammals aren’t fish!

    Could you put whales in there? I am really curious where whales end up. Whales are fish in the real TAXONOMY right?

  14. stcordova: Why is a molecular clock unwarranted, just because it doesn’t agree with a foregone conclusion? You do see the epicycles and ad hoc rationalizations piling up don’t you?

    It’s unwarranted because outgroup comparisons show that it is. You can’t just assume a clock. You have to first show a reason to believe it.

    We could use, for example the 43 genes used in the study that at least looks in agreement with what I’ve been saying.

    No it doesn’t. That study shows a monophyletic Sarcopterygii that includes tetrapods.

  15. stcordova,

    Interesting. I don’t know what’s happening here, but note that when you include the outgroup you can see that mammals are evolving faster than other taxa, so there goes the clock.

    It isn’t clear to me why you are still not recovering the same tree that your favorite 43-locus paper does. Perhaps, despite all your BLAST skills, you are using non-orthologous sequences. Perhaps you still don’t have enough taxa. I sincerely doubt that it’s because cytochrome c is different from all other genes.

  16. Rumraket:

    Yeah good luck with that.

    Freaking look a the diagram. Do the tetrapods look like they nest together under the teliostomi clade even with John’s suggested adjustment. You think adding a bird here and there is going to put humans under the teleostomi clade. I already cited a study that used 43 genes and it agrees with what I said. You want to close your eyes to the molecular data, be my guest.

  17. OK, Sal, I’ve spotted one of your problems. At least some of your sequences, probably all of them, aren’t cytochrome c at all. They’re cytochrome c oxidase I. You do know that’s a different protein, right?

  18. stcordova: I already cited a study that used 43 genes and it agrees with what I said.

    No, it doesn’t. Your inability to read a tree is getting in your way here.

  19. John Harshman:

    Yeah, you don’t know what your own tree shows. That’s the problem.

    Yes I do, and apparently you’re in denial. You whined about the me dropping the shark gene. Well I put a shark back in, and even higher quality sequence to boot. You whined about more tetrapods. Well I added one, I could add more, but how about you tell the readers if you think such changes will somehow put the tetrapods into the Teleostomi clade?

    You whine about mid point rooting, and not having the shark as the outgroup. I put the shark in as the out group removed the midpoint rooting. Did it put tetrapods in the postion of the Teliostomi clade? NO NO NO!

    For the readers benefit. This is the teleostomi clade:
    https://en.wikipedia.org/wiki/Teleostomi

    The clades under it are:
    Actinopterygii (ray finned fishes)
    Sarcopterygii (lobe finned fishes)

    Actinopterygii (ray finned fishes) include salmon and strugeons. Now look where the salmon and strugeons are in the diagram!

    Sarcopterygii (lobe finned fishes) include coelcanths and lungfish and supposedly the tetrapods. The Coelecanths and Lungfish are there but the tetrapods are — Yikes kind of in a sister relation under some vertebrate clade, just like the Linnaen taxnomy. Gee, that seemed to be comparable to the conclusion of a molecular study I cited with 43 genes, but that study didn’t come right out and point to the even more devastating conclusion.

    Then Allan Miller weighs in on other matters rather than actually deal with the generated cladogram.

    C’mon John, if you really wanted to refute what I’m saying, you’d do the data runs yourself with sequences of your choice, but you won’t. Maybe deep down you know that whatever you do, short of sketchy data manipulation, those tetrapods aren’t going to end up under the Teleostomi clade.

    Posture and bluff all you want, but you and I know who is holding the stronger hand in this round.

    It should be fairly evident in light of not just this data but studies that included the 43 genes that tetrapods don’t nest within Teleostomi nor should they belong in Sarcopterygii.

  20. John Harshman:
    OK, Sal, I’ve spotted one of your problems. At least some of your sequences, probably all of them, aren’t cytochrome c at all. They’re cytochrome c oxidase I. You do know that’s a different protein, right?

    You can’t make this up.

  21. stcordova: It should be fairly evident in light of not just this data but studies that included the 43 genes that tetrapods don’t nest within Teleostomi nor should they belong in Sarcopterygii.

    You need to look at that study again. Try harder to read and understand the tree.

  22. John Harshman:

    OK, Sal, I’ve spotted one of your problems. At least some of your sequences, probably all of them, aren’t cytochrome c at all. They’re cytochrome c oxidase I. You do know that’s a different protein, right?

