The adaptive radiation of New Zealand’s skinks and geckos is associated with distinct viromes

Background New Zealand is home to over 120 native endemic species of skinks and geckos that have evolved through adaptive radiation over the last 24 million years, likely driven by the exploitation of diverse habitats formed during the Miocene. The recent adaptive radiation of animal hosts may facilitate viral host-switching, likely reflecting their close genetic relationships and therefore relatively low barriers for cross-species virus transmission. Conversely, as animal hosts adapt to new niches, even within specific geographic locations, so too could their viruses. Consequently, animals that have niche-specialised following adaptive radiations may be expected to harbour distinct viruses. Through a metatranscriptomic analysis of eight of New Zealand’s native skink and gecko species, as well as the only introduced lizard species, the rainbow skink ( Lampropholis delicata ), we aimed to reveal the diversity of viruses in these hosts and determine whether and how the adaptive radiation of skinks and geckos in New Zealand has impacted virus diversity and evolution. Results We identified a total of 15 novel reptilian viruses spanning 11 different viral families, across seven of the nine species sampled. Notably, we detected no viral host-switching among the native hosts analysed, even between those sampled from the same geographic location. This is compatible with the idea that host speciation has likely resulted in isolated, niche-constrained viral populations that have prevented cross-species transmission. Using a protein structural similarity-based approach, we further identified a highly divergent bunya-like virus that potentially formed a new family within the Bunyavirales . Conclusions This study has broadened our understanding of reptilian viruses within New Zealand and illustrates how niche adaptation may limit viral-host interactions.