Bandicoot fossils and DNA elucidate lineage antiquity amongst xeric-adapted Australasian marsupials

Bandicoots (Peramelemorphia) are a unique order of Australasian marsupials whose sparse fossil record has been used as prima facie evidence for climate change coincident faunal turnover. In particular, the hypothesized replacement of ancient rainforest-dwelling extinct lineages by antecedents of xeric-tolerant extant taxa during the late Miocene (~10 Ma) has been advocated as a broader pattern evident amongst other marsupial clades. Problematically, however, this is in persistent conflict with DNA phylogenies. We therefore determine the pattern and timing of bandicoot evolution using the first combined morphological + DNA sequence dataset of Peramelemorphia. In addition, we document a remarkably archaic new fossil peramelemorphian taxon that inhabited a latest Quaternary mosaic savannah-riparian forest ecosystem on the Aru Islands of Eastern Indonesia. Our phylogenetic analyses reveal that unsuspected dental homoplasy and the detrimental effects of missing data collectively obscure stem bandicoot relationships. Nevertheless, recalibrated molecular clocks and multiple ancestral area optimizations unanimously infer an early diversification of modern xeric-adapted forms. These probably originated during the late Palaeogene (30–40 Ma) alongside progenitors of other desert marsupials, and thus occupied seasonally dry heterogenous habitats long before the onset of late Neogene aridity.


Diagnosis.
Lemdubuoryctes is distinguished from all currently extant bandicoot genera (plus Chaeropus), the early Pliocene cf. Peroryctes tedfordi 33 , early-middle Miocene Kutjamarcoot 14 , Madju 13 , Liyamayi 12 , Crash 12 , Galadi amplus 18 , and late Oligocene Bulungu campbelli 16 by its retention of a 'complete' centrocrista with continuous postparacristae-premetacristae on all upper molars. The centrocrista is incomplete on M3 of the early Miocene Galadi speciosus 17 , and is formed by residual buccal crests on M3 of the early Miocene Bulungu palara 15 . Galadi grandis 18 also from the early Miocene, and Bulungu muirheadae 16 the oldest known late Oligocene bandicoot, possess 'complete' centrocristae along their upper molar rows but differ from Lemdubuoryctes in the presence of two mental foramina on the dentary, and the absence of anterior cingulae on M2-4 respectively. The lack of an elevated talonid separates Lemdubuoryctes from the latest Miocene-early Pliocene Ischnodon. Finally, oblique orientation of the posthypocristid relative to the lower molar row contrasts with late Oligocene-early Miocene Yarala 19,21 . Etymology. 'Lemdubu' from the type locality, and 'oryctes' (ορυκτης, masculine) for 'digger'; species name refers to its endemic occurrence on the Aru Islands.
Description of the new fossil taxon. Both the holotype (Western Australian Museum [WAM] 14.9.6) and referred (WAM 14.9.9) maxillae of Lemdubuoryctes (Fig. 2) display tooth eruption and molar wear indicative of adult animals (this is most extreme in WAM 14.9.9). The remnant palatal shelf on WAM 14.9.9 preserves a vacuity in the molar region. The base of the zygomatic arch is level with the alveolar margin. The antorbital fossa extends posteriorly from above the M3 to behind the M4; this differs from many extant peramelemorphians, as well as Bulungu palara 15 and Galadi speciosus 17 , but can be intraspecifically variable 13 . Posterior expansion of the antorbital fossa   Supplementary Fig. S1), some Echymipera rufescens (e.g. Australian Museum [AM] S1866) 35 , Yarala burchfieldi 20 , and osteologically mature Madju 13 specimens. The antorbital fossa of Macrotis is uniquely elevated above the tooth row 11 . The anterior opening of the infraorbital canal in WAM 14.9.6 extends to the P3 alveolus (or the posterior margin of the M1 in WAM 14.9.9). This is similar to most bandicoots (including B. palara) 15 , in which the infraorbital canal usually has an expansive exit over the M1-P3. The infraorbital canal opens immediately above the P3 in Y. burchfieldi 20 and species of Galadi 17,18 .
