Why is Poncirus not considered Citrus?

[Lauta_hibrid]

Good morning! With this exhaustive research work I started to get interested in the genetics of citrus... but there is something I had overlooked, why was Poncirus used as an external group to Citrus, while all the other genera were reconsidered as synonyms of Citrus and for which it is proposed that they should be changed to Citrus. What reason makes a single branch, with a single species and perfectly interfertile with citrus, be placed as external to the genus? Before, it was considered that Poncirus could be Citrus trifoliata, that is, they included it. It should be noted that Severina is also another external group, but this is logical since Severina belongs to an independent branch in which other species of the genus Atalantia are found (basically Severina would be synonymous with Atalantia).
https://www.nature.com/articles/nature25447

Does anyone have a clearer idea of ​​why it is considered a "non-Citrus" here?

[BorisR]

The claim that Poncirus trifoliata (Citrus trifoliata) does not belong to the same genus as other citrus fruits is controversial and debatable among botanists. Many combine them into one genus. This can be found in many other articles, or for example on the POWO website.

I note that PT does not perfectly interbreed with other citrus fruits, many hybrids produce only nucellar seeds without forming sexual ones. Successful sexual interbreeding is not the only criterion of the species. There are many examples of species that produced sexual offspring, but were not combined by taxonomists. The closest example to us is the Neanderthals, some of whose DNA is in our genes. This is even more common among plants than among animals. There is also morphology, ecology, genetics, and apparently they give botanists reason to doubt the unity of PT and other citruses.
 
I wouldn't attach so much importance to it. Biological systematics is just an attempt to sort out a complex and continuous nature. That's how the human brain gets used to understanding everything. But this is a simplification and collisions are inevitable . An analogy can be given with dividing a rainbow into a certain number of colors. But why is it right to draw the border here, and not a little further, or not accept that there are hundreds, thousands of colors? Therefore, I think that arguing about taxonomy is not very productive. The main thing is that when we communicate with each other, we understand what we are talking about.

[bussone]

Good morning! With this exhaustive research work I started to get interested in the genetics of citrus... but there is something I had overlooked, why was Poncirus used as an external group to Citrus, while all the other genera were reconsidered as synonyms of Citrus and for which it is proposed that they should be changed to Citrus. What reason makes a single branch, with a single species and perfectly interfertile with citrus, be placed as external to the genus? Before, it was considered that Poncirus could be Citrus trifoliata, that is, they included it. It should be noted that Severina is also another external group, but this is logical since Severina belongs to an independent branch in which other species of the genus Atalantia are found (basically Severina would be synonymous with Atalantia).
https://www.nature.com/articles/nature25447

Does anyone have a clearer idea of ​​why it is considered a "non-Citrus" here?

This seems to fluctuate with thinking in whatever era you're looking at. Poncirus has been in and out before (once Citrus trifoliata). We're currently in a phase where citrus-adjacent genii are collapsing back into citrus (already happened with microcitrus and eremocitrus and it seems fortunella as well). There's some effort to reclassify poncirus as citrus.

Florida will probably support it, because it means they can use poncirus hybrids for juice without having to declare it transgenic.

Incidentally, poncirus is not monospecific. There is also poncirus polyandra (would be citrus polytrifolia, as "polyandra" is already taken).

[mikkel]

There is also the newly discovered Citrus pubinervia, which belongs to Poncirus rather than Citrus, but is placed in Citrus in the first description because the authors place all Poncirus in Citrus.

In this paper, Poncirus is treated as an outgroup because Poncirus lies outside the clusters of all other Citrus. In the diagram, Poncirus is not even within the diagram shown.
This is the reason why it is considered as not belonging to Citrus in the paper.

"Poncirus, a subject of continuous controversy since it was originally proposed to be within the genus Citrus is clearly a distinct clade that is separate from Citrus based on sequence divergence and whole-genome phylogeny."

However, Kew lists Poncirus trifoliata as Citrus trifoliata.

[bussone]

There is also the newly discovered Citrus pubinervia, which belongs to Poncirus rather than Citrus, but is placed in Citrus in the first description because the authors place all Poncirus in Citrus.

In this paper, Poncirus is treated as an outgroup because Poncirus lies outside the clusters of all other Citrus. In the diagram, Poncirus is not even within the diagram shown.
This is the reason why it is considered as not belonging to Citrus in the paper.

"Poncirus, a subject of continuous controversy since it was originally proposed to be within the genus Citrus is clearly a distinct clade that is separate from Citrus based on sequence divergence and whole-genome phylogeny."

