Taxonomy Discussion Thread

The paper is here: Phylogenomic systematics of the spotted skunks (Carnivora, Mephitidae, Spilogale): Additional species diversity and Pleistocene climate change as a major driver of diversification

Figure 2 is a map showing distribution of their seven species plus an extra clade (Sonora, inside the range of one of the named species).

Relevant paragraph on splits from the Discussion:

Although the most recent mammal taxonomic compendiums recognize four species of spotted skunks (S. angustifrons, S. gracilis, S. putorius, and S. pygmaea; Wozencraft, 2005; Dragoo, 2009; Burgin et al., 2018) our phylogenetic analyses support the presence of seven species. This includes the splitting of S. gracilis sensu stricto into two distinct species, the Rocky Mountain spotted skunk S. gracilis confined to the western United States and Baja Peninsula which includes the currently recognized subspecies S. g. gracilis, S. g. amphialus, S. g. latifrons, S. g. lucasana, S. g. martirensis, and S. phenax and the desert spotted skunk S. leucoparia in the southern US and northern Mexico, which includes the entire distribution of the currently recognized subspecies S. g. leucoparia. The eastern spotted skunk S. putorius sensu stricto is also split into two distinct species, the prairie spotted skunk S. interrupta found in the central U.S. east of the Rocky Mountains and west of the Mississippi River and the Alleghany spotted skunk S. putorius which inhabits Appalachia and the southeastern US east of the Mississippi River, encompassing the range of two currently recognized subspecies S. p. putorius and S. p. ambarvalis. The southern spotted skunk, S. angustifrons sensu stricto also represents two species, the southern spotted skunk S. angustifrons found south of the Trans-Volcanic Mexican Belt into Central America but excluding the Yucatán Peninsula and encompassing four of the five recognized subspecies (S. a. angustifrons, S. a. celeris, S. a. elata, and S. a. tropicalis), and the endemic Yucatán spotted skunk S. yucatanensis which is elevated from the previously recognized subspecies S. a. yucatanensis. The pygmy spotted skunk S. pygmaea consists of a single species, rounding out the seven extant species of Spilogale.
 
So I have a taxonomy question: I am working on Madagascar for my Fantasy Zoo. Amphibiaweb has Cophyla and Platypelis as two separate genera within the Microhylid subfamily Cophylinae (Madagascar narrow-mouthed frogs). All of IUCN Redlist, ITIS and Wikipedia put all these species in Cophyla. The collapse of Platypelis into Cophyla seems to have resulted from these articles in 2015 and 2016: https://www.biotaxa.org/Zootaxa/article/view/zootaxa.3937.1.3
https://onlinelibrary.wiley.com/doi/full/10.1111/cla.12118
But other articles since have continued to use both, for example: Figure 1. Maximum Likelihood phylogenetic tree of Platypelis and...
AMNH has a good discussion of the state of the issue: https://amphibiansoftheworld.amnh.org/Amphibia/Anura/Microhylidae/Cophylinae/Cophyla

So which do is use at my fantasy zoo?

I should add it's a necessary decision since some don't have vernacular names. I suppose the easiest option is to use both genus names for those species some put in Platypelis, e.g., Platypelis/Cophyla speciesname or Cophyla/Platypelis speciesname.
 
Gomphothere said:
So I have a taxonomy question: I am working on Madagascar for my Fantasy Zoo. Amphibiaweb has Cophyla and Platypelis as two separate genera within the Microhylid subfamily Cophylinae (Madagascar narrow-mouthed frogs). All of IUCN Redlist, ITIS and Wikipedia put all these species in Cophyla. The collapse of Platypelis into Cophyla seems to have resulted from these articles in 2015 and 2016: https://www.biotaxa.org/Zootaxa/article/view/zootaxa.3937.1.3
https://onlinelibrary.wiley.com/doi/full/10.1111/cla.12118
But other articles since have continued to use both, for example: Figure 1. Maximum Likelihood phylogenetic tree of Platypelis and...
AMNH has a good discussion of the state of the issue: https://amphibiansoftheworld.amnh.org/Amphibia/Anura/Microhylidae/Cophylinae/Cophyla

So which do is use at my fantasy zoo?

I should add it's a necessary decision since some don't have vernacular names. I suppose the easiest option is to use both genus names for those species some put in Platypelis, e.g., Platypelis/Cophyla speciesname or Cophyla/Platypelis speciesname.
Click to expand...
Broadly speaking it seems like keeping them as separate genera is based on osteology, and lumping them is based on genetics. It doesn't really matter from a Fantasy Zoo listing perspective though, because whether you call a species Platypelis cowanii or Cophyla cowanii there isn't going to be any confusion - whichever name you use is still only applicable to that one species.

