Carnivora (lions, tigers and bears, among others) represent a medium-sized order within Mammalia. It is noteworthy for the charismatic appeal of many of its members as well as the large diversity harbored within it. With its inclusion of both terrestrial and aquatic species, Carnivora is one of few mammalian orders to occur naturally on all the continents. It also presents one of the largest size ranges of any mammalian order among its extant representatives at some five to six orders of magnitude between the Least Weasel (Mustela nivalis, 35 to 250 g) and the Southern Elephant Seal (Mirounga leonina, 2200 to 5000 kg).
With its publication, the carnivore supertree of Bininda-Emonds et al
] provided the first complete species-level phylogeny of this diverse mammalian order that was based on a robust, repeatable methodology. In the intervening 10 years, the carnivore supertree has formed the basis for numerous studies illuminating the biology of this group, including its macroevolution and conservation biology (for example, [2
]); morphological, molecular and behavioral evolution (for example, [5
]); and disease and parasite risk (for example, [9
]). Although the method used to construct the tree, supertree construction (sensu
]), was controversial at the time and arguably remains so to this day, the same cannot be said for the phylogenetic relationships presented in the supertree, which largely mirrored the current opinion of the day accurately (for example, compare with [12
]). That being said, the pattern of relationships pictured in the carnivore supertree are now out-of-date in several places due to three main factors: taxonomic changes within Carnivora leading to a different set of accepted species; information from additional data sources, primarily DNA sequence data; and methodological limitations in the original analysis.
The original carnivore supertree was based on the 273 species recognized by Wozencraft [13
]. In the meantime, however, the number of recognized species has increased to at least 286 [14
], in part due to new discoveries, but largely due to changes in taxonomic opinion resulting in both the splitting and lumping together of previous species (but with more of the former).
At the time that data collection for the initial carnivore supertree was concluded (January 1996), the molecular revolution was still in its infancy. The amount of DNA sequence data for the group available in GenBank amounted to only 677 sequences for 48 species [15
]. By March 2004, the data set had increased to 1,984,623 sequences for 197 species [15
] and by December 2007 it had increased further to cover a total 248 species. (The number of sequences becomes difficult to compare because of the fusion of accessions by the National Center for Biotechnology Information. For instance, > 99% of the nearly two million sequences from 2004 derive from the domestic dog genome project and are now superseded by the genome sequences for that species.) Although molecular data have largely reaffirmed phylogenetic relationships within Carnivora obtained using phenotypic data, they have also toppled some long-held traditional groupings and sets of relationships. Particularly noteworthy changes include Mephitidae being elevated out of Mustelidae [16
forming the sister group to all remaining feliform carnivores [18
being more closely related to Felidae than to Viverridae [19
]; and the monophyly of the Malagasy Viverridae and Herpestidae as Eupleridae [20
]. Of these now widely accepted hypotheses, robust evidence was only available for the first two in 1996 (for example, [16
]), and only starting to gain acceptance among carnivore systematists.
Finally, the analyses for the carnivore supertree were also hindered by several methodological limitations. First, a number of assumptions of monophyly were made, in part for computational reasons. Because an analysis of 273 species simultaneously was impractical at the time, a compartmentalized approach (sensu
]) was taken instead, such that the supertree was a composite formed from a family-level supertree to which individual supertrees for each of the families (and Lutrinae and Mephitinae within Mustelidae) were grafted. Thus, the monophyly of these groups could not be contradicted, even if some evidence to the contrary existed at the time (for example, as for Nandinia
with respect to Viverridae). In addition, where a source tree contained a higher-level taxon as a terminal taxon, the tree was coded as if all constituent species of that taxon were present as an unresolved node. Although this assumption of monophyly could still be contradicted, the monophyly of the higher-level taxon was nonetheless artificially up-weighted through this procedure. Both sets of assumptions now represent avoidable 'appeals to authority' (sensu
]). Second, as correctly pointed out by Gatesy et al
], there was no attempt to correct for potential data duplication between the source trees, meaning that more commonly used data sources were effectively up-weighted. Finally, the paucity of available sequence data meant that the molecular divergence time estimates were derived by mapping relative branch lengths from the source publications on to the topology of the supertree, even when the two topologies conflicted. Although these shortcomings are real, they fortunately appear to have had little negative impact empirically; as mentioned, both the topology of the tree as well as the estimated divergence time estimates were uncontroversial.
The goal of this study is to produce an updated version of the carnivore supertree that accounts for both current taxonomic opinion and additional data sources (primarily DNA sequence data, but also additional phenotypic data) as well as corrects for the shortcomings present in the original analysis by using the best available methodology and analytical methods. As with the original analysis, supertree construction still represents the only robust methodology able to include as much of the phylogenetic database as possible so as to provide a complete phylogenetic estimate for all extant Carnivora species. We are confident that the updated carnivore supertree will form an important foundation for understanding the biology of this order for some time to come.