The search of the final MRP supertree matrix from the full analysis recovered 17 most parsimonious trees of length 8150.935 (the tree length is not a whole number because of the downweighting procedure used to account for the presence of nonmonophyletic families in some source trees; see Methods). The strict consensus of the 17 trees is highly resolved, with the only conflict occurring within the hystricognath rodents. The 50% majority rule consensus is illustrated here (Figure ), with those branches that collapse in the strict consensus identified by asterisks. There are no unsupported novel clades (sensu
]). Repeating the analysis with the extinct Nesophontidae and Plesiorycteropodidae deleted from the original source trees has no effect on the higher-level relationships among the extant taxa.
The supertree presented here is highly congruent with most recent estimates of placental phylogeny at both the inter- and intraordinal levels [8
]. However, because the primary goal of our analyses was to investigate ordinal composition and interordinal relationships, we did not include single order source trees in our dataset. As such, the intraordinal relationships presented here are not based on the maximum amount of data available. Although even this amount of data has yielded relationships that are largely congruent with current phylogenetic opinion, we would recommend the use of relevant supertrees (e.g. [26
]) or other similarly comprehensive phylogenies for intraordinal relationships.
Four principal clades, or 'superorders', are present: Afrotheria (rQS = +0.112), Xenarthra (rQS = +0.052), Laurasiatheria (rQS = +0.186) and Euarchontoglires (rQS = -0.085). In upholding the monophyly of these superorders, this supertree supports the hypothesis that plate tectonics have been crucial in the early evolution of modern placentals [40
]. The superorders may have undergone their initial divergences in biogeographical areas that were separate throughout much of the Cretaceous and Cenozoic: Afrotheria in Afro-Arabia, Xenarthra in South America, and both Euarchontoglires and Laurasiatheria in Laurasia [40
]. However, recent studies suggest that a number of fossil 'condylarths' from Laurasia are afrotherian [18
], conflicting with a strict tectonic-based interpretation of placental phylogeny. Regardless, these four superorders indicate that morphological convergence has been more pervasive than previously thought [8
In agreement with most recent phylogenetic analyses of placental mammals, the supertree upholds the monophyly of 16 of the 18 extant orders recognised in Wilson and Reeder [7
]. Although a 'seed tree' that assumes monophyly of all 18 of these orders (including Artiodactyla and Lipotyphla) was included as a source tree (see Methods), the 16 that are monophyletic in the supertree are supported by between 17 (Sirenia) and 156 (Primates) other source trees. Lipotyphla is polyphyletic, with Afrosoricida in Afrotheria and Eulipotyphla (here including the extinct Nesophontidae) in Laurasiatheria, and Artiodactyla is paraphyletic with respect to Cetacea.
The supertree supports Afrotheria as the sister to the remaining superorders, in agreement with most nuclear and nuclear + mitochondrial trees (e.g. [43
]). A recent analysis of retroposon integrations [16
] supported a xenarthran root, congruent with morphological evidence for a split between Xenarthra and all other extant placentals (Epitheria) [46
], although alternatives could not be statistically rejected. Within Afrotheria, the first split is between Paenungulata (rQS = +0.121) and Afroinsectiphilia (rQS = -0.019; here including the extinct Plesiorycteropodidae). Within Paenungulata, Procaviidae (Hyracoidea) and Dugongidae + Trichechidae (Sirenia) are sister taxa (rQS = -0.014), in agreement with some sequence data (e.g. [13
]) and retroposons [47
]. Within Afroinsectiphilia, the supertree recovers both Afrosoricida (rQS = +0.023) and Afroinsectivora (Afrosoricida + Macroscelididae; rQS = -0.029), with Orycteropodidae (Tubulidentata) as the sister to Afroinsectivora; this is again congruent with most sequence data (e.g. [8
]), although chromosome-painting supports monophyly of (Macroscelididae + Orycteropodidae) [48
] and retroposons support monophyly of (Afrosoricida + Orycteropodidae) [47
]. Based on source trees from MacPhee [35
] and Asher et al
], Plesiorycteropodidae is recovered as the sister to Orycteropodidae, indicating that the extinct bibymalagasy is afrotherian, as might be suspected from its known distribution (the Holocene of Madagascar; [35
]) and from features of its astragalus that are shared with a number of extant afrotherians [35
]. Relationships within Xenarthra, the only superorder that is currently also supported by morphology, are congruent with both morphological [49
] and molecular [14
Euarchonta (rQS = +0.058) and Glires (rQS = -0.112) are both monophyletic, together forming the clade Euarchontoglires. The low rQS value for Glires probably reflects the inclusion of source trees that support rodent polyphyly or paraphyly (e.g. [50
]), although morphological [18
] and most recent molecular phylogenies [17
] support rodent monophyly, as recovered here. Tupaiidae (Scandentia) form the sister group to a Cynocephalidae (Dermoptera) + Primates clade. The supertree topology within Euarchontoglires, at both the inter- and intra-ordinal levels, is highly congruent with most recent, mainly molecular evidence [17
Within Laurasiatheria, a monophyletic Eulipotyphla (rQS = +0.018) is the sister to the remaining taxa. This contradicts the hypothesis that Erinaceidae (hedgehogs) are basal placentals, as has been suggested by mitochondrial trees (e.g. [50
]),. A Solenodontidae + Nesophontidae (rQS = -0.001) clade is congruent with biogeographic evidence, as both taxa are known only from the West Indies, but compelling evidence for the true affinities of Nesophontidae is still lacking [36
]; the position advocated for it here is based on only three source trees. A sister-group relationship between Erinaceidae and Soricidae (shrews) to the exclusion of Talpidae (true moles) agrees with most molecular estimates (e.g. [53
