Author Contributions:
MG and RR designed the study. RK designed and performed sampling of soil
arthropods and sorting of morphospecies. AG identified insect samples.
MG did the screening, barcoding, sequencing and analysis of the data. MG
and RR wrote the paper.
Figure 1 : A) Rarefaction curve of morphospecies found (in
black) showing species richness in the soil arthropod community. Colored
lines represent expected number of morphospecies. B) The distribution of
three endosymbionts screened across different host arthropod orders.
Figure 2 : Phylogenetic analysis of (A) Wolbachia, (B)Cardinium and (C) Arsenophonus found, shown with some
known sequences for better resolution. Wolbachia phylogenetic
tree was constructed using MLST data in ClonalFrame with 50% majority
rule consensus. Cardinium and Arsenophonus phylogeny was
made in MEGA7 using 16S rRNA gene fragment. Dotted nodes
represent bootstrap value >50. Wolbachia infections
are shown as STs whereas Cardinium and Arsenophonus are
labelled with host taxa that they infected. Infections obtained in this
study are in BOLD. Brugia malayi, Amoebophilus asiaticus andProteus mirabilis were taken as outgroup for Wolbachia ,Cardinium and Arsenophonus phylogenetic analysis,
respectively.
Figure 3 : Association between infected host (left) and
endosymbiont (right) phylogeny with (A) Wolbachia A supergroup,
(B) Wolbachia B supergroup, (C) Cardinium and (D)Arsenophonus Host phylogeny was constructed by MrBayes using
partial CO1 sequences. Black dots represent clade credibility
value >70. Phylogenetic relationship between differentWolbachia strains was interpreted through ClonalFrame.Cardinium and Arsenophonus 16S rDNA phylogeny was
constructed using MEGA7. Correlation between the two phylogenies suggest
phylogenetic incongruence and extensive horizontal transfer across host
taxa.
Figure 4 : Maximum likelihood phylogenetic trees of coxA(left), concatenated MLST dataset (centre) and gatB (right) gene
made using MEGA7. Black dots represent bootstrap value >50.Wolbachia ST-N2 and ST-560 clustered with B supergroup in
concatenated MLST phylogenetic tree whereas in coxA phylogenetic
tree, these strains clustered with A supergroup indicating recombination
between Wolbachia supergroup A and B. Similarly, ST-552 clustered
with F supergroup in concatenated MLST tree, but the individualgatB gene tree shows it to be from A supergroup, indicating
recombination between A and F supergroup. These three cases (ST-N2,
ST-560, and ST-552) represents between supergroup recombination of gene
or gene segment.
Table 1 : Allele profiles of MLST genes for 36 unique
host-Wolbachia combinations. (Bold numbers represent new alleles
and STs).
Table 2 : Recombination events detected in the WolbachiaMLST sequences. Putative breakpoints indicate concatenated sequences of
MLST genes in the order (gatB-coxA-hcpA-ftsZ-fbpA ). p-value was
kept at < 0.01.