The presence of clonal and population structure within a dataset results in genome-wide LD that can confound screens for epistatic interactions based on LD patterns. To minimize the effect of population structure we first removed closely related strains within our global collection of 1,103 isolates (Yang et al., 2019a) to generate a non-redundant set of 469 genomes that each differed from each other by more than 2,000 SNPs (Figure 1a). As previously described, the sample is subdivided into four distinct populations, which have different, although currently overlapping, geographical distributions (Yang et al., 2019a). These four populations are clearly visible in Principle Coordination Analysis (PCoA) of the SNP variants in this dataset (Figure 1b). The great majority of strains in our sample are from the Asian population, VppAsia, so we excluded isolates from other populations. We then used fineSTRUCTURE (Lawson et al., 2012) to look for signals of clonal structure within the remaining isolates, iteratively removing isolates until all of the isolates were assigned to a single population (Materials and methods), leading to a discovery dataset of 198 strains (Figure 1c, Figure 1—figure supplement 1).

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Using the discovery dataset, we performed a Fisher exact test of associations between all pairwise combinations of 151,957 SNP variants within the core and 14,486 accessory genome elements. As has been observed previously (Cui et al., 2015), most of strong associations occurred between sites within 3 kb on the chromosome (Figure 2). In order to exclude associations that arise only due to physical linkage, we excluded all sets of associations that spanned less than 3 kb, including between accessory genome elements. This left us with 452,849 interactions with P < 10^-10, which grouped into 90 interaction groups (IG, a set of SNP/accessory gene connected by at least one significant interaction), all of which involved at least one accessory-genome element, with 8 also including core genome SNPs and 35 including multiple genome regions. In total these IGs included 1,873 SNPs in 100 core genes and 1,460 accessory genome elements (Table 1). Interacting SNPs were enriched for non-synonymous variants (26% vs. 16%, P < 0.01, Fisher exact test), which is consistent with natural selection being the force generating the linkage disequilibrium we detected.

Figure 2

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The largest interaction group 1 (IG1) accounted for the majority of interacting SNPs (82%) as well as a significant fraction of accessory genome elements (23%), while IG2-IG90 generally consisted of a small number of interacting SNPs (0-297) and accessory genes (2-128). IG1 is shown in Figure 3, Figure 3—figure supplements 1–3, Figure 4 and Supplementary file 1, while IG2-IG90 are displayed in Figure 5, Figure 5—figure supplement 1, Figure 6 and Supplementary file 2. In order to interpret these associations in a broader ecological and geographical context, we performed further analyses on the interactions that we identified in the discovery dataset on the non-redundant set of 469 strains.

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IG1 involves a large number of pairwise interactions, presenting a challenge for interpretation. We filtered the results to remove putatively-non-causal interactions using ARACNE (Margolin et al., 2006), but this only reduced the number of interactions from 414,785 to 103,241, which is still far too many to interpret (Supplementary file 1). However, hierarchical clustering revealed that strains fall into four distinct ‘ecogroups’ (EGs) based on IG1 variants (Figure 3a,b). Three of these groups, EG1a, EG1b and EG1d have a large number of variants (50-965) that are associated with them, and we used the clustering to sort these variants into tiers, with ‘Tier 1’ (T1) corresponding to the variants that showed the strongest association for each EG (Figure 3, Table 2, Supplementary file 2). Associated variants also show other patterns, for example, Tier“Other 1’ (O-1) variants distinguish EG1a and EG1b from other EGs, with some exceptions; O-2 variants distinguish EG1a and EG1d from other EGs, also with exceptions; O-3 variants are polymorphic in EG1b and EG1c but mostly fixed in EG1a and EG1d (Figure 3a,b). Similar but not identical structuring of strains was obtained if clustering was performed only using core genome SNPs (Figure 3—figure supplement 1a) or accessory genome elements (Figure 3—figure supplement 1b).

