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Open Access Highly Accessed Research article

A glimpse on the pattern of rodent diversification: a phylogenetic approach

Pierre-Henri Fabre12*, Lionel Hautier3, Dimitar Dimitrov1 and Emmanuel J P Douzery2

Author Affiliations

1 Center for Macroecology, Evolution and Climate (CMEC, Department of Biology), Zoological Museum, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark

2 Institut des Sciences de l’Evolution (ISEM, UMR 5554 CNRS-IRD), Université Montpellier II, Place E. Bataillon - CC 064 - 34095 Montpellier Cedex 5, France

3 Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK

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BMC Evolutionary Biology 2012, 12:88  doi:10.1186/1471-2148-12-88

Published: 14 June 2012

Additional files

Additional file 1:

Figure S1. Rodent species level evolutionary tree. Species-level phylogenetic topology based on the highest-likelihood tree inferred from the 11-gene supermatrix, and combined with the taxonomic information of Wilson and Reeder (2005).

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Additional file 2:

Figure S2. Cladogram depicting the highest-likelihood topology for the Ctenohystrica. Circles at nodes represent bootstrap support (circles: black 100-95%, white 95-70%, gray 70-50%). Maximum likekihood tree (lnL=-714749.2). Displayed clade are highlighted using the simplified full ML topology on the left side of the figure. Molecular marker sampling is depicted for each taxa to the right of the tree. Names of the genes are given. Genes sampled for our dataset (Table 2) are marked in black square while missing genes are symbolized by white squares. Triangles indicate significant (P < 0.05) and marginal (0.05 < P < 0.1) shifts in diversification rate (SDR) as inferred by Δ1. LA = Diatomyidae, CT = Ctenodactylidae, TH = Thryonomyidae, PE = Petromuridae, CU = Cuniculidae, DASYPROC = Dasyproctidae, DI = Dinomyidae, CHINCHILLID = Chinchillidae. Bootstrap for all nodes and topology can be found in Additional file 14.

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Additional file 3:

Figure S3. Cladogram depicting the highest-likelihood topology for the Octodontoidea. See Additional file 2: Figure S2 for details of the legend. AB = Abrocomidae, CA = Capromyidae.

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Additional file 4:

Figure S4. Cladogram depicting the highest-likelihood topology for the Sciuroidea. See Additional file 2: Figure S2 for details of the legend. AP = Aplodontidae, RA = Ratufinae, SI = Sciurillinae.

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Additional file 5:

Figure S5. Cladogram depicting the highest-likelihood topology for the Xerinae. See Additional file 2: Figure S2 for details of the legend.

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Additional file 6:

Figure S6. Cladogram depicting the highest-likelihood topology for the Castorimorpha. See Additional file 2: Figure S2 for details of the legend. CAS = Castoridae.

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Additional file 7:

Figure S7. Cladogram depicting the highest-likelihood topology for the mouse-related clade. See Additional file 2: Figure S2 for details of the legend. PED = Pedetidae, ANO = Anomaluroidea, PLA = Platacanthomyidae, Rhy = Rhyzomyidae, Spalac = Spalacidae, CAL = Calomyscidae, LOP = Lophiomyinae.

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Additional file 8:

Figure S8. Cladogram depicting the highest-likelihood topology for Sigmodontinae [part 1] + Tylomyinae. See Additional file 2: Figure S2 for details of the legend. Tyl = Tylomyinae, Ich = Ichthyomyini, Rei = Reithrodontini.

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Additional file 9:

Figure S9. Cladogram depicting the highest-likelihood topology for Sigmodontinae [part 2]. See Additional file 2: Figure S2 for details of the legend. Tyl = Tylomyinae, Ich = Ichthyomyini, Rei = Reithrodontini, Phy = Phyllotini.

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Additional file 10:

Figure S10. Cladogram depicting the highest-likelihood topology for Neotominae. See Additional file 2: Figure S2 for details of the legend. Och = Ochrotomyini, Baiom = Baiomyini.

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Additional file 11:

Figure S11. Cladogram depicting the highest-likelihood topology for Arvicolinae. See Additional file 2: Figure S2 for details of the legend. Pro = Prometheomyini, Dic = Dicrostonychini, Ond = Ondatrini, Plio = Pliomyini, Arv = Arvicolini, Ell = Ellobiusini, Lag = Lagurini.

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Additional file 12:

Figure S12. Cladogram depicting the highest-likelihood topology for Murinae [part 1]. See Additional file 2: Figure S2 for details of the legend. Mic = Micromys division, Cru = Crunomys division, Max = Maxomys division, Mel = Melasmothrix division, Hydrom = Hydromyines division, Con = Conilurines division, Urom = Uromyines division.

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Additional file 13:

Figure S13. Cladogram depicting the highest-likelihood topology for Murinae [part 2]. See Additional file 2: Figure S2 for details of the legend. Mic = Micromys division, Mil = Millardia division, Col = Colomys division, Cre = Cremnomys division, Gol = Golunda, Oen = Oenomys division, Hyb = Hybomys division, Mi = Micaelamys division, Das = Dasymys division, Mal = Malacomys division, Stenocep = Stenocephalemys division.

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Additional file 14:

ML RaxML topology.

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Additional file 15:

Rodentia species list names.

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Additional file 16:

Rodentia accession numbers by gene.

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Additional file 17:

Rodentia accession numbers by taxonomic group (Sheet 1: MYODONTA + ANOMALUROMORPHA; Sheet 2: SCIUROIDEA; Sheet 3: CTENOHYSTRICA; Sheet 4: CASTORIMORPHA).

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Additional file 18:

Loci used in each molecular dating analysis (see Material and Methods).

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