\articletype Original Articles Non-invasive genetic sampling is particularly useful for the genetic monitoring of rare, protected, or elusive species that require accurate evaluation of their conservation status. However, non-invasive samples often contain degraded DNA, leading to important data losses and high genotyping error rates. These samples have already been validated as a suitable source of DNA for genetic studies on a very discreet species, the rock ptarmigan (Lagopus muta). But, there is currently no specific protocol for producing high-quality data with minimal losses and errors for this species. Thus, this study aimed to improve non-invasive sampling and laboratory protocols for genetic monitoring of mountain Galliformes populations. To this end, we collected 338 fecal samples over two years in the French Alps and analyzed the impact of sample freshness and weather conditions on genotyping success and genotyping error rates for 19 microsatellites. Our study shows that the use of non-invasive samples can be optimized from the field phase onwards. We highlight the importance of collecting well-preserved and fresh fecal samples, preferably on days without rain and on snow-covered ground. We then demonstrated that laboratory procedures could also be optimized for fecal samples containing uric acid, in particular by using a well-adapted extraction protocol. In addition, the panel of microsatellite markers can be reduced to the 14 best quality markers in order to obtain higher quality final data without loss of information. This study provides a series of recommendations aimed at improving genotyping success and ensuring the quality of results, while reducing costs. We aim to encourage genetic studies using non-invasive samples for monitoring rock ptarmigan or mountain Galliformes species, and are confident that following these procedures will facilitate the transition to genomic monitoring.

Non-invasive genetic sampling is particularly useful for the genetic monitoring of rare, protected, or elusive species that require accurate evaluation of their conservation status. However, non-invasive samples often contain degraded DNA, leading to important data losses and high genotyping error rates. These samples have already been validated as a suitable source of DNA for genetic studies on a very discreet species, the rock ptarmigan (Lagopus muta). But, there is currently no specific protocol for producing high-quality data with minimal losses and errors for this species. Thus, this study aimed to improve non-invasive sampling and laboratory protocols for genetic monitoring of mountain Galliformes populations. To this end, we collected 338 fecal samples over two years in the French Alps and analyzed the impact of sample freshness and weather conditions on genotyping success and genotyping error rates for 19 microsatellites. Our study shows that the use of non-invasive samples can be optimized from the field phase onwards. We highlight the importance of collecting well-preserved and fresh fecal samples, preferably on days without rain and on snow-covered ground. We then demonstrated that laboratory procedures could also be optimized for fecal samples containing uric acid, in particular by using a well-adapted extraction protocol. In addition, the panel of microsatellite markers can be reduced to the 14 best quality markers in order to obtain higher quality final data without loss of information. This study provides a series of recommendations aimed at improving genotyping success and ensuring the quality of results, while reducing costs. We aim to encourage genetic studies using non-invasive samples for monitoring rock ptarmigan or mountain Galliformes species, and are confident that following these procedures will facilitate the transition to genomic monitoring.