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PlantFiles How-to's: Taxonomy changes coming in the PDB

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Terry

Terry
Murfreesboro, TN
(Zone 7a)


January 7, 2004
4:43 PM

Post #746752

For all who are interested, it would seem that the taxonomists have made some fairly important decisions about the family Leguminosae, and we're not following these guidelines as they were intended.

Leguminosae did not simply changed to Fabaceae, as we (I?) originally thought. Instead, all genera within the family now fall into one of three sub-families: Caesalpiniaceae, Mimosaceae, and Papilionaceae.

What this means is that in a few days, all references to Fabaceae will be removed from the PDB, to be replaced by one of these families. Before we make this change, we (the PDB editors) thought we'd give the DG membership at large an opportunity to voice any concerns that you have about this change. If you have questions, now's the time to raise them.

On a related note, we're overdue for changing Hemerocallis to Hemerocallidaceae (from Liliaceae). Again - if there are any dissenting opinions, we'd like to hear from you now, rather than after we make the changes en masse.

The virtual "floor" is now open to questions and comments...
Monocromatico
Rio de Janeiro
Brazil
(Zone 11)


January 7, 2004
6:20 PM

Post #746851

I donīt think the Fabaceae family needs to be changed. The recent phylogenetical studies made by the Angiosperm Phylogeny Group (here: http://www.mobot.org/MOBOT/Research/APweb/orders/fabalesweb.htm#Fabales ), using the most advanced molecular techniques, show that the 3 subfamilies of Fabaceae form a close and monophyletical group that can be confortably considered as a single family. The 3 subfamilies are closest to each other than to any other family, so they are being considered as it traditionally is, a big family hsaring the same general characteristics with 3 distinct groups based basically on the floral morphology.

These molecular studies are still confusing regarding many groups (like what they did to my Theaceae... those #@#$), but in this case, it comes to the same conclusions that many traditional taxonomists were stating before.
Baa

January 8, 2004
9:24 AM

Post #747418

Monocromatico

What we're doing is tidying up and coming into line with the ICBN rules. We can't leave things as they are in the PDB, we have some genera listed under 2 or even 3 family names because of the confusion on how to use the ex-Leguminosae family names that has prevailed these recent years.

We can choose to use only Fabaceae as a family name for all the related genera or we can use the 3 sub-family names (but not Fabaceae), at present we are using the 4, it's causing problems and is technically wrong.

Monocromatico
Rio de Janeiro
Brazil
(Zone 11)


January 8, 2004
3:10 PM

Post #747600

I have noticed that mani Leguminosae are listed under different family names. My point is that all those taxa are summed up into one family, acording to those recent studies, the family Fabaceae. To rename these families to make them stay under the ICBN rules, the most safe option could be only renaming all the Leguminosae/Caes./Pap./Mim./Fab. into "Fabaceae". I wouldnīt put them into "Fabaceae", "Caesalpinaceae" and "Mimosaceae", because these taxa are being proved to not constitute true families, only part of the big family "Fabaceae".

Since we are on it, thereīs another family that got major changes after the molecular studies. I think that around half of the Scrophulariaceae fell into the formerly small family Plantaginaceae (which, now, became a huge family). The traditional specialists on Scrophulariaceae are going crazy about it, but they donīt have means to prove it wrong.

Terry

Terry
Murfreesboro, TN
(Zone 7a)


May 13, 2004
7:00 PM

Post #869182

Well, apparently I dropped the conversational ball here. To wrap things up, please consider this a last call for input: any other ideas/opinions/suggestions on the ex-Leguminosae family issue?

The good news is that Hemerocallis are in their own family now, and Scrophulariaceae may well be next up to bat...

Horseshoe
Efland, NC
(Zone 7a)

May 13, 2004
7:57 PM

Post #869282

It's very hard for my pea-brain (hehe, no, I did NOT mean to make that pun!) to understand all these new (long) words.

How will we know what falls into those 3 new categories? Is there a "cheat sheet" somewhere?

