Sex chromosomes in vertebrates range from highly heteromorphic (as in most birds and mammals) to strictly homomorphic (as in many fishes, amphibians, and non-avian reptiles). Reasons for these contrasted evolutionary trajectories remain unclear, but species such as common frogs with polymorphism in the extent of sex-chromosome differentiation may potentially deliver important clues. By investigating 92 common-frog populations from a wide range of elevations throughout Switzerland, we show that sex-chromosome differentiation strongly correlates with alleles at the candidate sex-determining gene Dmrt1. Y-specific Dmrt1 haplotypes cluster into two main haplogroups, Y_A and Y_B, with a phylogeographic signal that parallels mtDNA haplotypes: Y_A populations, with mostly well-differentiated sex chromosomes, occur primarily south of the main alpine ridge that bisects Switzerland, while Y_B populations, with mostly undifferentiated (proto-)sex chromosomes, occur north of this ridge. Elevation has only a marginal effect, opposing previous suggestions of a major role for climate on sex-chromosome differentiation. The Y-haplotype effect might result from differences in the penetrance of alleles at the sex-determining locus (such that sex reversal and ensuing X-Y recombination are more frequent in Y_B populations), and/or fixation of an inversion on Y_A (as supported by the empirical observation that Y_A haplotypes might not recombine in XY_A females).

Adult frogs (Rana temporaria) were phenotypically sexed and DNA was collected from buccal swabs. Juvenile samples were collected as eggs, hatched in the lab, and euthanized for DNA extraction. Genetic data is from 3 panels of microsatellites on Chr01, inside and outside the candidate sex-determining gene (Dmrt1). Alleles were called in GeneMapper 4.0 (Fisher Scientific), and Y haplotypes (Dmrt) were defined by comparing sexed adult samples. Differentiated vs. undifferentiated chromosomes were called via a threshold of Y-like alleles across Chr01 (outside Dmrt), in individuals with a Dmrt-Y genotype. 

Missing and null alleles are coded as 0. Other missing data is coded as NA. In the column 'Genotype', XYA0 and XYB0 indicate undifferentiated (by the threshold method) Y chromosomes with the corresponding Dmrt-Y haplotype; XYA and XYB indicate differentiated Y chromosomes with the corresponding Dmrt-Y haplotype; XX indicates no Dmrt-Y haplotype is present.