2.5 Individual and population genetic diversity
Genome-wide genetic diversity was measured at both individual and
population level. For the individual level, genome-wide observed
heterozygosity (H O) was calculated by averaging
the values of both variant and non-variant sites. The genotype data that
include both variant and non-variant sites were re-analysed, and
mono/bi-allelic SNPs with read depth ranging from 4 to 24 were retained
for estimation of genetic diversity. H O at each
locus was calculated as the generalized gametic heterozygosity which
estimates the probability of randomly sampling two different alleles
from an individual (Meirmans et al., 2018; Moody et al., 1993). Hence, a
bi-allelic SNP had a H O value of 1 for diploids,
and 2/3 for triploids because of three homologous chromosomes. For
population level, genome-wide
nucleotide diversity (π) was
calculated using the R package PopGenome (Pfeifer et al., 2014)
with a 10 kb window size.
2.6 Detection ofruns of homozygosity
(ROH)
To assess whether inbreeding occurred in invasive populations, the
genome-wide inbreeding level of each individual was estimated by
detecting the total length and number of ROHs using the R packagedetectRUNs (Biscarini et al., 2018). As ROHs were detected only
based on the genotype state (homozygous/heterozygous), the triploid VCF
file was converted into diploid format which could be analyzed withdetectRUNs . The following constraints were applied to the
sliding-window-based run detection: (1) The minimum number of SNPs in a
ROH was 138 for diploids and 116 for triploids which was determined by
the method described in Purfield et al. (2012) (Purfield et al., 2012).
(2) One heterozygote and two missing genotypes were allowed in a window.
(3) The maximum gap between consecutive SNPs was 300 kb. (4) The minimum
length of a run was 500 kb. (5) The minimum SNP density was set to one
SNP per 100 kb. The genomic inbreeding coefficient based on ROHs
(F ROH) was calculated following the method
described in McQuillan et al. (2008) (McQuillan et al., 2008):F ROH,i =L ROH/L AUTO, whereL ROH is the total length of ROHs in individuali , and L AUTO is the length of autosomal
genome, here assumed to be 1.54 Gb. The ROH segment length
(E (LIBD-H |gcA )) represents
the number of generations from the common ancestor (gcA ),
estimated asE (LIBD-H |gcA )=
41/(2gcA ) (Curik et al.,
2014) assuming that 1 cM is roughly equivalent to 0.41 Mb (Liu et al.,
2017a).