    Well, how about that, I actually used a different gene than cytochrome C. Thanks for the fix and correcting my mistake.

    But you know the hits are still likely homologous right, they are just a different gene. But now I will be more methodical. I’ll select high identity entries.

    Any bets whether it will put Tetrapods into Sarcopterygii? One way to find out is to redo with Cytochrome C Oxidase I. This time, I realized I can leverage Entrez to get good orthologs.

    Thank you for the free-of-charge technical corrections. I’ll do a run in short order. Then we can try some other genes.

    For a change this was a good discussion.

  23. stcordova,

    Then Allan Miller weighs in on other matters rather than actually deal with the generated cladogram.

    Wha? I was responding to points made. Points made by, among others, you. There is no point me joining in on the cladistic detail; it’s John’s field.

  24. Allan Miller: Wha? I was responding to points made. Points made by, among others, you. There is no point me joining in on the cladistic detail; it’s John’s field.

    LOL. Yeah, why can’ t you stay on topic, like Sal does 😀

  25. Since I’m rebuilding the first Cladogram on Cytochrome-C Oxidase rather than Cytochrome-C, here are some technical details. I chose the gene because it had some nice size, it coded for something with 520 residues.

    Nothing is stopping me from also doing a cladogram with cytochrome-C or other genes like RAG1.

    Anyway, thanks to John Harsman for his technical correction of my mistake as it will improve the quality of the discussion about my hypothesis that Tetrapods should not nest in the Teleostomi clade and that saying Tetrapods are Sarcopterygiians is an equivocation and abuse of labeling, it doesn’t match the spirit of what is actually represented in phylogenetic gene trees.

    https://en.wikipedia.org/wiki/Cytochrome_c_oxidase#/media/File:Cytochrome_C_Oxidase_1OCC_in_Membrane_2.png

    The enzyme cytochrome c oxidase or Complex IV, EC 1.9.3.1 is a large transmembrane protein complex found in bacteria and the mitochondrion of eukaryotes.

    It is the last enzyme in the respiratory electron transport chain of mitochondria (or bacteria) located in the mitochondrial (or bacterial) membrane. It receives an electron from each of four cytochrome c molecules, and transfers them to one oxygen molecule, converting molecular oxygen to two molecules of water. In the process, it binds four protons from the inner aqueous phase to make water and in addition translocates four protons across the membrane, in the process, helping to establish a transmembrane difference of proton electrochemical potential that the ATP synthase then uses to synthesize ATP.

    It’s actually a beautiful looking protein.

  26. stcordova: Well, how about that, I actually used a different gene than cytochrome C.Thanks for the fix and correcting my mistake.

    This should be a wakeup call for you: you are not competent to do what you are trying to do. Ignorance is not a fault, but the arrogant assumption that you aren’t ignorant certainly is. You will have to learn a lot more before you’re capable of doing what you’ve been claiming to do here.

    But you know the hits are still likely homologous right, they are just a different gene.But now I will be more methodical.I’ll select high identity entries.

    It’s not just a different gene, it’s a mitochondrial gene. In animals, mitochondria evolve much faster than nuclear genes. This means that in order to get a decent analysis you have to work much harder. You may need a better model, and you certainly need a much denser taxon sample, in order to achieve reasonable results.

    Any bets whether it will put Tetrapods into Sarcopterygii? One way to find out is to redo with Cytochrome C Oxidase I.This time, I realized I can leverage Entrez to get good orthologs.

    Again, you need a much bigger taxon sample before you can hope for valid results when you’re using mitochondrial genes.

    For a change this was a good discussion.

    Unfortunately, you don’t seem to be drawing the proper lesson.

  27. stcordova,

    We might wonder why there’s a squid-specific way of passing an electron, and a rabbit way, and a shark way … as I’ve said before, I find it remarkable that low-level (albeit vital) function can get anywhere near convergence on the morphological tree – lactate dehydrogenase, DNA polymerase – as well as this intron, that SINE … they all vend to vary in this same curious way in taxa. And not just in ours.

  28. stcordova: saying Tetrapods are Sarcopterygiians is an equivocation and abuse of labeling, it doesn’t match the spirit of what is actually represented in phylogenetic gene trees.

    “The spirit”?? What do you think you mean by that? Tetrapods are sarcopterygians because Sarcopterygia shows up as monophyletic on phylogenetic trees; pretty much all of them except for your little attempts here.