However, Kew lists Poncirus trifoliata as Citrus trifoliata.

You may want to link the paper. =)

[mikkel]

I am referring to the paper linked in Lauta_hibrid first post above

[mikkel]

pubinervia:

https://phytotaxa.mapress.com/pt/article/view/phytotaxa.523.3.4

[Ilya11]

Xpubinervia sequence analysis
http://fruitsci.zzgss.cn/english/html/down/2024-10-21/2566.html

[Lauta_hibrid]

Thank you for all your contributions. Maybe I did not express myself clearly in what my question was. My question was not about science in general and taxonomy, but it was within the research work. In it, it clarifies a lot about what the pure species were, what evolutionary closeness they had and about elucidating the hybrid origin of many species that we use in everyday life. But with such an extensive work and with so many researchers, they all make the decision to include everything in Citrus except Poncirus. In taxonomy there is the fight against forming paraphyletic groups, that is, if the ancestor is Citrus, all the descendants, of the later branches of the tree must be called Citrus... that is why if the first branch is Citrus, the ones below have to be equal, and hence Emerocitrus, Microcitrus, Fortunella, etc., cannot exist as different genera.  and if we put together the tree as they propose, they would all be of the Citrus genus, but a branch with one species (or two) would be isolated... and if you go further back you would find a branch that makes up another tree which is the Atalantia genus (where there is a branch which is Severina). That is where my question comes in... why do they leave one species alone and then come another tree with the Atalantias... or would Citrus, Poncirus and Atalantia be left alone... that seemed strange to me. Does anyone know the criteria of these researchers?

[mikkel]

I think this is the relevant statement of the paper:

"Poncirus, a subject of continuous controversy since it was originally proposed to be within the genus Citrus is clearly a distinct clade that is separate from Citrus based on sequence divergence and whole-genome phylogeny."

Poncirus is treated as an outgroup because Poncirus is outside the clusters of all other Citrus.  This leads the authors to the conclusion to separate Poncirus. In the images as in the principal coordinate analysis, Poncirus is not even inside the diagram shown. It forms a cluster far outside the other citrus groups.
I think this is the reason why it is considered as not belonging to Citrus in the paper.
Also in the cladogram Poncirus is placed basal to all Citrus. Which means that the researchers consider Poncirus to be older than Citrus. Poncirus would not be a split-off, but a sister genus to Citrus.

Concerning P.polyandra and pubinervia it is somewhat more complex. Because, as in the paper linked by Ilya, an introgression of C. maxima could be demonstrated in pubinervia (I can't remember for polyandra at the moment). This leads to a difficulty in the classification. obviously both are Poncirus representatives, on the other hand the hybridisation with maxima is a connection to Citrus. This is also noticeable in the certain clusters. pubinervia tends to group with Citrus in some parameters. In pubinervia, this is expressed by an assignment to Citrus and by labelling the hybrid origin with an X.
Whether a marginal, long-ago introgression and since then a separate development of pubinervia and polyandra justifies labelling as a hybrid species is a complex discussion. (Btw. I don't think that's a good idea, as introgressions are often found in plants)

[bussone]

I think this is the relevant statement of the paper:

"Poncirus, a subject of continuous controversy since it was originally proposed to be within the genus Citrus is clearly a distinct clade that is separate from Citrus based on sequence divergence and whole-genome phylogeny."

Poncirus is treated as an outgroup because Poncirus is outside the clusters of all other Citrus.  This leads the authors to the conclusion to separate Poncirus. In the images as in the principal coordinate analysis, Poncirus is not even inside the diagram shown. It forms a cluster far outside the other citrus groups.
I think this is the reason why it is considered as not belonging to Citrus in the paper.
Also in the cladogram Poncirus is placed basal to all Citrus. Which means that the researchers consider Poncirus to be older than Citrus. Poncirus would not be a split-off, but a sister genus to Citrus.

Concerning P.polyandra and pubinervia it is somewhat more complex. Because, as in the paper linked by Ilya, an introgression of C. maxima could be demonstrated in pubinervia (I can't remember for polyandra at the moment). This leads to a difficulty in the classification. obviously both are Poncirus representatives, on the other hand the hybridisation with maxima is a connection to Citrus. This is also noticeable in the certain clusters. pubinervia tends to group with Citrus in some parameters. In pubinervia, this is expressed by an assignment to Citrus and by labelling the hybrid origin with an X.
Whether a marginal, long-ago introgression and since then a separate development of pubinervia and polyandra justifies labelling as a hybrid species is a complex discussion. (Btw. I don't think that's a good idea, as introgressions are often found in plants)

I think the literature backs the idea that polyandra is a mutation of poncirus trifoliata.

