More on species complexes

I’d like to canvas curator opinion about the use of the iNat species complex rank.

The curators guide includes …
o Species complex is monophyletic (i.e. sibling groups of species)
o Complex is recognized in the literature
o A named subgenus, section, or series does not already exist for the group …

Modern phylogenetic analysis in my group, the fungi, often uncovers cryptic species-level diversity within taxa that were historically treated under a single name. Often these cryptic species reflect biogeographical divisions, but not always.

In addition, we quite often find that taxa that are grouped into tight clades, where morphological distinctiveness may, or may not distinguish species in the clade, i.e. closely related species are sometimes morphologically indistinguishable and at other times (surprisingly) they have clear/stable differences.

I’m sure there are other groups where the same issues arise.

So my questions are these:

  1. Do you think that ‘species complex’ should be applied to both these cases? Or only the first where morphology alone does not easily separate the (phylogenetic) species? And then what about ‘mixed bags’?

  2. If you include the latter situation, where morphology can be quite different between closely related species, then ‘species complex’ can easily become a means of labelling clades. Is that appropriate or not?

  3. What level of evidence is required to justify the introduction of a complex?

    a. Does the ‘complex’ need to be quoted in multiple peer reviewed publications (by different authors), or just used on the web somewhere?
    b. Does a source need to explicitly refer to a (cryptic) complex, or does the use of words like ‘the xxxx group of species’ count as a valid proxy for the term species complex?

  4. Can an iNat species complex stand alone in the iNat hierarchy with just the nominate species as a subordinate taxon (so it can at least be used for observations) or do all the relevant taxa need to be included as subordinates?

  5. If introduction of a complex requires all iNat subordinates to be included then good practice would be to ensure that primary cited sources not only mention/introduce the complex, but also establish the boundaries of the complex and enumerate the species within it. i.e. it would not be adequate to reference a work that uses the complex name but does not define what it is (which is why it might stand alone).

I have clear opinions on all these questions but I’m willing to change my views, and the way I curate, depending on the consensus.

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I can only speak from my limited experience as a noctuid identifier. Often a group of species is so visually similar that they cannot be told apart by visual characteristics. I often use Xestia c-nigum & dolosa as an example. Some of the Euxoa spp. are so variable and similar that they are often grouped into a complex. These are generally the result of peer reviewed papers, but I do not know for sure if the complexes have been formally named in papers. Certainly with something like E. comosa there is a named group that includes several species or sub-species, most of which are geographically separated. Although not always by much.

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  1. In my opinion complexes should only be created if they are useful. If range itself can separate two species, a complex does not seem useful. If they overlap and can only be separated genetically, that’s exactly the use case for a complex.
  2. see above
  3. Best if it comes from the literature. I don’t think they need to use the word complex verbatim, but group would be valid IMO. Cryptic does not need to be stated.
  4. No. All taxa in the complex need to be grafted to the complex.
  5. A complex is not useful unless its membership is clear.
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I would agree with this approach.

I would add that I think one source is enough, but it should definitely be from the literature.

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I also agree that to add a new complex to iNat it should typically be already used by at least one external authoritative source. I’d also need to recheck but am unsure that all species groups are necessarily equivalent to complexes?

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  1. How you define easily separable may vary. The important morphological characteristics may be clear and consistent, but not captured in iNat observations for whatever reason. I think macromorphologically similar (bonus points for “historically confused or synonymized”) and monophyletic is appropriate.

  2. That does seem to be how it’s used in most cases anyway. There’s not a lot of consistency in how below genus clades are represented like this - section, subgenus, species complex, group, pick your favorite I guess. I don’t think I’ve ever seen a justification offered for which one gets used in a publication.

  3. One paper. How often do you get two papers on the same genus? I would hate to wait around for that.

  4. All known subordinate species ought to be included. I’m sure some potential members will get left out just because they were not investigated at all in the reference publication. Suggesting a species ID should not conflict with a broader ID of complex. It’s pretty annoying and defeats the point!

  5. I agree. It needs to have been defined, not just mentioned, so citations should include both relevant sources.

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This mostly agrees with my current practice, although I think I would expect to see the complex utilised by more than the person who introduced it. Like all taxonomic opinions I think they should be underpinned by consensus affirmation - at least to the extent that is possible in mycology.

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For interpreting the curator guide on when complexes can be used, I’ve followed this:

The other species group thread is also relevant, and I think there are a couple other threads about complexes on the forum.

