September 12
Higher Phylogeny: The current TiF higher phylogeny attempts to avoid grouping orders that don't belong together. A number of relevant papers have appeared since I last revisited it. Sad to say, most have not really indicated solid improvements over the current TiF phylogeny. One that seemed promising to me was Kuhl et al. (2021), but after spending a lot of time studying it, I just wasn't convinced by some of their higher-level groupings. In other words, the Hoatzin problem is still a problem!
Pluvialidae: I've changed the attribution of Pluvialidae from MacGillivray 1852 to Wood 1836.
[
Pluvialidae, Charadriiformes, 3.06b]
Sulidae: I've also changed the attribution of Sulidae from to Wood 1836.
[
Sulidae, Aequornithes II, 3.08]
Indo-Atlantic Shag Phylogeny, Yet Again! Although I'd thought I'd been backed into an unpleasant position, that turned out to not be so. First, Keith Bennett explained to me that my conclusions about the glacial maxima and cormorant survival were just wrong.
That shifted my big problem to the condition of the estimated phylogeny from Rawlence et al. (2022). Almost all of it had insufficient posterior support, which made many nodes essentially meaningless. However, in their supplementary information, I noticed Figure S1.1.F. The key information is in the phylogeny below.
Although they use 10 genes in their full analysis, 5 nuclear and 5 mitochondrial, the nuclear genes introduce a lot of noise while adding little insight. We can see that in the poor posterior probabilities. In contrast, the mitochondrial tree (Fig. S1.1.F) is pretty clean. Most nodes have posterior probabilities of 98% and above. It's almost the same tree as in their article. The biggest discrepancy is the position of the Crozet melanognis sample. See the abstracted tree in the cormorant account. Even though the position is odd, its support, though weak, is much stronger here. Other than improved posterior probabilities, The New Zealand portion is unaffected.
Dividing the Indo-Atlantic clade into species and subspecies as before, I ended up with
Falkland Cormorant, L. albiventer
Imperial Cormorant, L. atriceps
South Georgia Shag, L. georgianus, with a possible unnamed subspecies in the South Orkneys
Crozet Shag, L. melanogenis
Antarctic Shag, L. bransfieldensis, including a and a possible subspecies of melanogenis on Marion and Prince Edward Islands
Subantarctic Shag, L. purpurascens including nivalis and verrucosus
This was a lot of complication to get a phylogeny that's pretty similar to the Aug. 6 update! However, I'm now much more confident about the basic phylogeny (except for the Crozet Shag). I've also put some material in the text to explain better why I lumped onslowi into L. chalconotus.
[Phalacrocoracidae, Aequornithes II, 3.08]
If I was Boyd, I would reduce the number of species of
Leucocarbo to seven (
atriceps, bougainvillii, campbelli, carunculatus, chalconotus, magellanicus and
ranfurlyi)
).
