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.