Using the “and/or” phrasing of the above quote and the guideline of usefulness for identification, I’ve taken a pretty liberal approach to species complexes. Ideally they should be groups/complexes that are delineated in publications. However, iNat uses BugGuide as a source and even if it’s not recognized in literature and the taxonomy isn’t particularly ambiguous, BugGuide has Eupeodes americanus/pomus as a difficult to identify group/species pair and that’s sufficient for me to add it to iNat since a lot of observations can only go down to that level. Similarly, even if Greater/Lesser Scaup is only an informal tricky species pair, it’s well established and used on eBird etc. so I’d support having it as a complex so that potentially thousands of observations can be identified lower than genus Aythya.

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It seems to me that usefulness is the key. It is about making difficult to ID species identifiable beyond genus. I don’t think they need to be formally defined in literature - but if they are not they should be discussed in a flag first so that the limits can be discussed.

I would like to see ‘Species Group’ implemented as discussed in the other thread but, until it is, ‘Complex’ seems like a reasonable substitute because both of these terms are somewhat informal in the way they are used in the literature (unlike ‘subgenus’). In some species only one sex may be easily distinguishable and this seems an appropriate use case too.

I suspect there may be a division in usage between different taxa. They seem to be used pretty liberally in the insects, but I can imagine people in other taxa may take a more formalised approach. This simply would reflect the varying degrees of usefulness for the concept among different taxa.

An example: in the genus Palloptera (Insecta, Diptera, Pallopteridae) we created a complex for P ustulata/anderssoni. These are regarded as impossible to reliably separate because of overlapping variability in the wing pattern (genitalia makes sure) - though there is a distinct tendency for each. There is nothing in the literature formally calling them a complex or anything else - but the alternative is to identify them as ‘Genus Palloptera’; a large genus of flies that are otherwise readily identifiable. Doing that would just make it difficult to pick out records of these species. As it is a well known issue this seems appropriate, and there are countless other examples.

There’s no point making a complex for A and B if their ranges do not overlap - unless it is a (e.g.) three-species complex with C that overlaps both.

Any complex should have more than one species descended from it - or what is the point of it? Best thing is to check whether there is a use for such a complex and, if there is, add species rather than removing the complex.

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I look at species complexes as particularly useful for venues like iNaturalist when photographic documentation is recognizably insufficient to distinguish taxa. In my mind, iNat should follow whatever formal taxonomic structure has been established in peer-reviewed literature, but the additional set of “species complexes” are simply a useful set of baskets in which the hold observations of those difficult groups. There use on BugGuide follows that strategy for many difficult groups. “Species complexes” for photographic repositories may or may not coincide in part with subgeneric taxonomy. I don’t really think they need to.
I also want to point out a subtlety of usage that I don’t think has been touched on in this discussion. I think species complexes are useful for two cases:

  1. When the best information available indicates that a set of 2 or more species truly cannot be separated; and
  2. When our current state of knowledge precludes the recognition/separation of species from photographic evidence.
    I have focused much of my interest and research into moth groups which have been relegated to that “Can’t Be Separated In Photographs” purgatory. I’m happy to acknowledge those cases in which the best minds have look at the issue in detail and come to that conclusion. But there are innumberable cases at least in the moth world where taxonomists and “museum experts” (my tongue-in-cheek pejorative) have made that assertion after being impressed/overwhelmed by the variability in patterns in a set of species and simply moved on to genitalic examination or biochemical analysis. I came to the moth world as a field biologist and birder. I still harbor the naive hopefulness that at least some sets of “inseparable” species complexes can in fact be teased apart. To the point of this thread, informal “species complexes” serve as useful buckets to collect such sets of observations together for future investigation and illumination.
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Agreed. But I would be slightly looser in saying not necessarily that photographic identification is precluded (either absolutely or due to lack of info), but also where it is often precluded (e.g. due to variability but where the extremes are sometimes separable), or indeed where a discussion on a flag concludes that they are sufficiently difficult to distinguish from photos that a complex would be useful. In other words, is it good to leave the boundaries of what is possible or not ‘fuzzy’.

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I’m also living in that purgatory, and agree with your points about a complexes usefulness in a venue like iNat. One other thing a complex does is reduce the likelihood of a wrong identification, but is more precise than Genus. Xestia contains a number of species that do not look alike. The Xestia c-nigrum/dolosa complex narrows it down to those two species which cannot be told apart visually. For an iNat identification I think that is preferable to the use of Genus.
I’m currently involved in a discussion about the identity of an Agrotis spp. where there is currently no consensus between two species, in spite of two very knowledgeable people offering their opinions. A finer ID would be preferable to Agrotis. Since it has been identified on Bugguide as species x, it is now part of their visual library, and it may or may not be the correct ID.
The pitfalls of purgatory!

