Phylogenetics is a frequently cited proof of evolution. Phylogenetic trees adorn our high school and college textbooks and are presented as somehow being an absolute fact in spite of the fact that almost all phylogeneticists themselves agree that no phylogeny can be proved. In fact, E.O Wiley, one of the premier evolutionary biologists of the 20th century wrote an entire book on phylogenetics which made the claim that phylogenies are hypotheses at best. In his view, it was only possible to determine the best approximation of phylogenetic trees, rather than demonstrate any of them conclusively.
Despite these flaws, evolutionists continue to present phylogenetic trees to the public as both authoritative and accurate. This is, of course, in spite of the fact that they are neither of those things. With that in mind, let us examine the four necessary assumptions of phylogenetics. The first three are drawn from a 1991 book on phylogenetics (Phylogeny, Ecology and Behavior, Daniel Brooks and Deborah McLennan) which lays out the case for phylogenies, while the fourth is so integral to phylogenetics that it is assumed at the outset.
The first assumption is that speciation events must be able to be reconstructed by following chains of traits. What this means is that it should, in theory, be possible to reconstruct all the splitting of species in a lineage based on the traits exhibited by the species that formed as a result of those events. There is all manner of problems with this assumption. The first and perhaps most obvious is that no one has a firm solid definition of what a species actually is, or how to define it. There are at least 32 different species concepts that vary widely in ideas and acceptance. The second problem is the assumption that some traits have not been lost in time. In other words, we cannot assume that a group of species still has all the traits its ancestors had. Some traits may have been lost.
The potential for lost traits plays strongly into assumption number two of phylogenetics, namely that there have been no extinctions in the group in question. This makes sense. If there have been extinctions, it is impossible to track the path of traits and thereby track the path of speciation. However, since we have not been keeping accurate scientific records since the beginning, and we know massive extinctions happened in the past, it is quite conceivable that extinctions have happened and we missed them. This throws every single phylogenetic tree ever constructed out the window. If even one extinction in a group was missed, it is impossible to accurately present a phylogenetic tree of that group.
The third assumption is that if speciation has been influenced by geography, then we should be able to trace the background of the original speciation event. What this means in practice is that, if the speciation that occurred was a result of geography, we should be able to determine why the event occurred and which species was ancestral. This assumption has less of an issue with it than the other two. However, again, it has the issue of assuming the topography and geography of a region have stayed the same since a given speciation event took place.
The fourth assumption underpins them all and is so critical that, if you kick it out, the entire foundation of phylogenetics collapses. That assumption is that there is at least some form of common ancestry in the group that can be traced in the first place. In the case of phylogenetics, this requires the assumption of evolution, either within a small group or within the broader group of living organisms. Since this assumption is false in the broad sense at least, it is impossible to correctly deduce a phylogeny of all life.
While the phylogeny of all life cannot be deduced, could it be possible to deduce a phylogeny of a small group? Perhaps but not with the current methods of phylogenetics. As demonstrated above, the other three underlying assumptions are incredibly unreliable as well. Therefore, phylogenetics ought to be rejected as a method of determining ancestry, particularly since it fails to take into account the Biblically-based concept of the baramin. Science would do much better to reject the outdated, failed methods of phylogeny and attempt to develop a more accurate assessment of organism relationships.