Although this 'canonical' tree of life is thought to exist by many evolutionary biologists, the actual details of the tree have never been agreed upon. There have been a multitude of different attempts to map out this tree of life but they vary so widely depending on which technique of classification is used and which particular method within each technique, that many biologists have given up on the idea of a 'canonical' tree altogether. In the 1960's chemist Linus Pauling and biologist Emile Zuckerkandl proposed a way of confirming rigorously the proof of 'macroevolution.' Since random mutations are thought to occur at regular intervals (the 'molecular clock'), you could date the divergence of one type of animal from another by the amount of difference in common genes. In other words there are genes that code for proteins that perform similar functions in all animals. As a result of mutations, so the theory goes, these proteins vary from each other by one or two or several amino acids which are the result, according to the theory, of mutations or errors, during the DNA replication process for these genes. If two animals from different phyla share proteins with lots of amino acid variations, that would indicate that these phyla diverged on the tree of life from each other a long time ago. Less amino acid variation would indicate a more recent divergence. If it turned out that the tree of life based on these 'molecular clock' calculations matched the tree of life based on shared anatomical features, than that would be hard proof, according to Pauling and Zuckerkandl, that macroevolutionary change was caused by random mutations. It didn't.
In fact the actual world of scientific attempts using both methods, or different attempts at using the same method, are so varied, and the different points of view so contentiously debated, that the world of tree classification, which is both large, in the number of scientists involved in it, and minuscule, in the myopic obsessiveness and pre-occupation of its participants, that it could best be described as, I believe the scientific term is, a hot mess.
Some of the problems arise from the fact that different proteins have very different mutation rates. Histone proteins, for instance, show almost no variation at all from one species to another, even from one phyla to another. Other proteins show modest variation and others show great variation. Depending on which protein you use to figure out divergence dates, you come up with an entirely different tree. Also, how do you classify different animals? Which body features do you focus on to make your tree? If you focus on one set of features you group animals together in one way leading to one type of tree, and if you focus on another set of features you wind up with a very different type of tree.
Just a side note here about molecular clocks. I read a defense of them from 'The Human Evolution Coloring Book' 2nd edition. The author contends that the molecular clock is actually the same for all molecules, it's just that some proteins cannot tolerate any mutations, so the organism that is the recipient of such a mutation dies instantly or at least before it can reproduce, so the mutation doesn't survive. In comparing horses to humans, they note that in the last ninety million years there have been no mutations in the histone protein which binds DNA and can tolerate no change in it's shape. For cytochrome C, which is an enzyme necessary for the oxidation of food, there is a 12% amino acid difference between horses and humans. And in fibrinopeptides, which aid in the blood clotting process by acting as spacers between the sticky surfaces of fibrinogen (at a certain point the fibrinopeptides are discarded and the separate sticky clumps of fibrinogen come together to form the larger clot) there is a difference between horses and humans of 86%.
Now this is in a coloring book, so beyond the purpose of learning about the molecular clock, it serves the function of re-enforcing the idea of evolution to children. Supposing all of the above to be true and that there is a consistent molecular clock of random mutations, which I don't believe for a moment; is this really a good defense of evolutionary theory? If the best that mutations can do is to be tolerated; if 86% of the amino acid composition of horse and human fibrinopeptides differ and yet they still perform the identical function, what does that say about mutations as the engine to drive macroevolutionary change? With the right teacher, these kiddies could go back over their coloring book and notice that mutations bring either death, disability or, at best, tolerance. Where are the mutations in all of this that improve or change the functioning of any of these proteins? How is the process of evolution forwarded one iota by any of this?
Of course if you try to create a tree of life using only actual fossils, with no speculation as to genetic or morphological divergence points, than you do not wind up with a tree at all. We can start with the fact that for at least the first three quarters of biological life, about three billion years, there was nothing but bacteria. These bacteria underwent tremendous adaptation to every climactic condition on this planet, but this was accomplished chemically and molecularly with no real morphological change. The next event in the fossil record is the appearance of some tiny animals in the Ediacaran period, over 550 million years ago. These were sponges, mollusks and worms that are very simple organisms in comparison to most modern day plants and animals, but represent a huge and inexplicable leap from bacteria, with no fossils of complexity intermediate to bacteria and Ediacarans ever found. Then we have the Cambrian explosion. Around five hundred and thirty million years ago, for a period of time less than seven million years (an eye blink in the four billion year old history of life) we have discovered treasure troves of highly complex animals with legs, gills, intestines, exo-skeletons, spines, tails, mouths, anuses and compound eyes (so much for both Darwin's and Dawkins' explanation of the gradual evolution of the eye). And more than that, the Cambrian menagerie is so varied, that it represents twenty-three of the twenty-six phyla, or basic body plans, of all the animals that populate the earth today.
