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"Lagging" IOC taxonomy (1 Viewer)

G

gusasp

Well-known member
In bed with heavy cold scanning through the latest Clements and IOC updates. It strikes me that although being really up to date concerning species splits, there are a bunch of higher level taxonomic changes that hasn't been implemented yet in the IOC list.

Just a quick comparison with Clements (which in turn also lags in several aspects) gives the following. Hoping for assessment in the upcoming update! ;)

Orders & families
– Turacos in its on order? Might be closer to bustards.
– Resolvement of Caprimulgiformes. Either split as AOU or lump with Apodiformes as Clements.
– Emu in cassowary family, recent split
– Ptillorrhoa & Cinclosoma to Cinclosomatidae, distant from whipbirds
– Separate Falcunculidae, not closest to Pachycephalidae?
– Megabyas & Bias in Vangidae
– Include Tephrodornithidae & Prionopidae in Vangidae: recent split and uncertainty where Philentoma goes.
– Parrotbills and allies to Paradoxornithidae, split older than other familiar splits in this clade.
– Split Alcippe in two, Schoeniparus to Pellorneidae, the rest to the laughingthrushes. (but where does Fulvetta ludlowi go?)
– Malia grata is a grassbird
– Hylia and Pholidornis in a family of their own close to cettids and long-tailed tits.
– Micromacronus are cisticolas.
– Plocepasser, Histurgops, Pseudonigrita & Philetarius are weavers.
– Gubernatix, Coereba, Porphyrospiza are tanagers.
– Oreothraupis is a bunting.

Genera
– Lump Oceanodroma, Leucocarbo, Siptornopsis, Gyalophylax, Simoxenops, Hyloctistes, Hylocryptus, Heliolais, Oreophilais, Pseudoalcippe, Horizorhinus, Lioptilus, Muscicapella, Oryzoborus

– Split Terenura, Cercomacra, Myrmeciza, Hylophilus, Coracina, Chlorophoneus, Lonchura (Spermestes)

– Plus:
Coturnix ypsilophora & Excalfactioria to Synoicus
Pseudobulweria rupinarum to Pterodroma
Neochen & Andean Goose to Oressochen
Porzana/Amaurornis-assemblage
Calidris-assemblage
Philydor ruficaudatum & lichtensteini to Anabacerthia
Automolus rubiginosus & rufipectus to Syndactyla
Deconychura stictolaema to Certhiasomus
Melidectes whitemanensis to Vosea
Monarcha rubiensis in Symposiachrus or not?
Atticora-assemblage
Timaliidae & Pellorneidae mess
Macronyx sharpei & Anthus chloris to Hemimacronyx

Comments?
 
Turacos are Musophagiformes now, close to Bustards. Both orders (Musophagiformes and Otidiformes) are close to Cuculiformes.

Oceanodroma has been split into more genera (Thalobata and Cymochorea, according to TiF). Surely that some authors (which ?) are lumping the monotypic Oceanodroma (O. furcata) into Hydrobates. I don't follow this concept because I'm stubborn and incorrigible.

Leucocarbo is a subgenus ? of Phalacrocorax.

Siptornopsis and Gyalophylax are paraphyletic with Synallaxis, so bye bye Siptornopsis and Gyalophylax.

Same remark for Oryzoborus (embedded in Sporophila) and Dolospingus fringilloides (now Sporophila fringilloides)

Oreophilais lump ? Not to my knowledge. Since when ?

Terenura is polyphyletic it seems to me (tell me if I wrong) , so the new genus Euchrepomis has been erected for callinota, sharpei, spodioptila and humeralis.

Cercomacra has been split into two genera : Cercomacra and Cercomacroides (laeta, parkeri, nigrescens, fuscicauda, serva and tyrannina)

Excalfactoria keep Excalfactoria. Why merge it into Synoicus ?
 
Phylloscopus & Seicercus still to sort out, though maybe waiting for more data.

Larus canus still awaiting splitting (not a genus, but long overdue all the same!).
 