  29. Sal, to John:

    Thank you for the free-of-charge technical corrections.

    This is Sal’s go-to defense mechanism when someone corrects a stupid error of his. He should be thinking “I just got my ass handed to me”, but instead he tries to spin it as if he’s pulling one over on his opponents by getting “free-of-charge” corrections.

  30. John Harshman:

    At least some of your sequences, probably all of them, aren’t cytochrome c at all.

    Hopefully ALL of them are cytochrome c oxidase, which means they are homolgous which means the diagram stands, I just mislabeled the gene, but a rose is a rose by any other name. The other proteins in the UNIPROT listing where I got them from were 5 times smaller, so it’s likely I did hit the actual homologs.

    However, to that end, before I move onto creating cladograms of other genes, I’ll go through the Cytochrome-C Cox1 more methodically.

    METHODS and MATERIALS

    To find orthologues of the gene of interest I start with this Cox1 which was the first entry used to generate above cladograms:

    >Neoceratodus forsteri (Australian lungfish) NP_387474.1
    MTITRWFFST NHKDIGTLYM IFGAWAGMVG TALSLLIRAE LSQPGALLGD
    DQIYNVLVTA HAFVMIFFMV MPIMIGGFGN WLIPLMIGAP DMAFPRMNNM
    SFWLLPPSFL LLLASSGVEA GAGTGWTVYP PLAGNLAHAG ASVDLTIFSL
    HLAGVSSILG SINFITTIIN MKPPAISQYQ TPLFIWSVMI TTILLLLSLP
    VLAAGITMLL TDRNLNTTFF DPAGGGDPIL YQHLFWFFGH PEVYILILPG
    YGMISHIVAY YSGKKEPFGY MGMVWAMMAI GLLGFIVWAH HMFTVGMDVD
    TRAYFTSATM IIAIPTGVKV FSWLATLHGG SIKWETPLLW ALGFIFLFTV
    GGLTGIVLAN SSLDIVLHDT YYVVAHFHYV LSMGAVFAIM GGFVHWFPLM
    TGYTLHNTWT KIHFGVMFIG VNLTFFPQHF LGLAGMPRRY SDYPDAYTLW
    NTVSSIGSLI SLVAVIMLLF IIWEAFAAKR EVMSIELSPT NVEWLHGCPP
    PHHTFEEPAF VQVQTSQR

    Then it’s a matter of BLASTING it against individual species and confirming I get the orthologous Cytochrome-C Cox1. This time I will attach accession numbers that readers can use to confirm the entries in Genbank.

  31. Here’s a cytochrome c-based phylogeny simply from the Uniprot “Tree” feature it makes when you get an alignment. I have no idea what kind of algorithm it uses to make the tree from the alignment.

    But it all looks fine to me. I just found a host of (actual) cytochrome c sequences and asked it to do the alignment.
    http://www.uniprot.org/align/A20171110F725F458AC8690F874DD868E4ED79B88D77E3EP

    The bacteria are all the most distantly related to each other and to everything else. I suppose this could indicate they might not be cytochrome c’s. Some of the annotation is horrible for bacterial strains.

    The fungi are together, but more closely related to the rest of the eukaryotes. The primates are together, and with the rat make up the mammals. The birds are together. The frog which makes up the amphibian, is the most distantly related tetrapod (from humans) so sits on a branch node closest to the tetrapod-defining node. Which is inside the Sarcopterygii together with the Coelacanth, with salmon (a ray finned fish) outside.

    That’s how Uniprot sorted them, but again I have no idea what algorithm or settings it uses.

  32. Rumraket:
    Picture is too small so here’s a link: https://i.imgur.com/ss71eSX.jpg.

    Your tree has a weird thing happening at the crucial node, i.e. where the coelacanth, salmon, and tetrapods meet. I can’t figure out if it’s a graphic glitch or if it’s generating negative-length branches. But it certainly doesn’t clearly show a monophyletic Sarcopterygii.

  33. Ok first, here is the cleaned up FASTA file of cytochrome-c COX1. I should mention I tried to put in Gallus gallus (chicken) and it mangled the phylogeny tree. Since John Harshman is and expert on birds maybe he can explain it. I assembled the orthologs according to my Methods and Material in the previous comment.

