Troubleshooting species complexes

A few thoughts for refining the new Species Complex taxon.

I think that species complexes should be given a unique name that is different from the name of the species that they are named after.

As an example, currently Dasysyrphus intrudens is the name of a species of hoverfly, and the name of a species complex that includes Dasysyrphus intrudens as its sole species. (Current research shows that what was once thought to be a single species is actually several species, but no other species have yet been described).

Another example is Laphria canis, which is the name of a species of robber fly and the name of a species complex that includes Laphria canis, as well as several other species that cannot be differentiated from photos.

Having two different taxa, one of which is the parent of the other, with the exact same name is a recipe for confusion. Currently, iNaturalist adds the word “Complex” in front of the name of a taxon if it is a species complex. However, this means that the name that is displayed when you ID something is not the actual name of the taxon, which creates other issues. For instance, if you do a search for “Complex Dasysyrphus intrudens”, which is currently the name that would be displayed as the ID on an observation page, it will result in no results, as the actual name of the species complex taxon is just “Dasysyrphus intrudens”.

My suggestion to solve this issue requires two changes:

  • A feature change where iNaturalist no longer adds “Complex” in front of the name of taxa that are species complexes
  • All species complexes be given a unique name. This could be accomplished by adding the word “complex” after the species name. I.e. the actual taxon name would be “Dasysyrphus intrudens complex”. This would mean that it would come up as an option if you started typing the genus name, which is the most likely thing that someone would type.

Note that the suggestions that come up when you type a name into the “Suggest an Identification” box do not come from the name of the taxon page, but from the names that are listed under “Names” under the Taxonomy tab on the taxon page. These names do not have to agree with the name of the taxon page. So, it is important that the name listed here is the right name.

As a second suggestion, I think that it would be worthwhile to have a warning pop up if someone IDs an observation as a species that is included in a species complex. The species within a species complex are still valid species, so they can’t be merged with the species complex. But the species complex exists because it is difficult or impossible to identify the species from a photo. So, except in extenuating circumstances, the species complex should be chosen as the ID over the species. But it is quite possible for many people, even those who are very familiar with the species, to not know that there is a species complex for that taxon on iNaturalist. So, observations will get put randomly in either the species, or the species complex, and it will require constant vigilance to correct this. A solution would be to prompt an ID’er to ensure that they really meant to chose the species instead of the species complex.

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One problem with using a three-part name like “Dasysyrphus intrudens complex” is that traditionally speaking, subspecies are written that way. Here on iNat we don’t use italics for the binomial name, the scientific name, so the word “complex” does not stand out from the rest of the name.

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This is a good point. I think the key things that need to be accomplished with the naming scheme for species complexes are:

  • Each valid taxon has a unique name
  • Species complex taxa are not hidden: they come up easily in searches and as suggestions, and they come up as a suggestion if you start by typing the genus name.
  • The naming scheme is consistent for different taxa
  • A species complex is identified as a species complex

I think that the naming scheme that is most consistent with literature is “Dasysyrphus intrudens species complex”. This is also the most logical name in my mind. Without the italics, it is a little less obvious which is the binomial name, but “Dasysyrphus intrudens species complex” is probably less likely to get confused with a subspecies than “Dasysyrphus intrudens complex”.

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I thought it might be useful to see what people have been doing for naming species complexes. So far, there are 149 species complexes on iNaturalist:

  • 79 are given the same name as a species that they include.
  • 18 are given a name with two or more species, usually hyphenated
  • 28 have “group” added to the end of their name, often hyphenated
  • 7 have “complex” added to the end of their name, usually hyphenated
  • 4 have “sensu lato” added to the end of their name
  • 3 have agg or aggr added to the end of their name
  • 1 is given a common name
  • 1 is designated with cf (confer, to be compared with)
  • 9 are just given a genus name

I think that it would be good to be consistent with this naming.

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I think the best way is that inaturalist adopts open nomenclature: https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.12594

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That is a good article. According to that article, following the accepted Open Nomenclature the proper qualifier is “species complex”, which is abbreviated as “complex”. It should come after the authority name, and not be italicized. For example, the proper name would be “Dasysyrphus intrudens (Osten Sacken, 1877) complex”.

But iNaturalist does not use the authority, nor italics, which would leave us with “Dasysyrphus intrudens complex”. That does seem to be the strategy used on GBIF. But, as susanhewitt pointed out, that could be confused as a subspecies. (There are some subspecies named complexa, so it is not an unreasonable confusion.)

I think that it would also be correct according to Open Nomenclature to use the full qualifier of “species complex”, instead of just the abbreviated “complex”. That would leave us with “Dasysyrphus intrudens species complex”, which seems less likely to be confused with a subspecies, and is also a naming scheme that one does see in the literature.

