Why is plant taxonomy so complicated?

Nature Talk
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Hi
I realize I might be asking a complicated question, but I’m going to give it a go anyway.

I’d like to know why there are so many problems with plant taxonomy. I’ve started studying plants about a year ago and I use different books and online sources. It’s rather frustrating that there are so many disagreements about taxonomy. One sources will describe two species and another source will say those are actually the same plant. Some sources use the accepted name, while others use a synonym.

It seems to me that this is more of a problem with plants than with animals.

Is there a reason for this?
Any good books out there to better understand this?
Can’t some kind of DNA test be used to decide if plants are different species? (I know this is probably very naive).

Thanks!

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I actually think plant (by which I mean Vascular Plant) taxonomy is at a really exciting point, where a global taxonomy is actually coming together as we speak and within reach.

In my mind, this is an important milestone towards getting a more stable taxonomy for any clade, because a lot of the disagreements you describe come from semi-overlapping regional taxonomies (which is where plants have been up to this point, ie Flora of North America etc.)

Vertebrates (ie the ~10k Birds, ~6k Mammals, ~10k Reptiles, ~8k Amphibians, & ~36k Fishes) have all had some form of Global List available for about the past 1 to 2 decades (e.g. Catalogue of Fishes, Amphibian Species of the World, Handbook of Mammals etc.).

There’s ~360k Vascular Plants, so pulling together a global list is a much bigger job than Vertebrates. Monocots and Gymnosperms have had global lists for a while but thats just a small fraction of Vascular Plants. Kew and MoBot tried a global list with the Plant List in 2008 but most people agree that it wasn’t quite ready for show time. Last year POWO came online which isn’t supposed to be fully ready for show time until 2020, but its close and getting better rapidly http://www.plantsoftheworldonline.org. I think when these global lists are available and usable, they get more buy in and become less controversial alongside regional floras (here in CA, disagreeing with our local Jepson Manual was sacrilege until very recently - maybe still is…)

Vascular Plants are in a much better place than insects (~1M species). For all but a few orders (eg Odonata, Orthoptera, etc.) and Families (Ants, Bees, Sphinx Moths, etc), we don’t have anything close to a global list, just a smattering of regional lists.

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Plants also hybridize, self fertilize and/or change ploidy more readily than other groups of organisms, which may further blur already cloudy species boundaries and make genetic differentiation via DNA testing more difficult.

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You think plants are hard… try fungi!

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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:

  1. Easy to apply and communicate
  2. 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:
https://www.allaboutbirds.org/mixed-wing-warblers-golden-wings-and-blue-wings-are-99-97-percent-alike-genetically/

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:

  1. 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.
  2. The process will always be difficult, fraught, uneven, frustrating, because that reflects the objective reality of the terrain over which the process treads.
  3. 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…

C

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my unpopular explanation:

because splitters exist.

I will leave it at that because too many people here have already had to read my rants :)

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We humans need simple, clear words to decribe plants, so we can communicate clearly. Real animals and plants have no need for our neat words. They evolve in sometimes unclear ways. Matching our words to real organisms inevitably leaves room for confusion and disagreement. I wish this weren’t true, but it is.

An inevitable result of evolution is that some times one species is dividing into two different species, but it hasn’t completed the process. Some of the individuals are clearly different, but others are not. Where to do draw the line? That choice is arbitrary.

DNA can help us evaluate whether populations are currently interbreeding or did so in the recent past, so it is a good clue about whether we should call organisms the same species or not. However, DNA is not a one-size-fits-all solution to the question of whether organisms are the same species or not. Sometimes very genetically similar organisms differ in one important way that prevent interbreeding and divides them into two different species. Sometimes a single species is highly variable. And sometimes . . .

Well, sometimes we have to find words (species/subspecies names) to fit, for example, plants that reproduce entirely (or almost entirely) without sex. Where do we draw the lines within such lineages? What criteria should we use? The very worst are those that produce seeds without sex most of the time (like blackberries or hawthorns) but sometimes do have sex and then that new genetic individual produces thousands of asexual seeds, essentially cloning itself, with those rare events of sexual reproduction. Those plants really mess with our species concepts.

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Although DNA doesn’t often do a good job of determining where to draw lines between species, it does a very good job or showing what’s related to what. Sometimes the relationships are different enough that we feel a need to change taxonomy, sometimes including species names. Sigh.

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Systematists do science in the search for the one true phylogeny. Taxonomists are file clerks. (I say that as someone who loves the complexities and arcane features of taxonomy.)

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A portion of the problem can be attributed to history: beginning with Linnaeus, binomials have been attached to vascular plants, with physically similar species grouped into genera. These genera were further grouped into families, families into orders, etc, based on physical features. Over time, other techniques have refined the groupings - cytology, anatomy, genetics, biochemistry, DNA (as you note), etc., have added to our knowledge, and led to re-arrangements. Yet taxonomy is a human enterprise, and ours is an argumentative species. So there is some disagreement over arrangements. This is a part of the problem, and because of it there will never be an absolute authority.

