Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia)

Abstract

One way to build larger, more comprehensive phylogenies is to combine the vast amount of phylogenetic information already available. We review the two main strategies for accomplishing this (combining raw data versus combining trees), but employ a relatively new variant of the latter : supertree construction. The utility of one supertree technique, matrix representation using parsimony analysis (MRP), is demonstrated by deriving a complete phylogeny for all 271 extant species of the Carnivora from 177 literature sources. Beyond providing a ' consensus ' estimate of carnivore phylogeny, the tree also indicates taxa for which the relationships remain controversial (e.g. the red panda ; within canids, felids, and hyaenids) or have not been studied in any great detail (e.g. herpestids, viverrids, and intrageneric relationships in the procyonids). Times of divergence throughout the tree were also estimated from 74 literature sources based on both fossil and molecular data. We use the phylogeny to show that some lineages within the Mustelinae and Canidae contain significantly more species than expected for their age, illustrating the tree's utility for studies of macroevolution. It will also provide a useful foundation for comparative and conservational studies involving the carnivores.

Evidence of a false thumb in a fossil carnivore clarifies the evolution of pandas

“…3). This fact agrees with views that postulate an independent family Ailuridae as a basal sister-group of Musteloidea (13)(14)(15)(16)(17). In all known carnivores, other than the pandas and Simocyon, the radial sesamoid retains its primitive state as a small, lens-shaped bone that develops on the tendon of the abductor pollicis longus muscle where it glides over the scapholunar.…”

“…Although most specialists now agree about the ursid affinities of the giant panda (11)(12)(13)(14), the position of the red panda has remained controversial. Molecular and morphological evidence has been interpreted by some to support a sister-group relationship with the Musteloidea (Procyonidae ϩ Mustelidae) as the family Ailuridae (13-17), whereas others include it in the Procyonidae, as the subfamily Ailurinae (18,19).…”

Darwin's abominable mystery: Insights from a supertree of the angiosperms

“…The matrices for all of the trees are then combined, and a tree search is performed on the combined matrix using parsimony (31,32). The best practice for supertree analyses is an active area of research (33), but MRP is widely recognized as one of the best current methods and has been successfully applied in a large number of studies (34)(35)(36).…”

From ‘third pole’ to north pole: a Himalayan origin for the arctic fox

“…Until recently, phylogenetic work on the Tibetan sand fox was unavailable and the only published assessment was based on a numerical classification of phenotypic characteristics, in which V. ferrilata was closest to the corsac fox (steppe fox) [25], as was also reflected, not surprisingly, in a supertree analysis of crown Carnivora [26]. However, a strict consensus of 12 trees by Zrzavý & Ř ičánková [27] from a combined dataset of morphology, cytochrome b and cytochrome c oxidase subunits I and II yielded no resolution (nearly all species of Vulpes fall within a multichotomy).…”