Nutcracker said:
Baffled - why split Sylvia from the info in that tree? There's only 3 Sylvia spp listed there, and they're monophyletic.
Click to expand...
Not from the info in that tree. ;)

In Clements, Myzornis, Pseudoalcippe, Horizorhinus and Lioptilus are all lumped with Sylvia, based on various studies. Parosphasma is not, but it is certainly embedded in the broad Sylvia as well if I believe the data that are in GenBank. In IOC, Myzornis, Parosphasma, Pseudoalcippe, Horizorhinus and Lioptilus are all treated as distinct. None of these can be distinct if Sylvia includes more than two (or more probably one) of the species it usually includes.
 
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l_raty said:
Not from the info in that tree. ;)

In Clements, Myzornis, Pseudoalcippe, Horizorhinus and Lioptilus are all lumped with Sylvia, based on various studies. Parosphasma is not, but it is certainly embedded in the broad Sylvia as well if I believe the data that are in GenBank. In IOC, Myzornis, Parosphasma, Pseudoalcippe, Horizorhinus and Lioptilus are all treated as distinct. None of these can be distinct if Sylvia includes more than two (or more probably one) of the species it usually includes.
Click to expand...

Thanks! Thought you were quoting from that tree ;) Where is this from then please?
 
Yew... NOT Myzornis, of course, how did I get this one in...? :(

(Mmh, I see - I copied all the sylviid taxa grouped ahead of Sylvia in the IOC list, without really checking. Myzornis is there in the list, despite it now appears to belong with Paradoxornithidae if these are separated from Sylviidae.)

The sources for the rest include:
  • Böhning-Gaese et al 2003 [abstract], 2006 [abstract] - Pseudoalcippe abyssinica sister to S. atricapilla + S. borin; all other Sylvia spp. more distant.
  • Gelang et al 2009 [abstract] [pdf] - they produced the only published Parophasma data; in the analysis, Parophasma is sister to Sylvia atricapilla, but no other Sylvia spp are included.
  • Johansson et al 2008 [abstract] [pdf] - Lioptilus nigricapillus closer to Pseudoalcippe abyssinica than to Sylvia atricapilla; given that (cf. Böhning-Gaese et al) Sylvia atricapilla is closer to Pseudoalcippe abyssinica than to the bunch of other Sylvia spp, this implies that Lioptilus is embedded in Sylvia as well.
  • Voelker et al 2009 [abstract] [pdf] - Horizorhinus dohrni sister to Pseudoalcippe abyssinica; these two sister to Sylvia borin; these three sister to Sylvia atricapilla; all other Sylvia spp more distant.
  • Voelker & Light 2011 [whole paper] - as in Voelker et al 2009.
  • Moyle et al 2012 [whole paper] - Horizorhinus dohrni sister to Lioptilus nigricapillus, these two sister Pseudoalcippe abyssinica; this group sister to Sylvia borin; no other Sylvia spp included, but given the above, this can only be consistent with the three non-Sylvia being embedded in Sylvia.
 
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Here is what I get with a subset of Sylvia and all the species that are traditionally not included in the genus.
There are some apparent problems in the published mitochondrial data (sequences of the same gene from different studies placing the same species in completely different positions; sequences of two mitochondrial genes placing the same specimen at completely different positions, etc.), but nothing obvious in the sequences I used here, to the exception of a somewhat suspect high variability in the cytb sequences of Sylvia borin -- it may be that some of the published sequences are a bit off, but I can't easily determine which ones.
The genes I used are nd2, cyt-b, myo, odc, rag1 and gapdh (i.e., all the genes sequenced for Parophasma, plus cyt-b).

My tree differs from that in Voelker & Light 2011 in that I recover S. borin and S. atricapilla as sister taxa (but with fairly low support only), while their tree contradicted this. (NB - The borin sequences I used are from their data set, so the difference doesn't come from there.)

*****
PS - the academia.edu link that I gave yesterday to the pdf of Voelker et al 2009 doesn't seem to have survived. This was a Google Scholar link, so perhaps the best thing to do is to link directly to [them]...? For me the pdf link on this page works even when I'm not logged in (neither in Google, nor in Academia). (Or you can go directly [here], but then you must log in to see the paper.)
 