Although fineSTRUCTURE did not detect any population structure within the discovery dataset, PCoA analysis of SNPs identifies axes of variation that reflect the ecogroup structure within EG1 (Figure 1d). PCo1, which explains 1.28% of the total SNP variance differentiates EG1a strains from the others while PCo2, which explains 1.06% of the variance differentiates the two distinct genotype clusters separated by O-3 variants (Figure 1d), with O-3-cluster 1 corresponding to SNP Allele 2 shown in Figure 3a. The phylogenetic analysis also reveals a split between EG1a and the remaining isolates (Figure 1a, c).

The reason that PCoA and phylogenetic analysis reveals population structure within the discovery dataset, while fineSTRUCTURE does not, is because the differentiated loci are sharply concentrated into a small number of chromosomal regions, while fineSTRUCTURE looks for evidence of higher sharing across the entire genome. Chromosome painting (Figure 3d) shows evidence for sharp peaks of differentiation of different EGs around the IG1 loci identified by our coadaptation scan, especially for EG1a strains, but with little evidence for differentiation elsewhere. This pattern is qualitatively distinct either for that observed between geographically differentiated populations or for clonally related strains, which show higher-than-expected copying probability (probability of genetic variants inherited from the same population or ecogroup) throughout the genome but without sharp peaks (Figure 3—figure supplement 2). These results are consistent with there being a common gene pool shared by all of the ecogroups within each V. parahaemolyticus population, with ecogroup structure being maintained by natural selection rather than barriers to gene flow.

The accessory genome elements are present in many of the same configurations as core genome SNPs, but with ecogroup structure explaining a much larger fraction of the overall variation. The first PCo accounts for around 10% of the variance, both for the discovery dataset and the non-redundant dataset, and nearly cleanly distinguishes EG1a strains from EG1b, c strains and from EG1d strains (Figure 1b,d). Geographically based population structure is correspondingly less important, with weak differentiation of two of the populations (VppAsia and VppX) from the other two evident within PCo2 (Figure 1b,d), which is consistent with our previous observation that few population-specific genes were identified (Yang et al., 2019a).

Within IG1, genes of COG classes M and N, cell wall biosynthesis and cell motility, are substantially overrepresented, relative to their overall frequency in the genome (COG M 32% vs 8%, COG N 13% vs 3%, P<0.01, Fisher exact test). 27% (509/1879) of the IG1 SNPs localize to the lateral flagella gene cluster (VPA1538-VPA1557). The variants are scattered widely in the heatmap in many different configurations, with Tier 1 and Tier 2 SNPs from lateral flagella gene cluster showing strong associations with EG1a (a-T1 and a-T2 variants) and EG1b (b-T1 and b-T2 variants) and other patterns (O-1 variants, Figure 3a, Table 2, Supplementary file 1). Consistent with this, hierarchical clustering based on the IG1 SNPs of lateral flagellar genes can also distinguish EG1a and EG1b strains (Figure 3—figure supplement 1c). The lateral flagellar locus is responsible for motility on surfaces and the different configurations, most involving multiple non-synonymous SNPs, suggests that there are several functionally distinct motility phenotypes encoded by different versions of the gene cluster. A phylogenetic analysis of variation at the lateral flagellar locus incorporating data from Vibrio genus shows that the locus has been inherited vertically within the species but with a substantially elevated rate of evolution in the EG1a version of the locus (Figure 3—figure supplement 3), which suggests that this version of the cluster has evolved a substantially new function.

EG1a strains are highly diverged compared to other EGs in the number of core SNPs (831 SNPs in 47 genes) and accessory genes (134 genes), including 114 fixed or nearly fixed non-synonymous differences (a-T1 and a-T2) at the lateral flagellar gene cluster. Additionally, EG1a strain has a particularly complex polymorphic genomic block (reference genome 2, genome block 13, Ref2-13, 82 kb, Figure 3d, Supplementary file 1) with substantial variation in gene content between strains, which in total constitutes for a large fraction of the gene content difference (60 genes). Among this genomic block, 14 genes were cell wall biosynthesis genes (COG M) and 5 genes are annotated as having Type II secretion related function.

