DOI: 10.5061/dryad.9s4mw6mpc
title: Data from: Genetic structure and climate niche differentiation among populations of Leopardus geoffroyi

description: 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 PID and therefore we discarded it from
 the analyses. Geographic origin of samples is provided as geographic
 coordinates (DATUM: GRS80).
description: 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. <em>Biological Journal of
 the Linnean Society</em>, <em>129</em>(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
 (NH<sub>4</sub>)<sub>2</sub>SO<sub>4</sub>, 0.1% (v/v) Tween 20); 2.5-3.75mM of MgCl<sub>2</sub>; 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.
description: # Data from: Genetic structure and climate niche differentiation among
 populations of Leopardus geoffroyi
 [https://doi.org/10.5061/dryad.9s4mw6mpc](https://doi.org/10.5061/dryad.9s4mw6mpc) Genotypes and geographic coordinates for 135 *Leopardus geoffroyi* samples, used in the manuscript ECE-2023-11-02018 submitted to BMC Ecology and Evolution. ## Description of the data and file structure Data is presented as an .xlsx file containing the following columns: ID: sample identification code. FCA742_1: allele 1 for microsatellite FCA742. FCA742_2: allele 2 for microsatellite FCA742. FCA391_1: allele 1 for microsatellite FCA391. FCA391_2: allele 2 for microsatellite FCA391. F53_1: allele 1 for microsatellite F53. F53_2: allele 2 for microsatellite F53. FCA723_1: allele 1 for microsatellite FCA723. FCA723_2: allele 2 for microsatellite FCA723. F146_1: allele 1 for microsatellite F146. F146_2: allele 2 for microsatellite F146. F42_1: allele 1 for microsatellite F42. F42_2: allele 2 for microsatellite F42. FCA424_1: allele 1 for microsatellite FCA424. FCA424_2: allele 2 for microsatellite FCA424. FCA453_1: allele 1 for microsatellite FCA453. FCA453_2: allele 2 for microsatellite FCA453. F124_1: allele 1 for microsatellite F124. F124_2: allele 2 for microsatellite F124. F98_1: allele 1 for microsatellite F98. F98_2: allele 2 for microsatellite F98. FCA441_1: allele 1 for microsatellite FCA441. FCA441_2: allele 2 for microsatellite FCA441. Lat: Latitude in degrees. Long: Longitude in degrees. Group: We divided samples into two groups, “historical” (period 1928−1990) and “contemporary” (period 1991−2015).