    I post the following for interested readers to process the data and independently review my findings. This time I added accession numbers to enable duplication of any results which I claim.

    >Neoceratodus forsteri (Australian lungfish) NP_387474.1
    MTITRWFFST NHKDIGTLYM IFGAWAGMVG TALSLLIRAE LSQPGALLGD
    DQIYNVLVTA HAFVMIFFMV MPIMIGGFGN WLIPLMIGAP DMAFPRMNNM
    SFWLLPPSFL LLLASSGVEA GAGTGWTVYP PLAGNLAHAG ASVDLTIFSL
    HLAGVSSILG SINFITTIIN MKPPAISQYQ TPLFIWSVMI TTILLLLSLP
    VLAAGITMLL TDRNLNTTFF DPAGGGDPIL YQHLFWFFGH PEVYILILPG
    YGMISHIVAY YSGKKEPFGY MGMVWAMMAI GLLGFIVWAH HMFTVGMDVD
    TRAYFTSATM IIAIPTGVKV FSWLATLHGG SIKWETPLLW ALGFIFLFTV
    GGLTGIVLAN SSLDIVLHDT YYVVAHFHYV LSMGAVFAIM GGFVHWFPLM
    TGYTLHNTWT KIHFGVMFIG VNLTFFPQHF LGLAGMPRRY SDYPDAYTLW
    NTVSSIGSLI SLVAVIMLLF IIWEAFAAKR EVMSIELSPT NVEWLHGCPP
    PHHTFEEPAF VQVQTSQR

    >Lepidosiren paradoxa (South American lungfish) NP_542458.1
    mtitrwlfst nhkdigtlym lfgawagmvg talsllirae lsqpgallgd dqifnvlvta
    hafvmiffmv mpimiggfgn wliplmigap dmafprlnnm sfwllppafl lllagsgvea
    gagtgwtvyp plagnlahag asvdltifsl hlagmssilg sinfittvin mkppaasqfq
    tplfiwsvmi ttvllllslp vlaagitmll tdrnlnttff dpagggdpil yqhlfwffgh
    pevyililpg fgmishivty ysgkkepfgy mgmvwamiai gllgfivwah hmftvgmdvd
    trayftsatm iiaiptgvkv fswlatlhgg aikwetpliw algfiflftv ggltgvvlan
    ssldimlhdt yyvvahfhyv lsmgavfaim aglvhwfplm tgytlhdtwt kihfgvtfig
    vnltffpqhf lglagmprry sdypdaytfw ntvssvgsvi smvavmlllf iiweafaskr
    evssiemtht naewlhgcpp pyhtfeepaf vqtqivn

    >Protopterus annectens (West African lungfish) YP_006884099.1
    mtltrwlfst nhkdigtlym vfgawagmvg talsllirae lsqpgallgd dqiynvlvta
    hafvmiffmv mpimiggfgn wliplmigap dmafprmnnm sfwllppsfl lllagsgvea
    gagtgwtvyp plasnlahag asvdltifsl hlagvssilg sinfittiin mkppaasqyq
    tplfiwsvmi ttvllllslp vlaagitmll tdrnlnttff dpagggdpil yqhlfwffgh
    pevyililpg fgmishivaf ysgkkepfgy mgmvwammai gllgfivwah hmftvgmdvd
    trayftsatm iiaiptgvkv fswlatlhgg aikwetpllw algfiflftv ggltgivlan
    ssldimlhdt yyvvahfhyv lsmgavfaim gglmhwfplm tgytlhdtwt kihfgvmflg
    vnltffpqhf lglagmprry sdypdaytlw ntlssvgsli slvavilllf iiweafaskr
    evnsieliyt nvewmhgcpp pyhtfeepaf vqiqr

    >Latimeria chalumnae (coelacanth) BAF43538.1
    mmitrwlfst nhkdigtlym ifgawagmvg talsllirae lsqpgallgd dqiynvvvta
    hafvmiffmv mpimiggfgn wliplmigap dmafprmnnm sfwllppsll lllassgvea
    gagtgwtvyp plagnlahag asvdltifsl hlagvssilg ainfittvin mkpptmtqyq
    tplfiwsvlv tavllllslp vlaagitmll tdrnlnttff dpagggdpil yqhlfwffgh
    pevyililpg fgmishivay ysgkkepfgy mgmvwammai gllgfivwah hmftvgmdvd
    trayftsatm iiaiptgvkv fswlatlhgg vtkwdtpllw algfiflftv ggltgivlan
    ssldiilhdt yyvvahfhyv lsmgavfaim gglvhwfplm tgytlhntwt kihfgvmftg
    vnltffpqhf lglagmprry sdypdaytlw ntvssigsli sliavimfmf ilweafsakr
    evlivemttt nvewlhgcpp phhtyeepaf vqar

