Flag for Taxon: Pacific chorus frog (Pseudacris regilla)
| Flagger | Content Author | Content | Reason | Flag Created | Resolved by | Resolution |
|---|---|---|---|---|---|---|
| loarie | Pacific chorus frog (Pseudacris regilla) |
time to lump? |
May. 16, 2019 18:41:10 +0000 | loarie |
Comments
2
or 3.
I commend your bravery. If we go with a "complex" does that mean we have to identify all of these at the complex level? That sounds annoying and confusing to all the people who couldn't give a toss about pedantic taxonomic messes due to poor sampling and inadequate peer review standards. It would also mean most of these records will not get shared with data partners like GBIF (won't qualify for RG unless people vote that the ID is as good as it can get). Or would a "complex" mean we only ID at the "complex" level at the range borders?
If we only use the "complexes" at the range borders then I guess I'm cool with 2. If not, I would prefer 1 because it's the clearest and easiest to use treatment for the largest amount of people (argument form utility), or 3 because it complies with ICZN rules (presumably; argument from authority).
Also worth considering: have P. sierra and P. hypochodriaca been adopted by major partner orgs, and/or have they been used in conservation statuses with legal ramifications? If either of those are true, then they have utility for conservation, supporting option 1 with complexes only at borders or option 3.
The complex would be the parent of the 3 species, so thats where the community ID would go for controversial obs, but I think in practice obs would only sit at the complex node when its not clear which child they should belong to (ie Bay Area obs would prob still mostly uncontroversially settle at P. sierra)
For an example of a complex in practice see:
https://www.inaturalist.org/taxa/857190
and as expected obs sitting at the complex node mostly are along the uncertain boundary (but looking at that, it is a pretty broad area)
https://www.inaturalist.org/observations?hrank=complex&locale=en&lrank=complex&preferred_place_id=7003&taxon_id=857190
I'm not a biologist, but I think every biologist I know in California is unhappy with this split. So based on that, I say go with no. 1 unless there are conservation issues like kueda mentioned. But I don't feel too strongly either way, as long as we're clear about the choice.
I'm also just a layman but I like option 1, since from what I've read online I agree that it seems like most actual biologists didn't agree with the spit in the first place. I've also never been a fan of splitting species when there's no reliable physical differences and no hard geographic boundary, I understand the logic behind it from a genetics standpoint but if they all look the same and can interbreed across their range do they really need to be split at that level, since naming species is just for human convenience anyway? Splitting them leads to these gradient/hybrid areas along the borders, where it's impossible for anyone to identify an individual to a species since they're going to be a genetic mix of the two defined species.
If option 1 is too radical then I think option 2 is also fine, since it at least lets us identify the frogs in those border areas as something beyond generic Pseudacris.
I wrote a journal post about this very issue.
https://www.inaturalist.org/journal/birdwhisperer/23244-treefrog-problems
And I live in a place that gets lots of treefrogs but I'm in an 'overlap' zone assuming that ranges are correct. As much as I believe that option one is the best, I still don't think it would be wise since we don't have solid proof that they are one species and vice versa. The one thing I know for sure is, there is a lot of room for future studies. And I think in till we have more information, I think a complex would be the best decision.
I definitely vote for a complex until further research is done. 2 for me.
Has a decision been made/discussed during the last 4 months? Coming from a guy who keeps finding frogs and identifying them to Pseudacris but identifiers keep fighting over it being Northern Pacific or Sierran.
Distinct morphological criteria for distinguishing P. hypochondriaca from its sister species the Northern Pacific Treefrog, Pseudacris regilla, have not yet been established. The controversial 2006 paper splitting the P. regilla taxon into three species had no range maps or morphological keys to distinguish the three "new" species, and relied on a very small MtDNA sampling missing most areas of the extensive range. "Phylogeography of Pseudacris regilla (Anura: Hylidae) in western North America, with a proposal for a new taxonomic rearrangement" in Molecular Phylogenetics and Evolution. 39 (2): 293–304 is not well accepted.
Also differing and conflicting range maps now vary widely on this group and where the splits are (some even show Pseudacris sierra in northern Utah, others claim all of western Utah as P. hypochondriaca.) Because the paper provided no maps or discussion of how to diagnose the species, it has been an extremely controversial taxonomic revision. It was discussed and the revisions summarily ignored in:
Dodd, C. K., Jr. 2013. Frogs of the United States and Canada. Volume 1. xxxi + 460.
