Non‐Invasive eDNA Reveals the Ecological and Genetic Status of the Western Capercaillie ( Tetrao urogallus aquitanicus ) in the Eastern Pyrenees

ABSTRACT Environmental changes and human activities in the Anthropocene era are likely to alter population size, structure, and genetic diversity of many species. Long‐term monitoring is therefore essential to assess these impacts and enable informed conservation strategies for threatened species. The Western Capercaillie ( Tetrao urogallus , L. 1758) is a mountainous species locally threatened by climate change, habitat fragmentation, and human disturbance. Traditional direct monitoring methods, such as lek counts, can be biased and cause disturbance, while molecular approaches are increasingly used for noninvasive population monitoring. Here, we focus on the eastern population of the subspecies T. u. aquitanicus , endemic to the Pyrenees, for which no molecular data have been generated so far. We conducted a molecular study based on 229 noninvasive samples (feces) to assess the ecological and genetic status of the local population in the Catalan nature reserves of the Pyrénées‐Orientales (Occitanie region, France). At the individual level, we assessed multi‐locus genotypes, sexing, inbreeding, stress level (Fecal Corticosterone Metabolites; FCMs) and diet. At the population level, we assessed sex ratio, genetic diversity and structure. We identified 62 individuals and estimated a population size of 79 individuals [95% CI = 68–92]. Of these, we identified 27 females, 18 males, and 17 individuals that we were unable to assign to a sex. Genetic diversity was low ( H O = 0.279, mean H E = 0.305) and inbreeding coefficient ( G IS = 0.085) was significantly higher than expected under random mating at population level. FCM levels were lower in birds of areas considered as disturbed by humans and metabarcoding revealed a geographic structuring of diet at the local scale, with individuals feeding on only one or a few plant species. Our results demonstrate that molecular, noninvasive approaches provide critical ecological and genetic insights, establishing a baseline to support informed conservation management of this threatened population.