Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

Abstract

BackgroundAlthough it has proven to be an important foundation for investigations of carnivoran ecology, biology and evolution, the complete species-level supertree for Carnivora of Bininda-Emonds et al. is showing its age. Additional, largely molecular sequence data are now available for many species and the advancement of computer technology means that many of the limitations of the original analysis can now be avoided. We therefore sought to provide an updated estimate of the phylogenetic relationships within all extant Carnivora, again using supertree analysis to be able to analyze as much of the global phylogenetic database for the group as possible.ResultsIn total, 188 source trees were combined, representing 114 trees from the literature together with 74 newly constructed gene trees derived from nearly 45,000 bp of sequence data from GenBank. The greater availability of sequence data means that the new supertree is almost completely resolved and also better reflects current phylogenetic opinion (for example, supporting a monophyletic Mephitidae, Eupleridae and Prionodontidae; placing Nandinia binotata as sister to the remaining Feliformia). Following an initial rapid radiation, diversification rate analyses indicate a downturn in the net speciation rate within the past three million years as well as a possible increase some 18.0 million years ago; numerous diversification rate shifts within the order were also identified.ConclusionsTogether, the two carnivore supertrees remain the only complete phylogenetic estimates for all extant species and the new supertree, like the old one, will form a key tool in helping us to further understand the biology of this charismatic group of carnivores.

A dynamic global equilibrium in carnivoran diversification over 20 million years

“…For example, more than 50 species in the extinct family Amphicyonidae are known between 22 and 2 Ma [44]. These extinct species cannot be included in the supertree analysis, which estimated rates of cladogenic events leading up to the extant subset of carnivorans [36]. By constrast, our estimates of diversification, [36] are reflective of the diversity dynamics for the extant carnivorans, then the modern lineages experienced a substantial increase in branching rates during a period when total carnivoran diversification was rather nondescript (figure 1).…”

“…A recent study of the entire Carnivora employing a supertree [36] reconstructed a sustained increase in diversification rates for Carnivora beginning at approximately 18 Ma, peaking at about 7.3 Ma and subsequently declining through the Late Miocene and Pliocene. However, excluding extinct taxa may hinder accurate reconstructions of diversification [3,42,43].…”

“…We augmented these data using compilations in Finarelli [25] and Démére et al [35], and added occurrences in the interval (1,0] Ma for extant species with at least one fossil occurrence [36]. We analysed data for 24 one-million-year time intervals and present results for 20 intervals (see the electronic supplementary material), between 22-21 Ma (our notation here signifies the time interval from 22 Ma to 21 Ma inclusive, and the same principle applies to notation throughout) and 3-2 Ma, coinciding approximately with the extent of the Miocene and Pliocene [37].…”

Habitat changes and changing predatory habits in North American fossil canids

“…We incorporated branch lengths in our composite phylogeny in million years before present 43,44 . In the case of living species, branches were scaled according to node dates estimates based on Nyakatura and Bininda-Emonds 45 . In the case of extinct taxa, fossil occurrence dates were compiled from various sources based on species locality and age information (Table 2), and the branch lengths were estimated from the first and last appearance of taxa (Supplementary Fig.…”

Musteloid carnivores from the upper Miocene of South-Western Bulgaria, and the phylogeny of the Mephitidae

“…Members of the Mephitidae, consisting today of the American skunks (Mephitis Geoffroy Saint-Hilaire and Cuvier, 1795, Spilogale Gray, 1865, and Conepatus Gray, 1837) and southAsian stink badgers (Mydaus Cuvier, 1821), were previously included in the Mustelidae but are now united in a family of their own, which is not more closely related to the Mustelidae than to some other Musteloidea (Dragoo and Honeycutt 1997;Finarelli 2008;Eizirik et al 2010;Nyakatura and Bininda-Emonds 2012;Catalano et al 2015). Their best-known osteologic feature is the lateral expansion of the epitympanic recess into the petrosal and squamosal, forming a large sinus that inflates the ventral part of the lateral side of the braincase, if not its ventral side.…”