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Electronic supplementary material: figures 1, 2 and 3.

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1 Electronic supplementary material: figures 1, 2 and 3

2 ESM Figure 1. Schematics of a jawbone of Ototylomys from the Loltún cave used in this study. The red shaded area, which includes all three molars and mandible bone, corresponds to the fragment used for DNA extraction. Length of molars Alveolar length of molars Mandibular foramen Tooth length Diastema distance Tooth depth

3 Outgroups 0.2 Loltún cave Ototylomys phyllotis AH4 AH1 AH2 AH3 AH5 AH6 ESM Figure 2. Maximum likelihood tree for ancient and modern sequences from Ototylomys phyllotis obtained with PhyML v3.1. AH are haplotypes from Loltún and H are Ototylomys phyllotis haplotypes from the study of Gutiérrez-García & Vázquez-Domínguez (2012). H74 H61 H63 H71 H69 H42 H66 H67 H65 H77 H76 H73 H75 H72 H89 H90 H87 H84 H85 H83 H82 H78 H79 H81 H80 H59 H60 H58 H54 H55 H52 H53 H56 H57 H51 H50 H49 H41 H42 H44 H45 H40 H47 H46 H31 H32 H34 H35 H36 H33 H37 H38 H39 H28 H29 H30 H26 H27 H18 H17 H15 H16 H14 H11 H12 H13 H9 H10 H19 H8 H6 H5 H3 H2 H24 H25 H4 H23 H22 H20 H21 H1

4 Population size (Ne) Time before present (million years ago) ESM Figure 3. Demographic results for the ancient sequences from the Loltún cave (Loltún clade), estimated by Bayesian skyline plot analysis.

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