]), but is only relatively weakly supported here (rQS = -0.004). Within the remaining taxa, Chiroptera (including a paraphyletic Microchiroptera with respect to Megachiroptera) are the sister group to Fereuungulata (rQS = +0.176). Carnivora and Manidae (Pholidota) together form Ferae (rQS = +0.039), with Cetartiodactyla and Perissodactyla as sister taxa (= Cetungulata; rQS = +0.081). Different molecular data continue to yield incompatible topologies within Fereuungulata (see [44
]); the topology favoured here is arguably more congruent with morphological data because the sister relationship between cetartiodactyls and perissodactyls requires only a single origin of 'ungulate' features within Laurasiatheria. However, a recent transposon analysis [54
] recovered a clade comprising carnivorans, perissodactyls and bats (pholidotans were not sampled, but are also probably members of this group), which has been named Pegasoferae. Artiodactyla is paraphyletic, with Whippomorpha (rQS = +0.139) as the sister to the ruminants, forming Cetruminantia (rQS = +0.127); Suidae + Tayassuidae (pigs + peccaries; rQS = +0.073) and Camelidae (camels) comprise successive sister groups. The cetartiodactylan topology is congruent with both molecular [10
] and combined morphological and molecular [11
Overall, our supertree topology is in much better agreement with the current consensus view of placental phylogeny than is that of LEA. Why? The three main possibilities are (a) that the LEA topology resulted from either poor and/or duplicated data, or assumptions of monophyly, which the Bininda-Emonds et al. [32
] guidelines have largely removed; (b) that other, minor, differences in the technical details of the two studies are responsible, or (c) that phylogenies published after March 1999 (the cut-off point of LEA) are more in agreement with the molecular consensus, and that these studies are now in a majority. Our subsidiary analysis – in effect, repeating the LEA analysis using the Bininda-Emonds et al. [32
] guidelines – can help discriminate between these three possibilities.
The subsidiary analysis found 5535 trees of length 4262.625, using the same 4:1 weighting scheme of LEA (see Methods). A strict consensus is fully resolved at the interordinal level (the only conflicts are within rodents and bats), and there are no novel unsupported clades. Again, although a 'seed tree' that assumes monophyly of the orders recognised by Wilson and Reeder [7
] was included as a source tree (see Methods), those that are monophyletic in the supertree are supported by between six (Sirenia) and 60 (Rodentia) other source trees. Figure is a 50% majority rule consensus, with branches that collapse in the strict consensus indicated by asterisks. The equally weighted analysis (not shown) recovers largely identical unrooted relationships, with neither Artiodactyla nor Lipotyphla recovered as monophyletic.
Artiodactyla is paraphyletic, with Cetacea and Hippopotamidae forming Whippomorpha. Support values (DI = 6; rQS = +0.099) indicate that this clade is relatively well-supported, and are similar to those for Ruminantia (DI = 7; rQS = +0.124). Whippomorpha and Ruminantia are sisters, forming Cetruminantia, which also has reasonable support (DI = 6; rQS = +0.111).
Lipotyphla is polyphyletic, with separate eulipotyphlan (DI = 7, rQS = +0.009) and afrosoricid (DI = 7, rQS = +0.002) clades. Significantly, Afrosoricida is part of a monophyletic Afrotheria (DI = 5, rQS = +0.045), the existence of which was controversial in 1999. Afrotheria was not recovered in the combined supertree of LEA, although it was present in their molecular-only supertree (their Figure ).
The two major changes from the LEA topology – Cetacea nesting within a paraphyletic Artiodactyla, and diphyly of Lipotyphla (both of which were recovered in the LEA molecular-only supertree) – seen in this reanalysis are both in better accord with the state of phylogenetic knowledge in 1999, and are in agreement with our full supertree (Figure ). They indicate that the potential problem of 'time-lag' in supertrees, where inclusion of older studies biases the supertree topology towards outdated views of relationships, is not an inherent limitation of the method.
Notably, the DI support values in this reanalysis are almost always lower, and in many cases greatly so, than their equivalents in the original combined LEA supertree. For example, DI support for the monophyly of the order Chiroptera, drops from 74 to 6, and similarly large drops are seen for Lagomorpha (69 to 5), Perissodactyla (139 to 10) and Rodentia (37 to 3). Some interordinal groupings also show reduced DI values (e.g. Glires, 26 to 5; Ferae, 21 to 7; Paenungulata, 108 to 25.5). These declines probably reflect the exclusion of some duplicate trees and, particularly, the avoidance of a priori assumptions of monophyly. As such, the DI values in this analysis are probably a more accurate indication of the actual support for each group.
Table lists the relative similarity of different topologies as measured by the normalised partition metric [55
] and 'explicitly agree' triplets. It indicates that both the application of the source tree selection protocol of Bininda-Emonds et al. [32
] and the inclusion of more recent source trees are important in explaining the differences between our updated supertree topology and the original LEA supertree. For instance, the 4:1 upweighted supertree from the subsidiary analysis ('LEA+P 4:1') is ~18% more similar to the large molecular tree of Murphy et al. ('MEA'; [17
]) than is the original LEA supertree, according to the normalised partition metric. This effect is attributable solely to the application of the protocol, which was sufficient to bring the LEA dataset in line with the molecular consensus in a number of key areas. The full supertree, however, was ~15% more similar again to the Murphy et al. [17
] tree. It is also only ~9% different from the large molecular and morphological analysis of Gatesy et al. ('GEA'; [11
]). These latter results reflect the inclusion of the more recent source trees published since the study by LEA. The 'explicitly agree' triplet scores confirm these findings.
Normalised partition metric [55,56] and 'explicitly agree' triplet scores of supertrees and supermatrices.