3.1 | Population genetic structure
The FST values were relatively low (ranging from 0 to
0.055) indicating a weak genetic structure between the different
populations (Table S1). A dendrogram constructed from the
FST (Figure S1) shows that the populations initially
clustered in pairs. However, sampling location is not a hierarchical
level of the population structure since only the populations sampled in
location 1 in 2011 and 2013 clustered together. The populations in
location 3 were sampled in the same plantations in 2011 and 2013 but the
plantations had been replanted between the two years and the
differentiation observed could thus result from genetic drift after
recolonization by P. fijiensis . Absence of clear hierarchical
structure reinforced our decision to consider data from samples
collected in 2011 and 2013 as spatial replicates but not as time series.
The nucleotide diversity (π), Watterson’s theta (Θ) and Tajima’s D
estimated for each population were similar in populations sampled in the
same year (in 2011 or in 2013) with Pool-Seq data. In populations
sampled in 2011, the median values of π and Θ ranged from 0.0001 to
0.0019 and from 0.0003 to 0.0017, respectively. In populations sampled
in 2013, the median values of π and Θ ranged from 0.0049 to 0.0072 and
from 0.0040 to 0.0061, respectively. The greater genetic diversity
detected in populations sampled in 2013 is certainly due to the fact
that more individuals were sampled in 2013. However, Tajima’s D
estimates were similar in the two sampling years, ranging from -0.429 to
0.055 and -0.316 to -0.005 in populations sampled in 2011 and 2013,
respectively. For individual sequencing data, the median values of π and
Θ were 0.0005 for both populations and both indices. Tajima’s D median
was 0.0006 for population CU1S2 and 0.0005 for population CU1R2. The
estimated values for all the indexes were lower with the individual
sequences, probably due to the smaller number of SNPs detected. The data
obtained by sequencing individuals were also used to estimate linkage
disequilibrium (LD) decay over the distance separating two SNPs in each
population. The distance corresponding to a LD decay of 50% was around
4 Kb when all the scaffolds
constituting the core genome ofP. fijiensis were taken into consideration (Figure S2). Overall,
no difference in the LD decay pattern was observed between the two
populations (CU1S2 and CU1S2). The association became random in sites
located 500 kb apart whatever the population.