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.
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).
The resolution of the trees in the article, unfortunately, doesn't really make them readable.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.)
Either that or split them all up in a number of families.
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.
Yes, that looks correct... Except that: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.
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.)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.
This is presumably based on nothing too.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.)
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?