Mammal tree of life still not resolved

Lesser hedgehog tenrec (Echinops telfairi)
A member of the superordinal clade Afrotheria
Photo by Wilfried Berns CC BY-SA

My studies of placental evolution were stimulated by the large-scale molecular phylogenetic analyses of mammals that appeared 15 years ago (e.g. here). Especially riveting was the revelation of four superordinal clades, among them Afrotheria. 

An excellent review of the progress made in molecular phylogenetics and phylogenomics in the last 15 years recently appeared under the heading "Mammal madness" (by Foley, Springer and Teeling here). 

Competing hypotheses on the root of the mammalian tree
From Mess and Carter (here) based on Springer (Chapter here)



Some of the uncertainties arising from the earlier work remain. Most striking is the failure unequivocally to root the tree. The three competing hypotheses shown above are still in play. While consensus is tipping in favour of Model A above, retroposon analysis provides similar support for all three.

This is not all. There remains uncertainty about the branch order within Laurasiatheria, which includes bats, carnivores, pangolins and even- and odd-toed ungulates.

Such uncertainties make it difficult to plot the evolution of fetal membranes and placentation. Thus the likelihood that the common ancestor of extant eutherians had an endotheliochorial placenta is greater under Model A than the other two hypotheses (shown here).

Concatenation and coalescence

Analysis of large data sets involves some fancy statistics. Foley et al. give a fair account of the pitfalls in concatenation, used in all the early papers, and coalescence. Coalescent methods require much more computer time and are not applicable to large data sets unless short cuts are taken. So far this has not worked out too well.

An article just appeared in Cladistics (here), which seems to demand a "correction," in reality a retraction, of a paper in PNAS based on a coalescent approach. The authors doth protest too much, methinks. As Foley et al. point out, some pretty weird results appeared in the early days of DNA studies, too.

Morphology and molecules

The attitude of some researchers to morphological data could also be more generous. Attempts to integrate morphology and molecules, such as O'Leary et al. (previous post) do throw up some counterintuitive results. But there are examples where fossils have been useful in bolstering hypotheses based on molecular data - the position of whales is a case in point (previous post). Similarly, Afrotheria is not well supported by morphology, but we have published an apparent synapomorphy in the form of the allantoic sac (here).

Moreover fossil calibrations are the key to solving another conflict, which concerns the timing of ordinal diversification of mammals. Deservedly this is given close attention in Foley et al.'s excellent review. The sort of fossils we are talking about are too old to yield ancient DNA so we have only morphology to go on.

Foley et al. finish on an optimistic note and predict the next 20 years of phylogenetic research "should result in the resolution and dating of the mammal tree of life."