The upper premolars of Lemdubuoryctes are double-rooted with diastemata between P1 and P2 (WAM 14.9.11), suggesting an elongate maxillary rostrum. The P3 exhibits marked size dimorphism consistent with sexual variation observed in some extant peramelids, most notably species of Peroryctes and Echymipera 34 ( Supplementary Fig. S1). We therefore interpret WAM 14.9.6 as a probable male because the P3 exceeds the M1 in occlusal area (Fig. 2B). The P3 is smaller than the M1 in WAM 14.9.9 and thus represents a potential female (Supplementary Table S1). Both P3 morphotypes are otherwise identical in their triangular basal outline with conical central cusp, weak posterolingual cingulum and incipient anterobasal cuspule.
At up to 14.89 mm in length (Supplementary Table S1), the complete M1-M4 row of Lemdubuoryctes (WAM 14.9.9) is equal to the largest living bandicoot Peroryctes broadbenti 34 . The M1 ( Fig. 2; Supplementary Fig. S2) is triangular in occlusal outline unlike the more quadrangular molars of peramelines, Chaeropus and Macrotis; the latter further distinguished by extreme lingual displacement of the metacone 27 . In Lemdubuoryctes, the metacone is positioned at the posterolabial margin of the trigon basin, which is bounded buccally by the paracone. A prominent protocone is situated lingually. There is no protoconule. The metaconule (metaconular hypocone) forms only a weak spur that connects the postprotocrista to the base of the metacone. This is compatible with extreme metaconular reduction seen in the stem peramelemorphians Yarala 19,21 , Bulungu 15,16 , and Galadi 17,18 , together with the early Pliocene cf. Peroryctes tedfordi 33 . Alternatively, living bandicoots 27 as well as species of Crash 12 , Madju 13 and Kutjamarcoot 14 elaborate the metaconule into an enamel flange that is demarcated from the protocone via a vertical trough ( Supplementary Fig. S1). Dasyuromorphian marsupial carnivores have a more prominent cusp-like metaconule 36 . Amongst bandicoots only Macrotis completely lacks a metaconular structure, but a small metaconule is present in the putative thylacomyid Liyamayi 12 .
The anterior cingulum on the M1 of Lemdubuoryctes is formed by the preprotocrista, which connects to the parastylar base. There is no posterior cingulum. The paracone lies directly behind the parastyle and the preparacrista runs posterobuccally towards the parastylar tip (a common trait amongst Peramelemorphia: see Supplementary Data, character 14). The postparacrista merges with the premetacrista to create a 'complete' centrocrista. The opposing buccal ectoflexus is shallowly incised between the remnants of stylar cusps B and D (there is no discernible stylar cusp E). Remarkably, there are broad ectolophs evident on the M2 and M3 that closely resemble those of the most ancient peramelemorphians Yarala kida 21 and Bulungu muirheadae 16 . In other fossils, the postparacrista and premetacrista gradually retract resulting in a ridge-like centrocrista on the M3 of B. palara 15 , and total division of the ectoloph in Bulungu campbelli 16 , Galadi 17,18 , Madju 13 and Kutjamarcoot 14 .
Remnants of the centrocrista also occur on the M1-3 of extant P. broadbenti ( Supplementary Fig. S1), less prominently on the M1-2 of Peroryctes raffrayana, and occasionally in E. rufescens 34 . Crests appear elsewhere on the M1-2 of Crash 12 and cf. P. tedfordi 33 , which also has a small 'stylar cusp C' , perhaps constituting another residual component.
The M2 and M3 of Lemdubuoryctes ( Fig. 2; Supplementary Fig. S2) differ from the M1 in their lingually positioned paracone, less distinct ectoflexus, and transversely oriented preparacrista that trends towards stylar cusp B, but retains contact with the parastylar tip via a subsidiary crest. This forms a truncated anterior cingulum comparable to that on the M2-3 of P. raffrayana 34 .
The M4 of Lemdubuoryctes ( Fig. 2; Supplementary Fig. S2) is reduced relative to the anterior molars and bears both a paracone and diminutive protocone. An anterobuccal cingulum is not visible but could be covered by matrix in WAM 14.9.9. The postprotocrista forms the posterior margin of the tooth and meets the postparacrista at stylar cups B.