EG1b strains are also associated with a large block, containing 34 accessory genes (Ref2-04, Figure 3d, Supplementary file 1), as well as a smaller number of lateral flagellar gene cluster SNPs and only one further accessory gene and SNPs in a single gene, 12 of the accessory genes are cell wall biosynthesis genes (COG M). EG1c has no clear defining features, there are 7 genes (Tier O-4, Supplementary file 1) that are found at high frequency (67%) in EG1c while being rare elsewhere (5%), but none come close to representing a fixed difference. Four of these genes are annotated as being transferases.

Tier O-1 includes 16 SNPs in lateral flagellar genes (VPA1548 and VPA1550) and 20 SNPs in the gene TonB (VP0163), which was associated with the energy transduction (Kuehl and Crosa, 2010). These SNPs are strongly associated, despite being on different chromosomes, suggesting a specific functional interaction. Tier O-2 includes 18 SNPs in two core genes encoding LuxR family transcriptional regulators (VPA1446-VPA1447), which is associated with c-di-GMP signaling and biofilm formation (Ferreira et al., 2012). Within Tier O-2, ARACNE identified an accessory gene group_3560 as being a driver locus, with a particularly large number of causal interactions. This gene codes for a polysaccharide biosynthesis/export protein and retains interactions with 9 genome blocks after filtering (Supplementary file 1). Tier O-3 contains SNPs that are at high frequency in strains containing the group_3560 gene but are rare in the rest of the dataset. The SNPs are in four genes coding multidrug resistance protein (VP0038), hypothetical protein (VP0039), lipase (VPA0859) and long-chain fatty acid transport protein (VPA0860) respectively.

EG1d was identified in our previous analysis (Cui et al., 2015). In the current dataset, it is differentiated from other strains at 5 SNPs in a transmembrane gene (VPA1081) and 45 accessory genes. A 23 gene block encoding T6SS (type VI secretion system, VP1391-VP1420, Ref1-10, d-T1) is present or partly present in all EG1d strains, and absent or largely absent in the other three EGs. Most EG1a-c strains instead encode a block of genes that are annotated as being cellulose synthesis related (Ref2-01, d-T2). It is notable, however, that there are no SNPs associated specifically with EG1d in the lateral flagellar genome region.

We performed a preliminary investigation of the phenotypic differences underlying EG1a by determining the motility, growth rate, and biofilm formation ability (Figure 4) of 11 strains (4 EG1a, 1 EG1b, 2 EG1c, 4 EG1d) on laboratory media. Because there are many unique variations in the lateral flagella gene cluster of EG1a isolates, we expected a different motility ability between EG1a and other isolates, but we failed to observe differences in swimming or swarming capability under the conditions tested (Figure 4a). However, EG1a strains revealed faster growth rate and significantly higher biofilm formation ability than EG1b-d strains (Figure 4b,c), and they revealed rough colony morphology, also an indication of increased biofilm formation, under low salinity (1% NaCl) culture condition (Figure 4c).

There are in total 60 EG1a strains in the global collection of 1,103 V. parahaemolyticus strains. All but one, a VppUS2 isolate, is from the VppAsia population, with the majority (n = 48, 80%) in this study coming from routine surveillance on food related environmental samples, including fish, shellfish, and water used for aquaculture. The strains revealed no clear geographical clustering pattern in China, as they can be isolated from all six provinces that under surveillance. Notably, only 4 EG1a strains were isolated from clinical samples, including wound and stool, representing a lower proportion than for EG1b-d isolates (453/1043), including if the two major pathogenic clonal lineages (CG1 and CG2) (Yang et al., 2019a) are removed (268/798), suggesting this ecogroup has low virulence potential in humans.

The most common type of interaction group is ‘genome island-like’, which is a single accessory genome region of between 3 kb (IG50) and 57 kb (IG38), of which there are 52 (Figure 5). For example, IG2 consists of 10 genes in a single block (VPA1700-VPA1709). Nine of the genes code for various functions related to carbohydrate metabolism and transport while the 10^th is a transcriptional regulator (Figure 6 and Supplementary file 2). Four strains have 9 out of the 10 genes but otherwise the genes are either all present or all absent in every strain. Interestingly, there appears to be a difference in frequency between VppAsia isolates and others, with the island present in 52% of VppAsia strains and 90% of others.

