Noninvasive sampling and genetic variability, pack structure, and dynamics in an expanding wolf population

Abstract

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Experimental evaluation of genetic predator identification from saliva traces on wildlife kills

“…Damage to DNA occurs as a function of time and environmental conditions, and is also affected by the tissue type (Pääbo et al 2004). However, appropriate practices have been developed to minimize and detect errors, including sample preservation Downloaded from https://academic.oup.com/jmammal/article-abstract/96/1/138/865057 by guest on 06 June 2019 methods that prevent extensive DNA damage and degradation, such as freezing, drying, or the use of buffers (Laird et al 1991;Seutin et al 1991;Frantzen et al 1998), DNA extraction methods that optimize yield and speed and prevent further degradation (Rohland and Hofreiter 2007;Rohland et al 2009), and appropriate laboratory practices (Navidi et al 1992;Taberlet et al 1996;Fernando et al 2003;Leonard 2008;Caniglia et al 2014). In particular, a multiple-tubes approach (Navidi et al 1992;Taberlet et al 1996) has become standard practice when samples have low DNA quantity or quality.…”

Non-invasive genetic sampling to predict wolf distribution and habitat suitability in the Northern Italian Apennines: implications for livestock depredation risk

“…1b). Samples were collected by more than 150 researchers, students, volunteers, and employees of Parks, Forestry Corps, and local or national administrations (Caniglia et al 2014). Sampling locations were georeferenced in the Universal Transverse of Mercator World Geodetic System (UTM WGS84 32N; Fig.…”

“…Scat, hair, urine and muscular tissue samples were individually stored at −20°C in 10 volumes of 95 % ethanol; saliva samples were dry-stored; blood samples were stored in a Tris/SDS buffer (Caniglia et al 2014). DNA was automatically extracted using a MULTIPROBE II EX Robotic Liquid Handling System (Perkin Elmer) and the QIAGEN stool and tissue extraction kits (Qiagen Inc, Hilden, Germany).…”

“…DNA was automatically extracted using a MULTIPROBE II EX Robotic Liquid Handling System (Perkin Elmer) and the QIAGEN stool and tissue extraction kits (Qiagen Inc, Hilden, Germany). Individual multilocus genotypes and gender of each sample were PCR-determined using 12 unlinked microsatellites, five uniparental markers (mtDNA control region and four Y-linked microsatellites), and a sex-specific restriction site in the ZFY/ ZFX gene, following the procedures and conditions reported by Caniglia et al (2014). In order to avoid the inclusion of false-presence occurrences, likely caused by the presence of free-ranging dogs or wolf × dog hybrids in the study area (Randi and Lucchini 2002), we then assigned each genotype to its possible population of origin (wolves, dogs, or hybrids) based on a Bayesian assignment test performed with STRUCTURE 2.3 (Falush et al 2003), using K=2 with the Badmixture^and the BI^models, without any prior population information.…”

“…In order to avoid the inclusion of false-presence occurrences, likely caused by the presence of free-ranging dogs or wolf × dog hybrids in the study area (Randi and Lucchini 2002), we then assigned each genotype to its possible population of origin (wolves, dogs, or hybrids) based on a Bayesian assignment test performed with STRUCTURE 2.3 (Falush et al 2003), using K=2 with the Badmixture^and the BI^models, without any prior population information. Hybrids were defined as those individuals having a proportion of membership qi≤0.95 to the wolf cluster and/or uniparental markers atypical for the Italian wolf population, following the careful recommendations reported in Caniglia et al (2014) that guarantee to reliably identify the first two generations of admixture (Caniglia et al 2013). …”