Genomic insights into the Montseny brook newt, a Critically Endangered glacial relict

The Montseny brook newt (Calotriton arnoldi) is an amphibian species endemic to a few isolated creeks within a small massif located in northeastern Spain. Such a tiny range, coupled with small population sizes, the outbreak of lethal emergent diseases, rampant aquifer overdraft, and the threat of global warming, make this relict salamandrid the most endangered amphibian in Europe. Although conservation efforts should always be guided by genomic studies, those are yet scarce among urodeles, hampered by the extreme sizes of their genomes. Here we present the third available genome assembly for the order Caudata, and the first genomic study of the species and its sister taxon, the Pyrenean brook newt (C. asper), based on 22 whole-genome and 132 ddRADseq samples. Our results reveal significant demographic oscillations which accurately mirrored Europe's climatic history, from the end of the Last Glacial Period to local and minor events such as the Little Ice Age. Although severe bottlenecks have led to depauperate genomic diversities and long Runs of Homozygosity along a gigantic genome, inbreeding might have been avoided by assortative mating strategies. Other life history traits, however, seem to have been less advantageous, and the lack of land dispersal has driven to exceptional levels of fragmentation, evidenced across main watersheds, but also at a finer scale through small waterfalls and modern roads.