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Old Tuesday 16th June 2020, 09:49   #251
AlexJB497
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Difficult to interpret much of it, but check out divergences in Pezoporus, perhaps time to resurrect Geopsittacus for Night Parrot?
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Old Tuesday 16th June 2020, 16:20   #252
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Originally Posted by l_raty View Post
Psittacella is one of the "differences between this tree and the trees that are in the paper that I do not really understand". Although I cannot read the names of the taxa on the trees that are in the paper, I see no basal branch in these trees that would match the basal position of Psittacella as in the .tre file.
The trees in the paper are both fully bifurcating supertrees that only include a subset of all parrot species (273 of the 413 species that were included in the analysis). These trees are a Maximum Agreement Subtree of the 960 Most Parsimonious Trees the authors obtained in their analysis. The Maximum Agreement Subtree, so far as I understand, removes any branches that conflict between the Most Parsimonious Trees, leaving only those taxa (273 species, in this case) that don't show any topological conflict among the Most Parsimonious Trees.

The tree in the supplementary data, on the other hand, includes all 413 species in the analysis. The authors made this tree by adding the remaining 140 species to the Maximum Agreement Subtree in a very conservative way: based on their least inclusive known taxonomy. For example, any Amazona species that weren't already in the 273-species tree were added at the node that's the last common ancestor of all Amazona species already in the tree. Members of genera that weren't represented in the 273-species tree at all were added "at the base node of the least inclusive clade that the taxon was known to be part of according to classification". For example, if a genus that isn't represented in the 273-species tree is known to be part of a certain subfamily, it was added at the base node of all the members of that subfamily in the tree.

What this means, basically, is that the position of Psittacella in the full supertree is completely uninformative it's not based on any new data, but solely on existing taxonomy.
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Old Tuesday 16th June 2020, 19:30   #253
LeNomenclatoriste
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Originally Posted by andrew147 View Post

As already mentioned, Geopsittacus should be resurrected - this data has it separating from Pezoporus 34 million years ago!
34 mya! it's enormous, so much. It doesn't match.
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Old Tuesday 16th June 2020, 21:25   #254
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Quote:
Originally Posted by D Halas View Post
The trees in the paper are both fully bifurcating supertrees that only include a subset of all parrot species (273 of the 413 species that were included in the analysis). These trees are a Maximum Agreement Subtree of the 960 Most Parsimonious Trees the authors obtained in their analysis. The Maximum Agreement Subtree, so far as I understand, removes any branches that conflict between the Most Parsimonious Trees, leaving only those taxa (273 species, in this case) that don't show any topological conflict among the Most Parsimonious Trees.
Yes, that looks correct... Except that:
- I don't read the caption to Fig. 2 ("Complete time-calibrated supertree" etc.) as saying this;
- the tree in Fig. 2 is (as the caption says) clearly time-calibrated, and I see nothing in the text suggesting they time-calibrated an MAST before adding the missing taxa to it.

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The tree in the supplementary data, on the other hand, includes all 413 species in the analysis. The authors made this tree by adding the remaining 140 species to the Maximum Agreement Subtree in a very conservative way: based on their least inclusive known taxonomy. For example, any Amazona species that weren't already in the 273-species tree were added at the node that's the last common ancestor of all Amazona species already in the tree. Members of genera that weren't represented in the 273-species tree at all were added "at the base node of the least inclusive clade that the taxon was known to be part of according to classification". For example, if a genus that isn't represented in the 273-species tree is known to be part of a certain subfamily, it was added at the base node of all the members of that subfamily in the tree.

What this means, basically, is that the position of Psittacella in the full supertree is completely uninformative – it's not based on any new data, but solely on existing taxonomy.
So they built a supertree from trees they found in the literature, some of which included Psittacella; then they ran an algorithm over the results that would have trimmed Psittacella from them due to conflicting topologies; and then the finally re-inserted Psittacella in the tree, in a position based exclusively on "classification"... (Thereby "inventing" a Psittacidae + Psittaculidae clade excluding Psittacella, based on... absolutely nothing at all.)

I knew I was not over-fond of supertrees...

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Old Tuesday 16th June 2020, 21:51   #255
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34 mya! it's enormous, so much. It doesn't match.
This is presumably based on nothing too.
(A supertree is created by merging the topologies of published trees, in a procedure that does not take branch lengths (or, for what matters, branch supports) into account. The result is a topology, without any age attached to it. This topology was then time-calibrated based on a number of published node age estimations. For Geopsittacus/Pezoborus, if the two taxa ended up sister in the supertree topology, but no age had been published for this particular split, the only thing the data are saying is that the age of the split must be somewhere between zero and the age of the clade.)
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Old Wednesday 17th June 2020, 08:56   #256
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Roughly, this tree is worth nothing
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Old Wednesday 17th June 2020, 10:13   #257
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Quote:

Originally Posted by LeNomenclatoriste View Post
34 mya! it's enormous, so much. It doesn't match.

Quote:
Originally Posted by l_raty View Post
This is presumably based on nothing too.
(A supertree is created by merging the topologies of published trees, in a procedure that does not take branch lengths (or, for what matters, branch supports) into account. The result is a topology, without any age attached to it. This topology was then time-calibrated based on a number of published node age estimations. For Geopsittacus/Pezoborus, if the two taxa ended up sister in the supertree topology, but no age had been published for this particular split, the only thing the data are saying is that the age of the split must be somewhere between zero and the age of the clade.)
There also is no fossil evidence to support this age.