Pragmatically should be P. regilla until the revision claims can be substantiated or dismissed based on more comprehensive research.
this paper addresses problematic reactionary taxonomy revisions based on limited genetic sampling
Species Delimitation in Herpetology
https://www.journalofherpetology.org/doi/full/10.1670/18-123?fbclid=IwAR0c60veHQGgwyI10kkI8CrxTOl1agqv5_YP2YZa9dthaa2_aC363wN5TS0
@uta_stansburiana This may be the thread you'd post your thoughts on. And perhaps to develop some new discussion, it has well been over a year since this flag was created and it sounds like we haven't even gotten close to coming to a decision on this taxon's status on iNat.
Yes, it'd be great to see one of these solutions applied.
I’m a little late here, but why is Pseudacris regilla still spit in iNaturalist? I normally understand why a certain taxonomy is followed, even if I don’t necessarily agree with it. However this one isn’t even supported by any of the data bases, AWS considered recognizing the split provisionally but stated that they are probably invalid while Amphibiaweb and the iucn don’t even recognize it, and there is literally no way to tell them apart with a photograph, so why does iNat continue to follow the split?
Does iNat take into account that these taxa were added provisionally? Just seems like even if they were valid, without known diagnostic criteria we can’t identify either of the three proposed species in a photograph and can only infer some identifications based on their location, despite not knowing the actual range delineations of any of the three proposed species. How are observers supposed to tell which of these three species are present in a specific area and where/if they overlap, hybridize, etc.?
We take external references at face value, so if AWS includes P. regilla sensu stricto, P. hypochondriaca, & P. sierra (which it does) thats what we would consider the status of the external reference. If we want to do something other than whats in the external reference than we would consider that a deviation from the external reference (e.g. P. regilla sensu lato)
What's interesting is that I read your link and it even says:
"Barrow, Ralicki, Emme, and Lemmon, 2014, Mol. Phylogenet. Evol., 75: 78–90, suggested that the distinction of this taxon [Pseudacris sierra], drawn on the basis of mtDNA, was not supported by nuDNA analysis. This suggests that this taxon will will ultimately be included into the synonymy of Pseudacris regilla."
So, it's even been admitted that the genetics data is not sound, and the Pseudacris spilt was premature.
Even if these taxa were valid, how would we distinguish them without any proper range or diagnostic information? If you were to find one of these frogs around a supposed grey area of their ranges. Which species would you assign it as? We can’t tell them apart visually so this doesn’t seems like the appropriate route.
Perhaps iNat should deviate, after all AWS considers recognizing these species in the future to be highly unlikely.
I'm still in favor of combining them, but I think adding a P. regilla complex is possibly the best compromise, since it would leave the individual species available to ID for anyone who wants to or in their obvious ranges, but also give us something to ID as in the grey areas beyond generic Pseudacris. Then when the species are hopefully officially recombined it will be easy to transfer all the complex IDs back into full P. regillas, along with all the sierras and hypochondriacas.
If we have to keep them separate than I think adding a complex is completely fine, however I still think that lumping them back together would be the most in line with current taxonomic understanding of this species.
The Amphibians of the World Pseudacris page that @loarie linked above notes that there's a 2021 study that supports the molecular evidence for the split, so it's clearly not the case that there is a current consensus about this. This recent study's citation is here: https://amphibiansoftheworld.amnh.org/Bibliography/J/Jadin-Orlofske-Jezkova-and-Blair-2021-Biol.-J.-Linn.-Soc.-132
Apparently that paper has only been cited one time according to google scholar…
Meanwhile you can pull up multitudes of papers with multiple citations that don’t even bother to even acknowledge a split. Most working herpetologists don’t even recognize these taxa.
Ultimately even if this study was to be accepted as valid, how are we to delineate the three species between one another? To date there have been no identifiable features or even full ranges given for any of these supposed species.
For this who want to read the research instead of link, here's the newest research.
https://academic.oup.com/biolinnean/article/132/3/612/6090220
I gave the newest paper a good read through, but there's still things that bother me. There is absolutely nothing proving that any of these "three" species are allopatrically breeding. All we have is 3 distinct unique haplotypes and that does not prove speciation. The researchers claim that the Columbia Basin (where I live) was one of their areas of high interest to test frogs, and we got a measly 5 samples to compare to and the locations as follows: Ellensburg, Moses Lake, Yakima (regilla) and Lewiston and La Grande (sierra). Now as the authors implied, these samples seem to imply that the Columbia Basin is regilla and the Blue Mountains are sierra, which is a nice geographic break and all... unless you're like me who sees a glaring problem. There is no geographic break. It doesn't matter where you are, if there's standing water for breeding, there's going to be treefrog. Pick a water drainage, any, and try to convince that the creek/river in the mountains sierra and those in the very creek/river in the valley is regilla. You're telling me these frogs are not interacting with each other? That is where we need to do DNA sampling, not 50+ miles away from range overlap. Because I'm willing to bet big bucks on the idea that they are likely hybridizing in these overlap zones and probably quite extensively. The only thing genetic sampling will do is prove haplotype swapping. But the lack of allopatric ranges, lack of vocal differentiation (which should be the driving factor for speciation, not genetics), and lack of morphological differences, all say that the Pacific Treefrog is just one species with 3 well-defined subspecies.