However, much of the name confusion is actually due, as noted up top, to history. As names - and groupings - are changed, and for various reasons, the “new” names are left out or not included in the various databases listing vascular plants. Luckily, when a taxon is renamed, a list of old names is attached to the new name as synonyms: “old” names are retained. So it pays to check a database such as the default iNaturalist vascular plant authority, Plants of the World Online (POWO), for synonyms. In fact a search of a name there will also return results for synonyms, and lead to POWO’s accepted name. Each entry in POWO includes a list of accepted synonyms.

I take comfort in two sayings: Thank Goodness for Synonymy, and a quote from an old Jefferson Airplane song, “Eskimo Blue Day”: “The human name doesn’t mean sh__ to a tree.” The tree cares not a whit what we call it.

(There’s much more to it than this as noted by others above, and hopefully below, but I hope this helps.)

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Excellent question and excellent replies above. The answer to the question about genetic tests is that in many cases it is possible to use a genetic test to decide if plants are different species–however, in those cases we often already know they are different for a lot of non-genetic reasons. The problem is trying to decide whether two very similar populations of plants deserve to be called different species. First it’s actually a huge computational challenge to comb through the mountains of genetic data required to compare closely related populations–although scientists are getting better at this. More fundamentally, however, even with access to all the genomes of all the individuals in the populations, we might still have trouble deciding whether those populations were different species!

One of the most eye-opening moments for me as a graduate student was realizing the inherent “fuzziness” of species as a concept. In the early part of the last century, I believe biologists were optimistic that a more or less universal definition of species could be found. However, the more we have studied genetics and non-vertebrate organisms the more complicated and problematic the concept of species has become.

If you have time, I highly recommend reading this short thought provoking essay on the species concept by Brent Mishler who is a botanist at UC Berkeley. Here’s a link to the PDF (let me know if you have trouble accessing)

“Species Are Not Uniquely Real Biological Entities” in Arp and Ayala, Contemporary Debates in Philosophy of Biology. 2010.

Dr. Mishler’s view is his own and I know many biologists probably disagree (it’s not really my area of expertise) but it’s a good, not too technical, overview of the conceptual problems that any species definition faces.

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Tl;dr: I don’t think there is a simple answer!

As a few people have said in various ways, there are several issues:

  • There is no universally accepted definition of a species. Groupings above that (genera, families) become even more artificial.
  • Some people expect that a given amount of morphological variability is to be expected within a species (look at humans!). Others (someone already brought in splitters) will make the argument that if something is distinctive enough to be referred to as an entity, we need a name for it, and often describe these as new species.
  • Some taxonomists don’t believe in infra-specific taxa: subspecies, varieties, forms, and so they describe everything as new species. Others (myself included) think that infra-specific taxa can be used effectively to explain the variation we observe in the plant world.
  • Unlike a majority of animals, plant hybrids are common and often perfectly viable, sometimes able to back-cross with the parent species. This allows for gene-flow even after populations have differentiated past the point where we’d consider them different species.
  • Plants don’t read taxonomy books and consequently don’t realise that we expect them to fit into these neat little named boxes we’ve created for them.
  • Unlike the situation with arthropods and fungi, where taxonomists barely keep up making sense of the vast number of unknown species, vascular plants at least are getting fairly well known. This leaves more time to argue about where one species/genus/family ends and the next one starts, and to refine the taxonomy to better reflect the evolutionary history of taxa.
  • Some groups are just hard. We keep expecting that if we throw the next whizz-bang new technology at the hard groups, they will magically resolve.

I hope these points make sense!

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@liesvanrompaey – I used to be troubled by the various taxonomies I ran across for various groups of organisms until I realized that any taxonomic arrangement that is proposed in the literature is a hypothesis (or theory, if you prefer) about relationships and thus can be tested and potentially rejected. The proposed arrangements are not necessarily correct (if any taxonomy can ultimately be considered correct), they are just an idea based on what we know. So I don’t get attached to any particular taxonomy, I simply use what I consider to be the best arrangement (which might not be the latest) or what is available for a particular purpose (e.g., whatever iNat is using).

Systematics is the science by which we try to understand evolutionary histories of organisms with various methods (genetic analyses, identifying morphological differences/similarities, biogeography, etc.). There actually is a right answer about the evolutionary history for any group of organisms, but we are still trying to get there. Based on information from systematics, we then try to fit these organisms into a human-created file system (Linnean taxonomy). There will always be disagreements about how to file these groups since taxonomy is not actually real in a biological sense. Maybe there are better systems out there (e.g., the PhyloCode, which apparently never really caught on) or that have yet to be invented. But for now we have Linnaeus’s system and we have to deal with its inadequacies and differences in opinion about how to apply it.

Good luck with your studies.

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Thank you for this reference! It helps clarify for me why statements such as

always rub me the wrong way. They oversimiplify.

As that reference clarifies, the natural entities to which we apply the term “species” are very real. What is arbitrary is the human decision about which of those natural entities to call a species, versus some other category in the Linnaean hierarchy of taxonomic ranks.

