Pedigree reconstruction
Parentage analysis was performed using a likelihood-based approach with the CERVUS software (version 3.0.7) (Kalinowski, Taper and Marshall, 2007), followed by the COLONY software (version 2.0.6.4) (Jones and Wang, 2010; Wang, 2004). Mitochondrial and Y chromosomal haplotype data were used for the selection of potential mother–offspring relationships and potential father–son relationships, respectively. Analyses were run systematically in accordance with a previous study (Shimozuru, et al. , 2019). First, all individuals, sampled during 1998–2020, were analyzed with CERVUS, which selected the most likely parent among the existing candidates. The same simulation parameters were set as in a previous study (Shimozuru, et al. , 2019). In the first step of the CERVUS analysis, we assigned a parent pair. The confidence level was set at 80%, and no mismatching was allowed in a parent–offspring combination (i.e., mother–father–offspring trio). One mismatch was allowed in a parent–offspring combination obtained at a ≥95% confidence level when the same mother and father were selected as the most likely parents (≤1 mismatch per pair) in maternity and paternity assignment analyses, respectively. If a parent pair could not be assigned due to a low (<80%) confidence level or the presence of ≥1 mismatching loci, we assigned maternity or paternity as a second step. The confidence level was set at 80%, and no mismatching was allowed in a mother/father–offspring combination. Furthermore, bears that were not assigned a mother and/or father in CERVUS were included in a parentage analysis using COLONY. The COLONY software generates hypothetical parents in a sib-ship reconstruction with the assumption that both females and males are promiscuous (Steyaert, et al. , 2012), which enables the assignment of parentage to individuals whose parent(s) were not present in the parent candidate data set. To reduce the possibility of multiple generations in the candidate offspring leading to a false parentage assignment, only bears that were sampled during 2019–2020 were included as candidate offspring in COLONY analyses.