Figure S1. Map of Ototylomys phyllotis area of study (yellow points represent sampling localities). Colours indicate phylogenetic major groups (PMG; see results) as follows: green, Yucatan Peninsula (YP); purple, Chiapas–Guatemala Highlands (CGH); blue, Central America Nucleus (CAN). Polygons indicate the phylogeographical groups (samovaG; see Results): Costa Rica (group 1), El Salvador (2), Belize (3), Guatemala highlands (4 and 7), Honduras and Nicaragua (5), El Salvador and Honduras (6), Chiapas highlands and Nicaragua (8), Honduras and Guatemala (9), and all Yucatan, Campeche and Tabasco haplotypes, together with two from northern Belize and Guatemala (10). Dotted lines indicate plausible barriers.


Figure S2. Mismatch distribution results estimated for expected frequencies under a sudden expansion model for samovaG groups: (a) group 5, (b) 8, (c) 9, (d) 10, and phylogenetic major groups: (e) Central America Nucleus, (f) Chiapas–Guatemala Highlands, and (g) Yucatan Peninsula.


Table S1. List of Ototylomys phyllotis individuals used in this study. Catalog number in the first column corresponds to the sample ID in the last column. GenBank accession numbers are indicated in the table and in the text.


Table S2. Net nucleotide divergence (Da ± SD; above diagonal) and p-uncorrected distance (below diagonal) between O. phyllotis phylogeographical groups (samovaG; see Table 2). Bold numbers and gray shading indicate highest and lowest divergence values, respectively.


Table S3. Inference of the phylogeographic structure obtained with the Nested Clade Phylogenetic Analysis and following the latest inference key (January 2011; for interpretation of evolutionary processes.

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