Estimation of kinship between F2 and captive
individuals
From the SNP set filtered by the criteria determined above, COLONY 2.0
(Jones and Wang, 2010), Sequoia (Huisman, 2017), and gRandma (Delomas
and Campbell, 2021) were used to estimate relationships between
F2 and captive individuals. COLONY 2.0 was used to
estimate FS and HS relationships between F0 individuals
and between F2 individuals. Both COLONY 2.0 and gRandma
were used to estimate GG relationships between F0 and
F2 individuals. Sequoia was used to estimate UANN
relationships between F1 and F2individuals. Here, HS, GG, and UANN have the same relatedness (Thompson,
1975). Although these three relationships are inherently genetically
indistinguishable without utilizing linkage information, it is important
to note that in this study, F0 consistently represents
the grandparent generation, F1 corresponds to the
uncle/aunt generation (parent generation), and F2represents the grandchild generation (Fig. 1). Therefore, if a
half-sibling (HS) relationship is estimated between F0and F2 individuals using COLONY 2.0, it actually
indicates a GG relationship (J. Wang, personal communication).
Specifically, all 62 individuals from the F0 and
F2 generations were included as candidate offspring in
COLONY 2.0, and if an HS relationship was estimated between
F0 and F2 individuals, it was considered
a GG relationship. Likewise, all 55 individuals from the
F1 and F2 generations were entered as
candidate offspring in COLONY 2.0, and UANN relationships were
considered as HS relationships.
For the COLONY 2.0 settings, both the allele dropout rate and error rate
were set to 0.01 based on the results of the preliminary considerations
alongside other filtering conditions (Table S6), and inbreeding was
considered. Other settings were the same as those used in the
consideration of filtering parameters (random mating was assumed,
estimation accuracy was very high, and run length was set to 3). From a
prior study, those relationships with a support probability of 0.8 or
greater in COLONY 2.0 were considered to be true kinship (Thow et al.,
2022).
gRandma can provide estimates for trio relationships between paternal
and maternal grandparents and one grandchild. The estimated GG trios are
then output with the Mendelian incompatibility (MI: the closer to 0, the
less genetic inconsistency) and the log likelihood ratio (LLR) of
assuming that the trio is unrelated. It is also possible to calculate
the false positive and false negative rates for each MI when the LLR
threshold is set to a certain value. In this study, the false positive
and false negative rates for each MI were calculated for LLR = 30, 50,
60, 70, 80, and 90 as candidates for the threshold, and LLR = 70 was
adopted because at this value the false positive rate was 0.06 and the
false negative rate was 0 when MI = 0 (Table S2). The results of the
kinship estimation are presented as “robust” if LLR ≥ 70 and MI = 0,
and “weak” if LLR < 70 and MI = 0 or LLR ≥ 70 and MI
> 0. A total of 62 individuals
(F0–F2) were used, the same as in the
estimation of GG using COLONY 2.0, and the filtering conditions were
also the same (MIN_DP = 5, MAX_DP = 50, MIN_MEAN_DP = 15, MIN_GQ ≥
30, CR > 0.9, MAF ≥ 0.03, HWE < 0.00001, HET ≤
0.7, LD ≤ 0.2). The allele dropout rate and error rate were both set to
0.01, the same as in COLONY 2.0.