Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades - PubMed (original) (raw)

Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades

Shani Blanga-Kanfi et al. BMC Evol Biol. 2009.

Abstract

Background: Rodentia is the most diverse order of placental mammals, with extant rodent species representing about half of all placental diversity. In spite of many morphological and molecular studies, the family-level relationships among rodents and the location of the rodent root are still debated. Although various datasets have already been analyzed to solve rodent phylogeny at the family level, these are difficult to combine because they involve different taxa and genes.

Results: We present here the largest protein-coding dataset used to study rodent relationships. It comprises six nuclear genes, 41 rodent species, and eight outgroups. Our phylogenetic reconstructions strongly support the division of Rodentia into three clades: (1) a "squirrel-related clade", (2) a "mouse-related clade", and (3) Ctenohystrica. Almost all evolutionary relationships within these clades are also highly supported. The primary remaining uncertainty is the position of the root. The application of various models and techniques aimed to remove non-phylogenetic signal was unable to solve the basal rodent trifurcation.

Conclusion: Sequencing and analyzing a large sequence dataset enabled us to resolve most of the evolutionary relationships among Rodentia. Our findings suggest that the uncertainty regarding the position of the rodent root reflects the rapid rodent radiation that occurred in the Paleocene rather than the presence of conflicting phylogenetic and non-phylogenetic signals in the dataset.

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Figures

Figure 1

Figure 1

ML tree (-ln likelihood = 85,018.88) obtained for the concatenated dataset under the GTR+Γ+I model of sequence evolution. For each node the ML bootstrap percentage (BP) and the Bayesian posterior probabilities (PP) are given at the right and left of the slash, respectively. Branches with maximal support value (i.e., BP = 100, PP = 1.0) are indicated by black dots.

Figure 2

Figure 2

Bootstrap support as a function of the maximum evolutionary rate of site retained in the data. S: the best topology with the squirrel-related clade at the base of the rodent tree; M: the best topology with the mouse-related clade at the base of the rodent tree; C: the best topology with Ctenohystrica at the base of the rodent tree. Nine datasets were considered: (1) all sites (6,255 base pairs (bps); rates range from -0.698 to 3.989); (2) sites with rate ≤ 3.5 (6,114 bps); (3) sites with rate ≤ 3.0 (6,058 bps); (4) sites with rate ≤ 2.5 (5,997 bps); (5) sites with rate ≤ 2.0 (5,896 bps); (6) sites with rate ≤ 1.5 (5,759 bps); (7) sites with rate ≤ 1 (5,444 bps); (8) sites with rate ≤ 0.5 (4,997 bps); and (9) sites with rate ≤ 0.0 (4,179 bps).

Figure 3

Figure 3

Bootstrap support as a function of the minimum CI of sites retained in the data. S: the best topology with the squirrel-related clade at the base of the rodent tree; M: the best topology with the mouse-related clade at the base of the rodent tree; C: the best topology with Ctenohystrica at the base of the rodent tree. Seven datasets were considered: (1) all sites (6,255 bps; CI range 0.0625–1); (2) sites with CI > 0.1 (6,210 bps); (3) sites with CI > 0.2 (5,864 bps); (4) sites with CI > 0.3 (5,432 bps); (5) sites with CI > 0.4 (4,833 bps); (6) sites with CI > 0.5 (4,119 bps); and (7) sites with CI > 0.6 (4,023 bps).

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