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Re: Proto-penguins lived with dinosaurs



Fordyce and friends took the [...] 62 Ma of *Waimanu manneringi*
(determined by traditional geological methods -- it's in a Danian
layer) as the date of the divergence between Sphenisciformes and...
whatever their molecular tree gives as the closest living relative.

Storks (bizarrely), followed by loons and procellariiforms:

Bizarre indeed, but when they take the stork out of their analysis nothing changes, they say.


The second calibration point is *Vegavis* at 66 Ma. That's fine (give or take a million years maybe). However, as they say in the supplementary information but not the text, they used a third calibration point: the divergence between cassowaries and emus at 30 to 35 Ma ago. This date may well be correct, but unfortunately it comes out of quite thin air. The _entire_ fossil evidence for this age is the fact that the oldest known emu is _twenty_-five Ma old.

Additionally, they get the ostrich as the basalmost ratite. If this is wrong, it may have pushed a lot of other divergences down, especially the basal divergence of Neornithes. The paper that announced the complete mitochondrial genomes of two moas and the partial one of an aepyornithid found a different topology, with ostriches less basal than rheas, maybe because the moa and elephant-bird sequences were included in that analysis. They are missing this time.

In addition to the (small) standard deviations, 95 % confidence intervals were calculated "but are not shown".

The program for estimating divergence dates does Bayesian analyses. This means you can choose a so-called prior; if possible, the program will bias its results toward the prior. Now, "the mean of the prior distribution for the time separating the ingroup root and the present (rt_tm)" is 84 Ma ago, and "the standard deviation of rttm" is 42 Ma ago. It is not explained where these numbers come from.

More importantly, however, "the length of time between the root and the present" is set a priori as 500 Ma. How does this work? The ingroup are Neornithes, and the outgroup is composed of 6 "reptiles", including 2 turtles -- so why not, like, 300 Ma???

Interestingly -- for a molecular tree -- the two crocodylians clade with the birds, while the turtles are in the basal trichotomy.

The internal branch lengths, especially in Neoaves minus Passeriformes, are _very_ short. This may mean that the used characters (complete mitochondrial genomes minus a few genes that were "excluded due to missing data") are not well suited for examining the relationships of the used taxa. Indeed some bootstrap values are rather low. Ratitae (with the ostrich as the sister-group to the rest, see above) has only 54, and Ratitae without the ostrich has 64. Neognathae, too, has only 67. The other bootstrap values below 78 are all in the following clade:

--92--85--falcon
  |   `--buzzard
  `--49--91--oystercatcher
      |   `--turnstone
      `--66--49--loon
          |   `--54--stork
          |      `--penguin
          `--99--albatross
             `--petrel

...which is arguably the most interesting one for the purposes of this paper. Let's put it this way... it is very honest to publish a bootstrap value of 49. Few people do that.