Personally I'd lean to the side of caution and keep them as separate genera.
 
Many European zoos keep Azara's Agouti. The following article suggests the species should be included within Dasyprocta variegata:

Journal of Mammalogy, 102(6):1548-1563 (2022). Uncovering species boundaries through qualitative and quantitative morphology in the genus Dasyprocta (Rodentia, Caviomorpha), with emphasis in D. punctata and D. variegata

Abstract
The genus Dasyprocta Illiger, 1811 includes at least 13 species of medium-sized caviomorph rodents, widely distributed from Mexico to northern Argentina. Despite being abundant, largely diurnal, and easily identifiable by their external traits, the taxonomy of this genus remains poorly understood. In this work, we reviewed the taxonomy of Dasyprocta along the Andes and adjoining lowland areas of the western Neotropics, including samples from Mexico to northern Argentina, with emphasis on two species largely confounded—sometimes considered as synonyms—during the last century: D. punctata Gray, 1842 and D. variegata Tschudi, 1845. In the construction of our taxonomic hypotheses, we use a purely morphological approach, emphasizing qualitative and quantitative cranial features and external traits (color patterns). The results of multivariate statistical analysis and differences in color patterns support the species-level validity of D. punctata and D. variegata. Within this latter nominal form, we also include those populations from northern Argentina and eastern Bolivia that recently were referred to D. azarae. Based on our results,
D.punctata (including bellula, callida, candelensis, chiapensis, chocoensis, colombiana, dariensis, isthmica, nuchalis, richmondi, underwoodi, yucatanica, and zuliae) extends from southern Mexico to Colombia, Ecuador, northernmost Peru, and western Venezuela, while D. variegata (including azarae, boliviae, and yungarum) is distributed from south–central Peru and southwestern Brazil to Bolivia and northwestern Argentina.

www.mammalogy.org
 
MikeG said:
Many European zoos keep Azara's Agouti. The following article suggests the species should be included within Dasyprocta variegata:
Click to expand...

Except that if the dates you indicate are correct, Dasyprocta azarae has priority (having been described in 1823) and therefore it is Dasyprocta variegata which would be subsumed!
 
MikeG said:
Many European zoos keep Azara's Agouti. The following article suggests the species should be included within Dasyprocta variegata:
Click to expand...
I haven't seen the full paper myself, but on Mammalwatching Vladimir Dinets has said he has read it and, despite what the abstract says, the authors actually haven't merged the two species at all.
 
Here’s a fun one for Brits; Scottish Crossbills have only been reliably identifiable in the field based on call, but over the past few years the call has apparently changed to a different call used in the same locations, but also found elsewhere. As there are no diagnostic genetic features known either, it is now impossible to identify any individual as belonging to this species! Place your bets as to whether it will continue to have a place on taxonomic lists...
 
Tetzoo Quizzer said:
Here’s a fun one for Brits; Scottish Crossbills have only been reliably identifiable in the field based on call, but over the past few years the call has apparently changed to a different call used in the same locations, but also found elsewhere. As there are no diagnostic genetic features known either, it is now impossible to identify any individual as belonging to this species! Place your bets as to whether it will continue to have a place on taxonomic lists...
Click to expand...

Crossbills are a rather complex lot all around taxonomically. Personally I don't particularly think the Cassia Crossbill deserves its elevated rank but that's just me.
 
I don’t think it’s JUST you!
To return to the Scottish Crossbill, I cannot see how it can be a species unless there is some kind of genetic underpinning leading to mate choice; let us say that intermediate billed birds make a particular call based on bill size, and mate choice is based on call. A “Scottish” morph could come into being, but members of the morph would not necessarily share ancestry; I would not regard this morph as a species (although it would be an interesting phenomenon).
 
How valid are the "species groups" of macaques? Is there any chance these could represent distinct genera? Always been curious considering macaques seem to have a lot of diversity for a single genus, would be curious to see any phylogenetic studies on this group.
 
Firstly, there is no definition of the spread of a genus. Putting all the Macaques into Macaca is one perfectly valid option, provided no other species is derived from the last common ancestor. Any other split into monophyletic groups is also valid. I agree, it would be interesting to see a full phylogeny and see it it shakes out into sensible groups.
 
I have a question regarding Gelada baboon (Theropithecus gelada) taxonomy: have there been any recent studies regarding the validity of the 2 proposed subspecies and an updated assessment of the new subspecies found in 1990?

