NewtCap: An Efficient Target Capture Approach to Boost Genomic Studies in Salamandridae (True Salamanders and Newts)

Salamanders have large and complex genomes, hampering whole genome sequencing. However, reduced representation sequencing provides a feasible alternative to obtain genome-wide data. We present NewtCap: a sequence capture bait set that targets <i>c</i>. 7 k coding regions across the genomes of all true salamanders and newts (the family Salamandridae, also known as "salamandrids"). We test the efficacy of NewtCap, originally designed for the Eurasian <i>Triturus</i> newts, in 30 species, belonging to 17 different genera that cover all main Salamandridae lineages. We also test NewtCap in two other salamander families. We discover that NewtCap performs well across all Salamandridae lineages (but not in the salamander families Ambystomatidae and Hynobiidae). As expected, the amount of genetic divergence from the genus <i>Triturus</i> correlates negatively to capture efficacy and mapping success. However, this does not impede our downstream analyses. We showcase the potential of NewtCap in the contexts of; (1) phylogenomics, by reconstructing the phylogeny of Salamandridae, (2) phylogeography, by sequencing the four closely related species comprising the genus <i>Taricha</i>, (3) hybrid zone analysis, by genotyping two <i>Lissotriton</i> species and different classes of interspecific hybrids, and (4) conservation genetics, by comparing <i>Triturus ivanbureschi</i> samples from several wild populations and one captive-bred population. Overall, NewtCap has the potential to boost straightforward, reproducible, and affordable genomic studies, tackling both fundamental and applied research questions across salamandrids.