Where are the predecessors? And you should know that the existence of a Cambrian explosion was known to Darwin, and he realized that it was a challenge to his entire theory. Therefore, there have been armies of evolutionary paleontologists who have explored the pre-Cambrian sedimentary layers on this planet as never before since Darwin expressed his concern, in the hopes of finding at least some fossils that would begin to explain the gradual, advantageous mutation by advantageous mutation scenario demanded by Darwinian evolution. Short of those few Ediacarans that I already mentioned, and bacteria which have been here unchanged for billions of years, there is nothing. In fact what was actually discovered after Darwin were two enormous Cambrian deposits, one in British Columbia, the Burgess shale, and one in China, the Chengjiang fossil site. Through the study of these remarkable deposits it has been determined that the Cambrian explosion was much wider, more varied and more compressed (the entire explosion taking place betweeen five and seven million years) than originally thought, which served to only make the Cambrian conundrum that much more difficult to yield a Darwinian solution.
Trying to explain the Cambrian explosion by molecular clocks; in other words taking the present day representatives of phyla found among Cambrian fossils and using the amount of amino acid differences to determine when these phyla diverged, we get results, depending on which proteins are measured, of divergences from a few billion years ago (even though there are absolutely no fossils for all that time to support this hypothesis) to a few million years ago, in other words over 500 million years after the Cambrian explosion. So much for molecular clocks!
Of course the Cambrian explosion is not the only mystery for Darwinians in the fossil record. In fact if you look at the record as a whole, it looks to be, in shape, more like a layer cake than a tree. Geologists used to date layers of rock simply by their elevation; those on the bottom were considered older and those on top were considered to be younger. Then, with the understanding of plate tectonics, the picture became murkier. Layers of sediment that were below the surface have commonly overrode the layers that were on the surface during plate shifts. How to date these sediments then? In 1815 a geologist, William Smith, studying the fossil strata exposed during the construction of a canal, offered a new idea to solve this dilemma of determining the age of rock layers. Since the fossil strata are so distinct from each other, so discontinuous, each one having whole new types of animals not present in earlier strata, and absent of so many types of animals from previous strata, that the easiest way of determining the age of rocks was by the fossils revealed in them. In other words a layer cake, not a tree, with each layer a different flavor from the other layers and the whole thing covered with a bacterial frosting. And that is a standard dating technique that geologists use to this day. "Chew upon this" my neo-Darwinian comrades!
I need to also mention convergent evolution. There are some animals that share an almost identical trait, but little else. For instance, moles and mole crickets have, structurally, almost identical forelimbs, but based on this we cannot classify moles with insects or mole crickets with mammals. Whales and bats share almost identical systems of echo location. Should we then move bats away from their squirrel neighbors and join the dolphins and porpoises on their branch of the tree of life, or shall we have the whales join the bats and squirrels on their branch? There are actually many of these situations, where identical or almost identical traits and features, and very complex features at that, turn up on completely different animals. Evolutionists have been forced to come up with the idea of convergent evolution; that after different animals diverged on the tree they underwent separately the identical sequential processes of accidental, random mutations leading to identical features on completely different body plans. If one evolutionary path of random mutations seems mathematically and logically impossible, try pondering the probability of the identical series of accidental mutations occuring two or three different times. Darwin's whole basis for constructing his tree of life was that similarity implies common ancestry. Now we are told that it does except in those cases, those very many cases, actually, when it does not.
I will mention one more thing before I get to the real point of this post. The tree is built based on the understanding that similarity implies descent from a common ancestor, yet as more and more genomes are studies, ORFans, or genes of unknown origin, have been sprouting up in every major group of organisms including plants, animals, eukaryotes and prokaryotes. They have homologous relationships with no known organisms. They are referred to as having a "de novo' origin," which is neo-Darwinian for "huh?" Is the tree of life now surrounded by a forest of slender saplings, or are the ORFans more like the entire Cambrian bestiary, hanging in air with no evolutionary roots at all?
To finally get to the real point of this post: even if a canonical tree of life were found; even if, as Pauling and Zuckerkandl had hoped, the molecular tree comported perfectly with the anatomical tree, would that give hard proof of "macro-evolution?" Absolutely not!
I don't know whether to call it a tautology or a self-fulfilling prophecy, but it has elements of both. If you define every amino acid change in a protein as a mutation, you are already assuming Darwinian evolution before you begin. What all these scientists are trying to prove, really, is that living organisms got here by random, accidental processes. By defining any differences in proteins as mutational you are assuming that those changes were random and accidental to begin with. Also, even if they were random mutations, all you have proved is that random mutations are associated with morphological change, not that they cause morphological change. Actually, all that you would have proven is that amino acid changes in proteins, whether accidental or intentional, are associated with morphological changes.
Since Pauling's and Zuckerkandl's premises are all grounded in neo-Darwinian theory to begin with, the theory is never actually tested. That is why, when the results come out and the molecular and anatomical results do not comport, the theory is never called into question, but the assumption is that the technique must be wrong. And that is why scientists have tried again using different proteins and different systems of classification, and tried again, and tried again, and are still trying.