Mandibular elements were referred to Lemdubuoryctes based on obvious morphological distinction from the sympatric bandicoots 29 Isoodon macrourus, E. rufescens and E. kalubu. Relative hypertrophy of the p3 differentiates presumed male (WAM 14.9.1) and female (WAM 14.9.3) specimens ( Fig. 3; Supplementary Fig. S3). The mandibular rami of Lemdubuoryctes ( Supplementary Fig. S4) are ventrally convex and up to 9.7 mm deep below the m3 (WAM 14.9.3). The single mental foramen is level with the midline of p1, and the mandibular symphysis extends to the middle of p2. The ascending ramus in WAM 14.9.1 is angled at ~45°; the mandibular foramen opens low on the medial surface and the masseteric fossa is well defined. The i3 root on WAM 14.9.3 is separated from the canine alveolus (3.9/1.8 mm in maximum length/width) by a 2 mm diastema. Another diastema (3.5 mm) intersperses between c1 and p1 with a narrower gap between p1 and p2. The length and height of p1-3 decrease anteriorly (Supplementary Table S2) and are coupled with progressive migration of the blade-like central cusp forward over the anterior root. There are no accessory cuspids.
The complete m1-4 row of Lemdubuoryctes ( Fig. 3; Supplementary Fig. S3) was up to 17.43 mm long (WAM 14.9.3: Supplementary Table S2), with marked constriction evident at the enamel crown-root interface (also visible on p1-3); this is typical of peramelemorphians except for Isoodon and Macrotis 27 . The m1 is laterally compressed with a bulbous trigonid incorporating a prominent paraconid, which is absent in Ischnodon 37 , living peramelines and Echymipera 27 . There are no median buccal cuspules between the trigonids and talonids as reported in Y. burchfieldi 19 . The anterior cingulid is reduced on m1-4 and the labial cingulids are weakly developed, similar to Peroryctes 34 ( Supplementary Fig. S1). The cristid obliqua terminates buccally against the posterior wall of the protoconid on m1-2 (rather than the metaconid as in many peramelines 27,38 ) but is more lingually positioned on the m3, and immediately adjacent to the metacristid notch on m4. The hypoconulid is situated directly posterior to the entoconid, and sunken well below the talonid basin on all lower molars (synapomorphies for Peramelemorphia 27 ). The posthypocristid is oblique to the molar row like that of P. raffrayana 34 Scientific RepoRts | 6:37537 | DOI: 10.1038/srep37537 ( Supplementary Fig. S1). The conical entoconids on m2-3 differ from the blade-like structures in P. raffrayana 34 ( Supplementary Fig. S1), some species of Microperoryctes (Supplementary Data, character 25), cf. P. tedfordi 33 and Y. kida 21 . A discrete entoconid and hypoconid on the reduced m4 talonid are additional differences relative to Y. burchfieldi 19 and B. campbelli 16 .
The petrosals of Lemdubuoryctes (WAM 14.9.13-WAM 14.9.15) were identified by their weakly inflated periotic hypotympanic sinuses (thus excluding I. macrourus 27 ), and large size relative to those of I. macrourus, E. rufescens and E. kalubu. They also bear small rostral tympanic and caudal tympanic processes, as well as shallow mastoid sinuses and epitympanic recesses ( Supplementary Fig. S5). The prominent ventral flange on the pars cochlearis is compatible with those of Y. burchfieldi 21 , B. palara 15 and P. raffrayana 34 .
Calcanea were assigned to Lemdubuoryctes on the basis of their substantial size and striking morphological distinction from those of I. macrourus, E. rufescens and E. kalubu. The largest referred calcaneum (WAM 14.9.16: Supplementary Fig. S6) is 22.2 mm in maximum length. The compact tuber calcis, oblique calcaneo-cuboid facet, and projecting calcaneum-austragalus facet incorporating a short triangular lateral shelf, are all reminiscent of the condition in Microperoryctes 39 and P. raffrayana (American Museum of Natural History [AMNH] 151936), but contrast with that of Echymipera 39 (Supplementary Fig. S6). Calcanea have not yet been described for any other fossil peramelemorphian.
