The marsupial mole (Notoryctes) is not a living dryolestoid. It is a marsupial, and Agnolin & Chimento draw conclusions in this manuscript that do not follow from the evidence they present. Despite the PeerJ-preprint header above this manuscript title ("not peer reviewed"), this manuscript was peer-reviewed, twice by me, and rejected both times. This version is the second iteration I've seen, having been contacted by editors at two different journals to review it. (PeerJ was #2.) Because I've seen references to this "preprint" crop up elsewhere on the web, linking to this site, I would like to make public my review of this paper (pasted below). I do not have any grudge against the authors, nor do I have any vested interest for or against the claim that the marsupial mole is a crown marsupial (or a late-surviving dryolestoid). I post these comments here solely because I would like to help anyone who is interested to understand the basis for the well-corroborated view that Notoryctes is in fact a marsupial mammal, contra the claims in this manuscript.
Robert Asher, Curator of Vertebrates and Senior Lecturer
Museum of Zoology, University of Cambridge
p.s. Here are a few papers w/ links dating to 1994 that provide evidence that the marsupial mole is indeed a marsupial. This is not an exhaustive list. Even analyses that don't sample fossils still place Notoryctes within therians (i.e., the clade of all marsupials & placentals), not stemward from it as the dryolestoid hypothesis would require. All but the first of the following citations (a book) are peer-reviewed journal articles and (unlike this manuscript) were not rejected by the scientific process of peer-review:
Szalay FS. 1994. Evolutionary History of the Marsupials and an Analysis of Osteological Characters. Cambridge Univ Press. http://www.cambridge.org/gb/academic/subjects/life-sciences/evolutionary-biology/evolutionary-history-marsupials-and-analysis-osteological-characters
Springer MS, Burk A, Kavanagh JR, Waddell VG, Stanhope MJ. The interphotoreceptor retinoid binding protein gene in therian mammals: implications for higher level relationships and evidence for loss of function in the marsupial mole. Proceedings of the National Academy of Sciences. 1997 Dec 9;94(25):13754-9.
Burk A, Westerman M, Kao DJ, Kavanagh JR, Springer MS. An analysis of marsupial interordinal relationships based on 12S rRNA, tRNA valine, 16S rRNA, and cytochrome b sequences. Journal of Mammalian Evolution. 1999 Dec 1;6(4):317-34.
Amrine-Madsen H, Scally M, Westerman M, Stanhope MJ, Krajewski C, Springer MS. Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials. Molecular phylogenetics and evolution. 2003 Aug 31;28(2):186-96.
Horovitz I, Sánchez-Villagra MR. A morphological analysis of marsupial mammal higher‐level phylogenetic relationships. Cladistics. 2003 Jun 1;19(3):181-212.
Asher RJ, Horovitz I, Sánchez-Villagra MR. 2004. First Combined Cladistic Analysis of Marsupial Mammal Interrelationships. Molecular Phylogenetics and Evolution 33: 240-250.
Phillips MJ, McLenachan PA, Down C, Gibb GC, Penny D. Combined mitochondrial and nuclear DNA sequences resolve the interrelations of the major Australasian marsupial radiations. Systematic Biology. 2006 Feb 1;55(1):122-37.
Kjer KM, Honeycutt RL. Site specific rates of mitochondrial genomes and the phylogeny of eutheria. BMC Evolutionary Biology. 2007 Jan 25;7(1):8. https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-7-8
Beck RM, Godthelp H, Weisbecker V, Archer M, Hand SJ. Australia's oldest marsupial fossils and their biogeographical implications. PLos one. 2008 Mar 26;3(3):e1858.
Nilsson MA, Churakov G, Sommer M, Van Tran N, Zemann A, Brosius J, Schmitz J. Tracking marsupial evolution using archaic genomic retroposon insertions. PLoS Biol. 2010 Jul 27;8(7):e1000436.
Meredith RW, Janečka JE, Gatesy J, Ryder OA, Fisher CA, Teeling EC, Goodbla A, Eizirik E, Simão TL, Stadler T, Rabosky DL. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science. 2011 Oct 28;334(6055):521-4.
