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Figure S1. Hierarchical analysis implemented with STRUCTURE. Seven genetic groups (A–G) were obtained after three rounds of analysis. Each individual (x-axis) is represented by a vertical bar showing the proportion of the individual’s genome that has been assigned to a k (genetic group). Black lines separate individuals from the 17 different sampling localities.

Figure S2. (1) Results from STRUCTURE HARVESTER, showing K = 3 for the first round of analysis including 17 sampling localities along Río Negro and Santa Cruz river basins. (2) Results from STRUCTURE HARVESTER, showing K = 3 for the second round of analysis including six sampling localities of the genetic cluster 1 within Río Negro. (3) Results from STRUCTURE HARVESTER, showing K = 3 for the second round of analysis including seven sampling localities within Santa Cruz River basin.

Table S1. Allelic frequencies per loci and per locality along Río Negro and Santa Cruz River. Pop 1: Villa Regina, Pop 2: Isla Jordan, Pop 3: Río Caleufu, Pop 4: Lago Meliquina, Pop 5: Lago Filo HuaHum, Pop 6: Confluencia Ríos Limay-Traful, Pop 7: Lago Nahuel Huapi, Pop 8: Lago Morenito, Pop 9: Lago Gutierrez, Pop 10: Lago Quillén, Pop 11: Piedra Buena, Pop 12: Condor Cliff (SC), Pop 13: Boca Río Santa Cruz, Pop 14: Lago Argentino, Pop 15: Arroyo Calafate, Pop 16:Lago Roca, Pop 17: Río Cangrejo (Lago Viedma). Bold alleles indicate unique alleles. H-W p indicate p-values for the H-W exact tests are for each locus and population.

Table S2. Paiwise FST between localities in (a) Río Negro basin and (b) Santa Cruz River basin. Localities are denoted by sampling site numbers detailed in Table 1 in order to allow cross-referencing throughout the paper. *Significantly different pairs (P < 0.05, permutation test).

Appendix S1. Paiwise FST between localities in Río Negro basin.

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