Phylogeny. Analysis of our morphological dataset (including molecular backbone constraints: Supplementary Fig. S7) produced both poor ingroup resolution and node support for the placement of fossil taxa ( Supplementary Figs S8 and S9). We attribute this to missing data and pervasive homoplasy, which was detected during construction of our matrix (see Methods) and subsequently examined via serial pruning of redundant fossils 40 and wildcards 41 (Supplementary Figs S10-S12). These procedures returned Lemdubuoryctes, together with Bulungu palara, Yarala burchfieldi and species of Galadi as labile stem peramelemorphians. This implies enormously protracted ghost lineages (Fig. 1), but no discrete character states served to unite these taxa as a clade. In fact, the only traits collectively distinguishing basal stem peramelemorphians from more crown-ward bandicoots were the deeply symplesiomorphic 20,25 presence of 'complete' centrocristae on M1-3 (although this is polymorphic in Galadi speciosus 17 and absent in G. amplus 18 ), and an alisphenoid-parietal contact on the lateral wall of the neurocranium (also evident in Madju 13 ). An alternatively derived squamosal-frontal contact is shared by all crown perameloids, and might be diagnostic for this radiation, but was not a major driver of our topologies (see Supplementary Data). Moreover, the monophyly of Yarala 21 as a separate sister grouping to Perameloidea was equivocal (Supplementary Table S3), leading us to question the taxonomic utility of Yaraloidea based on these primitive states alone 3,20,21 .
Our assessments of extant bandicoot morphology were consistent with DNA 1,4 in returning the xeric-adapted Macrotis lagotis as the most divergent living peramelemorphian (Supplementary Fig. S13). On the other hand, alternate grouping of the extinct arid-zone chaeropodid Chaeropus within Peramelinae (Supplementary Fig. S14) suggests that either extensive dental/osteological convergence 3 , or incomplete characterization of its scant mitochondrial sequence data 43 confound its relationships. Interestingly, inclusion of the extinct desert-adapted thylacomyid, Macrotis leucura, promoted extensive topological degradation (Supplementary Fig. S15). This might be due to its curious 'peramelid-like' dental attributes (see matrix scores in Supplementary Data), which could again denote either homoplasy, or the retention of ancestral perameloid states.
Trees generated by the concatenated dataset of morphology + DNA were identical to those produced by DNA alone 1 , but with amplified support values for weak nodes demonstrating overall signal congruence. This was most notable at the nodes excluding Macrotis lagotis from Peramelidae, and positioning of the Seram bandicoot Rhynchomeles prattorum within Echymipera (Supplementary Fig. S16). Successive deletion of molecular information for major clades 44 pinpointed residual morphological conflict over a paraphyletic Peroryctinae + Echymiperinae, and repositioning of Chaeropodidae within Peramelinae (Supplementary Table S4). This concurs with previous studies [14][15][16][17]45 , which have placed Macrotis and Chaeropus outside of Peramelidae using a molecular backbone, but not with morphology on its own. As expected, the introduction of fossils completely degraded node support ( Supplementary Fig. S17), and revealed long-branch effects in the clumped redistribution of taxa ( Supplementary Fig. S18). Sequential deletion of highly homoplastic dental-dependant terminals did improve these results (Supplementary Figs S19 and S20), but still failed to yield stable positioning of fossils, perhaps because they integrate insufficient cranial-postcranial skeletal data to accurately discriminate relationships.