Attachments

  • Sylviidae-nd2-cytb-myo-odc-rag1-gapdh.pdf
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Colombia is a good sample, as it includes 20% of the world's species.

In the latest XL spreadsheet checklist we did, we include notes comparing all changes on our list from IOC and SACC and BirdLife. You can see from this comparison that IOC has not paid so much attention recently to higher level taxonomy; and that SACC "lag along way behind" on splits. Although SACC would probably say that none of them are valid or that no one has produced a proposal yet.

https://www.researchgate.net/public...n_occurrencestatus_Listado_de_Aves_de_Colombi


Thomas
 
gusasp said:
In bed with heavy cold scanning through the latest Clements and IOC updates. It strikes me that although being really up to date concerning species splits, there are a bunch of higher level taxonomic changes that hasn't been implemented yet in the IOC list.

Just a quick comparison with Clements (which in turn also lags in several aspects) gives the following. Hoping for assessment in the upcoming update! ;)

Orders & families
– Turacos in its on order? Might be closer to bustards.
– Resolvement of Caprimulgiformes. Either split as AOU or lump with Apodiformes as Clements.
– Emu in cassowary family, recent split
– Ptillorrhoa & Cinclosoma to Cinclosomatidae, distant from whipbirds
– Separate Falcunculidae, not closest to Pachycephalidae?
– Megabyas & Bias in Vangidae
– Include Tephrodornithidae & Prionopidae in Vangidae: recent split and uncertainty where Philentoma goes.
– Parrotbills and allies to Paradoxornithidae, split older than other familiar splits in this clade.
– Split Alcippe in two, Schoeniparus to Pellorneidae, the rest to the laughingthrushes. (but where does Fulvetta ludlowi go?)
– Malia grata is a grassbird
– Hylia and Pholidornis in a family of their own close to cettids and long-tailed tits.
– Micromacronus are cisticolas.
– Plocepasser, Histurgops, Pseudonigrita & Philetarius are weavers.
– Gubernatix, Coereba, Porphyrospiza are tanagers.
– Oreothraupis is a bunting.

Genera
– Lump Oceanodroma, Leucocarbo, Siptornopsis, Gyalophylax, Simoxenops, Hyloctistes, Hylocryptus, Heliolais, Oreophilais, Pseudoalcippe, Horizorhinus, Lioptilus, Muscicapella, Oryzoborus

– Split Terenura, Cercomacra, Myrmeciza, Hylophilus, Coracina, Chlorophoneus, Lonchura (Spermestes)

– Plus:
Coturnix ypsilophora & Excalfactioria to Synoicus
Pseudobulweria rupinarum to Pterodroma
Neochen & Andean Goose to Oressochen
Porzana/Amaurornis-assemblage
Calidris-assemblage
Philydor ruficaudatum & lichtensteini to Anabacerthia
Automolus rubiginosus & rufipectus to Syndactyla
Deconychura stictolaema to Certhiasomus
Melidectes whitemanensis to Vosea
Monarcha rubiensis in Symposiachrus or not?
Atticora-assemblage
Timaliidae & Pellorneidae mess
Macronyx sharpei & Anthus chloris to Hemimacronyx

Comments?
Click to expand...
Laggards we are!

Tracking subfamilial radiations by revising the genera of birds definitely challenges us. We tend to favor a conservative approach given the rapidly changing protocols and surprises from new genomics. Also, we prefer to wait for a comprehensive revision of a family rather than adopt new partial phylogenies, with exceptions for compelling cases of paraphyly. Such excuses aside, revisions of the ordinal classification of the IOC list are underway and will be posted early next year. We also will update many genera, including a review of the helpful lists posted on this forum.

Looking ahead, a fully resolved hierarchical phylogeny of world birds will soon require attention to the names of many more branches. Increased use of subgenera instead of more genera may be a constructive first step in this daunting task.
 
One other thing that would be useful would be addition of suprafamilial classification, in Passeriformes at least (Corvoidea, Sylvoidea, Passeroidea, etc.), please :t:
 
l_raty said:
Yew... NOT Myzornis, of course, how did I get this one in...? :(

(Mmh, I see - I copied all the sylviid taxa grouped ahead of Sylvia in the IOC list, without really checking. Myzornis is there in the list, despite it now appears to belong with Paradoxornithidae if these are separated from Sylviidae.)
Click to expand...