Where to draw the genus line is not clear. Basically everything agrees that citrus, fortunella, and poncirus are fairly distant from atalantia, the preferred nearest aurantiodae (the ones I saw didn't use citropsis, which can hybridize). It's generally agreed that fortunella is closer to citrus than poncirus is, and farther from poncirus than from citrus. But it's not necessarily a ton closer. Fortunella has recently tended to be grouped within citrus, but that waxes and wanes.

If poncirus is freely hybridizing in the wild with citrus, it would tend to support it being a distant accession within citrus.

[mikkel]

If poncirus is freely hybridizing in the wild with citrus, it would tend to support it being a distant accession within citrus.

not necessarily, at least in the study cited here trifoliata does not cluster with Citrus. In the study linked by ilya, at least pubinervia clusters with Citrus, which is attributed to introgression with maxima.
Citropsis can also hybridise with Citrus, although only with wakonai. However, there is no doubt that it is not Citrus.
Interbreeding does not necessarily indicate the same generic affiliation.

[bussone]

If poncirus is freely hybridizing in the wild with citrus, it would tend to support it being a distant accession within citrus.

not necessarily, at least in the study cited here trifoliata does not cluster with Citrus. In the study linked by ilya, at least pubinervia clusters with Citrus, which is attributed to introgression with maxima.
Citropsis can also hybridise with Citrus, although only with wakonai. However, there is no doubt that it is not Citrus.
Interbreeding does not necessarily indicate the same generic affiliation.

Fortunella only clusters with citrus if you assume it's citrus. If you don't, it clusters separately as well.

Citropsis *can* hybridize with citrus, but does not in the wild. Poncirus apparently does.

[mikkel]

Fortunella only clusters with citrus if you assume it's citrus. If you don't, it clusters separately as well.

Please don't get me wrong, I only want to answer thematically, that which seems logical to me, and by no means be unkind., but I don't think that's right.
In consequence, this means that the assumption determines the result. Such an investigation would be of no use.
Cluster analyses are based on the genetic parameters investigated and the clusters identified are determined by the genetic signature.
Which clusters are formed naturally depends on the gene sequences analysed. This means that different conclusions can be drawn depending on the genetic sequences analysed. Such results still need to be categorised and interpreted  This is described very well in the study linked by Ilya.

Citropsis *can* hybridize with citrus, but does not in the wild. Poncirus apparently does.

That's true, of course. It is a question of where the generic boundary is drawn. Is the focus on the possibility of spontaneous intercompatibility or is it on the genetic signatures? This is ultimately a decision that has to be made and even then there are still ambiguities and possibilities for interpretation.

[Lauta_hibrid]

Thanks to everyone for contributing, it has left me less confused. There are human criteria as to where something begins and ends, and therefore decisions are made based on the age of the separation of the branch that forms Poncirus and on broad genetic differentiation. Taxonomic classification is a classification system and decisions are made or ideas are postulated, there are no absolutes. Interfertility is a criterion but it does not justify the assignment of a genus, we can see this in Anona, which has countless species but is almost impossible to cross. Regarding Citropsis, it is possible to hybridize with Citrus but it is very difficult, and these crosses reach a point of sterility. I do not know of any cross that can give a next generation as far as I know. I myself tried to cross Triphasia with limequat and only got somatic plants, taking into account that Eutis limequat is very easy to hybridize and very unlikely to produce somatic embryos, however it gave me 5 seedlings identical to Eutis.  Here I am attaching a diagram that I downloaded some time ago, showing the related species and closely related genera. I had marked them, showing those for which there is evidence of crossbreeding.

In theory, if citropsis can be crossed, all the inner branches can too. With triphasia it would be too far to achieve it. There is evidence of crosses with Severina, Atalantia, citropsis and when my limonia gives me the green we will see if I can achieve the cross 💪☺️

[bussone]

In consequence, this means that the assumption determines the result. Such an investigation would be of no use.
Cluster analyses are based on the genetic parameters investigated and the clusters identified are determined by the genetic signature.
Which clusters are formed naturally depends on the gene sequences analysed. This means that different conclusions can be drawn depending on the genetic sequences analysed. Such results still need to be categorised and interpreted  This is described very well in the study linked by Ilya.

That bedevils all of these studies -- the answer depends on the comparison groups.