That said, and as I think @charlie and other field-going botanists and plant ecologists would agree, I know a species when I see it. (And a corollary: I know an arbitrary species when I see it!) I see both ambiguous and unambiguous ones every day (usually more of the latter). So maybe this is where application of the Linnaean species rank will end up if the PhyloCode (see reference above) ever gains wide acceptance – the “Practical Species Concept” of Cronquist and similar thinkers.

Would you agree that each necessarily encompasses the other? Taxonomists need something to file; Systematists need something to call the entities they study (even if provided by PhyloCode taxonomists of the future).

Yep. And thanks for asking it. I hope the variety of perspectives it has and will provoke here lead to better understanding among the larger community!

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Ho, boy, what a topic! My most distilled answer to “why is plant taxonomy so complicated?” is that’s because plants are very complicated! Each population of every species is subjected to a unique set of selective pressures acting on the particular genetic characters of that population at that particular time. As a function of this, populations may either converge or diverge, creating local races and variations. Humans, reacting to these similarities and differences, interpret them in different ways, hence the eternal debate between splitters and lumpers. Having dealt with this for decades, my own perspective is to favor moderation, not heading too radically toward either splitting or lumping. That being said, I strongly object to the view that “splitters” are the problem. I actually think the opposite view has more validity, and that we need to be aware that there is still much to learn and document in the natural world before it is destroyed or much diminished by the “Anthropocene”, as defined by E. O. Wilson. To think otherwise for me is either naive or deliberately donning blinders in order to “keep things simple.” The world is an amazingly complex and ever-changing place, and we who study biodiversity need to remain humble and flexible and always willing to learn from it.

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It’s complicated because of geneticists. Their work has changed the original purpose of taxonomy with considerations that were not foreseen. Interesting to see someone take the other side and say “the problem is history”, very disrespectful of Linnaeus. There is an attitude right now that “science is golden”, or “a particular science is golden” instead of an omnipotent view from future generations that this is a time of competing factions. Geneticists have found something to do; I wish my own field had more grants and individual notoriety. In the Archaeology vs. History debate the reason for saying “the problem is history” is competition, and the next official statement is “there is no competition”. Don’t trust any institution that says “the problem is our own history books”, it’s like saying “there is no change, we were always right”. The short-term gains for taxonomy are fleeting because we will only come to realize our dependence on words; they are gains for today’s situation only. I see a lot of facts used to promote the things an individual cares about, but I don’t see anyone admitting that facts are also trends. If the problem is history then a historian can’t assemble their own case as you have done and therefore there is no learning.

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Yes! The joy of discovery and biodiversity! I applaud the systematist who digs into all available evidence to test a hypothesis and then refine what we know about relationships within taxa and various lineages. Documenting with evidence a distinct lineage is exciting. Their conclusions can be re-tested by others, but a split with evidence and peer review, is us narrowing in on the vast biodiversity that makes this world an even richer place to exist. I say split away ;-) with testable repeatable peer reviewed evidence!

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Hi @liesvanrompaey, thanks for the question! I had the fortunate opportunity to examine the relationship of a group of sedges and DNA was extremely informative. It is truly an eye-opening experience to see the conserved DNA distinctions in one lineage compared to a very closely related and often cryptic sibling species. Systematists are building on the shoulders of their predecessors and through hypothesis making and testing, improving our understanding of the breadth of biodiversity that exists. Frustrating at times for learning names, but also exciting and part of the spirit of discovery that many of us iNaters share. I haven’t read through all this thread yet to see if any book recommendations have been made, but a Plant Systematics textbook would be informative (but a slog to read). I can look through my old files (grad school) and see if there are journal articles I can recommend.
-Derek

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It is never useful to generalise :wink:

More specifically, however, plant taxonomists had plenty to disagree about before modern phylogenetics hit the scene, and the main difference was that back then we were just guessing based on morphological and functional traits.

I have to agree with @calloftheloon:

I also had the opportunity to work on a group with a taxonomy that had been established since the 19th century, and was based on morphological characters that were poorly chosen and uninformative. As a result the taxonomy of the group was totally artificial and pretty useless. The advent of DNA-based phylogenies allowed the construction of a backbone against which to test the usefulness of morphological traits to taxonomy.

Separately:

Can you elaborate on how this is disrespectful, please? Taxonomy has moved beyond Linnaeus’ artificial groupings (i.e. Heptandria Monogyna) and into natural families that attempt to reflect the natural affinities of the groups since even before Darwin’s theory of Evolution by Natural Selection was published. Even after this, virtually every taxonomic treatment uses a classification that attempts to reconstruct the evolutionary history of the groups. One thing taxonomy has never been about is remaining static and pretending to be the one and final word.

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Changes in taxonomy usually come because newer researchers disagree with old treatments, or find new outbreaks in “evidence” to justify speciation. Taxonomy is pretty fluid, although not nearly as much as it used to be when people were renaming genera constantly. Now when genera are reclassified, it is generally for good reasoning (genetics, or a more comprehensive treatment then has been done previously).

At the end of the day, you only really need to learn one name – it will still work as a synonym in various ways. The only issue is when a single species becomes many.

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