Yeah, I can't believe you posted that either Laurent. ;)

1) I know TiF places Myzornis in Paradoxornithidae but my understanding was it was placed in a trichotomy with Paradoxornithidae on the one hand and Sylviidae on the other.
Sorry, I don't recall which paper left me with that impression.

2) From your limited Sylvia tree Laurent I can't see a need to lump all the African species in Sylvia with Blackcap and Garden Warbler. Why not leave them in separate genera with all the rest in Curruca, or alternatively lump Horizorhinus, Lioptilus, Pseudoalcippe & Parophasma in a single sister genus to Sylvia?
 
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Acanthis said:
1) I know TiF places Myzornis in Paradoxornithidae but my understanding was it was placed in a trichotomy with Paradoxornithidae on the one hand and Sylvidae on the other.
Sorry, I don't recall which paper left me with that impression.
Click to expand...

Oh yes I see Myzornis is basal to the Paradoxornithidae in https://www.researchgate.net/publication/262014937_PasserineTree

Btw. I don't have a problem with Paradoxornithidae being included in Sylviidae, nor Leiotrichidae & Pellorneidae being restitched back into Timaliidae.
Thoughts, opinions anyone?
 
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Acanthis said:
Yeah, I can't believe you posted that either Laurent. ;)

1) I know TiF places Myzornis in Paradoxornithidae but my understanding was it was placed in a trichotomy with Paradoxornithidae on the one hand and Sylvidae on the other.
Sorry, I don't recall which paper left me with that impression.
Click to expand...
It's no excuse, but I was cooking at the same time I wrote the post. I apparently succeeded copying and formatting the list without actually reading the names it included -- I couldn't believe it either when I re-read it later in the evening. ;)
Gelang et al 2009 [pdf] had a trichotomy. I was going to add a link to Price et al 2014, but you found it yourself. :t:
Clements has Myzornis in Paradoxornithidae as well.

2) From your limited Sylvia tree Laurent I can't see a need to lump all the African species in Sylvia with Blackcap and Garden Warbler. Why not leave them in separate genera with all the rest in Curruca, or alternatively lump Horizorhinus, Lioptilus, Pseudoalcippe & Parophasma in a single sister genus to Sylvia?
Click to expand...
Currently, IOC use a more or less traditional circumscription (Parisoma lumped with Sylvia, the other African genera kept valid).
Clements has apparently been following the course suggested in the primary literature: the African genera have been found one at a time embedded in the traditional Sylvia, and each time the suggested solution was to lump the single offending taxon. As they split Paradoxornithidae (with Myzornis), their Sylviidae is now just a very large genus Sylvia (>30 species), plus the monotypic Parophasma. Sooner or later a tree showing Parophasma to be embedded in Sylvia will be published -- so, if they keep following the same logic, they'll end up with a monogeneric Sylviidae.

A two-species Sylvia would make sense to me, but this requires that these two species are indeed sister.
(I guess I could try to see how support behaves if I add more data. I was mainly looking for the relationships of Parophasma when I assembled the data set for the last tree: I used the genes available for this genus, then added cytb because only cytb and nd2 were available for Horizonrhinus, and this taxon seemed to float when represented by nd2 only. In this data set, borin is, just like Horizorhinus, represented by cytb and nd2 only. But I now see that a couple of other genes are available for borin, atricapilla, Lioptilus and Pseudoalcippe, which could be added as well.)
I'm not sure I'd be that comfortable with Sylvia for atricapilla only and Epilais for borin only.
 
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LeNomenclatoriste said:
I have also suggested the use of genus Epilais. 8-P, but as subgenus of Sylvia only if Horizorhinus, Pseudoalcippe etc... are treated as subgenera too.
Click to expand...

I like your thinking Monsieur :t: particularly if Curruca (à la TiF) with all those subgenera is taken into account too.

As an aside I've long wanted to buy 'Sylvia Warblers' by Helbig et al but felt it was incomplete.
Hopefully a newer edition will be produced one day with all the additional species
 
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