Genome islands are often associated with transmission mechanisms such as phage and plasmids (Dobrindt et al., 2004). In our data, one example is IG14 which contains 4 genes annotated as being phage related and a further 19 hypothetical proteins (Figure 6). In the reference strain, 16 of the genes occur in a single block VP1563-VP1586, while 7 genes are present elsewhere in the genome. 56% of the 469 strains had none of the 23 genes, while 36% had more than 12 of them and 8% had between 1 and 5, which presumably represent remnants of an old phage infection. Only one gene (VP1563) in IG14 was found in appreciable frequency in strains that had none of the other genes. This gene might represent cargo of the phage infection that is able to persist for extended periods in the absence of infection due to a useful biological function of its own. Alternatively, it might additionally be transmitted by other mechanisms.

Another common interaction is incompatibility between different accessory genome elements, which is found in total 24 of the interaction groups (Figure 5). For example, in IG3 (Figure 6), all of the 469 strains either have the gene yniC, which is annotated as being a phosphorylated carbohydrates phosphatase, or at least 4 out of a set of 5 genes VP0363-VP0367 that includes a phosphotransferase and a dehydrogenase in the same genome location. Only one strain has both sets of genes. This interaction also involves a core genome SNP, in the adjacent gene VP0368, which is annotated as being a mannitol repressor protein. Another pattern is found in IG42 (Figure 6), where there are three genes (polar flagellar sheath protein and hypothetical proteins) that are mutually incompatible in our data, and 12% strains have none of the three genes.

Amongst interaction groups other than IG1, class G, encoding carbohydrate transport and metabolism are substantially overrepresented (22% vs 6%, p<0.01, Fisher exact test, Figure 5a), particularly amongst groups involving incompatibilities. There are also differences in GC content between accessory genes in IGs and others, with IGs having higher mean values, especially in compatibility IGs (Figure 5a).

We compared our results for core genome interactions with those obtained by SuperDCA, a method that uses Direct Coupling Analysis to identify causal interactions (Morcos et al., 2011; Puranen et al., 2018), using the default settings for the algorithm. To make the results as directly comparable as possible we used the same 198 isolates that were used for the Fisher exact test. The most important discrepancy is that although SNPs associated with a specific group of strains, EG1a, involves perfect associations, with P values as low as 1.4×10⁻³⁰, the coupling strengths are lower than for the other groups we identified and none appear amongst the top 5,000 couplings (Figure 7a, Figure 7—figure supplement 1). This discrepancy is due the large number of SNPs involved with similar association patterns, which means that coupling values are distributed between them. Excluding EG1a SNPs, there is a strong correlation between SuperDCA coupling strengths and Fisher exact test P values (Figure 7a). At a stringent cutoff of 10^-2.2, SuperDCA identifies the same multi-locus interactions as Fisher exact test does at P < 10^-10, with a few SNPs excluded (Figure 7b). The significance thresholds for both the Fisher exact test and SuperDCA could be relaxed to identify a substantially larger number of true-positive hits, at the likely expense of some false ones, but we do not investigate these associations further here. We also compared our results with those obtained by SpydrPick, a model-free method based on mutual information (MI) (Pensar et al., 2019). The Fisher exact test P value is almost perfectly correlated with the MI statistic used by SpydrPick for this data (Figure 7a).

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A recent debate about whether the accessory genome evolves neutrally (Vos and Eyre-Walker, 2017; Andreani et al., 2017; Shapiro, 2017) highlighted how little we know about the functional importance of much of the DNA in bacterial chromosomes. Using the same statistical threshold to assess significance, our interaction screen identifies many more examples of coadaptation between different accessory genome elements than of interactions between the core and accessory genomes or within the core genome, implying that natural selection has a central role in determining accessory genome composition.

