Table S1. Ocelots sampled in the US and Mexico that were used for population structure analysis in this study. Ten additional ocelots were genotyped for Y microsatellites but were excluded from this table because they were not used to asses autosomal and mtDNA diversity.

Table S2. The chromosomal position of 41 autosomal microsatellites in the domestic cat genetic linkage and radiation hybrid maps that were screened in ocelots (NCBI Map Viewer Build 0.1, Menotti-Raymond et al., 2003a,b; 2009; Davis et al., 2009). Microsatellites in bold were selected for population structure analysis. PCR results (res.) are coded as; +=robust amplification, -=no amplification, and M.A.=multiple amplicons of different size. PCR conditions (cond.) refer to whether the primers were fluorescently labeled directly on the 5′ end (1) or using a dye-labeled m13 tag (2).

Table S3. Genetic diversity among 25 autosomal microsatellites in three ocelot populations sampled from 1991–2005. Abbreviations: Ca = Cameron County, Texas; Wi = Willacy County, Texas; Mx = Mexico; HO = observed heterozygosity, HE = expected heterozygosity; AN = effective alleles.

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