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Looking back into species complex definitions, I’d also be okay with a more flexible use of complexes based on usefulness, although it’s still ideal when the complex happens to be used in external sources as well.

Thanks again cooperj for writing up this question, and writing it with so much care, following our conversation on my new Inocybe “Complex” names.

My thoughts on your question:

(1) I agree with kevinfaccenda that usefulness is key. In other words, “are there observations where this ID is possible but a more specific ID is not?” But I think they’re pretty much all useful.

I can imagine a referred-to but useless “complex”, where a distinct blue species, red species, and yellow species are genetically close… but how often does that happen? My impression (from mushrooms) is that more or less any time someone has referred to a “complex” or a “group”, there are going to be some photos of members which few or no people can confidently ID to species. I’d love to hear a counterexample!

(2) It seems like everyone agrees that complexes should be monophyletic. In other words, they SHOULD be clades. So the question is really something like, “is it okay for ‘complex’ names to refer to large/high-ranked/arbitrary clades?”
Large - Who cares? If a thousand species are morphologically inseparable, they’re equally a complex as a pair of species that are morphologically inseparable.
High-ranked - Definitely not - it needs to stay as the lowest rank above species so iNat can maintain a simple hierarchy of ranks.
Arbitrary - All taxa can be arbitrarily large or small; taxonomists can and do vary and disagree in their circumscriptions of taxa, and I assume iNat is handling that fine for sections, genera, families, etc. But it makes sense to add some extra demand(s) on “complexes”, because they’re not formal taxa so are subject to even more inconsistency. We already have two, along with the rank-respecting requirement:
A. (presumed) monophyly
B. (some) interspecific indistinguishability
I actually think the fourth:
C. a reference in the literature
is a hindrance. I’m only speaking from the perspective of mycology, but it’s pretty easy, and pretty common, for semi-amateurs and professionals with access to DNA sequencing to determine, long pre-publication, that what was been called a single species is a group of genetically distinct relatives. On Mushroom Observer, any user can create any “group”/“complex” name (or any name at all, for that matter). And we do, and it makes observations that much less wrong, with minimal debate, much less conflict, if any. So I think A and B are plenty, given iNat’s barrier to curatorship, and especially with @matthewvosper’s suggestion of a flag for discussion on pre-literature complexes, C as such can and should be skipped.

(3) see (1) and (2)

(4) I think we have to distinguish between “what is ideal” and “what should be required”. An enumeration of species is obviously ideal, but I don’t see why it should be required. Like @sarahduhon says, species often haven’t been enumerated in literature; often species besides the nominate one are undescribed; and even when neither apply - I agree with @matthewvosper that adding species (or requesting a “defense”) is a better response than removing the complex. iNat doesn’t require curators adding a new genus to enumerate its species.

(5) see (4)

Other thoughts, to minimize the annoyance of having “Genus species” proposals overriden by “Complex Genus species” proposals:

  • As far as I can tell from my time with mycology, “group” and “complex” are interchangeable. “Complex” feels unnecessarily, well… complex, especially with iNat’s intentions for accessiblity to laypeople. So I agree with @matthewvosper that calling it a “group” would be better.
  • Even better (I’m probably overstepping my boundaries even further as a sort-of new user here) would be to move it after the species name, soften it with grey-colored text, and set it somehow as the default suggestion for proposals. It should be easier to propose the less specific (more likely) name, not harder.
  • Obviously there should be some restraint in proposing a “taxon split” that overrides all existing proposals, and when that isn’t done obviously some restraint should still be had in manually overriding proposals on other people’s observations. We should have some kind of awareness that there really are multiple options consistent with the geography and appearance. My approach on Mushroom Observer is “innocent until proven guilty” (species until “proven” group) for other people’s existing species-named observations, and “guilty until proven innocent” for creating my own new observations.
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The point here is that species already in the iNat dictionary need to be added to
the complex.
For example here is one of several recent additions of a complex
Complex Inocybe cincinnata · iNaturalist
and yet even the nominate species has not been added …
Inocybe cincinnata (Collared Fibrecap) · iNaturalist

Also, adding complexes where there is no published use, perhaps just ‘findings’ from sequencing projects, has the same dangers as adding unpublished names. It is a slippery slope to chaos.

There are also many examples of complexes where the members are in fact readily identifiable, even if only from range restrictions and/or ecology. Those are key factors that drive the emergence of complexes.

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That explicitly goes against the rules for creation of complexes per the rules. You should get the blessing from a staff member before you start making anything which isn’t mentioned in the literature.

