Perhaps, but maybe not. In this case I suppose the results are nearly identical either way.
It’s not a parsimony tree, given the fractional branch lengths. Could be neighbor joining. Conceivably maximum likelihood. Wait, there’s a negative branch. Scratch likelihood. It’s got to be some distance method.
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It’s from here: Evolution - Species, Genetics, Trees | Britannica
This is what it says in relation to the figure:
Distance methods
A “distance” is the number of differences between two taxa. The differences are measured with respect to certain traits (i.e., morphological data) or to certain macromolecules (primarily the sequence of amino acids in proteins or the sequence of nucleotides in DNA or RNA). The two trees illustrated in the figure were obtained by taking into account the distance, or number of amino acid differences, between three organisms with respect to a particular protein. The amino acid sequence of a protein contains more information than is reflected in the number of amino acid differences. This is because in some cases the replacement of one amino acid by another requires no more than one nucleotide substitution in the DNA that codes for the protein, whereas in other cases it requires at least two nucleotide changes. The table shows the minimum number of nucleotide differences in the genes of 20 separate species that are necessary to account for the amino acid differences in their cytochrome c. An evolutionary tree based on the data in the table, showing the minimum numbers of nucleotide changes in each branch, is illustrated in the complementary figure.
The relationships between species as shown in the figure correspond fairly well to the relationships determined from other sources, such as the fossil record. According to the figure, chickens are less closely related to ducks and pigeons than to penguins, and humans and monkeys diverged from the other mammals before the marsupial kangaroo separated from the nonprimate placentals. Although these examples are known to be erroneousrelationships, the power of the method is apparent in that a single protein yields a fairly accurate reconstruction of the evolutionary history of 20 organisms that started to diverge more than one billion years ago.
Morphological data also can be used for constructing distance trees. The first step is to obtain a distance matrix based on a set of morphological comparisons between species or other taxa. For example, in some insects one can measure body length, wing length, wing width, number and length of wing veins, or another trait. The most common procedure to transform a distance matrix into a phylogeny is called cluster analysis. The distance matrix is scanned for the smallest distance element, and the two taxa involved (say, A and B) are joined at an internal node, or branching point. The matrix is scanned again for the next smallest distance, and the two new taxa (say, C and D) are clustered. The procedure is continued until all taxa have been joined. When a distance involves a taxon that is already part of a previous cluster (say, E and A), the average distance is obtained between the new taxon and the preexisting cluster (say, the average distance between E to A and E to B). This simple procedure, which can also be used with molecular data, assumes that the rate of evolution is uniform along all branches.
Other distance methods (including the one used to construct the tree in the figure of the 20-organism phylogeny) relax the condition of uniform rate and allow for unequal rates of evolution along the branches. One of the most extensively used methods of this kind is called neighbour-joining. The method starts, as before, by identifying the smallest distance in the matrix and linking the two taxa involved. The next step is to remove these two taxa and calculate a new matrix in which their distances to other taxa are replaced by the distance between the node linking the two taxa and all other taxa. The smallest distance in this new matrix is used for making the next connection, which will be between two other taxa or between the previous node and a new taxon. The procedure is repeated until all taxa have been connected with one another by intervening nodes.
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The relevant bit is “Science, vol 165, Jan. 20, 1967, p. 281”. Look that one up.
From what I can gather it’s the Fitch–Margoliash method used to construct the tree(which is well explained in the paper), and the one shown is the best among a mere 40 different trees tested by the algorithm, which I suppose was standard for 1967 computers?
So a least-squares method, as I had supposed. Yes, searches have become faster and more extensive since 1967.
ok. i got your point. you are basically asking why there should be a connection between morphology and enzymatic activity (supposedly there is no connection between the two). so all we need to find is that there is a connection between the two. am i right?
The scientists are using math, @Robert_Byers1. Their math has been soundly executed and explained, albeit in a form that a majority of folks have not studied.
You are asserting that you can grasp these concepts without grappling with the math. This assertion is completely, 100% wrong.
Instead of shouting with all caps, you would do better to go back, read the papers carefully, and ask questions about the math you might not understand.
If you just keep shouting and avoid doing the hard work, I will be forced to assume that your posts about science are not worth reading.
Best,
Chris
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Showing a connection would be a first step in a bigger job before you, but yes that would be one of the things you would have to do. After you have found this putative connection you think there is, then you need to demonstrate that this connection should constrain tree-topologies to agree.