Unsurprisingly, given the extensive literature highlighting the importance of genomic islands to functional diversity of bacteria (Dobrindt et al., 2004), the most common form of adaptation detected by our screen is the coinheritance of accessory genome elements located in the same region of the genome. Based on a minimum size threshold of 3 kb, we find 52 (56%) such interactions, the largest of which is 57 kb (Figure 5).

Previous approaches to detecting genome islands emphasize traits associated with horizontal transmission, for example based on differences in GC content with the core genome, the presence of phage-related genes or other markers of frequent horizontal transfer (Langille et al., 2010). Our approach, based simply on co-occurrence identifies a wider range of coinherited units and suggests that many islands have functions related to carbohydrate metabolism.

Amongst interactions not involving physical linkage, the most common is incompatibility of different accessory genome elements, representing 27% (24/90) of our IGs. For example, two different versions of a phosphorous-related pathway, one involving one gene, the other involving 5 (IG3, Figure 6).

We propose that the rarity of interactions between core and accessory genome in our scan reflects the evolution of ‘plug and play’-like architecture for frequently transferred genetic elements. Accessory genome elements are more likely to establish themselves in new host genomes if they are functional immediately on arrival in a diversity of genetic backgrounds. Furthermore, from the point of view of the host bacteria, acquisition of essential functions in new environments is more likely if diverse accessory genome elements in the gene pool are functional as soon as they are acquired. These selection pressures will tend to promote a genomic architecture that facilitates casual gain and loss of genetic elements from particular genomes (Figure 8a).

When an accessory genome element with an important protein coding function arrives in a new genome, it is likely that some optimization of gene regulation will be possible, coordinating the expression of the gene with others in the genome. This can lead to longer-lasting associations between genetic elements (Figure 8b). We found 8 different interaction groups involving core and accessory genome regions. One simple example included a regulatory gene VP0368 and an accessory genome element (IG3, Figure 6). In this example, it is feasible for the core genome SNP and the associated accessory element to be transferred together between strains in a single recombination event. Where coadaptation involves two or more separate genome regions, this makes assembling fit combinations more difficult and is likely to slow down the rate at which strains gain and lose the accessory genome elements involved. The difficulty of evolving the trait de novo is likely to slow down the rate at which it is gained and loss, which in turn makes further coadaptation at additional genes more likely.

IG1d, is an example of a complex coadaptation involving multiple core and accessory genome regions. A large majority of strains in our dataset (439/469, EG1d) either carry a cluster of genes encoding a T6SS, or a cluster encoding cellulose biosynthesis genes (EG1a-c), but few strains have genes from both clusters (Figure 3a). Cells uses the T6SS to inject toxins into nearby bacteria (Salomon et al., 2013) and cellulose production to coat themselves in a protective layer (Tischler and Camilli, 2004). Incompatibility might have a functional basis, for example because cellulose production prevents the T6SS functioning efficiently, or an ecological one, for example because cells that attack others do not need to defend themselves. The evolution of dissimilar strategies has led to differentiation in gene/SNP frequencies in a large number of regions. Strains that do not have the T6SS use at least three distinct sets of strategies, corresponding to ecogroups EG1a, EG1b and EG1c, encoded by alleles that are rare or absent in EG1d strains.

EG1a variants differ from the other interaction groups in our coadaptation screen in both the number of associated regions and the strength of the associations. The interaction group includes 454 SNPs in the lateral flagellar gene cluster (VPA1538-1557, 18 kb, Figure 3c), a further 917 core genome SNPs in 62 genes and 152 accessory genes in 35 clusters. Many of the variants represent fixed or nearly fixed differences between EG1a and other strains (a-T1 and a-T2). These include loci encoding flagellar genes, T2SS and other membrane transport elements. There are also 285 loci (27%, a-T3) in weaker disequilibrium, typically because they are polymorphic in EG1a or the other EGs. Many of these variants are likely to represent more recently evolved coadaptations. Some of these genes are also associated with flagella or the T2SS related function but also encompass a broader range of functional categories, including cell division and amino acid transport and metabolism (Table 2, Supplementary file 1).

