Abstract
Non-recombining regions often have profound effects on genome evolution, resulting in structures such as sex chromosomes and supergenes. Amongst the strangest examples are balanced lethal systems, such as that found in newts of the genus Triturus. These systems halve reproductive output, and the evolution of such a deleterious trait is difficult to explain. For Triturus, an intriguing model proposes that the balanced lethal system evolved from an ancestral Y-chromosome. To test this hypothesis, we identify the Y-chromosome of Triturus and verify whether it, or the balanced lethal system, is homologous to the Y-chromosome of its sister genus Lissotriton, which does not possess the balanced lethal system. We identify a set of candidate Y-linked markers in Triturus ivanbureschi and validate the male specificity of the markers in all major clades of Triturus. We place the Y-linked markers on a high-density linkage map of T. ivanbureschi that we construct with 7,233 RADseq markers. We then place both the Triturus and Lissotriton Y-linked regions within previously constructed target capture linkage maps that include genes linked to the balanced lethal system. We observe that neither the Triturus balanced lethal system, nor the Triturus Y-chromosome are homologous to the Lissotriton Y-chromosome. This is the first molecular evidence of a transition between Y-chromosome systems within salamanders. However, unless additional sex chromosome turnover events are involved, our data does not support a sex chromosome origin of the balanced lethal system.