Divergence times and ancestral areas. We utilized a DNA dataset with expanded outgroup sampling of diprotodontian, notoryctemorphan and dasyuromorphian taxa to correlate the timeframes and settings for peramelemorphian intra-clade divergences. Alternative fossil constraints (Supplementary Table S5) and Bayesian random local clocks 46 (Supplementary Fig. S21) were also implemented to assess possible sources of overestimation 16 . Despite these tests, our analyses demonstrated an unequivocal origination of the crown bandicoot total-group during the mid-Paleocene around 60 Ma (Table 1; Supplementary Tables S6-S8; Supplementary Figs S22-S30). This corroborates the discovery of possible stem peramelemorphian fossils from the early Eocene 3,9,47 , but massively predates previous molecular estimates 1,4 by up to 40 Ma. In accordance, diversifications amongst chaeropodid, thylacomyid and peramelid family-level clades seem to have commenced in the middle Eocene to Oligocene (~40-30 Ma). These epochs coincide with the tectonic isolation of Australia and instigation of the circum-Antarctic current, which propagated seasonally cool-dry climates and the spread of sclerophyllous vegetation 48 Tables S9-S12). Unanimous inference of a post early-middle Miocene (after ~20 Ma) rainforest-woodland radiation amongst peroryctines and echymiperines likewise coincides with uplift of the New Guinean landmass and onset "greenhouse" climates 49 , which propagated higher rainfall and coastal/riparian vegetation 50 . In contrast, our analyses failed to pinpoint an emergent habitat for peramelines. We attribute this to their rapid expansion into openly vegetated environments 1,3,51 , compounded by methodological dependence of our probability matrices upon predefined species distribution codes. These are particularly sensitive to highly dispersive organisms, as well as significant area changes through time 52 . In our case this included the pronounced middle-late Miocene (after ~16 Ma) resurgence of cool-dry climates, and Pliocene predominance of mosaic vegetation, especially incorporating intra-continental grasslands which proliferated across Australia during this interval 50 .

Discussion
The 'complete' centrocristae delimiting broad ectolophs, and extreme metaconular reduction on the M1-3 of Lemdubuoryctes are virtually identical to the conditions found in the most ancient fossil bandicoots Yarala kida 21 and Bulungu muirheadae 16 . As shown here, these unexpected state expressions have radical implications for bandicoot phylogeny in placing Lemdubuoryctes as an exceptionally late-surviving stem-grade peramelemorphian. Moreover, the presence of both residual centrocrista and metaconules on the upper molars of the early-middle Miocene Bulungu 15,16 and Galadi 17,18 , as well as the early Pliocene cf. Peroryctes tedfordi 33 , and extant species of Peroryctes and Echymipera 34 shows that these symplesiomorphies were persistent throughout bandicoot evolution, and could represent examples of repeated convergent atavism. Although postulated 3,16,18,27 , such rampant homoplasy has never previously been demonstrated within the fundamental discriminative features of the peramelomorphian dentition. Equally as significant is our topological nesting of Bulungu campbelli amongst living perameloids 3 , which implies a corresponding appearance of advanced dental traits within the stratigraphically earliest bandicoot lineages. Bulungu campbelli is a late Oligocene species (Etadunna Formation Zone C: 24.6− 24.1 Ma 53 ) that approximates the oldest known fossil peramelemorphian taxon B. muirheadae (Etadunna Formation Zone B: 24.9− 24.6 Ma 53 ). Bulungu campbelli is also important because it predates what is usually regarded as the most plesiomorphic bandicoot Yarala kida (Wipajiri Formation equivalent: < 24 Ma 53,54 ). Our new phylogenetic arrangement therefore pushes back the feasible minimum age for crown Peramelemorphia by more than 20 Ma (previous molecular clock constraints have used an upper limit of 4.36 Ma based on cf. Peroryctes tedfordi 1,3,[22][23][24], and also infers a pectinate pattern of past higher-level diversity (Fig. 1) that challenges the traditional yaraloid versus perameloid clade/time-division model 3,9,10,[19][20][21]27 .