Our laboratory phenotype experiments (Figure 4) suggest that biofilm formation is likely to be a key trait underlying the different ecological strategies of EG1a and other EGs. However, the variation in phenotypic response at different salinity levels, and the absence of measurable difference in swarming behavior despite the large genetic difference within the lateral flagella genes, highlight some of the manifold difficulties of interpreting natural variation using phenotypes measured under laboratory conditions.

Despite the extensive differences that have accumulated between EG1a strains and the other EGs, there is no evidence of restricted gene flow in most of the genome (Figure 3d). Even within the flagellar gene cluster, strongly differentiated regions are separated by a weakly differentiated one (Figure 3c), implying that the coadaptation is being maintained by selection in the face of frequent recombination. Initial divergence in flagellar function is likely to have led to ecological differentiation, which led to bacteria for example having different nutritional inputs or requirements and a broadening of the functional categories undergoing divergent selection.

How can the difference between EG1a variants and the other interaction groups in both the number of associations and their strength be explained? V. parahaemolyticus is ubiquitous in shellfish in warm coastal waters, within which it occurs at densities of around 1,000 cells per gram, so a back of the envelope calculation suggests there are likely to be substantially more than 10¹⁵ bacteria in the VppAsia population. The species also has a high estimated effective population size (Yang et al., 2018; Cui et al., 2015) and has strong codon bias, which is often argued to be evidence that even tiny selective coefficients can drive adaptation (Sharp et al., 2005). Furthermore, recombination only breaks up linkage disequilibrium between loci slowly. Therefore, weaker and more variable patterns of association found for associations other than EG1a variants is unlikely to be a simple consequence of the ineffectiveness of selection and is instead likely to reflect complexity in the fitness landscape.

Strains gain flexibility by being able to switch between or modulate genomically encoded strategies by homologous recombination. The evolution of promiscuity, and plug and play-like architecture is self-reinforcing because the presence of strains using multiple strategies in the population also favors the presence of accessory genes and core gene haplotypes that have high or intermediate fitness on a wide range of different genetic backgrounds.

On the other hand, an absence of intermediate genotypes in the population can favor the evolution of fastidiousness, with particular accessory genes and haplotypes becoming essential components of some genetic backgrounds but deleterious on others. A likely scenario is that EG1a initially involved epistatic interactions between lateral flagellar variants and one or more additional loci elsewhere in the genome. Additional SNP differences accumulated making the two different versions of the lateral flagellar locus functionally more distinct. Greater functional distinctiveness of the two phenotypes in turn generated divergent selection pressures at additional loci, which led to further coadaptation, which made the phenotypes of the ecogroups still more distinct.

These arguments imply that the evolution of fastidiousness, like the evolution of promiscuity, can be self-reinforcing. At some point in the differentiation of EG1a strains from the remaining ones, the coadaptation of the core loci to each other is likely to have become more-or-less irreversible (Figure 8c). In this respect, the interaction between loci resembles the human institution of marriage, which has historically been thought of as an irreversible bond, although this notion loosened in the Christian world following the reign of King Henry VIII in England.

Running the tape forward, it is easy to envisage the number of coadapted regions of the genome within EG1a undergoing progressive enlargement, until the entire genome becomes differentiated. As coadapted regions become more numerous, the proportion of recombination events between eco-groups that are maladaptive will increase, which might prompt the evolution of mechanistic barriers to genetic exchange between them (Figure 8d).

Mechanisms by which new bacterial species arise are frequently discussed in the literature (Shapiro et al., 2012; Fraser et al., 2009; Falush et al., 2006) but there is currently little data on how the process unfolds. EG1a isolates are of interest both as an example of an intermediate stage of divergence, prior to speciation, and because it suggests that substantial adaptive divergence between gene pools can precede any barriers to genetic exchange, other than natural selection at the loci involved. This – unique to our knowledge – example is exciting because the distinct signature of selection should make it possible to dissect the genetic basis of coadaptation in unprecedented detail. Broadly similar patterns of differentiation including ‘genomic islands of speciation’ have been observed for example between ecomorphs of cichlid fishes (Malinsky et al., 2015), but the evolution of ecomorphs has been facilitated by fish preferring to mate with similar individuals, which will have also inevitably lead to some level of differentiation at neutral loci throughout the genome.

