Dataset containing information for Geoffroy's cat (Leopardus geoffroyi) samples from Argentina, Uruguay, Brazil and Bolivia, genotyped for 11 microsatellites markers. Markers FCA441 and F124 showed evidence of linkage, but the former had higher P_ID and therefore we discarded it from the analyses. Geographic origin of samples is provided as geographic coordinates (DATUM: GRS80).

Samples consisted of preserved tissues obtained from museum specimens, fresh muscle and blood samples collected from road-killed and captured wild individuals, respectively, and feces collected in the field. Collection dates ranged from 1928 to 2015, and we divided samples into two groups: “historical” (period 1928−1990) and “contemporary” (period 1991−2015). The year 1990 was used as the limit to separate samples before and after export ban on native cats in Argentina.

We extracted DNA following Gómez Fernández, M. J., Fameli, A., Rojo Gómez, J., Pereira, J. A., & Mirol, P. (2020). Phylogeographical spatial diffusion analysis reveals the journey of Geoffroy’s cat through the Quaternary glaciations of South America. Biological Journal of the Linnean Society, 129(3), 603-617.

We used a panel of eleven microsatellite loci (F42, F53, F98, F124, F146, FCA391, FCA424, FCA441, FCA453, FCA723, FCA742) developed for domestic cats. PCR amplifications were performed individually using the M13-tailed primer method to label amplicons with 5′-fluorescent tags (6-FAM, HEX or NED). Each microsatellite amplification reaction included negative controls, they were carried out on a 12μl reactions mix containing 1.8-2.2μl of DNA; 1X Taq buffer; (750mm Tris-HCl, 200mM (NH₄)₂SO₄, 0.1% (v/v) Tween 20); 2.5-3.75mM of MgCl₂; 0.08mM of each dNTP; 0.24 pmoles of M13-tailed forward primer; 4 pmoles of reverse primer, 6 pmoles of M13-fluorescent primer; 0.2mg/ml of BSA and 0.6U of Taq DNA polymerase (Fermentas). Thermocycling conditions were as follow: 94ºC for 5 min; 10 cycles (touchdown) of 94ºC for 40 s, 60-51ºC for 40 s, 72ºC for 60 s; 15 cycles of 94ºC for 40 s,  (i) 53.4ºC (F42, F124, F146, FCA391, FCA441, FCA723, FCA742), (ii) 52.5°C (F53, FCA453), (iii) 51.7°C (FCA424) or (iv) 50°C  (F98) for 40 s, 72ºC for 60 s; 10 cycles of 94ºC for 40 s, 48ºC for 30 s, 72ºC for 40 s and a final extension at 72ºC for 5 min. We arranged PCR products in two multiplexes according to allele size and fluorescent dye.

We used a MegaBACE 1000 automated sequencer (GE Healthcare) and an automated sequencer ABI3100 (Macrogen Inc., Korea) to perform fragment analysis, in conjunction with MEGABACE FRAGMENT PROFILER 1.2 software (Amersham Biosciences) and Geneious v.6.0. Two researchers analyzed fragments independently and in case of differences in allele calling, a consensus was reached by repeating amplification.

For fecal and museum samples, we built a consensus genotype based on the results of independent PCRs: a heterozygous genotype was assigned when supported by at least two PCRs yielding the same result, whereas a homozygous genotype was assigned after obtaining the same result in three PCRs. We performed downstream analyses including only samples successfully genotyped for at least seven out of 11 markers.