Biological classification aims at conflicting goals which do not appear to conflict – identifiable distinctions which correspond with evolutionary descent. Life which looks or behaves similarly may be very distantly related at best, as is often the instance in cases of convergent evolution.
Genetic analysis shows traces which suggest heritage, but this too has often proven misleading or confusing – forensic evidence which wrongly convicts. The problem becomes especially acute with organisms which selectively pick up genes from the environment and incorporate them. This dilemma applies to all early life, when genetic expertise was de rigueur to surviving in an every-changing world. But it does not stop there. Cross-species genetic transfers have been a driver of evolution for all life forms. The likely culprit is viruses, which regularly infect their hosts with new genic material.
Horizontal transfer, differing from the normal parent-offspring transfer, has had an enormous impact on mammalian evolution. ~ Australian geneticist David Adelson
Setting aside the genetic perspective, categorizing is problematic when trying to make evolutionary sense. Consider those with backbones.
We are accustomed to consider vertebrates in commonly known and understood categories such as fish, amphibians and reptiles. But phylogenetic analyses demonstrate quite convincingly that these are not natural categories, if by natural we mean that each constitutes a group, all of whose members can be traced to a single ancestral lineage, that is, a group that is monophyletic. The recent elimination of birds as a group and the recognition of “birds” as flying dinosaurs, while fully justified, illustrates the shoals on the course we are navigating. “Fish” is a name for a polyphyletic group of animals that share many features, but a single evolutionary origin is not one of them. ~ Brian Hall and Benedikt Hallgrímsson
Amphibians arose from among a group of lobe-finned fish. How to distinguish the more-derived lobe-finned fish that gave rise to these first tetrapods? Because the most derived lobe-finned genus of fish is Panderichthys, some refer to an even more derived taxon as “postpanderichthyid stem tetrapods” – a breathtaking name for devotees only. “Fish-like amphibians” is at least somewhat memorable; but such labeling of descents into a new major group is less descriptive than it seems, as mammals-to-be illustrate.
The old term “mammal-like reptiles” was once used for those reptiles recognized as having given rise to mammals. It is no longer considered appropriate because: 1) these creatures (therapsids) consist of multiple independent evolutionary lines, only a few which bequeathed mammals; 2) the term confuses a crown group (the culmination of an lineage) with a stem group (a lineage that gave rise to another group); and 3) the attribution makes it sound like some reptiles were trying to become mammals, and so struck a mammalian pose.
Many long-standing taxonomic groups are paraphyletic: they do not include all descendants of a common ancestor. A famous example is reptiles, which cladistically includes both birds and mammals. Among humanity’s closest relatives, the family of “great apes” is paraphyletic in excluding humans.
Conversely, paleoanthropologists go through some pains to delineate between those humanoid creatures that supposedly did not beget humanity, such as Neanderthals, and those that did: hominins. Considering the crossbreeding that went on (including with Neanderthals), the exercise is quaint.
In the finale, the problem is that you can’t square the circle of identifying groups of organisms with an eye toward descent, as the reality of evolution is seldom so simple as to be simply labeled. Humans are considered a single species, but not by any reasonable definition of what a species is. The attribution is political, and an acknowledgement that biological classification is a social convention, not a scientific discovery.
It is really laughable to see what different ideas are prominent in various naturalists minds, when they speak of ‘species’. It all comes from trying to define the undefinable. ~ Charles Darwin
Evolution is a messy business, defiant to easy tagging. Forgetting heritage for the moment, there is any even more fundamental problem inherent in classifying extant groups in a world with biological diversity beyond imagination: where do you draw the lines? To even begin, you have to have some consistent concept of species. There isn’t one.
There are n+1 definitions of ‘species’ in a room of n biologists. ~ Australian science philosopher John Wilkins