Genetic diversity of the Pseudomonas population
Representative Neighbour-Joining (NJ) trees are shown in Figure 2 and
Figure 3A. The Pseudomonas population was clearly separated into
two major clusters according to origin of isolation, i.e., Oxford or
Auckland (ANOSIM in PRIMER, r = 0.477, P < 0.001
(Fig. 3B); Libshuff in Mothur, dCXYScore 0.0254, P <
0.0001). The Oxford cluster contains the reference strain, P.
fluorescen s SBW25, which was separately isolated from the phyllosphere
of sugar beet grown in the same field. Interestingly, the Oxford cluster
contains few isolates from Auckland, and vice versa (highlighted by
asterisk in Fig. 2).
A total of 44 and 37 unique STs (81 in total) were detected in the
Oxford and Auckland populations, respectively (Table 3). The two
populations had no shared STs. However, when the closely related STs
were grouped into OTUs at the distance level of 0.06, four shared OTUs
were identified for the 11 and 15 OTUs present in the population of
Oxford and Auckland, respectively (Table 3). The Oxford population
displayed lower levels of nucleotide sequence polymorphism (Fig. 3C),
and lower diversity in terms of the Simpson’s index on the basis of both
unique STs and OTUs (Fig. 3D). Single likelihood ancestor counting
(SLAC) analysis indicated no sites under positive or negative selection
for these housekeeping genes.
Recombination, as mentioned above, was detected in a single gene
(gapA ) but not in the concatenated sequence by the likelihood
permutation test. However, when the analysis was performed with data
from Oxford and Auckland separately, significant levels of recombination
were noted in the concatenated sequence, particularly for the Oxford
population; these were further supported by single breakpoint
recombination analysis using the 10340 model (Table 3). Further GARD
analysis revealed two breakpoints with significant topological
incongruence, indicating recombination breakpoints between the MLSA
genes (Fig. 4A).
Recombination events can be utilized to separate the isolates into
populations on the basis of ancestry, i.e. the presence of linked
alleles in multiple isolates mandates that they have shared ancestry to
some degree. Obviously, multiple sources of ancestry can be present in
any one isolate. Ancestral analysis performed in STRUCTURE found
evidence of six ancestral populations, and their distributions at the
level of the population and isolate are presented in Figure 4B and 4C,
respectively. Few isolates were “highly recombinant” without any
predominant source of their ancestry (8% in total, mostly from Oxford).