I realize that this is going to be a somewhat unsatisfying and maybe even annoying answer, but as far as I can tell the complexity accurately reflects the objective reality of evolution… which is unsatisfying for our order-seeking, narrative-oriented brains.
The crux of the issue is a platitude at this point, but one that may people still don’t seem to take seriously: “Species” are artificial constructs. I know this isn’t a new idea, and I’m not claiming that it’s radical nor is it intended to be disheartening, defeatist, or rabble-rousing.
Species hypotheses necessarily involve judgement calls presented with variously strong arguments using multiple lines of evidence (DNA is only one, and is not a silver bullet – there is no Yes/No test, because there is no objective reality underlying the idea of a species).
Further complicating matters, species concepts are intended to serve two (unfortunately inherently conflicting) purposes. They are ideally:
- Easy to apply and communicate
- Reflective of evolutionary history
If you want a great example of just how unintuitive the species concept is even for something as straightforward as a big, charismatic vertebrate, check out the case study with Golden-winged and Blue-winged Warblers:
Their songs, ecology, and appearance all intuitively align with our idea of “different species”. And we even try to make conservation decisions to keep up healthy populations of Golden-winged Warblers (which are declining).
But… genetics (and not just barcoding, but actual whole-genome evidence) suggest that they should be considered part of the same taxonomic unit if we use other bird species/subspecies groups as stabilizing metrics.
I’ve started to harbor a lot of probably untenable, radical notions about taxonomy, that I can boil down to this:
- Species taxonomy is objectively and foundationally flawed, but still completely necessary. Numerically-named taxa are fine for ecologists and evolutionary biologists, but the common people of the world want/need/deserve names.
- The process will always be difficult, fraught, uneven, frustrating, because that reflects the objective reality of the terrain over which the process treads.
- That doesn’t mean we shouldn’t make the various processes and systems easier, more stable, more consistent, and more efficient where possible: Getting rid of formally and/or culturally enforced requirements that species names conform to proper Latin, requiring images and descriptions of species to be publicly available in a consolidated source, having committees to stabilize adoption of new nomenclature/systematic research.
Anyways, I hope this doesn’t cause anyone to come after me with pitchforks or exile me for heresy. I still play by the rules as they exist (mostly), but would like to initiate a lot of changes in those rules…