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Are there any published examples of complexes/species groups (but not subgenera) containing even over 100 species? I’m unsure although hadn’t assumed so, and assumed that a subgenus would typically just be created somewhat in place of a complex in that case (if not already). Speaking of subgenera, one general point is that creating complexes/species groups should only be considered after considering if there are or should be subgenera and if a subgenus still includes too many species. For example in sweat bees, there’s subgenus Dialictus which includes many species, as well as fairly small complexes like complex L. pilosum.

I think iNat’s current system at least defines the taxonomic rank itself which would be used in such cases as a complex. So making any proposed change to that would in principle require suggesting changing the site’s default formatting. Speaking of formatting, I’d like to get opinions/consensus on what’s proper capitalization, italicization, and formatting for subgenera (- when treated like a species group) and complexes. e.g. iNat has:

Complex Lasioglossum pilosum [non italic]. Should this be “Complex L. pilosum,” “L. pilosum complex,” or the same as it is now?

Fuscatus-group Paper Wasps [non italic, a subgenus described as similar to or as being a species group] Since fuscatus refers to a species (P. fuscatus) should this ideally not be capitalized, i.e. “fuscatus-group Paper Wasps”? Also, why is this subgenus being called a group (recalling species group) at all if it’s a subgenus? Note that these questions are asking what the ideal formatting should be, whether or not compatible with iNat’s current default formatting.

I’d like to clarify one thing I said above. Yes at the moment I think it’s reasonable to implement a species group using the ‘complex’ taxon, only because ‘species group’ doesn’t exist in iNat. I think the ideal is that both should exist. I know of at least one large genus where we felt the need to implement ‘species group’ using ‘section’, because the genus is divided into well defined subgenera, which contain well defined species groups, which contain well defined complexes, all of which are useful to the identifier! (I speak of Platycheirus) If you agree that ‘species group’ should exist, there is a feature request for it here.

On naming, the curator guide gives clear examples - the name should be written in full with only the genus capitalised. I’m not sure what you mean with the reference to subgenera - these are a much more ‘formal’ regulated rank, I don’t think a complex or species group should be implemented as a subgenus. The example you give is not really appropriate - the subgenus is called Fuscopolistes and is a recognised subgenus. ‘Fuscatus-group Paper Wasps’ is given as a ‘Common Name’. I’m not sure of the history. I would hazard a guess that it was called a species group before being made a formal subgenus and that specialists commonly refer to it in that manner - but we should not be raising ‘groups’ to ‘Subgenera’ ourselves.

What it means for a complex to be ‘recognised in the literature’ (as per the curator guide) is a bit fuzzier I think: it can be mentioned almost in passing that such-and-such a species is part of a complex with A, B and C, without a ‘Species such-and-such complex’ being formally declared anywhere (the curator guide even gives instructions on determining a name for complexes), sometimes there is simply an awareness that two species are indistinguishable e.g. apart from genitalia. I think this should count as evidence of ‘recognition’ if specialists on the site agree. They are rarely formally declared and named in the same way as e.g. Subgenera. So I think there is discretion - what we should absolutely not be doing is creating complexes left, right and centre for everything we think looks a bit similar, and I think that is the point. There should be evidence of the general recognition of a complex, and it should be implemented sparingly, and only if useful to identifiers.

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Just to clarify here that ‘species group’ in this sense seems to be a well understood/used term in insect taxonomy, and I can see why it might be needed, but there is no clear usage of this concept for plants, fungi etc.

I also assume species group and complex (but not subgenus) are typically used interchangeably/synonymously on iNat. To clarify re: terminology or capitalization, I also meant iNat’s taxonomic system controls some formatting of all taxa added at each rank for the ranks themselves. So when we create a taxon it requires determining what rank we’d ideally want it to be, and which iNat rank we’ll need to use to add it. Which are ideally the same, but occasionally an arbitrary or ambiguous rank must be used. e.g. When SARS-CoV-2 was added (which is difficult to assign to one rank even in literature) it’s longer common name became italicized based on the iNat rank formatting, despite that it isn’t in taxonomic nomenclature. I think I agree Fuscopolistes (which I didn’t create) should primarily be considered a subgenus, but would like to recheck publications. Anyway, I was implying or asking if iNat’s formatting may have been what resulted in capitalizing “Fuscatus-group” (vs. “fuscatus-group”), i.e. resulted in unavoidable capitalization.

I also agree that the way species groups/complexes are defined in literature can be brief. And that discretion should be used in creating taxa. That said, there also remain many groups/complexes which could help ID to add. e.g. Adding the three known potter wasp tribes so subfamily IDs can be refined to them, and adding the three known subgenera of the genus Pterocheilus for example.

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