    >Latimeria menadoensis (Menado coelacanth) YP_220643.2
    mmitrwlfst nhkdigtlym ifgawagmvg talsllirae lsqpgallgd dqiynvivta
    hafvmiffmv mpvmiggfgn wliplmigap dmafprmnnm sfwllppsll lllassgvea
    gagtgwtvyp plasnlahag asvdltifsl hlagvssilg ainfittvin mkpptmtqyq
    tplfiwsvlv tavllllslp vlaagitmll tdrnlnttff dpagggdpil yqhlfwffgh
    pevyililpg fgmishivay ysgkkepfgy mgmvwammai gllgfivwah hmftvgmdvd
    trayftsatm iiaiptgvkv fswlatlhgg vtkwdtpllw algfiflftv ggltgivlan
    ssldiilhdt yyvvahfhyv lsmgavfaim gglvhwfplm tgytlhntwt kihfgvmftg
    vnltffpqhf lglagmprry sdypdaytlw ntvssigsli sliavimfmf ilweafsakr
    evlivemttt nvewlhgcpp phhtyeepaf vqar

    >Leucoraja erinacea (little skate) YP_004935520.1
    mainrwlfst nhkdigtlyl ifgawagmvg tglsllirae lsqpgsllgd dqiynvlvta
    hafvmiffmv mpimiggfgn wlvplmigsp dmafprmnnm sfwllppsfl lllasagvea
    gagtgwtvyp plagnlahag asvdltifsl hlagissila sinfittiin mkppaisqyq
    tplfvwsilv ttvlllmalp vlaagitmll tdrnlnttff dpagggdpil yqhlfwffgh
    pevyililpg fgmishvvay ysgkkepfgy mgmvwammai gllgfivwah hmftvgmdvd
    trayftsatm iiaiptgvkv fswlatlhgg sikwetpllw algfiflftv ggltgivlan
    ssldivlhdt yyvvahfhyv lsmgavfaim agfvhwfplf tgytlhstwa kiqfsimfig
    vnltffpqhf lglagmprry sdypdaytlw nvvssigsli slvaviillf iiweafaskr
    evlsielsnt nvewlhgcpp pyhtyeepaf vqvqqpay

    >Scoliodon macrorhynchos (Pacific spadenose shark) YP_006460407.1
    mainrwlfst nhkdigtlyl ifgawagmvg talsllirae lgqpgsllgd dqiynvivta
    hafvmiffmv mpimiggfgn wlvplmigap dmafprmnnm sfwllppsfi lllasagvea
    gagtgwtvyp plasnlahag psvdlaifsl hlagvssila sinfittiin mkppaisqyq
    tplfvwsilv ttvllllslp vlaagitmll tdrnlnttff dpagggdpil yqhlfwffgh
    pevyililpg fgmishvvay ysgkkepfgy mgmvwammai gllgfivwah hmftvgmdvd
    trayftsatm iiaiptgvkv fswlatlhgg sikwdtpllw algfiflftv ggltgivlan
    ssldivlhdt yyvvahfhyv lsmgavfaim agfihwfpli sgftlhqtwt kiqftvmfig
    vnltffpqhf lglagmprry sdypdaytlw nvissigsli slvavimllf iiweafaskr
    evlsvelpyt niewlhgcpp pyhtyeepaf vqvqrspf

    >Xenopus tropicalis (tropical clawed frog) YP_203372.1
    maitrwlfst nhkdigtlyl vfgawagmvg talsllirae lsqpgtllgd dqiynvivta
    hafimiffmv mpimiggfgn wliplmigap dmafprmnnm sfwllppsfl lllassgvea
    gagtgwtvyp plagnlahag asvdltifsl hlagvssilg ainfitttin mkppamsqyq
    tplfvwsvli tavllllslp vlaagitmll tdrnlnttff dpagggdpvl yqhlfwffgh
    pevyililpg fgmishivty ysgkkepfgy mgmvwammsi gllgfivwah hmftvdlnvd
    trayftsatm iiaiptgvkv fswlatmhgg tikwdapmlw algfiflftv ggltgivlan
    ssldivlhdt yyvvahfhyv lsmgavfaim ggfvhwfplf tgytlhetwa kihfgvmfag
    vnltffpqhf lglagmprry sdypdaytlw ntvssvgsli slvavimmmf iiweafaakr
    evtlteltst niewlhgcpp pyhtfeepaf vqihpshn