I never knew it but the "Fabaceae (Bean) Family" seems to include trees (Redbud, locust, coffee tree, for example). I've always, in my limited way, looked at legumes as garden beans and/or alfalfa type plants. Is this why the 3 categories are being put into play, to better define the variety of plant life that are somewhat related?

Baa

May 13, 2004
9:07 PM

Post #869357

Shoe

Yes there are cheat sheets to this, thank goodness!

The reasons we're looking into this is to try and dissolve some of the confusion around. As there are 4 correct family names for Legumes but the nomenclature rules say you must use one system or the other (either the blanket Fabaceae or the other three) we're trying to keep the PDB as current/correct as possible.

Other horticultural entities are favouring the 3 names rather than Fabaceae. As time goes on, more and more entries will come into the PDB under one of those 3 family names. However, Fabaceae still stands as a correct name and some places will hold out on the Fabaceae fort. We need to have a clear policy on how the family names are represented in the PDB.
Another reason is
If you were trying to search Mimosa in the PDB and wanted to narrow it down, you'd click on the Mimosa in one of the plant entries.

so you click on an entry which has

Family - Mimosaceae
Genus - Mimosa

Yoru search is limited to all Mimosa entries which also have Mimosaceae as a family name. It won't bring up the entries that have Fabaceae as a family name!

Terry

Terry
Murfreesboro, TN
(Zone 7a)


May 13, 2004
9:26 PM

Post #869465

Baa, maybe it would help if we lined out which genera will/would fall under each family name? I've gotta scoot for a couple hours, but I'll be glad to help research it and get a list up and running tonight.

Unless there is a strong and steady breeze blowing from the Fabaceae-only direction within the taxonomic community, I'm leaning (from a purely pragmatic standpoint) at separating them now. As messy as it will be, I'd rather do that and then possibly be faced with "lumping" them back under Fabaceae (if need be), versus lumping them together now and separating them later when there are who-knows-how-many-more entries?
Horseshoe
Efland, NC
(Zone 7a)

May 13, 2004
11:30 PM

Post #869588

Thanks Baa...that makes good sense! Much obliged!

Ya'll know I don't do many entries but this is good info (for me) to know for when (or if) I ever get my ducks in a row (and also to pass on to others).

I sure would like to figger out which of those 3 choices refer to all the wonderful tasty beans I grow and eat! I'll be learning from this thread. Thanks ya'll!

Baa

May 13, 2004
11:48 PM

Post #869614

Shoe that would be Papilionaceae which is the largest of the three and the pea flower shape family. Which reminds me, I didn't get around to planting the edible peas this year ... sigh. A case of too many plants, so little garden.

Terry

Terry
Murfreesboro, TN
(Zone 7a)


May 14, 2004
12:52 AM

Post #869692

Baa was already ahead of me, and gathered these up:

Papilionaceae
Abrus
Adenocarpus
Adesmia
Amicia
Ammopiptanthus
Amorpha
Anarthrophyllum
Anthyllis
Apios
Arachis
Argyrocytisus
Astracantha
Astragalus
Baphia
Baptisia
Bolusafra
Bolusanthus
Bossiaea
Brachysema
Brya
Burtonia
Butea
Cajanus
Calicotome
Calophaca
Calpurnia
Camoensia
Campylotropis
Canavalia
Caragana
Carmichaelia
Carmispartium
Castanospermum
Centrolobium
Centrosema
Chamaecytisus
Chamaespartium
Chesneya
Chordospartium
Chorizema
Chronanthus
Cicer
Cladrastis
Clianthus
Clitoria
Codariocalyx
Colutea
Coralia
Corallospartium
Coronilla
Crotalaria
Cytisophyllum
Cytisus
Cytisus
Dalbergia
Dalea
Daviesia
Derris
Desmodium
Dillwynia
Dipogon
Dipteryx
Dolichos
Dorycnium
Dumasia
Ebenus
Echinospartum
Edwardsia
Erinacea
Erythrina
Eutaxia
Eysenhardtia
Galactia
Galega
Gastrolobium
Genista
Genista
Geoffroea
Gliricidia
Glycine
Glycyrrhiza
Gompholobium
Goodia
Gueldenstaedtia
Halimodendron
Hardenbergia
Hedysarum
Herminiera
Hippocrepis
Hovea
Hypocalyptus
Indigofera
Inocarpus
Jacksonia
Kennedia
Kummerowia
Lablab
Laburnocytisus
Laburnum
Lathyrus
Lebeckia
Lens
Lespedeza
Liparia
Lonchocarpus
Lotononis
Lotus
Lupinaster
Lupinus
Lygos
Maackia
Macrotyloma
Medicago
Melilotus
Millettia
Mucuna
Mundulea
Myrospermum
Myroxylon
Notospartium
Olneya
Onobrychis
Ononis
Ornithopus
Orobus
Otholobium
Oxylobium
Oxytropis
Pachyrhizus
Parochetus
Pericopsis
Petteria
Phaseolus
Physostigma
Pickeringia
Piptanthus
Piscidia
Pisum
Platylobium
Platymiscium
Podalyria
Podocytisus
Poecilanthe
Psophocarpus
Psoralea
Pterocarpus
Pueraria
Pultenaea
Retama
Rhynchosia
Robinia
Sabinea
Sarothamnus
Scorpiurus
Securigera
Sesbania
Sophora
Spartium
Sphenostylis
Stizolobium
Strongylodon
Sutherlandia
Swainsona
Sweetia
Taverniera
Templetonia
Tephrosia
Tetragonolobus
Thermopsis
Tipuana
Trifolium
Trigonella
Ulex
Vicia
Vigna
Vilmorinia
Viminaria
Virgilia
Wisteria
Xanthocercis

Caesalpiniaceae
Afzelia
Anthonotha
Bauhinia
Brownea
Caesalpinia
Cassia
Ceratonia
Cercidium
Cercis
Chamaecrista
Colophospermum
Delonix
Gleditsia
Gymnocladus
Humboldtia
Hymenaea
Labichea
Parkinsonia
Pterolobium
Schizolobium
Schotia
Senna
Tamarindus

Mimosaceae
Acacia
Albizia
Anadenanthera
Calliandra
Cylicodiscus
Desmanthus
Dichrostachys
Entada
Enterolobium
Inga
Leucaena
Lysiloma
Mimosa
Neptunia
Paraserianthes
Parkia
Pentaclethra
Piptadeniastrum
Pithecellobium
Plathymenia
Prosopis
Racosperma
Schrankia
Stryphnodendron
Xylia

There may be a few others, but I think she's done a fantastic job (as always ;o) of gathering most of them...
Ulrich
Manhattan Beach, CA
(Zone 11)

May 14, 2004
12:58 AM

Post #869697

To me it always will be the Pea Family just as "Beijing" will always be Peking, and "Myanmar" will always be Burma.
Horseshoe
Efland, NC
(Zone 7a)

May 14, 2004
1:50 AM

Post #869760

Goon'ness gracious! So much to choose from! No wonder this needs to be divided into threes!

Thanks Terry. Thanks Baa. (By the way, I'll be picking edible peas tomorrow, I'll be thinking of you!)

Terry

Terry
Murfreesboro, TN
(Zone 7a)


September 20, 2004
2:56 PM

Post #1058274

FYI...for those of you adding new ex-Leguminosae entries in the PDB, please be aware that we have made this change; new entries should use the genera/family list posted above.
Monocromatico
Rio de Janeiro
Brazil
(Zone 11)


September 20, 2004
4:01 PM

Post #1058357

I donīt like this :^(

But then, it could be worse, it could be about Euphorbiaceae, which was split into 4 new families :^P
Baa