The survival of Lemdubuoryctes on what is today a rainforest prevalent 28 island refuge, seemingly accords with the most ancient peramelemorphian habitats 12,13,[16][17][18] . However, the stratigraphical horizons containing Lemdubuoryctes fossils date from prior to inundation of the Torresian Plain after the Last Glacial Maximum [28][29][30][31] . At this time, the Aru Islands were a limestone plateau surrounded by open savannah plains with dense riparian forest restricted to topographic lows along fault-controlled 'sungai' channels [28][29][30][31] . The fossil bandicoot species from these settings are dominated by both Lemdubuoryctes and Isoodon macrourus, the latter being an extant grassland-open woodland inhabitant. On the other hand, Echymipera rufescens which presently occupies lowland rainforests on the Aru Islands 29 is comparatively rare, and E. kalubu which typifies rainforests and anthropogenic grasslands in high rainfall areas, has been tentatively identified from a few teeth but these post-date the Holocene marine transgression 29 . The numerical abundance of Lemdubuoryctes at Liang Lemdubu and Liang Nabulei Lisa, coupled with palynomorph evidence 28 , and its associated open savannah-moist forest vertebrate assemblage 29 , could therefore suggest a preference for heterogenous habitats. This pointedly compliments zoogeographic correlations of the late Pleistocene Aru Islands with mosaic ecotones in northern Australia and the Trans-Fly region of southern New Guinea 28,29 , as well as the reconstructed palaeoenvironments ascribed to other plesiomorphic Pliocene-Pleistocene bandicoots 3,27,55,56 . In stark contrast, early to middle Miocene peramelemorphians are usually considered to have been rainforest specialists, a conclusion based on associated mammalian faunas 57 , and most tellingly, their archaic craniodental morphologies 12,13,[16][17][18] . This key premise underlies the Miocene 'bottleneck' hypothesis, under which environmentally constrained stem taxa were replaced by crown perameloid lineages 9,10,16,[19][20][21]27 that more successfully adjusted to changing climates 4,22,23 and dietary competition with emergent dasyurid marsupial carnivores and rodents migrating from Asia 3,15,[17][18][19] . Conversely, the discovery of Lemdubuoryctes reveals that these phenomena in fact did not prevent the survival of archetypal peramelemorphians through to the terminal Pleistocene-Holocene. In addition, our demonstration of profound antiquity for modern desert-living bandicoot lineages (a result unaffected by alternative constraint parameters  Supplementary Tables S6-S8. or variation in substitution rate 16 : Supplementary Tables S6-S8; Supplementary Figs S21-S30), indicates that increasing aridity during the late Neogene likely did not initiate the genesis of crown Perameloidea, although it probably assisted in perameline intra-clade habitat expansion and localized speciation events. The undeniable rarity of definitive crown perameloid fossils in pre-Pliocene sediments might therefore be explained by sampling biases and/or incompletely documented collections 3,27,58,59 , as well as ecological underrepresentation 60 . Indeed, our tree-based ancestral area optimisations (Supplementary Tables S9-S12; Supplementary Figs S31-S34) infer that the seminal radiation of modern bandicoots accompanied widespread australidelphian niche dispersals into drier mosaic settings, perhaps such as mallee (Eucalyptus) woodlands that spread through Central Australia from the late Oligocene 50,61 . The scarcity of crown bandicoot antecedents in intensively studied fluvial or karstic contexts 54,57,58 with higher preservation potential thus becomes understandable, as does the ecologically disjunct DNA-based phylogeny of living peramelemorphians. This now clearly captures one of the most deeply divergent radiations of xeric-adapted marsupials 1,3,4,[22][23][24]32 , and reinforces a biota-wide exaptive response to late Neogene aridity 62 , including diversification amongst clades that had already maintained substantial habitat disparity for many millions of years.