In other words, not just that there is SOME physiological consequence on anatomy derived from (say) the activity of some enzyme. We know there are such connections. For example, if you have certain metabolic diseases caused by mutations in certain enzymes, this can result in stunted bone growh or muscle development (and many other possibilities). So it is not merely that you need to show that one has some effect on the other, but that the effect it has functionally demands that phylogenetic trees that can be derived from the species that have these genes should be forced to match each other.
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ok. here is apaper that show a connection between supposedly morphology-neutral genes and morphology:
“Evidence for an ancient adaptive episode of convergent molecular evolution”
first note that this happen in similar creatures (snakes and agamid lizards). so we probably will not find it among a lizard and any kind of mammal or a fish or a bird. this fact alove prove that similar morphology also effect similar non- morphological genes. it also show that there is a connection between morphology and these genes:
“The molecular convergence between snakes and agamid lizards may thus have driven by similar adaptive pressures on metabolic function affecting both lineages”
since metabolic function may be effected by the creature morphology.
Nope. In fact it’s evidence against that claim, because snakes are more similar morphologically to their actual relatives, iguanid lizards, than they are to their convergent buddies, agamids. Congratulations: your citation argues against your point. It’s a difficult point, but creationists in my experience manage it more often than you might expect.
Sorry, no. They’re affected (with an “a” not an “e”; spelling pet peeve) by the creature physiology.
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not so fast. the fact that this convergent took place in very similar creatures indeed prove that there is a correlation between morphology and enzymatic function. otherwise we should find such a convergent between far species like mammals or birds or fishes. but as far as i know we dont. we only find it between these snakes and lizards.
and isnt physiology a part of the creature morphology?
Why do you consider snakes and agamids “very similar” but do not consider iguanids also similar? This says nothing about such a correlation.
No. Words have meanings.
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sure that they are similar. but i try to show that the similarity can be affected by the morphology and that its not just neutral difference. so by showing that these traits are adaptive in similar species we have evidence that they arent realy neutral.
does physiology have no connection to the creature morphology?
You’re not being asked to show just SOME connection. We already know metabolism can and does affect morphology in various ways, it’s just that we have no evidence this connection constrains them to yield similar trees. You’re being asked to show that the connection would generally be expected to force phylogenetic trees to agree on the same topology even if the species did not share a common genealogical relationship. The paper you reference shows the opposite, that in this case some of the mitochondrial gene trees diverge from the morphological one instead of agree, because some mitochondrial genes have evolved convergently with another, less morphologically similar group.
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The first sentence’s meaning is obscure. The second sentence is not in contention.
Of course it does. But connection is not identity. My phone is currently connected to a wall socket, but nobody would say that my phone is a wall socket.
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The Fitch/Margoliash tree was constructed by an early program of Fitch’s that had a number of limitations. It did not do a very thorough search among tree topologies and branch lengths, and it did not restrict branch lengths to be nonnegative. Nevertheless the tree is pretty good for its time, though with some weird placement of rattlesnake and of kangaroo. Fitch was so annoyed at the rattlesnake result that he got the protein for that species requenced. It was corrected but still came out in a not-so-great place. Note that the matrix of distances is not any measure used today but is a count of the smallest number of nucleotide substitutions that could get you from that protein sequence to the other. They are not corrected for unobserved parallel or reversed changes, though in making the tree Fitch appears to have done something like that (his “corrected mutation distance”). One can redo the tree by using an alignment of the protein sequences and using a distance measure such as the Jones-Taylor-Thornton distance, and use the Fitch-Margoliah method program Fitch from my PHYLIP package, or similar capabilities in PAUP* or MEGA.
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several things. first: can you show me that there is no real connection between similar morphology and similar enzyme sequence?
second: my example indeed doesnt fit with the accepted phylogeny. but its still very close to the real phylogeny. remember that we dont find it in many other species that arent reptiles. and since these reptiles are a small group out of all creatures it show that there is a very close connection between morphology and enzymatic function. reptiles have about 10,000 species out of total 9 million species on earth. so the chance that these sequences will convergent only in reptiles is very small if its suppose to be morphology-free.
What do you mean by “real phylogeny”? I thought you were a creationist.
Sorry, but there’s a simple alternative explanation. Convergence in closely related species is more likely than in distantly related ones because the former are starting from similar places, i.e. similar protein sequences, and they are also more likely to encounter similar selective conditions and respond to them in similar ways. Nothing to do with a connection between enzyme sequence and morphology, other than the phylogenetic connection.
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why is that matter if we start with similar sequence?
why? because they are more similar creatures?