That’s the message of a new paper in Nature that compiled sequence data from 4,510 mammalian species

No, they did not.They took the literature, compiled a supertree from the (hopefully) phylogenetic analyses they found there, got sequences of 66 genes for as many mammals as possible, and then used those sequence data plus 30 calibration points to estimate some divergence dates on that supertree.That’s right: apart from its size, it’s just yet another attempt at molecular dating.And not a very good one. The age of the basal divergence (between the monotremes and the rest) was fixed at a rather arbitrary date out of the range of ages the oldest known fossil on the monotreme side of the split could have. The other ages were only used as minimal ages; maximal ages were not used, thus providing no protection against too old divergence date estimates. Of course maximal ages cannot be derived from the fossil record as easily as minimal ages, but the fossil record from some epochs is good enough to let us interpret absence of evidence as evidence of absence with more than 50 % confidence.There are only three outgroups, increasing the risk that the lengths of these branches could have detrimental effects on the branch lengths in the ingroup…No, it is not an earth-shattering paper, despite having been published as an “Article” (rather than “Letter”) in Nature.

Number 15 at Pharyngula (where I give a link to the supplementary information of the paper, which is free-access; also, Diacodexis pakistanensis is now Gujaratia pakistanensis):

[…] I downloaded the first part of the supplementary information. Table 3 of http://www.nature.com/nature/journal/v446/n7135/extref/nature05634-s1.pdf lists the calibration points. It contains (at least) the following mistakes:- Monotrematum is probably not a crown-group monotreme. Thus, Monotremata may be younger than 63.6 Ma.- Tribosphenomys is far from being a crown-group rodent! Rodentia (unlike Rodentiamorpha) is younger than 57.25 Ma (…and I wonder where they got such a precise date…). Note that the reference Bininda-Emonds et al. cite makes this quite clear (it coins the name Rodentiamorpha).- Not that I knew anything, but I’d be quite surprised if Eodendrogale were a crown-group scandentian. Thus, the crown-group of Scandentia may well be younger than 44.5 Ma.- Same for Dendrotherium being a crown-group dermopteran.- The genus Tarsius is 44.5 Ma old? Difficult to believe. I’d say a name change is in order.- Diacodexis is a paraphyletic series of species around the base of Cetartiodactyla (which means that at least some of those species should get new genus names). Putting “Diacodexis sp.” into Suiformes does therefore not look defensible to me, but I’ll try to find the reference.- Obviously, Pakicetus is not a crown-group whale. The crown-group of Cetacea (Autoceta) is much younger.- Eomanis is far from a crown-group pangolin…- I’d be very surprised if Ageinia turned out to be a crown-group bat. Thus, chances are high that the crown-group of Chiroptera is younger than 52.2 Ma.- I’d be surprised if Riostegotherium turned out to be a crown-group dasypodid. But that’s outside my area of knowledge.- The crown-group of Tubulidentata consists only of Orycteropus. Obviously Myorycteropus can’t be part of that…- Nortedelphys was indeed described as a didelphimorphian, but I don’t buy it. It’s “the tooth, the whole tooth, and nothing but the tooth” (as usual in the Mesozoic). In any case, considering it a crown didelphimorphian really stretches it.- Paucituberculata… all extant paucituberculates are caenolestids, and the fossil is most likely not one of those…- I bet the fossil notoryctid is outside the crown-group.Much sloppier work than I imagined.

Just for the record, I stand by that latter remark.Comment 18 at Pharyngula:

and my point is that seeing a mammalian radiation prior to the K/T boundary should not be a surprising result —

But a placental and a marsupial radiation in the Cretaceous areNortedelphys and a few more problematic crumbs), no matter how common the remains of other mammals are, and no matter how small those are.

Comment 23 at Pharyngula (note that, in addition to the two isolated teeth, Monotrematum is also known from at least one small nondescript jaw fragment):

David – is there another use of the term “crown” in the picture?

No. For example, you’ll see they put divergence between Tachyglossidae and Ornithorhynchidae ( = the origin of crown-group Monotremata) very shortly after the K-Pg boundary; clearly the Paleocene Monotrematum was considered an ornithorhynchid (or a tachyglossid, but there’s no way to compare two isolated teeth to an echidna, so they clearly didn’t do that).

Comment 41 at Pharyngula:

Wow, that is a huge mistake. Are we sure they weren’t using Pakicetus to give a minimum age for the divergence of the Cetecea *stem* group? That would make a lot more sense.

Yes, but look at the tree: they put the divergence between baleen whales and toothed whales into what seems to be the Eocene. Or have a look at their calibration point for Monotrematum, the only known Paleocene monotreme — the divergence between Tachyglossidae and Ornithorhynchidae is right after the K-Pg boundary, fitting the age of Monotrematum, so Bininda-Emonds et al. seem to consider M. an ornithorhynchid.

This study would be more impressive if they had compared the crown group frequency to some kind of null model.

I agree.Note how little time passed between reception and acceptance (just over 3 months) and between acceptance and publication (just under 2). That’s very fast.[…]

Proto-placentalians may have been minor members of the fauna, as Mr. Marjanovic indicates, but they still could have been divided into several lineages that gave rise to different modern placental orders after the age of the dinosaurs.

This is of course correct; neither the fossil record nor our current knowledge of it are complete. But have another look at the tree: I count not two, not five, not ten, but forty-two lineages of Cretaceous placentals and marsupials, and those are just those that happen to have left extant descendants. That so many lineages were present in the Cretaceous but are so far absent from the fossil record is not probable. (I can’t do the math off the top of my head, but it can be done — a paper has recently been submitted which does something like this for amphibians.)

This paper will come out in a few months in Acta Palaeontologica Polonica.Comment 42 at Pharyngula (note that the echidnas = tachyglossids do have a fossil record in Australia that reaches back to the Miocene):

I should have mentioned that the only certain fossil ornithorhynchids are Miocene and younger. There are no known fossil tachyglossids (apparently the group evolved in the underexplored New Guinea). There are no known fossil monotremes from the Eo- or Oligocene (or for that matter the Late Cretaceous… there are several from the Early Cretaceous, however). Thus, Bininda-Emonds et al. have obviously used Monotrematum to calibrate the divergence between Ornithorhynchidae and Tachyglossidae.

Comment 54 at Pharyngula:

[…]The latest word on the gastornithids — Diatryma is a junior synonym of Gastornis — is that they were herbivores, eating e. g. palm hearts.[…]

Comment 2 at Sandwalk:

You are right that it was not a good idea to fix the age of the root at 166.2 Ma, and that the cladogenesis may well have happened earlier. However, most of the other calibration points are too old because the phylogenetic positions of the fossils in question were misinterpreted. Bininda-Emonds et al. regularly mistook stem-group representatives for crown-group members. For example, the one they took as the oldest rodent is the oldest rodentiamorph, as the paper they cite makes clear — Rodentia is younger than that, and Rodentiamorpha includes Rodentia plus its closest extinct relatives. For more, please see my comment over at Pharyngula: [URL deleted — see top of this comment]This miscalibration pushes most, maybe all, divergence dates too far into the past. I’m sure this more than offsets the effect of the probably too young root.Using only minimal ages for the calibration points and no maximal ages may not have been a good idea either. There are rich Late Cretaceous mammal faunas which lack any trace of placentals or marsupials — in some of those cases I think absence of evidence should be regarded as evidence of absence of a radiation.