In V. parahaemolyticus, it has been possible to distinguish clearly between adaptive processes, reflecting fitness interactions between genes and neutral ones, reflecting clonal and population structure. This has allowed us to provide a description of the landscape of coadaptation, involving multiple simple interactions and a small number of complex ones. We have focused on interactions that generate strong linkage disequilibrium, but weaker and more complex polygenic ones also have the potential to provide biological insight.

Most bacteria have population structure that deviates more markedly from panmixia (Yang et al., 2018). In some species, this is likely due to smaller effective population sizes, lower recombination rates or mechanistic barriers to genetic exchange between strains. However, coadaptation can itself generate genome-wide linkage disequilibrium that might be difficult to distinguish from clonal or population structure. Because the linkage disequilibrium associated with IG1 is highly localized within the genome, it can, on careful inspection be clearly be attributed to selection, but in other bacteria patterns are likely to be less straightforward, making it challenging to understand to whether adaptive processes drive population structure, or vice versa. Natural selection is the jewel of evolution but distinguishing it from other processes requires in depth understanding of the relevant biology in addition to suitable data and statistical methods.

Totally 1,103 global V. parahaemolyticus genomes were used in this work, which also were analyzed in our other study (Yang et al., 2019a). To reduce clonal signals, we firstly made a ‘non-redundant’ dataset of 469 strains, in which no sequence differed by less than 2,000 SNPs in the core genome. They were attributed to 4 populations, VppAsia (383 strains), VppX (43), VppUS1 (18) and VppUS2 (21) based on fineSTRUCTURE result (Lawson et al., 2012). We then focused on VppAsia which has more strains, to generate a genome dataset in which strains represent a freely recombining population. We selected 386 genomes from 469 non-redundant genome dataset, including all the 383 VppAsia genomes and 3 outgroup genomes which were randomly selected from VppX, VppUS1 and VppUS2 population, respectively. These 386 genomes were used in Chromosome painting and fineSTRUCTURE analysis (Lawson et al., 2012) as previously described (Cui et al., 2015). Initial fineSTRUCTURE result revealed multiple clonal signals still exist, thus we selected one representative genome from each clone, combined them with the remaining genomes and repeated the process. After 14 iterations, we got a final dataset of 201 genomes with no trace of clonal signals, involving 198 VppAsia genomes that were used in further analysis (Figure 1—figure supplement 1).

The copying probability (probability of genetic variants inherited from the same population or ecogroup) value of each strain at each SNP was generated by Chromosome painting with ‘-b’ option, and the average copying probability value of a given strain group (e.g. EG1a) at each SNP was used in Figure 3d and Figure 3—figure supplement 2.

We re-called SNPs for 198 VppAsia genomes by aligning the assembly against reference genome (RIMD 2210633) using MUMmer (Delcher et al., 2003) as previous described (Cui et al., 2015; Yang et al., 2019b). Totally 565,466 bi-allelic SNPs were identified and 151,957 bi-allelic SNPs with minor allele frequency >2% were used in coadaptation detection. We re-annotated all the assemblies using Prokka (Seemann, 2014), and the annotated results were used in Roary (Page et al., 2015) to identify the pan-genome and gene presence/absence, totally 41,052 pan-genes were found and 14,486 accessory genes (present in >2% and<98% strains) were used in coadaptation detection. The pan-gene protein sequences of Roary were used to BLAST (BLASTP) against COG (Galperin et al., 2015) and KEGG (Kanehisa and Goto, 2000) database to obtain further annotation.

The Neighbour-joining trees were built by using the TreeBest software (http://treesoft.sourceforge.net/treebest.shtml) based on sequences of concatenated SNPs, and were visualized by using online tool iTOL (Letunic and Bork, 2016).

