2.6.2 Population-level estimates of selfing rates
Selfing rates were estimated using three methods [i.e.,s(g2), s(ML) and s(BES) ] from the microsatellite data of 613
individuals of 22 natural populations (see section 2.3). First, selfing
rates and associated 95% CI were estimated using the reciprocal of the
two-locus heterozygosity disequilibrium (s(g2) ) and a Maximum
Likelihood (s(ML) ) estimator, both implemented in RMES (David,
Pujol, Viard, & Goudet,
2007) by running
10000 iterations. Both s(g2) and s(ML) estimate
correlation among loci, providing complementary information about
identity disequilibrium and selfing rate. Given that estimation of
selfing using s(g2) and s(ML) can be biased due to the
removal of homozygous loci (David et al.,2007), we
compared these selfing rates with a model-based Bayesian estimation of
selfing that makes use of all loci regardless of heterozygosity (BES
v0.1.3; Redelings et
al., 2015).
Standard deviations were estimated using 10000 bootstrap iterations. To
test if population-level estimates of selfing rates are positively
correlated with the frequency of homostyles in natural populations, we
used generalized additive models where frequency of homostyles was used
as independent variable and specifying a Beta distribution for the
estimates of selfing rates as implemented in the R package ‘gamlss’
v5.1.6 (Rigby, Stasinopoulos, & Lane,, 2005).