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Parrots (1 Viewer)

Peter Kovalik

Well-known member
Slovakia
BirdLife Taxonomy: Blue-backed Parrot (Tanygnathus sumatranus) is being split: assessment of newly recognised taxa.

Following a taxonomic reassessment, Blue-backed Parrot (Tanygnathus sumatranus) has been split into Azure-rumped Parrot (T. sumatranus) and Blue-backed Parrot (T. everetti) (see Arndt et al., 2019). The newly-split Blue-backed Parrot is found in the Philippines, while Azure-rumped Parrot is extant in Indonesia (Arndt et al., 2019).

The exact habitat requirements for the newly-split T. everetti have not been investigated, but it is very likely to inhabit tropical, lowland and montane forests, similar to T. sumatranus (del Hoyo et al., 1997). These species may also inhabit mangrove swamps, and can also tolerate degraded forests (del Hoyo et al., 1997). The population size of the pre-split species is unknown, but it is described as common to very common (del Hoyo et al., 1997). These species are not known to have many threats, but they may be at risk of habitat loss from deforestation (Tracewski et al., 2016).

The pre-split species was previously listed as Least Concern (BirdLife International, 2020). However, following the taxonomic split, new range sizes suggest that both species warrant a thorough reassessment. We have therefore reassessed both species against each criterion here.
 

Peter Kovalik

Well-known member
Slovakia
Smith, Mauck, Benz, Andersen. 2018. Uneven missing data skews phylogenomic relationships within the lories and lorikeets. [BioRxiv preprint]

Brian Tilston Smith, William M Mauck, III, Brett W Benz, Michael J Andersen, Uneven missing data skews phylogenomic relationships within the lories and lorikeets, Genome Biology and Evolution, , evaa113, https://doi.org/10.1093/gbe/evaa113

Abstract:

The resolution of the Tree of Life has accelerated with advances in DNA sequencing technology. To achieve dense taxon sampling, it is often necessary to obtain DNA from historical museum specimens to supplement modern genetic samples. However, DNA from historical material is generally degraded, which presents various challenges. In this study, we evaluated how the coverage at variant sites and missing data among historical and modern samples impacts phylogenomic inference. We explored these patterns in the brush-tongued parrots (lories and lorikeets) of Australasia by sampling ultraconserved elements in 105 taxa. Trees estimated with low coverage characters had several clades where relationships appeared to be influenced by whether the sample came from historical or modern specimens, which were not observed when more stringent filtering was applied. To assess if the topologies were affected by missing data, we performed an outlier analysis of sites and loci, and a data reduction approach where we excluded sites based on data completeness. Depending on the outlier test, 0.15% of total sites or 38% of loci were driving the topological differences among trees, and at these sites, historical samples had 10.9x more missing data than modern ones. In contrast, 70% data completeness was necessary to avoid spurious relationships. Predictive modeling found that outlier analysis scores were correlated with parsimony informative sites in the clades whose topologies changed the most by filtering. After accounting for biased loci and understanding the stability of relationships, we inferred a more robust phylogenetic hypothesis for lories and lorikeets.

[pdf]
 

Jim LeNomenclatoriste

Taxonomy and zoological nomenclature
France
I seem to be seeing nth study that will solve nothing from a taxonomic point of view. One wonders if Eos wouldn't become a synonym of Trichoglossus

|8||
 
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Peter Kovalik

Well-known member
Slovakia
Burgio, K.R, K.E. Davis, L.M. Dreiss, L.M. Cisneros, B.T. Klingbeil, S.J. Presley, and M.R. Willig (2019), Phylogenetic supertree and functional trait database for all extant parrots, Data in Brief 24, DOI: 10.1016/j.dib.2019.103882.