    >Xenopus victorianus (Lake Victoria clawed frog) YP_006883487.1
    maitrwlfst nhkdigtlyl vfgawagmvg talsllirae lsqpgtllgd dqiynvivta
    hafimiffmv mpimiggfgn wlvplmigap dmafprmnnm sfwllppsfl lllassgvea
    gagtgwtvyp plagnlahag asvdltifsl hlagvssilg ainfitttin mkppamsqyq
    tplfvwsvli tavllllslp vlaagitmll tdrnlnttff dpagggdpvl yqhlfwffgh
    pevyililpg fgmishivty ysgkkepfgy mgmvwammsi gllgfivwah hmftvdlnvd
    trayftsatm iiaiptgvkv fswlatmhgg tikwdapmlw algfiflftv ggltgivlan
    ssldimlhdt yyvvahfhyv lsmgavfaim ggfihwfplf tgytlhetwa kihfgvmfag
    vnltffpqhf lglagmprry sdypdaytlw ntvssvgsli slvavimmmf iiweafaakr
    evtlteltst niewlhgcpp pyhtfeepaf vqiqssnn

    >Homo sapiens (human) AEG23663.1
    mfadrwlfst nhkdigtlyl lfgawagvlg talsllirae lgqpgnllgn dhiynvivta
    hafvmiffmv mpimiggfgn wlvplmigap dmafprmnnm sfwllppsll lllasamvea
    gagtgwtvyp plagnyshpg asvdltifsl hlagvssilg ainfittiin mkppamtqyq
    tplfvwsvli tavllilslp vlaagitmll tdrnlnttff dpagggdpil yqhlfwffgh
    pevyililpg fgmishivty ysgkkepfgy mgmvwammsi gflgfivwah hmftvgmdvd
    trayftsatm iiaiptgvkv fswlatlhgs nmkwsaavlw algfiflftv ggltgivlan
    ssldivlhdt yyvvahfhyv lsmgavfaim ggfihwfplf sgytldqtya kihftimfig
    vnltffpqhf lglsgmprry sdypdayttw nilssvgsfi sltavmlmif miweafaskr
    kvlmveepsm nlewlhgcpp pyhtfeepvy mks

    >Macropus giganteus (eastern gray kangaroo) YP_009154379.1
    mfitrwlfst nhkdigtlyl lfgawagmvg talsllirae lgqpgtllgd dqiynvivta
    hafvmiffmv mpimiggfgn wlvplmigap dmafprmnnm sfwllppsfl lllasstvea
    gagtgwtvyp plagnlahag asvdlaifsl hlagvssilg ainfittiin mkppalsqyq
    tplfvwsvmi tavllllslp vlaagitmll tdrnlnttff dpagggdpil yqhlfwffgh
    pevyililpg fgmishivty ysgkkepfgy mgmvwammsi gflgfivwah hmftvgldvd
    trayftsatm iiaiptgvkv fswlatlhgg nikwspallw algfiflfti ggltgivlan
    ssldivlhdt yyvvahfhyv lsmgavfaim ggfvhwfplf tgytlndlwa kihfsimfvg
    vnmtffpqhf lglsgmprry sdypdayttw nvissigsfi sltavilmvf iiweafaskr
    evstvelttt niewlhgcpp pyhtfeqpaf ikv

    >Loxodonta africana (African savanna elephant) NP_009281.1
    mfanrwlyst nhkdigtlyl lfgawagmvg tafsilirae lgqpgsllgd dqiynvivta
    hafvmiffmv mpimiggfgn wliplmigap dmafprmnnm sfwllppsfl lllassmvea
    gagtgwtvyp plagnlahag asvdltifsl hlagvssils ainfittiin mkppamsqyh
    mplfvwsili tavllllslp vlaagitmll tdrnlnttff dpagggdpil yqhlfwffgh
    pevyililpg fgmvshivty ysgkkepfgy mgmvwammsi gflgfivwah hmftvgmdvd
    trayftsatm iiaiptgvkv fswlatlhgg nikwspammw algfiflfti ggltgivlan
    ssldivlhdt yyvvahfhyv lsmgavfaim ggfihwfplf sgytlnytwa kiqflvmfig
    vnltffpqhf lglsgmprry sdypdaytaw ntassmgsfi slvavilmvf miweafaskr
    evsvmelttt nvewlngcpp phhtfeepay vksns