Methods
Dataset construction. Peramelemorphian morphological phylogenies have suffered from persistently inadequate resolution [12][13][14][15][16][17][18] prompting weighting of dental data via homologous sets 63 and incremental qualitative subdivisions 64 . We therefore compiled a de novo matrix that emphasized partition sampling 65 across 93 cranial-dental and postcranial characters assembled for demonstrable extant outgroup dasyurid/didelphid marsupials 66  The concatenated series of 9977 DNA sequence nucleotides representing five nuclear (ApoB, BRCA1, IRBP, RAG1, vWF) and three mitochondrial genes (12 S rRNA, cytochrome b and the 3′ portion of 16 S rRNA) was used to: (1) produce a backbone tree ( Supplementary Fig. S7) that determined the best-supported position of fossils relative to the living species topology; and (2) compute a combined (non-weighted) total evidence analysis that examined effects of morphological data on molecular nodes. Laboratory procedures, DNA sequence derivation/alignment, and model testing of separate gene/codon regions were described in Westerman et al. 1,68 . Phylogenetic analysis. We implemented a six-stage strategy to manage the detrimental effects of incomplete fossils and characters 69 . (1) Initial selection of operational taxonomic units [OTUs] specifically targeted extant taxa with overlapping coverage of morphological and DNA sampling 70 . Fossil OTUs included only the most complete genus-level exemplars for branching lineages (Bulungu 16 , Galadi 18 , Madju 13 ) as well as those species critical for molecular clock calibrations (Yarala kida, cf. Peroryctes tedfordi, Perameles bowensis) 1,4 or uncontested crown clade referral (Perameles sobbei) 3,38,45 . (2) Excessively incomplete DNA characters were removed in morphology-only analyses to examine the effects of extinct taxa with numerous missing entries 71 . A manual screen for redundant taxa (safe taxonomic reduction 40 ) identified all OTUs that degraded strict consensus resolution and pinpointed instability caused by missing data versus character conflict 72 . (3) The 'amb-' option was implemented during all PAUP* v4.0b10 73 parsimony searches to eliminate ambiguous zero length branches 74 . (4) A posteriori screening of wildcard taxa produced a strict reduced consensus profile based on the semi-strict Adams consensus (where wildcards do not obscure adequately supported nodes 40,41 ) and assessments of relative character support at affected nodes 74 . (5) Bootstrapping and branch (Bremer) decay indices were alternately employed with and without wildcard exclusion to test the impact of mobile OTUs upon support measures. (6) Sequential exclusion of fossils incorporating numerous missing entries for cranial and postcranial characters was used to assess the effects of sub-sampling and long-branch attraction 74 within the total evidence framework 70 .
Parsimony trees and bootstrap frequencies (1000 repetitions) were computed using heuristic searches with TBR (tree-bisection-reconnection) branch swapping and 100 random-addition replicates. The molecular scaffold enforced monophyly for clades receiving ≥ 70% partitioned maximum likelihood bootstrap, and ≥ 0.95 Bayesian posterior probability support. Bremer values were calculated for unconstrained morphological data with TNT v1.1 75 , which also cross-referenced MP topologies via a 'New Technology Search' with sectorial searches, drift, and tree fusing enabled. Results were then processed using a 'Traditional Search' option with TBR. DELTRAN character state optimisation was preferentially employed for tree construction, but unequivocal synapomorphies were shared by both DELTRAN and ACCTRAN outputs (see Supplementary Data).

Molecular clocks.
Time-trees were generated in BEAST2 78 with uncorrelated relaxed lognormal clocks. A Bayesian random local clock model was also used to test for overestimation imposed by punctuated shifts in substitution rate 46 . We used traditional node dating to assess contested 16 ingroup constraints for Peramelemorphia, Chaeropodidae, Thylacomyidae, Peroryctinae + Echymiperinae, Peramelinae and Isoodon + Perameles. Minimum and maximum fossil calibrations (Supplementary Table S5) were compiled according to best practice protocols 79 . Analyses incorporated a birth-death model and normal priors imposed on soft bounds with 95% distribution between the minimum and maximum. MCMC analyses were run for 50 × 10 6 generations with a 25% burn-in for tree summaries. Runs were terminated when ESS values reached > 200 for all estimated parameters.
Ancestral areas. Because the precise topological placement and habitat preferences of fossil peremelemorphians are uncertain, we used a non-ultrametric Bayesian DNA tree sub-sample of extant taxa, and alternative S-DIVA (tree dataset) versus Bayesian Binary MCMC (condensed tree accommodating topological uncertainty) approaches implemented in RASP ver. 3.2 80 to infer ancestral habitat dispersal patterns. Four Markov Chains (default heating values) were run twice over 5 × 10 6 generations with sampling frequency and burn-in fixed at 500. Among-site rate variation was set to 'gamma' and state frequencies utilized a 'fixed (JC)' model. Habitat codings were generalized to accommodate for non-exclusivity, but broadly adhered to defined vegetation units 50