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. 2012 Feb 27:10:12.
doi: 10.1186/1741-7007-10-12.

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

Katrin Nyakatura  1 , Olaf R P Bininda-Emonds
Affiliations

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

Katrin Nyakatura et al. BMC Biol. .

Abstract

Background: Although 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.

Results: In 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.

Conclusions: Together, 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.

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Figures

Figure 1
Figure 1
The complete carnivore supertree showing the best estimates of the divergence times. The major carnivore lineages counterclockwise from the top left are Canidae (red), Pinnipedia (pink), Mephitidae (orange), Procyonidae (yellow), Mustelidae (light green), Ailuridae (black), Ursidae (dark green), Nandiniidae (black), Hyaenidae (light blue), Eupleridae (dark blue), Herpestidae (light purple), Viverridae (dark purple), Prionodontidae (grey) and Felidae (brown); outgroup taxa have been omitted (see Figure 2). Time intervals are in units of 5 Ma.
Figure 2
Figure 2
Phylogenetic relationships and divergence-time estimates among the major carnivore lineages and within the smaller families. Nodes are individually numbered, with node bars indicating 95% confidence intervals on the divergence time estimates (in Ma before present).
Figure 3
Figure 3
Phylogenetic relationships and divergence times estimates within Canidae. Nodes are individually numbered, with node bars indicating 95% confidence intervals on the divergence time estimates (in Ma before present).
Figure 4
Figure 4
Phylogenetic relationships and divergence times estimates within Pinnipedia (Odobenidae, Otariidae, and Phocidae). Nodes are individually numbered, with node bars indicating 95% confidence intervals on the divergence time estimates (in Ma before present).
Figure 5
Figure 5
Phylogenetic relationships and divergence times estimates within Mephitidae. Nodes are individually numbered, with node bars indicating 95% confidence intervals on the divergence time estimates (in Ma before present).
Figure 6
Figure 6
Phylogenetic relationships and divergence times estimates within Procyonidae. Nodes are individually numbered, with node bars indicating 95% confidence intervals on the divergence time estimates (in Ma before present).
Figure 7
Figure 7
Phylogenetic relationships and divergence times estimates within Mustelidae. Nodes are individually numbered, with node bars indicating 95% confidence intervals on the divergence time estimates (in Ma before present).
Figure 8
Figure 8
Phylogenetic relationships and divergence times estimates within Eupleridae and Herpestidae. Nodes are individually numbered, with node bars indicating 95% confidence intervals on the divergence time estimates (in Ma before present).
Figure 9
Figure 9
Phylogenetic relationships and divergence times estimates within Viverridae. Nodes are individually numbered, with node bars indicating 95% confidence intervals on the divergence time estimates (in Ma before present).
Figure 10
Figure 10
Phylogenetic relationships and divergence times estimates within Felidae. Nodes are individually numbered, with node bars indicating 95% confidence intervals on the divergence time estimates (in Ma before present).
Figure 11
Figure 11
Phylogenetic relationships among Carnivora as inferred from a partitioned maximum likelihood supermatrix analysis. The tree includes all 229 carnivore species for which molecular sequence data from the 74 gene data sets were available from GenBank. Taxon names have been omitted for clarity and the orientation of the tree parallels that in Figure 2 as far as possible. Green branches indicate clades also occurring on the full matrix representation parsimony supertree, whereas red branches indicate conflicting clades; branch lengths do not reflect divergence times or amount of sequence divergence. Most of the conflict between the two trees derives from three unusual results from the supermatrix analysis: 1) a paraphyletic Vulpes nesting within Canini within Canidae, 2) a paraphyletic Mephitidae and Ailurus fulgens nesting within Procyonidae, and 3) a placement of Eira barbara away from Gulo + Martes and within Lutrinae.
Figure 12
Figure 12
Lineages-through-time plots for the carnivores (a) as a whole and (b) for the individual families. In (a), the thick black line indicates the number of lineages through time according to the best divergence time estimates, with the grey area indicating the numbers according to the upper and lower 95% confidence intervals on these dates; the red lines present the slopes for the three different time segments indicated by goodness-of-fit tests. In (b), only the plots according to the best divergence time estimates are presented.
Figure 13
Figure 13
Net diversification rates through time across all carnivores. Rates were localized to bins of 0.25 Ma (stepped line) or modeled as a function of time using generalized additive models (solid curve with 95% confidence intervals presented as dashed curves).
See this image and copyright information in PMC

Comment in

  • Do we still need supertrees?
    von Haeseler A. von Haeseler A. BMC Biol. 2012 Feb 27;10:13. doi: 10.1186/1741-7007-10-13. BMC Biol. 2012. PMID: 22369571 Free PMC article.

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