    >Thunnus obesus (bigeye tuna) YP_003587610.1
    maitrwffst nhkdigtlyl vfgawagmvg talsllirae lsqpgallgd dqiynvivta
    hafvmiffmv mpimiggfgn wliplmigap dmafprmnnm sfwllppsfl lllassgvea
    gagtgwtvyp plagnlahag asvdltifsl hlagvssilg ainfittiin mkpaaisqyq
    tplfvwavli tavllllslp vlaagitmll tdrnlnttff dpagggdpil yqhlfwffgh
    pevyililpg fgmishivay ysgkkepfgy mgmvwammai gllgfivwah hmftvgmdvd
    trayftsatm iiaiptgvkv fswlatlhgg avkwetpllw aigfiflftv ggltgivlan
    ssldivlhdt yyvvahfhyv lsmgavfaiv aafvhwfplf tgytlhstwt kihfgvmfvg
    vnltffpqhf lglagmprry sdypdaytlw ntissigsli slvavimflf iiweafaakr
    evmsveltst nvewlhgcpp pyhtfeepaf vlvqsd

    >Katsuwonus pelamis (skipjack tuna) ADA69876.1
    maitrwffst nhkdigtlyl vfgawagmvg talsllirae lsqpgallgd dqiynvivta
    hafvmiffmv mpimiggfgn wliplmigap dmafprmnnm sfwllppsfl lllassgvea
    gagtgwtvyp plagnlahag asvdltifsl hlagvssilg ainfittiin mkpaaisqyq
    tplfvwavli tavllllslp vlaagitmll tdrnlnttff dpagggdpil yqhlfwffgh
    pevyililpg fgmishivay yagkketfgy mgmvwammai gllgfivwah hmftvgmdvd
    trayftsatm iiaiptgvkv fswlatlhgg avkwetpllw aigfiflftv ggltgivlan
    ssldivlhdt yyvvahfhyv lsmgavfaiv aafvhwfplf tgytlhstwt kihfgvmivg
    vnltffpqhf lglagmprry sdypdaytlw ntissigsli slvavimflf iiweafaakr
    evmsveltat nvewlhgcpp pyhtfeepaf vlvqsd

    >Paradactylodon mustersi (Paghman mountain salamander) YP_626701.1
    mmitrwlfst nhkdigtlyl vfgawagmvg talsllirae lsqpstllgd dqiynvivta
    hafvmiffmv mpvmiggfgn wlvplmigap dmafprmnnm sfwllppsfl llmassgvea
    gagtgwtvyp plagnlahag asvdltifsl hlagissilg ainfittsin mkppsmsqyq
    tplfvwsvli taillllslp vlaagitmll tdrnlnttff dpagggdpvl yqhlfwffgh
    pevyililpg fgmishivty ysakkepfgy mgmvwammsi gllgfivwah hmftvdlnvd
    trayftsatm iiaiptgvkv fswlatmhgg sikwdaamlw algfiflftv ggltgiilan
    ssldivlhdt yyvvahfhyv lsmgavfaim ggfvhwfplf sgftlhptws kihfgvmfig
    vnltffpqhf lglagmprry sdypdaytlw ntvssigsli slvavimmmf iiweafaskr
    evlttelsft niewlhgcpp pyhtfeepsf vqarvy

    >Acipenser gueldenstaedtii (Russian sturgeon) YP_002808661.1
    maitrwffst nhkdigtlyl vfgawagmvg talsllirae lsqpgallgd dqiynvivta
    hafvmiffmv mpimiggfgn wlvplmigap dmafprmnnm sfwllppsfl lllassgvea
    gagtgwtvyp plagnlahag asvdltifsl hlagvssilg ainfittiin mkppavsqyq
    tplfvwsvli tavllllslp vlaagitmll tdrnlnttff dpagggdpil yqhlfwffgh
    pevyililpg fgmishivay yagkkepfgy mgmvwammai gllgfivwah hmftvgmdvd
    trayftsatm iiaiptgvkv fswlatlhgg sikwdtpllw algfiflftv ggltgivlan
    ssldivlhdt yyvvahfhyv lsmgavfaim gafvhwfplf tgytlhgtws kihfavmfvg
    vnltffpqhf lglagmprry sdypdayalw ntvssigsli slvavimflf ilweafaakr
    evmsvelttt nvewlhgcpp pyhtyeepaf vqvqsts