September 20, 2004
4:40 PM

Post #1058407

Monocromatico, what don't you like about it? Instead of having one huge family to contend with we have 3 smaller families, are following the ICBN rules regarding the family and current horticultural useage. Or is it because you disagree with the split in general, which we have no control over.
Monocromatico
Rio de Janeiro
Brazil
(Zone 11)


September 20, 2004
5:03 PM

Post #1058445

I disagree with the split in 3 families. It may be practical to separate all those genera into smaller groups, but I agree with the phylogenetic analysis and see them as one big family.
Baa

September 20, 2004
5:25 PM

Post #1058474

Ahh so it's not so much the PDB using the 3 subfamilies but the actual nomenclature change, I agree it's confusing to have one main family and then split into subfamilies and then say you can't use one name if you are using the other 3. However, the family changes (and their nomenclatural useage) are it's something we hortics will just have to ride until the botanists decide on something else ;)
Todd_Boland
St. John's, NL
(Zone 5b)



March 2, 2005
2:31 AM

Post #1315639

As Terry mentioned, if the Fabaceae is causing such grief, wait until the Scrophulariaceae is attacked!...that will no doubt cause considerable confusion as well.
spklatt
Ottawa, ON
(Zone 5a)

March 2, 2005
2:32 AM

Post #1315646

Darn these plants for not fitting into our neat little human-devised boxes! ;-)

Terry

Terry
Murfreesboro, TN
(Zone 7a)


March 2, 2005
6:12 PM

Post #1316558

I think we've finally got a handle on the ex-Leguminosae issue. Can't say I'm looking forward to the Scrophulariaceae brouhaha...
Baa

March 2, 2005
6:50 PM

Post #1316613

I don't think Scrophulariaceae will be anywhere near the confusing issue that Leguminosae is who's main problem was the rules about how to use the names. It appears that Scropulariaceae, Orobanchaceae and Plantaginaceae the main families in question will be a relatively straight forward transition to their old genera.
inanda
Winnipeg, MB
(Zone 2b)

March 6, 2005
11:06 AM

Post #1322633

Big thank you Terry re changing hemerocallis away from liliaceae. It has been driving me mad here.
Inanda
Fog_in_the_Mist
Lordsburg, NM
(Zone 7b)

March 20, 2005
10:19 PM

Post #1350524

So who won that round - lumpers or spliters?
Ulrich
Manhattan Beach, CA
(Zone 11)

March 31, 2005
5:29 AM

Post #1374182

Why can't they leave well enough alone? Nobody was confused when it was the Pea Family. They just re-name stuff to act important and avoid going out to get a real job! LOL

Terry

Terry
Murfreesboro, TN
(Zone 7a)


March 31, 2005
12:00 PM

Post #1374394

Now Ulrich...the ornery part of me agrees with you.

But on the other hand, the taxonomists provide an important service to us mere gardeners. We would be even more confused if there weren't groups providing oversight and standards so we can know we're both talking about the same pea, whether it's called Leguminosae, Fabaceae or Papiloniaceae ;o)
Ulrich
Manhattan Beach, CA
(Zone 11)

April 1, 2005
2:33 AM

Post #1376332

Calling me 'ornery', eh? Well, you got me pegged.

kooger

kooger
Oostburg, WI
(Zone 5b)

April 3, 2005
5:57 PM

Post #1381164

Nope, she didn't call you 'ornery' ... she just said the 'ornery' part of HER agrees with you ... and you get to draw your own conclusions, or assume something (and you know what they say about someone who assumes something...) ROTFLOL
Ulrich
Manhattan Beach, CA
(Zone 11)

April 4, 2005
6:38 AM

Post #1382254

Makes a donkey out of you and me? LOL

kooger

kooger
Oostburg, WI
(Zone 5b)

April 5, 2005
1:39 PM

Post #1385077

got it! LOL
paalexan
Las Cruces, NM

December 12, 2006
9:25 AM

Post #2992118

Posting late, since I happen across this.

