at nSSR loci
We found a total number of 210 alleles using the 14 nSSR (corresponding
to 15 diploid genotypes, see above), with the lowest number observed in
Banda (N A = 68) and the highest in Bacan
(N A = 176). The mean number of alleles per
population (N M) ranged from 5.00 to 11.73 across
the five populations (Table 1). We found a lower genetic diversity in
Ambon and Banda than in Ternate, Tidore and Bacan, as shown by the
rarefied allelic richness statistics (AR (k=46),
Table 1). The inbreeding coefficient (F IS) values
were found to be significantly greater than zero in Ambon, Ternate, and
Bacan, indicating a signal of inbreeding.
The global genetic structure among populations as measured by theF ST was 0.069. Meanwhile, the pairwiseF ST between populations ranged from 0.012
(between Ternate and Bacan) to 0.182 (between Ambon and Tidore) (Table
2). The genetic structure within populations (F STamong sub-populations) was globally relatively low
(F ST values from 0.008 in Bacan to 0.040 in
Tidore; see details in Supplementary Table S2).
Bayesian-clustering analyses suggest that the most likely number of
intra-specific genetic clusters within our data set is 2 (Supplementary
Figure S2). Individuals from Ambon and Banda are assigned to a first
genetic cluster (Figure 2A / 2C), referred as the ‘Southern Moluccas
cluster’ hereafter, whereas individuals from Ternate, Tidore and Bacan
are generally assigned to a second genetic cluster, that we name the
‘Northern Moluccas cluster’ (F ST = 0.089 between
the two clusters). A part of these individuals show variable admixture
proportions (probability of assignation to a cluster between 0.2 and
0.9) with the Southern Moluccas cluster (31%, 4%, and 26%,
respectively for Ternate, Tidore and Bacan).
Our STRUCTURE results also indicate that the Northern Moluccas cluster
is further subdivided into two groups at K = 3 (Figure 2), with
the first cluster (2a) including Ternate, Tidore, and part of Bacan
individuals (78%), and a second cluster (2b) including 22% of
individuals from Bacan island (F ST = 0.055
between cluster 2a and 2b). We further investigated this by running an
additional analysis in STRUCTURE with individuals from the Northern
Moluccas cluster (N = 160), and also Bacan island (N = 75;
Supplementary Table S3). This additional analysis indicated K = 2
as the most plausible solution (Supplementary Figure S3), supporting the
subdivision of the North Moluccas cluster into 2a and 2b as observed in
the previous analysis.
Genetic diversity and population structure of M. fragrans