    >Salmo salar (Atlantic salmon) NP_008447.1
    maitrwffst nhkdigtlyl vfgawagmvg talsllirae lsqpgallgd dqiynvivta
    hafvmiffmv mpimiggfgn wliplmigap dmafprmnnm sfwllppsfl lllassgvea
    gagtgwtvyp plagnlahag asvdltifsl hlagissilg ainfittiin mkppaisqyq
    tplfvwavlv tavllllslp vlaagitmll tdrnlnttff dpagggdpil yqhlfwffgh
    pevyililpg fgmishivay ysgkkepfgy mgmvwammai gllgfivwah hmftvgmdvd
    trayftsatm iiaiptgvkv fswlatlhgg sikwetpllw algfiflftv ggltgivlan
    ssldivlhdt yyvvahfhyv lsmgavfaim gafvhwfplf tgytlhstwt kihfgimfig
    vnltffpqhf lglagmprry sdypdaytlw ntissigsli slvavimflf ilweafaakr
    evasiemtst nvewlhgcpp pyhtfeepaf vqvqas

  34. John Harshman:

    Why don’t you just search GenBank for “Cytochrome c oxidase subunit I”?

    That would be the best way assuming the annotations are correct. Just for my own piece of mind I was just being thorough. The hits I got with my more painstaking method still returned “Cytochrome c oxidase subunit I”, so that was assuring.

    Thanks for you help. Much appreciated.

    Still, I can’t account for why my gallus gallus hit blew up the cladogram.

    Rather than fix it, I could go on to another gene, like THE cytochrome-C. Other genes suggested were RAG1, or whatever.

  35. John Harshman: Your tree has a weird thing happening at the crucial node, i.e. where the coelacanth, salmon, and tetrapods meet. I can’t figure out if it’s a graphic glitch or if it’s generating negative-length branches. But it certainly doesn’t clearly show a monophyletic Sarcopterygii.

    Yes that does look weird. The same thing seem to be happening close to the mammal-alligator node. And all the way out at the three bacteria node there’s another glitch. How annoying.

  36. stcordova: Ok first, here is the cleaned up FASTA file of cytochrome-c COX1. I should mention I tried to put in Gallus gallus (chicken) and it mangled the phylogeny tree. Since John Harshman is and expert on birds maybe he can explain it.

    See what I mean? After being shown that you’re incompetent, you just blow it off and blithely continue. Putting in a chicken shouldn’t mangle anything. You did something wrong, but I don’t know what it was.

  37. stcordova: Ok, there are various trees that can be run. ML, NJ, minL, whatever. I’ll just post a few of them.

    What your tree shows, incidentally, is that your data/method are incapable of resolving the four-way polytomy among lungfish, coelacanth, actinopterygians, and tetrapods. Do you know what the little numbers next to the nodes mean?

  38. John Harshman to Rumraket:

    I can’t figure out if it’s a graphic glitch or if it’s generating negative-length branches. But it certainly doesn’t clearly show a monophyletic Sarcopterygii.

    No kidding. No Shitake Mushrooms too.

  39. Rumraket,

    I just had a little play with one of your sequences, one of the Salmon sequences. BLAST found a few other paralogs in the salmon, and orthologs in rainbow trout but also among the top hits … Caligus rogercresseyi. Never heard of it, turns out it’s a sea louse. It’s a parasite of … wait for it … salmon, and rainbow trout. This looks like HGT to me. So here’s an example where common descent is reasonably inferred from sequence alignment – not of the entire organisms of course, but of the gene. Yet if we just looked at this gene, we might be misled into nesting sea lice with salmonids.

    Some might think that destroys the entire enterprise. Anomalies? How dare there be anomalies!

  40. Do you know what the little numbers next to the nodes mean?

    Confidence level (interval).

    But, there are other methods, and one can add more bootstrap support.

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