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I think the better way is to following the International Code of Zoological Nomenclature here:

6.2. Names of aggregates of species or subspecies

A specific name may be added in parentheses after the genus-group name, or be interpolated in parentheses between the genus-group name and the specific name, to denote an aggregate of species within a genus-group taxon…

https://www.iczn.org/the-code/the-international-code-of-zoological-nomenclature/the-code-online/

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And I think that the species complex must have ability to receive “green” research level automatically when it received enough numbers of ID.

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If I understand this correctly, Unisexual Mole Salamander is a Complex of Ambystoma platineum, nothagenes and tremblayi. Can these salamanders be distinguished in the field from the other unisexual polyploid Ambystoma jeffersonianum, laterale, texanum, barbouri and tigrinum salamanders? From what I have read, this is not possible with drawing blood for genetic analysis. The documentation that goes with something like Unisexual Mole Salamander [Complex] needs to be very clear about what is included in the Complex and in this case, that identification cannot be determined in the field.
The next thing for me is that the diploid (bisexual) mole salamanders are not in a Complex and are listed by species. Again, from what I have read, identification is not always possible or accurate between species in the field.
Sorry, long preamble, here are my points.
I think the name of the Complex has to be unique, very clear and come up in a name search. I think that “Unisexual Mole Salamander“ should be renamed to “Ambystoma Mole Salamander Complex, Polyploid Unisexual”
That the documentation accessed on clicking “view” is very clear about what is the definition of a member of the Complex. If identification can’t be concluded in the field, what general methods need to be used, like genetic analysis.

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This is a unique situation, and the unisexual mole salamander is currently in the iNat taxonomy as if it is a species (or hybrid, since they’re treated the same way [edit: technically it looks like it is in as a hybrid]) rather than a species complex, even though it is labeled as a complex in its “scientific name” (although it’s also labelled as a hybrid there…). https://www.inaturalist.org/flags/79019

The difficulty with making it a complex in iNat’s taxonomy is that while the unisexual hybrids are monophyletic, the group of pure species involved is not (if I understand that term and the research correctly). Tiger Salamander (A. trigrinum) is part of the unisexual complex, but the three other tiger salamander species that were split off from it are not. I don’t think iNat taxonomy can handle Tiger Salamander being included in both the tiger salamander complex and the unisexual hybrid complex at the same time.

But yes, I agree the labeling is confusing and is resulting in inconsistent application of the taxon.

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Point taken on the uniqueness of the salamander situation. I will re-state my comments without the example:

I think the name of the Complex has to be unique, very clear and come up in a name search. This allows observers to see it as an option. The nomenclature might not be correct but it needs to work.

That the documentation accessed on clicking “view” is very clear about what is the definition of a member of the Complex. If identification can’t be concluded in the field, it should state what general methods need to be used, like genetic analysis.

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I only joined iNaturalist recently so I missed the “flag” conversation. Right now, I identify my observations of Blue-spotted salamanders as Blue-spotted salamanders with no speculation on if they are diploid, polyploid, unisexual or bisexual. The identification is by what the salamander most closely resembles.

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Welcome to iNaturalist and to the forum! Without more guidance I don’t see an issue with doing it that way. There are discussions elsewhere on the forum about providing identification tips as you make an ID, such as here.

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I completely agree with prokhozhyj about giving species complexes the ability to attain research grade status. I was also thinking this. I see two reasons why this is desirable:

  • The species complex rank is used when it is expected to be impossible to determine the species from a photo, except in extenuating circumstances. If an observation has received a species complex ID, that is the best that can be expected for that taxon on iNaturalist, so there is no reason to devalue that observation compared to other observations.
  • It will remove an incentive to provide false accuracy and ID the observation to the species level, when this cannot be done for that species.

I also agree with ebarr about the importance of having good documentation about the species complex. This needs to provide, at a minimum, which species are included, and an explanation as to the issues with differentiating the individual species within the species complex. I think that it should also include a reference, but perhaps this does not fit with iNaturalist. It seems like the place for this documentation would be in the “About” tab on the taxon page for the species complex? It would replace, or be added to, the Wikipedia write-up on the species that is automatically added when the taxon page is created.

It would be good to provide a template on what documentation needs to be provided for a Species Complex taxon. This could be combined with instructions for naming a Species Complex. Ideally there would be an iNaturalist feature that provided these instructions when someone created a Species Complex taxon. Either forcing them to follow the standard, or at least making sure that they knew what the standard was. For taxa of any other rank, iNaturalist has established what authority we should use. But for Species Complexes, it seems to just be a free-for-all. So providing some structure in how they are defined seems important.

Regarding prokhozhyj’s suggestion about using the ICZN standard for subgenera or superspecies, I think that there are some issues with this. In this scheme, the Dasysyrphus intrudens species complex would be named “Dasysyrphus (intrudens)”.

A subgenus or a superspecies has been described and published, and has an authority. It is based on assumed evolutionary relationships, and should be monophyletic. A species complex is different, it is not a described taxon, and it is not necessarily monophyletic. It is based on taxonomic uncertainty and/or morphological similarity. If there is a valid subgenus or superspecies that would provide the same function, we should use that instead of a species complex. We are only using a species complex when the preferred subgenus/superspecies option is not available. As I understand it, neither ICZN or ICN provides direction for qualifiers like species complex.