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Old Wednesday 15th July 2020, 15:19   #258
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Lorikeets

Leo Joseph , Jon Merwin & Brian Tilston Smith (2020): Improved systematics of lorikeets reflects their evolutionary history and frames conservation priorities, Emu - Austral Ornithology, DOI: 10.1080/01584197.2020.1779596

Abstract:

A well-supported genus-level classification of any group of organisms underpins downstream understanding of its evolutionary biology and enhances the role of phylogenetic diversity in guiding its conservation and management. The lorikeets (Psittaciformes: Loriini) are parrots for which genus-level systematics (phylogenetic relationships and classification) has long been unstable and unsatisfactory. Instability has manifested through frequently changing compositions of some genera (e.g. Trichoglossus and Psitteuteles). Other genera (e.g. Charmosyna, Vini) have become so large that their phenotypic heterogeneity alone at least questions whether they are monophyletic assemblages that genera should comprise. Recent molecular phylogenetic and phenotypic studies have improved the framework with which to rationalise genus-level systematics in lorikeets but some trenchant uncertainty has remained. Here we utilise published genomic data and tetrahedral analysis of plumage colour to develop a full review of the genus-level classification of lorikeets. Using existing phylogenetic relationships and a newly estimated time-calibrated tree for lorikeets, we show where paraphyletic assemblages have misled the classification of genera. We assign six species to three new genera and six other species to four previously described generic names that have been in synonymy in recent literature. Our taxonomic revision brings a new perspective informing and guiding the conservation and management of the lorikeets and their evolutionary biology.

Three new genera:
- Saudareos Joseph, Merwin and Smith gen. nov.
[S. ornata, S. iris, S. flavoviridis and S. johnstoniae]
- Synorhacma Joseph, Merwin and Smith gen. nov
[Synorhacma multistriata]
- Charmosynoides Joseph, Merwin and Smith gen. nov.
[Charmosynoides margarethae]

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Old Wednesday 15th July 2020, 17:44   #259
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Lorikeets; Joseph et al. 2020. Etymologies of new genera.
Synorhacma is an anagram of genus Charmosyna.
Charmosynoides is genus Charmosyna + Gr. -oides, resembling.
Saudareos has the look of an anagram involving genus Eos, but I am currently stumped. Ideas, anyone?
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Old Wednesday 15th July 2020, 17:48   #260
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Quote:
Originally Posted by James Jobling View Post
Lorikeets; Joseph et al. 2020. Etymologies of new genera.
Synorhacma is an anagram of genus Charmosyna.
Charmosynoides is genus Charmosyna + Gr. -oides, resembling.
Saudareos has the look of an anagram involving genus Eos, but I am currently stumped. Ideas, anyone?
Derived from Saudara the Bahasa for "sister" and genus Eos, sister of Eos

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Old Wednesday 15th July 2020, 18:27   #261
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Le N.
Many thanks for your quick reply (if you send me a private post with your given name, I shall be happy to acknowledge this contribution - and in the future). If you have access to the paper, can you tell me the type of Saudareos (in the list I use ornata, flavoviridis, and johnstoniae are in Trichoglossus, but iris is in Psitteuteles).
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Old Wednesday 15th July 2020, 18:34   #262
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I didn't do much, just downloaded the article and read it. To know the type species, I can send to you

Last edited by LeNomenclatoriste : Wednesday 15th July 2020 at 18:38.
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Old Wednesday 15th July 2020, 19:06   #263
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Let's face it, Saudareos is a horrible name. Personally I would have preferred a name like Ptilopsittacus, emphasizing their feather-shaped tongue shared by many genera

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Old Friday 17th July 2020, 17:20   #264
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Le N.
Many thanks for your quick reply (if you send me a private post with your given name, I shall be happy to acknowledge this contribution - and in the future). If you have access to the paper, can you tell me the type of Saudareos (in the list I use ornata, flavoviridis, and johnstoniae are in Trichoglossus, but iris is in Psitteuteles).
They designate ornatus as the type species of Saudareos.
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Old Friday 24th July 2020, 03:53   #265
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This is a really fascinating paper, so much to take in. The three taxonomic rearrangements for Indonesian taxa that I'm most interested in I noticed the following:

flavotectus (Wetar race of Marigold Lorikeet) more closely related to weberi (Leaf/Flores Lorikeet), than those it is currently placed with (capistratus and fortis) in current taxonomic arrangements, though does make sense when looking at plumage. No taxonomic authority had previously picked up on that.

meyeri and flavoviridis (Sulawesi & Sula) should be considered separate species, given meyeri is more closely related to the sympatric ornata (this is one that Birdlife and Indonesian Archipelago field guide already split).

It's a shame riciniata wasn't included in the study to compare with squamata and obiensis, as this is a likely split.

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Old Monday 27th July 2020, 18:30   #266
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Macaws

Proposal (869) to SACC

Revise Linear Sequence of Macaws
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Old Monday 3rd August 2020, 17:43   #267
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Proposal 873 to SACC

Modify species limits in Forpus: (A) Treat Forpus crassirostris as a separate species from F. xanthopterygius, and (B) Treat Forpus spengeli as a separate species from F. passerinus
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Old Monday 3rd August 2020, 17:57   #268
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Pamela Rasmussen has been busy writing proposals! I think that was no 2 or 3 during the last two days

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