Analysis of relationships by COLONY 2.0 and Sequoia
We conducted kinship analysis using COLONY 2.0 and Sequoia and found
that Sequoia produced lower reliability of kinships for all types of
relationships compared to COLONY 2.0. This is because COLONY 2.0
estimates kinships by calculating the likelihood for the entire set of
individuals (Wang, 2004, 2012), whereas Sequoia identifies the most
likely kinship based on a threshold likelihood ratio between the first
and second most likely relationships for a given pair (Huisman, 2017),
which is less powerful than the COLONY 2.0 calculation. Moreover, the
target population in this study was considered to be highly inbred,
making COLONY 2.0 more suitable for this study as it can account for
inbreeding. Nevertheless, almost all the pairs estimated as FS or HS by
Sequoia were similarly estimated by COLONY 2.0, whereas four out of
eight UANN pairs were estimated only by Sequoia. This can be attributed
to COLONY 2.0 originally lacking a function to estimate UANN
relationships. The family of two F2 individuals was
identified solely through UANN relationships, and therefore we
incorporated the results from Sequoia along with those from COLONY 2.0.
We identified 10 pairs of FS or HS among the 15 F0individuals, indicating that the natural population was highly inbred,
making it challenging to determine the detailed kinships of a
reintroduced population. Despite these difficulties, we were able to
identify almost all of the F2 families by combining the
estimated GG, UANN, and FS relationships between F2individuals. However, despite sampling all possible grandparents for the
F2 individuals analyzed, GG relationships were not
estimated for all F2 individuals using COLONY 2.0. This
is likely because COLONY 2.0 assumes hypothetical parents when
estimating kinship (Steyaert et al., 2012), resulting in inconsistencies
when attempting to estimate individuals that originally have a GG
relationship by regarding them as HS.