This study of most of rutaceae places poncirus pretty comfortably within a citrus genra that also includes fortunella, eremocitrus, microcitrus, and clymenia, although its internal sorting of those within citrus isn't very confident.
https://onlinelibrary.wiley.com/doi/10.1002/tax.12543

That draws an outgroup line at limonia/feroniella, with citropsis a ways outside that. (Basically the line sits at oranges vs wood apples, and we are thusly comparing apples to oranges) Aurantioideae is annoyingly promiscuous.

It seems generally to be found that poncirus's nearest extant relative is ichangensis.

[mikkel]

Crossbreeding Citropsis with Citrus was unsuccessful for a long time, and it was only recently (around 15 years ago) that wakonai was discovered that fertile hybrids could be produced. Malcolm W Smith, one of the discoverers of wakonai, achieved this in Bundaberg.

https://journals.ashs.org/jashs/view/journals/jashs/138/1/article-p57.xml

[bussone]

Crossbreeding Citropsis with Citrus was unsuccessful for a long time, and it was only recently (around 20 years ago) that wakonai was discovered that fertile hybrids could be produced. Malcolm W Smith, one of the discoverers of wakonai, achieved this in Bundaberg.

https://journals.ashs.org/jashs/view/journals/jashs/138/1/article-p57.xml

This thesis has a photo of an earlier somatic cross Smith mentions. ('Nova' mandarin (Citrus reticulata Blanco + Citropsis gilletiana))
https://ufdcimages.uflib.ufl.edu/UF/E0/05/07/33/00001/NIELSEN_E.pdf

Update from Smith.
https://era.daf.qld.gov.au/id/eprint/13750/1/IH_2024_1_4_Smith%20et%20al_01.pdf

They have some complicated Australian crosses which involve poncirus now (they need the CTV resistance).

[Lauta_hibrid]

 

Crossbreeding Citropsis with Citrus was unsuccessful for a long time, and it was only recently (around 15 years ago) that wakonai was discovered that fertile hybrids could be produced. Malcolm W Smith, one of the discoverers of wakonai, achieved this in Bundaberg.

https://journals.ashs.org/jashs/view/journals/jashs/138/1/article-p57.xml

in that work he mentions that they are sterile, although the novel thing was that they formed fruit, but they are sterile both in pollen and in the inability to form seeds. I never understood why crosses are made with things like Mandarina Nova, it would be better with Poncirus or Citranges... 🤷. but I don't know, worry, give me citropsis and I challenge you! haha. I thought someone was selling seeds on Ebay, but it was very doubtful. and yes, I also saw the fruit of the somatic hybrid. what I also didn't understand is why chromosome duplication is not done in sexual hybrids, that has managed to recover fertility in many cases, since their chromosomes would once again have the parity necessary for meiosis.  (maybe it was done but I don't know the documentation... who knows) but well, I will continue with my attempts to cross triphasia which is even further away than citropsis... and limonia is still young, but it would be fantastic to see what comes out if I mix it with citrus (it is more closely related than Citropsis). Luckily I already have my monoembryonic Poncirus 💪

[mikkel]

Update from Smith.
https://era.daf.qld.gov.au/id/eprint/13750/1/IH_2024_1_4_Smith%20et%20al_01.pdf

They have some complicated Australian crosses which involve poncirus now (they need the CTV resistance).

great! Thank you for posting!

[bussone]

Crossbreeding Citropsis with Citrus was unsuccessful for a long time, and it was only recently (around 15 years ago) that wakonai was discovered that fertile hybrids could be produced. Malcolm W Smith, one of the discoverers of wakonai, achieved this in Bundaberg.

https://journals.ashs.org/jashs/view/journals/jashs/138/1/article-p57.xml

in that work he mentions that they are sterile, although the novel thing was that they formed fruit, but they are sterile both in pollen and in the inability to form seeds. I never understood why crosses are made with things like Mandarina Nova, it would be better with Poncirus or Citranges... 🤷.

Smith discusses that in a later work. Sometimes species won't cross directly, but will cross as a member of a hybrid. Poncirus and the Australian citrus dislike crossing directly, but can cross if a mandarin is a hybrid-member. Thus a poncirus-mandarin hybrid can be made to cross with Australian species or Australian hybrids. Basically the mandarin acts as a buffer or mediator for the cross and appears to provide tolerance to distant outcrossings.

Two prior distant outcrossings used mandarins -- a Nova (reticulata) and an unnamed sunki.

[Lauta_hibrid]

For those who are interested in these crosses with poncirus or Citropsis and Australian citrus, I am leaving you this graph with plants to scale to see the results. It is a pity that it is very difficult to find photos of these experiments.