General rules:
1) Anything ending in "-aceae" is a family, except for eight conserved names that remain valid because they were in such prominent and long-standing use;
2) Anything ending in "-ideae" is a subfamily;
3) All families and subfamilies are named for genera within them (except for the conserved names mentioned above).

The current most widely accepted taxonomy:

The family Fabaceae can also be called Leguminosae--both names are valid, since Leguminosae is one of the seven conserved names. The family Fabaceae has three subfamilies: Caesalpinoideae, Faboideae, and Mimosoideae. Cercideae is sometimes recognized as well, containing Cercis & Bauhinia; more often it is lumped into Faboideae. Papilionoideae is equivalent to Faboideae, but is an illegitimate name because of rule "3"--there is no plant genus "Papilio", and you can't name a plant family after an insect genus.

The names "Papilionaceae", "Mimosaceae", and "Caesalpinaceae" derive from taxonomists who recognize these as separate families. Under this arrangement, "Papilionaceae" should be called "Fabaceae", for the reason mentioned above.

In differentiating the three subfamilies, here's the gist:
Faboideae: flower pea-like--strongly zygomorphic with four apparent petals; ten stamens, these forming a tube; stamens in the tube may be fused together (most often in a 9 + 1 pattern) or free from each other; the stamens are usually included within the "keel", which is a fusion of what were once two separate petals;
Caesalpinoideae: flower varying from actinomorphic to moderately zygomorphic, with five distinct petals; 5 or more stamens, these always free from each other, never forming a tube, never hidden between petals;
Mimosoideae: flower actinomorphic, with five small fused petals; stamens 10 or more, usually free from each other, many times longer than the petals; flowers in dense inflorescences, these either round or elongate.

Clear as mud? The three subfamilies are very easy to distinguish 99% of the time...

Patrick Alexander

This message was edited Dec 14, 2006 5:36 PM

Resin

Resin
Northumberland
United Kingdom
(Zone 9a)

December 12, 2006
9:31 AM

Post #2992122

[quote]Clear as mud?[/quote]

Actually, that's the clearest and best explanation I've seen anywhere! Nicely done.

Resin
paalexan
Las Cruces, NM

December 12, 2006
9:34 AM

Post #2992124

BTW, if you wanted to keep up with modern taxonomy, a few other changes would be necessary. I don't really know to what extent that's your goal, though. Also worth mentioning that I certainly wouldn't recommend trying to stay on the bleeding edge of the nomenclature, but there are a number of recent changes that are well-supported and generally accepted. The most notable of these at the family level--or at least the hardest for most people to swallow--is the shift of most members of Scrophulariaceae to Plantaginaceae. At the genus level, a change that's particularly near to my heart--since I work on the things--is the move of most North American former Arabis to Boechera.

Patrick Alexander
paalexan
Las Cruces, NM

December 12, 2006
9:53 PM

Post #2993907

Thanks Resin--guess you were posting while I was writing that reply above.

Patrick Alexander
Baa

December 14, 2006
6:42 PM

Post #2998978

Paalexan

Thank you for your interesting post. I do have a question though :)

You wrote and I quote

"The names "Papilionaceae", "Mimosaceae", and "Caesalpinaceae" derive from taxonomists who recognize these as separate families. Under this arrangement, "Papilionaceae" should be called "Fabaceae", for the reason mentioned above."

Which paper or group does this come from, as my understanding of the International Code of Botanical Nomenclature is different.

We are aware of the other changes to family names and have been working on them when and where we can, I have been particularly absent this year which I hope to redress in the new year. I can tell you though that we do not claim to be current right up to the minute because we'd be chasing our own tails much of the time and botanical nomenclature changes very often don't filter down to horticulture very quickly. As we are "For Gardeners, By Gardeners" we go with the horticultural flow rather than the botanical rapids (and then we'd have to choose a system to follow), otherwise the PlantFiles would end up making very little sense to anyone and difficult for members to know which name for their entry is the most current in botanical circles :)
paalexan
Las Cruces, NM

December 15, 2006
4:21 AM

Post #3000340

The general rule that higher-level taxon names have to be based on the names of genera contained within them is in the ICBN somewhere, but I don't know where offhand.

