Authors: Skrbinsek, Tomaz; Boyer, Frederic;Fumagalli, Luca;Iosif, Ruben;Jelenčič, Maja;Konec, Marjeta;Pazhenkova, Elena;Promberger, Barbara;Taberlet, Pierre;De Barba, Marta;

For many wildlife species, noninvasive genetic sampling is the backbone of abundance and distribution monitoring and is being increasingly included into routine monitoring programs. In most cases the markers of choice are microsatellites, which are in many aspects ideal for the purpose, but the way they’re commonly analyzed is labor-intensive and subjective, making large studies and collaboration between laboratories difficult. An alternative using high-throughput sequencing has been recently proposed, and we applied it to several large studies of brown bears, analyzing 7916 noninvasive and 1971 tissue samples. The method proved to be efficient and cost effective, providing fast and reliable genotyping with low manual labor, making it easily scalable to large studies. Since genotypes are based on DNA sequences, they can be readily transferred between laboratories and will be independent from the DNA sequencing technology used in the future, fostering collaboration and longitudinal studies. Besides providing a thorough real-world test, we have optimized the procedure for application of the method to other species and developed protocols for grey wolf and Eurasian lynx. The method has a great potential not only for ecological research, but also for routine wildlife monitoring programs that require rapid, cost-effective genotyping of large numbers of samples.