This continues a series on species. The previous episodes introduced the topic, provided an intuitive classification of species concepts, and dealt with biological, genotypic cluster and "typological" species.
The term "phylogenetic" became so popular after phylogenetic systematics gained ascendency in the systematic and taxonomic community that several quite unrelated species concepts were published under that label. In the previous post you may have noticed that I call something the autoapomorphic species concept following this list compiled by a philosopher of science although it was really published as “The phylogenetic species concept (sensu Wheeler and Platnick)”. Not only does that clarification in the brackets nicely demonstrate the problem of homonymy here, but I am also unsure what exactly is so phylogenetic about a concept considering species to be groups of samples with a unique character combination.
I will therefore limit this post to discussing the so-called phylogenetic species concepts that demand species be monophyletic (i.e. the Phylogenetic Taxon Species in the list mentioned above), although that necessarily means that I will in part reiterate what I already wrote before.
The basic idea is alluringly simple: all supraspecific taxa should be monophyletic so it would only be consistent if the species themselves also were monophyletic. The US American bryologist Brent Mishler is among those who push this to its logical conclusion: Species are not a unique or special level in the classificatory hierarchy of life, they are simply another clade (Mishler, 2010). Others argue that species are unique, but what makes them unique is merely that they are the lowest clade that one can resolve.
But there is a problem right there: what about asexually reproducing organisms? In purely asexually reproducing groups, everything down
to the individual (and of course its cell lines) is monophyletic because there are no reticulations, ever. Okay, in that case Mishler's idea to abandon species would make sense, just like biological and mate recognition species do not really exist in asexual organisms.
However, there are much more severe problems with making everything monophyletic in sexually reproducing groups. First, we are talking about clades, i.e. monophyletic groups, of what precisely? To make species monophyletic, the items forming the clade must be something below the species level, so they must be populations or individuals. But then the deal-breaker becomes immediately obvious: in sexually reproducing organisms, the relationships between populations and between individuals are tokogenetic instead of phylogenetic, and that means that they cannot be monophyletic or non-monophyletic. The latter concepts simply do not apply in a tokogenetic structure, just like "scored a goal" does not apply to a marathon runner. That is why phylogenetic systematics does not group individuals but species into monophyletic groups - the relationships between species are predominantly phylogenetic, with few reticulations, the relationships between individuals mostly aren't.
Finally, even if one were to redefine the word monophyletic in a way to make it applicable to sexually reproducing individuals or populations, there is also an epistemological problem with the idea of inferring clades of them. We infer the existence of clades from characters, the so-called synapomorphies. Those are novel characters that we assume to first have evolved in the common ancestor of a clade, and the common inheritance of those characters by all its descendants is the evidence for them being a clade in the first place, i.e. for them all being descended from that common ancestor.
In reality, things are a bit more complicated. Characters, whether molecular or morphological, show some degree of homoplasy, either through reversals or parallelism. For example, the possession of four legs is the synapomorphy for the tetrapods, the land-living vertebrates, although several groups of tetrapods have lost some or all of these legs, such as snakes. Phylogenetic analysis with all available characters shows the snakes to be part of the tetrapods, and although they secondarily lost the character in question their ancestors still had it so it is still a synapomorphy for the group the snakes belong to.
The question that we need to consider here is the justification for assuming that synopomorphies allow us to identify clades: why can we assume that all the descendants of one ancestral species will (at first at least) inherit a given synapomorphy, and that members of other clades won't? Well, because a clade is the group of all descendants of one biological species, a lineage that does not interbreed with others any more. This is crucial: if the ancestor of a clade can be a sexually reproducing individual or population instead of a reproductively isolated species, there is no epistemological warrant for inferring the clade from characters. To provide a stark example, it would be entirely possible (although statistically unlikely) that I have inherited no genetic material whatsoever from my maternal grandfather: The Y chromosome comes from the paternal grandfather, the mitochondria from the maternal grandmother, and due to the stochastic nature of recombination it could happen that all chromosomes that I inherited from my mother are the set she inherited from her mother.
If we use the bizarro-definition of the term monophyly as forced onto tokogenetic systems then my mother, my uncle, my brother, myself and my two cousins would be a "monophyletic (not really)" group because we were all the descendants of my maternal grandfather, but under the scenario described in the previous paragraph it would be impossible to infer my membership in that "clade (not really)" using any character whatsoever.
Again, statistically unlikely, but if we are talking about a few more generations situations like this become inevitable. That is important. Talking of clades and trying to infer them is only possible if the ancestor is a group of individuals in which the character later identified as a synapomorphy became fixed, otherwise they could have had descendants that did not inherit the character. That means, at some point there was no interbreeding anymore with anybody who did not have that character, so the ancestor must have been a biological species. Consequently, talking about monophyly of anything below the level of biological species does not make sense. Consequently, "monophyletic" species do not make sense. Except, of course, for asexually reproducing individuals.
Mishler BD, 2010. Species are not uniquely real biological entities, pp. 110-122 in Ayala FJ & Arp R (eds.), Contemporary Debates in Philosophy of Biology. Blackwell Publishing.