Identification of Y-chromosome turnover in newts fails to support a sex chromosome origin for the Triturus balanced lethal system

Non-recombining regions of the genome often have profound effects on the course of evolution, resulting in phenomena such as sex chromosomes and supergenes. Amongst the strangest examples are naturally occurring balanced lethal systems, which halve reproductive output. The evolution of such a deleterious trait is difficult to explain. European newts of the genus Triturus possess a balanced lethal system derived from the presence of unique non-functional alleles of essential genes within the non-recombining region of heteromorphic chromosome 1. In Triturus newts the genetic basis of sex determination currently unknown but an intriguing model proposes that the Triturus 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 T. ivanbureschi via a sex-associative approach and place them on a high-density linkage map that we construct with 7,233 RADseq markers. We validate male specificity of the markers across the genus, and 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 is homologous to the Lissotriton Y-chromosome. We thus show 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.