Abstract:

We present a complete dataset from the literature on functional traits including morphological measurements, dietary information, foraging strategy, and foraging location for all 398 extant species of parrots. The morphological measurements include: mass, total length, wing chord, culmen length, tarsus length, and tail length. The diet data describe whether each species is known to consume particular food items (e.g. nectar, berries, and carrion), foraging strategy data describes how each species captures or accesses food, and foraging location data describe the habitat from which each species finds food (e.g. ground, canopy, and subcanopy). We also present a time-calibrated phylogenetic supertree that contains all 398 extant species as well as 15 extinct species (413 total species). These data are hosted on the Figshare data depository (https://figshare.com/s/6cdf8cf00793deab7ba6).
 

Jim LeNomenclatoriste

Taxonomy and zoological nomenclature
France
Burgio, K.R, K.E. Davis, L.M. Dreiss, L.M. Cisneros, B.T. Klingbeil, S.J. Presley, and M.R. Willig (2019), Phylogenetic supertree and functional trait database for all extant parrots, Data in Brief 24, DOI: 10.1016/j.dib.2019.103882.

Abstract:

We present a complete dataset from the literature on functional traits including morphological measurements, dietary information, foraging strategy, and foraging location for all 398 extant species of parrots. The morphological measurements include: mass, total length, wing chord, culmen length, tarsus length, and tail length. The diet data describe whether each species is known to consume particular food items (e.g. nectar, berries, and carrion), foraging strategy data describes how each species captures or accesses food, and foraging location data describe the habitat from which each species finds food (e.g. ground, canopy, and subcanopy). We also present a time-calibrated phylogenetic supertree that contains all 398 extant species as well as 15 extinct species (413 total species). These data are hosted on the Figshare data depository (https://figshare.com/s/6cdf8cf00793deab7ba6).

Could someone send me the different figures included in the zip file but in pdf format please, I have no possibility to extract or read these files ?
 

l_raty

laurent raty
Could someone send me the different figures included in the zip file but in pdf format please, I have no possibility to extract or read these files ?
The resolution of the trees in the article, unfortunately, doesn't really make them readable.
There are 7 files on FigShare, which you can download together as a .zip, or separately -- so that, in principle, there should be no need to extract them. None of these files is a figure, but one is a .tre tree file. I have attached a visualization of the latter in FigTree. (The numbers should represent the ages of nodes in million years.)
(I see differences between this tree and the trees that are in the paper that I do not really understand, so take it for what it's worth.)
 

Attachments

  • 5.ParrotSupertree.tre.pdf
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gusasp

Well-known member
The resolution of the trees in the article, unfortunately, doesn't really make them readable.
There are 7 files on FigShare, which you can download together as a .zip, or separately -- so that, in principle, there should be no need to extract them. None of these files is a figure, but one is a .tre tree file. I have attached a visualization of the latter in FigTree. (The numbers should represent the ages of nodes in million years.)
(I see differences between this tree and the trees that are in the paper that I do not really understand, so take it for what it's worth.)

Very interesting if this is correct, with Psittacella outside Psittacidae+Psittaculidae! Certainly an argument for uniting Psittacidae and Psittaculidae again. Either that or split them all up in a number of families.
 

Jim LeNomenclatoriste

Taxonomy and zoological nomenclature
France
Either that or split them all up in a number of families.

Isolate Psittacella in its own family, Psittacellidae.

Curious, they also find Mascarinus paraphyletic with Coracopsis. And, I wonder if we couldn't combine Alisterus, Aprosmictus and Polytelis in one: Polytelis.
 
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l_raty

laurent raty
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.
 

AlexJB497

Member
Difficult to interpret much of it, but check out divergences in Pezoporus, perhaps time to resurrect Geopsittacus for Night Parrot?
 

D Halas

Well-known member
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.
 

l_raty

laurent raty
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.

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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l_raty

laurent raty
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.)
 

Fred Ruhe

Well-known member
Netherlands
Quote:

Originally Posted by LeNomenclatoriste View Post
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.)

There also is no fossil evidence to support this age.

Fred
 

Peter Kovalik

Well-known member
Slovakia
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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James Jobling

Well-known member
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?
 

Jim LeNomenclatoriste

Taxonomy and zoological nomenclature
France
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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