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The first criterion in the user guide for the creation of a species complex is …
**

  • Species complex is monophyletic (i.e. sibling groups of species)

**

https://www.inaturalist.org/pages/curator+guide

I would be happy to see this requirement relaxed. In the fungi we have many instances of identical-looking species which are not monophyletic.

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They can achieve research grade level, just as genus level records can. You simply need to vote the Id can not be improved (when and where that vote is appropriate is a separate discussion).

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Thanks! I did not realize this, it is a great tip.

However, for the purposes of improving species complexes, I think that it would be best to make it more user friendly, so that it works for any iNaturalist user and doesn’t require a work-around from someone that understands the details of the iNaturalist platform. A quick glance through observations that have been ID’ed to a species complex level shows many examples of observations with 2 ID’s, but I don’t see any with Research Grade status, so this trick isn’t being consistently applied.

It should almost always be the case that a species complex ID cannot be improved to a species ID, as that is the only reason to create a species complex taxon on iNaturalist. According to the Open Nomenclature definition that josecamx referenced, a species complex is qualifier that shows that it is “not wanted, or found useful, to go further into the identification”: https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.12594

Although it could be possible that a species level ID is possible in part of the range of a species, but not in the rest of the range, if some members of the species complex are more geographically restricted than others. In that case, the species complex ID might be inappropriate to apply in that geographic region. Although I don’t see that as a big issue, already there are cases where a subspecies ID might be possible, but still a species ID is considered Research Grade. And the solution to that might be to label the species complex as not native in that region, so it would be automatically flagged as out of range.

I know that it is sometimes stated in literature that a species complex must be monophyletic, but I have always found this to be a strange assertion. It is also sometimes explicitly stated in literature that species complexes do not have to be monophyletic. There is no official guideline for it, as it isn’t recognized by ICZN or ICN, so people can define it however they want. Species complexes are probably generally monophyletic, because they are a group of very similar species. But the grouping is based on morphological similarity and taxonomic uncertainty, not evolutionary history, so it stands to reason that it won’t always be monophyletic.

A species complex is created for practical purposes, so it makes sense to me to not artificially restrict it to being monophyletic. Note that this agrees with the Open Nomenclature that josecamx referenced: https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.12594

But regardless, I don’t think this changes anything regarding a species complex not being a subgenus or superspecies, so we shouldn’t name a species complex as if it was one of those taxonomic groups.

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It should be noted that “species complexes” may be used on iNat for what would more be accurately termed “species groups” because there is currently no better label for that level of taxonomy in the system, so definitions from other sources won’t perfectly match how the concept is applied here.
I agree that the taxon level will generally be used for groups that are difficult to ID from photos though. In a true species complex it may not be possible to separate species even with a specimen, if I understand correctly.

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Thanks for everyone’s input. To summarize the discussion, here are the issues that I think have been identified, and some suggested solutions.

Identified issues to solve:

  1. The name of each species complex should be unique. It should not be the same as a valid species or other taxon on iNaturalist.
  2. The naming protocol for species complexes should be consistent.
  3. The rank of species complex is also being used for “species groups”. These taxa could potentially have a different naming protocol.
  4. The name that iNaturalist displays for the species complex should be the actual name that iNaturalist is using for that taxa, so that it comes up in a search.
  5. The name of the species complex should come up as a suggestion when someone starts typing in the name of the representative species
  6. There should be documentation for each species complex that explains what is contained within the complex and some explanation as to why the complex was created.
  7. Observations that are identified to the rank of species complex should automatically receive Research Grade status in the same way as observations identified to the species rank.

Suggested solutions:

  1. All species be named as the representative species followed by “complex” if it is a species complex, and “group” if it is a species group. Eg. “Dasysyrphus intrudens complex” and “Chrysoperla carnea group”. This follows the accepted Open Nomeclature.
  2. Alternately, to prevent confusion with subspecies, the word “species” could be added for all names, creating “Dasysyrphus intrudens species complex” and “Chrysoperla carnea species group”.
  3. When someone creates a new species complex, there is a prompt that either recommends or forces them to follow this naming scheme.
  4. A template is created that outlines what documentation is required to create a species complex on iNaturalist. When someone creates a new species complex, there is a prompt that either recommends or forces them to fill out this template.
  5. All iNaturalist users who have already created a species complex are contacted, and asked to edit these taxa to bring them up to the new standard.
  6. A feature change so that the word “Complex” is not added in front of the name of species complexes.
  7. A feature change so that if someone tries to identify an observation to the rank of species when a species complex exists, they are prompted to confirm whether or not that level of ID is possible.
  8. A feature change so that observations identified to the rank of species complex automatically receive Research Grade status in the same way as observations identified to the species rank.
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