Totally 151,957 bi-allelic SNPs and 14,486 accessory genes identified from 198 independent VppAsia genomes were used in coadaptation detection by three methods. Firstly, we used Fisher exact test to detect the linkage disequilibrium of each SNP-SNP, SNP-accessory gene, and accessory gene-gene pair. Presence or absence of an accessory gene were considered as being alternate alleles. Each variant locus (SNP or accessory gene) has two alleles, major and minor, of which major represents the allele shared by majority of isolates. For each pair of loci X and Y, the number of combinations between X_major-Y_major, X_major-Y_minor, X_minor-Y_major, X_minor-Y_minor were separately counted and used in the contingency table to calculate the Fisher exact test P value. It took 3 days to finish all the coadaptation detection in a computer cluster using 21 cores and 2 Gb memory.

We also used SuperDCA (Puranen et al., 2018) and SpydrPick (Pensar et al., 2019) to detect the coadaptation between SNPs, using the same subset of 198 strains to make the analysis as comparable as possible. SuperDCA is based on direct coupling analysis (DCA) model (Morcos et al., 2011), a model to predict protein residue-residue contact from multiple sequence alignment, which has recently been extended to genome-wide epistasis analysis within bacterial populations. The demanding computation requirements hampered the direct application of DCA methods in big genome dataset. SuperDCA introduced optimized parallel inference algorithm, which is much faster than earlier DCA methods and is scalable for up to 10⁵ variants. However, it still took 25 days to finish the detection by using 32 cores and 86 Gb memory.

SpydrPick is based on mutual information (MI), an information theoretic measure of mutual dependence between two variants. Pairwise analysis of variants using SpydrPick is scalable to core genome SNP and pan-genome-wide analysis. SpydrPick took one hour to finish the calculation using 32 cores and 1 Gb memory.

We removed coadaptation pairs with distance less than 3 kb to minimize the influence of physical linkage. All identified SNPs in this study were located in the core genome, therefore the physical distance between SNP pairs can be calculated according to their position in the reference genome. To define the distance between accessory genes, and between SNP and accessory gene, we mapped the sequence of accessory genes against available 19 complete maps of the V. parahaemolyticus genomes to acquire their corresponding position, and then the gene that failed to be found in complete reference genomes were then mapped to the draft genomes. If the accessory genes pair or SNP- accessory gene pair was found located in a same chromosome or same contig of a draft genome, then the distance between paired variants could be counted according to their position in the chromosome or contig. The distance between paired variants that located in different chromosomes or contigs was counted as larger than 3 kb and such pairs were kept in further analysis. Circos (Krzywinski et al., 2009) was used to visualize the networks of coadaptation SNPs in Figure 7b and Figure 7—figure supplement 1.

To identify the homologous sequences of V. parahaemolyticus lateral flagellar gene cluster (VPA1538-1557) in the Vibrio genus, we downloaded all available Vibrio genome assemblies in NCBI, then aligned the nucleotide sequence of lateral flagellar gene cluster of V. parahaemolyticus (NC_004605 1639906–1657888) against Vibrio genome dataset (excluding V. parahaemolyticus) by using BLASTN. Totally 46 Vibrio genomes revealed above than 60% coverage on lateral flagella region in V. parahaemolyticus genome and was used in phylogeny rebuilding. We also included three randomly selected strains from EG1a and EG1b-d respectively for comparison. In total 3,000 SNPs were identified in this region and were used for NJ tree construction.

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

This work is supported by the National Key Research and Development Program of China (No. 2017YFC1601503 and 2018YFC1603902), National Key Program for Infectious Diseases of China (No. 2018ZX10101003 and 2018ZX10714–002), Sanming Project of Medicine in Shenzhen (No. SZSM201811071), the National Natural Science Foundation of China (No. 31770001) and the Key Research Program of the Chinese Academy of Sciences (No. ZDRW-ZS-2017–1). DF is funded by a Medical Research Council Fellowship as part of the MRC CLIMB consortium for microbial bioinformatics (No. MR/M501608/1), Shanghai Municipal Science and Technology Major Project (No. 2019SHZDZX02).

© 2020, Cui et al.

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