Here here @birdwhisperer!
I wasn't invited to this, but I came to submit a request for a complex idea and was pleasantly surprised to see this discussion. At the very least, it seems clear that the split was premature. And based on that, I would support iNaturalist returning to the previous status quo (sensu lato) until it is more settled. The complex option would also give a suitable compromise since it would allow us to move past the unsatisfying genus level identifications in the supposed inter-grade zones.
ASW has lumped Pseudacris hypochondriaca and Pseudacris sierra back into Pseudacris regilla! I assume everyone is on board with following ASW and making this lump on iNat aswell?
https://amphibiansoftheworld.amnh.org/Amphibia/Anura/Hylidae/Hylinae/Pseudacris/Pseudacris-regilla
temporary deviation https://www.inaturalist.org/taxon_framework_relationships/22680
I'm down.
I think I've made my opinion on the subject rather clear, let's go for it. Also, for those who care, I do have a rough draft written up about the complex that I was going to try and publish to the opinion section of a herp journal but if ASW has already lumped them, it's kind of a moot point. But if anyone is interested in reading my 6-page comment on how none of the science supports a three-species concept, I can send a pdf your way.
@birdwhisperer that is my kind of reading! MavetheGreat@gmail.com
Phew! Adding in @johngsalamander since he's an actual biologist who does a lot of PNW chorus frog IDs, in case he has any thoughts. I'm definitely for it, but I'm just an amateur.
Thanks @alexb0000. This is an interesting discussion and one that has been coming for a long time. I am happy to share my thoughts, but certainly don't want to pick fights with anyone.
My approach to cryptic species is that I want to see strong genetic differentiation. The Jadin et al. 2021 paper's biggest shortcoming is they only used a few genes, instead of generating utilizing genome-scale data which would allow resolution on the questions of hybridization/introgression. That being said, their methods are sound even if some people disagree with their interpretation of the data. The divergence among the three taxa is also very young (1.4 and 0.8 mya). For a vertebrate capable of significant dispersal this is a little bit recent for a species split unless reproductive barriers have arisen. Had I done that study with that data, I would have avoided making a call on the taxonomy. Particularly as they weren't able to compare their findings to the nuclear discordance found by Barrow et al. (2014). Nevertheless, Jadin et al. (2021) seem to interpret the current accepted taxonomy to favor the three-species solution (possibly based on the SSAR species list, which has its own controversies that I do not wish to engage upon), and therefore failing to overturn this concept may have been the conservative approach in their minds.
For @birdwhisperer, I would encourage you to submit your manuscript to a peer-reviewed journal if you believe you have complied substantial information with well supported hypotheses. ASW, while a good resource created by good scientists is not peer-reviewed, so putting forth something in that sphere. The presence of Jadin et al.'s paper negates your statement that "none of the science" supports a three-species concept, rather that currently deficiencies exist in needed areas (geographic sampling in the "boundaries", and multilocus sampling complete with analyses of hybridization/introgression), which could truly support or refute the presence of a single species. Your work may be appropriate to submit as a response to the 2021 paper in the same journal, but I would urge to ensure your writing to be objective and pragmatic. Also if you are truly willing to "bet big bucks" one the one species concept, you are welcome to donate those big bucks to my lab and one of my grad students can do their Master's on it :-)
As for iNat's treatment, I do not see any reason not to follow ASW if that is the general policy anyways. It is clear that ASW is aware of Jadin et al. (2021) and still favors the single-species concept due to a lack of convincing data. So I guess @loarie 's option #1. It doesn't sound like there is any pushback on that option, so may be the best choice for now until further science arises to the contrary. Option #2 to implement a 'complex' wouldn't be terrible (see the ratsnakes or gray treefrogs), but given all the above discussion, I think #1 is still the best option for the inat community.
If I'm understanding correctly, sounds like everyone is onboard with following ASW and lumping Pseudacris sierra and Pseudacris hypochondriaca into Pseudacris regilla making it sensu lato. I'll go ahead and make that change soon
I favor P. regilla instead of inclusion of P. sierra and P. hypochondriaca until further genetic clarification, along with narrowed distribution boundaries if separate species exist within California [yes I'm California biased :) ].