Archer M, Beck R, Gott M, Hand S, Godthelp H, Black K. Australia's first fossil marsupial mole (Notoryctemorphia) resolves controversies about their evolution and palaeoenvironmental origins. Proceedings of the Royal Society of London B: Biological Sciences. 2011 May 22;278(1711):1498-506.
O’Meara RN, Thompson RS. Were there Miocene meridiolestidans? Assessing the phylogenetic placement of Necrolestes patagonensis and the presence of a 40 million year meridiolestidan ghost lineage. Journal of Mammalian Evolution. 2014 Sep 1;21(3):271-84.
Beck RM, Warburton NM, Archer MI, Hand SJ, Aplin KP. Going underground: postcranial morphology of the early Miocene marsupial mole Naraboryctes philcreaseri and the evolution of fossoriality in notoryctemorphians. Memoirs of Museum Victoria. 2016;74:151-71.
Mitchell KJ, Pratt RC, Watson LN, Gibb GC, Llamas B, Kasper M, Edson J, Hopwood B, Male D, Armstrong KN, Meyer M. Molecular phylogeny, biogeography, and habitat preference evolution of marsupials. Molecular biology and evolution. 2014 Sep 1;31(9):2322-30.
Review of Agnolin & Chimento manuscript for PeerJ
by Robert Asher, Department of Zoology, University of Cambridge
As in the previous version of this manuscript, the authors are still convinced that the marsupial mole is not actually a marsupial but a non-therian holdover of otherwise extinct dryolestoids. Such "lazarus taxa" (Dawson et al. 2006 on Laonastes, or Rougier et al. 2012 and O'Meara & Thompson 2014 on Necrolestes) are exciting, and indeed as the authors point out, the Miocene Necrolestes has recently been compellingly placed among dryolestoids after decades of ambiguity regarding its affinities.
In contrast, and contra the arguments in this paper, there is nowhere near the same level of ambiguity regarding the systematics of Notoryctes (a living mammal) as there was for Necrolestes (a Miocene fossil). There is actually a recent mitogenomic paper (Kjer & Honeycutt 2007, not cited here) that shows Notoryctes at the marsupial root, but this is a far cry from claiming that it isn't* a marsupial. Lines 28-30 of this MS state "authors include it among Australian marsupial clades, mainly by biogeographic reasons". No, authors include it among Australian marsupial clades primarily because of genetic, anatomical, and biogeographic evidence. Agnolin & Chimento discuss previous work on the systematics of Notoryctes over the last few decades and note the variety of hypotheses on its affinities. However, they inaccurately downplay what actually is a substantial consensus that it is in fact a marsupial. This consensus is not arbitrary, but based on evidence: for example, the 35kb alignment across 164 placentals, marsupials, and monotremes from Meredith et al. 2011, showing that Notoryctes is a marsupial, almost always within the australidelphian radiation, in agreement with just about every other phylogeny of mammals that samples this taxon published over the last decade (e.g., Amrine-Madsen et al. 2003; Horovitz & Sánchez-Villagra 2003; Nilsson et al. 2004, Asher et al. 2004; Phillips et al. 2006; Beck et al. 2008, etc.). To imply that disagreement across these studies regarding Notoryctes' affinities with dasyuromorphs or peramelians is evidence for genuine uncertainty about the status of Notoryctes as a marsupial (lines 93-135) is absurd.
Fossil evidence such as Naraboryctes shows that the main cusp of notorycid upper molars is the metacone (Archer et al. 2011: fig. 1). The authors devote a whole section trying to disprove Archer et al's conclusions, claiming "Archer et al. (2010 [sic]) do not report a single unique apomorphy uniting Notoryctes and Naraboryctes". This is nonsense. Please look briefly at the figures of the humerus, ulna (Archer et al. 2011: fig. 4), jaw or upper dentition (fig. 3) of Naraboryctes. Based on comparative anatomy, Archer et al. correctly identified this fossil as a notoryctid.
I hesitate to suggest (because they might believe it) that what these authors really should consider is that the entire dryolestoid radiation is actually part of Australidelphia. I.e., Notoryctes is not a Lazarus taxon, but rather dryolestoids comprise a 150ma ghost lineage of largely South American notoryctids dating to the Jurassic. This wild claim is supported by more data (e.g., anatomy & DNA placing Notoryctes among australidelphians) than the even wilder claims advanced in this paper.