And as a follow up, are there any pure Theropithecus gelada gelada in captivity? ZooTierliste states a few EU zoos have them, though a source is lacking.
Is there any plan by EAZA and San Diego or Bronx to select this lineage? Or will they keep on having stock of uncertain lineage?
 
Mickey said:
I have a question regarding Gelada baboon (Theropithecus gelada) taxonomy: have there been any recent studies regarding the validity of the 2 proposed subspecies and an updated assessment of the new subspecies found in 1990?

And as a follow up, are there any pure Theropithecus gelada gelada in captivity? ZooTierliste states a few EU zoos have them, though a source is lacking.
Is there any plan by EAZA and San Diego or Bronx to select this lineage? Or will they keep on having stock of uncertain lineage?
Click to expand...

I would be highly surprised if the entire ex-situ stock wasn't intermixed by this point.

~Thylo
 
Mickey said:
I have a question regarding Gelada baboon (Theropithecus gelada) taxonomy: have there been any recent studies regarding the validity of the 2 proposed subspecies and an updated assessment of the new subspecies found in 1990?
Click to expand...

As a non-native English speaker, I may not explain this perfectly, but my understanding is that this paper suggests that the samples from geladas kept in European zoos fall within the central lineage. The paper can be found here: https://onlinelibrary.wiley.com/doi/full/10.1111/mec.17514

I’m not fully confident in my interpretation because my background in biology is limited, so if anyone could briefly summarize what this paper indicates about the subspecies of zoo geladas, I would really appreciate it.

For context, another paper (not open access) appears to show on its phylogenetic tree that most zoo samples cluster with the central lineage, with two samples grouping with the northern lineage. Here is the link: https://www.researchgate.net/public...ation_and_chromosomal_polymorphism_in_geladas

If I’ve misunderstood anything, please feel free to correct me.
 
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Veno said:
As a non-native English speaker, I may not explain this perfectly, but my understanding is that this paper suggests that the samples from geladas kept in European zoos fall within the central lineage. The paper can be found here: https://onlinelibrary.wiley.com/doi/full/10.1111/mec.17514

I’m not fully confident in my interpretation because my background in biology is limited, so if anyone could briefly summarize what this paper indicates about the subspecies of zoo geladas, I would really appreciate it.

For context, another paper (not open access) appears to show on its phylogenetic tree that most zoo samples cluster with the central lineage, with one sample grouping with the northern lineage. Here is the link: https://www.researchgate.net/public...ation_and_chromosomal_polymorphism_in_geladas

If I’ve misunderstood anything, please feel free to correct me.
Click to expand...

The content of both of these papers seem to support the existence of three subspecies: gelada (northern), obscurus (central), and arsi (southern).

The first starts out by saying that zoo populations mostly cluster with the central (obscurus) population, but then later on they seem to conclude that they entirely cluster with the central population. This reads a little confusing to me, but again their conclusion is that captive Geladas would be the obscurus subspecies. This would make the most sense to me to be honest, as this subspecies seems to have the largest range and is the one most accessible to exporters working out of Addis Ababa where I would assume most exports from Ethiopia were coming from. I find myself confused again, however, when they say their zoo samples came from 5 US zoos when there are only 3 zoos in all of North America with Geladas. Considering they only ever talk about Stuttgart and the EAZA after that, I can only assume "US" was a typo(?). I suppose it doesn't matter much, as the North American stock is managed as part of the EAZA population.

The second paper--which was actually published two years earlier--makes things sound more confusing. It certainly doesn't help that only the abstract and figures are available. One figure indicates that they sampled animals from four zoos, but the identity of these zoos is not given here. The figure indicates that 15 zoo Gelada all clustered within the central (obscurus) population. The figure does also clearly state that two individual zoo Geladas from "Zoo 1" did hold a single haplotype from the northern (gelada) population. Unfortunately, without access to the full context within the paper, it's difficult to say for whether this is proof of cross-breeding in captivity. From afar, it does seem to indicate that zoo populations descend primarily from obscurus animals, but there may have been some small admixture of gelada as well.

To answer @Mickey's original question, I don't think there is any evidence of any zoo Geladas being the nominate subspecies at this time.

~Thylo
 
Chlidonias said:
I haven't seen the full paper myself, but on Mammalwatching Vladimir Dinets has said he has read it and, despite what the abstract says, the authors actually haven't merged the two species at all.
Click to expand...
Indeed. The abstract is confusing, only a part of the former Dasyprocta azarae are included in D. variegata.
It is therefore important to read the article BEFORE posting wrong information in a taxonomic change!
 
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