I need to add Jadin et al. 2021 to my critic to be fair and complete (I'm surprised they didn't use more robust genetics 15 years on from Recuero et al. 2006, considering Barrow et al. 2014).
@loarie, based on your comment 7 months ago, I thought we were moving to Pseudacris regilla sensu lato and have been making identifications as such (though most of them have been in the Pseudacris regilla sensu stricto range anyway. Is there an update here?
Is there any progress on getting this lump done?
Seconded, now that reptile observations have died down I'm working on tackling a lot of the non-research grade amphibian observations and would love a better way to classify all these.
alright this is now committing - might take a while https://www.inaturalist.org/taxon_changes/138983
Anyone consult Amphibiaweb? It is a superior resource.
Pseudacris regilla (Baird & Girard, 1852)
Pacific Treefrog, Pacific Chorus Frog
Subgenus: Hyliola
family: Hylidae
subfamily: Hylinae
genus: Pseudacris
Species Description: Baird, S. F., Girard, C. (1852). "Descriptions of new species of reptiles, collected by the U.S. Exploring Expedition under the command of Capt. Charles Wilkes, U.S.N., First Part—including the species from the western part of America." Proceedings of the Academy of Natural Sciences of Philadelphia 6, 174–177.
Taxonomic Notes: Duellman, Marion, and Hedges (2016) proposed resurrecting the unused name Hyliola for western North American tree frogs Pseudacris regilla and P. cadaverina. Faivovich et al. (Faivovich J, Pereyra MO, Luna MC, Hertz A, Blotto BL, Vasquez-Almarzan CR, McCranie JR, Sanchez DA, Baeta D, Araujo-Vieira K, Kohler G, Kubicki B, Campbell JA, Frost DR, Wheeler WC, and Haddad CFB. 2018. On the monophyly and relationships of several genera of Hylini (Anura: Hylidae: Hylinae), with comments on recent taxonomic changes in hylids. South American Journal of Herpetology 13:1-32.) says: "All results published in the last 12 years obtained the P. cadaverina + P. regilla clade as the sister taxon of the remaining species of Pseudacris. As such, the resurrection of Hyliola is both congruent with our phylogenetic knowledge, and optional on the same grounds. Given the optional nature of the recognition of Hyliola and the lack of any substantial discussion as to its taxonomic utility, we see no reason to follow it." Recuero et al. (2006, Mol Phylog Evol) on the basis of limited mtDNA and old allozyme data, divided this taxon into three: P. hypochondriaca in Baja California and southern California, P. sierra in central California, and P. regilla restricted to northwestern California and more northerly regions. However, central California was poorly sampled and it is impossible to determine the borders of the putative species. Furthermore, there are irregularities in the distribution of mtDNA haplotypes that call the taxonomic decision into question. The entire complex badly needs to be studied using fine scale sampling and nuclear gene sequences.
Hi @twake63, isn't this just further support for what others have posted and is being implemented, or are we overlooking something?
Thanks @loarie, glad to see this go through!
Ok this has finished processing - https://www.inaturalist.org/taxon_changes/138983
thanks all
Pseudacris regilla sensu lato now in 5th place for amphibians
https://www.inaturalist.org/observations?place_id=any&subview=map&view=species&iconic_taxa=Amphibia
Woo hoo!
If anyone wants to help - many of these obs sitting at genus from the pacific coast can prob be safely ID'd https://www.inaturalist.org/observations/identify?verifiable=true&page=1&spam=false&place_id=any&iconic_taxa%5B%5D=Amphibia&taxon_id=24253&user_id=&project_id=&lrank=genus&swlng=-128.47090721441285&swlat=20.45879629004768&nelng=-108.78340721441283&nelat=53.219766057369235&lat=&lng=&radius=
especially those outside of the range of California Tree Frog (Pseudacris cadaverina)
Non-biologist layperson here who would like to update the Pacific tree frog and P. sierra Wikipedia pages if no one else does. My understanding is that the consensus is leaning towards not necessarily doing away with P. sierra completely, but basically going back to using P. regilla more widely for the time being (basically putting the burden of proof on further genetic research). Is that a correct understanding, and if so, what would be a good reference/citation for this? Amphibiaweb and ASW 6.2?