It looks like I might be wrong about Papilionaceae, though. In some dinking around I came across a paper (I'd stick a link here, but the forum software is mis-rendering it...) discussing family names that violate this rule, and I guess the eight conserved names I knew about (Leguminosae, Umbelliferae, Palmae, Gramineae, Cruciferae, Guttiferae, Compositae, Labiatae) aren't the only ones. Apparently Papilionaceae is another improperly-formed name that has been conserved.

With name changes in general... yeah, there's a balance between being correct and being comprehensible. I'm not sure where exactly you guys want to strike that balance on PlantFiles. The horticultural community in particular tends to be very slow to incorporate new taxonomy, but my view tends to be someone's gotta start using names that reflect new information, or else we'll be stuck in the past indefinitely. I don't know a thing about how PlantFiles works in terms of this, but one helpful approach would be to leave entries under older names, but have these forward you to the current name. Then, for instance, you could leave the name Arabis tricornuta in there, but have it forward you to Pennellia tricornuta... and hopefully people could still find things just fine, as well as being aware of some of what's going on with the taxonomy.

Patrick Alexander

This message was edited Dec 14, 2006 10:25 PM
Baa

December 15, 2006
9:43 AM

Post #3000560

Thanks for your reply.

We already list synonyms which are searchable on the PF so those members working with older names still have a chance to find the entry, of course this isn't entirely perfect as it requires the synonymy in the first place and for brevity's sake, we only allow 5 synonyms per entry, (the rest can be made in a comment which are not currently searchable).

I understand what you mean about someone leading the way for newer nomenclature and if it was the case that new entries were only created by a restricted group of members this may be achievable with a lot of research. This would also mean that the group would also need to have a keen interest in taxonomy, a subject which as you will know is not one that is overly enthused about in a positive manner by many gardeners *G*

In many respects, while I have my ideas on how I would shape the PF were it my own work, I do think that it's beauty lies in the fact that it isn't a dry and dusty, set in stone, database but a living, breathing work on plants based on peoples gardening and local flora experiences. To focus on the taxonomical aspect in an effort to lead the way would be to take the PF out of the reach of a lot of members and it's the myriad of contributing members that make the PF what it is in the first place.

We're always open to new suggestions and information on how to walk that fine line between being as current or correct as humanly possible and ensuring the PF is accessable to all. :)
paalexan
Las Cruces, NM

December 16, 2006
10:27 PM

Post #3004807

"This would also mean that the group would also need to have a keen interest in taxonomy, a subject which as you will know is not one that is overly enthused about in a positive manner by many gardeners."

Yeah, I've noticed that. :-)

A couple changes that could be made without inconveniencing gardeners in the least (because most gardeners don't care a whit about these species!) would be moving Arabis thaliana to Arabidopsis thaliana and Arabis tricornuta to Pennellia tricornuta. Also, Cheilanthes aliena should be Notholaena aliena.

Patrick Alexander

Baa

December 21, 2006
10:21 AM

Post #3015947

Thanks for letting us know :) I've made the name changes, they should show up soon.
ginger749

October 7, 2007
6:40 PM

Post #4057992

Why is it that interesting threads like this just die ?
Is it because yall can't agree ?
Or is it now all set in concrete and nothing more needs to be said ?
So many Questions so little time .
ginger749

October 19, 2007
3:42 AM

Post #4099723

I guess no one is watching this thread any longer .
I found it very interesting reading .
mystic
Ewing, KY
(Zone 6a)


October 20, 2007
2:03 AM

Post #4102852

ginger749, have you looked at the date on this thread? These things where done along time ago. I agree it's a great thread and we refer to it often. There is really no reason to keep it bumped to the top anymore since it was a change that was made a couple years ago. I think that is why nobody replied.


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