Quantifying rarity of intraspecific diversity at multiple spatial scales by combining fine-grain citizen-based data across national boundaries

Quantifying rarity at the intraspecific level is an important task for conservation biologists because rare phenotypes have a higher extinction risk than common ones. However, quantitative assessments of rarity are lacking at this level, preventing to adequately protect rare and endangered variants that are part of the pool of common species. Our aim was to take benefit of high-resolution volunteer-based occurrence data to assess quantitatively rarity patterns of facultative paedomorphosis, in the Alpine newt (Ichthyosaura alpestris). This polyphenism is composed of two morphs, a rare adult phenotype retaining gills and a common phenotype metamorphosing. We included multiple spatial scales (i.e., resolution) and combined 15,613 occurrence records from the atlas databases of the seven countries in the European Alps to understand how spatial scale may affect rarity metrics. Our analyses revealed that the rarer phenotype was 292 times rarer than the common phenotype, occupying a very small and fragmented area of occupancy. Yet, rarity depended on the spatial resolution of the data. Rarity estimates were up to 1,300 times lower at the coarser than at the finer spatial scale. Both the rarity of the rare phenotype and the presence of threats (i.e., fish introductions) make paedomorphs critically endangered whereas the common phenotype was widespread at all spatial scales. Altogether, these results show how rarity metrics can differ between spatial scales for rare and common organisms, suggesting that fine-grain data should be used to assess intraspecific rarity. They also show that combining datasets from distribution atlases is efficient to estimate rarity.