https://amphibiaweb.org/cgi/amphib_query?where-genus=Pseudacris&where-species=regilla
https://amphibiansoftheworld.amnh.org/Amphibia/Anura/Hylidae/Hylinae/Pseudacris/Pseudacris-regilla
@bayareawalker,
Personally I think more robust genetic methods and more sampling (spatially) would be helpful. I'm not a geneticist but I've read a lot of articles on species genetics and I get the impression that mtDNA may not be the best method these days for drawing species lines. I think the western pond turtle research from very responsible scientists over a 10-20 year time period represents very well some misleading conclusions from mtDNA to better conclusions with nDNA and whole genome. And to add to my critique, Jaden et al. 2021 has a great title, but they seem to have done the exact same analysis as Recuero et al. 2006 that is being highly critiqued, and they didn't sample in areas to clarify potential species boundaries (the sampling was completely opportunistic based on other, on-going research, not targeted), https://academic.oup.com/biolinnean/article/132/3/612/6090220.
I summarized some of articles not agreeing with the 3 species concept and include the citations: https://www.inaturalist.org/journal/cnddb_brian/63094-why-no-one-really-knows-what-name-to-use-for-tree-frogs-in-california. Of note:
"Other folks are skeptical of the split. Barrow et al. (2014) studied nuclear and mitochondrial DNA and concluded, "Our results, though limited in geographic scope, do not support the species designations suggested by Recuero et al. (2006) for mtDNA lineages of the P. regilla complex." Stebbins and McGinnis (2018), the most recent edition of the famous Peterson Field Guide series, states, "...some herpetologists believe that no obvious differences exist among the proposed new species groups, and that additional studies are needed. We concur with this view." Currently (March 2022), the Society for the Study of Amphibians and Reptiles (SSAR), the keepers of the names for North America (taxonomy & nomenclature), still have the 3 proposed species list in their database, hence it appearing on iNaturalist, but also note under the P. hypochondriaca record, "Barrow et al. (2014) suggested that the distinction of P. hypochondriaca and P. sierra, drawn on the basis of mtDNA, was not supported by nuDNA analysis. This suggests that this taxon will ultimately be included in the synonymy of Pseudacris regilla." "
SSAR (the keepers of the names) has not produced a list for awhile and they took down their online database. They wanted to have a new list by end of the 2023, but that has not happened yet. https://ssarherps.org/publications/north-american-checklist/
AMNH does not include P. sierra and appears to conclude, "Nevertheless, as suggested by Barrow et al., 2014, considerable work on the Pacific Coast of the USA is warranted." AMNH has a lot of cited literature references, https://amphibiansoftheworld.amnh.org/Amphibia/Anura/Hylidae/Hylinae/Pseudacris/Pseudacris-regilla
If I was updating Wikipedia, I would not say that the other species concepts are invalid. I would present the issues around what is currently known, what the shortcomings are, and ideally what future research would be to help clarify the issues. Seems like a big challenge.
Sincerely,
Brian
(my 2 cents which may or may not be on target and can be discarded at will)
:)
@bayareawalker, as a fellow layperson my understanding is this reversion is just iNat's response to the question and doesn't represent an "official" decision. I agree with @cnddb_brian's summary that the other species shouldn't be removed or merged or anything on Wikipedia at this point, but maybe just have sections noting that they may be invalid and/or aren't universally agreed upon based on the stuff he cited.
Hi top 10 Pseudacris regilla (sensu lato) identifiers
@alexb0000, @calebcam, @dominic, @john8, @mikepatterson, @gregpauly @biohexx1, @kueda, @tiwane
we split Pseudacris regilla (sensu lato) into Pseudacris regilla (sensu stricto), Pseudacris sierra, and Pseudacris hypochondriaca several years ago because we were trying to keep in sync with Amphibian Species of the World
AmphibiaWeb has still not accepted this split because "it is impossible to determine the borders of the putative species"
Also no one is questioning that Pseudacris regilla (sensu stricto), Pseudacris sierra, and Pseudacris hypochondriaca is not a monophyletic group (specifically they make up a distinct clade sister to Pseudacris cadaverina)
There's been continued confusion IDing these species along the unknown boundaries, and some people continue to use Pseudacris regilla (sensu stricto) as if it were Pseudacris regilla (sensu lato)
We now have 2 new tools that may help:
1) Deviation - we're now using Taxon Frameworks for amphibians which makes it pretty straightforward to deviate from Amphibian Species of the World and go with Pseudacris regilla (sensu lato)
2) Complexes - because these taxa make up a distinct clade, we could also add a node of rank 'complex' between Genus Pseudacris and these 3 species.
We can also (3) status quo
I vote for 1 or 2. Are folks in favor of 1, 2, or 3?